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Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease BMC Biol. (IF 5.4) Pub Date : 2024-04-23 Nick Quinn-Bohmann, Jose A. Freixas-Coutin, Jin Seo, Ruth Simmons, Christian Diener, Sean M. Gibbons
The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case–control results has made the identification of consistent and generalizable URT-disease associations difficult. In order to address this issue, we assembled 26 independent 16S rRNA gene amplicon sequencing
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Pangenome analysis reveals transposon-driven genome evolution in cotton BMC Biol. (IF 5.4) Pub Date : 2024-04-23 Xin He, Zhengyang Qi, Zhenping Liu, Xing Chang, Xianlong Zhang, Jianying Li, Maojun Wang
Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE
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Hypoxia exposure blunts angiogenic signaling and upregulates the antioxidant system in endothelial cells derived from elephant seals BMC Biol. (IF 5.4) Pub Date : 2024-04-23 Kaitlin N. Allen, Julia María Torres-Velarde, Juan Manuel Vazquez, Diana D. Moreno-Santillán, Peter H. Sudmant, José Pablo Vázquez-Medina
Elephant seals exhibit extreme hypoxemic tolerance derived from repetitive hypoxia/reoxygenation episodes they experience during diving bouts. Real-time assessment of the molecular changes underlying protection against hypoxic injury in seals remains restricted by their at-sea inaccessibility. Hence, we developed a proliferative arterial endothelial cell culture model from elephant seals and used RNA-seq
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Fast and accurate variant identification tool for sequencing-based studies BMC Biol. (IF 5.4) Pub Date : 2024-04-22 Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang
Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness. We present QuickVariants
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Recognition of nonself is necessary to activate Drosophila’s immune response against an insect parasite BMC Biol. (IF 5.4) Pub Date : 2024-04-22 Alexandre B. Leitão, Ramesh Arunkumar, Jonathan P. Day, Nancy Hanna, Aarathi Devi, Matthew P. Hayes, Francis M. Jiggins
Innate immune responses can be activated by pathogen-associated molecular patterns (PAMPs), danger signals released by damaged tissues, or the absence of self-molecules that inhibit immunity. As PAMPs are typically conserved across broad groups of pathogens but absent from the host, it is unclear whether they allow hosts to recognize parasites that are phylogenetically similar to themselves, such as
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Listeria-vectored cervical cancer vaccine candidate strains reduce MDSCs via the JAK-STAT signaling pathway BMC Biol. (IF 5.4) Pub Date : 2024-04-19 Yunwen Zhang, Yao Lei, Qian Ou, Mengdie Chen, Sicheng Tian, Jing Tang, Ruidan Li, Qian Liang, Zhaobin Chen, Chuan Wang
Immunosuppressive status is prevalent in cancer patients and increases the complexity of tumor immunotherapy. It has been found that Listeria-vectored tumor vaccines had the potential ability of two-side regulatory effect on the immune response during immunotherapy. The results show that the combined immunotherapy with the LM∆E6E7 and LI∆E6E7, the two cervical cancer vaccine candidate strains constructed
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Genomic insights into the seawater adaptation in Cyprinidae BMC Biol. (IF 5.4) Pub Date : 2024-04-19 Ying Wang, Xuejing Zhang, Jing Wang, Cheng Wang, Fei Xiong, Yuting Qian, Minghui Meng, Min Zhou, Wenjun Chen, Zufa Ding, Dan Yu, Yang Liu, Yumei Chang, Shunping He, Liandong Yang
Cyprinidae, the largest fish family, encompasses approximately 367 genera and 3006 species. While they exhibit remarkable adaptability to diverse aquatic environments, it is exceptionally rare to find them in seawater, with the Far Eastern daces being of few exceptions. Therefore, the Far Eastern daces serve as a valuable model for studying the genetic mechanisms underlying seawater adaptation in Cyprinidae
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Prediction of blood–brain barrier penetrating peptides based on data augmentation with Augur BMC Biol. (IF 5.4) Pub Date : 2024-04-19 Zhi-Feng Gu, Yu-Duo Hao, Tian-Yu Wang, Pei-Ling Cai, Yang Zhang, Ke-Jun Deng, Hao Lin, Hao Lv
