Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jose Carlos Montanes, Marta Huertas, Xavier Messeguer, M. Mar Alba
Summary: The formation of new genes can occur through gene duplication or de novo formation from noncoding sequences. Both mechanisms show similarities in terms of low sequence constraints in the initial evolutionary stages, high turnover rates at the species level, and comparable persistence rates in deeper branches. Additionally, de novo proteins tend to have an excess of substitutions between charged amino acids, leading to rapid loss of their initial highly basic character.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Madiha Zaynab, Jiaofeng Peng, Yasir Sharif, Mohammed Albaqami, Rashid Al-Yahyai, Mahpara Fatima, Muhammad Azhar Nadeem, Khalid Ali Khan, Saqer S. Alotaibi, Ibrahim A. Alaraidh, Hassan O. Shaikhaldein, Shuangfei Li
Summary: This study conducted a comprehensive analysis of DDP proteins in the potato genome, identifying 10 DDP genes and studying their characteristics in terms of phylogenetics, gene duplication, expression profiles, and promoter regions involved in stress response. The research revealed that StDDP genes were distributed across different clades, and exhibited various expression patterns in response to heat stress and salt stress. Real-time qPCR results indicated that StDDPs played significant roles in potato growth and development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Gabriela Giannina Schaefer, Lukas Joerg Grebe, Robin Schinkel, Bernhard Lieb
Summary: The study reveals multiple gene duplications and intron gains within Caenogastropoda, indicating these as general features of Apogastropoda hemocyanins. While exon-intron structures are consistent within Tectipleura lineages, they vary significantly within Caenogastropoda and even among paralogous hemocyanin genes of the same species. This suggests that intron accumulation occurred gradually within Caenogastropoda, leading to a multitude of introns.
JOURNAL OF MOLECULAR EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Melendez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones
Summary: Studying the evolutionary history of gene families is important for understanding gene origin, evolution, and their implications for functional studies. The sirtuin gene family, involved in aging-related functions, has a complex duplicative history, but our results provide a well-resolved phylogeny and shed light on the repertoire of sirtuin genes among vertebrates. We identified a new member (SIRT3.2) that was lost in amniotes but retained in other jawed vertebrates, and its experimental analysis revealed its mitochondrial location and deacetylase activity similar to mammalian SIRT3.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Satoshi Fukuchi, Tamotsu Noguchi, Hiroto Anbo, Keiichi Homma
Summary: This study found that longer internal exons tend to encode intrinsically disordered regions (IDRs) in eukaryotes. Based on this finding, the "small bang model" was proposed, suggesting that early eukaryotic genes lacked introns and mostly encoded single structural domains (SDs). However, through exon division and elongation, IDRs were acquired and eventually led to the last common ancestor of eukaryotes. This model explains the dichotomy between prokaryotic and eukaryotic proteins and highlights the selective advantage conferred by IDRs.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Hui Liu, Hai-Meng Lyu, Kaikai Zhu, Yves Van de Peer, Zong-Ming (Max) Cheng
Summary: This study identified multiple gene families in plant genomes containing intronless or intron-poor genes, which play important roles in response to drought and salt stress, epigenetic processes, and plant development. The origin, evolution, and potential functions of these intronless and intron-poor sub-families provide insights into plant genome evolution and gene functional divergence.
Article
Biochemistry & Molecular Biology
Maoshuang Ran, Yulian Shi, Boning Li, Heng Xiang, Meilin Tao, Xianzhi Meng, Tian Li, Chunfeng Li, Jialing Bao, Guoqing Pan, Zeyang Zhou
Summary: This study characterized 19 serpins in the microsporidian Nosema bombycis and found that they play vital roles in pathogen-host interactions. The comparative genomic analysis revealed that microsporidia serpins were only found in the genus Nosema and there were gene duplications in Nosema antheranae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Negin Mirghasemi, Elena Fanelli, Salar Jamali, Mohammed Mehdi Sohani, Francesca De Luca
Summary: The study characterized and evolution of three ss-1,4-endoglucanase genes in the root-lesion nematode Pratylenchus loosi, showing they resulted from gene duplication followed by sequence and gene structure diversification. The Pl-eng-2 gene was fully determined and found to be localized in the secretory esophageal glands of all life stages, while Pl-eng-3 and Pl-eng-4 were only partially sequenced, with loss of the linker domain and carbohydrate-binding domain during evolution.
