Articles

Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana

Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. P...

Authors: Sony Kumari, Sandeep Yadav, Debadutta Patra, Sharmila Singh, Ananda K. Sarkar and Kishore C. S. Panigrahi

Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes

Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target ...

Authors: Fazhe Yan, Xuelin Yu, Zhongqu Duan, Jinyuan Lu, Ben Jia, Yuyang Qiao, Chen Sun and Chaochun Wei

Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. Although its usage grows every year, little is known on this plant’s geno...

Authors: Matteo Schiavinato, Richard Strasser, Lukas Mach, Juliane C. Dohm and Heinz Himmelbauer

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies

Anti-CD3 immunotherapy was initially approved for clinical use for renal transplantation rejection prevention. Subsequently, new generations of anti-CD3 antibodies have entered clinical trials for a broader sp...

Authors: Isabel Garcia Sousa, Kelly Cristina Rodrigues Simi, Manuela Maragno do Almo, Maryani Andressa Gomes Bezerra, Gero Doose, Tainá Raiol, Peter F. Stadler, Steve Hoffmann, Andréa Queiroz Maranhão and Marcelo Macedo Brigido

Honey bee (Apis mellifera) larval pheromones may regulate gene expression related to foraging task specialization

Foraging behavior in honey bees (Apis mellifera) is a complex phenotype that is regulated by physiological state and social signals. How these factors are integrated at the molecular level to modulate foraging be...

Authors: Rong Ma, Juliana Rangel and Christina M. Grozinger

geneHummus: an R package to define gene families and their expression in legumes and beyond

During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technolo...

Authors: Jose V. Die, Moamen M. Elmassry, Kimberly H. LeBlanc, Olaitan I. Awe, Allissa Dillman and Ben Busby

The first evidence of global meat phosphoproteome changes in response to pre-slaughter stress

Pre-slaughter stress (PSS) impairs animal welfare and meat quality. Dark, firm and dry (DFD) are terms used to designate poor quality meats induced by PSS. Protein phosphorylation can be a potentially signific...

Authors: Ariadna Mato, Raquel Rodríguez-Vázquez, María López-Pedrouso, Susana Bravo, Daniel Franco and Carlos Zapata

Transcriptome profiling of Puccinellia tenuiflora during seed germination under a long-term saline-alkali stress

Puccinellia tenuiflora is the most saline-alkali tolerant plant in the Songnen Plain, one of the three largest soda saline-alkali lands worldwide. Here, we investigated the physicochemical properties of saline-al...

Authors: Xiaoxue Ye, Hao Wang, Xiuling Cao, Xuejiao Jin, Fuqiang Cui, Yuanyuan Bu, Hua Liu, Wenwu Wu, Tetsuo Takano and Shenkui Liu

Analysis of the equine “cumulome” reveals major metabolic aberrations after maturation in vitro

Maturation of oocytes under in vitro conditions (IVM) results in impaired developmental competence compared to oocytes matured in vivo. As oocytes are closely coupled to their cumulus complex, elucidating aber...

Authors: Jasmin Walter, Fabian Huwiler, Claudia Fortes, Jonas Grossmann, Bernd Roschitzki, Junmin Hu, Hanspeter Naegeli, Endre Laczko and Ulrich Bleul

Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

Atrazine is widely used in agriculture and is a known endocrine disrupting chemical. Atrazine can seep into the water body through surface, posing a potential threat to the aquatic ecological environment and h...

Authors: Fang Wang, Qian-wen Yang, Wen-Jie Zhao, Qi-Yan Du and Zhong-Jie Chang

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food i...

Authors: Abdul Fatah A. Samad, Reyhaneh Rahnamaie-Tajadod, Muhammad Sajad, Jaeyres Jani, Abdul Munir Abdul Murad, Normah Mohd Noor and Ismanizan Ismail

Systematic analysis of the lysine succinylome in the model medicinal mushroom Ganoderma lucidum

Ganoderma lucidum, one of the best-known medicinal mushrooms in the world, produces more than 400 different bioactive compounds. However, the regulation of these bioactive compounds biosynthesis is still unclear....

