Article
Biochemistry & Molecular Biology
Wen-Lin Ho, Jie-rong Huang
Summary: Aromatic residues are frequently found in the intrinsically disordered regions (IDRs) of RNA binding proteins (RBPs) and are often conserved among chordates. These residues play a crucial role in protein liquid-liquid phase separation (LLPS) and contribute to the formation of higher-order oligomers. This suggests that aromatic residues have played a significant role in the evolution of protein folding and biomolecular condensate assembly.
Article
Biochemistry & Molecular Biology
Haley I. Merritt, Nicholas Sawyer, Andrew M. Watkins, Paramjit S. Arora
Summary: This study aims to determine the requirements for binding an intrinsically disordered region (IDR) by its native binding partner, in order to develop minimal protein mimics that can regulate IDR interactions. The findings suggest that key binding residues on partner protein surfaces play a crucial role in determining their folding, and targeting the globular protein partners of IDRs may be more effective.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Steffen Luedeke, Philipp Lohner, Lara G. Stuehn, Martin U. Betschart, Matthias C. Huber, Andreas Schreiber, Stefan M. Schiller
Summary: Research has shown that coacervation of Elastin-like proteins occurs sharply when a certain number of repeat units has acquired beta-turn conformation, which is retained even after polypeptide assembly. This conformational threshold may have implications for other protein assembly processes and the design of protein-based smart materials.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Yumeng Liu, Xiaolong Wang, Bin Liu
Summary: Intrinsically disordered proteins/regions (IDPs/IDRs) are important for biological functions, and accurate prediction is crucial for protein structure and function predictions. However, most existing methods tend to predict fully ordered proteins as disordered, ignoring the fact that most newly sequenced proteins are fully ordered. The proposed RFPR-IDP method, trained on both ordered and disordered proteins, outperforms existing predictors in predicting both ordered and disordered proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Tanuj Handa, Debanjan Kundu, Vikash Kumar Dubey
Summary: The importance of protein structure in performing biological functions optimally is being challenged by the emergence of intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs). Understanding the evolutionary and functional significance of these proteins is crucial in studying various organisms. This review highlights the importance of IDPs in the physiology of specific organisms and establishes a positive correlation between IDPs and their relevance in human health and future medicine. Extensive research on IDPs and IDPRs will greatly contribute to expanding the field of structural biology, aiding in the comprehension of protein folding, misfolding, associated diseases, and drug design.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Andras Micsonai, Eva Moussong, Nikoletta Murvai, Agnes Tantos, Orsolya Toke, Matthieu Refregiers, Frank Wien, Jozsef Kardos
Summary: This article proposes a method for classifying disorder and order based on the analysis of far-UV CD spectroscopy data. The method only requires CD data at three wavelength points, making it useful for experimental verification of proteins without a stable tertiary structure.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Mughair Abdul Aziz, Miloofer Sabeem, M. Sangeeta Kutty, Shafeeq Rahman, Maitha Khalfan Alneyadi, Alia Binghushoom Alkaabi, Eiman Saeed Almeqbali, Faical Brini, Ranjit Vijayan, Khaled Masmoudi
Summary: In this study, five date palm LEA2 genes were cloned and functionally characterized, and three of them were found to enhance the thermostability of enzymes, suggesting their potential as target molecules for heat stress tolerance in plants.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Wen-Lin Ho, Hsuan-Cheng Huang, Jie-rong Huang
Summary: Conserved residues in protein homolog sequence alignments are important for structure or function. However, alignment often fails for intrinsically disordered proteins or regions due to lack of structure. This study proposes a method to retrieve common features in intrinsically disordered regions to identify functionally important residues. The trained model successfully predicts critical residues, allowing for improved understanding of protein functions.
Article
Biochemistry & Molecular Biology
Sushmita Basu, Ranjit Prasad Bahadur
Summary: This study explores the relationship between protein structure, function, and evolution, revealing different evolutionary characteristics among different classes of DRs in IDPs. Short IDRs show lower conservation, while functional classes requiring flexibility and specificity evolve slower. Amino acids promoting disorder evolve faster, with Pro, Gly, Ile, and Phe exhibiting unique coevolving nature in IDPs.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Virology
Melissa N. Webby, Nicole Herr, Esther M. M. Bulloch, Michael Schmitz, Jeremy R. Keown, David C. Goldstone, Richard L. Kingston
Summary: The paramyxoviral phosphoprotein plays a crucial role in RNA synthesis, with a stable structure and dynamic linker, facilitating interactions between the polymerase and genomic RNA. The protein's C-terminal region exhibits a gradual disorder-to-order transition at the interface between the structured binding domain and disordered linker.
