journal
https://read.qxmd.com/read/38414038/membranes-are-functionalized-by-a-proteolipid-code
#21
JOURNAL ARTICLE
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 that lipids sort proteins after forming stable membrane subregions independently of proteins.
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38414014/the-cytoskeleton-adaptor-protein-sorbs1-controls-the-development-of-lymphatic-and-venous-vessels-in-zebrafish
#22
JOURNAL ARTICLE
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
BACKGROUND: 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. RESULTS: We show that Sorbs1 is required for secondary sprouting and emergence of several vascular structures specifically derived from the axial vein...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38414012/genomics-insights-into-flowering-and-floral-pattern-formation-regional-duplication-and-seasonal-pattern-of-gene-expression-in-camellia
#23
JOURNAL ARTICLE
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
BACKGROUND: 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 as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38413974/primary-cilia-promote-the-differentiation-of-human-neurons-through-the-wnt-signaling-pathway
#24
JOURNAL ARTICLE
Andrea Coschiera, Masahito Yoshihara, Gilbert Lauter, Sini Ezer, Mariangela Pucci, Haonan Li, Alan Kavšek, Christian G Riedel, Juha Kere, Peter Swoboda
BACKGROUND: 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 cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38413947/evolution-of-ancient-satellite-dnas-in-extant-alligators-and-caimans-crocodylia-reptilia
#25
JOURNAL ARTICLE
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
BACKGROUND: 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 catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38413944/gene-flow-and-an-anomaly-zone-complicate-phylogenomic-inference-in-a-rapidly-radiated-avian-family-prunellidae
#26
JOURNAL ARTICLE
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
BACKGROUND: 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. RESULTS: 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 resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38408987/circrna-identification-and-feature-interpretability-analysis
#27
JOURNAL ARTICLE
Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Ren Qi, Lei Xu
BACKGROUND: 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 a more accurate computational framework to predict circRNAs and analyse their looping characteristics is crucial for systematic annotation...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38408951/functional-characterization-of-nbs-lrr-genes-reveals-an-nbs-lrr-gene-that-mediates-resistance-against-fusarium-wilt
#28
JOURNAL ARTICLE
Yunpeng Cao, Wanzhen Mo, Yanli Li, Yao Xiong, Han Wang, Yingjie Zhang, Mengfei Lin, Lin Zhang, Xiaoxu Li
BACKGROUND: 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 tree. RESULTS: Here, we identified 239 NBS-LRR genes across two tung tree genomes: 90 in V...
February 27, 2024: BMC Biology
https://read.qxmd.com/read/38378561/tumor-mutational-burden-assessment-and-standardized-bioinformatics-approach-using-custom-ngs-panels-in-clinical-routine
#29
JOURNAL ARTICLE
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, Jennifer Wong, Christophe Le Tourneau, Ivan Bièche, Nicolas Servant, Maud Kamal, Julien Masliah-Planchon
BACKGROUND: 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. RESULTS: FFPE/frozen tumor samples from various origins were sequenced in the frame of the Institut Curie (IC) Molecular Tumor Board using an in-house next-generation sequencing (NGS) panel...
February 20, 2024: BMC Biology
https://read.qxmd.com/read/38378556/population-genomics-of-agrotis-segetum-provide-insights-into-the-local-adaptive-evolution-of-agricultural-pests
#30
JOURNAL ARTICLE
Ping Wang, Minghui Jin, Chao Wu, Yan Peng, Yanjin He, Hanyue Wang, Yutao Xiao
BACKGROUND: 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 to new environments. It is thus a good model for studying the adaptive evolution of pest species...
February 20, 2024: BMC Biology
https://read.qxmd.com/read/38369493/predicting-thresholds-for-population-replacement-gene-drives
#31
JOURNAL ARTICLE
Anna Janzen, Ratnasri Pothula, Adam Sychla, Nathan R Feltman, Michael J Smanski
BACKGROUND: 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 a wild-type population. RESULTS: Here we use a single generation fitness assay to compare the fecundity, mating preferences, and temperature-dependent relative fitness to wild-type of two distinct genotypes of EGI agents...
February 19, 2024: BMC Biology
https://read.qxmd.com/read/38369453/weathered-granites-and-soils-harbour-microbes-with-lanthanide-dependent-methylotrophic-enzymes
#32
JOURNAL ARTICLE
Marcos Y Voutsinos, Jacob A West-Roberts, Rohan Sachdeva, John W Moreau, Jillian F Banfield
BACKGROUND: 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. RESULTS: Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock...
February 19, 2024: BMC Biology
https://read.qxmd.com/read/38360697/a-combination-of-conserved-and-diverged-responses-underlies-theobroma-cacao-s-defense-response-to-phytophthora-palmivora
#33
JOURNAL ARTICLE
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
BACKGROUND: 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 crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L...
February 16, 2024: BMC Biology
https://read.qxmd.com/read/38360623/adars-regulate-cuticle-collagen-expression-and-promote-survival-to-pathogen-infection
#34
JOURNAL ARTICLE
Alfa Dhakal, Chinnu Salim, Mary Skelly, Yarden Amichan, Ayelet T Lamm, Heather A Hundley
BACKGROUND: 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 animals to infection are largely lacking. RESULTS: Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans...
February 16, 2024: BMC Biology
https://read.qxmd.com/read/38360607/genome-wide-comparative-methylation-analysis-reveals-the-fate-of-germ-stem-cells-after-surrogate-production-in-teleost
#35
JOURNAL ARTICLE
Rigolin Nayak, Roman Franěk, Audrey Laurent, Martin Pšenička
BACKGROUND: 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 changes, is rarely acquired. Germ cells develop in close contact with supporting somatic cells during gametogenesis in vertebrates, and we hypothesize that the recipient's gonadal environment may cause epigenetic changes in produced gametes and progeny...
February 16, 2024: BMC Biology
https://read.qxmd.com/read/38355587/female-behavior-drives-the-formation-of-distinct-social-structures-in-c57bl-6j-versus-wild-derived-outbred-mice-in-field-enclosures
#36
JOURNAL ARTICLE
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
BACKGROUND: 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. RESULTS: Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures...
February 14, 2024: BMC Biology
https://read.qxmd.com/read/38355543/a-human-stomach-cell-type-transcriptome-atlas
#37
JOURNAL ARTICLE
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
BACKGROUND: 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 to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single-cell sequencing-based atlases...
February 14, 2024: BMC Biology
https://read.qxmd.com/read/38331819/convergent-genomic-signatures-associated-with-vertebrate-viviparity
#38
JOURNAL ARTICLE
Rhiannon V Eastment, Bob B M Wong, Matthew D McGee
BACKGROUND: 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; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale...
February 8, 2024: BMC Biology
https://read.qxmd.com/read/38331785/enolase-of-streptococcus-suis-serotype-2-promotes-biomolecular-condensation-of-ribosomal-protein-sa-for-hbmecs-apoptosis
#39
JOURNAL ARTICLE
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
BACKGROUND: 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 apoptosis. However, the mechanism that activates RPSA translocation to the cell surface and induces ENO-mediated HBMEC apoptosis is unclear...
February 8, 2024: BMC Biology
https://read.qxmd.com/read/38317233/an-lqt2-related-mutation-in-the-voltage-sensing-domain-is-involved-in-switching-the-gating-polarity-of-herg
#40
JOURNAL ARTICLE
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
BACKGROUND: 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 activated by positive membrane potentials (depolarization), whereas HCN conducts inward current and is activated by negative membrane potentials (hyperpolarization)...
February 5, 2024: BMC Biology
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