BMC BIOLOGY 是一本涵盖生物学所有领域的广泛期刊。我们的内容包括研究文章、新方法和工具。 BMC BIOLOGY 还发布评论、问答和评论。

BMC Biology is a comprehensive journal that covers all areas of biology. We publish research articles, introductions to new methods and tools, as well as reviews, Q&A, and commentaries.

BMC Biology 是一本涵盖生物学各个领域的综合性期刊。我们提供研究文章、新方法和工具的介绍，同时也发布评论、问答和综述文章。

BMC Biology

Abstract Background The synthetic chemical 1,4-dioxane is used as industrial solvent, food, and care product additive. 1,4-Dioxane has been noted to influence the nervous system in long-term animal experiments and in humans, but the molecular mechanisms underlying its effects on animals were not previously known. Results Here, we report that 1,4-dioxane potentiates the capsaicin-sensitive transient receptor potential (TRP) channel TRPV1, thereby causing hyperalgesia in mouse model. This effect was abolished by CRISPR/Cas9-mediated genetic deletion of TRPV1 in sensory neurons, but enhanced under inflammatory conditions. 1,4-Dioxane lowered the temperature threshold for TRPV1 thermal activation and potentiated the channel sensitivity to agonistic stimuli. 1,3-dioxane and tetrahydrofuran which are structurally related to 1,4-dioxane also potentiated TRPV1 activation. The residue M572 in the S4-S5 linker region of TRPV1 was found to be crucial for direct activation of the channel by 1,4-dioxane and its analogs. A single residue mutation M572V abrogated the 1,4-dioxane-evoked currents while largely preserving the capsaicin responses. Our results further demonstrate that this residue exerts a gating effect through hydrophobic interactions and support the existence of discrete domains for multimodal gating of TRPV1 channel. Conclusions Our results suggest TRPV1 is a co-receptor for 1,4-dioxane and that this accounts for its ability to dysregulate body nociceptive sensation.

Xiaoyi Mo

Qiang Liu

Luna Gao

Chang Xie

Xin Wei

Peiyuan Pang

Quan Tian

Yue Gao

Youjing Zhang

Yuanyuan Wang

Tianchen Xiong

Bo Zhong

Dongdong Li

Jing Yao

The industrial solvent 1,4-dioxane causes hyperalgesia by targeting capsaicin receptor TRPV1

tRFs, 14 to 32 nt long single-stranded RNA derived from mature or precursor tRNAs, are a recently discovered class of small RNA that have been found to be present in diverse organisms at read counts comparable to miRNAs. Currently, there is a debate about their biogenesis and function.This is the first meta-analysis of tRFs. Analysis of more than 50 short RNA libraries has revealed that tRFs are precisely generated fragments present in all domains of life (bacteria to humans), and are not produced by the miRNA biogenesis pathway. Human PAR-CLIP data shows a striking preference for tRF-5s and tRF-3s to associate with AGO1, 3 and 4 rather than AGO2, and analysis of positional T to C mutational frequency indicates these tRFs associate with Argonautes in a manner similar to miRNAs. The reverse complements of canonical seed positions in these sequences match cross-link centered regions, suggesting these tRF-5s and tRF-3s interact with RNAs in the cell. Consistent with these results, human AGO1 CLASH data contains thousands of tRF-5 and tRF-3 reads chimeric with mRNAs.tRFs are an abundant class of small RNA present in all domains of life whose biogenesis is distinct from miRNAs. In human HEK293 cells tRFs associate with Argonautes 1, 3 and 4 and not Argonaute 2 which is the main effector protein of miRNA function, but otherwise have very similar properties to miRNAs, indicating tRFs may play a major role in RNA silencing.

