Article
Materials Science, Multidisciplinary
Ya Wang, Yuxiao Wang, Ting-Ting Li, Xiaomeng Wang, Hai-Tao Ren, Ching-Wen Lou, Jia-Horng Lin
Summary: In this article, a self-healing conductive material was prepared using polyaniline as the conductive substance with oxidized nanocellulose and polyacrylamide. The material showed high fracture stress, electrical conductivity, and self-healing efficiency at room temperature.
ACS APPLIED POLYMER MATERIALS
(2023)
Editorial Material
Cell Biology
Ina Kirmes, Steven Zuryn
Summary: The integrity of mitochondrial DNA is crucial for energy synthesis. A recent study reveals a vicious cycle of mtDNA replication within dysfunctional mitochondria that propagates genomes with deleterious mutations.
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yao Houndonougbo, Bethany Pugh, Kandise VanWormer, Caitlin April, Nicholas Burgis
Summary: ITPA protein is crucial for removing noncanonical purine nucleoside triphosphates, with mutations P32T and R178C altering the protein's structure and dynamics, and affecting its activity. Detailed molecular dynamic simulations provide insights into the impact of these mutations on ITPA function.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Yong-Bi Fu, Gregory W. Peterson, Carolee Horbach
Summary: Conserving millions of plant germplasm accessions in genebanks worldwide is crucial for securing future food supply. However, long-term conservation also comes with genetic costs. By studying several crop collections, we found that there were deleterious and adaptive mutations present, and that the number of deleterious mutations increased while the number of adaptive mutations decreased with longer storage time. This has implications for understanding mutational dynamics and genetic costs in conserved germplasm and for long-term germplasm management.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Shinji Sasaki, Toshio Watanabe, Takayuki Ibi, Kiyotoshi Hasegawa, Yoichi Sakamoto, Shunsuke Moriwaki, Kazuhito Kurogi, Atsushi Ogino, Takanori Yasumori, Hiroyuki Wakaguri, Eiji Muraki, Youko Miki, Yuichi Yoshida, Yoshinobu Inoue, Ichiro Tabuchi, Ken Iwao, Taichi Arishima, Keisuke Kawashima, Manabu Watanabe, Sumio Sugano, Yoshikazu Sugimoto, Yutaka Suzuki
Summary: The intensive use of a few elite sires in cattle has led to an increased risk of deleterious recessive traits. By analyzing SNP array data and exome sequencing, researchers identified deleterious recessive haplotypes in Japanese Black cattle, some of which affect embryonic survival. The study found specific candidate mutations in genes like IARS, CDC45, and CLDN16 associated with these deleterious haplotypes.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Mengdie Yan, Chenlu Xu, Yang Sun, Huilin Pan, Hong Li
Summary: The addition of PEO in aqueous electrolytes has been found to improve the cycling stability and Coulombic efficiency of Zn anodes, but the overpotential and long-term stability are significantly influenced by different anions. The choice of salt anions in aqueous electrolytes with PEO additives plays a crucial role in tuning the reaction kinetics and stability of Zn anodes.
Article
Biology
Sara Catalini, Barbara Rossi, Mariagrazia Tortora, Paolo Foggi, Alessandro Gessini, Claudio Masciovecchio, Fabio Bruni
Summary: This study investigated the hydrogen bonding of water and water/salt mixtures around a proline-based tripeptide model using UVRR, revealing the significant roles of cations and fluoride/chloride anions in affecting the conformational stability of proline residues. The spectroscopic data suggested that cations alter the solvation shell at the carbonyl site of proline, while fluoride and chloride ions promote the strongest interactions at the C = O site of proline, leading to greater stabilization of the trans conformers of the tripeptide.
Article
Biochemistry & Molecular Biology
Brandon Havranek, Shahidul M. Islam
Summary: The majority of disease-causing genetic variations in the human genome are due to non-synonymous single nucleotide polymorphisms (nsSNPs). This study focused on investigating the pathogenic effect of 14 nsSNPs in the merlin FERM domain, identifying G197C and L234R mutations as deleterious mutations associated with mild and severe forms of NF2. Molecular dynamics simulations showed that mutant structures were more flexible than the wildtype, with the L234R mutation exhibiting greater structural instability, potentially impacting merlin's ability to regulate the Hippo signaling pathway.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Energy & Fuels
Mingwei Xia, Wei Chen, Jing Wu, Yingquan Chen, Haiping Yang, Xu Chen, Danchen Zhu, Hanping Chen
Summary: This study elucidated the unique effect of organic salt porogen on biomass char intermediates, providing a novel precursor-universal and efficient approach for carbon material preparation.
