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Modeling antibody drug conjugate potential using a granzyme B antibody fusion protein BMC Biol. (IF 5.4) Pub Date : 2024-03-14 Trevor S. Anderson, Amanda L. McCormick, Savanna L. Smith, Devin B. Lowe
Antibody drug conjugates (ADCs) constitute a promising class of targeted anti-tumor therapeutics that harness the selectivity of monoclonal antibodies with the potency of cytotoxic drugs. ADC development is best suited to initially screening antibody candidates for desired properties that potentiate target cell cytotoxicity. However, validating and producing an optimally designed ADC requires expertise
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DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits BMC Biol. (IF 5.4) Pub Date : 2024-03-14 Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, Pier-Luc Dudemaine, David Gagné, Jean-Philippe Roy, Marc-André Sirard, Eveline M. Ibeagha-Awemu
DNA methylation has been documented to play vital roles in diseases and biological processes. In bovine, little is known about the regulatory roles of DNA methylation alterations on production and health traits, including mastitis. Here, we employed whole-genome DNA methylation sequencing to profile the DNA methylation patterns of milk somatic cells from sixteen cows with naturally occurring Staphylococcus
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Cytoplasmic genome contributions to domestication and improvement of modern maize BMC Biol. (IF 5.4) Pub Date : 2024-03-13 Shuai Cao, Huanhuan Zhang, Yang Liu, Yi Sun, Z. Jeffrey Chen
Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been
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The pharyngeal taste organ of a blood-feeding insect functions in food recognition BMC Biol. (IF 5.4) Pub Date : 2024-03-13 Isabel Ortega-Insaurralde, José Manuel Latorre-Estivalis, Andre Luis Costa-da-Silva, Agustina Cano, Teresita C. Insausti, Héctor Salas Morales, Gina Pontes, Martín Berón de Astrada, Sheila Ons, Matthew DeGennaro, Romina B. Barrozo
Obligate blood-feeding insects obtain the nutrients and water necessary to ensure survival from the vertebrate blood. The internal taste sensilla, situated in the pharynx, evaluate the suitability of the ingested food. Here, through multiple approaches, we characterized the pharyngeal organ (PO) of the hematophagous kissing bug Rhodnius prolixus to determine its role in food assessment. The PO, located
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The fitness trade-off between growth and stress resistance determines the phenotypic landscape BMC Biol. (IF 5.4) Pub Date : 2024-03-13 Dongsan Kim, Chae Young Hwang, Kwang-Hyun Cho
A central challenge in biology is to discover a principle that determines individual phenotypic differences within a species. The growth rate is particularly important for a unicellular organism, and the growth rate under a certain condition is negatively associated with that of another condition, termed fitness trade-off. Therefore, there should exist a common molecular mechanism that regulates multiple
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An odorant receptor mediates the avoidance of Plutella xylostella against parasitoid BMC Biol. (IF 5.4) Pub Date : 2024-03-13 Yipeng Liu, Sai Zhang, Song Cao, Emmanuelle Jacquin-Joly, Qiong Zhou, Yang Liu, Guirong Wang
Ecosystems are brimming with myriad compounds, including some at very low concentrations that are indispensable for insect survival and reproduction. Screening strategies for identifying active compounds are typically based on bioassay-guided approaches. Here, we selected two candidate odorant receptors from a major pest of cruciferous plants—the diamondback moth Plutella xylostella—as targets to screen
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Mitochondrial perturbation in immune cells enhances cell-mediated innate immunity in Drosophila BMC Biol. (IF 5.4) Pub Date : 2024-03-13 Laura Vesala, Yuliya Basikhina, Tea Tuomela, Anssi Nurminen, Emilia Siukola, Pedro F. Vale, Tiina S. Salminen
Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, production of reactive oxygen species, stress responses, inflammation and immunity. However, the role of mitochondrial metabolism in immune cells and tissues shaping the innate immune responses are not yet fully understood. We investigated the effects of tissue-specific mitochondrial perturbation
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Reconstructing the ancestral gene pool to uncover the origins and genetic links of Hmong–Mien speakers BMC Biol. (IF 5.4) Pub Date : 2024-03-13 Yang Gao, Xiaoxi Zhang, Hao Chen, Yan Lu, Sen Ma, Yajun Yang, Menghan Zhang, Shuhua Xu
Hmong–Mien (HM) speakers are linguistically related and live primarily in China, but little is known about their ancestral origins or the evolutionary mechanism shaping their genomic diversity. In particular, the lack of whole-genome sequencing data on the Yao population has prevented a full investigation of the origins and evolutionary history of HM speakers. As such, their origins are debatable.