The blood–brain barrier serves as a critical interface between the bloodstream and brain tissue, mainly composed of pericytes, neurons, endothelial cells, and tightly connected basal membranes. It plays a pivotal role in safeguarding brain from harmful substances, thus protecting the integrity of the nervous system and preserving overall brain homeostasis. However, this remarkable selective transmission
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GATA3 functions downstream of BRCA1 to promote DNA damage repair and suppress dedifferentiation in breast cancer BMC Biol. (IF 5.4) Pub Date : 2024-04-16 Xuejie Wang, Feng Bai, Xiong Liu, Bin Peng, Xingzhi Xu, Hongquan Zhang, Li Fu, Wei-Guo Zhu, Bin Wang, Xin-Hai Pei
Inadequate DNA damage repair promotes aberrant differentiation of mammary epithelial cells. Mammary luminal cell fate is mainly determined by a few transcription factors including GATA3. We previously reported that GATA3 functions downstream of BRCA1 to suppress aberrant differentiation in breast cancer. How GATA3 impacts DNA damage repair preventing aberrant cell differentiation in breast cancer remains
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A cilia-bound unconventional secretory pathway for Drosophila odorant receptors BMC Biol. (IF 5.4) Pub Date : 2024-04-12 Najat Dzaki, Mattias Alenius
Post-translational transport is a vital process which ensures that each protein reaches its site of function. Though most do so via an ordered ER-to-Golgi route, an increasing number of proteins are now shown to bypass this conventional secretory pathway. In the Drosophila olfactory sensory neurons (OSNs), odorant receptors (ORs) are trafficked from the ER towards the cilia. Here, we show that Or22a
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Targeting of REST with rationally-designed small molecule compounds exhibits synergetic therapeutic potential in human glioblastoma cells BMC Biol. (IF 5.4) Pub Date : 2024-04-12 Svetlana B. Panina, Joshua V. Schweer, Qian Zhang, Gaurav Raina, Haley A. Hardtke, Seungjin Kim, Wanjie Yang, Dionicio Siegel, Y. Jessie Zhang
Glioblastoma (GBM) is an aggressive brain cancer associated with poor prognosis, intrinsic heterogeneity, plasticity, and therapy resistance. In some GBMs, cell proliferation is fueled by a transcriptional regulator, repressor element-1 silencing transcription factor (REST). Using CRISPR/Cas9, we identified GBM cell lines dependent on REST activity. We developed new small molecule inhibitory compounds
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Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis BMC Biol. (IF 5.4) Pub Date : 2024-04-12 Guoyun Zhang, Yating Song, Ning Chen, Jihua Wei, Jianguo Zhang, Caiyun He
As an endemic shrub of the Qinghai-Tibetan Plateau (QTP), the distribution of Hippophae tibetana Schlecht. ranges between 2800 and 5200 m above sea level. As the most basal branch of the Hippophae genus, H. tibetana has an extensive evolutionary history. The H. tibetana is a valuable tree for studying the ecological evolution of species under extreme conditions. Here, we generated a high-quality chromosome-level
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A network of transcription factors in complex with a regulating cell cycle cyclin orchestrates fungal oxidative stress responses BMC Biol. (IF 5.4) Pub Date : 2024-04-12 Yanze Kan, Zhangjiang He, Nemat O. Keyhani, Ning Li, Shuaishuai Huang, Xin Zhao, Pengfei Liu, Fanqin Zeng, Min Li, Zhibing Luo, Yongjun Zhang
Response to oxidative stress is universal in almost all organisms and the mitochondrial membrane protein, BbOhmm, negatively affects oxidative stress responses and virulence in the insect fungal pathogen, Beauveria bassiana. Nothing further, however, is known concerning how BbOhmm and this phenomenon is regulated. Three oxidative stress response regulating Zn2Cys6 transcription factors (BbOsrR1, 2
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Nuclear lamina component KAKU4 regulates chromatin states and transcriptional regulation in the Arabidopsis genome BMC Biol. (IF 5.4) Pub Date : 2024-04-12 Yaxin Cao, Hengyu Yan, Minghao Sheng, Yue Liu, Xinyue Yu, Zhongqiu Li, Wenying Xu, Zhen Su
The nuclear lamina links the nuclear membrane to chromosomes and plays a crucial role in regulating chromatin states and gene expression. However, current knowledge of nuclear lamina in plants is limited compared to animals and humans. This study mainly focused on elucidating the mechanism through which the putative nuclear lamina component protein KAKU4 regulates chromatin states and gene expression
