MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays by Alan F. Rubin, Jeremy Stone, Aisha Haley Bianchi, Benjamin J. Capodanno, Estelle Y. Da, Mafalda Dias, Daniel Esposito, Jonathan Frazer, Yunfan Fu, Sally B. Grindstaff, Matthew R. Harrington, Iris Li, Abbye E. McEwen, Joseph K. Min, Nick Moore, Olivia G. Moscatelli, Jesslyn Ong, Polina V. Polunina, Joshua E. Rollins, Nathan J. Rollins, Ashley E. Snyder, Amy Tam, Matthew J. Wakefield, Shenyi Sunny Ye, Lea M. Starita, Vanessa L. Bryant, Debora S. Marks, Douglas M. Fowler

“…Abstract Multiplexed assays of variant effect (MAVEs) are a critical tool for researchers and clinicians to understand genetic variants. Here we describe the 2024 update to MaveDB ( https://www.mavedb.org/ ) with four key improvements to the MAVE community’s database of record: more available data including over 7 million variant effect measurements, an improved data model supporting assays such as saturation genome editing, new built-in exploration and visualization tools, and powerful APIs for data federation and streamlined submission and access. …”
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Dataset of speech produced with delayed auditory feedbackOpen Science FrameworkOpen Science Framework by Matthias Heyne, Monique C. Tardif, Alexander Ocampo, Ashley P. Petitjean, Emily J. Hacker, Caroline N. Fox, Megan A. Liu, Madeline Fontana, Vincent Pennetti, Jason W. Bohland

“…To our knowledge, there are currently no publicly available research datasets containing recordings of speech produced with DAF. Here we describe a large dataset of speech produced with DAF using modern experimental methods with systematic controls and varied speaking materials, including phonotactically legal, nonword syllable sequences and American English sentences. …”
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Nicotinamide mononucleotide restores impaired metabolism, endothelial cell proliferation and angiogenesis in old sedentary male mice by Kevin Kiesworo, Thomas Agius, Michael R. Macarthur, Martine Lambelet, Arnaud Lyon, Jing Zhang, Guillermo Turiel, Zheng Fan, Sènan d’Almeida, Korkut Uygun, Heidi Yeh, Sébastien Déglise, Katrien de Bock, Sarah J. Mitchell, Alejandro Ocampo, Florent Allagnat, Alban Longchamp

“…Summary: Aging is accompanied by a decline in neovascularization potential and increased susceptibility to ischemic injury. Here, we confirm the age-related impaired neovascularization following ischemic leg injury and impaired angiogenesis. …”
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Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background by Evangelista, Charlotte, Kamenova, Stefaniya, Diaz Pauli, Beatriz, Sandkjenn, Joakim, Vøllestad, Leif Asbjørn, Edeline, Eric, Trosvik, Pål, de Muinck, Eric Jacques

“…Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. …”
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Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling by David Kim, Chad M. Vanderbilt, Soo-Ryum Yang, Subhiksha Nandakumar, Khedoudja Nafa, Rusmir Feratovic, Natasha Rekhtman, Ivelise Rijo, Jacklyn Casanova, Anita Yun, A. Rose Brannon, Michael F. Berger, Marc Ladanyi, Oscar Lin, Maria E. Arcila

“…However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. …”
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Abnormal cytoskeletal remodeling but normal neuronal excitability in a mouse model of the recurrent developmental and epileptic encephalopathy-susceptibility KCNB1-p.R312H variant by Alessandro Bortolami, Elena Forzisi Kathera-Ibarra, Anastasia Balatsky, Mansi Dubey, Rusheel Amin, Srinidi Venkateswaran, Stefania Dutto, Ishan Seth, Adam Ashor, Angel Nwandiko, Ping-Yue Pan, David P. Crockett, Federico Sesti

“…Abstract Integrin_K+ Channel_Complexes (IKCs), are implicated in neurodevelopment and cause developmental and epileptic encephalopathy (DEE) through mechanisms that were poorly understood. Here, we investigate the function of neocortical IKCs formed by voltage-gated potassium (Kv) channels Kcnb1 and α5β5 integrin dimers in wild-type (WT) and homozygous knock-in (KI) Kcnb1 R312H(+/+) mouse model of DEE. …”
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Development of a cell-penetrating peptide-based nanocomplex for long-term delivery of intact mitochondrial DNA into epithelial cells by Kyrie Wilson, Charles Holjencin, Hwaran Lee, Balasubramaniam Annamalai, Masaaki Ishii, Jeremy L. Gilbert, Andrew Jakymiw, Bärbel Rohrer