Pankaj Kumar

Jordan Anaya

Suresh B Mudunuri

Anindya Dutta

BMC Biol

Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets

tRNA衍生RNA片段的Meta分析揭示其具有进化保守性并与AGO蛋白结合以识别特定RNA靶标

Abstract Background Verticillium wilt, caused by the fungus Verticillium dahliae , is a soil-borne vascular fungal disease, which has caused great losses to cotton yield and quality worldwide. The strain KRS010 was isolated from the seed of Verticillium wilt-resistant Gossypium hirsutum cultivar “Zhongzhimian No. 2.” Results The strain KRS010 has a broad-spectrum antifungal activity to various pathogenic fungi as Verticillium dahliae , Botrytis cinerea , Fusarium spp., Colletotrichum spp., and Magnaporthe oryzae , of which the inhibition rate of V. dahliae mycelial growth was 73.97% and 84.39% respectively through confrontation test and volatile organic compounds (VOCs) treatments. The strain was identified as Bacillus altitudinis by phylogenetic analysis based on complete genome sequences, and the strain physio-biochemical characteristics were detected, including growth-promoting ability and active enzymes. Moreover, the control efficiency of KRS010 against Verticillium wilt of cotton was 93.59%. After treatment with KRS010 culture, the biomass of V. dahliae was reduced. The biomass of V. dahliae in the control group (Vd991 alone) was 30.76-folds higher than that in the treatment group (KRS010+Vd991). From a molecular biological aspect, KRS010 could trigger plant immunity by inducing systemic resistance (ISR) activated by salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Its extracellular metabolites and VOCs inhibited the melanin biosynthesis of V. dahliae . In addition, KRS010 had been characterized as the ability to promote plant growth. Conclusions This study indicated that B. altitudinis KRS010 is a beneficial microbe with a potential for controlling Verticillium wilt of cotton, as well as promoting plant growth.

Yujia Shan

Dan Wang

Fu-Hua Zhao

Jian Song

He Zhu

Yue Li

Xiao-Jun Zhang

Xiao-Feng Dai

Dongfei Han

Jie-Yin Chen

Insights into the biocontrol and plant growth promotion functions of Bacillus altitudinis strain KRS010 against Verticillium dahliae

解淀粉芽孢杆菌KRS010株对大丽轮枝菌的生物防治及植物促生功能研究

Abstract Background 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 the difference in eye size between D. mauritiana and its sibling species D. simulans. Results We confirmed that D. mauritiana have rapidly evolved larger eyes as a result of more and wider ommatidia than D. simulans since they recently diverged approximately 240,000 years ago. The functional impact of eye size, and specifically ommatidia size, is often only estimated based on the rigid surface morphology of the compound eye. Therefore, we used 3D synchrotron radiation tomography to measure optical parameters in 3D, predict optical capacity, and compare the modelled vision to in vivo optomotor responses. Our optical models predicted higher contrast sensitivity for D. mauritiana , which we verified by presenting sinusoidal gratings to tethered flies in a flight arena. Similarly, we confirmed the higher spatial acuity predicted for Drosophila simulans with smaller ommatidia and found evidence for higher temporal resolution. Conclusions Our study demonstrates that even subtle differences in ommatidia size between closely related Drosophila species can impact the vision of these insects. Therefore, further comparative studies of intra- and interspecific variation in eye morphology and the consequences for vision among other Drosophila species, other dipterans and other insects are needed to better understand compound eye structure–function and how the diversification of eye size, shape, and function has helped insects to adapt to the vast range of ecological niches.

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

Evolution of compound eye morphology underlies differences in vision between closely related Drosophila species

复眼形态的演化在近缘果蝇物种视觉差异中的作用

Abstract The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.

Sanzhima Garmaeva

Trishla Sinha

Alexander Kurilshikov

Jingyuan Fu

Cisca Wijmenga

Alexandra Zhernakova

Studying the gut virome in the metagenomic era: challenges and perspectives

在宏基因组学时代研究肠道病毒组：挑战与展望

Abstract Background The harmonious operation of many insect societies depends upon colony-wide dissemination of a non-volatile pheromone produced by a single queen, which informs workers of her presence. This represents a major challenge in large colonies. Honeybee colonies, which can exceed 60,000 bees, are believed to solve this challenge using ‘messenger’ workers that actively relay the queen pheromone throughout the hive. However, little is known about the structure and effectiveness of the underlying relay network or the biology of messaging. Results Here, we combine automated tracking with modelling to address these outstanding questions. We find that both queen movement and worker messaging play fundamental roles in queen pheromone dissemination. Fine-grained analyses of worker behaviour confirmed the existence of active messaging, as physical contacts with the queen caused workers to move faster and straighter, thereby accelerating pheromone transmission. Finally, we show that messaging follows a stereotypical developmental trajectory, resulting in an age-dependent hierarchical relay network, with the most intense messaging observed between three and five days of age, when workers undergo a suite of physiological changes associated with queen rearing. Conclusions These results suggest that the individuals that contribute most to advertising the presence of the queen are also the ones that control queen production.