Authors: Guangyuan Wang, Lili Xu, Hao Yu, Jie Gao and Lizhong Guo

Relation between DNA ionization potentials, single base substitutions and pathogenic variants

It is nowadays clear that single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, d...

Authors: Fabrizio Pucci and Marianne Rooman

VarI-COSI 2018: a forum for research advances in variant interpretation and diagnostics

Authors: Yana Bromberg, Emidio Capriotti and Hannah Carter

Assessing cell-specific effects of genetic variations using tRNA microarrays

By definition, effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid. Recent examples indicate tissue-specif...

Authors: Christine Polte, Daniel Wedemeyer, Kathryn E. Oliver, Johannes Wagner, Marcel J. C. Bijvelds, John Mahoney, Hugo R. de Jonge, Eric J. Sorscher and Zoya Ignatova

PhenPath: a tool for characterizing biological functions underlying different phenotypes

Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or ...

Authors: Giulia Babbi, Pier Luigi Martelli and Rita Casadio

Benchmarking subcellular localization and variant tolerance predictors on membrane proteins

Membrane proteins constitute up to 30% of the human proteome. These proteins have special properties because the transmembrane segments are embedded into lipid bilayer while extramembranous parts are in differ...

Authors: Tommaso Orioli and Mauno Vihinen

Recurrent miscalling of missense variation from short-read genome sequence data

Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels...

Authors: Matthew A. Field, Gaetan Burgio, Aaron Chuah, Jalila Al Shekaili, Batool Hassan, Nashat Al Sukaiti, Simon J. Foote, Matthew C. Cook and T. Daniel Andrews

A clinically validated whole genome pipeline for structural variant detection and analysis

With the continuing decrease in cost of whole genome sequencing (WGS), we have already approached the point of inflection where WGS testing has become economically feasible, facilitating broader access to the ...

Authors: Nir Neerman, Gregory Faust, Naomi Meeks, Shira Modai, Limor Kalfon, Tzipora Falik-Zaccai and Alexander Kaplun

What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization

Egg quality can be defined as the egg ability to be fertilized and subsequently develop into a normal embryo. Previous research has shed light on factors that can influence egg quality. Large gaps however rema...

Authors: Caroline T. Cheung, Thao-vi Nguyen, Aurélie Le Cam, Amélie Patinote, Laurent Journot, Christelle Reynes and Julien Bobe

Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

The synthetic 17α-ethinylestradiol (EE2) is a common estrogenic pollutant that has been suspected to affect the demography of river-dwelling salmonids. One possibility is that exposure to EE2 tips the balance ...

Authors: Oliver M. Selmoni, Diane Maitre, Julien Roux, Laetitia G. E. Wilkins, Lucas Marques da Cunha, Etienne L. M. Vermeirssen, Susanne Knörr, Marc Robinson-Rechavi and Claus Wedekind

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are mi...

Authors: Keoni Saint-Pé, Maeva Leitwein, Laurence Tissot, Nicolas Poulet, Bruno Guinand, Patrick Berrebi, Geoffrey Marselli, Jean-Marc Lascaux, Pierre-Alexandre Gagnaire and Simon Blanchet

Transcriptional characterisation of the Exaiptasia pallida pedal disc

Biological adhesion (bioadhesion), enables organisms to attach to surfaces as well as to a range of other targets. Bioadhesion evolved numerous times independently and is ubiquitous throughout the kingdoms of ...

Authors: Peter A. Davey, Marcelo Rodrigues, Jessica L. Clarke and Nick Aldred

PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequenc...

Authors: Sean P. Gordon, Joshua J. Levy and John P. Vogel

Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers

Replication stress (RS) gives rise to DNA damage that threatens genome stability. RS can originate from different sources that stall replication by diverse mechanisms. However, the mechanism underlying how dif...