Article
Biochemistry & Molecular Biology
Zachary A. Digby, Yuhui Chen, Khalil Akkaoui, Joseph B. Schlenoff
Summary: Salt bridges, pairings between oppositely charged amino acids, play a crucial role in protein folding and interactions. This study focuses on the properties of biopolyelectrolyte complexes (BioPECs) formed by poly-L-arginine (PLR) and poly-L-lysine (PLK) with sodium triphosphate (STPP), as well as by polypeptide-only combinations. The results show that these materials exhibit solid, even glassy, characteristics. Additionally, the BioPECs made with different polypeptides and additives display distinct melting events and structural features.
Article
Biochemical Research Methods
Lihua Wang, Tao Zhang, Lihong Yu, Chun-Hou Zheng, Wenguang Yin, Junfeng Xia, Tiejun Zhang
Summary: This study proposes a computational model, seDSM, which uses a selective ensemble to predict deleterious synonymous mutations. The model constructs candidate base classifiers using balanced training subsets and selects classifiers with high diversity for integration. Experimental results demonstrate the outstanding predictive performance of seDSM.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Song Zhang, Zhenghuai Feng, Chunhui Jiang, Xiaojun Yu, Jianke Pan, Juan Du, Zhiyu Jiang, Yuan Chen, Tianli Wang
Summary: In this study, a series of chiral epsilon-benzosultams bearing phosphorus functionalities were synthesized successfully. Control experiments were conducted to elucidate the plausible reaction mechanism of this chemical transformation.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Sahithya Phani Babu Vemulapalli, Stefan Becker, Christian Griesinger, Nasrollah Rezaei-Ghaleh
Summary: The presence of salt bridges between Arg5 and its nearby negatively charged residues in the N-terminal region of Aβ is correlated with less extended structures. Ser8 phosphorylation promotes Aβ aggregation, and density functional theory calculations demonstrate how negatively charged phosphoserine 8 influences the network of adjacent salt bridges.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
V. L. Furer, A. E. Vandyukov, S. R. Kleshnina, S. E. Solovieva, I. S. Antipin, V. Kovalenko
Summary: The vibrational spectra of p-hexasulfonatocalix[6]arene hexasodium salt (SC6) and p-tert-butylcalix[6]arene (TB6) were studied, allowing to distinguish bands of tert-butyl and sulfonate groups. The structure and vibrational spectra of the SC6 molecule were calculated for different conformations, with the compressed cone conformation being the most stable. The replacement of tert-butyl groups with sulfonate groups resulted in an increase in the cavity size of calixarene molecules and changes in supramolecular properties.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Physical
U. Likhitha, B. Narayana, B. K. Sarojini, S. Madan Kumar, T. Karthick
Summary: DL-tartaric acid and dimethylamine were used to create a hybrid salt-pseudopolymorph molecule, with the main intermolecular interactions demonstrated by simulating the FTIR spectrum, and the crystal structure characterized by complementary hydrogen bonds and one-dimensional anionic chains.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Rahul Singh, Vijay Kumar Bhardwaj, Jatin Sharma, Pralay Das, Rituraj Purohit
Summary: The study focuses on the overexpression of CDK2 in relation to cancer, aiming to design new inhibitors to suppress cancer cell proliferation. Comparison with standard inhibitors showed Ligand2 as a potential selective inhibitor for CDK2, with low side effects, based on ligand efficiency and binding affinity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Integrative & Complementary Medicine
Rahul Singh, Vijay Kumar Bhardwaj, Jatin Sharma, Rituraj Purohit, Sanjay Kumar
Summary: Tea polyphenols have the potential to inhibit the NSP16 protein of SARS-CoV-2, making them a potential antiviral medication.