Thomas O. Richardson

Tomas Kay

Laurent Keller

Nathalie Stroeymeyt

Pheromone relay networks in the honeybee: messenger workers distribute the queen’s fertility signal throughout the hive

蜜蜂中的信息素接力网络：信使工蜂在整个蜂巢中传递蜂王的生育信号

Abstract Background Plastids are usually involved in photosynthesis, but the secondary loss of this function is a widespread phenomenon in various lineages of algae and plants. In addition to the loss of genes associated with photosynthesis, the plastid genomes of colorless algae are frequently reduced further. To understand the pathways of reductive evolution associated with the loss of photosynthesis, it is necessary to study a number of closely related strains. Prototheca , a chlorophyte genus of facultative pathogens, provides an excellent opportunity to study this process with its well-sampled array of diverse colorless strains. Results We have sequenced the plastid genomes of 13 Prototheca strains and reconstructed a comprehensive phylogeny that reveals evolutionary patterns within the genus and among its closest relatives. Our phylogenomic analysis revealed three independent losses of photosynthesis among the Prototheca strains and varied protein-coding gene content in their ptDNA. Despite this diversity, all Prototheca strains retain the same key plastid functions. These include processes related to gene expression, as well as crucial roles in fatty acid and cysteine biosynthesis, and membrane transport. Conclusions The retention of vestigial genomes in colorless plastids is typically associated with the biosynthesis of secondary metabolites. In contrast, the remarkable conservation of plastid membrane transport system components in the nonphotosynthetic genera Prototheca and Helicosporidium provides an additional constraint against the loss of ptDNA in this lineage. Furthermore, these genes can potentially serve as targets for therapeutic intervention, indicating their importance beyond the evolutionary context.

Kacper Maciszewski

Gabriela Wilga

Tomasz Jagielski

Zofia Bakuła

Jan Gawor

Robert Gromadka

Anna Karnkowska

Reduced plastid genomes of colorless facultative pathogens Prototheca (Chlorophyta) are retained for membrane transport genes

无色兼性病原菌原藻（绿藻门）的简化质体基因组保留了膜转运基因

The mutualistic beneficial relationship between legume plants and rhizobia enables the growth of plants in nitrogen-limiting conditions. Rhizobia infect legumes through root hairs and trigger nodule organogenesis in the cortex. The plant hormone cytokinin plays a pivotal role in regulating both rhizobial infection and the initiation of nodule development. However, the mechanism used by the cytokinin output module to control symbiosis remains poorly documented. In this study, we identified a cytokinin signaling output component encoded by the Type-B RESPONSE REGULATOR (RRB) gene, LjRRB12, which is expressed in Lotus japonicus nodule primordia and young nodules. Disruption of LjRRB12 leads to a reduction in nodulation and to an increase in the number of infection threads. Overexpression of LjRRB12D76E, an active form of the LjRRB12 protein, induces nodule-like structures in wild type and hit1 (hyperinfected 1/lotus histidine kinase 1) mutants but not in nin2 (nodule inception 2) mutants. Additionally, we utilized nCUT&Tag and EMSA to demonstrate that LjRRB12 can bind a CE (cytokinin response element) from the LjNIN promoter. Our results provide a deeper understanding of nodule organogenesis by establishing a link between the cytokinin signal and the transcriptional regulation of LjNIN.

