Article
Biochemistry & Molecular Biology
Yuanyuan Huang, Yanfei Wu, Han Hu, Bangzhuo Tong, Jie Wang, Siyu Zhang, Yanyi Wang, Jicong Zhang, Yue Yin, Shengkun Dai, Wenjuan Zhao, Bolin An, Jiahua Pu, Yaomin Wang, Chao Peng, Nan Li, Jiahai Zhou, Yan Tan, Chao Zhong
Summary: This study describes a technological workflow that facilitates the design and development of engineered living materials (ELMs) through the integration of bioinformatics, structural biology, and synthetic biology technologies. By developing a bioinformatics software called Bacteria Biopolymer Sniffer (BBSniffer), the researchers are able to identify bacteria and biopolymers of interest. Using genetic manipulation and structural characterization, a programmable bacterium was identified in the industrial workhorse Corynebacterium glutamicum, enabling the design of ELMs.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biology
Parth Sarker, Arnob Mitro, Hammadul Hoque, Md. Nazmul Hasan, G. M. Nurnabi Azad Jewel
Summary: In this study, potential therapeutic targets for Elizabethkingia anophelis were investigated using genomic analysis and molecular dynamics simulation. The identified targets have the potential to develop novel antimicrobial drugs for treating infections caused by this deadly pathogen and preventing disease progression.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Immunology
Shahla Shahbazi, Samira Sabzi, Narjes Noori Goodarzi, Sepideh Fereshteh, Negin Bolourchi, Bahman Mirzaie, Farzad Badmasti
Summary: This study utilized reverse vaccinology approach to identify potential immunogenic targets against C. jeikeium and developed a multi-epitope vaccine, which needs further experimental analysis to confirm safety, immunoreactivity, and efficacy.
MICROBIAL PATHOGENESIS
(2022)
Article
Immunology
Guoqiang Liu, Guisong He, Jie Zhang, Zhongmin Zhang, Liang Wang
Summary: This study identifies key genes in osteoarthritis synovial tissue and discovers that the SCRG1 gene can serve as a diagnostic marker for osteoarthritis. Additionally, SCRG1 is involved in regulating immune pathways, making it a potential therapeutic target for osteoarthritis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anila Hoda, Mirela Lika (Cekani), Valbona Kolaneci
Summary: This study utilized bioinformatics tools and in silico methods to analyze deleterious nsSNPs of the HGF gene. Five nsSNPs were found to have the most significant impact on the structure and function of the HGF protein. Analysis of gene-gene and protein-protein interactions revealed the importance of HGF in multiple pathways and co-expressions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Vasavi Garisetti, Anantha Krishnan Dhanabalan, Gayathri Dasararaju
Summary: GPR88 is an orphan GPCR receptor that is a potential target for central nervous system disorders. This study focuses on predicting its protein structure and screening for novel ligands, which can contribute to the development of new treatments.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Liza Vinhoven, Frauke Stanke, Sylvia Hafkemeyer, Manuel Manfred Nietert
Summary: This study used a compound database and a systems biology model to identify targets for the treatment of cystic fibrosis. Through inverse screening methods, 1038 potential target-compound pairings were found.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Tomasz Wolkowicz, Katarzyna Zacharczuk, Aleksandra Anna Zasada
Summary: Infections caused by non-toxigenic Corynebacterium diphtheriae have been increasing in Poland, with the most common strains being ST8 biovar gravis. This study analyzed 30 strains isolated between 2017 and 2022, as well as six previously isolated strains, using classic methods and whole genome sequencing. The appearance of new strains in 2022 and the isolation of the first non-toxigenic tox gene-bearing strain suggest that C. diphtheriae should be considered a pathogen of special public health concern in Poland.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Neurosciences
William Renthal, Alexander Chamessian, Michele Curatolo, Steve Davidson, Michael Burton, Sulayman Dib-Hajj, Patrick M. Dougherty, Allison D. Ebert, Robert W. Gereau, Andre Ghetti, Michael S. Gold, Gwendolyn Hoben, Daniela Maria Menichella, Philippe Mercier, Wilson Z. Ray, Daniela Salvemini, Rebecca P. Seal, Stephen Waxman, Clifford J. Woolf, Cheryl L. Stucky, Theodore J. Price
Summary: Chronic pain is a debilitating disease with limited treatment options. Understanding pain cells and networks in humans is crucial for translating knowledge from animal models to therapeutic applications. A multi-institutional collaboration is proposed to address this challenge rigorously and ethically.
