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Hire Dr. Hamed P.

Australia

USD 65 /hr

Scientific & Medical Writer | PhD Biomedical Scientist | Literature Reviews, Data Analysis & Publication Support

Profile Summary

I am a researcher with a PhD in Biomedical Sciences from Macquarie University, where my work focused on the cellular and molecular toxicity of the environmental cyanotoxin BMAA. My research involved studying oxidative stress, mitochondrial dysfunction, DNA damage, and ferroptosis using cell culture models, fluorescence microscopy, Western blotting, immunocytochemistry, ELISA, and proteomics workflows. I have hands-on expertise in LC-MS/MS and HPLC method development, liquid-liquid extraction, metabolite analysis, and experimental optimization (Design-of-Experiments). My work integrates biochemical assays and analytical platforms to investigate toxin exposure and cellular stress responses. Before my PhD, I completed an MSc and BSc in Microbiology, working on extraction and quantification of microbial metabolites and chromatographic assay development. I have contributed to projects involving microbial natural products and environmental exposure-related health impacts. I have authored 40+ peer-reviewed publications, including review and research articles across toxicology, microbial products, bioenergy-related topics, and pollutant-linked health effects (3,676 citations, h-index 27). I have experience in scientific writing, figure preparation, peer-review, and literature synthesis, and have collaborated with research groups in Australia, the US, China, Malaysia, Germany, France, etc. I am available for projects involving: 1-Cell culture & molecular toxicology workflows 2-LC-MS/MS & HPLC method support and data interpretation 3-Proteomics data interpretation and pathway analysis (IPA) 4-Scientific writing, literature review, and manuscript editing 5-Experimental design and analytical method optimisation My approach is focused on rigorous methodology, clear data interpretation, and accurate scientific communication.

Subject Matter Expertise

• ☆ Analytical Chemistry
• ☆ Liquid Chromatography/HPLC
• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Industrial Microbiology
• ☆ Microbiological Assays
• ☆ Bacteriology
• ☆ Gram-Negative Bacteria
• ☆ Gram-Positive Bacteria
• ☆ Biostatistics
• ☆ Biochemistry
• ☆ Biochemical Assays
• ☆ Apoptosis
• ☆ Oxidative Stress & Mitochondrial Function
• ☆ Enzyme Activity Assays
• ☆ Molecular Biology
• ☆ Biomarkers
• ☆ Proteomics
• ☆ PCR
• ☆ DNA Damage & Repair
• ☆ Cell Biology
• ☆ Cell-Based Assays
• ☆ Cytochemistry
• ☆ Neuroscience
• ☆ Cognitive Neuroscience
• ☆ Biotechnology & Bioengineering
• ☆ Microbial Biotechnology
• ☆ Biomass & Bioenergy
• ☆ Microscopy
• ☆ Light Microscopy
• ☆ Electron Microscopy
• ☆ Fluorescence Microscopy
• ☆ Cell Culture
• ☆ Primary Cells
• ☆ Industrial Biotechnology
• ☆ Bioenergy & Biofuels
• ☆ Microbial Fermentation
• ☆ Blotting

Services

• Writing

Writing Medical Writing, Technical Writing, Newswriting

Work Experience

Scientific Communications Specialist

BioNexora Pty Ltd

March 2025 - Present

Research Assistant - Research Associate

Biofuels Research Team (BRTeam)

June 2018 - December 2019

Research Assistant - Research Associate

University of Tehran

April 2014 - November 2017

Editing Manager

University of Tehran

January 2016 - June 2017

Education

PhD (Medicine and Health Sciences)

Macquarie University

December 2019 - Present

Master of Science (Microbiology) (Microbiology)

University of Tehran

February 2011 - September 2013

Bachelor of Science (Microbiology) (Microbiology)

University of Pune

August 2006 - April 2009

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

The roles of the kynurenine pathway in COVID-19 neuropathogenesis @article{cb87f7163fc74d6b9636e3d326cc30d2, title = "The roles of the kynurenine pathway in COVID-19 neuropathogenesis", abstract = "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly contagious respiratory disease Corona Virus Disease 2019 (COVID-19) that may lead to various neurological and psychological disorders that can be acute, lasting days to weeks or months and possibly longer. The latter is known as long-COVID or more recently post-acute sequelae of COVID (PASC). During acute COVID-19 infection, a strong inflammatory response, known as the cytokine storm, occurs in some patients. The levels of interferon‐γ (IFN‐γ), interferon-β (IFN-β), interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are particularly increased. These cytokines are known to activate the enzyme indoleamine 2,3-dioxygenase 1 (IDO-1), catalysing the first step of tryptophan (Trp) catabolism through the kynurenine pathway (KP) leading to the production of several neurotoxic and immunosuppressive metabolites. There is already data showing elevation in KP metabolites both acutely and in PASC, especially regarding cognitive impairment. Thus, it is likely that KP involvement is significant in SARS-CoV-2 pathogenesis especially neurologically.", keywords = "COVID-19, Kynurenine pathway, Long COVID, Neurological manifestations, SARS-CoV-2, Tryptophan", author = "Mona Dehhaghi and Mostafa Heydari and Panahi, {Hamed Kazemi Shariat} and Lewin, {Sharon R.} and Benjamin Heng and Brew, {Bruce J.} and Guillemin, {Gilles J.}", note = "Copyright the Author(s) 2024. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2024", month = oct, doi = "10.1007/s15010-024-02293-y", language = "English", volume = "52", pages = "2043--2059", journal = "Infection", issn = "0300-8126", publisher = "Springer, Springer Nature", number = "5", } . Infection.

Targeting microRNAs as a promising anti-cancer therapeutic strategy against traffic-related air pollution-mediated lung cancer @article{8728f5c041ae442f8471a31f7a26b7af, title = "Targeting microRNAs as a promising anti-cancer therapeutic strategy against traffic-related air pollution-mediated lung cancer", abstract = "Air pollutants are increasingly emitted into the atmosphere because of the high dependency of humans on fossil-derived fuels. Wind speed and direction assisted high dispersibility and uncontrolled nature of air pollution across geo-/demographical borders, making it one of the major global concerns. Besides climate change, air pollution has been found to be associated with various diseases, such as cancer. Lung cancer, which is the world{\textquoteright}s most common type of cancer, has been found to be associated with traffic-related air pollution. Research and political efforts have been taken to explore green/renewable energy sources. However, these efforts at the current intensity cannot cope with the increasing need for fossil fuels. More specifically, political tensions such as the Russian-Ukraine war, economic tension (e.g., China-USA economic tensions), and other issues (e.g., pandemic, higher inflation rate, and poverty) significantly hindered phasing out fossil fuels. In this context, an increasing global population will be exposed to traffic-related air pollution, which justifies the current uptrend in the number of lung cancer patients. To combat this health burden, novel treatments with higher efficiency and specificity must be designed. One of the potential “life changer” options is microRNA (miRNA)-based therapy to target the expression of oncogenic genes. That said, this review discusses the association of traffic-related air pollution with lung cancer, the changes in indigenous miRNAs in the body during lung cancer, and the current status of miRNA therapeutics for lung cancer treatment. We believe that the article will significantly appeal to a broad readership of oncologists, environmentalists, and those who work in the field of (bio)energy. It may also gain the policymakers{\textquoteright} attention to establish better health policies and regulations about air pollution, for example, by promoting (bio)fuel exploration, production, and consumption.", keywords = "Lung cancer, MicroRNA, Nitrogen oxides, Non-coding RNA, Particulate matter, Treatment", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Guillemin, {Gilles J.} and Wanxi Peng and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2024", month = jun, doi = "10.1007/s10555-023-10142-x", language = "English", volume = "43", pages = "657--672", journal = "Cancer and Metastasis Reviews", issn = "0167-7659", publisher = "Springer", number = "2", } . Cancer and Metastasis Reviews.

Nanotechnology applications in biodiesel processing and production @article{0c3ef3caeb5f46d49e675419935da9d5, title = "Nanotechnology applications in biodiesel processing and production: a comprehensive review", abstract = "The wide application of diesel engines globally and the resulting exhaust emissions have been the driving force behind producing eco-friendly alternatives to fossil diesel. Biodiesel derived from triglycerides is a promising replacement for fossil diesel due to less contribution to greenhouse gases and other harmful emissions. Transesterification is a widely adopted production method for converting triglycerides into alkyl esters, primarily owing to its superior conversion efficiency. Both homogeneous and heterogeneous catalysts, as well as enzymes, can be utilized to catalyze this process. However, commonly used catalysts often exhibit significant technical, economic, and environmental challenges, which can compromise the sustainability aspects of biodiesel production. Consequently, efforts are being directed towards developing sustainable catalysts in alignment with the United Nations Sustainable Development Goals. Among the proposed solutions, the application of nanomaterials has emerged as a promising avenue to address the limitations of conventional catalysts in the transesterification reaction. Compared with conventional catalysts, nanocatalysts have a substantially higher surface-to-volume ratio, amplifying the catalytic activity and eliminating many intrinsic limitations. In addition to their increased surface-to-volume ratio, nanocatalysts provide enhanced activity, stability, and reusability, along with greater resistance to saponification. Moreover, nanomaterials can enhance lipid extraction from feedstocks, especially from third-generation resources, due to the lack of toxicity and, subsequently, less environmental concern. While achieving promising outcomes, advancing nanotechnology as an environmentally friendly and economical approach to processing feedstocks and biodiesel production necessitates continued scrutiny. This issue is due to the potential for nanomaterials to infiltrate living systems, giving rise to various safety concerns. Thus, this review summarizes the opportunities and limitations of the mainstream applications of nanotechnology in biodiesel research.", keywords = "Biodiesel production, Nanocatalyst, Nanomaterials, Oil extraction, Sustainable production, Transesterification", author = "{Kazemi Shariat Panahi}, Hamed and Homa Hosseinzadeh-Bandbafha and Mona Dehhaghi and Yasin Orooji and Omid Mahian and Hossein Shahbeik and Mohammadali Kiehbadroudinezhad and Kalam, {Md Abul} and Hassan Karimi-Maleh and {Salehi Jouzani}, Gholamreza and Changtong Mei and Guillemin, {Gilles G.} and Nizami, {Abdul Sattar} and Yajing Wang and Gupta, {Vijai Kumar} and Lam, {Su Shiung} and Junting Pan and Kim, {Ki Hyun} and Wanxi Peng and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2024", month = mar, doi = "10.1016/j.rser.2023.114219", language = "English", volume = "192", pages = "1--27", journal = "Renewable and Sustainable Energy Reviews", issn = "1364-0321", publisher = "Elsevier", } . Renewable and Sustainable Energy Reviews.