Jingjing Cao

Yu Zhou

Tao Tian

Jie Ji

Yan Deng

Yuhao Guan

Yongmei Qi

Longxiang Wang

Longlong Wang

Yibo Huang

Qiuling Fan

Deqiang Duanmu

Type-B response regulator RRB12 regulates nodule formation in Lotus japonicus

B型响应调控因子RRB12调控百脉根根瘤形成

RNA velocity, as an extension of trajectory inference, is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. However, existing RNA velocity methods are limited by the batch effect because they cannot directly correct for batch effects in the input data, which comprises spliced and unspliced matrices in a proportional relationship. This limitation can lead to an incorrect velocity stream. This paper introduces VeloVGI, which addresses this issue innovatively in two key ways. Firstly, it employs an optimal transport (OT) and mutual nearest neighbor (MNN) approach to construct neighbors in batch data. This strategy overcomes the limitations of existing methods that are affected by the batch effect. Secondly, VeloVGI improves upon VeloVI's velocity estimation by incorporating the graph structure into the encoder for more effective feature extraction. The effectiveness of VeloVGI is demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb tissue, as well as on several public datasets. The results show that VeloVGI outperformed other methods in terms of metric performance.

Zhaoyang Huang

Xinyang Guo

Jie Qin

Lin Gao

Fen Ju

Chenguang Zhao

Liang Yu

Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data

基于多批次网络的精确RNA速度估计揭示批次单细胞RNA-seq数据中的复杂谱系

The complete mitochondrial respiratory chain is a precondition for maintaining cellular energy supply, development, and metabolic balance. Due to the evolutionary differentiation of complexes and the semi-autonomy of mitochondria, respiratory chain subunits have become critical targets for crop improvement and fungal control. In fungi, mitochondrial complex I mediates growth and metabolism. However, the role of this complex in the pathogenesis of phytopathogenic fungi is largely unknown. In this study, we identified the NADH: ubiquinone oxidoreductase 24-kDa subunit (VdNuo1) of complex in vascular wilt pathogen, Verticillium dahliae, and examined its functional conservation in phytopathogenic fungi. Based on the treatments with respiratory chain inhibitors, the mitochondria-localized VdNuo1 was confirmed to regulate mitochondrial morphogenesis and homeostasis. VdNuo1 was induced during the different developmental stages in V. dahliae, including hyphal growth, conidiation, and melanized microsclerotia development. The VdNuo1 mutants displayed variable sensitivity to stress factors and decreased pathogenicity in multiple hosts, indicating that VdNuo1 is necessary in stress tolerance and full virulence. Comparative transcriptome analysis demonstrated that VdNuo1 mediates global transcriptional effects, including oxidation and reduction processes, fatty acid, sugar, and energy metabolism. These defects are partly attributed to impairments of mitochondrial morphological integrity, complex assembly, and related functions. Its homologue (CgNuo1) functions in the vegetative growth, melanin biosynthesis, and pathogenicity of Colletotrichum gloeosporioides; however, CgNuo1 does not restore the VdNuo1 mutant to normal phenotypes. Our results revealed that VdNuo1 plays important roles in growth, metabolism, microsclerotia development, stress tolerance, and virulence of V. dahliae, sharing novel insight into the function of complex I and a potential fungicide target for pathogenic fungi.

Huan Li

Ying Liu

Ya-Hong Wang

Ruo-Cheng Sheng

Zhi-Qiang Kong

Steven J. Klosterman

Krishna V. Subbarao

Feng-Mao Chen

Dan-Dan Zhang

The 24-kDa subunit of mitochondrial complex I regulates growth, microsclerotia development, stress tolerance, and virulence in Verticillium dahliae

线粒体复合物I的24-kDa亚基调控维管束轮枝菌的生长、微菌核发育、胁迫耐受性和致病性

Abbreviation	BMC Biol
Journal Impact	4.43
Quartiles(Global)	BIOLOGY(Q1)

ISSN	1741-7007
h-index	129
Top Journals	Yes

Publication Information	Publisher: BioMed Central Ltd，Publishing cycle: Irregular，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 2003，Proportion of original research papers: 98.94%，Self Citation Rate:0.00%， Gold OA Rate: 99.88%
Journal Fees	$3390Details
Average review cycle	网友分享经验：平均3.0个月
Average recruitment ratio	网友分享经验：约50%

BMC Biology

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