Review
Biochemistry & Molecular Biology
K. M. Taufiqul Arif, Rachel K. Okolicsanyi, Larisa M. Haupt, Lyn R. Griffiths
Summary: Contemporary computational miRNA-target prediction tools are essential in identifying potential targets for miRNAs, but they often generate numerous false-positive predictions. The lack of a standardized approach and satisfactory sensitivity, specificity, and overall efficiency in single tools calls for a systematic combination of selective online tools to develop an effective prediction scheme for miRNA-target identification.
Article
Microbiology
Abiodun Joseph Fatoba, Moses Okpeku, Matthew Adekunle Adeleke
Summary: This study aimed to identify novel drug targets against Mycoplasma genitalium infection by analyzing unique metabolic pathways and essential proteins. The research found seven potential druggable proteins involved in specific metabolic pathways of the pathogen, which could lead to the development of potent drugs for eradicating M. genitalium.
Article
Biochemical Research Methods
Tomas Alarcon, Josep Sardanyes, Antoni Guillamon, Javier A. Menendez
Summary: Tumour cell heterogeneity poses a major obstacle for targeted anti-cancer therapies, with limited strategies available to mitigate its undesirable impact on clinical outcomes. A computational approach has been developed to design combinatorial therapies against chromatin modifiers, with promising results in circumventing therapeutic challenges posed by tumour heterogeneity. Combinatorial strategies involving modulators of histone H3K4 and H3K27 demethylases are predicted to be more effective in managing non-uniform responses of heterogeneous cancer cell populations.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Genetics & Heredity
Kavita Sharma, Prithvi Singh, Md Amjad Beg, Ravins Dohare, Fareeda Athar, Mansoor Ali Syed
Summary: The aim of the study is to update knowledge on primary treatment of hypertension and identify critical miRNA-mRNA-TF interactions through systematic bioinformatics analysis. Molecular modeling and docking were used to identify therapeutic targets, with telmisartan and limonin identified as potential compounds to combat the impact of hypertension. The study provides novel insight into the etiology of hypertension by identifying mRNAs, miRNAs, and associated pathways.
Article
Multidisciplinary Sciences
Ishita Mallick, Pradnya Panchal, Smita Kadam, Priyanka Mohite, Juergen Scheele, Werner Seiz, Amit Agarwal, Om Prakash Sharma
Summary: Asthma is a common chronic lung disorder with significant global burden. This study identified IL-13 as the most important therapeutic target for asthma, supported by extensive analysis of scientific literature and patient datasets. Additionally, other potential targets such as TNF, VEGFA, and IL-18 were identified, but require further clinical testing and experimental validation.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Vanessa L. Goettl, Ina Schmitt, Kristina Braun, Petra Peters-Wendisch, Volker F. Wendisch, Nadja A. Henke
Summary: This study constructed a library for the repression of 74 genes of C. glutamicum using CRISPRi technology, targeting important genes involved in metabolic pathways. The results showed that CRISPRi-mediated gene repression can increase carotenoid pigment biosynthesis, while deletion of certain genes can significantly enhance pigment production.
Article
Biotechnology & Applied Microbiology
Luisa Martins Trindade, Licia Torres, Isabel David Matos, Vivian Correia Miranda, Luis Claudio Lima de Jesus, Gregorio Cavalcante, Jonathan Junio de Souza Oliveira, Geovanni Dantas Cassali, Pamela Mancha-Agresti, Vasco Ariston de Carvalho Azevedo, Tatiani Uceli Maioli, Valbert Nascimento Cardoso, Flaviano dos Santos Martins, Simone de Vasconcelos Generoso
Summary: Intestinal mucositis is a common side effect of cancer treatment, and the current management options are not very effective. Recent research suggests that the gut microbiota plays a role in the development and severity of mucositis. Therefore, the use of probiotics and paraprobiotics may have potential therapeutic effects on intestinal mucositis.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Biotechnology & Applied Microbiology
Jessica C. das D. Ribeiro, Mariana M. Drumond, Pamela Mancha-Agresti, Joao P. F. Guimaraes, Daiane da C. Ferreira, Maria I. A. Martins, Pedro M. de M. Murata, Andressa C. de Carvalho, Raquel T. Pereira, Valdir Ribeiro Junior, Vasco A. de C. Azevedo, Luciana de P. Naves
Summary: This experiment evaluated the effects of probiotics on the performance and intestinal health of broilers exposed to heat stress. The results showed that diets containing non-commercial probiotics improved weight gain and feed conversion in broilers.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Biochemistry & Molecular Biology
Syed Shah Hassan, Rida Shams, Ihosvany Camps, Zarrin Basharat, Saman Sohail, Yasmin Khan, Asad Ullah, Muhammad Irfan, Javed Ali, Muhammad Bilal, Carlos M. Morel
Summary: In this study, potential drug targets for Burkholderia cepacia complex (BCC) were identified through the analysis of proteomic data. Two potential BCC targets were found using computational modeling and library screening techniques. These findings are of great significance for the development of novel therapies for BCC infections.