Article
Plant Sciences
Shanshan Dong, Jin Yu, Li Zhang, Bernard Goffinet, Yang Liu
Summary: Based on transcriptome data analysis of 38 liverworts, we re-evaluated the phylogeny of liverworts and provided evidence for ancient hybridizations and incomplete lineage sorting that shaped their deep evolutionary history. The study also found no evidence of whole-genome duplication events during the deep evolution of liverworts.
Article
Biochemistry & Molecular Biology
Shanshan Yao, Jiulin Chan, Yue Xu, Shimei Wu, Linlin Zhang
Summary: This study explored the immune diversity and specificity of invertebrates based on the lophotrochozoan RLRs, a major component in antiviral immune recognition. The analysis of genomes revealed that the N-terminal domains of lophotrochozoan RLRs showed the most striking diversity, evolved independently by domain grafting. Exon-intron structures were found to be prevalent in the domain grafting, resulting in the generation of non-canonical N-terminal domains. Transcriptomic studies showed that many non-canonical RLRs display immune-related expression patterns. Positive selection was observed in two RLRs, possibly a result of host defense selection pressure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Madiha Zaynab, Yasir Sharif, Zhaoshi Xu, Sajid Fiaz, Rashid Al-Yahyai, Hamad. A. Yadikar, Najla Amin T. Al Kashgry, Sameer H. Qari, Monther Sadder, Shuangfei Li
Summary: In this study, 30 DUF668 genes were identified in the soybean genome, distributed across fifteen chromosomes. Phylogenetic analysis classified these genes into three groups. Gene structure analysis showed that some of these genes lacked introns. Subcellular localization results indicated that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane.
Article
Plant Sciences
N. F. Weeden, M. Lavin, S. Abbo, C. J. Coyne, K. Mcphee
Summary: An analysis of sequence variation in a fragment of the STAYGREEN (SGR) locus in Pisum fulvum revealed 57 alleles, most of which differed in indel structure. The SGR sequence was found to be a more reliable indicator of accession identity than morphological characteristics. The study also showed that P. fulvum accessions can be divided into two allele groups.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Daffodil M. Canson, Aimee L. Davidson, Miguel de la Hoya, Michael T. Parsons, Dylan M. Glubb, Olga Kondrashova, Amanda B. Spurdle
Summary: SpliceAI is a widely used splicing prediction tool and we developed the SpliceAI-10k calculator (SAI-10k-calc) to extend its use for predicting various types of splicing aberrations with high accuracy. The SAI-10k-calc has 95% sensitivity and 96% specificity for predicting variants that impact splicing, and it performs well in predicting pseudoexon and partial intron retention. The automated amino acid sequence prediction feature allows for efficient identification of variants that may lead to mRNA nonsense-mediated decay or truncated proteins during translation.
Article
Biochemistry & Molecular Biology
Stepanka Nedvedova, Davide De Stefano, Olivier Walker, Maggy Hologne, Adriana Erica Miele
Summary: Genome sequencing of the human parasite Schistosoma mansoni revealed a gene superfamily called micro-exon gene (meg) that encodes secreted MEG proteins. Through bioinformatics tools and phylogenetic analysis, this study identified conserved patterns in the sequences of highly variable MEG proteins and classified them into two subfamilies. It also proposed revisiting the common names and annotations of MEGs to avoid duplication and misunderstandings.