Review
Biophysics
Orkid Coskuner-Weber, Sule Irem Caglayan
Summary: Computer simulations are used to study the secondary structure properties of proteins, but the choice of simulation protocol, technique, and force field parameters can impact the predicted results for disordered proteins. Research shows that different simulation techniques yield similar results for ordered proteins, but consensus is still needed to develop simulation techniques and force field parameter sets for disordered proteins.
BIOPHYSICAL REVIEWS
(2021)
Article
Chemistry, Analytical
Nazeer Hasan, Mohammad Imran, Dhara Jain, Athar Shamim, Sarwar Beg, Prashant Kesharwani, Gaurav Jain, Farhan J. Ahmad
Summary: The paper describes the development and validation of a simple and reliable HPLC method for simultaneous estimation of 5-FU and CBD. The method showed good linearity, precision, specificity, and robustness. It could be effectively used for quantification of these drugs in various in vitro and in vivo studies.
CURRENT ANALYTICAL CHEMISTRY
(2022)
Article
Education, Scientific Disciplines
Tej Pratap Singh, Navneet Verma, Farhan Jalees Ahmad, Phool Chandra, Gaurav Kumar Jain
Summary: This study evaluated the wound healing potential of raloxifene nanoemulsion gel in a rat model. The results showed that the raloxifene nanoemulsion gel can enhance breaking strength, tensile strength, and wound contraction in incision wounds, as well as promote re-epithelialization, neo-vascularization, fibroblast proliferation, and collagen deposition. It demonstrates significant wound healing potential.
INDIAN JOURNAL OF PHARMACEUTICAL EDUCATION AND RESEARCH
(2022)
Article
Pharmacology & Pharmacy
Nazeer Hasan, Mohammad Imran, Afsana Sheikh, Suma Saad, Gaurav Chaudhary, Gaurav Kumar Jain, Prashant Kesharwani, Farhan J. Ahmad
Summary: This review discusses the potential of cannabis in treating cancer, its safety profile, and the advancements in using nanotechnology to improve its therapeutic efficacy. It also explores the role of cannabinoids in different cancers and provides information on completed and ongoing clinical trials.
JOURNAL OF DRUG TARGETING
(2022)
Article
Multidisciplinary Sciences
Sheldon D'Silva, Shreya Chakraborty, Bratati Kahali
Summary: Genome wide association studies (GWAS) focus on single variant effects in additive genetic models, but only explain part of the heritability of complex traits. This study conducted epistasis analysis for BMI associated SNPs and identified two significant pairwise interactions, highlighting the influence of neuronal genes and implicating the coordinated expression of associated genes in liver, pancreas, and adipose tissues.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Bharti Vyas, Ratul Bhowmik, Mymoona Akhter, Farhan Jalees Ahmad
Summary: This study used computational analysis to identify potential mutations associated with hereditary glutathione reductase deficiency and other diseases. Structural and evolutionary analyses suggested that the mutations may alter the structure and function of the GSR protein. Additionally, genetic studies found that certain variations were associated with obstructive heart defects and hereditary anemia.
SCIENTIFIC REPORTS
(2022)
Article
Pharmacology & Pharmacy
Syed Mohammad Danish, Anshul Gupta, Urooj Ahmad Khan, Nazeer Hasan, Farhan Jalees Ahmad, Musarrat Husain Warsi, Ahmed M. Abdelhaleem Ali, Ameeduzzafar Zafar, Gaurav Kumar Jain
Summary: Intranasal cerium oxide nanoparticles (CNPs) have the potential to improve cognitive function in Alzheimer's disease (AD) through their antioxidant effect.
Article
Engineering, Chemical
Muzaffar Iqbal, Mohammad Raish, Ajaz Ahmad, Essam A. Ali, Yousef A. Bin Jardan, Mushtaq A. Ansari, Mudassar Shahid, Abdul Ahad, Khalid M. Alkharfy, Fahad I. Al-Jenoobi
Summary: The study found that when Ibrutinib interacts with Sinapic acid, it may influence the pharmacokinetics of Ibrutinib and result in increased bioavailability. This may be due to the inhibition of IBR metabolism in the liver and intestines by SA.
