Article
Biotechnology & Applied Microbiology
Hitomi Omachi, Takeshi Terahara, Kunihiko Futami, Satoshi Kawato, Chiaki Imada, Kaeko Kamei, Tomonori Waku, Akihiro Kondo, Takeshi Naganuma, Tri Winarni Agustini, Takeshi Kobayashi
Summary: Experiments on V. salexigens strains from different sources showed similar bacteriocin encoding sequences, with some strains sharing sequence homology with human gut bacteria. This suggests a widespread distribution of bacteriocin-producing V. salexigens strains in diverse environments.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Jeong Min Yoo, Ji Hoon Song, Robie Vasquez, In-Chan Hwang, Jae Seung Lee, Dae-Kyung Kang
Summary: In this study, a novel bacteriocin named agilicin C7 was isolated from Ligilactobacillus agilis C7 and showed inhibitory activity against L. monocytogenes. Agilicin C7 is a glycoprotein with wide pH and thermal stability and can be stable in various organic solvents. It destroys L. monocytogenes by damaging the integrity of the cell envelope, indicating that agilicin C7 is a novel amylase-sensitive anti-listerial Class IId bacteriocin.
FOOD SCIENCE OF ANIMAL RESOURCES
(2023)
Article
Biochemical Research Methods
Bindiya Ellathuparambil Saidumohamed, Anitharaj Pottekkat Baburaj, Tina Kollannoor Johny, Unnikrishnan Babukuttan Sheela, Maya Sreeranganathan, Sarita Ganapathy Bhat
Summary: This study focuses on a magainin-2 like bacteriocin with anticancer action, produced by Bacillus safensis strain SDG14 isolated from the gut of marine fish, which inhibited lung carcinoma cells and demonstrated anti-apoptotic action by docking with apoptotic receptors DR5 and TGF-beta.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Computer Science, Artificial Intelligence
Lan Li, De-chuan Zhan, Xin-chun Li
Summary: Federated Learning (FL) is a method that aims to generate a global shared model by collaborating with decentralized edge computing devices with privacy considerations. However, FL faces challenges due to non-IID data partitioning across heterogeneous devices, causing divergence in local updates and difficulties in aggregation. In this paper, the authors propose a statistically principled probability-corrected loss and the sharing of fixed prototypes to handle non-IID FL with balanced and imbalanced global data. Experimental results demonstrate the superiority of their methods.
Review
Infectious Diseases
Jiahui Wu, Xia Zhou, Qiaoqiao Chen, Zhiqiang Chen, Jinyu Zhang, Lele Yang, Yuxuan Sun, Guohui Wang, Jianfeng Dai, Tingting Feng
Summary: This review provides an overview of tick defensins, including their structural classification and antimicrobial function. Tick defensins exhibit broad-spectrum antimicrobial activities against various pathogens and are considered novel candidates or targets for controlling infectious diseases.
INFECTIOUS DISEASES OF POVERTY
(2022)
Article
Mathematics
M. Rostami, S. F. Shariati, A. Sahami
Summary: In this study, we demonstrate that a matrix algebra LMIp(A) is a dual Banach algebra. Additionally, we prove the equivalence between the Connes amenability of LMIp(C) and the finiteness of I, and that LMIp(C) is always pseudo-Connes amenable for any 1 ≤ p ≤ 2.
JOURNAL OF MATHEMATICS
(2022)
Article
Microbiology
Preeti Sharma, Sumanpreet Kaur, Bhupinder Singh Chadha, Raminderjit Kaur, Manpreet Kaur, Sukhraj Kaur
Summary: Enterocin 12a is a novel bacteriocin with anticancer properties against human cancer cell lines. It selectively inhibits the proliferation of cancer cells in a dose-dependent manner and induces apoptosis-like morphological changes, while having negligible activity towards non-malignant cells. Further evaluation in animal models is recommended to explore its potential as an anticancer agent.