MOLECULAR DIVERSITY
(2023)
Review
Immunology
Mohamed Ahmed Raslan, Sara Ahmed Raslan, Eslam Mansour Shehata, Amr Saad Mahmoud, Nagwa A. Sabri, Khalid J. Alzahrani, Fuad M. Alzahrani, Saleh Alshammeri, Vasco Azevedo, Kenneth Lundstrom, Debmalya Barh
Summary: This systematic review investigated the value and success of COVID-19 vaccination in children. The majority of adverse events reported were mild to moderate, and most were unrelated to vaccination. Different types of vaccines provided excellent protection against COVID-19 in children. Further studies are needed to confirm the long-term safety and effectiveness of vaccinations.
Article
Microbiology
Danitza Xiomara Romero-Calle, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tome, Thiago J. J. Sousa, Leila Thaise Santana de Oliveira Santos, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Raquel Guimaraes Benevides, Thiago M. M. Venancio, Craig Billington, Aristoteles Goes-Neto
Summary: In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. A strain of Salmonella enterica serovar Enteritidis SE3 was isolated from soil in Santo Amaro, Brazil, an area contaminated with heavy metals and organic waste. The genome analysis of this strain revealed the presence of important resistance and virulence genes, which are crucial for controlling Salmonella and heavy metal pollution in the region.
Article
Genetics & Heredity
Alessandra Lima, Ana Carolina Barbosa Caetano, Raquel Hurtado Castillo, Roselane Gonsalves dos Santos, Diego Lucas Neres Rodrigues, Thiago de Jesus Sousa, Rodrigo Bentes Kato, Marcus Vinicius Canario Viana, Anne Cybelle Pinto Gomide, Flavia Figueira Aburjaile, Sandeep Tiwari, Arun Jaiswal, Alfonso Gala-Garcia, Nubia Seyffert, Thiago Luiz de Paula Castro, Bertram Brenig, Mateus Matiuzzi da Costa, Elaine Maria Seles Dorneles, Yves Le Loir, Vasco Azevedo
Summary: This study performed comparative genomic analyses of 73 Staphylococcus aureus genomes from different hosts, including 12 genomes isolated from sheep. The study revealed the genomic specialization and the role of specific genes in establishing infection in ovine mastitis-associated S. aureus.
Article
Plant Sciences
Parvinderdeep S. Kahlon, Andrea Foerner, Michael Muser, Mhaned Oubounyt, Michael Gigl, Richard Hammerl, Jan Baumbach, Ralph Hueckelhoven, Corinna Dawid, Remco Stam
Summary: Natural plant populations show polymorphism and intraspecific variation in resistance against pathogens. Perception of pathogen-associated molecular patterns or elicitors can activate defence responses, and this variation was evaluated in the wild tomato species Solanum chilense. The diversity in basal and elicitor-induced levels of reactive oxygen species and phytohormones was measured in 83 plants from nine populations. Geographical origin influenced the effect of individual components on infection frequency of Phytophthora infestans, with a direct correlation found between ethylene responses and resistance in the southern coastal region.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Health Care Sciences & Services
Alissa Brauneck, Louisa Schmalhorst, Mohammad Mahdi Kazemi Majdabadi, Mohammad Bakhtiari, Uwe Voelker, Jan Baumbach, Linda Baumbach, Gabriele Buchholtz
Summary: This article summarizes the legal questions and concerns related to federated learning (FL) systems in medical research. The study found that FL can meet the legal requirements of the General Data Protection Regulation (GDPR) by combining secure multiparty computation (SMPC) and differential privacy (DP) as privacy-enhancing technologies, providing a secure technical solution.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2023)
Article
Microbiology
Monique Ferrary Americo, Andria dos Santos Freitas, Tales Fernando da Silva, Luis Claudio Lima de Jesus, Fernanda Alvarenga Lima Barroso, Gabriela Munis Campos, Rhayane Cristina Viegas Santos, Gabriel Camargos Gomes, Rafael Assis, Enio Ferreira, Pamela Mancha-Agresti, Juliana Guimaraes Laguna, Jean-Marc Chatel, Rodrigo Dias de Oliveira Carvalho, Vasco Azevedo
Summary: Mucositis is a gastrointestinal inflammation caused by chemotherapy treatments that severely affects patient's quality of life. Probiotic strains have shown promising results as an alternative treatment, and targeting the site of inflammation could be explored further. This study evaluated the anti-inflammatory effect of GDF11 delivered by Lactococcus lactis strains and found that the recombinant lactococci strains improved intestinal damage and reduced goblet cell degeneration in a murine model of mucositis induced by 5-FU. These strains also reduced neutrophil infiltration and exhibited immunomodulation of inflammatory markers, suggesting their potential as a gene therapy for 5-FU-induced intestinal mucositis.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Sankaran Venkatachalam, Nisha Murlidharan, Sowmya R. Krishnan, C. Ramakrishnan, Mpho Setshedi, Ramesh Pandian, Debmalya Barh, Sandeep Tiwari, Vasco Azevedo, Yasien Sayed, M. Michael Gromiha
Summary: AIDS is a challenging infectious disease with a need for understanding drug resistance mechanisms. A new double-insertion mutation (L38HL) in HIV subtype C protease was investigated for its potential in inducing drug resistance towards the protease inhibitor Saquinavir (SQV). Computational techniques revealed that the L38HL mutation increased flexibility in certain regions and decreased binding affinity of SQV compared to wild-type. The mutation also resulted in a wide opening at the binding site and altered flap dynamics, leading to decreased interactions with the binding site and a potential drug resistance phenotype.