Review
Biochemistry & Molecular Biology
Syed M. Kawish, Shwetakshi Sharma, Waleed H. Almalki, Saad Alghamdi, Obaid Afzal, Imran Kazmi, Abdulmalik S. A. Altamimi, Fahad A. Al-Abbasi, Sarwar Beg, Farhan J. Ahmad
Summary: The pharmaceutical industry is advancing towards personalized medicine through innovation in drug development. Three-dimensional printing technology has enabled the manufacturing of personalized dosage forms, opening up new possibilities for discovering compounds and technologies.
CURRENT DRUG METABOLISM
(2022)
Article
Instruments & Instrumentation
Pavitra Solanki, Mohd Danish Ansari, Mohd Iqbal Alam, Mohd Aqil, Farhan J. Ahmad, Yasmin Sultana
Summary: This study developed an orally effective nanoformulation of disodium pamidronate for the treatment of osteoporosis. Through rational design and optimization, a commercially potential self nano-emulsifying drug delivery system (SNEDDS) was developed, which showed improved oral bioavailability and enhanced anti-osteoporotic activity. The study provided significant achievements in the treatment of postmenopausal osteoporosis and may lead to the use of nanotherapeutic-driven emerging biodegradable carriers-based drug delivery.
DRUG DELIVERY AND TRANSLATIONAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Anuja Jain, Tina Begum, Shandar Ahmad
Summary: Identifying the molecular features of host Toll-like receptors (TLRs), which are responsible for sensing pathogen nucleic acids, is important for understanding host defense mechanisms. We found that these features directly correlate with the strand specificity of the pathogen nucleic acids, but cannot fully explain the selectivity of pathogenic molecular patterns. Using machine learning, we developed a model that accurately predicts the strand specificity of TLRs based on protein-derived features.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Shreya Chakraborty, Bratati Kahali
Summary: Cognitive functioning is influenced by genetic factors, and metabolic risk factors can accelerate cognitive decline with age. This study aims to identify the genetic basis of cognition by analyzing data from whole-exome sequencing of 157,160 individuals. The findings reveal 20 loci associated with cognitive domains, implicating genes related to oxidative stress, synaptic plasticity, and neuroinflammation. The study also identifies interactions between APOE variants and LRP1, AMIGO1, and ITPR3, as well as their roles in amyloid beta and lipid/glucose metabolism pathways. The results highlight the importance of neuronal genes in cognition during aging.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Neha Vinayak, Shandar Ahmad
Summary: High quality and numerous data are essential for machine learning models. This study examines the issue using low-dimensional data sets and random forest as the classification model. The authors provide an initial estimate for the optimal data size requirement and observe that ML models can still perform well even with some class label errors.
ADVANCED NETWORK TECHNOLOGIES AND INTELLIGENT COMPUTING, ANTIC 2022, PT II
(2023)
Article
Computer Science, Information Systems
Hanif Amal Robbani, Alhadi Bustamam, Risman Adnan, Shandar Ahmad
Summary: This paper proposes an EKFAC preconditioned SGLD algorithm (EKSGLD), which improves the optimization process and combines the advantages of second-order optimization and the approximate Bayesian method. Experimental results show that EKSGLD outperforms existing preconditioning methods in terms of predictive accuracy and calibration.
Article
Oncology
Farhan Ahmad, Shalini Singh, Niraj Kumari
Summary: Spontaneous regression (SR) is relatively rare in non-small-cell lung cancer, especially with adenocarcinoma histology. Various mechanisms have been postulated, but the exact underlying mechanism is still uncertain.
JOURNAL OF CANCER RESEARCH AND THERAPEUTICS
(2022)
Article
Genetics & Heredity
Dana Mary Varghese, Ruth Nussinov, Shandar Ahmad
Summary: Moonlighting proteins are capable of performing multiple autonomous functions. In this study, human moonlighting DNA-binding proteins (mDBPs) were investigated and found to be distinguishable from other proteins with the same DNA-binding function. A machine learning model was developed to predict mDBPs from other DBPs with high accuracy.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
