Article
Biochemistry & Molecular Biology
Zhenyu Ma, Mingyue Li, Huaning Zhang, Baihui Zhao, Zihui Liu, Shuonan Duan, Xiangzhao Meng, Guoliang Li, Xiulin Guo
Summary: High temperature reduces crop production, especially wheat. A novel splice variant, TaHsfA2-7-AS, was induced by heat and positively regulated thermotolerance in wheat. TaHsfA2-7-AS encodes a truncated isoform and its expression is up-regulated during heat shock.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Yule Wang, Yuduan Ding, Qian Zhao, Chen Wu, Cecilia H. Deng, Jingru Wang, Yufan Wang, Yanfang Yan, Rui Zhai, Yar-Khing Yauk, Fengwang Ma, Ross G. Atkinson, Pengmin Li
Summary: This study found that the synthesis of phlorizin and trilobatin in apple are controlled by single genes. Differential promoter activities of PGT1 and PGT2 genes determine the accumulation patterns of DHC glycosides. Transcription factors MYB8L and PRR2L control the DHC glycoside patterns in different tissues. Furthermore, DHC glycoside production is essential during apple seed development.
Article
Biology
Mukulika Ray, Ashley Mae Conard, Jennifer Urban, Pranav Mahableshwarkar, Joseph Aguilera, Annie Huang, Smriti Vaidyanathan, Erica Larschan
Summary: Sex-specific splicing is crucial for sex determination and sexual dimorphism. Our study reveals that widespread sex-specific transcript diversity occurs at early developmental stages.
Review
Endocrinology & Metabolism
Panyisha Wu, Moya Zhang, Nicholas J. G. Webster
Summary: Alternative RNA splicing is an important biological process that has been linked to various clinical syndromes, but its applicability to common diseases is still uncertain. This review focuses on the changes in alternative RNA splicing in fatty liver disease and the role of splicing regulation in disease progression.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Genetics & Heredity
He Zhang, Baoai Han, Xingxing Han, Yuying Zhu, Hui Liu, Zhiyong Wang, Yanfen Cui, Ran Tian, Zicong Gao, Ruinan Tian, Sixin Ren, Xiaoyan Zuo, Jianfei Tian, Fei Zhang, Ruifang Niu
Summary: Recent evidence suggests that splicing factors (SFs) and alternative splicing (AS) play important roles in cancer progression. This study constructed SF-risk-models and AS-risk-models in different BRCA subtypes, providing potential multidimensional biomarkers for the diagnosis, prognosis, and treatment of BRCA. The functional roles of the selected SFs were found to be highly context-dependent among different BRCA subtypes.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Wenhao Li, Weike Zeng, Xiayang Jin, Huiming Xu, Xingyan Fang, Zhijie Ma, Gangjian Cao, Ruizhe Li, Liuyin Ma
Summary: This study analyzed the transcriptome dynamics of Tibetan sheep ovaries under high-altitude stress and found that high-altitude stress suppressed the expression of follicular development marker genes, impaired the LH/FSH signaling pathway, and affected alternative splicing of transcription factors and RNA processing factors. This research is important for understanding the mechanism of reduced fertility in animals under high-altitude stress.
Article
Plant Sciences
Bing He, Lin Meng, Lina Tang, Weicong Qi, Fengqin Hu, Yuanda Lv, Wenjing Song
Summary: This study investigated the transcriptome changes in roots and shoots of allopolyploid Nicotiana tabacum under K+ deficiency, revealing significant alterations in root architecture and IAA content. Analysis of alternative splicing (AS) events showed a tissue-specific response to K+ deficiency, with differentially alternatively spliced genes playing a unique regulatory role in plants' adaptation to low potassium conditions. The study also identified DAS transcription factors that were involved in response to auxin signaling, highlighting the functional significance of AS events in regulating root growth and architecture.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Jianzhao Li, Xinhui Yan, Mudassar Ahmad, Wenjie Yu, Zhizhong Song, Junbei Ni, Qinsong Yang, Yuanwen Teng, Hongxia Zhang, Songling Bai
Summary: The study found that alternative splicing of the PpDAM1 gene may play a crucial role in the pear flower bud dormancy process in 'Dangshansu' pear tree.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Virology
Dania Lavysh, Vladimir Mekler, Evgeny Klimuk, Konstantin Severinov
Summary: This study investigated the temporal pattern of gene expression during Salmonella enterica serovar Newport bacteriophage 7-11 infection and compared it to the previously determined transcription strategy of Escherichia coli phage phiEco32. The results revealed the presence of eight promoters in 7-11 phage and the absence of middle promoters and shut-off of sigma(70)-dependent transcription.