Article
Chemistry, Organic
Ratnesh Kumar, Abhishek Kumar, Ambrish Kumar Srivastava, Goutam Brahmachari, Neeraj Misra
Summary: This study presents a comparative experimental and theoretical investigation on a synthetic analog of a biologically relevant compound. Spectral and structural properties were analyzed, and a simple and efficient synthesis method was proposed. The results obtained from both experimental and computational approaches confirm the importance of this compound in the field of drug discovery.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Chemistry, Organic
Krishna Kant Yadav, Abhishek Kumar, Amarendra Kumar, Goutam Brahmachari, Neeraj Misra
Summary: Theoretical calculations and experimental measurements were conducted on three phosphonate compounds. The results showed good agreement between calculated and experimental vibrational frequencies, and molecular docking studies revealed their potential as effective drugs.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Biochemistry & Molecular Biology
Beiping Miao, Diamanto Skopelitou, Aayushi Srivastava, Sara Giangiobbe, Dagmara Dymerska, Nagarajan Paramasivam, Abhishek Kumar, Magdalena Kuswik, Wojciech Kluzniak, Katarzyna Paszkowska-Szczur, Matthias Schlesner, Jan Lubinski, Kari Hemminki, Asta Foersti, Obul Reddy Bandapalli
Summary: In this study, a novel germline variant in the PTK7 gene associated with genetic predisposition to colorectal cancer was identified through whole-exome sequencing. Further investigations revealed the oncogenic function of PTK7, including increased cell proliferation, migration, and invasion, inhibition of apoptosis pathways, and activation of AKT signaling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
P. Travis Courtney, Rishi Deka, Nikhil Kotha, Daniel R. Cherry, Mia A. Salans, Tyler J. Nelson, Abhishek Kumar, Elaine Luterstein, Anthony T. Yip, Vinit Nalawade, J. Kellogg Parsons, A. Karim Kader, Tyler F. Stewart, Brent S. Rose
Summary: Active surveillance may not be safe for patients with intermediate-risk prostate cancer, as it may increase the risk of metastasis and prostate cancer-specific mortality. However, carefully selected patients with favorable intermediate-risk prostate cancer may be suitable for active surveillance.
JOURNAL OF THE NATIONAL COMPREHENSIVE CANCER NETWORK
(2022)
Article
Peripheral Vascular Disease
Srinidhi Shanmugasundaram, Aleksander Kubiak, Aleena Dar, Abhishek Shrinet, Nirav Chauhan, Humza Haque, Abhishek Kumar, Pratik A. Shukla
Summary: This study evaluated the incidence of large bore hemodialysis catheter malfunction in COVID-19 patients. The results showed a high rate of dysfunction in temporary dialysis catheters in patients with COVID-19 infection. Catheters placed via a femoral vein access had a higher risk of dysfunction and required earlier replacement.
JOURNAL OF VASCULAR ACCESS
(2023)
Article
Otorhinolaryngology
Rohith S. Voora, Bharat A. Panuganti, Mitchell Flagg, Tyler Nelson, Nikhil V. Kotha, Edmund M. Qiao, Alexander S. Qian, Abhishek Kumar, Tyler F. Stewart, Brent Rose, Joseph Califano, Philip A. Weissbrod, Loren K. Mell, Ryan K. Orosco
Summary: Recurrence patterns in T4a laryngeal squamous cell cancer (LSCC) differ between patients treated with chemoradiotherapy (CRT) and those who undergo surgery. Surgery is associated with lower rates of locoregional and distant recurrence, improved overall and larynx cancer mortality outcomes.
OTOLARYNGOLOGY-HEAD AND NECK SURGERY
(2022)
Article
Oncology
Lizhen Zhu, Beiping Miao, Dagmara Dymerska, Magdalena Kuswik, Elena Bueno-Martinez, Lara Sanoguera-Miralles, Eladio A. Velasco, Nagarajan Paramasivam, Matthias Schlesner, Abhishek Kumar, Ying Yuan, Jan Lubinski, Obul Reddy Bandapalli, Kari Hemminki, Asta Foersti
Summary: Whole-genome sequencing and functional characterization studies on colorectal cancer families identified CYBA and TRPM4 as candidate predisposition genes that mechanistically involve intestinal barrier integrity through reactive oxygen species and mucus biology, converging in chronic bowel inflammation, a known risk factor for colorectal cancer.