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Differentiation is accompanied by a progressive loss in transcriptional memory BMC Biol. (IF 5.4) Pub Date : 2024-03-12 Camille Fourneaux, Laëtitia Racine, Catherine Koering, Sébastien Dussurgey, Elodie Vallin, Alice Moussy, Romuald Parmentier, Fanny Brunard, Daniel Stockholm, Laurent Modolo, Franck Picard, Olivier Gandrillon, Andras Paldi, Sandrine Gonin-Giraud
Cell differentiation requires the integration of two opposite processes, a stabilizing cellular memory, especially at the transcriptional scale, and a burst of gene expression variability which follows the differentiation induction. Therefore, the actual capacity of a cell to undergo phenotypic change during a differentiation process relies upon a modification in this balance which favors change-inducing
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Author Correction: Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia BMC Biol. (IF 5.4) Pub Date : 2024-03-12 Zhikang Hu, Zhengqi Fan, Sijia Li, Minyan Wang, Mingchuan Huang, Xianjin Ma, Weixin Liu, Yupeng Wang, Yifan Yu, Yaxuan Li, Yingkun Sun, Xinlei Li, Jiyuan Li, Hengfu Yin
Author Correction: BMC Biology 22 50, (2024) https://doi.org/10.1186/s12915-024-01851-y In the original article [1], the respective images for Figs. 2 and 3 are erroneously transposed and should be treated as having been swapped over. Hu Z, et al. Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia. BMC Biol. 2024;22:50
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Introgressions lead to reference bias in wheat RNA-seq analysis BMC Biol. (IF 5.4) Pub Date : 2024-03-07 Benedict Coombes, Thomas Lux, Eduard Akhunov, Anthony Hall
RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative
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Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations BMC Biol. (IF 5.4) Pub Date : 2024-03-06 Qiuxia Sun, Mengge Wang, Tao Lu, Shuhan Duan, Yan Liu, Jing Chen, Zhiyong Wang, Yuntao Sun, Xiangping Li, Shaomei Wang, Liuyi Lu, Liping Hu, Libing Yun, Junbao Yang, Jiangwei Yan, Shengjie Nie, Yanfeng Zhu, Gang Chen, Chuan-Chao Wang, Chao Liu, Guanglin He, Renkuan Tang
The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han
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A CTL − Lys immune function maintains insect metamorphosis by preventing gut bacterial dysbiosis and limiting opportunistic infections BMC Biol. (IF 5.4) Pub Date : 2024-03-06 Pei Xiong, Wen-Wen Wang, Xu-Sheng Liu, Yu-Feng Wang, Jia-Lin Wang
Gut bacteria are beneficial to the host, many of which must be passed on to host offspring. During metamorphosis, the midgut of holometabolous insects undergoes histolysis and remodeling, and thus risks losing gut bacteria. Strategies employed by holometabolous insects to minimize this risk are obscure. How gut bacteria affect host insects after entering the hemocoel and causing opportunistic infections
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Integrative systems biology of wheat susceptibility to Fusarium graminearum uncovers a conserved gene regulatory network and identifies master regulators targeted by fungal core effectors BMC Biol. (IF 5.4) Pub Date : 2024-03-05 Florian Rocher, Samir Dou, Géraldine Philippe, Marie-Laure Martin, Philippe Label, Thierry Langin, Ludovic Bonhomme
Plant diseases are driven by an intricate set of defense mechanisms counterbalanced by the expression of host susceptibility factors promoted through the action of pathogen effectors. In spite of their central role in the establishment of the pathology, the primary components of plant susceptibility are still poorly understood and challenging to trace especially in plant-fungal interactions such as
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Origin and diversity of Capsella bursa-pastoris from the genomic point of view BMC Biol. (IF 5.4) Pub Date : 2024-03-05 Aleksey A. Penin, Artem S. Kasianov, Anna V. Klepikova, Denis O. Omelchenko, Maksim S. Makarenko, Maria D. Logacheva
Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of