“…Gene therapy approaches for mitochondrial DNA (mtDNA)-associated damage/diseases have thus far been limited, and despite advancements in single gene therapy for mtDNA mutations and progress in mitochondrial transplantation, no method exists for restoring the entire mtDNA molecule in a clinically translatable manner. Here, we present for the first time a strategy to deliver an exogenous, fully intact, and healthy mtDNA template into cells to correct endogenous mtDNA mutations and deletions, with the potential to be developed into an efficient pan-therapy for inherited and/or acquired mtDNA disorders. …”
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Dutch Validation of the Self-Evaluation of Negative Symptoms Scale (SNS) by Tim van Brouwershaven, Anika Poppe, Gerdina Hendrika Maria Pijnenborg, André Aleman, Nynke Boonstra, Shiral Gangadin, Sonia Dollfus, Wim Veling, Stynke Castelein, Jan Alexander de Vos, Edith Liemburg, PHAMOUS-researchers, Lisette van der Meer

“…Self-rating scales, like the Self-Evaluation of Negative Symptoms (SNS), could complement observer ratings by adding information from the patient’s perspective. Here, we aim to evaluate the psychometric properties of the Dutch translation of the SNS and the relationship between the SNS and functional outcomes. …”
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Transient Decrease in Circulatory Testosterone and Homocysteine Precedes the Development of Metabolic Syndrome Features in Fructose-Fed Sprague Dawley Rats by Anil Sakamuri, Sujatha Pitla, Uday Kumar Putcha, Sugeedha Jayapal, Sailaja Pothana, Sai Santosh Vadakattu, Nagabhushan Reddy Konapalli, Siva Sankara Vara Prasad Sakamuri, Ahamed Ibrahim

“…Increased fructose consumption is linked to the development of metabolic syndrome (MS). Here we investigated the time course of development of MS features in high-fructose-fed Sprague Dawley rats along with circulatory testosterone and homocysteine levels. …”
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Nitrous Oxide Emissions from Smallholders’ Cropping Systems in Sub-Saharan Africa by Shaankua E. Lemarpe, Collins M. Musafiri, Joseph M. Macharia, Milka N. Kiboi, Onesmus K. Ng’etich, Chris A. Shisanya, Jeremiah Okeyo, Elizabeth A. Okwuosa, Felix K. Ngetich

“…We reviewed the state of N2O emissions from selected cropping systems, drivers that significantly influence N2O emissions, and probable soil N2O emissions mitigation options from 30 studies in SSA cropping systems have been elucidated here. The review outcome indicates that coffee, tea, maize, and vegetables emit N2O ranging from 1 to 1.9, 0.4 to 3.9, 0.1 to 4.26, and 48 to 113.4 kg N2O-N ha-1 yr−1, respectively. …”
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Heterochromatic gene silencing controls CD4+ T cell susceptibility to regulatory T cell-mediated suppression in a murine allograft model by Julie Noguerol, Karl Laviolette, Margot Zahm, Adeline Chaubet, Ambrine Sahal, Claire Détraves, Romain Torres, Clothilde Demont, Véronique Adoue, Carine Joffre, Florence Cammas, Joost PM van Meerwijk, Olivier P. Joffre

“…However, how Tconv translate Treg-dependent suppressive signals at the chromatin level remains largely unknown. Here we show, using a murine bone marrow allograft model in which graft rejection is coordinated by CD4+ T cells and can be inhibited by Treg, that Treg-mediated T cell suppression involves Heterochromatin Protein 1 α (HP1α)-dependent gene silencing. …”
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C5a-C5aR1 axis mediates lung inflammation and fibrosis induced by single-walled carbon nanotubes via promoting neutrophils recruitment by Jiaojiao Zhu, Xiang Zhang, Lanlan Li, Hongxu Yang, Hang Liu, Danyang Wu, Zikai Liu, Bin Liu, Tong Shen

“…However, the molecular mechanisms of single-walled CNT (SWCNT)-provoked lung injury remain to be elucidated. Here, we established a mice model of SWCNT-induced lung injury by intratracheal instillation and found that C5a-C5a receptor-1 (C5aR1) signaling was significantly activated along with abundant neutrophils recruitment in lungs at early phase post SWCNT administration, which were positively correlated with early lung inflammation and late pulmonary fibrosis. …”
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Identification of immune-associated genes with altered expression in the spleen of mice enriched with probiotic species using RNA-seq profiling by Anh Duc Truong, Ha Thi Thanh Tran, Nhu Thi Chu, Lanh Phan, Hoai Thi Phan, Thu Huong Dang, Hoang Vu Dang, La Anh Nguyen