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Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae BMC Biol. (IF 5.4) Pub Date : 2024-04-10 Charles Ross Lindsey, Andrew H. Knoll, Matthew D. Herron, Frank Rosenzweig
Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved
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Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation BMC Biol. (IF 5.4) Pub Date : 2024-04-10 Irina Abnizova, Carine Stapel, Rene te Boekhorst, Jimmy Tsz Hang Lee, Martin Hemberg
Regulation of transcription is central to the emergence of new cell types during development, and it often involves activation of genes via proximal and distal regulatory regions. The activity of regulatory elements is determined by transcription factors (TFs) and epigenetic marks, but despite extensive mapping of such patterns, the extraction of regulatory principles remains challenging. Here we study
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High incidence of imperforate vagina in ADGRA3-deficient mice BMC Biol. (IF 5.4) Pub Date : 2024-04-08 Jone Marita Kvam, Maja Lind Nybo, Lola Torz, Riia Karolina Sustarsic, Kristian Høj Reveles Jensen, John Erik Nielsen, Hanne Frederiksen, Sarina Gadgaard, Katja Spiess, Steen Seier Poulsen, Jesper Skovhus Thomsen, Pamela Cowin, Martin Blomberg Jensen, Takeshi Kurita, Mette Marie Rosenkilde
Ten percent of the female population suffers from congenital abnormalities of the vagina, uterus, or oviducts, with severe consequences for reproductive and psychological health. Yet, the underlying causes of most of these malformations remain largely unknown. ADGRA3 (GPR125) is involved in WNT signaling and planar cell polarity, mechanisms vital to female reproductive tract development. Although ADGRA3
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Bacterial accumulation in intestinal folds induced by physical and biological factors BMC Biol. (IF 5.4) Pub Date : 2024-04-05 Jinyou Yang, Toma Isaka, Kenji Kikuchi, Keiko Numayama-Tsuruta, Takuji Ishikawa
The gut microbiota, vital for host health, influences metabolism, immune function, and development. Understanding the dynamic processes of bacterial accumulation within the gut is crucial, as it is closely related to immune responses, antibiotic resistance, and colorectal cancer. We investigated Escherichia coli behavior and distribution in zebrafish larval intestines, focusing on the gut microenvironment
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Insights for disease modeling from single-cell transcriptomics of iPSC-derived Ngn2-induced neurons and astrocytes across differentiation time and co-culture BMC Biol. (IF 5.4) Pub Date : 2024-04-02 D. Das, S. Sonthalia, G. Stein-O.’Brien, MH. Wahbeh, K. Feuer, L. Goff, C. Colantuoni, V. Mahairaki, D. Avramopoulos
Trans-differentiation of human-induced pluripotent stem cells into neurons via Ngn2-induction (hiPSC-N) has become an efficient system to quickly generate neurons a likely significant advance for disease modeling and in vitro assay development. Recent single-cell interrogation of Ngn2-induced neurons, however, has revealed some similarities to unexpected neuronal lineages. Similarly, a straightforward
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Molecular control of cellulosic fin morphogenesis in ascidians BMC Biol. (IF 5.4) Pub Date : 2024-04-02 Maxence Lanoizelet, Christel Elkhoury Youhanna, Agnès Roure, Sébastien Darras
The tunicates form a group of filter-feeding marine animals closely related to vertebrates. They share with them a number of features such as a notochord and a dorsal neural tube in the tadpole larvae of ascidians, one of the three groups that make tunicates. However, a number of typical chordate characters have been lost in different branches of tunicates, a diverse and fast-evolving phylum. Consequently
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Cue-driven microbial cooperation and communication: evolving quorum sensing with honest signaling BMC Biol. (IF 5.4) Pub Date : 2024-04-02 Tamás Czárán, István Scheuring, István Zachar, Szabolcs Számadó