Article
Biochemistry & Molecular Biology
Xueqing Wang, Quanlong Jiang, Yuanyuan Song, Zhidong He, Hongdao Zhang, Mengjiao Song, Xiaona Zhang, Yumin Dai, Oezlem Karalay, Christoph Dieterich, Adam Antebi, Ligang Wu, Jing-Dong J. Han, Yidong Shen
Summary: Ageing is a complex process with different features in different tissues. This study isolated cells from different tissues in worms and analyzed the transcriptomic changes during ageing, revealing the diversity of ageing across tissues and identifying tissue-specific longevity regulators. Additionally, novel factors controlling intestinal barrier integrity and sarcomere structure during ageing were discovered.
Article
Multidisciplinary Sciences
Suqin Zhu, Dianliang Lin, Zhoujie Ye, Xiaojing Chen, Wenwen Jiang, Huiling Xu, Song Quan, Beihong Zheng
Summary: Endometrial decidualization is crucial for maintaining pregnancy, and GOLPH3 plays a role in regulating gene expression and alternative splicing in human endometrial stromal cells. Through bioinformatics analysis, it was found that GOLPH3 affects the transcriptional level and alternative splicing events in hESCs, particularly in pathways related to endometrial decidualization.
Article
Biochemistry & Molecular Biology
Anabelle Planques, Vanessa Oliveira Moreira, David Benacom, Clemence Bernard, Laurent Jourdren, Corinne Blugeon, Florent Dingli, Vanessa Masson, Damarys Loew, Alain Prochiantz, Ariel A. Di Nardo
Summary: This study explores the functional roles of OTX2 in adult choroid plexus, highlighting its importance in processes such as cell signaling, adhesion, and regulation of secreted factors. OTX2 is shown to impact immune responses, stress reactions in the choroid plexus, and influence the mRNA isoforms of proteins involved in oxidative stress response and DNA repair. Mass spectrometry analysis also reveals potential OTX2 protein partners in the choroid plexus and other target regions, involved in cell adhesion, chromatin structure, and RNA processing. Overall, OTX2 plays crucial roles in regulating choroid plexus function and brain homeostasis throughout life.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Immunology
Jianli Zhou, Qiao Zhang, Yuzhen Zhao, Yuchen Song, Yanan Leng, Moxian Chen, Shaoming Zhou, Zhaoxia Wang
Summary: Inflammatory bowel disease (IBD) is a group of chronic diseases including Crohn's disease and ulcerative colitis, which have a global impact on both children and adults. The burden of IBD is increasing worldwide, and the costs associated with it are high. The pathogenesis of IBD is still unclear, but is believed to be related to environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. This article reviews the research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Yunqi Chao, Yonghui Jiang, Mianling Zhong, Kaiyan Wei, Chenxi Hu, Yifang Qin, Yiming Zuo, Lili Yang, Zheng Shen, Chaochun Zou
Summary: Alternative splicing plays a crucial role in regulating gene expression patterns post-transcriptionally, particularly in adipogenesis. Aberrant expression and alterations in splicing regulators are linked to mutations in obesity-related genes, indicating their potential role in diet-induced obesity and metabolic dysregulation. Research on the splicing machinery's interaction with obesity and metabolic disorders provides insights for potential therapeutic strategies in clinical settings.
CELL AND BIOSCIENCE
(2021)
Review
Plant Sciences
Xiao-Xiao Liu, Qian-Huan Guo, Wei-Bo Xu, Peng Liu, Kang Yan
Summary: Plants use diverse strategies and complex regulations to adapt to changing environmental conditions. In addition to direct gene transcription regulation, alternative splicing plays a crucial role in coping with various stresses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Behavioral Sciences
Neeraj Kumar Sharma, Sukhdeep Kaur, Rajesh Kumar Goel
EPILEPSY & BEHAVIOR
(2020)
Article
Cell Biology
Wesley L. Crouse, Swapan K. Das, Thu Le, Gregory Keele, Katie Holl, Osborne Seshie, Ann L. Craddock, Neeraj K. Sharma, Mary E. Comeau, Carl D. Langefeld, Gregory A. Hawkins, Richard Mott, William Valdar, Leah C. Solberg Woods
Summary: This study conducted transcriptomic analysis in metabolically active tissues of outbred heterogeneous stock (HS) rats and humans, identifying consensus genes and networks associated with body weight/body mass index (BW/BMI). The identified genes and networks are involved in various metabolic processes, expanding our understanding of the genetics underlying obesity.