Biomass to biofuels using hydrothermal liquefaction @article{277ab16ba14445aaa4e1bf25b79e0d9e, title = "Biomass to biofuels using hydrothermal liquefaction: a comprehensive review", abstract = "The utilization of renewable fuel alternatives holds promise for reducing the financial burden of regulatory compliance and the social responsibility associated with greenhouse gas emissions. Hydrothermal liquefaction (HTL) is one of the most versatile technologies for converting renewable biomass feedstocks (especially in the wet state) into biofuel (biocrude oil) in a compact plant. Therefore, this review is devoted to thoroughly reviewing and critically discussing biocrude oil production from biomass feedstocks through the HTL process. This review starts by discussing the principles of biomass HTL processing and product upgrading, aiming to provide a grounded and broad understanding of current developments in this domain. The data reported in the published literature are analyzed and visualized in order to scrutinize the effects of the main process parameters on the quantity, quality, cost, and environmental impacts of resultant biofuels. Higher biocrude oil yields are obtained at temperatures, pressures, and residual times between 300 and 350 °C, 24–27 MPa, and 15–25 min, respectively. Concerning yield and calorific value, biocrude oil derived from homogeneous catalysts demonstrates figures of 23.6 % and 32.1 MJ/kg, whereas that from heterogeneous catalysts exhibits percentages of 66.8 % and 40 MJ/kg, respectively. The challenges and prospects for the future development of biocrude oil are also discussed. HTL has a long way to go before being used for biofuel production on a large scale. Future studies appear to be directed towards the use of HTL technology under the biorefinery framework to maximize the exploitation of biomass into value-added products, while minimizing waste generation.", keywords = "Biocrude oil, Biofuel, Biomass feedstock, Catalyst, Hydrothermal liquefaction, Upgrading", author = "Hossein Shahbeik and {Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Guillemin, {Gilles J.} and Alireza Fallahi and Homa Hosseinzadeh-Bandbafha and Hamid Amiri and Mohammad Rehan and Deepak Raikwar and Hannes Latine and Bruno Pandalone and Benyamin Khoshnevisan and Christian Sonne and Luigi Vaccaro and Nizami, {Abdul Sattar} and Gupta, {Vijai Kumar} and Lam, {Su Shiung} and Junting Pan and Rafael Luque and Bert Sels and Wanxi Peng and Meisam Tabatabaei and Mortaza Aghbashlo", year = "2024", month = jan, doi = "10.1016/j.rser.2023.113976", language = "English", volume = "189", pages = "1--38", journal = "Renewable and Sustainable Energy Reviews", issn = "1364-0321", publisher = "Elsevier", number = "Part B", } . Renewable and Sustainable Energy Reviews.

Nanomaterials and their role in advancing biodiesel feedstock production @article{018db5db6a784bfa8eef73e5d4bbba77, title = "Nanomaterials and their role in advancing biodiesel feedstock production: a comprehensive review", abstract = "Sustainable socio-economic development largely depends on the sustainability of the energy supply from economic, environmental, and public health perspectives. Fossil fuel combustion only meets the first element of this equation and is hence rendered unsustainable. Biofuels are advantageous from a public health perspective, but their environmental and economic sustainability might be questioned considering the conflicts surrounding their feedstocks, including land use change and fuel vs. food conflict. Therefore, it is imperative to put more effort into addressing the downsides of biofuel production using advanced technologies, such as nanotechnology. In light of that, this review strives to scrutinize the latest developments in the application of nanotechnology in producing biodiesel, a promising alternative to fossil diesel with proven environmental and health benefits. The main focus is placed on nanotechnology applications in the feedstock production stage. First, the latest findings concerning the application of nanomaterials as nanofertilizers and nanopesticides to improve the performance of oil crops are presented and critically discussed. Then, the most promising results reported recently on applying nanotechnology to boost biomass and oil production by microalgae and facilitating microalgae harvesting are reviewed and mechanistically explained. Finally, the promises held by nanomaterials to enhance animal fat production in livestock, poultry, and aquaculture systems are elaborated. Despite the favorable features of using nanotechnology in biodiesel feedstock production, the presence of nanoparticles in living systems is also associated with important health and environmental challenges, which are critically covered and discussed in this work.", keywords = "Animal fat, Biodiesel, Feedstock production, Microalgae oil, Nanotechnology, Oil crops", author = "Homa Hosseinzadeh-Bandbafha and Panahi, {Hamed Kazemi Shariat} and Mona Dehhaghi and Yasin Orooji and Hossein Shahbeik and Omid Mahian and Hassan Karimi-Maleh and Alawi Sulaiman and Changtong Mei and Mohammadali Kiehbadroudinezhad and Nizami, {Abdul Sattar} and Guillemin, {Gilles G.} and Lam, {Su Shiung} and Wanxi Peng and Xiangmeng Chen and Kim, {Ki Hyun} and Mortaza Aghbashlo and Meisam Tabatabaei", note = "Copyright BRTeam 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2023", month = sep, doi = "10.18331/BRJ2023.10.3.4", language = "English", volume = "10", pages = "1901--1932", journal = "Biofuel Research Journal", issn = "2292-8782", publisher = "Green Wave Publishing of Canada", number = "3", } . Biofuel Research Journal.

Current and emerging applications of saccharide-modified chitosan @article{6a6452566cfb4e009c6a3997236cdf8b, title = "Current and emerging applications of saccharide-modified chitosan: a critical review", abstract = "Chitin, as the main component of the exoskeleton of Arthropoda, is a highly available natural polymer that can be processed into various value-added products. Its most important derivative, i.e., chitosan, comprising β-1,4-linked 2-amino-2-deoxy-β-d-glucose (deacetylated d-glucosamine) and N-acetyl-d-glucosamine units, can be prepared via alkaline deacetylation process. Chitosan has been used as a biodegradable, biocompatible, non-antigenic, and nontoxic polymer in some in-vitro applications, but the recently found potentials of chitosan for in-vivo applications based on its biological activities, especially antimicrobial, antioxidant, and anticancer activities, have upgraded the chitosan roles in biomaterials. Chitosan approval, generally recognized as a safe compound by the United States Food and Drug Administration, has attracted much attention toward its possible applications in diverse fields, especially biomedicine and agriculture. Despite some favorable characteristics, the chitosan's structure should be customized for advanced applications, especially due to its drawbacks, such as low drug-load capacity, low solubility, high viscosity, lack of elastic properties, and pH sensitivity. In this context, derivatization with relatively inexpensive and highly available mono- and di-saccharides to soluble branched chitosan has been considered a {"}game changer{"}. This review critically scrutinizes the emerging technologies based on the synthesis and application of lactose- and galactose-modified chitosan as two important chitosan derivatives. Some characteristics of chitosan derivatives and biological activities have been detailed first to understand the value of these natural polymers. Second, the saccharide modification of chitosan has been discussed briefly. Finally, the applications of lactose- and galactose-modified chitosan have been scrutinized and compared to native chitosan to provide an insight into the current state-of-the research for stimulating new ideas with the potential of filling research gaps.", keywords = "Drug delivery, galactosylated chitosan, hydrogel, lactose, wound dressing", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Hamid Amiri and Guillemin, {Gilles J.} and Gupta, {Vijai Kumar} and Ahmad Rajaei and Yadong Yang and Wanxi Peng and Junting Pan and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2023", month = sep, doi = "10.1016/j.biotechadv.2023.108172", language = "English", volume = "66", pages = "1--23", journal = "Biotechnology Advances", issn = "0734-9750", publisher = "Elsevier", } . Biotechnology Advances.

Applications of nanotechnology in biodiesel combustion and post-combustion stages @article{45cfdd442e914f95a28c5ebb588fbdb0, title = "Applications of nanotechnology in biodiesel combustion and post-combustion stages", abstract = "Diesel fuel exhibits high efficiency, durability, and profitability for combustion engines but remains a major source of airborne pollutants, including particulate matter and nitrogen oxides. To address the urgent need for alternative energy sources and reduce greenhouse gas emissions, biodiesel has been developed as a potential replacement for petrodiesel. However, biodiesel combustion has its drawbacks, especially the emission of nitrogen oxides, which hinder its ability to replace petrodiesel sustainably. Nanotechnology has been proposed as a promising solution to improve biodiesel combustion and enhance its competitiveness against petrodiesel. Various studies have shown that both metallic and non-metallic nanoparticles can potentially enhance biodiesel performance during combustion, improving fuel combustion efficiency by 11.7% and 13.4% while reducing air pollutants such as carbon monoxide by 24.2% and 24.8% and unburned hydrocarbons by 11.5% and 25.3%, respectively. While both types of nanoparticles can potentially reduce greenhouse gas and particulate matter emissions, their impact on nitrogen oxide emissions varies. Non-metallic nanoparticles are more successful in reducing nitrogen oxide emissions, achieving reductions of up to 13.0%, while metallic nanoparticles have been shown to increase nitrogen oxides by 0.8% on average. In the post-combustion phase, nanoparticles can filter pollution from diesel engines with more than 99% efficiency, reducing friction, enhancing engine durability, preventing deposit formation, and reducing maintenance costs. However, using nanoparticles in biodiesel has several drawbacks, including toxicity to humans and ecosystems, high prices, lack of standardization, and limited understanding of their long-term effects. Further research is needed to address these constraints and ensure the safe and effective use of nanoparticles in biodiesel combustion. The potential benefits of nanotechnology for improving biodiesel combustion and reducing emissions can make this research field an exciting avenue for future research and development.", keywords = "Biodiesel, Combustion, Health risk, Nanotechnology, Nitrogen oxides, Sustainability", author = "Homa Hosseinzadeh-Bandbafha and {Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Yasin Orooji and Hossein Shahbeik and Omid Mahian and Hassan Karimi-Maleh and Kalam, {Md Abul} and {Salehi Jouzani}, Gholamreza and Changtong Mei and Abdul-Sattar Nizami and Guillemin, {Gilles G.} and Gupta, {Vijai Kumar} and Lam, {Su Shiung} and Yadong Yang and Wanxi Peng and Junting Pan and Ki-Hyun Kim and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2023", month = aug, doi = "10.1016/j.rser.2023.113414", language = "English", volume = "182", pages = "1--17", journal = "Renewable and Sustainable Energy Reviews", issn = "1364-0321", publisher = "Elsevier", } . Renewable and Sustainable Energy Reviews.

Oncolytic viruses as a promising therapeutic strategy against the detrimental health impacts of air pollution @article{9f2ee436a71b44f6ab652479ca0215a0, title = "Oncolytic viruses as a promising therapeutic strategy against the detrimental health impacts of air pollution: the case of glioblastoma multiforme", abstract = "Human livelihood highly depends on applying different sources of energy whose utilization is associated with air pollution. On the other hand, air pollution may be associated with glioblastoma multiforme (GBM) development. Unlike other environmental causes of cancer (e.g., irradiation), air pollution cannot efficiently be controlled by geographical borders, regulations, and policies. The unavoidable exposure to air pollution can modify cancer incidence and mortality. GBM treatment with chemotherapy or even its surgical removal has proven insufficient (100% recurrence rate; patient's survival mean of 15 months; 90% fatality within five years) due to glioma infiltrative and migratory capacities. Given the barrage of attention and research investments currently plowed into next-generation cancer therapy, oncolytic viruses are perhaps the most vigorously pursued. Provision of an insight into the current state of the research and future direction is essential for stimulating new ideas with the potentials of filling research gaps. This review manuscript aims to overview types of brain cancer, their burden, and different causative agents. It also describes why air pollution is becoming a concerning factor. The different opinions on the association of air pollution with brain cancer are reviewed. It tries to address the significant controversy in this field by hypothesizing the air-pollution-brain-cancer association via inflammation and atopic conditions. The last section of this review deals with the oncolytic viruses, which have been used in, or are still under clinical trials for GBM treatment. Engineered adenoviruses (i.e., DNX-2401, DNX-2440, CRAd8-S-pk7 loaded Neural stem cells), herpes simplex virus type 1 (i.e., HSV-1 C134, HSV-1 rQNestin34.5v.2, HSV-1 G207, HSV-1 M032), measles virus (i.e., MV-CEA), parvovirus (i.e., ParvOryx), poliovirus (i.e., Poliovirus PVSRIPO), reovirus (i.e., pelareorep), moloney murine leukemia virus (i.e., Toca 511 vector), and vaccinia virus (i.e., vaccinia virus TG6002) as possible life-changing alleviations for GBM have been discussed. To the best of our knowledge, this review is the first review that comprehensively discusses both (i) the negative/positive association of air pollution with GBM; and (ii) the application of oncolytic viruses for GBM, including the most recent advances and clinical trials. It is also the first review that addresses the controversies over air pollution and brain cancer association. We believe that the article will significantly appeal to a broad readership of virologists, oncologists, neurologists, environmentalists, and those who work in the field of (bio)energy. Policymakers may also use it to establish better health policies and regulations about air pollution and (bio)fuels exploration, production, and consumption.", keywords = "Atopic condition, Brain tumor, Clinical trial, Glioblastoma multiforme, Inflammation, Traffic-related air pollution, Virus-cell interaction", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Lam, {Su Shiung} and Wanxi Peng and Mortaza Aghbashlo and Meisam Tabatabaei and Guillemin, {Gilles J.}", year = "2022", month = nov, doi = "10.1016/j.semcancer.2021.05.013", language = "English", volume = "86", pages = "1122--1142", journal = "Seminars in Cancer Biology", issn = "1044-579X", publisher = "Academic Press", number = "Part 3", } . Seminars in Cancer Biology.