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The cytoskeleton adaptor protein Sorbs1 controls the development of lymphatic and venous vessels in zebrafish BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Alexandra Veloso, Anouk Bleuart, Louise Conrard, Tanguy Orban, Jonathan Bruyr, Pauline Cabochette, Raoul F. V. Germano, Giel Schevenels, Alice Bernard, Egor Zindy, Sofie Demeyer, Benoit Vanhollebeke, Franck Dequiedt, Maud Martin
Lymphangiogenesis, the formation of lymphatic vessels, is tightly linked to the development of the venous vasculature, both at the cellular and molecular levels. Here, we identify a novel role for Sorbs1, the founding member of the SoHo family of cytoskeleton adaptor proteins, in vascular and lymphatic development in the zebrafish. We show that Sorbs1 is required for secondary sprouting and emergence
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Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Zhikang Hu, Zhengqi Fan, Sijia Li, Minyan Wang, Mingchuan Huang, Xianjin Ma, Weixin Liu, Yupeng Wang, Yifan Yu, Yaxuan Li, Yingkun Sun, Xinlei Li, Jiyuan Li, Hengfu Yin
The formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well
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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae) BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Zhiyong Jiang, Wenqing Zang, Per G. P. Ericson, Gang Song, Shaoyuan Wu, Shaohong Feng, Sergei V. Drovetski, Gang Liu, Dezhi Zhang, Takema Saitoh, Per Alström, Scott V. Edwards, Fumin Lei, Yanhua Qu
Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene–Pleistocene boundary. Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage
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Primary cilia promote the differentiation of human neurons through the WNT signaling pathway BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Andrea Coschiera, Masahito Yoshihara, Gilbert Lauter, Sini Ezer, Mariangela Pucci, Haonan Li, Alan Kavšek, Christian G. Riedel, Juha Kere, Peter Swoboda
Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell’s immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor
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Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia) BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Vanessa C. Sales-Oliveira, Rodrigo Zeni dos Santos, Caio Augusto Gomes Goes, Rodrigo Milan Calegari, Manuel A. Garrido-Ramos, Marie Altmanová, Tariq Ezaz, Thomas Liehr, Fabio Porto-Foresti, Ricardo Utsunomia, Marcelo B. Cioffi
Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full
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Membranes are functionalized by a proteolipid code BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Troy A. Kervin, Michael Overduin
Membranes are protein and lipid structures that surround cells and other biological compartments. We present a conceptual model wherein all membranes are organized into structural and functional zones. The assembly of zones such as receptor clusters, protein-coated pits, lamellipodia, cell junctions, and membrane fusion sites is explained to occur through a protein-lipid code. This challenges the theory
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Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Yunpeng Cao, Wanzhen Mo, Yanli Li, Yao Xiong, Han Wang, Yingjie Zhang, Mengfei Lin, Lin Zhang, Xiaoxu Li
Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii and its resistant counterpart, Vernicia montana, offer significant resources for the functional characterization and discovery of novel NBS-LRR genes in tung
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CircRNA identification and feature interpretability analysis BMC Biol. (IF 5.4) Pub Date : 2024-02-27 Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Ren Qi, Lei Xu
Circular RNAs (circRNAs) can regulate microRNA activity and are related to various diseases, such as cancer. Functional research on circRNAs is the focus of scientific research. Accurate identification of circRNAs is important for gaining insight into their functions. Although several circRNA prediction models have been developed, their prediction accuracy is still unsatisfactory. Therefore, providing