PHYSIOLOGICAL GENOMICS
(2022)
Article
Engineering, Electrical & Electronic
Subodh Kumar, Ankit Rajpal, Neeraj Kumar Sharma, Sheetal Rajpal, Anand Nayyar, Naveen Kumar
Summary: Coronary heart disease is a leading cause of mortality worldwide. This paper proposes a robust semi-blind watermarking scheme, ROSEmark, for authenticating ECG records transmitted through networked devices. Experimental results demonstrate that ROSEmark outperforms competitors in terms of fidelity and robustness, making it suitable for real-time applications such as telemedicine.
DIGITAL SIGNAL PROCESSING
(2022)
Article
Biochemistry & Molecular Biology
Alistaire D. Ruggiero, Ravichandra Vemuri, Masha Block, Darla DeStephanis, Matthew Davis, Jeff Chou, Abigail Williams, Ashlynn Brock, Swapan Kumar Das, Kylie Kavanagh
Summary: Obesity affects 650 million people worldwide, often accompanied by metabolic syndrome. The study found that healthy obesity is characterized by an increased ratio of M2 to M1 macrophages and increased expression of lipid handling genes in subcutaneous adipose tissue. The findings suggest that M2 macrophages and fatty acid oxidation could be potential targets for improving metabolic health in obese individuals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Rekha Kumari, Rozi Sharma, Neeraj Kumar Sharma, Deepak Pant, Piyush Malaviya
Summary: Chemical fertilizers increase crop production in the short term but decrease soil fertility in the long run. Recycling nutrient-rich poultry manure into biochar and using it as a soil amendment, along with irrigation using greywater, can enhance soil properties and promote plant growth. This study demonstrated that applying poultry biochar and 100% greywater irrigation improved soil nutrient content and crop growth, highlighting the potential of biochar and greywater management for sustainable agriculture.
ENVIRONMENTAL TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Peng Xu, Minghui Wang, Neeraj K. Sharma, Mary E. Comeau, Martin Wabitsch, Carl D. Langefeld, Mete Civelek, Bin Zhang, Swapan K. Das
Summary: This study conducted a multiscale gene network analysis of adipose and muscle tissues in African and European populations to reveal the cell-type-specific molecular signatures of insulin resistance. The research identified two adipocyte subtype-enriched modules and modules enriched for stem cells and fibro-adipogenic progenitors that showed opposite insulin sensitivity responses. The study also pinpointed key drivers of insulin resistance through the integration of gene co-expression and causal networks.
Article
Engineering, Biomedical
Neeraj Kumar Sharma, Subodh Kumar, Naveen Kumar
Summary: The extensive use of telemedicine has increased the exchange of medical data via insecure networks. This paper proposes HGSmark, a watermarking scheme for ECG signals, to address the security and authenticity concerns. The proposed scheme utilizes the HGS algorithm to optimize the embedding strength values and employs a wrapping-based FDCT and SVD for watermarking. Experimental results show that HGSmark achieves high performance in terms of imperceptibility and robustness compared to other state-of-the-art watermarking schemes for ECG signals.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2023)
Article
Multidisciplinary Sciences
Debarpan Bhattacharya, Neeraj Kumar Sharma, Debottam Dutta, Srikanth Raj Chetupalli, Pravin Mote, Sriram Ganapathy, C. Chandrakiran, Sahiti Nori, K. K. Suhail, Sadhana Gonuguntla, Murali Alagesan
Summary: This paper introduces the Coswara dataset, which contains diverse respiratory sounds and rich meta-data recorded from 2635 individuals between April 2020 and February 2022. The dataset includes nine sound categories associated with breathing, cough, and speech variants. The rich meta-data includes demographic information and health information related to COVID-19 symptoms, pre-existing respiratory ailments, comorbidity, and SARS-CoV-2 test status. The paper also presents the manual annotation of audio quality and the training and evaluation of a COVID-19 classifier to analyze the impact of various factors on detection performance.