Synthesis of liquid biofuels from biomass by hydrothermal gasification @article{5d4083df469b40e49307f4eac670e6e6, title = "Synthesis of liquid biofuels from biomass by hydrothermal gasification: a critical review", abstract = "Liquid transportation biofuel production is a promising strategy to reduce greenhouse gas emissions. Hydrothermal gasification (HTG) has shown great potential as an effective method for valorizing wet biomass. The high-quality syngas produced using the HTG process can be chemically/biochemically converted to liquid biofuels. Therefore, this paper aims to comprehensively review and critically discuss syngas production from biomass using the HTG process and its conversion into liquid biofuels. The basics and mechanisms of biomass HTG processing are first detailed to provide a comprehensive and deep understanding of the process. Second, the effects of the main operating parameters on the performance of the HTG process are numerically analyzed and mechanistically discussed. The syngas cleaning/conditioning and Fischer-Tropsch (FT) synthesis are then detailed, aiming to produce liquid biofuels. The economic performance and environmental impacts of liquid biofuels using the HTG-FT route are evaluated. Finally, the challenges and prospects for future development in this field are presented. Overall, the maximum total gas yield in the HTG process is obtained at temperature, pressure, and residence time in the range of 450–500 °C, 28–30 MPa, and 30–60 min, respectively. The highest C5+ liquid hydrocarbon selectivity in the FT process is achieved at temperatures between 200 and 240 °C. Generally, effective conversion of biomass to syngas using the HTG process and its successful upgrading using the FT process can offer a viable route for producing liquid biofuels. Future studies should use HTG technology in the biorefinery context to maximize biomass valorization and minimize waste generation.", keywords = "Catalyst, Fischer-tropsch synthesis, Hydrothermal gasification, Liquid biofuels, Supercritical water, Syngas", author = "Hossein Shahbeik and Wanxi Peng and {Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Guillemin, {Gilles J.} and Alireza Fallahi and Hamid Amiri and Mohammad Rehan and Deepak Raikwar and Hannes Latine and Bruno Pandalone and Benyamin Khoshnevisan and Christian Sonne and Luigi Vaccaro and Nizami, {Abdul Sattar} and Gupta, {Vijai Kumar} and Lam, {Su Shiung} and Junting Pan and Rafael Luque and Bert Sels and Meisam Tabatabaei and Mortaza Aghbashlo", year = "2022", month = oct, doi = "10.1016/j.rser.2022.112833", language = "English", volume = "167", pages = "1--24", journal = "Renewable and Sustainable Energy Reviews", issn = "1364-0321", publisher = "Elsevier", } . Renewable and Sustainable Energy Reviews.

A comprehensive review on anaerobic fungi applications in biofuels production @article{ef1c5bda77a84c0b82dfaaa2188d6859, title = "A comprehensive review on anaerobic fungi applications in biofuels production", abstract = "Anaerobic fungi (Neocallimastigomycota) are promising lignocellulose-degrading microorganisms that can be exploited by the biofuel industry. While natural production of ethanol by these microorganisms is very low, there is a greater potential for their use in the biogas industry. More specifically, anaerobic fungi can contribute to biogas production by either releasing holocellulose or reducing sugars from lignocelluloses that can be used as a substrate by bacteria and methanogens involved in the anaerobic digestion (AD) process or by metabolizing acetate and formate that can be directly consumed by methanogens. Despite their great potential, the appropriate tools for engineering anaerobic fungi have not been established yet. The first section of this review justifies how the biofuel industry can benefit from using anaerobic fungi and is followed by their taxonomy. In the third section, the possibility of using anaerobic fungi for the consolidated production of bioethanol is briefly discussed. Nevertheless, the main focus of this review is on the upstream and mainstream effects of bioaugmentation with anaerobic fungi on the AD process. The present review also scrutinizes the constraints on the way of efficient engineering of anaerobic rumen fungi. By providing this knowledge, this review aims to help research in this field with identifying the challenges that must be addressed by future experiments to achieve the full potentials of these promising microorganisms. To sum up, the pretreatment of lignocelluloses by anaerobic fungi can prevent carbohydrate loss due to respiration (compared to white-rot fungi). Following fungal mixed acid fermentation, the obtained slurry containing sugars and more susceptible holocellulose can be directly consumed by AD microorganisms (bacteria, methanogens). The bioaugmentation of anaerobic fungi into the AD process can increase methane biosynthesis by >3.3 times. Despite this, for the commercial AD process, novel genetic engineering techniques and kits must be developed to efficiently improve anaerobic fungi viability throughout the AD process.", keywords = "Anaerobic digestion, Anaerobic rumen fungi, Bioaugmentation, Bioethanol, Biogas, Neocallimastigomycota", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Guillemin, {Gilles J.} and Gupta, {Vijai Kumar} and Lam, {Su Shiung} and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2022", month = jul, day = "10", doi = "10.1016/j.scitotenv.2022.154521", language = "English", volume = "829", pages = "1--12", journal = "Science of the Total Environment", issn = "0048-9697", publisher = "Elsevier", } . Science of the Total Environment.

The role of kynurenine pathway and NAD+ metabolism in myalgic encephalomyelitis/chronic fatigue syndrome @article{6fe73d8ba5514d8f8395375568087cf5, title = "The role of kynurenine pathway and NAD+ metabolism in myalgic encephalomyelitis/chronic fatigue syndrome", abstract = "Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious, complex, and highly debilitating long-term illness. People with ME/CFS are typically unable to carry out their routine activities. Key hallmarks of the disease are neurological and gastrointestinal impairments accompanied by pervasive malaise that is exacerbated after physical and/or mental activity. Currently, there is no validated cure of biomarker signature for this illness. Impaired tryptophan (TRYP) metabolism is thought to play significant role in the pathobiology of ME/CFS. TRYP is an important precursor for serotonin and the essential pyridine nucleotide nicotinamide adenine dinucleotide (NAD+). TRYP has been associated with the development of some parts of the brain responsible for behavioural functions. The main catabolic route for TRYP is the kynurenine pathway (KP). The KP produces NAD+ and several neuroactive metabolites with neuroprotective (i.e., kynurenic acid (KYNA)) and neurotoxic (i.e., quinolinic acid (QUIN)) activities. Hyperactivation of the KP, whether compensatory or a driving mechanism of degeneration can limit the availability of NAD+ and exacerbate the symptoms of ME/CFS. This review discusses the potential association of altered KP metabolism in ME/CFS. The review also evaluates the role of the patient's gut microbiota on TRYP availability and KP activation. We propose that strategies aimed at raising the levels of NAD+ (e.g., using nicotinamide mononucleotide and nicotinamide riboside) may be a promising intervention to overcome symptoms of fatigue and to improve the quality of life in patients with ME/CFS. Future clinical trials should further assess the potential benefits of NAD+ supplements for reducing some of the clinical features of ME/CFS. ", keywords = "gut microbiota, Kynurenine pathway, myalgic encephalomyelitis/chronic fatigue syndrome, NAD+, tryptophan", author = "Mona Dehhaghi and Panahi, {Hamed Kazemi Shariat} and Bahar Kavyani and Benjamin Heng and Vanessa Tan and Nady Braidy and Guillemin, {Gilles J.}", note = "Copyright the Author(s) 2021. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2022", month = may, day = "18", doi = "10.14336/AD.2021.0824", language = "English", volume = "13", pages = "698--711", journal = "Aging and Disease", issn = "2152-5250", publisher = "International Society on Aging and Disease", number = "3", } . Aging and Disease.

Neuropathological mechanisms of β-N-methylamino-L-alanine (BMAA) with a focus on iron overload and ferroptosis @article{dc5bef4f595b4f44b706f40303ffdc0c, title = "Neuropathological mechanisms of β-N-methylamino-L-alanine (BMAA) with a focus on iron overload and ferroptosis", abstract = "The incidence of neurodegenerative diseases and cyanobacterial blooms is concomitantly increasing worldwide. The cyanotoxin β-N-methylamino-L-alanine (BMAA) is produced by most of the Cyanobacteria spp. This cyanotoxin is described as a potential environmental etiology factor for some sporadic neurodegenerative diseases. Climate change and eutrophication significantly increase the frequency and intensity of cyanobacterial bloom in water bodies. This review evaluates different neuropathological mechanisms of BMAA at molecular and cellular levels and compares the related studies to provide some useful recommendations. Additionally, the structure and properties of BMAA as well as its microbial origin, especially by gut bacteria, are also briefly covered. Unlike previous reviews, we hypothesize the possible neurotoxic mechanism of BMAA through iron overload. We also discuss the involvement of BMAA in excitotoxicity, TAR DNA-binding protein 43 (TDP-43) translocation and accumulation, tauopathy, and other protein misincorporation and misfolding.", keywords = "Excitotoxicity, Ferroptosis, Iron overload, TAR DNA-binding protein 43 (TDP-43), Tauopathy, β-N-methylamino-L-alanine (BMAA)", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Benjamin Heng and Lane, {Darius J. R.} and Bush, {Ashley I.} and Guillemin, {Gilles J.} and Tan, {Vanessa X.}", year = "2022", month = apr, doi = "10.1007/s12640-021-00455-6", language = "English", volume = "40", pages = "614--635", journal = "Neurotoxicity Research", issn = "1029-8428", publisher = "Springer, Springer Nature", number = "2", } . Neurotoxicity Research.

Bioethanol production from food wastes rich in carbohydrates @article{801df854e87f47ad93ca68548ea6bd07, title = "Bioethanol production from food wastes rich in carbohydrates", abstract = "The inefficient food processing and food leftover management strategies often lead to the wastage of untapped carbohydrate-rich feedstocks. The conversion of these feedstocks into bioethanol can mitigate the emission of greenhouse gases (GHGs) while providing a sustainable and eco-friendly method for disposing of food wastes. In light of the above, the current review scrutinizes various types of food wastes (homogeneous and heterogeneous) and pretreatment methods (physical, chemical, physicochemical, and biological) for their valorization into bioethanol. The main constraints to commercial production of food-waste-derived bioethanol, that is, the requirement for sterilization and collection of feedstocks, are also discussed. The former issue can be addressed by developing an optimized solid-state fermentation process. Employing selective conditions to enrich bioethanol-producing microorganisms can increase the feasibility of this process configuration while inhibiting ethanol-consuming strains. The feedstock collection issue can be minimized by determining the hot spots that are in the vicinity of the large food processing sites.", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Guillemin, {Gilles J.} and Gupta, {Vijai Kumar} and Lam, {Su Shiung} and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2022", month = feb, doi = "10.1016/j.cofs.2021.11.001", language = "English", volume = "43", pages = "71--81", journal = "Current Opinion in Food Science", issn = "2214-7993", publisher = "Elsevier", } . Current Opinion in Food Science.