Article
Biotechnology & Applied Microbiology
Ruilian Li, Jinsong Duan, Yicheng Zhou, Jiawei Wang
Summary: Class IId (lactococcin-like) bacteriocins and class IIa (pediocin-like) bacteriocins induce membrane leakage and cell death by binding to the mannose phosphotransferase system (man-PTS) on target cells. Class IId bacteriocins specifically target lactococcal cells, while class IIa bacteriocins target diverse bacterial cells except lactococcal cells.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio Maldonado-Barragan, Estibaliz Alegria-Carrasco, Maria del Mar Blanco, Ana Isabel Vela, Jose Francisco Fernandez-Garayzabal, Juan Miguel Rodriguez, Alicia Gibello
Summary: Lactococcus garvieae is an emerging pathogen that causes infectious diseases in animals and potentially in humans. In this study, two gene clusters encoding novel bacteriocins were identified in a plasmid of a clinical isolate. These bacteriocins exhibited inhibitory activity against L. garvieae strains and other bacteria, and they may use a mannose uptake system as a receptor. Interestingly, they were highly active against their own host.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Mihye Seol, Taejoon Kim
Summary: Due to non-IID datasets used in local training of federated learning, performance degradation occurs. An efficient algorithm is proposed to enhance performance by addressing the negative effects of non-IID datasets. The proposed algorithm reduces intra-client class imbalance and mitigates inter-client class imbalance by adjusting client class distributions and amount of local training data. Additionally, it dynamically controls batch size and learning rate to improve efficiency. Evaluation shows a 20% higher accuracy compared to existing algorithms, with less resource usage.
Article
Biochemistry & Molecular Biology
Marta Worzakowska, Malgorzata Sztanke, Krzysztof Sztanke
Summary: This study investigates the thermal properties and decomposition process of a new class of potential anticancer drugs containing asymmetrical triazine template. The experimental methods used were differential scanning calorimetry (DSC) and simultaneous thermogravimetry/differential scanning calorimetry (TG/DTG/DSC) coupled online with Fourier transform infrared spectroscopy (FTIR) and quadrupole mass spectrometry (QMS). The results show that the melting points of the compounds depend on the position and type of substituents, but not on the furnace atmosphere. The compounds exhibit high thermal stability in both inert and oxidizing conditions, with most of them being more stable in oxidizing conditions. The pyrolysis process releases volatiles such as NH3, HNCO, HCN, CO, CO2, H2O, NO2, aromatic amine derivatives, alkenes, and HCl, while the oxidative decomposition process emits NH3, CO2, CO, HCN, HNCO, H2O, aromatics, HCl, N-2, NO2, NH2OH, and (CN)(2). The decomposition is initiated by a radical mechanism and involves the cleavage of C-N and C-C bonds (inert conditions) as well as the reaction of volatiles and residues with oxygen (oxidizing conditions).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Xiaoyan Chen, Angela Winstead, Hongtao Yu, Jiangnan Peng
Summary: Taccalonolides are a new class of microtubule stabilizers derived from plants of the Tacca genus, showing effectiveness against drug-resistant tumors. Through structural modification via semi-synthesis, their anti-proliferation potency can be significantly increased. The unique mechanism of covalently binding to microtubules and resistance circumvention mechanisms make taccalonolides a promising area of research in cancer therapy.
Article
Biotechnology & Applied Microbiology
Kankamol Kerdkumthong, Wannarat Chanket, Phanthipha Runsaeng, Sutthipong Nanarong, Kawinnath Songsurin, Phonprapavee Tantimetta, Chanan Angsuthanasombat, Aratee Aroonkesorn, Sumalee Obchoei
Summary: This study demonstrates the anticancer properties of two recombinant bacteriocins, rhamnosin and lysostaphin, against cholangiocarcinoma cell lines. The bacteriocins inhibit cell growth, especially in gemcitabine-resistant cells, and induce apoptosis through the upregulation of proapoptotic genes. This is the first report on the anticancer effects of rhamnosin and lysostaphin.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Food Science & Technology
Fanqiang Meng, Xiaoyu Zhu, Haizhen Zhao, Ting Nie, Fengxia Lu, Zhaoxin Lu, Yingjian Lu
Summary: A novel class III bacteriocin gene, NX371, was identified and expressed from Lactobacillus acidophilus with significant antimicrobial activity against various foodborne pathogens. The study demonstrated that NX371 exhibited thermal and pH stability, effectively inhibiting the growth of pathogens in milk and cheese.
