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  • Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles
    BMC Biol. (IF 6.765) Pub Date : 2021-01-14
    Hao-Sen Li; Xue-Fei Tang; Yu-Hao Huang; Ze-Yu Xu; Mei-Lan Chen; Xue-Yong Du; Bo-Yuan Qiu; Pei-Tao Chen; Wei Zhang; Adam Ślipiński; Hermes E. Escalona; Robert M. Waterhouse; Andreas Zwick; Hong Pang

    Horizontal gene transfer (HGT) has been documented in many herbivorous insects, conferring the ability to digest plant material and promoting their remarkable ecological diversification. Previous reports suggest HGT of antibacterial enzymes may have contributed to the insect immune response and limit bacterial growth. Carnivorous insects also display many evolutionary successful lineages, but in contrast

    更新日期:2021-01-14
  • Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics
    BMC Biol. (IF 6.765) Pub Date : 2021-01-14
    Congyu Lu; Zheng Zhang; Zena Cai; Zhaozhong Zhu; Ye Qiu; Aiping Wu; Taijiao Jiang; Heping Zheng; Yousong Peng

    Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which

    更新日期:2021-01-14
  • Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity
    BMC Biol. (IF 6.765) Pub Date : 2021-01-13
    Kristyna Pluhackova; Andreas Horner

    Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high

    更新日期:2021-01-13
  • Current cancer driver variant predictors learn to recognize driver genes instead of functional variants
    BMC Biol. (IF 6.765) Pub Date : 2021-01-13
    Daniele Raimondi; Antoine Passemiers; Piero Fariselli; Yves Moreau

    Identifying variants that drive tumor progression (driver variants) and distinguishing these from variants that are a byproduct of the uncontrolled cell growth in cancer (passenger variants) is a crucial step for understanding tumorigenesis and precision oncology. Various bioinformatics methods have attempted to solve this complex task. In this study, we investigate the assumptions on which these methods

    更新日期:2021-01-13
  • An updated tribal classification of Lamiaceae based on plastome phylogenomics
    BMC Biol. (IF 6.765) Pub Date : 2021-01-08
    Fei Zhao; Ya-Ping Chen; Yasaman Salmaki; Bryan T. Drew; Trevor C. Wilson; Anne-Cathrine Scheen; Ferhat Celep; Christian Bräuchler; Mika Bendiksby; Qiang Wang; Dao-Zhang Min; Hua Peng; Richard G. Olmstead; Bo Li; Chun-Lei Xiang

    A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally

    更新日期:2021-01-08
  • Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp
    BMC Biol. (IF 6.765) Pub Date : 2021-01-06
    Sarah Farhat; Phuong Le; Ehsan Kayal; Benjamin Noel; Estelle Bigeard; Erwan Corre; Florian Maumus; Isabelle Florent; Adriana Alberti; Jean-Marc Aury; Tristan Barbeyron; Ruibo Cai; Corinne Da Silva; Benjamin Istace; Karine Labadie; Dominique Marie; Jonathan Mercier; Tsinda Rukwavu; Jeremy Szymczak; Thierry Tonon; Catharina Alves-de-Souza; Pierre Rouzé; Yves Van de Peer; Patrick Wincker; Stephane Rombauts;

    Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from

    更新日期:2021-01-07
  • Lethal (2) giant discs (Lgd)/CC2D1 is required for the full activity of the ESCRT machinery
    BMC Biol. (IF 6.765) Pub Date : 2020-12-22
    Miriam Baeumers; Kristina Ruhnau; Thomas Breuer; Hendrik Pannen; Bastian Goerlich; Anna Kniebel; Sebastian Haensch; Stefanie Weidtkamp-Peters; Lutz Schmitt; Thomas Klein

    A major task of the endosomal sorting complex required for transport (ESCRT) machinery is the pinching off of cargo-loaded intraluminal vesicles (ILVs) into the lumen of maturing endosomes (MEs), which is essential for the complete degradation of transmembrane proteins in the lysosome. The ESCRT machinery is also required for the termination of signalling through activated signalling receptors, as

    更新日期:2020-12-22
  • Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats
    BMC Biol. (IF 6.765) Pub Date : 2020-12-21
    Octavio M. Palacios-Gimenez; Julia Koelman; Marc Palmada-Flores; Tessa M. Bradford; Karl K. Jones; Steven J. B. Cooper; Takeshi Kawakami; Alexander Suh

    Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read

    更新日期:2020-12-22
  • Publisher Correction: Spontaneous regression of micro-metastases following primary tumor excision: a critical role for primary tumor secretome
    BMC Biol. (IF 6.765) Pub Date : 2020-12-16
    Lee Shaashua; Anabel Eckerling; Boaz Israeli; Gali Yanovich; Ella Rosenne; Suzana Fichman-Horn; Ido Ben Zvi; Liat Sorski; Rita Haldar; Ronit Satchi-Fainaro; Tamar Geiger; Erica K. Sloan; Shamgar Ben-Eliyahu

    An amendment to this paper has been published and can be accessed via the original article.