Engineered bacteria for valorizing lignocellulosic biomass into bioethanol @article{c55494e032c34b4caa7820243e3e1dd0, title = "Engineered bacteria for valorizing lignocellulosic biomass into bioethanol", abstract = "Appropriate bioprocessing of lignocellulosic materials into ethanol could address the world's insatiable appetite for energy while mitigating greenhouse gases. Bioethanol is an ideal gasoline extender and is widely used in many countries in blended form with gasoline at specific ratios to improve fuel characteristics and engine performance. Although the bioethanol production industry has long been operational, finding a suitable microbial agent for the efficient conversion of lignocelluloses is still an active field of study. Among available microbial candidates, engineered bacteria may be promising ethanol producers while may show other desired traits such as thermophilic nature and high ethanol tolerance. This review provides the current knowledge on the introduction, overexpression, and deletion of the genes that have been performed in bacterial hosts to achieve higher ethanol yield, production rate and titer, and tolerance. The constraints and possible solutions and economic feasibility of the processes utilizing such engineered strains are also discussed.", keywords = "Bioethanol, Consolidated bioprocessing, Gasoline extender, Metabolic engineering, Second generation feedstock, Thermophilic bacteria", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Somayeh Dehhaghi and Guillemin, {Gilles J.} and Lam, {Su Shiung} and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2022", month = jan, doi = "10.1016/j.biortech.2021.126212", language = "English", volume = "344", pages = "1--12", journal = "Bioresource Technology", issn = "0960-8524", publisher = "Elsevier", number = "Part A", } . Bioresource Technology.

The effects of nanoadditives on the performance and emission characteristics of spark-ignition gasoline engines @article{e81f2c4737b54500a49a3c4e4a495f60, title = "The effects of nanoadditives on the performance and emission characteristics of spark-ignition gasoline engines: a critical review with a focus on health impacts", abstract = "Gasoline is currently the main fuel of choice in many cities worldwide, and hence, the consequent exposure to its emissions, i.e., CO, NOX, unreacted hydrocarbons, particulate matters, lead, sulfur dioxide, and ozone, is inevitable. Among the various solutions put forth to mitigate the toxic gasoline-related air pollution, while improving fuel performance at the same time, is the application of nanoparticles. Considering the above, the present paper aims to review and critically discuss the improvements made in engine performance and exhaust emission parameters by adding nanosized fuel additives in gasoline. Overall, the addition of fuel nanoadditives enhances the thermo-physical properties of the fuel and improves combustion characteristics. Moreover, the inclusion of the fuel nanoadditives generally results in early combustion and shortened ignition delay. In more detail, the optimum quantity of fuel nanoadditives is associated with improvements in ignition characteristics and reductions in exhaust emissions. The present work also scrutinizes the adverse health effects of various gasoline-related emissions. Finally, possible mechanisms underlying the improvements in gasoline properties and its combustion in the presence of nanoadditives are also reviewed and discussed.", keywords = "Fuel nanoadditive, Gasoline, Health impact, Spark-ignition engines, Traffic-related air pollution", author = "Mona Dehhaghi and {Kazemi Shariat Panahi}, Hamed and Mortaza Aghbashlo and Lam, {Su Shiung} and Meisam Tabatabaei", year = "2021", month = jun, day = "15", doi = "10.1016/j.energy.2021.120259", language = "English", volume = "225", pages = "1--24", journal = "Energy", issn = "0360-5442", publisher = "Elsevier", } . Energy.

The gut microbiota, kynurenine pathway, and immune system interaction in the development of brain cancer @article{555009375b57416c8f01d3cf0dc7c9d2, title = "The gut microbiota, kynurenine pathway, and immune system interaction in the development of brain cancer", abstract = "Human gut microbiota contains a large, complex, dynamic microbial community of approximately 1014 microbes from more than 1,000 microbial species, i.e., equivalent to 4 × 106 genes. Numerous evidence links gut microbiota with human health and diseases. Importantly, gut microbiota is involved in the development and function of the brain through a bidirectional pathway termed as the gut-brain axis. Interaction between gut microbiota and immune responses can modulate the development of neuroinflammation and cancer diseases in the brain. With respect of brain cancer, gut microbiota could modify the levels of antioxidants, amyloid protein and lipopolysaccharides, arginase 1, arginine, cytochrome C, granulocyte–macrophage colony-stimulating factor signaling (GM-CSF), IL-4, IL-6, IL-13, IL-17A, interferon gamma (IFN-γ), reactive oxygen species (ROS), reactive nitrogen species (e.g., nitric oxide and peroxynitrite), short-chain fatty acids (SCFAs), tryptophan, and tumor necrosis factor-β (TGF-β). Through these modifications, gut microbiota can modulate apoptosis, the aryl hydrocarbon receptor (AhR), autophagy, caspases activation, DNA integrity, microglia dysbiosis, mitochondria permeability, T-cell proliferation and functions, the signal transducer and activator of transcription (STAT) pathways, and tumor cell proliferation and metastasis. The outcome of such interventions could be either oncolytic or oncogenic. This review scrutinizes the oncogenic and oncolytic effects of gut microbiota by classifying the modification mechanisms into (i) amino acid deprivation (arginine and tryptophan); (ii) kynurenine pathway; (iii) microglia dysbiosis; and (iv) myeloid-derived suppressor cells (MDSCs). By delineating the complexity of the gut-microbiota-brain-cancer axis, this review aims to help the research on the development of novel therapeutic strategies that may aid the efficient eradication of brain cancers.", keywords = "3-dioxygenase-1, anti-tumor T-cells, glioblastoma, gut microbiota, indoleamine 2, kynurenine pathway, myeloid-derived suppressor cells, tryptophan", author = "Mona Dehhaghi and {Kazemi Shariat Panahi}, Hamed and Benjamin Heng and Guillemin, {Gilles J.}", note = "Copyright the Author(s) 2020. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2020", month = nov, day = "19", doi = "10.3389/fcell.2020.562812", language = "English", volume = "8", pages = "1--15", journal = "Frontiers in Cell and Developmental Biology", issn = "2296-634X", publisher = "Frontiers Media SA", } . Frontiers in Cell and Developmental Biology.

A comprehensive review of engineered biochar @article{f535721bbbbb408cb20dbb7565524d07, title = "A comprehensive review of engineered biochar: production, characteristics, and environmental applications", abstract = "A sustainable management of environment and agriculture is crucial to protect soil, water, and air during intensified agriculture practices as well as huge industrial and transportation activities. A promising tool to address these challenges could be the application of biochar, a carbonaceous product of biomass pyrolysis. The efficiency of biochar could be improved through physical, chemical and microbial procedures. Engineered biochar could then be applied for various applications ranging from sustainable agriculture to pollution remediation and catalytic reactions. Biochar engineering allows achieving biochar properties which are optimum for specific applications and/or under specific conditions. This would lead to harnessing the favorable features of biochar and to enhance its efficiency while simultaneously minimizing the existing tradeoffs. This review covers the production and applications of engineered biochar by summarizing great deals of research and knowledge on the field. Unlike previous reviews, herein biochar physical and chemical properties and the factors affecting them (i.e., biomass nature and pyrolysis conditions) have been discussed in detail. Moreover, the contributions of each physical and chemical activation/modification method to improving biochar characteristics with respect to environmental applications have been specifically scrutinized. By providing the state-of-the-art knowledge about engineered biochar production, properties, and applications, this review aims to help research in this field for identification of the culprits that must be addressed in future experiments.", keywords = "Charcoal, Designer biochar, Environmental management, Functional group, Green and sustainable remediation, Physical and chemical characteristics", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Ok, {Yong Sik} and Nizami, {Abdul Sattar} and Benyamin Khoshnevisan and Mussatto, {Solange I.} and Mortaza Aghbashlo and Meisam Tabatabaei and Lam, {Su Shiung}", year = "2020", month = oct, day = "10", doi = "10.1016/j.jclepro.2020.122462", language = "English", volume = "270", pages = "1--29", journal = "Journal of Cleaner Production", issn = "0959-6526", publisher = "Elsevier", } . Journal of Cleaner Production.

(2020). A comprehensive review of engineered biochar: production, characteristics, and environmental applications . Journal of Cleaner Production.

(2020). Herpetosiphon Secondary Metabolites Inhibit Amyloid-β Toxicity in Human Primary Astrocytes . Journal of Alzheimer's Disease.

In-situ recovery of persipeptides from Streptomyces zagrosensis fermentation broth by enhanced adsorption @article{77d0190b58bd46a4a1e6ccbc63a00b65, title = "In-situ recovery of persipeptides from Streptomyces zagrosensis fermentation broth by enhanced adsorption", abstract = "Background: Drug discovery process is growing considerably due to the noteworthy resource of natural products. Persipeptides A and B are cyclopeptide antibiotics, which are produced by Streptomyces zagrosensis UTMC 1154. Although extraction of culture broth with the help of solvent has been optimized previously, no effort for in-situ extraction of persipeptides has been done yet. Objective: To produce a high quantity of persipeptides for further drug evaluation, it is crucial to design approaches aimed at improvement of the extraction yield. Materials and Methods: Amberlite XAD-16N was employed into the fermentation culture medium of S. zagrosensis in order to enhance the in-situ extraction of persipeptides. Effects of resin content (%), resin addition time (h), and fermentation time (day) were investigated by a two-level full factorial experimental design. Results: The main factors of resin content (%) and the interaction of resin content (%) with resin addition time (day) were found to be important using ANOVA. The results showed the amount of 0.33 % (w.v-1) amberlite XAD-16N added at 27.2 h post-inoculation was the most effective combination to increase the efficiency of in-situ adsorption capacity of persipeptides. Conclusions: The provided method requires 3.3 g resin and 200 mL methanol for the extraction of persipeptides from each liter of fermentation culture of S. zagrosensis in less than 15 min. Apart from cost-efficiently and simplicity, this procedure enhanced the recovery of persipeptides by 7 % and 3 times, compared to ISP2 medium without any resin after 4 and 7 days of fermentation, respectively. Therefore, this method can be regarded as a cost-efficient enhancement approach for the production of these newly-discovered metabolites before implementing the genetic manipulation or intensive media optimization, demanding considerable time and effort.", keywords = "Amberlite Resin, Experimental design, Full factorial optimization, In situ metabolic extraction, Natural product, Persipeptides", author = "Panahi, {Hamed Kazemi Shariat} and Fatemeh Mohammadipanah and Farzaneh Rahmati and Aliakbar Tarlani and Javad Hamedi", note = "Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2020", month = apr, doi = "10.30498/ijb.2020.125909.2231", language = "English", volume = "18", pages = "1--10", journal = "Iranian Journal of Biotechnology", issn = "1728-3043", publisher = "National Institute of Genetic Engineering and Biotechnology", number = "2", } . Iranian Journal of Biotechnology.