Authors: Xinxing Lyu, Megan Chastain and Weihang Chai

Screening of genes encoding adhesion factors and biofilm production in methicillin resistant strains of Staphylococcus aureus isolated from Palestinian patients

Intercellular adhesion and biofilm production by Staphylococcus aureus makes these bacteria resistant to antimicrobial therapy. Here, Methicillin-resistant Staphylococcus aureus (MRSA) strains were characterized ...

Authors: Kifaya Azmi, Walaa Qrei and Ziad Abdeen

Alternative polyadenylation produces multiple 3’ untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons

Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterizat...

Authors: Mohamed Doulazmi, Cyril Cros, Isabelle Dusart, Alain Trembleau and Caroline Dubacq

Validation of 46 loci associated with female fertility traits in cattle

Subfertility is one challenge facing the dairy industry as the average Holstein heifer conception rate (HCR), the proportion of heifers that conceive and maintain a pregnancy per breeding, is estimated at 55–6...

Authors: Jennifer N. Kiser, Elizabeth M. Keuter, Christopher M. Seabury, Mahesh Neupane, Joao G. N. Moraes, Joseph Dalton, Gregory W. Burns, Thomas E. Spencer and Holly L. Neibergs

Genome-wide identification and characterization of ABA receptor PYL/RCAR gene family reveals evolution and roles in drought stress in Nicotiana tabacum

Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regul...

Authors: Ge Bai, He Xie, Heng Yao, Feng Li, Xuejun Chen, Yihan Zhang, Bingguan Xiao, Jun Yang, Yongping Li and Da-Hai Yang

Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize

Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expressi...

Authors: Xiaocong Zhang, Sidi Xie, Jienan Han, Yu Zhou, Chang Liu, Zhiqiang Zhou, Feifei Wang, Zixiang Cheng, Junjie Zhang, Yufeng Hu, Zhuanfang Hao, Mingshun Li, Degui Zhang, Hongjun Yong, Yubi Huang, Jianfeng Weng…

Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus

The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential...

Authors: Nai-Tong Yu, Hui-Min Xie, Yu-Liang Zhang, Jian-Hua Wang, Zhongguo Xiong and Zhi-Xin Liu

De novo sequencing of tree peony (Paeonia suffruticosa) transcriptome to identify critical genes involved in flowering and floral organ development

Tree peony (Paeonia suffruticosa Andrews) is a globally famous ornamental flower, with large and colorful flowers and abundant flower types. However, a relatively short and uniform flowering period hinders the ap...

Authors: Shunli Wang, Jie Gao, Jingqi Xue, Yuqian Xue, Dandan Li, Yanren Guan and Xiuxin Zhang

Systematic evaluation of RNA-Seq preparation protocol performance

RNA-Seq is currently the most widely used tool to analyze whole-transcriptome profiles. There are numerous commercial kits available to facilitate preparing RNA-Seq libraries; however, it is still not clear ho...

Authors: Hsueh-Ping Chao, Yueping Chen, Yoko Takata, Mary W. Tomida, Kevin Lin, Jason S. Kirk, Melissa S. Simper, Carol D. Mikulec, Joyce E. Rundhaug, Susan M. Fischer, Taiping Chen, Dean G. Tang, Yue Lu and Jianjun Shen

Computer genomics research at the bioinformatics conference series in Novosibirsk

Authors: Yuriy L. Orlov, Elvira R. Galieva and Alexander V. Melerzanov

Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries

Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of various DNA regulatory elements and their mutant variants. The assays are based on construction of highly diverse plas...

Authors: Evgeniya S. Omelina, Anton V. Ivankin, Anna E. Letiagina and Alexey V. Pindyurin

The difference in serum proteomes in schizophrenia and bipolar disorder

Purpose of study is revealing significant differences in serum proteomes in schizophrenia and bipolar disorder (BD).

Authors: Liudmila Smirnova, Alexander Seregin, Irina Boksha, Elena Dmitrieva, German Simutkin, Elena Kornetova, Olga Savushkina, Anastasia Letova, Nikolay Bokhan, Svetlana Ivanova and Victor Zgoda

Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increas...