    更新日期:2020-12-16
  • Oxidative stress mediates thalidomide-induced pain by targeting peripheral TRPA1 and central TRPV4
    BMC Biol. (IF 6.765) Pub Date : 2020-12-14
    Francesco De Logu; Gabriela Trevisan; Ilaria Maddalena Marone; Elisabetta Coppi; Diéssica Padilha Dalenogare; Mustafa Titiz; Matilde Marini; Lorenzo Landini; Daniel Souza Monteiro de Araujo; Simone Li Puma; Serena Materazzi; Gaetano De Siena; Pierangelo Geppetti; Romina Nassini

    The mechanism underlying the pain symptoms associated with chemotherapeutic-induced peripheral neuropathy (CIPN) is poorly understood. Transient receptor potential ankyrin 1 (TRPA1), TRP vanilloid 4 (TRPV4), TRPV1, and oxidative stress have been implicated in several rodent models of CIPN-evoked allodynia. Thalidomide causes a painful CIPN in patients via an unknown mechanism. Surprisingly, the pathway

    更新日期:2020-12-15
  • Feedback inhibition of AMT1 NH4+-transporters mediated by CIPK15 kinase
    BMC Biol. (IF 6.765) Pub Date : 2020-12-14
    Hui-Yu Chen; Yen-Ning Chen; Hung-Yu Wang; Zong-Ta Liu; Wolf B. Frommer; Cheng-Hsun Ho

    Ammonium (NH4+), a key nitrogen form, becomes toxic when it accumulates to high levels. Ammonium transporters (AMTs) are the key transporters responsible for NH4+ uptake. AMT activity is under allosteric feedback control, mediated by phosphorylation of a threonine in the cytosolic C-terminus (CCT). However, the kinases responsible for the NH4+-triggered phosphorylation remain unknown. In this study

    更新日期:2020-12-15
  • Resilin matrix distribution, variability and function in Drosophila
    BMC Biol. (IF 6.765) Pub Date : 2020-12-14
    Steven Lerch; Renata Zuber; Nicole Gehring; Yiwen Wang; Barbara Eckel; Klaus-Dieter Klass; Fritz-Olaf Lehmann; Bernard Moussian

    Elasticity prevents fatigue of tissues that are extensively and repeatedly deformed. Resilin is a resilient and elastic extracellular protein matrix in joints and hinges of insects. For its mechanical properties, Resilin is extensively analysed and applied in biomaterial and biomedical sciences. However, there is only indirect evidence for Resilin distribution and function in an insect. Commonly, the

    更新日期:2020-12-15
  • Competition for nutritional resources masks the true frequency of bacterial mutants
    BMC Biol. (IF 6.765) Pub Date : 2020-12-14
    Henrique Iglesias Neves; Gabriella Trombini Machado; Taíssa Cristina dos Santos Ramos; Hyun Mo Yang; Ezra Yagil; Beny Spira

    It is widely assumed that all mutant microorganisms present in a culture are able to grow and form colonies, provided that they express the features required for selection. Unlike wild-type Escherichia coli, PHO-constitutive mutants overexpress alkaline phosphatase and hence can hydrolyze glycerol-2-phosphate (G2P) to glycerol and form colonies on plates having G2P as the sole carbon source. These

    更新日期:2020-12-14
  • A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells
    BMC Biol. (IF 6.765) Pub Date : 2020-12-14
    Nicholas Brookhouser; Toan Nguyen; Stefan J. Tekel; Kylie Standage-Beier; Xiao Wang; David A. Brafman

    Adenine base editors (ABE) enable single nucleotide modifications without the need for double-stranded DNA breaks (DSBs) induced by conventional CRIPSR/Cas9-based approaches. However, most approaches that employ ABEs require inefficient downstream technologies to identify desired targeted mutations within large populations of manipulated cells. In this study, we developed a fluorescence-based method