A comprehensive review on recent biological innovations to improve biogas production, Part 1 @article{2926a41cc1854c628bdf8bc3800d284a, title = "A comprehensive review on recent biological innovations to improve biogas production, Part 1: upstream strategies", abstract = "This study reviews the innovations and optimizations in biogas production from the biological perspective reported by recently published patents and research works. The proposed biological strategies can be categorized into three different groups, i.e., upstream, mainstream, and downstream approaches. In the first part of this review, upstream strategies, including pretreatments by fungal, microbial consortium, and enzymatic as well as some other biological methods including microaeration, composting, ensiling, and genetic and metabolic engineering are discussed in detail. The impacts of upstream strategies on biogas production as well as their potentials in further improving the biogas industry are comprehensively scrutinized. Despite their promising impacts on biogas production, such biological innovations are time-consuming and require extra equipment and facilities that should be addressed in future studies. Overall, most information on biogas production has been generated through lab-scale investigations and not by commercial plants, undermining the commercial value of these data for the right decision-making. Pilot data would be necessary for techno-economic analyses with acceptable accuracies. Therefore, the future efforts should be directed toward providing the missing data for re-engineering designs, calculations, and life cycle assessment (LCA) of the newly designed biogas plants.", keywords = "Anaerobic digestion, Biogas production, Biological treatment, Lignocellulose, Pretreatment, Upstream strategy, Environmental management, Greenhouse gas (GHG) emissions, Renewable energy, electricity generation", author = "Meisam Tabatabaei and Mortaza Aghbashlo and Elena Valijanian and {Kazemi Shariat Panahi}, Hamed and Nizami, {Abdul Sattar} and Hossein Ghanavati and Alawi Sulaiman and Safoora Mirmohamadsadeghi and Keikhosro Karimi", year = "2020", month = feb, day = "1", doi = "10.1016/j.renene.2019.07.037", language = "English", volume = "146", pages = "1204--1220", journal = "Renewable Energy", issn = "0960-1481", publisher = "Elsevier", } . Renewable Energy.

A comprehensive review on recent biological innovations to improve biogas production, Part 2 @article{57eaaa4a6b5b4e16a8fead9ab494c969, title = "A comprehensive review on recent biological innovations to improve biogas production, Part 2: mainstream and downstream strategies", abstract = "This review is aimed at detailing and discussing biological innovations and optimizations including upstream, mainstream, and downstream approaches in biogas production elaborated in the recently published patents and research papers. In the first part of this review, upstream strategies including pretreatments by fungal, microbial consortium, and enzymatic as well as some other biological methods including microaeration, composting, ensiling, and genetic and metabolic engineering were comprehensively presented and duly discussed. Despite the fact that these approaches hold great promise for improving the quantity and quality of the evolved biogas, the need for more processing time and extra equipment are the main drawbacks of such strategies. In the second part of this review, mainstream and downstream strategies are reviewed, and their merits and limitations are outlined. Bioaugmentation, anaerobic co-digestion, and integrated biogas production are evaluated as mainstream strategies. Finally, downstream biological approaches used for removal of CO2, H2S, and other impurities are reviewed and discussed. Among the mainstream biological techniques, bioaugmentation is highly advised to accelerate start-up periods at commercial scale while anaerobic co-digestion is recommended to not only enhance biogas yield throughout the operation but also to take advantage of different waste streams. Such mainstream strategies could contribute to improving the economic facets of biogas plants. Despite their currently underdeveloped status, downstream techniques for biological removal of biogas impurities are expected to replace their physiochemical counterparts at industrial scale in future owing to increasingly stringent environmental regulations.", keywords = "Anaerobic digestion, Biogas production, Biological innovations, Downstream strategies, Mainstream strategies, Methane production, Environmental management, Microorganisms", author = "Meisam Tabatabaei and Mortaza Aghbashlo and Elena Valijanian and {Kazemi Shariat Panahi}, Hamed and Nizami, {Abdul Sattar} and Hossein Ghanavati and Alawi Sulaiman and Safoora Mirmohamadsadeghi and Keikhosro Karimi", year = "2020", month = feb, day = "1", doi = "10.1016/j.renene.2019.07.047", language = "English", volume = "146", pages = "1392--1407", journal = "Renewable Energy", issn = "0960-1481", publisher = "Elsevier", } . Renewable Energy.

(2020). A comprehensive review on recent biological innovations to improve biogas production, Part 1: Upstream strategies . Renewable Energy.

(2020). A comprehensive review on recent biological innovations to improve biogas production, Part 2: Mainstream and downstream strategies . Renewable Energy.

Conversion of residues from agro-food industry into bioethanol in Iran @article{7aa27af277b64647aa07cb43398ee12d, title = "Conversion of residues from agro-food industry into bioethanol in Iran: an under-valued biofuel additive to phase out MTBE in gasoline", abstract = "It is obvious that Iran agricultural industry, unlike Brazil and USA, cannot afford to provide conventional biomass, i.e. sugary or starchy biomass for bioethanol production, mainly due to climatic and geographic conditions. With some exception of date (fruit), first-generation ethanol production triggers food vs. fuel debates in Iran and put nation to hunger. Agricultural products including apple, barley, carrot, corn, grape, orange, potato, rice, sugar beet, sugarcane, and wheat are consumed domestically, exported, or even lost because of poor harvesting and processing conditions such as transportation or packaging. These products may alone generate 21.56 million ton per annum green wastes upon processing in the food industry. Every year about 5.4 billion liters of bioethanol can be produced by establishing second-generation ethanol plants next to the food processing sectors. Seventy-seven-percent of this amount of bioethanol can easily support 5% ethanol (E5) policy to phase out the consumption of 4.2 billion liters methyl tert-butyl ether (MTBE) for raising the octane number of gasoline in the country. If more comprehensive policy is adopted, larger quantities of lignocellulosic feedstocks can be gathered from agro as well as forestry practices. Second-generation bioethanol technology can help Iran to tackle air pollution in its big cities and to address the adverse effects of MTBE on its populations and ecosystem. The other advantages are improvement of fuel security, mitigation of climate change, and development of economy. The motivation can be created through passing a framework policy to cut fossil fuel subsidies, to mandate bioethanol blends in gasoline, and to impose carbon taxes. Development of coherent socially and environmentally relevant strategies and facilitation of investment in bioethanol industry are also necessary.", keywords = "Fermentation, Greenhouse gas, Hydrolysis, Lignocellulose, Liquid biofuel, Pretreatment, Saccharification, Bioethanol, Renewable energy, Biomass, Microorganisms, Fuel additive, Gasohol, MTBE, Air pollution", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Mortaza Aghbashlo and Keikhosro Karimi and Meisam Tabatabaei", year = "2020", month = jan, day = "1", doi = "10.1016/j.renene.2019.06.081", language = "English", volume = "145", pages = "699--710", journal = "Renewable Energy", issn = "0960-1481", publisher = "Elsevier", } . Renewable Energy.

Herpetosiphon secondary metabolites inhibit amyloid-β toxicity in human primary astrocytes @article{164b44f445e14addbdd5d538c18b04a6, title = "Herpetosiphon secondary metabolites inhibit amyloid-β toxicity in human primary astrocytes", abstract = "Background: The accumulation of extracellular plaques containing amyloid-β protein (Aβ) in the brain is one of the main pathological hallmarks of Alzheimer's disease (AD). Aβ peptide can promote the production of highly volatile free radicals and reactive oxygen species (ROS) that can induce oxidative damage to neurons and astrocytes. At present, numerous studies have investigated the neuroprotective and glioprotective effects of natural products derived from plants, animals, and microorganisms. Objective: We investigated the glioprotective effect of secondary metabolites obtained from Herpetosiphon sp. HM 1988 against Aβ40-induced toxicity in human primary astrocytes. Methods: The protective effect of bacterial secondary metabolites against Aβ40-induced inducible nitric oxide synthase (iNOS) activity was evaluated using the citrulline assay. To confirm the iNOS activity, nitrite production was assessed using the fluorometric Griess diazotization assay. Intracellular NAD+ depletion and lactate dehydrogenase (LDH) release in human primary astrocytes were also examined using well-established spectrophotometric assays. Results: Our results indicate that Aβ40 can induce elevation in iNOS and LDH activities, nitrite production, and cellular energy depletion. Importantly, extract of Herpetosiphon sp. HM 1988 decreased iNOS activity, nitrite production, and LDH release. In addition, metabolites of the strain were able to restore cellular energy deficits through inhibition of NAD+ depletion mediated by Aβ40. Conclusion: These findings suggest that Herpetosiphon metabolites may represent a promising, novel source for the prevention of Aβ toxicity in AD.", keywords = "Alzheimer{\textquoteright}s disease, amyloid-β, Herpetosiphon, inducible nitric oxide synthase, natural products, oxidative stress", author = "Mona Dehhaghi and {Kazemi Shariat Panahi}, Hamed and Nady Braidy and Guillemin, {Gilles J.}", year = "2020", month = jan, day = "1", doi = "10.3233/JAD-200116", language = "English", volume = "76", pages = "423--433", journal = "Journal of Alzheimer's Disease", issn = "1387-2877", publisher = "IOS Press", number = "1", } . Journal of Alzheimer's Disease.

(2020). Conversion of residues from agro-food industry into bioethanol in Iran: An under-valued biofuel additive to phase out MTBE in gasoline . Renewable Energy.

A state-of-the-art review on the application of nanomaterials for enhancing biogas production @article{af3caf84618b439db9514f26678feae8, title = "A state-of-the-art review on the application of nanomaterials for enhancing biogas production", abstract = "Anaerobic digestion (AD) of organic wastes is among the most promising approaches used for the simultaneous treatment of various waste streams, environment conservation, and renewable bioenergy generation (biomethane). Among the latest innovations investigated to enhance the overall performance of this process both qualitatively and quantitatively, the application of some nanoparticles (NPs) has attracted a great deal of attention. Typically, the NPs of potential benefit to the AD process could be divided into three groups: (i) zero-valent iron (ZVI) NPs, (ii) metallic and metal oxides NPs, and (iii) carbon-based NPs. The present review focuses on the latest findings reported on the application of these NPs in AD process and presents their various mechanisms of action leading to higher or lower biogas production rates. Among the NPs studies, ZVI NPs could be regarded as the most promising nanomaterials for enhancing biogas production through stabilizing the AD process as well as by stimulating the growth of beneficial microorganisms to the AD process and the enzymes involved. Future research should focus on various attributes of NPs when used as additives in biogas production, including facilitating mixing and pumping operations, enriching the population and diversity of beneficial microorganisms for AD, improving biogas release, and inducing the production and activity of AD-related enzymes. The higher volume of methane-enriched biogas would be translated into higher returns on investment and could therefore, result in further growth of the biogas production industry. Nevertheless, efforts should be devoted to decreasing the price of NPs so that the enhanced biogas and methane production (by over 90%, compared to control) would be more economically justified, facilitating the large-scale application of these compounds. In addition to economic considerations, environmental issues are also regarded as major constraints which should be addressed prior to widespread implementation of NP-augmented AD processes. More specifically, the fate of NPs augmented in AD process should be scrutinized to ensure maximal beneficial impacts while adverse environmental/health consequences are minimized.", keywords = "Anaerobic digestion (AD), Biogas, Mechanism of action, Nanoparticle, Techno-economic analysis, Zero-valent iron (ZVI), Microorganisms, Renewable energy, Waste to energy, Environmental management", author = "Mona Dehhaghi and Meisam Tabatabaei and Mortaza Aghbashlo and {Kazemi Shariat Panahi}, Hamed and Nizami, {Abdul Sattar}", year = "2019", month = dec, day = "1", doi = "10.1016/j.jenvman.2019.109597", language = "English", volume = "251", pages = "1--14", journal = "Journal of Environmental Management", issn = "0301-4797", publisher = "Academic Press", } . Journal of Environmental Management.

(2019). A state-of-the-art review on the application of nanomaterials for enhancing biogas production . Journal of Environmental Management.

(2019). A review on green liquid fuels for the transportation sector: a prospect of microbial solutions to climate change . Biofuel Research Journal.