Article
Computer Science, Artificial Intelligence
Jinxiang Ou, Yunheng Shen, Feng Wang, Qiao Liu, Xuegong Zhang, Hairong Lv
Summary: This article proposes a method called AggEnhance to enhance the aggregation in federated learning, aiming to solve the issues of poor aggregated result and slow convergence speed caused by non-IID data distributions. By synthesizing reliable samples from local models and adjusting the aggregated result, our method achieves noticeable improvements in convergence on real data, without requiring additional data transmission or process modification, and maintaining the same level of security as the original algorithm.
ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY
(2022)
Article
Biochemical Research Methods
Nishant Kumar, Sumeet Patiyal, Shubham Choudhury, Ritu Tomer, Anjali Dhall, Gajendra P. S. Raghava
Summary: In this study, a high-precision method for predicting, designing, and scanning T1DM associated peptides was developed. By using alignment and machine learning techniques, this method provides accurate results. A web server and standalone server were also developed for practical use.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Sumeet Patiyal, Anjali Dhall, Khushboo Bajaj, Harshita Sahu, Gajendra P. S. Raghava
Summary: This paper describes a method called Pprint2 for predicting RNA-interacting residues in proteins. The study found that positively charged amino acids are more prominent in these residues. By using evolutionary profiles and convolutional neural network, the researchers developed a final model that performed well on the validation dataset.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Anjali Dhall, Sumeet Patiyal, Shubham Choudhury, Shipra Jain, Kashish Narang, Gajendra P. S. Raghava
Summary: Tumor Necrosis Factor alpha (TNF-a) is a pleiotropic pro-inflammatory cytokine that plays a crucial role in immune cell signaling pathways. This study aimed to predict and design TNF-a inducing epitopes using an in silico tool. The proposed models achieved high predictive performance in identifying TNF-a inducing peptides in both human and mouse hosts. Additionally, potential TNF-a inducing peptides were identified in proteins of HIV-1, HIV-2, SARS-CoV-2, and human insulin.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biology
Leimarembi Devi Naorem, Neelam Sharma, Gajendra P. S. Raghava
Summary: This study aims to develop a model for accurately predicting IL-5 inducing antigenic regions in proteins. The study identified certain residues, such as Ile, Asn, and Tyr, that dominate IL-5 inducing peptides. Alignment-based methods provided high precision but limited coverage, while alignment-free methods, including machine learning models, improved performance. The hybrid model combining alignment-based and alignment-free methods achieved excellent results on the validation dataset.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Sadhana Tripathi, Neelam Sharma, Leimarembi Devi Naorem, Gajendra P. S. Raghava
Summary: Over the years, numerous vaccines have been developed against viral infections, but a comprehensive database providing detailed information on viral vaccines has been lacking. In this review, we introduce our freely accessible database ViralVacDB, which includes details of viral vaccines, their types, routes of administration, and approving agencies. This repository systematically covers additional information on 422 viral vaccines, including 145 approved vaccines and 277 in clinical trials. We believe that this database will greatly benefit researchers and professionals in pharmaceuticals and immuno-informatics.
DRUG DISCOVERY TODAY
(2023)
Article
Endocrinology & Metabolism
Dashleen Kaur, Akanksha Arora, Sumeet Patiyal, Gajendra Pal Singh Raghava
Summary: Hmrbase2 is a comprehensive platform that provides extensive information on hormones, which is essential for the therapeutics and diagnostics of hormonal diseases.