“…Objective Probiotics are living microorganisms that can provide health benefits when consumed. Here, we investigated the effects of probiotics on gene expression in the spleen of mice using RNA-sequencing analysis between negative control and probiotic groups (including 4 Lactobacillus strains: Lactobacillus fermentum, L. casei, L. plantarum, and L. brevis). …”
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Novel introductions of human-origin H3N2 influenza viruses in swine, Chile by Belen Monserrat Agüero, Naomi Ariyama, Felipe Berrios, Nikita Enciso, Barbara Quezada, Rafael A. Medina, Rafael A. Medina, Victor Neira, Victor Neira

“…In Chile, H1N2 and H3N2 subtypes were introduced in the swine population before the H1N1 2009 pandemic, and the H1N1 was introduced from the H1N1pdm09 by successive reverse zoonotic events. Here, we report two novel introductions of IAV H3N2 human-origin in Chilean swine during 2023. …”
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Protective mechanism of quercetin compounds against acrylamide-induced hepatotoxicity by Linzi Li, Xueying Lei, Lin Chen, Ya Ma, Jun Luo, Xuebo Liu, Xinglian Xu, Guanghong Zhou, Xianchao Feng

“…However, whether quercetin compounds can attenuate AA-induced liver injury and the specific mechanism are not clear. Here, we studied the mechanism and structure-activity relationship of quercetin compounds in reducing AA-induced hepatotoxicity in vivo and in vitro. …”
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Overexpressing the ClpC AAA+ unfoldase accelerates developmental cycle progression in Chlamydia trachomatis by Aaron A. Jensen, Saba Firdous, Lei Lei, Derek J. Fisher, Scot P. Ouellette

“…We previously reported that the Caseinolytic protease (Clp) system is essential for chlamydial growth. Here, we reveal a surprising function for ClpC, an unfoldase, in driving production of infectious chlamydiae during the chlamydial developmental cycle.…”
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Generation of INS-jGCaMP7f knock-in Ca2+ reporter human embryonic stem cell line, GZLe001-C, using CRISPR/Cas9-based gene targeting by Xin Liu, Feng Zhang, Deqi Chen, Jiaxiang Yin, Zirong Bi, Lihua Chen, Jiawei Yan, Qifei Dong, Wei Peng, Tao Xu, Yanying Guo, Haopeng Lin, Huisheng Liu

“…As a member of the single-fluorophore genetically encoded calcium indicators (GECIs), jGCaMP7f is widely applied to investigate intracellular Ca2+ concentrations. Here, we established an INS-jGCaMP7f knock-in H1 human embryonic stem cell (hESC) line by integrating jGCaMP7f gene into insulin locus via CRISPR/Cas9 system. …”
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Radar internal reflection horizons from multisystem data reflect ice dynamic and surface accumulation history along the Princess Ragnhild Coast, Dronning Maud Land, East Antarctica by Inka Koch, Reinhard Drews, Steven Franke, Daniela Jansen, Falk Marius Oraschewski, Leah Sophie Muhle, Vjeran Višnjević, Kenichi Matsuoka, Frank Pattyn, Olaf Eisen

“…Therefore, an ice dynamic and accumulation history are imprinted in the internal ice stratigraphy, which can be imaged by radar in the form of internal reflection horizons (IRHs). Here, IRHs were derived from radar data combined across radar platforms (airborne and ground-based) in coastal eastern Dronning Maud Land (East Antarctica), comprising three ice rises and adjacent two ice shelves. …”
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Determinants of survival of the bovine blastocyst to cryopreservation stress: treatment with colony stimulating factor 2 during the morula-to-blastocyst transition and embryo sex by Froylan Sosa, Jeremy Block, Yao Xiao, Peter J. Hansen

“…Earlier research indicates that CSF2 can regulate genes involved in cellular stress responses and block apoptosis. Here, we tested whether addition of 10 ng/mL CSF2 at day 5 of development would increase the survival of blastocysts harvested at day 7 and subjected to vitrification. …”
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Increased DNA Copy Number Variation Mosaicism in Elderly Human Brain by Darine Villela, Claudia K. Suemoto, Renata Leite, Carlos Augusto Pasqualucci, Lea T. Grinberg, Peter Pearson, Carla Rosenberg

“…The sizes of the variants described here were in the 150–760 kb range, and importantly, nearly all of them were present in the Database of Genomic Variants (common variants). …”
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