Article
Computer Science, Artificial Intelligence
Anne Hartebrodt, Richard Rottger, David B. Blumenthal
Summary: Federated learning (FL) is a privacy-aware alternative to classical cloud-based machine learning. The article presents a federated singular value decomposition algorithm suitable for GWAS, which addresses both privacy and computational requirements.
DATA MINING AND KNOWLEDGE DISCOVERY
(2023)
Article
Food Science & Technology
Marine Mantel, Tales Fernando da Silva, Rafael Gloria, Daniele Vassaux, Katia Duarte Vital, Valbert Nascimento Cardoso, Simone Odilia Antunes Fernandes, Eric Guedon, Yves Le Loir, Ana Maria Caetano Faria, Malvyne Rolli-Derkinderen, Vasco Azevedo, Gwenael Jan
Summary: Inflammatory bowel diseases (IBD) are a growing concern in western countries due to gut microbiota dysbiosis and loss of immunomodulatory bacteria. Probiotic products containing selected immunomodulatory bacterial strains, such as Propionibacterium freudenreichii, can mitigate IBD. The role of dairy matrix components in fermented dairy products and their effects on IBD remain unknown. This study found that P. freudenreichii-fermented milk, particularly with the presence of dairy fat, can prevent colitis and opens new perspectives for developing immunomodulatory functional fermented foods.
JOURNAL OF FUNCTIONAL FOODS
(2023)
Article
Computer Science, Information Systems
Priyankar Bose, Pratip Rana, Preetam Ghosh
Summary: This paper discusses attention-based deep learning approaches on vision-language multimodal data, including models, performances, and evaluation metrics. A comprehensive review was conducted on 75 articles from 2015 to 2022, discussing current tasks, datasets, application areas, and future directions.
Review
Biochemistry & Molecular Biology
Ligen Yu, Mohd Khanapi Abd Ghani, Alessio Aghemo, Debmalya Barh, Matteo Bassetti, Fausto Catena, Gaetano Gallo, Ali Gholamrezanezhad, Mohammad Amjad Kamal, Amos Lal, Kamal Kant Sahu, Shailendra K. Saxena, Ugo Elmore, Farid Rahimi, Chiara Robba, Yuanlin Song, Zhengyuan Xia, Boxuan Yu
Summary: This study analyzed keywords and found that factors such as the immune system and nutrition are related to COVID-19. It proposed that the human immune system is a complex system that employs self-destruct and rebuild strategies to fight microbial infections. Microbial infections may be self-limiting and provide essential nutrition for the patient. The study also discussed possible strategies to mitigate COVID-19, including vaccination.
CURRENT MEDICINAL CHEMISTRY
(2023)
Article
Cell & Tissue Engineering
Caroline C. C. Picoli, Patricia Rocha Martins, Xiao Lin Casey Wong, Thamires Righi, Pedro P. G. Guimaraes, Mauro C. X. Pinto, Jaime H. H. Amorim, Vasco A. C. Azevedo, Silma Regina Pereira, Alexandre Kanashiro, Fabio Cardoso Cruz, Rodrigo R. R. Resende, Akiva Mintz, Paul S. S. Frenette, Alexander Birbrair
Summary: Understanding the bone marrow niche is crucial for maintaining hematopoietic stem cells. This study presents a new method, called "whole bone subcutaneous transplantation", to precisely study the bone marrow niche in transgenic animals. By labeling cells, researchers were able to identify specific cellular components of the niche and found that certain cells play an important role in maintaining hematopoietic stem cells.
STEM CELL REVIEWS AND REPORTS
(2023)