A comprehensive review on electricity generation and GHG emission reduction potentials through anaerobic digestion of agricultural and livestock/slaughterhouse wastes in Iran @article{0d82b942e8484e5c838d349ac087dbc4, title = "A comprehensive review on electricity generation and GHG emission reduction potentials through anaerobic digestion of agricultural and livestock/slaughterhouse wastes in Iran", abstract = "Agricultural and livestock/slaughterhouse wastes are produced in huge quantities and could be promising sources for electricity generation to partially reduce dependence on fossil-oriented electricity. In light of that, the state of the production for these wastes in different parts of the globe was first presented. Subsequently, various waste-to-energy technologies and their electricity generation feasibility from both environmental and economic perspectives were reviewed. Finally, electricity generation and greenhouse gas (GHG) reduction potentials through anaerobic digestion of the above-mentioned wastes generated in each province of Iran in 2016 were investigated as a case study. Accordingly, Khuzestan province with the highest amount of agro-wastes (7.61 million tons) and Sistan and Baluchestan province with the highest amount of livestock/slaughterhouse wastes (10.69 million tons) had the maximum electricity generation potentials of 82.83 MW and 164.23 MW, respectively. Moreover, the country's total potentials for electricity generation from these wastes was determined at 2848.26 MW. Based on the life cycle assessment (LCA) results, a minimum of 10,693.5 thousand tons CO2eq/yr could be avoided by valorizing these wastes into electricity in Iran. This would be translated into 1.5% reduction of Iran's annual GHG emissions; a promising achievement given Iran's international GHGs reduction commitment. Moreover, if a short-term time horizon would be considered for electricity generation from these wastes, the reduction rate could reach 24,153 thousand tons CO2eq/yr, i.e., 3.39% reduction of Iran's annual GHG emissions. To the best of our knowledge, this is the first report scrutinizing electricity generation potentials from both agricultural and livestock/slaughterhouse wastes in Iran while assessing the consequent GHG emission reduction potentials. The outcomes of the study could assist policy makers with decisions aimed at taking advantage of these resources while the platform introduced pave the way for other researchers to conduct similar studies in different parts of the world.", keywords = "IRAN, Electric power production, Environmental management, Anaerobic digestion, Slaughtering and slaughterhouses, Livestock, Greenhouse gas mitigation, Agricultural waste, Consequential LCA, Global warming, Life cycle assessment, Livestock/slaughterhouse wastes, Waste management, Renewable energy, Biogas, Methane, Microorganism", author = "Mohammad Shirzad and {Kazemi Shariat Panahi}, Hamed and Dashti, {Behrouz B.} and Rajaeifar, {Mohammad Ali} and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2019", month = sep, day = "1", doi = "10.1016/j.rser.2019.05.011", language = "English", volume = "111", pages = "571--594", journal = "Renewable and Sustainable Energy Reviews", issn = "1364-0321", publisher = "Elsevier", } . Renewable and Sustainable Energy Reviews.

Reactor technologies for biodiesel production and processing @article{ab00ce201b914349b61bdd8c4d26c229, title = "Reactor technologies for biodiesel production and processing: a review", abstract = "Diesel engines are preferred over spark ignition counterparts for heavy-duty applications and power generation plants because of their higher efficiency, durability, and productivity. Currently, the research interests have been propelled towards renewable and sustainable diesel fuels such as biodiesel in order to address the environmental and energy security challenges associated with these energy systems. However, the most challenging issue concerning large-scale production of biodiesel is its relatively high cost over fossil-based diesel owing to high feedstock and manufacturing costs. Therefore, cost-effective and eco-friendly biodiesel production technologies should be necessarily developed and continuously improved in order to make this biofuel more competitive vs. its petroleum counterpart. Accordingly, this paper comprehensively reviews biodiesel manufacturing techniques from natural oils and fats using conventional and advanced technologies with an in-depth state-of-the-art focus on the utmost important unit, i.e., transesterification reactor. The effects of the main influential parameters on the transesterification process are first discussed in detail in order to better understand the mechanisms behind each reactor technology. Different transesterification reactors; e.g., tubular/plug-flow reactors, rotating reactors, simultaneous reaction-separation reactors, cavitational reactors, and microwave reactors are then scrutinized from the scientific and practical viewpoints. Merits and limitations of each reactor technology for biodiesel production are highlighted to guide future R&D on this topic. At the end of the paper, the sustainability aspects of biodiesel production are comprehensively discussed by emphasizing on the biorefinery concept utilizing waste-oriented oils.", keywords = "Biodiesel, Economic impacts and policies, Intensification, Reactor technology, Sustainability, Transesterification, Air pollution, Climate change, Renewable energy, Sustainable energy, Environmental management", author = "Meisam Tabatabaei and Mortaza Aghbashlo and Mona Dehhaghi and Panahi, {Hamed Kazemi Shariat} and Arash Mollahosseini and Mehdi Hosseini and Soufiyan, {Mohamad Mojarab}", year = "2019", month = sep, day = "1", doi = "10.1016/j.pecs.2019.06.001", language = "English", volume = "74", pages = "239--303", journal = "Progress in Energy and Combustion Science", issn = "0360-1285", publisher = "Elsevier", } . Progress in Energy and Combustion Science.

Shifting fuel feedstock from oil wells to sea @article{991df69899b44047bef0c62ba16eac06, title = "Shifting fuel feedstock from oil wells to sea: Iran outlook and potential for biofuel production from brown macroalgae (ochrophyta; phaeophyceae)", abstract = "Finding renewable alternative energy resources for fossil fuels substitution has become very vital due to the serious challenges faced by humankind at present such as environmental pollution, greenhouse gas emissions, climate change, crude oil price volatility, and fossil fuels exhaustion. Macroalgae (seaweeds) are fast-growing marine plants, providing several harvests per year without the need for arable land, fertilizer, and fresh water. Various types of ecosystems like coral reefs, mangrove forests, and rocky shores can efficiently host the seaweeds production systems. These characteristics have made them highly suitable feedstocks for third-generation bioethanol production. Iran has a huge potential in renewable energy resources owing to its unique geographical location and climatic features. The country borders with the Caspian Sea in the north and with the Persian Gulf and the Gulf of Oman in the south. Seaweeds farming can also play a key role in mitigating air pollution, increasing employment rate, sustaining fossil fuel resources, bioremediating contaminated water, and improving marine ecosystem in the Persian Gulf and the Gulf of Oman. In the present article, macroalgae diversity, cultivation, and their conversion and upgrading technologies into bioethanol in Iran are scrutinized and discussed. Finally, the potential of Bushehr (the Persian Gulf) and Chabahar (the Gulf of Oman) coastlines for macroalgae cultivation is investigated. These locations receive the annual solar radiation in the range of 1680‒1753 kWh/m2 and the photosynthetically active radiation (PAR) in the range of 2.6‒2.71 GJ/m2/year with 3051‒3311.9 h sunshine per annum. Furthermore, the nutrient-rich and calm water with relatively stable pH, salinity, and temperature make these coasts suitable for macroalgae farming. A potential yield up to 147‒153 t/ha/year can be obtained if proper native/engineered species, well-situated sites, and compatible cultivation techniques are selected.", keywords = "Fermentation, Iran, Macroalgae farming, Saccharification, Seaweed, Third-generation bioethanol", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Mortaza Aghbashlo and Keikhosro Karimi and Meisam Tabatabaei", year = "2019", month = sep, day = "1", doi = "10.1016/j.rser.2019.06.023", language = "English", volume = "112", pages = "626--642", journal = "Renewable and Sustainable Energy Reviews", issn = "1364-0321", publisher = "Elsevier", } . Renewable and Sustainable Energy Reviews.

Recent updates on the production and upgrading of bio-crude oil from microalgae @article{544a0f73b867494b9ea72e60bddd3c9c, title = "Recent updates on the production and upgrading of bio-crude oil from microalgae", abstract = "Although currently microalgae biomass is not considered as a sustainable feedstock for biofuel production, future developments of microalgae cultivation and harvest could make the commercial application of such fast-growing photosynthetic biomass economically and environmentally feasible. This article aims at reviewing thermochemical conversion of microalgae into bio-crude oil through pyrolysis and hydrothermal liquefaction technologies. Subsequently, possible solutions to overcome the constraints to achieve the sustainable conversion of microalgae biomass are discussed in detail. The drawbacks of bio-crude oil as a transportation fuel and the technologies required for its upgrading are highlighted. Currently, microalgae-derived bio-crude oil is inferior to biodiesel and diesel in terms of quality, thus cannot be used as a transportation or jet fuel. It requires catalytic upgrading steps and further processing, including durable and cost-effective catalysts with strong regenerative capabilities.", keywords = "Catalytic upgrading, Hydrogenation, Hydrothermal liquefaction, Pyrolysis, Sustainability, Thermochemical conversion, biocrude oil, Bio-oil, microalgae, Upgrading technique, Refinery, Wastewater treatment", author = "{Kazemi Shariat Panahi}, Hamed and Meisam Tabatabaei and Mortaza Aghbashlo and Mona Dehhaghi and Mohammad Rehan and Nizami, {Abdul Sattar}", year = "2019", month = sep, day = "1", doi = "10.1016/j.biteb.2019.100216", language = "English", volume = "7", pages = "1--17", journal = "Bioresource Technology Reports", issn = "2589-014X", publisher = "Elsevier", } . Bioresource Technology Reports.

(2019). Shifting fuel feedstock from oil wells to sea: Iran outlook and potential for biofuel production from brown macroalgae (ochrophyta; phaeophyceae) . Renewable and Sustainable Energy Reviews.

(2019). Recent updates on the production and upgrading of bio-crude oil from microalgae . Bioresource Technology Reports.

(2019). A comprehensive review on electricity generation and GHG emission reduction potentials through anaerobic digestion of agricultural and livestock/slaughterhouse wastes in Iran . Renewable and Sustainable Energy Reviews.

(2019). Reactor technologies for biodiesel production and processing: A review . Progress in Energy and Combustion Science.

Microorganisms, tryptophan metabolism, and kynurenine pathway @article{419bb3f136c441ec83c2bc9c4150fd80, title = "Microorganisms, tryptophan metabolism, and kynurenine pathway: a complex interconnected loop influencing human health status", abstract = "The kynurenine pathway is important in cellular energy generation and limiting cellular ageing as it degrades about 90% of dietary tryptophan into the essential co-factor NAD+ (nicotinamide adenine dinucleotide). Prior to the production of NAD+, various intermediate compounds with neuroactivity (kynurenic acid, quinolinic acid) or antioxidant activity (3-hydroxykynurenine, picolinic acid) are synthesized. The kynurenine metabolites can participate in numerous neurodegenerative disorders (Alzheimer disease, amyotrophic lateral sclerosis, Huntington disease, and Parkinson disease) or other diseases such as AIDS, cancer, cardiovascular diseases, inflammation, and irritable bowel syndrome. Recently, the role of gut in affecting the emotional and cognitive centres of the brain has attracted a great deal of attention. In this review, we focus on the bidirectional communication between the gut and the brain, known as the gut-brain axis. The interaction of components of this axis, namely, the gut, its microbiota, and gut pathogens; tryptophan; the kynurenine pathway on tryptophan availability; the regulation of kynurenine metabolite concentration; and diversity and population of gut microbiota, has been considered.", keywords = "gut microbiota, gut-brain axis, indoleamine 2,3-dioxygenase, kynurenine pathway, neurodegenerative disorder, tryptophan", author = "Mona Dehhaghi and {Kazemi Shariat Panahi}, Hamed and Guillemin, {Gilles J.}", note = "Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2019", month = jun, day = "19", doi = "10.1177/1178646919852996", language = "English", volume = "12", pages = "1--10", journal = "International Journal of Tryptophan Research", issn = "1178-6469", publisher = "Libertas Academica Ltd.", } . International Journal of Tryptophan Research.