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Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine BMC Biol. (IF 5.4) Pub Date : 2024-02-20 Célia Dupain, Tom Gutman, Elodie Girard, Choumouss Kamoun, Grégoire Marret, Zahra Castel-Ajgal, Marie-Paule Sablin, Cindy Neuzillet, Edith Borcoman, Ségolène Hescot, Céline Callens, Olfa Trabelsi-Grati, Samia Melaabi, Roseline Vibert, Samantha Antonio, Coralie Franck, Michèle Galut, Isabelle Guillou, Maral Halladjian, Yves Allory, Joanna Cyrta, Julien Romejon, Eleonore Frouin, Dominique Stoppa-Lyonnet
High tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an anti-PD-1, received FDA-approval for the treatment of unresectable/metastatic tumors with high TMB as determined by the FoundationOne®CDx test. It remains to be determined how TMB can also be calculated using other tests. FFPE/frozen tumor samples from various origins were
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Population genomics of Agrotis segetum provide insights into the local adaptive evolution of agricultural pests BMC Biol. (IF 5.4) Pub Date : 2024-02-20 Ping Wang, Minghui Jin, Chao Wu, Yan Peng, Yanjin He, Hanyue Wang, Yutao Xiao
The adaptive mechanisms of agricultural pests are the key to understanding the evolution of the pests and to developing new control strategies. However, there are few studies on the genetic basis of adaptations of agricultural pests. The turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) is an important underground pest that affects a wide range of host plants and has a strong capacity to adapt
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Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes BMC Biol. (IF 5.4) Pub Date : 2024-02-19 Marcos Y. Voutsinos, Jacob A. West-Roberts, Rohan Sachdeva, John W. Moreau, Jillian F. Banfield
Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. Although there have been many studies
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Predicting thresholds for population replacement gene drives BMC Biol. (IF 5.4) Pub Date : 2024-02-19 Anna Janzen, Ratnasri Pothula, Adam Sychla, Nathan R. Feltman, Michael J. Smanski
Threshold-dependent gene drives (TDGDs) could be used to spread desirable traits through a population, and are likely to be less invasive and easier to control than threshold-independent gene drives. Engineered Genetic Incompatibility (EGI) is an extreme underdominance system previously demonstrated in Drosophila melanogaster that can function as a TDGD when EGI agents of both sexes are released into
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Genome-wide comparative methylation analysis reveals the fate of germ stem cells after surrogate production in teleost BMC Biol. (IF 5.4) Pub Date : 2024-02-16 Rigolin Nayak, Roman Franěk, Audrey Laurent, Martin Pšenička
Surrogate production by germline stem cell transplantation is a powerful method to produce donor-derived gametes via a host, a practice known as surrogacy. The gametes produced by surrogates are often analysed on the basis of their morphology and species-specific genotyping, which enables conclusion to be drawn about the donor’s characteristics. However, in-depth information, such as data on epigenetic
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A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora BMC Biol. (IF 5.4) Pub Date : 2024-02-16 Noah P. Winters, Eric K. Wafula, Benjamin J. Knollenberg, Tuomas Hämälä, Prakash R. Timilsena, Melanie Perryman, Dapeng Zhang, Lena L. Sheaffer, Craig A. Praul, Paula E. Ralph, Sarah Prewitt, Mariela E. Leandro-Muñoz, Diego A. Delgadillo-Duran, Naomi S. Altman, Peter Tiffin, Siela N. Maximova, Claude W. dePamphilis, James H. Marden, Mark J. Guiltinan
Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding
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ADARs regulate cuticle collagen expression and promote survival to pathogen infection BMC Biol. (IF 5.4) Pub Date : 2024-02-16 Alfa Dhakal, Chinnu Salim, Mary Skelly, Yarden Amichan, Ayelet T. Lamm, Heather A. Hundley
In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant
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A human stomach cell type transcriptome atlas BMC Biol. (IF 5.4) Pub Date : 2024-02-14 S. Öling, E. Struck, M. Noreen-Thorsen, M. Zwahlen, K. von Feilitzen, J. Odeberg, F. Pontén, C. Lindskog, M. Uhlén, P. Dusart, L. M. Butler