Authors: Xiao-Qing Huang, Xiao-Hong Lu, Man-Hong Sun, Rong-Jun Guo, Anne D. van Diepeningen and Shi-Dong Li

Comparative proteomic analysis of Tibetan pig spermatozoa at high and low altitudes

To illuminate the mechanisms underlying the high-altitude tolerance of Tibetan pig spermatozoa, proteomes of spermatozoa from Tibetan pigs raised in high and low altitudes were compared using a tandem mass tag...

Authors: Yanling Zhao, Xiaoli Lu, Zhipeng Cheng, Mengfang Tian, Yangzong Qiangba Qiang, Qiang Fu and Zili Ren

Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube

The bHLH (basic helix-loop-helix) transcription factor is one of the largest families of transcription factors in plants, containing a large number of members with diverse functions. Chinese jujube (Ziziphus juju...

Authors: Hongtai Li, Weilin Gao, Chaoling Xue, Yao Zhang, Zhiguo Liu, Yu Zhang, Xianwei Meng, Mengjun Liu and Jin Zhao

Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes

Sequencing of microbiomes has accelerated the characterization of the diversity of CRISPR-Cas immune systems. However, the utilization of next generation short read sequences for the characterization of CRISPR...

Authors: Tony J. Lam and Yuzhen Ye

Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level

The usage of different synonymous codons reflects the genome organization and has been connected to parameters such as mRNA abundance and protein folding. It is also been established that mutations targeting s...

Authors: Eugenio F. Fornasiero and Silvio O. Rizzoli

Genomic reconstruction of σ⁵⁴ regulons in Clostridiales

The σ⁵⁴ factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ⁵⁴ is present in many Clostridiales species that have ...

Authors: Xiaoqun Nie, Wenyue Dong and Chen Yang

Identification and differential expression analysis of anthocyanin biosynthetic genes in leaf color variants of ornamental kale

Anthocyanins perform diverse biological functions in plants and are beneficial to human health. Leaf color is the most important trait of ornamental kale and the characteristics of changes in leaf color make i...

Authors: Ning Guo, Shuo Han, Mei Zong, Guixiang Wang, Shuning Zheng and Fan Liu

Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large ...

Authors: Xin Wen, Yadong Hu, Xinyu Zhang, Xiaozhen Wei, Tao Wang and Shaowu Yin

Transcriptomic analysis of differentially expressed genes in the oviduct of Rhacophorus omeimontis provides insights into foam nest construction

The production of foam nests is one of the strategies that has evolved to allow some anuran species to protect their eggs and larvae. Despite considerable knowledge of the biochemical components of and constru...

Authors: Wei Zhang, Li Huang, Jun Li, Yinghua Li, Shichao Wei, Ling Cai and Hua Wu

Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine

Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tok...

Authors: Katlyn Borgers, Jheng-Yang Ou, Po-Xing Zheng, Petra Tiels, Annelies Van Hecke, Evelyn Plets, Gitte Michielsen, Nele Festjens, Nico Callewaert and Yao-Cheng Lin

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size ...

Authors: Marco Meola, Etienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud and Christophe Chassard

Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum

Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing...

Authors: Huiru Sun, Hengling Wei, Hantao Wang, Pengbo Hao, Lijiao Gu, Guoyuan Liu, Liang Ma, Zhengzheng Su and Shuxun Yu

Microarray analysis of infectious bronchitis virus infection of chicken primary dendritic cells

Avian infectious bronchitis virus (IBV) is a major respiratory disease-causing agent in birds that leads to significant losses. Dendritic cells (DCs) are specialised cells responsible for sampling antigens and...

Authors: Jian Lin, Zhisheng Wang, Jialu Wang and Qian Yang

Correction to: ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation

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Authors: Viktor A. Shamanskiy, Valeria N. Timonina, Konstantin Yu. Popadin and Konstantin V. Gunbin