    更新日期:2020-12-14
  • Analysis of urinary exosomal metabolites identifies cardiovascular risk signatures with added value to urine analysis
    BMC Biol. (IF 6.765) Pub Date : 2020-12-14
    Marta Agudiez; Paula J. Martinez; Marta Martin-Lorenzo; Angeles Heredero; Aranzazu Santiago-Hernandez; Dolores Molero; Juan Manuel Garcia-Segura; Gonzalo Aldamiz-Echevarria; Gloria Alvarez-Llamas

    Subclinical atherosclerosis may result in fatal cardiovascular (CV) events, but the underlying mechanisms and molecular players leading to disease are not entirely understood. Thus, novel approaches capable of identifying the factors involved in pathological progression and providing a better understanding of the subjacent mechanisms are needed. Extracellular vesicles (EVs) have been shown to have

    更新日期:2020-12-14
  • Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates
    BMC Biol. (IF 6.765) Pub Date : 2020-12-07
    Tiago R. Simões; Michael W. Caldwell; Stephanie E. Pierce

    The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative

    更新日期:2020-12-07
  • An optimized base editor with efficient C-to-T base editing in zebrafish
    BMC Biol. (IF 6.765) Pub Date : 2020-12-03
    Yu Zhao; Dantong Shang; Ruhong Ying; Hanhua Cheng; Rongjia Zhou

    Zebrafish is a model organism widely used for the understanding of gene function, including the fundamental basis of human disease, enabled by the presence in its genome of a high number of orthologs to human genes. CRISPR/Cas9 and next-generation gene-editing techniques using cytidine deaminase fused with Cas9 nickase provide fast and efficient tools able to induce sequence-specific single base mutations

    更新日期:2020-12-03
  • Crystal structure of the yeast heterodimeric ADAT2/3 deaminase
    BMC Biol. (IF 6.765) Pub Date : 2020-12-03
    Xiwen Liu; Ruoyu Chen; Yujie Sun; Ran Chen; Jie Zhou; Qingnan Tian; Xuan Tao; Zhang Zhang; Guan-zheng Luo; Wei Xie

    The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms

    更新日期:2020-12-03
  • Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization
    BMC Biol. (IF 6.765) Pub Date : 2020-12-02
    Yan Zhao; Luhao Dong; Conghui Jiang; Xueqiang Wang; Jianyin Xie; Muhammad Abdul Rehman Rashid; Yanhe Liu; Mengyao Li; Zhimu Bu; Hongwei Wang; Xin Ma; Silong Sun; Xiaoqian Wang; Cunyao Bo; Tingting Zhou; Lingrang Kong

    The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its

    更新日期:2020-12-02
  • Vickermania gen. nov., trypanosomatids that use two joined flagella to resist midgut peristaltic flow within the fly host
    BMC Biol. (IF 6.765) Pub Date : 2020-12-02
    Alexei Y. Kostygov; Alexander O. Frolov; Marina N. Malysheva; Anna I. Ganyukova; Lyudmila V. Chistyakova; Daria Tashyreva; Martina Tesařová; Viktoria V. Spodareva; Jana Režnarová; Diego H. Macedo; Anzhelika Butenko; Claudia M. d’Avila-Levy; Julius Lukeš; Vyacheslav Yurchenko

    The family Trypanosomatidae encompasses parasitic flagellates, some of which cause serious vector-transmitted diseases of humans and domestic animals. However, insect-restricted parasites represent the ancestral and most diverse group within the family. They display a range of unusual features and their study can provide insights into the biology of human pathogens. Here we describe Vickermania, a

    更新日期:2020-12-02
  • Prediction of the incubation period for COVID-19 and future virus disease outbreaks
    BMC Biol. (IF 6.765) Pub Date : 2020-11-30
    Ayal B. Gussow; Noam Auslander; Yuri I. Wolf; Eugene V. Koonin

    A crucial factor in mitigating respiratory viral outbreaks is early determination of the duration of the incubation period and, accordingly, the required quarantine time for potentially exposed individuals. At the time of the COVID-19 pandemic, optimization of quarantine regimes becomes paramount for public health, societal well-being, and global economy. However, biological factors that determine

    更新日期:2020-12-01
  • First evidence of convergent lifestyle signal in reptile skull roof microanatomy
    BMC Biol. (IF 6.765) Pub Date : 2020-11-30
    Roy Ebel; Johannes Müller; Till Ramm; Christy Hipsley; Eli Amson

    The study of convergently acquired adaptations allows fundamental insight into life’s evolutionary history. Within lepidosaur reptiles—i.e. lizards, tuatara, and snakes—a fully fossorial (‘burrowing’) lifestyle has independently evolved in most major clades. However, despite their consistent use of the skull as a digging tool, cranial modifications common to all these lineages are yet to be found.