The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast
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Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures BMC Biol. (IF 5.4) Pub Date : 2024-02-14 Caleb C. Vogt, Matthew N. Zipple, Daniel D. Sprockett, Caitlin H. Miller, Summer X. Hardy, Matthew K. Arthur, Adam M. Greenstein, Melanie S. Colvin, Lucie M. Michel, Andrew H. Moeller, Michael J. Sheehan
Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science. Using
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Convergent genomic signatures associated with vertebrate viviparity BMC Biol. (IF 5.4) Pub Date : 2024-02-08 Rhiannon V. Eastment, Bob B. M. Wong, Matthew D. McGee
Viviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years;
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Enolase of Streptococcus suis serotype 2 promotes biomolecular condensation of ribosomal protein SA for HBMECs apoptosis BMC Biol. (IF 5.4) Pub Date : 2024-02-08 Hexiang Jiang, Yi Sun, Fengyang Li, Xibing Yu, Siyu Lei, Sulan Du, Tong Wu, Xuan Jiang, Junhui Zhu, Jun Wang, Yalu Ji, Na Li, Xin Feng, Jingmin Gu, Wenyu Han, Lei Zeng, Liancheng Lei
Ribosomal protein SA (RPSA) of human brain microvascular endothelial cells (HBMECs) can transfer from the cytosol to the cell surface and act as a receptor for some pathogens, including Streptococcus suis serotype 2 (SS2), a zoonotic pathogen causing meningitis in pigs and humans. We previously reported that SS2 virulence factor enolase (ENO) binds to RPSA on the cell surface of HBMECs and induces
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Bright lights, big synapses: fluorescent proteins let neurons shine BMC Biol. (IF 5.4) Pub Date : 2024-02-05 Brian D. Ackley
The availability of fluorescent proteins to visualize neurons and synapses has revolutionized our understanding of these key structures in brains. Here, I will discuss the new insights gleaned from the use of genetically encoded fluorescent molecules to study synapses inside living organisms.
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A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families BMC Biol. (IF 5.4) Pub Date : 2024-02-05 Jiaxiang Hu, Linfei Song, Mengfei Ning, Xinyu Niu, Mengying Han, Chuze Gao, Xingwei Feng, Han Cai, Te Li, Fangtao Li, Huifang Li, Daoqing Gong, Weitao Song, Long Liu, Juan Pu, Jinhua Liu, Jacqueline Smith, Honglei Sun, Yinhua Huang
The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck’s adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). We herein reported
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Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar BMC Biol. (IF 5.4) Pub Date : 2024-02-05 An Vanden Broeck, Tim Meese, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester, Filip Van Nieuwerburgh
Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we
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An LQT2-related mutation in the voltage-sensing domain is involved in switching the gating polarity of hERG BMC Biol. (IF 5.4) Pub Date : 2024-02-05 Zhipei Liu, Feng Wang, Hui Yuan, Fuyun Tian, Chuanyan Yang, Fei Hu, Yiyao Liu, Meiqin Tang, Meixuan Ping, Chunlan Kang, Ting Luo, Guimei Yang, Mei Hu, Zhaobing Gao, Ping Li
Cyclic Nucleotide-Binding Domain (CNBD)-family channels display distinct voltage-sensing properties despite sharing sequence and structural similarity. For example, the human Ether-a-go-go Related Gene (hERG) channel and the Hyperpolarization-activated Cyclic Nucleotide-gated (HCN) channel share high amino acid sequence similarity and identical domain structures. hERG conducts outward current and is
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The functional role of spatial anisotropies in ensemble perception BMC Biol. (IF 5.4) Pub Date : 2024-02-05 Natalia A. Tiurina, Yuri A. Markov, David Whitney, David Pascucci
The human brain can rapidly represent sets of similar stimuli by their ensemble summary statistics, like the average orientation or size. Classic models assume that ensemble statistics are computed by integrating all elements with equal weight. Challenging this view, here, we show that ensemble statistics are estimated by combining parafoveal and foveal statistics in proportion to their reliability