Article
Acoustics
Neeraj Kumar Sharma, Unal Ege Gaznepoglu, Thomas Robotham, Emanuel A. P. Habets
Summary: This letter presents a reaction time analysis of a sound lateralization test, showing that stimuli from the sides yield quicker reactions and better class accuracy than from the front. Congruent ITD-ILD cues significantly improved both metrics, while opposing ITD-ILD cues resulted in slower responses driven by ITD. These findings corroborate the integrated processing of binaural cues and promote the use of multiple congruent binaural cues in headphone reproduction.
JASA EXPRESS LETTERS
(2023)
Article
Endocrinology & Metabolism
Thu Hong-Le, Wesley L. Crouse, Gregory R. Keele, Katie Holl, Osborne Seshie, Michael Tschannen, Ann Craddock, Swapan K. Das, Alexandria M. Szalanczy, Bailey McDonald, Michael Grzybowski, Jason Klotz, Neeraj K. Sharma, Aron M. Geurts, Chia-Chi Chuang Key, Gregory Hawkins, William Valdar, Richard Mott, Leah C. Solberg Woods
Summary: Using outbred HS rats, expression data, and mediation analysis, we identified QTLs and candidate gene mediators for various metabolic traits. Through physiological and expression QTL mapping, we identified 14 SNP-based pQTLs and 19 haplotype-based pQTLs, with 10 in common. Mediation analysis revealed Grk5, Krtcap3, Ilrun, and Rfx6 as candidate mediators for specific pQTLs. Further verification using gene knockdown/out models confirmed the role of Grk5 and Krtcap3 as regulators of obesity.
Article
Endocrinology & Metabolism
Sreejon S. Das, Swapan K. Das
Summary: This study compared genes and biological pathways affected by obesity in European and African ancestry populations using data from transcriptome-wide analyses on skeletal muscle tissues. It identified common obesity-associated transcripts and biological pathways across ethnicities, as well as unique obesity-associated processes in either African or European ancestry populations. Integration of SNP-to-Gene analyses predicted 316 critical target genes for obesity-associated genetic variants, suggesting their role in causing obesity.
INTERNATIONAL JOURNAL OF OBESITY
(2023)
Proceedings Paper
Automation & Control Systems
Neeraj Kumar Sharma, Saikat Chakrabarti, Ankush Sharma
Summary: The conventional transmission system state estimation assumes balanced loads at the transmission distribution boundary, but in reality, distribution feeders have inherently unbalanced loading, especially with the inclusion of small-scale renewable energy sources. Unbalanced loading can cause voltage variation at the boundary and adjacent nodes inside the transmission system. The traditional state estimation method is unable to handle unbalanced nodes. Therefore, this paper proposes a method to detect and identify unbalanced nodes in the transmission system and quickly update their states using a quasi-Newton approach.
2022 22ND NATIONAL POWER SYSTEMS CONFERENCE, NPSC
(2022)
Proceedings Paper
Acoustics
Debarpan Bhattacharya, Debottam Dutta, Neeraj Kumar Sharma, Srikanth Raj Chetupalli, Pravin Mote, Sriram Ganapathy, C. Chandrakiran, Sahiti Nori, K. K. Suhail, Sadhana Gonuguntla, Murali Alagesan
Summary: This paper describes a COVID-19 detection tool based on the analysis of respiratory sound samples and health symptoms. Users can upload relevant information to a cloud server via a website application, and within a minute, receive a COVID-19 probability score. This tool provides a potential solution for large-scale population testing.
Article
Anesthesiology
Neeraj Kumar Sharma, Nagendra Singh Chouhan, Manish Bansal, Praveen Chandra, Ajmer Singh, Rajiv Juneja, Yatin Mehta, Naresh Trehan
Summary: Patients with severe symptomatic tricuspid regurgitation (TR) often experience high morbidity and mortality rates. Transcatheter caval valve implantation (CAVI) is emerging as an effective therapeutic option for restricting TR backflow, especially in cases where surgical correction is not feasible.
ANNALS OF CARDIAC ANAESTHESIA
(2021)