Human tick-borne diseases in Australia @article{956842842ea341698daa3f63cf060601, title = "Human tick-borne diseases in Australia", abstract = "There are 17 human-biting ticks known in Australia. The bites of Ixodes holocyclus, Ornithodoros capensis, and Ornithodoros gurneyi can cause paralysis, inflammation, and severe local and systemic reactions in humans, respectively. Six ticks, including Amblyomma triguttatum, Bothriocroton hydrosauri, Haemaphysalis novaeguineae, Ixodes cornuatus, Ixodes holocyclus, and Ixodes tasmani may transmit Coxiella burnetii, Rickettsia australis, Rickettsia honei, or Rickettsia honei subsp. marmionii. These bacterial pathogens cause Q fever, Queensland tick typhus (QTT), Flinders Island spotted fever (FISF), and Australian spotted fever (ASF). It is also believed that babesiosis can be transmitted by ticks to humans in Australia. In addition, Argas robertsi, Haemaphysalis bancrofti, Haemaphysalis longicornis, Ixodes hirsti, Rhipicephalus australis, and Rhipicephalus sanguineus ticks may play active roles in transmission of other pathogens that already exist or could potentially be introduced into Australia. These pathogens include Anaplasma spp., Bartonella spp., Burkholderia spp., Francisella spp., Dera Ghazi Khan virus (DGKV), tick-borne encephalitis virus (TBEV), Lake Clarendon virus (LCV), Saumarez Reef virus (SREV), Upolu virus (UPOV), or Vinegar Hill virus (VINHV). It is important to regularly update clinicians' knowledge about tick-borne infections because these bacteria and arboviruses are pathogens of humans that may cause fatal illness. An increase in the incidence of tick-borne infections of human may be observed in the future due to changes in demography, climate change, and increase in travel and shipments and even migratory patterns of birds or other animals. Moreover, the geographical conditions of Australia are favorable for many exotic ticks, which may become endemic to Australia given an opportunity. There are some human pathogens, such as Rickettsia conorii and Rickettsia rickettsii that are not currently present in Australia, but can be transmitted by some human-biting ticks found in Australia, such as Rhipicephalus sanguineus, if they enter and establish in this country. Despite these threats, our knowledge of Australian ticks and tick-borne diseases is in its infancy.", keywords = "anaplasmosis, arbovirus, babesiosis, bartonellosis, Lyme-like disease, Q fever, rickettsial infection, tick paralysis", author = "Mona Dehhaghi and {Kazemi Shariat Panahi}, Hamed and Holmes, {Edward C.} and Hudson, {Bernard J.} and Richard Schloeffel and Guillemin, {Gilles J.}", note = "Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2019", month = jan, day = "28", doi = "10.3389/fcimb.2019.00003", language = "English", volume = "9", pages = "1--17", journal = "Frontiers in Cellular and Infection Microbiology", issn = "2235-2988", publisher = "Frontiers Media SA", } . Frontiers in Cellular and Infection Microbiology.

(2019). Human Tick-Borne Diseases in Australia . Frontiers in Cellular and Infection Microbiology.

A review on green liquid fuels for the transportation sector @article{ef9a231698c14e76aa030a39c64eccc2, title = "A review on green liquid fuels for the transportation sector: a prospect of microbial solutions to climate change", abstract = "Environmental deterioration, global climate change, and consequent increases in pollution-related health problems among populations have been attributed to growing consumption of fossil fuels in particular by the transportation sector. Hence, replacing these energy carriers, also known as major contributors of greenhouse gas emissions, with biofuels have been regarded as a solution to mitigate the above-mentioned challenges. On the other hand, efforts have been put into limiting the utilization of edible feedstocks for biofuels production, i.e., first generation biofuels, by promoting higher generations of these eco-friendly alternatives. In light of that, the present review is aimed at comprehensively assessing the role and importance of microorganisms such as bacteria and yeasts as catalysts for sustainable production of liquid biofuels including bioethanol, biomethanol, biobutanol, bio-ammonia, biokerosene, and bioglycerol. Various aspects of these biofuels, i.e., background, chemical synthesis, microbial production (including exploitation of wild and metabolically-engineered species), and product recovery as well as the derivatives produced from these biofuels which are used as fuel additives are thoroughly covered and critically discussed. Furthermore, the industrial features of these green liquid fuels including the industrial practices reported in the literature and the challenges faced as well as possible approaches to enhance these practices are presented.", keywords = "Bio-jet fuel, Biobutanol, Bioethanol, Biofuel, Fuel additive, Microbial metabolite, Sustainable energy, Fermentation, Greenhouse gas (GHG) emissions, Environmental management, Transportation fuel, Renewable energy, Microorganisms, Natural product", author = "Panahi, {Hamed Kazemi Shariat} and Mona Dehhaghi and Kinder, {James E.} and Ezeji, {Thaddeus Chukwuemeka}", year = "2019", month = jan, day = "1", doi = "10.18331/BRJ2019.6.3.2", language = "English", volume = "6", pages = "995--1024", journal = "Biofuel Research Journal", issn = "2292-8782", publisher = "Green Wave Publishing of Canada", number = "3", } . Biofuel Research Journal.

(2019). Microorganisms, Tryptophan Metabolism, and Kynurenine Pathway: A Complex Interconnected Loop Influencing Human Health Status . International Journal of Tryptophan Research.

(2018). Potential of Acid-Activated Bentonite and SO3H-Functionalized MWCNTs for Biodiesel Production From Residual Olive Oil Under Biorefinery Scheme . Frontiers in Energy Research.

Potential of acid-activated bentonite and SO3H-functionalized MWCNTs for biodiesel production from residual olive oil under biorefinery scheme @article{ff6f786def534865a59d53caeb674f3f, title = "Potential of acid-activated bentonite and SO3H-functionalized MWCNTs for biodiesel production from residual olive oil under biorefinery scheme", abstract = "Application of acid-activated bentonite and SO3H-functionlized multiwall carbon nanotubes (SO3H-MWCNTs) for lowering free fatty acids (FFAs) content of low-quality residual olive oil, prior to alkali-catalyzed transesterification was investigated. The used bentonite was first characterized by Scanning Electron Microscopy (SEM), Inductively Coupled Plasma mass spectrometry (ICP-MS), and X-ray fluorescence (XRF), and was subsequently activated by different concentrations of H2SO4 (3, 5, and 10 N). Specific surface area of the original bentonite was measured by Brunauer, Emmett, and Teller (BET) method at 45 m2/g and was best improved after 5 N-acid activation (95-98°C, 2 h) reaching 68m2/g. MWCNTs was synthesized through methane decomposition (Co-Mo/MgO catalyst, 900°C) during the chemical vapor deposition (CVD) process. After two acid-purification (HCl, HNO3) and two deionized-water-neutralization steps, SO3H was grafted on MWCNTs (concentrated H2SO4, 110°C for 3 h) and again neutralized with deionized water and then dried. The synthesized SO3H-MWCNTs were analyzed using Fourier-Transform Infrared Spectroscopy (FTIR) and Transmission Electron Microscopy (TEM). The activated bentonite and SO3H-MWCNTs were utilized (5 wt.% and 3 wt.%, respectively), as solid catalysts in esterification reaction (62°C, 450 rpm; 15:1 and 12:1 methanol-to-oil molar ratio, 27 h and 8 h, respectively), to convert FFAs to their corresponding methyl esters. The results obtained revealed an FFA to methyl ester conversion of about 67% for the activated bentonite and 65% for the SO3H-MWCNTs. More specifically, the acid value of the residual olive oil was decreased significantly from 2.5 to 0.85 and 0.89 mg KOH/g using activated bentonite and SO3H-MWCNTs, respectively. The total FFAs in the residual olive oil after esterification was below 0.5%, which was appropriate for efficient alkaline-transesterification reaction. Both catalysts can effectively pretreat low-quality oil feedstock for sustainable biodiesel production under a biorefinery scheme. Overall, the acid-activate bentonite was found more convenient, cost-effective, and environment-friendly than the SO3H-MWCNTs.", keywords = "Acid-activated bentonite, Biodiesel production, Biorefinery, High free fatty acid, SOH-functionlized multiwall carbon nanotube (SOH-MWCNTs), Waste olive oil", author = "Hadi Rahimzadeh and Meisam Tabatabaei and Mortaza Aghbashlo and Panahi, {Hamed Kazemi Shariat} and Alimorad Rashidi and Goli, {Sayed Amir Hossein} and Mostafa Mostafaei and Mehdi Ardjmand and Nizami, {Abdul Sattar}", note = "Copyright the Author(s) 2018. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2018", month = dec, day = "17", doi = "10.3389/fenrg.2018.00137", language = "English", volume = "6", pages = "1--10", journal = "Frontiers in Energy Research", issn = "2296-598X", publisher = "Frontiers Research Foundation", number = "DEC", } . Frontiers in Energy Research.

Microorganisms’ footprint in neurodegenerative diseases @article{9710de800ffb4de9a893ff96ec395ab9, title = "Microorganisms{\textquoteright} footprint in neurodegenerative diseases", abstract = "Advancement of science has gifted the human a longer life; however, as neuron cells do not regenerate, the number of people with neurodegeneration disorders rises with population aging. Neurodegeneration diseases occur as a result of neuronal cells loss caused by environmental factors, genetic mutations, proteopathies and other cellular dysfunctions. The negative direct or indirect contributions of various microorganisms in onset or severity of some neurodegeneration disorders and interaction between human immune system and pathogenic microorganisms has been portrayed in this review article. This association may explain the early onset of neurodegeneration disorders in some individuals, which can be traced through detailed study of health background of these individuals for infection with any microbial disease with neuropathogenic microorganisms (bacteria, fungi, viruses). A better understanding and recognition of the relation between microorganisms and neurodegeneration disorders may help researchers in development of novel remedies to avoid, postpone, or make neurodegeneration disorders less severe.", keywords = "Gut microbiota, Microbial infection, Neurodegeneration disease, Neuroinflammation, Neuropathogenic microorganisms, Neurovirulence", author = "Mona Dehhaghi and {Kazemi Shariat Panahi}, Hamed and Guillemin, {Gilles J.}", note = "Copyright the Author(s) 2018. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.", year = "2018", month = dec, day = "4", doi = "10.3389/fncel.2018.00466", language = "English", volume = "12", pages = "1--17", journal = "Frontiers in Cellular Neuroscience", issn = "1662-5102", publisher = "Frontiers Media SA", } . Frontiers in Cellular Neuroscience.

(2018). Microorganisms’ Footprint in Neurodegenerative Diseases . Frontiers in Cellular Neuroscience.

An image analysis-aided method for redundancy reduction in differentiation of identical Actinobacterial strains @article{339557578cef433e80b8ec45afd784c0, title = "An image analysis-aided method for redundancy reduction in differentiation of identical Actinobacterial strains", abstract = "Aim: To simplify the recognition of Actinobacteria, at different stages of the growth phase, from a mixed culture to facilitate the isolation of novel strains of these bacteria for drug discovery purposes. Materials & methods: A method was developed on Gabor transform, and machine learning using k-Nearest Neighbors and Naive Bayes classifier, Logitboost, Bagging and Random Forest to automatically categorize the colonies. Results: A signature pattern was inferred by the model, making the differentiation of identical strains possible. Additionally, higher performance, compared with other classification methods was achieved. Conclusion: This automated approach can contribute to the acceleration of the drug discovery process while it simultaneously can diminish the loss of budget due to the redundancy occurred by the inexperienced researchers.", keywords = "Actinobacteria, classification, colony pattern, drug discovery, Gabor transform, high-throughput isolation", author = "Hedieh Sajedi and Fatemeh Mohammadipanah and {Shariat Panahi}, {Hamed Kazemi}", year = "2018", month = mar, day = "1", doi = "10.2217/fmb-2016-0096", language = "English", volume = "13", pages = "313--329", journal = "Future Microbiology", issn = "1746-0913", publisher = "Taylor & Francis", number = "3", } . Future Microbiology.