    更新日期:2020-12-01
  • Genome plasticity in Paramecium bursaria revealed by population genomics
    BMC Biol. (IF 6.765) Pub Date : 2020-11-30
    Yu-Hsuan Cheng; Chien-Fu Jeff Liu; Yen-Hsin Yu; Yu-Ting Jhou; Masahiro Fujishima; Isheng Jason Tsai; Jun-Yi Leu

    Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused

    更新日期:2020-12-01
  • miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling
    BMC Biol. (IF 6.765) Pub Date : 2020-11-27
    Bin Zhang; Lilin Zhao; Jing Ning; Jacob D. Wickham; Haokai Tian; Xiaoming Zhang; Meiling Yang; Xiangming Wang; Jianghua Sun

    Survival to cold stress in insects living in temperate environments requires the deployment of strategies that lead to physiological changes involved in freeze tolerance or freeze avoidance. These strategies may consist of, for instance, the induction of metabolic depression, accumulation of cryoprotectants, or the production of antifreeze proteins, however, little is known about the way such mechanisms

    更新日期:2020-11-27
  • Mapping the past, present and future research landscape of paternal effects
    BMC Biol. (IF 6.765) Pub Date : 2020-11-27
    Joanna Rutkowska; Malgorzata Lagisz; Russell Bonduriansky; Shinichi Nakagawa

    Although in all sexually reproducing organisms an individual has a mother and a father, non-genetic inheritance has been predominantly studied in mothers. Paternal effects have been far less frequently studied, until recently. In the last 5 years, research on environmentally induced paternal effects has grown rapidly in the number of publications and diversity of topics. Here, we provide an overview

    更新日期:2020-11-27
  • Colored visual stimuli evoke spectrally tuned neuronal responses across the central nervous system of zebrafish larvae
    BMC Biol. (IF 6.765) Pub Date : 2020-11-27
    Chiara Fornetto; Natascia Tiso; Francesco Saverio Pavone; Francesco Vanzi

    Visually guided behaviors such as optomotor and optokinetic responses, phototaxis, and prey capture are crucial for survival in zebrafish and become apparent after just a few days of development. Color vision, which in zebrafish is based on a spatially anisotropic tetrachromatic retina, provides an additional important component of world representation driving fundamental larval behaviors. However

    更新日期:2020-11-27
  • Paxillin mediates ATP-induced activation of P2X7 receptor and NLRP3 inflammasome
    BMC Biol. (IF 6.765) Pub Date : 2020-11-26
    Wenbiao Wang; Dingwen Hu; Yuqian Feng; Caifeng Wu; Yunting Song; Weiyong Liu; Aixin Li; Yingchong Wang; Keli Chen; Mingfu Tian; Feng Xiao; Qi Zhang; Weijie Chen; Pan Pan; Pin Wan; Yingle Liu; Huiyao Lan; Kailang Wu; Jianguo Wu

    Extracellular adenosine triphosphate (ATP), a key danger-associated molecular pattern (DAMP) molecule, is released to the extracellular medium during inflammation by injured parenchymal cells, dying leukocytes, and activated platelets. ATP directly activates the plasma membrane channel P2X7 receptor (P2X7R), leading to an intracellular influx of K+, a key trigger inducing NLRP3 inflammasome activation

    更新日期:2020-11-27
  • Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda
    BMC Biol. (IF 6.765) Pub Date : 2020-11-26
    Lian Xu; Jian Yang; Meng Xu; Dai Shan; Zhongdao Wu; Dongjuan Yuan

    Nematodes have evolved to survive in diverse ecological niches and can be a serious burden on agricultural economy, veterinary medicine, and public health. Antioxidant enzymes in parasitic nematodes play a critical role in defending against host oxidative stress. However, the features of the evolution of antioxidant enzymes in the phylum Nematoda remain elusive. Here, we systematically investigated

    更新日期:2020-11-27
  • Omission of non-poly(A) viral transcripts from the tissue level atlas of the healthy human virome
    BMC Biol. (IF 6.765) Pub Date : 2020-11-25
    Signe Altmäe; Nerea M. Molina; Alberto Sola-Leyva