Quorum sensing (QS) is the ability of microorganisms to assess local clonal density by measuring the extracellular concentration of signal molecules that they produce and excrete. QS is also the only known way of bacterial communication that supports the coordination of within-clone cooperative actions requiring a certain threshold density of cooperating cells. Cooperation aided by QS communication
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Publisher Correction: 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 : 2024-04-01 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
Correction: BMC Biology 22, 35 (2024) https://doi.org/10.1186/s12915-024-01809-0 The production team of the original article [1] mistakenly carried forward the following errors which have since been amended: • The ORCIDs of all authors post-first author were mistakenly omitted. • The term, ‘two by four’ was changed to ‘2 × 4’. • Two instances of the term ‘ad libitum’ were italicised. • The sentence
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MAPK-dependent control of mitotic progression in S. pombe BMC Biol. (IF 5.4) Pub Date : 2024-03-25 Ana Belén Iglesias-Romero, Terersa Soto, Ignacio Flor-Parra, Silvia Salas-Pino, Gabriel Ruiz-Romero, Kathleen L. Gould, José Cansado, Rafael R. Daga
Mitogen-activated protein kinases (MAPKs) preserve cell homeostasis by transducing physicochemical fluctuations of the environment into multiple adaptive responses. These responses involve transcriptional rewiring and the regulation of cell cycle transitions, among others. However, how stress conditions impinge mitotic progression is largely unknown. The mitotic checkpoint is a surveillance mechanism
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Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea) BMC Biol. (IF 5.4) Pub Date : 2024-03-22 Qi Zhang, Yi-Wen Lu, Xin-Yu Liu, Ye Li, Wei-Nan Gao, Jing-Tao Sun, Xiao-Yue Hong, Renfu Shao, Xiao-Feng Xue
Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters—some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could
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Single-cell RNA sequencing integrated with bulk RNA sequencing analysis identifies a tumor immune microenvironment-related lncRNA signature in lung adenocarcinoma BMC Biol. (IF 5.4) Pub Date : 2024-03-22 Yuqing Ren, Ruhao Wu, Chunwei Li, Long Liu, Lifeng Li, Siyuan Weng, Hui Xu, Zhe Xing, Yuyuan Zhang, Libo Wang, Zaoqu Liu, Xinwei Han
Recently, long non-coding RNAs (lncRNAs) have been demonstrated as essential roles in tumor immune microenvironments (TIME). Nevertheless, researches on the clinical significance of TIME-related lncRNAs are limited in lung adenocarcinoma (LUAD). Single-cell RNA sequencing and bulk RNA sequencing data are integrated to identify TIME-related lncRNAs. A total of 1368 LUAD patients are enrolled from 6
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OsmiR319-OsPCF5 modulate resistance to brown planthopper in rice through association with MYB proteins BMC Biol. (IF 5.4) Pub Date : 2024-03-22 Bo Sun, Yanjie Shen, Lin Zhu, Xiaofang Yang, Xue Liu, Dayong Li, Mulan Zhu, Xuexia Miao, Zhenying Shi
The brown planthopper (BPH) is a kind of piercing-sucking insect specific to rice, with the damage tops the list of pathogens and insects in recent years. microRNAs (miRNAs) are pivotal regulators of plant–environment interactions, while the mechanism underlying their function against insects is largely unknown. Here, we confirmed that OsmiR319, an ancient and conserved miRNA, negatively regulated
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Evolution of compound eye morphology underlies differences in vision between closely related Drosophila species BMC Biol. (IF 5.4) Pub Date : 2024-03-19 Alexandra D. Buffry, John P. Currea, Franziska A. Franke-Gerth, Ravindra Palavalli-Nettimi, Andrew J. Bodey, Christoph Rau, Nazanin Samadi, Stefan J. Gstöhl, Christian M. Schlepütz, Alistair P. McGregor, Lauren Sumner-Rooney, Jamie Theobald, Maike Kittelmann
Insects have evolved complex visual systems and display an astonishing range of adaptations for diverse ecological niches. Species of Drosophila melanogaster subgroup exhibit extensive intra- and interspecific differences in compound eye size. These differences provide an excellent opportunity to better understand variation in insect eye structure and the impact on vision. Here we further explored
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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;