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Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo BMC Biol. (IF 5.4) Pub Date : 2024-02-05 E. C. Solar Venero, M. B. Galeano, A. Luqman, M. M. Ricardi, F. Serral, D. Fernandez Do Porto, S. A. Robaldi, B. A. Z. Ashari, T. H. Munif, D. E. Egoburo, S. Nemirovsky, J. Escalante, B. Nishimura, M. S. Ramirez, F. Götz, P. M. Tribelli
Staphylococcus aureus (SA) and Pseudomonas aeruginosa (PA) cause a wide variety of bacterial infections and coinfections, showing a complex interaction that involves the production of different metabolites and metabolic changes. Temperature is a key factor for bacterial survival and virulence and within the host, bacteria could be exposed to an increment in temperature during fever development. We
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Donor template delivery by recombinant adeno-associated virus for the production of knock-in mice BMC Biol. (IF 5.4) Pub Date : 2024-02-02 Graham Duddy, Katherine Courtis, Juliette Horwood, Jessica Olsen, Helen Horsler, Tina Hodgson, Sunita Varsani-Brown, Abdullah Abdullah, Laura Denti, Hollie Lane, Fabio Delaqua, Julia Janzen, Molly Strom, Ian Rosewell, Katharine Crawley, Benjamin Davies
The ability of recombinant adeno-associated virus to transduce preimplantation mouse embryos has led to the use of this delivery method for the production of genetically altered knock-in mice via CRISPR-Cas9. The potential exists for this method to simplify the production and extend the types of alleles that can be generated directly in the zygote, obviating the need for manipulations of the mouse
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Migrasomal autophagosomes relieve endoplasmic reticulum stress in glioblastoma cells BMC Biol. (IF 5.4) Pub Date : 2024-01-30 Seon Yong Lee, Sang-Hun Choi, Yoonji Kim, Hee-Sung Ahn, Young-Gyu Ko, Kyunggon Kim, Sung Wook Chi, Hyunggee Kim
Glioblastoma (GBM) is more difficult to treat than other intractable adult tumors. The main reason that GBM is so difficult to treat is that it is highly infiltrative. Migrasomes are newly discovered membrane structures observed in migrating cells. Thus, they can be generated from GBM cells that have the ability to migrate along the brain parenchyma. However, the function of migrasomes has not yet
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Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes BMC Biol. (IF 5.4) Pub Date : 2024-01-29 Alex Z. Zaccaron, Ioannis Stergiopoulos
Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes
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A computational model of circRNA-associated diseases based on a graph neural network: prediction and case studies for follow-up experimental validation BMC Biol. (IF 5.4) Pub Date : 2024-01-29 Mengting Niu, Chunyu Wang, Zhanguo Zhang, Quan Zou
Circular RNAs (circRNAs) have been confirmed to play a vital role in the occurrence and development of diseases. Exploring the relationship between circRNAs and diseases is of far-reaching significance for studying etiopathogenesis and treating diseases. To this end, based on the graph Markov neural network algorithm (GMNN) constructed in our previous work GMNN2CD, we further considered the multisource
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The midgut epithelium of mosquitoes adjusts cell proliferation and endoreplication to respond to physiological challenges BMC Biol. (IF 5.4) Pub Date : 2024-01-29 M. L. Taracena-Agarwal, B. Hixson, S. Nandakumar, A. P. Girard-Mejia, R. Y. Chen, L. Huot, N. Padilla, N. Buchon
Hematophagous mosquitoes transmit many pathogens that cause human diseases. Pathogen acquisition and transmission occur when female mosquitoes blood feed to acquire nutrients for reproduction. The midgut epithelium of mosquitoes serves as the point of entry for transmissible viruses and parasites. We studied midgut epithelial dynamics in five major mosquito vector species by quantifying PH3-positive