    A recent paper in BMC Biology entitled “A tissue level atlas of the healthy human virome” by Kumata et al. describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project. Using a workflow that maps the GTEx sequences to the human genome, then screens unmapped sequences to detect viral transcripts, the authors present a quantitative analysis of

    更新日期:2020-11-25
  • Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites
    BMC Biol. (IF 6.765) Pub Date : 2020-11-24
    Marco Schmidt; Tiago Maié; Edgar Dahl; Ivan G. Costa; Wolfgang Wagner

    The complex composition of different cell types within a tissue can be estimated by deconvolution of bulk gene expression profiles or with various single-cell sequencing approaches. Alternatively, DNA methylation (DNAm) profiles have been used to establish an atlas for multiple human tissues and cell types. DNAm is particularly suitable for deconvolution of cell types because each CG dinucleotide (CpG

    更新日期:2020-11-25
  • CloneSifter: enrichment of rare clones from heterogeneous cell populations
    BMC Biol. (IF 6.765) Pub Date : 2020-11-24
    David Feldman; FuNien Tsai; Anthony J. Garrity; Ryan O’Rourke; Lisa Brenan; Patricia Ho; Elizabeth Gonzalez; Silvana Konermann; Cory M. Johannessen; Rameen Beroukhim; Pratiti Bandopadhayay; Paul C. Blainey

    Many biological processes, such as cancer metastasis, organismal development, and acquisition of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. While large-scale barcoding with NGS

    更新日期:2020-11-25
  • Open questions: how do engineered nanomaterials affect our cells?
    BMC Biol. (IF 6.765) Pub Date : 2020-11-24
    Daniela Barrios; Laura Segatori

    Our cells have evolutionarily conserved mechanisms that battle foreign and toxic materials to maintain cellular homeostasis and viability. How do these cellular machineries respond to engineered nanomaterials?

    更新日期:2020-11-25
  • System-wide molecular dynamics of endothelial dysfunction in Gram-negative sepsis
    BMC Biol. (IF 6.765) Pub Date : 2020-11-24
    Xavier Gallart-Palau; Aida Serra; Siu Kwan Sze

    Inflammation affecting whole organism vascular networks plays a central role in the progression and establishment of several human diseases, including Gram-negative sepsis. Although the molecular mechanisms that control inflammation of specific vascular beds have been partially defined, knowledge lacks on the impact of these on the molecular dynamics of whole organism vascular beds. In this study,

    更新日期:2020-11-25
  • Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
    BMC Biol. (IF 6.765) Pub Date : 2020-11-23
    Luisa Henkel; Benedikt Rauscher; Barbara Schmitt; Jan Winter; Michael Boutros

    In recent years, large-scale genetic screens using the CRISPR/Cas9 system have emerged as scalable approaches able to interrogate gene function with unprecedented efficiency and specificity in various biological contexts. By this means, functional dependencies on both the protein-coding and noncoding genome of numerous cell types in different organisms have been interrogated. However, screening designs

    更新日期:2020-11-23
  • Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation
    BMC Biol. (IF 6.765) Pub Date : 2020-11-20
    Lorraine A. Draper; Feargal J. Ryan; Marion Dalmasso; Pat G. Casey; Angela McCann; Vimalkumar Velayudhan; R. Paul Ross; Colin Hill

    It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the

    更新日期:2020-11-21
  • Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat
    BMC Biol. (IF 6.765) Pub Date : 2020-11-20
    Jingya Yuan; Wu Jiao; Yanfeng Liu; Wenxue Ye; Xiue Wang; Bao Liu; Qingxin Song; Z. Jeffrey Chen

    Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid

    更新日期:2020-11-21
  • In vivo imaging of injured cortical axons reveals a rapid onset form of Wallerian degeneration
    BMC Biol. (IF 6.765) Pub Date : 2020-11-18
    Alison Jane Canty; Johanna Sara Jackson; Lieven Huang; Antonio Trabalza; Cher Bass; Graham Little; Maria Tortora; Shabana Khan; Vincenzo De Paola

    Despite the widespread occurrence of axon and synaptic loss in the injured and diseased nervous system, the cellular and molecular mechanisms of these key degenerative processes remain incompletely understood. Wallerian degeneration (WD) is a tightly regulated form of axon loss after injury, which has been intensively studied in large myelinated fibre tracts of the spinal cord, optic nerve and peripheral