HORMONES-INTERNATIONAL JOURNAL OF ENDOCRINOLOGY AND METABOLISM
(2023)
Article
Biochemistry & Molecular Biology
Piyush Baindara, Trinath Chowdhury, Dinata Roy, Mahitosh Mandal, Santi M. Mandal
Summary: The coronavirus disease 2019 (COVID-19) has spread rapidly worldwide, causing millions of infections and hundreds of deaths. In this study, a surfactin-like lipopeptide produced by a probiotic bacterial strain Bacillus clausii TS was isolated and purified. The purified lipopeptide showed efficient binding and inhibition of SARS-CoV-2 spike (S1) protein, and thermodynamic analysis confirmed its inhibitory binding. Molecular docking, dynamics, and simulation experiments further demonstrated the potential of surfactin as a drug agent for targeting the spike protein of SARS-CoV-2 and other emerging variants.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Microbiology
Suchet Aggarwal, Anjali Dhall, Sumeet Patiyal, Shubham Choudhury, Akanksha Arora, Gajendra P. S. Raghava
Summary: Phage therapy is a viable alternative to antibiotics for treating drug-resistant bacterial infections. This study aims to accurately predict phage-host interactions to identify potential bacteriophage candidates for treatment. Various models, including alignment-based, alignment-free, hybrid, and ensemble models, were developed and achieved high accuracy rates, with the ensemble model reaching up to 93.5% accuracy on the validation dataset.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Roy Dinata, Piyush Baindara
Summary: In this study, a novel defensin-like bacteriocin called LS25 was identified and its immunogenic and physiochemical properties were investigated using immunoinformatic tools. LS25 was found to have potential as an adjuvant or carrier protein for subunit vaccine development.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Nishant Kumar, Nisha Bajiya, Sumeet Patiyal, Gajendra P. S. Raghava
Summary: This paper provides a comprehensive review of the identification of B-cell epitopes (BCEs), covering experimental techniques, historical perspectives, and computational methods. The overall challenge of identifying BCEs is also discussed.
Article
Biochemical Research Methods
Akanksha Arora, Sumeet Patiyal, Neelam Sharma, Naorem Leimarembi Devi, Dashleen Kaur, Gajendra P. S. Raghava
Summary: Non-invasive diagnostics and therapies are important for minimizing patient discomfort. Exosomal proteins are identified as potential biomarkers. This study presents a model for predicting exosomal proteins based on machine learning and sequence motifs. The hybrid model outperforms existing methods and a web server and standalone software have been developed for researchers to predict and discover exosomal proteins.
Article
Biochemical Research Methods
Akshara Pande, Sumeet Patiyal, Anjali Lathwal, Chakit Arora, Dilraj Kaur, Anjali Dhall, Gaurav Mishra, Harpreet Kaur, Neelam Sharma, Shipra Jain, Salman Sadullah Usmani, Piyush Agrawal, Rajesh Kumar, Vinod Kumar, Gajendra P. S. Raghava
Summary: In the past 30 years, numerous protein features have been discovered for protein annotation. To integrate these features, we developed a method called Pfeature, which can compute over 200,000 features for predicting protein function, residue-level annotation, and chemically modified peptides. Pfeature includes six major modules: composition, binary profiles, evolutionary information, structural features, patterns, and model building.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Review
Medicine, General & Internal
Piyush Baindara, Sriradha Ganguli, Ranadhir Chakraborty, Santi M. Mandal
Summary: The vast surface area of the respiratory system is the initial contact site for microbes and foreign particles. Respiratory secretions contain host defense peptides (HDPs) that play a crucial role in the body's defense against respiratory infections. Understanding the regulation of HDPs during respiratory disorders can provide alternative methods for combating respiratory viral infections.
CLINICS AND PRACTICE
(2023)
Article
Biology
Anjali Dhall, Sumeet Patiyal, Harpreet Kaur, Gajendra P. S. Raghava
Summary: Advancements in cancer immunotherapy have shown significant outcomes in treating cancers. To design effective immunotherapy, it's important to understand immune response of a patient based on its genomic profile. However, analyses to do that requires proficiency in the bioinformatic methods. Here, we are providing a web-based resource that gives scientists with no bioinformatics expertise, the ability to obtain the prognostic biomarkers for different cancer types at different levels.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Chemistry, Applied
Mohd Yusuf, Soniya Rani, Udeep Chawla, Piyush Baindara, Samera Ali Siddique, Khushboo Nirala, Mohammad Asif
Summary: Obesity, diabetes, and cancer are significant health concerns globally. Adiponectin, a protein that regulates these diseases, is a potential drug target. Herbal compounds, such as curcumin, can modulate adiponectin activity, although the underlying mechanisms are unclear. Understanding the activation mechanism of adiponectin can aid in the development of new herbal drugs for obesity, diabetes, and cancer.
BIOINTERFACE RESEARCH IN APPLIED CHEMISTRY
(2023)