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Organellar electrophysiology: DNA nanodevices charging at the unmeasured BMC Biol. (IF 5.4) Pub Date : 2024-01-26 Senthil Arumugam
Organellar ion channels are regulators of key processes of cellular homeostasis as well as being involved in diseases including cancer, neurological disorders and virus infection. Individual organelle-level electrophysiology has until recently only been performed using isolated organelles, removing any direct physiological context. New DNA-based nanodevices — Clensor (chloride sensor), RatiNa (sodium
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Two decades of population genomics: will we ever agree on bacterial species? BMC Biol. (IF 5.4) Pub Date : 2024-01-26 William P. Hanage
We have never known more about the genetic variation that characterizes life on earth, which is stored in ever-growing databases, many of which are publicly accessible. Yet, an accessible database does not mean that information is readily usable or interpretable. Here, I consider how the last two decades of gene and genome sequencing have advanced our understanding specifically of pathogen variation
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Dimensions of genome dynamics in fungal pathogens: from fundamentals to applications BMC Biol. (IF 5.4) Pub Date : 2024-01-26 Daniel Croll
Fungi are ubiquitous in most ecosystems and are at the origin of serious pathogen outbreaks in humans and crops. Investigation of pathogen genomes over the past decade led to a paradigm shift of our understanding of the disease agents and provided a fertile ground for fundamental insights into drivers of genome dynamics and expression of traits.
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Differentiated genomic footprints suggest isolation and long-distance migration of Hmong-Mien populations BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Guanglin He, Peixin Wang, Jing Chen, Yan Liu, Yuntao Sun, Rong Hu, Shuhan Duan, Qiuxia Sun, Renkuan Tang, Junbao Yang, Zhiyong Wang, Libing Yun, Liping Hu, Jiangwei Yan, Shengjie Nie, Lanhai Wei, Chao Liu, Mengge Wang
The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded
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Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Eilis Hannon, Emma L. Dempster, Jonathan P. Davies, Barry Chioza, Georgina E. T. Blake, Joe Burrage, Stefania Policicchio, Alice Franklin, Emma M. Walker, Rosemary A. Bamford, Leonard C. Schalkwyk, Jonathan Mill
Due to interindividual variation in the cellular composition of the human cortex, it is essential that covariates that capture these differences are included in epigenome-wide association studies using bulk tissue. As experimentally derived cell counts are often unavailable, computational solutions have been adopted to estimate the proportion of different cell types using DNA methylation data. Here
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The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Sergei S. Ryazansky, Chujia Chen, Mark Potters, Anastasia N. Naumenko, Varvara Lukyanchikova, Reem A. Masri, Ilya I. Brusentsov, Dmitriy A. Karagodin, Andrey A. Yurchenko, Vitor L. dos Anjos, Yuki Haba, Noah H. Rose, Jinna Hoffman, Rong Guo, Theresa Menna, Melissa Kelley, Emily Ferrill, Karen E. Schultz, Yumin Qi, Atashi Sharma, Stéphane Deschamps, Victor Llaca, Chunhong Mao, Terence D. Murphy, Elina
Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. In this study, we used
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Mitochondrial genomes revisited: why do different lineages retain different genes? BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Anzhelika Butenko, Julius Lukeš, Dave Speijer, Jeremy G. Wideman
The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to
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Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Carlos F. Estevez-Castro, Murillo F. Rodrigues, Antinéa Babarit, Flávia V. Ferreira, Elisa G. de Andrade, Eric Marois, Rodrigo Cogni, Eric R. G. R. Aguiar, João T. Marques, Roenick P. Olmo