    更新日期:2020-11-19
  • Correction to: Genome-enabled insights into the biology of thrips as crop pests
    BMC Biol. (IF 6.765) Pub Date : 2020-11-16
    Dorith Rotenberg; Aaron A. Baumann; Sulley Ben-Mahmoud; Olivier Christiaens; Wannes Dermauw; Panagiotis Ioannidis; Chris G. C. Jacobs; Iris M. Vargas Jentzsch; Jonathan E. Oliver; Monica F. Poelchau; Swapna Priya Rajarapu; Derek J. Schneweis; Simon Snoeck; Clauvis N. T. Taning; Dong Wei; Shirani M. K. Widana Gamage; Daniel S. T. Hughes; Shwetha C. Murali; Samuel T. Bailey; Nicolas E. Bejerman; Christopher

    An amendment to this paper has been published and can be accessed via the original article.

    更新日期:2020-11-16
  • Protein kinase A controls yeast growth in visible light
    BMC Biol. (IF 6.765) Pub Date : 2020-11-16
    Mikael Molin; Katarina Logg; Kristofer Bodvard; Ken Peeters; Annabelle Forsmark; Friederike Roger; Anna Jörhov; Neha Mishra; Jean-Marc Billod; Sabiha Amir; Mikael Andersson; Leif A. Eriksson; Jonas Warringer; Mikael Käll; Anders Blomberg

    A wide variety of photosynthetic and non-photosynthetic species sense and respond to light, having developed protective mechanisms to adapt to damaging effects on DNA and proteins. While the biology of UV light-induced damage has been well studied, cellular responses to stress from visible light (400–700 nm) remain poorly understood despite being a regular part of the life cycle of many organisms.

    更新日期:2020-11-16
  • Insertion variants missing in the human reference genome are widespread among human populations
    BMC Biol. (IF 6.765) Pub Date : 2020-11-13
    Young-gun Lee; Jin-young Lee; Junhyong Kim; Young-Joon Kim

    Structural variants comprise diverse genomic arrangements including deletions, insertions, inversions, and translocations, which can generally be detected in humans through sequence comparison to the reference genome. Among structural variants, insertions are the least frequently identified variants, mainly due to ascertainment bias in the reference genome, lack of previous sequence knowledge, and

    更新日期:2020-11-15
  • Echolocating bats can adjust sensory acquisition based on internal cues
    BMC Biol. (IF 6.765) Pub Date : 2020-11-09
    Arjan Boonman; Itai Rieger; Eran Amichai; Stefan Greif; Ofri Eitan; Aya Goldshtein; Yossi Yovel

    Sensory systems acquire both external and internal information to guide behavior. Adjustments based on external input are much better documented and understood than internal-based sensory adaptations. When external input is not available, idiothetic—internal—cues become crucial for guiding behavior. Here, we take advantage of the rapid sensory adjustments exhibited by bats in order to study how animals

    更新日期:2020-11-12
  • Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection
    BMC Biol. (IF 6.765) Pub Date : 2020-11-09
    Peter D. Olson; Alan Tracey; Andrew Baillie; Katherine James; Stephen R. Doyle; Sarah K. Buddenborg; Faye H. Rodgers; Nancy Holroyd; Matt Berriman

    Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end

    更新日期:2020-11-09
  • Neuronal surface P antigen (NSPA) modulates postsynaptic NMDAR stability through ubiquitination of tyrosine phosphatase PTPMEG
    BMC Biol. (IF 6.765) Pub Date : 2020-11-06
    Sofía Espinoza; Sebastián B. Arredondo; Francisca Barake; Francisco Carvajal; Fernanda G. Guerrero; Fabian Segovia-Miranda; David M. Valenzuela; Ursula Wyneken; Alejandro Rojas-Fernández; Waldo Cerpa; Loreto Massardo; Lorena Varela-Nallar; Alfonso González

    Cognitive dysfunction (CD) is common among patients with the autoimmune disease systemic lupus erythematosus (SLE). Anti-ribosomal P autoantibodies associate with this dysfunction and have neuropathogenic effects that are mediated by cross-reacting with neuronal surface P antigen (NSPA) protein. Elucidating the function of NSPA can then reveal CD pathogenic mechanisms and treatment opportunities. In