JOURNAL OF TRADITIONAL AND COMPLEMENTARY MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Sachin Kumar, Vijay Kumar Bhardwaj, Shweta Guleria, Rituraj Purohit, Sanjay Kumar
Summary: This study utilized a structure-guided consensus approach to improve the enzymatic properties of Cu,Zn SOD from the high-altitude plant Potentilla atrosanguinea. The T97D substitution in SOD led to improved dimer stability and catalytic efficiency compared to the wild-type (WT), as validated by computational and experimental tools. This mutation not only enhanced enzyme thermostability but also laid the groundwork for designing SODs with improved kinetics by exploring interface residues as potential targets.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Article
Biochemical Research Methods
Priyank Shukla, Preeti Pandey, Bodhayan Prasad, Tony Robinson, Rituraj Purohit, Leon G. D'Cruz, Murtaza M. Tambuwala, Ankur Mutreja, Jim Harkin, Taranjit Singh Rai, Elaine K. Murray, David S. Gibson, Anthony J. Bjourson
Summary: This study utilizes immuno-informatics tools and bioinformatics databases to identify potential immunogenic epitopes of SARS-CoV-2 and validates their binding and interaction with HLA proteins. These findings have significant implications for the development of globally effective SARS-CoV-2 vaccines.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Chemistry, Physical
Vijay Kumar Bhardwaj, Pralay Das, Rituraj Purohit
Summary: In this study, the potential of plant-derived semi-synthetic molecules as selective inhibitors of CDK5 was evaluated using computational methods. The results suggest that two of these molecules have the ability to selectively inhibit CDK5 and could be potential candidates for the treatment of neurodegeneration, cancer, and diabetes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Vijay Kumar Bhardwaj, Rituraj Purohit
Summary: The proliferating cell nuclear antigen (PCNA) is a nononcogenic mediator of DNA replication that regulates cellular functions and pathways through protein-protein interactions. This study explores the binding modes and affinity of molecules with PCNA and identifies potential lead molecules to inhibit its protein-protein interactions.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sachin Kumar, Vijay K. Bhardwaj, Rahul Singh, Pralay Das, Rituraj Purohit
Summary: This study discovered a compound that can efficiently bind to the DENV-2 C protein through virtual ligand screening. Molecular docking and dynamics simulations revealed strong interactions between the compound and DENV-2 C protein. The findings suggest that this compound could be a potential therapeutic molecule for treating dengue complications.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Article
Biology
Rahul Singh, Vijay Kumar Bhardwaj, Pralay Das, Dhananjay Bhattacherjee, Grigory V. Zyryanov, Rituraj Purohit
Summary: This study investigated the potential binding mechanisms of 1,2,3-triazole scaffolds with SARS-CoV-2 M-pro using molecular dynamics and enhanced sampling simulations. The results showed interactions between the scaffolds and key residues of M-pro, with comparable binding free energy to experimental inhibitors.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Multidisciplinary Sciences
Prakriti Kashyap, Vijay Kumar Bhardwaj, Mahima Chauhan, Varun Chauhan, Asheesh Kumar, Rituraj Purohit, Arun Kumar, Sanjay Kumar
Summary: This study aimed to identify peptides that can inhibit the main protease (M-pro) of SARS-CoV-2, and a ricin-based peptide from barley (BRIP) was found to effectively inhibit M-pro and show potential therapeutic effects against SARS-CoV-2. Molecular docking and MD simulations revealed the favorable binding site and stable interactions between M-pro and BRIP. The findings provide new insights into inhibitor development against COVID-19.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Mahima Chauhan, Vijay Kumar Bhardwaj, Asheesh Kumar, Vinod Kumar, Pawan Kumar, M. Ghalib Enayathullah, Jessie Thomas, Joel George, Bokara Kiran Kumar, Rituraj Purohit, Arun Kumar, Sanjay Kumar
Summary: This study demonstrates that theaflavin 3-gallate effectively targets the M-pro of SARS-CoV-2, thereby limiting viral replication in vitro.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Rahul Singh, Vijay K. Bhardwaj, Rituraj Purohit
Summary: This study investigates the potential of six turmeric derivatives as inhibitors for the coronavirus Nsp15 using computer-based methods. The results show that these compounds have stable interactions and high binding affinity with Nsp15, indicating their potential as modulators for Nsp15 inhibition.
CELL BIOCHEMISTRY AND FUNCTION
(2022)
Article
Biochemistry & Molecular Biology
Ankita Dhiman, Rituraj Purohit
Summary: This study aimed to enhance the acid resistance of Serratiopeptidase through computational interventions. The N412D mutant was identified as the most stable mutant with negative electrostatic potential, which can stabilize Serratiopeptidase amid extreme pH values.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Bhanu Sharma, Dhananjay Bhattacherjee, Grigory Zyryanov, Rituraj Purohit
Summary: Phosphodiesterase 10A (PDE10A) is an important drug target for neurological conditions. In this study, a series of compounds were explored as PDE10A inhibitors using computational methods, and 3h and 3j were identified as promising candidates. The results showed that these compounds formed stable complexes with PDE10A.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Rahul Singh, Sachin Kumar, Vijay Kumar Bhardwaj, Rituraj Purohit
Summary: This study analyzed the interaction ability of aminoarylbenzosuberene (AAB) molecules with DprE1 and identified a promising molecule (AAB4) as a potential lead against tuberculosis. AAB4 showed better inhibition potency and stability compared to co-crystallized inhibitors and also inhibited a drug-resistant mutant. These findings suggest the potential of AAB4 as a therapeutic option for tuberculosis.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Rahul Singh, Vijay Kumar Bhardwaj, Pralay Das, Rituraj Purohit
Summary: Aminoarylbenzosuberene (AAB) molecules were analyzed in silico to develop potent inhibitors for 11 beta-Hydroxysteroid dehydrogenase (11 beta-HSD1) protein. AAB4 molecule showed stronger interactions and binding affinity compared to the standard inhibitors.
CHEMICAL COMMUNICATIONS
(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.