Article
Oncology
Nikhil Kotha, Abhishek Kumar, Tyler J. Nelson, Edmund M. Qiao, Alex S. Qian, Rohith S. Voora, Rana R. McKay, Tyler F. Stewart, Brent S. Rose
Summary: The study investigated factors associated with treatment discontinuation in MIBC patients undergoing CRT, finding that factors such as creatinine clearance, incomplete TURBT, and nonpreferred chemotherapy were associated with discontinuation. Patients who discontinued radiation had higher mortality rates compared to those who completed radiation.
ADVANCES IN RADIATION ONCOLOGY
(2022)
Article
Oncology
Tyler J. Nelson, Caroline A. Thompson, Jingjing Zou, Abhishek Kumar, Prangrawee Sangchan, Casey W. Williamson, Lucas K. Vitzthum, Andrew B. Sharabi, James D. Murphy, Carole A. Fakhry, Loren K. Mell
Summary: The study aimed to validate the nomograms developed by NRG Oncology in oropharyngeal squamous cell carcinoma (OPSCC) patients. The results showed that these nomograms were effective in predicting progression-free survival (PFS) and overall survival (OS), supporting their broader applicability in OPSCC patients undergoing definitive radiotherapy.
Article
Dentistry, Oral Surgery & Medicine
Khaled Al-Manei, Nabeel Almotairy, Kholod Khalil Al-Manei, Anastasios Grigoriadis, Abhishek Kumar
Summary: This study investigated the force regulation of incisor teeth treated with AMS during an unpredictable force control task. The results showed that AMS-treated incisors had lower peak force and peak force rate during the initial time-segment compared to the contralateral control teeth. However, there were no significant differences in holding force and coefficient of variability between the AMS-treated teeth and their controls during the later time-segment.
JOURNAL OF ORAL REHABILITATION
(2022)
Article
Oncology
Nikhil V. Kotha, Abhishek Kumar, Tyler J. Nelson, Edmund M. Qiao, Alex S. Qian, Rohith S. Voora, Rana R. Mckay, Brent S. Rose, Tyler F. Stewart
Summary: This study suggests that a short-term delay in definitive therapy may not affect long-term outcomes for patients with MIBC undergoing CRT. It provides information to aid patients and clinicians navigate the unique challenges of MIBC care in both pandemic and non-pandemic times.
UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS
(2022)
Retraction
Multidisciplinary Sciences
Sushmita Das, Ashish Kumar, Abhishek Mandal, Kumar Abhishek, Sudha Verma, Ajay Kumar, Pradeep Das
SCIENTIFIC REPORTS
(2022)
Article
Dentistry, Oral Surgery & Medicine
George Homsi, Anna Karlsson, Nabeel Almotairy, Mats Trulsson, Abhishek Kumar, Anastasios Grigoriadis
Summary: This study investigated the association between subjective and objective measures of masticatory function in patients with bimaxillary implant-supported prostheses. The results showed that although patients with implant prostheses performed poorly in objective tests, there was a lack of agreement between subjective and objective measures of mastication.
JOURNAL OF ORAL REHABILITATION
(2023)
Article
Engineering, Multidisciplinary
Somnath Kumar, K. K. Keshari, A. Deva, R. K. Singh, S. Roy, V. Kumar, S. Toppo, K. Abhishek, N. Pradhan
Summary: Clogging of sub entry nozzle is a recurring issue in continuous casting of low carbon aluminum deoxidized steel. A new modernized SMS shop faced a major problem of nozzle clogging, resulting in abrupt abortion of sequence casting. The high incidences of SEN clogging led to a loss of productivity. The study found that dendritic clusters of alumina originating from deoxidation and reoxidation of aluminum during secondary refining were the likely cause of SEN clogging. Optimization of the Ca treatment process was also required for successful continuous casting.
JOURNAL OF FAILURE ANALYSIS AND PREVENTION
(2023)