    更新日期:2020-11-06
  • Spontaneous regression of micro-metastases following primary tumor excision: a critical role for primary tumor secretome
    BMC Biol. (IF 6.765) Pub Date : 2020-11-06
    Lee Shaashua; Anabel Eckerling; Boaz Israeli; Gali Yanovich; Ella Rosenne; Suzana Fichman-Horn; Ido Ben Zvi; Liat Sorski; Rita Haldar; Ronit Satchi-Fainaro; Tamar Geiger; Erica K. Sloan; Shamgar Ben-Eliyahu

    Numerous case studies have reported spontaneous regression of recognized metastases following primary tumor excision, but underlying mechanisms are elusive. Here, we present a model of regression and latency of metastases following primary tumor excision and identify potential underlying mechanisms. Using MDA-MB-231HM human breast cancer cells that express highly sensitive luciferase, we monitored

    更新日期:2020-11-06
  • Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression
    BMC Biol. (IF 6.765) Pub Date : 2020-11-06
    Ulfar Bergthorsson; Caroline J. Sheeba; Anke Konrad; Tony Belicard; Toni Beltran; Vaishali Katju; Peter Sarkies

    Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood

    更新日期:2020-11-06
  • Modelling the Wolbachia incompatible insect technique: strategies for effective mosquito population elimination
    BMC Biol. (IF 6.765) Pub Date : 2020-11-06
    D. E. Pagendam; B. J. Trewin; N. Snoad; S. A. Ritchie; A. A. Hoffmann; K. M. Staunton; C. Paton; N. Beebe

    The Wolbachia incompatible insect technique (IIT) shows promise as a method for eliminating populations of invasive mosquitoes such as Aedes aegypti (Linnaeus) (Diptera: Culicidae) and reducing the incidence of vector-borne diseases such as dengue, chikungunya and Zika. Successful implementation of this biological control strategy relies on high-fidelity separation of male from female insects in mass

    更新日期:2020-11-06
  • Natural food intake patterns have little synchronizing effect on peripheral circadian clocks
    BMC Biol. (IF 6.765) Pub Date : 2020-11-06
    Xiaobin Xie; Ayaka Kukino; Haley E. Calcagno; Alec M. Berman; Joseph P. Garner; Matthew P. Butler

    Circadian rhythms across mammalian tissues are coordinated by a master clock in the suprachiasmatic nucleus (SCN) that is principally entrained by light-dark cycles. Prior investigations have shown, however, that time-restricted feeding (TRF)—daily alternation of fasting and food availability—synchronizes peripheral clocks independent of the light-dark cycle and of the SCN. This has led to the idea

    更新日期:2020-11-06
  • Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes
    BMC Biol. (IF 6.765) Pub Date : 2020-11-04
    Ryan T. Bell; Yuri I. Wolf; Eugene V. Koonin

    DNA and RNA of all cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and

    更新日期:2020-11-04
  • Correction to: InsP3R-SEC5 interaction on phagosomes modulates innate immunity to Candida albicans by promoting cytosolic Ca 2+ elevation and TBK1 activity
    BMC Biol. (IF 6.765) Pub Date : 2020-11-02
    Long Yang; Wenwen Gu; King-Ho Cheung; Lan Yan; Benjamin Chun-Kit Tong; Yuanying Jiang; Jun Yang

    An amendment to this paper has been published and can be accessed via the original article.

    更新日期:2020-11-02
  • Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature
    BMC Biol. (IF 6.765) Pub Date : 2020-10-30
    Anna Maria Langmüller; Viola Nolte; Ruwansha Galagedara; Rodolphe Poupardin; Marlies Dolezal; Christian Schlötterer

    Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of

    更新日期:2020-10-30
  • The selectivity filter of the mitochondrial protein import machinery
    BMC Biol. (IF 6.765) Pub Date : 2020-10-29
    Sebastian Kreimendahl; Jan Schwichtenberg; Kathrin Günnewig; Lukas Brandherm; Joachim Rassow

    The uptake of newly synthesized nuclear-encoded mitochondrial proteins from the cytosol is mediated by a complex of mitochondrial outer membrane proteins comprising a central pore-forming component and associated receptor proteins. Distinct fractions of proteins initially bind to the receptor proteins and are subsequently transferred to the pore-forming component for import. The aim of this study was

    更新日期:2020-10-30
  • The CBP KIX domain regulates long-term memory and circadian activity
    BMC Biol. (IF 6.765) Pub Date : 2020-10-29
    Snehajyoti Chatterjee; Christopher C. Angelakos; Ethan Bahl; Joshua D. Hawk; Marie E. Gaine; Shane G. Poplawski; Anne Schneider-Anthony; Manish Yadav; Giulia S. Porcari; Jean-Christophe Cassel; K. Peter Giese; Jacob J. Michaelson; Lisa C. Lyons; Anne-Laurence Boutillier; Ted Abel