Hedieh Sajedi, Fatemeh Mohammadipanah, Hamed Kazemi Shariat Panahi(2018). An image analysis-aided method for redundancy reduction in differentiation of identical Actinobacterial strains . Future Microbiology. 13. (3). p. 313--329. Future Medicine Ltd

Development of a reversed-phase liquid chromatographic assay for the quantification of total persipeptides in fermentation broth @article{d79898714d764803b47821b771c254a7, title = "Development of a reversed-phase liquid chromatographic assay for the quantification of total persipeptides in fermentation broth", abstract = "The emergence and prevalence of multi-drug-resistant bacterial strains increase the potential for outbreaks of incurable infections. The discovery of novel antibiotics and pharmacological preparations requires the identification of novel bioactive small molecules. A specific, sensitive, and reliable quantification method using high-performance liquid chromatography (HPLC) with UV detection was developed for the determination of total persipeptides (A and B), which are cyclic pentapeptides found in the fermentation broth of Streptomyces zagrosensis UTMC 1154 that exhibit bioactivity against methicillin-resistant Staphylococcus aureus (MRSA). A simple liquid–liquid extraction (LLE) method using butanol was employed to extract persipeptides from the fermentation broth prior to HPLC analysis. The chromatographic separation of persipeptides and the internal standard, virginiamycin, was achieved with a gradient of acetonitrile and water on a C18 reversed-phase analytical column in a 25-min analytical run utilizing a flow rate of 0.8 mL min−1 and detection at 210 nm. The whole assay was validated, and the method presented a linear response range with a regression coefficient of determination R2 of 0.9996 for the quantification of persipeptides in the concentration range of 3.9–250.0 µg mL−1, as well as extraction recoveries ranging from 54.78 ± 9.83 % to 56.45 ± 16.33 %. The bias and the precision of the proposed method were <10 %. The detection and quantification limits for the persipeptides were 27 and 83 µg L−1, respectively.", keywords = "Assay development, HPLC, Liquid-liquid extraction, Peptide antibiotics, Persipeptides, Drug discovery, Method validation, Method development, Stability analysis, Robustness testing, Fermentation", author = "Fatemeh Mohammadipanah and {Kazemi Shariat Panahi}, Hamed and Fatemeh Imanparast and Javad Hamedi", year = "2016", month = oct, day = "1", doi = "10.1007/s10337-016-3140-y", language = "English", volume = "79", pages = "1325--1332", journal = "Chromatographia", issn = "0009-5893", publisher = "Springer, Springer Nature", number = "19-20", } . Chromatographia.

Panahi, H.K.S., Mohammadipanah, F. and Dehhaghi, M., 2016. Optimization of extraction conditions for liquid-liquid extraction of persipeptides from Streptomyces zagrosensis fermentation broth. Eur Chem Bull, 5, pp.408-415 .

Mohammadipanah, F., Kazemi Shariat Panahi, H., Imanparast, F., Hamedi, J., Mohammadipanah, F., Kazemi Shariat Panahi, H., Imanparast, F., Hamedi, J.(2016). Development of a Reversed-Phase Liquid Chromatographic Assay for the Quantification of Total Persipeptides in Fermentation Broth . Chromatographia. 79. (19-20). p. 1325-1332.

Seyed Hamed Kazemi Shariat Panahi, Fatemeh Mohammadipanah, Mona Dehhaghi(2016). Optimization of extraction conditions for liquid-liquid extraction of persipeptides from Streptomyces zagrosensis fermentation broth . European Chemical Bulletin. 5. (9). p. 408--415. Deuton-X Ltd.

BOOK CHAPTER

Biodiesel production systems @inbook{831a0581e68e4de685d78fe08324e9f4, title = "Biodiesel production systems: real-world reactor technologies and processes", abstract = "Biodiesel is a promising substitution for diesel for solving greenhouse gas emissions and traffic-related air pollution. If well-developed, switching to biodiesel can have other socioeconomic advantages, including energy security, job growth, and eco-friendly conversion of used-cooking oil. However, the biodiesel production industry currently has much lower economic feasibility than that of the petrochemical diesel industry. Some countries have been trying to encourage biodiesel production and consumption by providing subsidies or increasing the price of diesel through higher taxation. These types of incentives may not be sustainable as they have a great economic burden on both the governments and civilians. Together with the current sophisticated condition of the world (e.g., wars, sanctions, pandemic), the need for quicker developments of the biodiesel industry to decrease the capital and production costs is more significantly felt than before. Therefore, this review scrutinizes the current development stages of the biodiesel industry from a production systems viewpoint. The chapter starts with an introduction justifying the need for this study and the general knowledge of biodiesel production technologies. This is followed by three separate sections scrutinizing rotating reactors (stirred tank reactors, spinning tube-in-tube reactors), simultaneous reaction-separation reactors, and cavitation reactors (sonochemical/ultrasonic reactors, hydrodynamic cavitation reactors, shockwave power reactors). By presenting real-world reactor technologies and processes, and their advantages and limitations, this chapter tries to gain the attention of a wider audience familiar with the biodiesel industry to stimulate further ideas and research in this field.", keywords = "Cavitation reactor, process intensification, reactive separation process, renewable energy, rotating reactor, transesterification", author = "{Kazemi Shariat Panahi}, Hamed and Mona Dehhaghi and Guillemin, {Gilles J.} and Gupta, {Vijai Kumar} and Mortaza Aghbashlo and Meisam Tabatabaei", year = "2023", month = jun, day = "30", doi = "10.1016/B978-0-12-820361-3.00004-8", language = "English", isbn = "9780128204856", pages = "91--118", editor = "Meisam Tabatabaei and Abdul-Sattar Nizami", booktitle = "Sustainable biodiesel", publisher = "Elsevier", } . Sustainable biodiesel.

Climate change and debilitating symptom complexes attributed to ticks in Australia @inbook{d734069d785b42ef9492472bc05af77e, title = "Climate change and debilitating symptom complexes attributed to ticks in Australia", abstract = "This expert opinion focuses on the impact of global warming and climate change on the spread and distribution of Australian ticks and the prevalence and intensity of associated human diseases.", author = "Mona Dehhaghi and Panahi, {Hamed Kazemi Shariat} and Richard Schloeffel and Bernard Hudson and Benjamin Ruiwen and Gilles Guillemin", year = "2021", month = dec, day = "15", doi = "10.1079/9781789249637.0056", language = "English", isbn = "9781789249637", series = "CABI Climate Change Series", publisher = "CABI International", pages = "391--399", editor = "Pat Nuttall", booktitle = "Climate, ticks and disease", } . Climate, ticks and disease.

Practical aspects of working with actinobacteria @inbook{defd2bae468c4d97b47977562db941aa, title = "Practical aspects of working with actinobacteria", abstract = "More than other bacteria Actinobacteria, especially the mycelium forming ones impress by their appearance, the color of the aerial mycelium, of the substrate mycelium and also of pigments that diffuse into the agar (Cross 1989; Krasil{\textquoteright}nikov 1979; K{\"u}ster 1976) and the morphology of their differentiation stages (Gottlieb 1961) which will be described in the later chapters. The aerial mycelium which makes them look like a fungus and the often three dimensional shape of the colony. The color of the aerial mycelium has been used by many groups for a first classification (Flaig and Kutzner 1960; Ettlinger et al. 1958; Shirling and Gottlieb 1966; Tresner and Backus 1963). The main classification groups are: white, grey white, cream (Streptomyces albus); yellow.-grey (Streptomyces griseus); rose, pale violet (Streptomyces fradiae, Microbispora rosea), rose-grey (Streptomyces lavendulae); pale brown, red brown (Streptomyces fragilis); pale blue, grey-blue (Streptomyces viridochromogenes); blue green (Streptomyces glaucescens, Actinomadura rubrobrunnea); pale green, green (Streptomyces prasinus, Microtetraspora viridis); pale grey, grey (Streptomyces violaceoruber, Microtetraspora glauca) (Blinov and Khokhlov 1970). By the description of the aerial mycelium color three points have to be kept in mind. The first is that the typical color is only expressed if the culture is also sporulating. Different species often sporulate on different media, so a number of agar cultures have to be prepared to get good results. The second is the diffusion of pigments from the substrate mycelium into the aerial mycelium which can have influences on the shade of the aerial mycelium. The third is the experience with many different Actinobacteria and their pigmentation, to do this grouping well. It is therefore very important to use the same media and culture conditions for all strains that will be compared. Over the years the use of the media from Shirling and Gottlieb (1966) from the “International Streptomyces Project/ISP” has been established in nearly all labs working with Actinobacteria (composition of media, see Sect. 11.2.1).", author = "Joachim Wink and Fatemeh Mohammadipanah and {Shariat Panahi}, {Hamed Kazemi}", year = "2017", month = jan, day = "1", doi = "10.1007/978-3-319-60339-1_11", language = "English", isbn = "9783319603384", pages = "329--376", editor = "Joachim Wink and Fatemeh Mohammadipanah and Javad Hamedi", booktitle = "Biology and biotechnology of actinobacteria", publisher = "Springer, Springer Nature", address = "United States", } . Biology and biotechnology of actinobacteria.

Biotechnological exploitation of actinobacterial members @inbook{1fcf03ce53c845beb5f88f732791f4d3, title = "Biotechnological exploitation of actinobacterial members", abstract = "Microbial-derived products, while do not have many environmental side effects of their synthetic counterparts, have proved more efficient than those synthetically obtained. The nature has provided a treasure of microorganisms with capabilities to produce vast variety of novel compounds. This ability has been arised during long last of evolution and adaptation to diverse chemical and physical microenviroments. Microbial-derived metabolites have made their own space in industries and therefore human life. Among these microorganisms, halophilic and halotolerant actinobacteria are recently gaining much attentions. Metabolites and biological functions from halophilic or halotolerant members of this phylum of bacteria may resolving the ever-increasing thirst of industry for metabolites with salttolerancy to cope a range of issues from environmental pollution to diseases and world's hunger. In the current chapter, it has been tried to introduce the less dealt group of halophilic and halotolerant actinobacteria, and shed light on their potential to be exploited in various industry sectors.", keywords = "Actinobacteria, Actinomycetes, Bioremediation, Compatible solutes, Enzymes, Pigments, Secondary metabolites, Fermentation, Halophilic bacteria, Biotechnology, Natural compound", author = "Javad Hamedi and Fatemeh Mohammadipanah and Panahi, {Hamed Kazemi Shariat}", year = "2015", month = sep, day = "16", doi = "10.1007/978-3-319-14595-2_3", language = "English", isbn = "9783319145945", series = "Sustainable Development and Biodiversity", publisher = "Springer, Springer Nature", pages = "57--143", editor = "Maheshwari, {Dinesh K.} and Meenu Saraf", booktitle = "Halophiles", address = "United States", } . Halophiles.

OTHER

Joachim Wink, Fatemeh Mohammadipanah, Hamed Kazemi Shariat Panahi(2017). Practical Aspects of Working with Actinobacteria . Biology and Biotechnology of Actinobacteria. p. 329--376. Springer International Publishing

Javad Hamedi, Fatemeh Mohammadipanah, Hamed Kazemi Shariat Panahi(2015). Biotechnological Exploitation of Actinobacterial Members . Halophiles. p. 57--143. Springer International Publishing