Mosquito borne viruses, such as dengue, Zika, yellow fever and Chikungunya, cause millions of infections every year. These viruses are mostly transmitted by two urban-adapted mosquito species, Aedes aegypti and Aedes albopictus. Although mechanistic understanding remains largely unknown, Aedes mosquitoes may have unique adaptations that lower the impact of viral infection. Recently, we reported the
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A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Yong Zhou, Nagarajan Kathiresan, Zhichao Yu, Luis F. Rivera, Yujian Yang, Manjula Thimma, Keerthana Manickam, Dmytro Chebotarov, Ramil Mauleon, Kapeel Chougule, Sharon Wei, Tingting Gao, Carl D. Green, Andrea Zuccolo, Weibo Xie, Doreen Ware, Jianwei Zhang, Kenneth L. McNally, Rod A. Wing
Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions
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The temporal association of CapZ with early endosomes regulates endosomal trafficking and viral entry into host cells BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Huazhang Zhu, Dawei Wang, Zuodong Ye, Lihong Huang, Wenjie Wei, Kui Ming Chan, Rongxin Zhang, Liang Zhang, Jianbo Yue
Many viruses enter host cells by hijacking endosomal trafficking. CapZ, a canonical actin capping protein, participates in endosomal trafficking, yet its precise role in endocytosis and virus infection remains elusive. Here, we showed that CapZ was transiently associated with early endosomes (EEs) and was subsequently released from the matured EEs after the fusion of two EEs, which was facilitated
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Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga BMC Biol. (IF 5.4) Pub Date : 2024-01-25 Victoria C. Moris, Lucie Bruneau, Jérémy Berthe, Anne-Catherine Heuskin, Sébastien Penninckx, Sylvia Ritter, Uli Weber, Marco Durante, Etienne G. J. Danchin, Boris Hespeels, Karine Van Doninck
The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. In this study, we analyzed
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Use of chitin:DNA ratio to assess growth form in fungal cells BMC Biol. (IF 5.4) Pub Date : 2024-01-17 Andrea Kovács-Simon, Helen N. Fones
Dimorphism, the ability to switch between a ‘yeast-like’ and a hyphal growth form, is an important feature of certain fungi, including important plant and human pathogens. The switch to hyphal growth is often associated with virulence, pathogenicity, biofilm formation and stress resistance. Thus, the ability to accurately and efficiently measure fungal growth form is key to research into these fungi
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A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes BMC Biol. (IF 5.4) Pub Date : 2024-01-17 Jessica A. Goodheart, Robin A. Rio, Neville F. Taraporevala, Rose A. Fiorenza, Seth R. Barnes, Kevin Morrill, Mark Allan C. Jacob, Carl Whitesel, Park Masterson, Grant O. Batzel, Hereroa T. Johnston, M. Desmond Ramirez, Paul S. Katz, Deirdre C. Lyons
How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel
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IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle BMC Biol. (IF 5.4) Pub Date : 2024-01-17 Jessica Marie Waite, Christopher Dardick
Plants adjust their growth orientations primarily in response to light and gravity signals. Considering that the gravity vector is fixed and the angle of light incidence is constantly changing, plants must somehow integrate these signals to establish organ orientation, commonly referred to as gravitropic set-point angle (GSA). The IGT gene family contains known regulators of GSA, including the gene
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The accumulation of modular serine protease mediated by a novel circRNA sponging miRNA increases Aedes aegypti immunity to fungus BMC Biol. (IF 5.4) Pub Date : 2024-01-17 Tengfei Lu, Yannan Ji, Mengmeng Chang, Xiaoming Zhang, Yanhong Wang, Zhen Zou
Mosquitoes transmit many infectious diseases that affect human health. The fungus Beauveria bassiana is a biological pesticide that is pathogenic to mosquitoes but harmless to the environment. We found a microRNA (miRNA) that can modulate the antifungal immunity of Aedes aegypti by inhibiting its cognate serine protease. Fungal infection can induce the expression of modular serine protease (ModSP)