    CREB-dependent transcription necessary for long-term memory is driven by interactions with CREB-binding protein (CBP), a multi-domain protein that binds numerous transcription factors potentially affecting expression of thousands of genes. Identifying specific domain functions for multi-domain proteins is essential to understand processes such as cognitive function and circadian clocks. We investigated

    更新日期:2020-10-30
  • TRIM25 promotes Capicua degradation independently of ERK in the absence of ATXN1L
    BMC Biol. (IF 6.765) Pub Date : 2020-10-28
    Derek Wong; Lisa Sogerer; Samantha S. Lee; Victor Wong; Amy Lum; Adrian B. Levine; Marco A. Marra; Stephen Yip

    Aberrations in Capicua (CIC) have recently been implicated as a negative prognostic factor in a multitude of cancer types through the derepression of targets downstream of the mitogen-activated protein kinase (MAPK) signaling cascade, such as oncogenic E26 transformation-specific (ETS) transcription factors. The Ataxin-family protein ATXN1L has previously been reported to interact with CIC in both

    更新日期:2020-10-30
  • Adaptive, diverse and de-centralized diagnostics are key to the future of outbreak response
    BMC Biol. (IF 6.765) Pub Date : 2020-10-28
    Quinn Matthews; Severino Jefferson Ribeiro da Silva; Masoud Norouzi; Lindomar José Pena; Keith Pardee

    The global spread of SARS-CoV-2 has shaken our health care and economic systems, prompting re-evaluation of long-held views on how best to deliver care. This is especially the case for our global diagnostic strategy. While current laboratory-based centralized RT-qPCR will continue to serve as a gold standard diagnostic into the foreseeable future, the shortcomings of our dependence on this method have

    更新日期:2020-10-30
  • Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy
    BMC Biol. (IF 6.765) Pub Date : 2020-10-28
    Kouta Mayanagi; Keisuke Oki; Naoyuki Miyazaki; Sonoko Ishino; Takeshi Yamagami; Kosuke Morikawa; Kenji Iwasaki; Daisuke Kohda; Tsuyoshi Shirai; Yoshizumi Ishino

    DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3′-5′ editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually

    更新日期:2020-10-30
  • Hyperactivated Wnt-β-catenin signaling in the absence of sFRP1 and sFRP5 disrupts trophoblast differentiation through repression of Ascl2
    BMC Biol. (IF 6.765) Pub Date : 2020-10-27
    Haili Bao; Dong Liu; Yingchun Xu; Yang Sun; Change Mu; Yongqin Yu; Chunping Wang; Qian Han; Sanmei Liu; Han Cai; Fan Liu; Shuangbo Kong; Wenbo Deng; Bin Cao; Haibin Wang; Qiang Wang; Jinhua Lu

    Wnt signaling is a critical determinant for the maintenance and differentiation of stem/progenitor cells, including trophoblast stem cells during placental development. Hyperactivation of Wnt signaling has been shown to be associated with human trophoblast diseases. However, little is known about the impact and underlying mechanisms of excessive Wnt signaling during placental trophoblast development

    更新日期:2020-10-30
  • Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)
    BMC Biol. (IF 6.765) Pub Date : 2020-10-26
    Irene Julca; Marina Marcet-Houben; Fernando Cruz; Jèssica Gómez-Garrido; Brandon S. Gaut; Concepción M. Díez; Ivo G. Gut; Tyler S. Alioto; Pablo Vargas; Toni Gabaldón

    Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event

    更新日期:2020-10-26
  • Unbiased PCR-free spatio-temporal mapping of the mtDNA mutation spectrum reveals brain region-specific responses to replication instability
    BMC Biol. (IF 6.765) Pub Date : 2020-10-23
    Emilie Kristine Bagge; Noriko Fujimori-Tonou; Mie Kubota-Sakashita; Takaoki Kasahara; Tadafumi Kato

    The accumulation of mtDNA mutations in different tissues from various mouse models has been widely studied especially in the context of mtDNA mutation-driven ageing but has been confounded by the inherent limitations of the most widely used approaches. By implementing a method to sequence mtDNA without PCR amplification prior to library preparation, we map the full unbiased mtDNA mutation spectrum

    更新日期:2020-10-26