Articles

Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many org...

Authors: Ni-Chiao Tsai, Tzu-Shu Hsu, Shang-Che Kuo, Chung-Ting Kao, Tzu-Huan Hung, Da-Gin Lin, Chung-Shu Yeh, Chia-Chen Chu, Jeng-Shane Lin, Hsin-Hung Lin, Chia-Ying Ko, Tien-Hsien Chang, Jung-Chen Su and Ying-Chung Jimmy Lin

Control of vein-forming, striped gene expression by auxin signaling

Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals,...

Authors: Anmol Krishna, Jason Gardiner, Tyler J. Donner and Enrico Scarpella

Self-organising human gonads generated by a Matrigel-based gradient system

Advances in three-dimensional culture technologies have led to progression in systems used to model the gonadal microenvironment in vitro. Despite demonstrating basic functionality, tissue organisation is ofte...

Authors: Elizabeth Oliver, João Pedro Alves-Lopes, Femke Harteveld, Rod T. Mitchell, Elisabet Åkesson, Olle Söder and Jan-Bernd Stukenborg

Viviparity and habitat restrictions may influence the evolution of male reproductive genes in tsetse fly (Glossina) species

Glossina species (tsetse flies), the sole vectors of African trypanosomes, maintained along their long evolutionary history a unique reproductive strategy, adenotrophic viviparity. Viviparity reduces their reprod...

Authors: Grazia Savini, Francesca Scolari, Lino Ometto, Omar Rota-Stabelli, Davide Carraretto, Ludvik M. Gomulski, Giuliano Gasperi, Adly M. M. Abd-Alla, Serap Aksoy, Geoffrey M. Attardo and Anna R. Malacrida

Species co-occurrence and management intensity modulate habitat preferences of forest birds

Species co-occurrences can have profound effects on the habitat use of species, and therefore habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organizat...

Authors: Marco Basile, Thomas Asbeck, João M. Cordeiro Pereira, Grzegorz Mikusiński and Ilse Storch

Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Authors: 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…

Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability

Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variabili...

Authors: Guillaume Le Goc, Julie Lafaye, Sophia Karpenko, Volker Bormuth, Raphaël Candelier and Georges Debrégeas

Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model

Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of ...

Authors: Hanako Ono, Yasuhito Arai, Eisaku Furukawa, Daichi Narushima, Tetsuya Matsuura, Hiromi Nakamura, Daisuke Shiokawa, Momoko Nagai, Toshio Imai, Koshi Mimori, Koji Okamoto, Yoshitaka Hippo, Tatsuhiro Shibata and Mamoru Kato

Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous s...

Authors: C. P. Stelzer, J. Blommaert, A. M. Waldvogel, M. Pichler, B. Hecox-Lea and D. B. Mark Welch

Insights into the evolutionary origin of the pineal color discrimination mechanism from the river lamprey

Pineal-related organs in cyclostomes, teleosts, amphibians, and reptiles exhibit color opponency, generating antagonistic neural responses to different wavelengths of light and thereby sensory information abou...

Authors: Seiji Wada, Emi Kawano-Yamashita, Tomohiro Sugihara, Satoshi Tamotsu, Mitsumasa Koyanagi and Akihisa Terakita

Competition-based screening helps to secure the evolutionary stability of a defensive microbiome

The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, ...

Authors: Sarah F. Worsley, Tabitha M. Innocent, Neil A. Holmes, Mahmoud M. Al-Bassam, Morten Schiøtt, Barrie Wilkinson, J. Colin Murrell, Jacobus J. Boomsma, Douglas W. Yu and Matthew I. Hutchings

Lepidoptera demonstrate the relevance of Murray’s Law to circulatory systems with tidal flow

Murray’s Law, which describes the branching architecture of bifurcating tubes, predicts the morphology of vessels in many amniotes and plants. Here, we use insects to explore the universality of Murray’s Law a...

Authors: Sandra R. Schachat, C. Kevin Boyce, Jonathan L. Payne and David Lentink

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation

Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms o...

Authors: Jana Sperschneider, Ashley W. Jones, Jamila Nasim, Bo Xu, Silke Jacques, Chengcheng Zhong, Narayana M. Upadhyaya, Rohit Mago, Yiheng Hu, Melania Figueroa, Karam B. Singh, Eric A. Stone, Benjamin Schwessinger, Ming-Bo Wang, Jennifer M. Taylor and Peter N. Dodds

Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

The world’s fast disappearing mangrove forests have low plant diversity and are often assumed to also have a species-poor insect fauna. We here compare the tropical arthropod fauna across a freshwater swamp an...

Authors: Darren Yeo, Amrita Srivathsan, Jayanthi Puniamoorthy, Foo Maosheng, Patrick Grootaert, Lena Chan, Benoit Guénard, Claas Damken, Rodzay A. Wahab, Ang Yuchen and Rudolf Meier

Caenorhabditis elegans exhibits positive gravitaxis

Gravity plays an important role in most life forms on Earth. Yet, a complete molecular understanding of sensing and responding to gravity is lacking. While there are anatomical differences among animals, there...

Authors: Wei-Long Chen, Hungtang Ko, Han-Sheng Chuang, David M. Raizen and Haim H. Bau

Single-cell analysis at the protein level delineates intracellular signaling dynamic during hematopoiesis

Hematopoietic stem and progenitor cell (HSPC) subsets in mice have previously been studied using cell surface markers, and more recently single-cell technologies. The recent revolution of single-cell analysis ...

Authors: Jinheng Wang, Chenggong Tu, Hui Zhang, Yongliang Huo, Eline Menu and Jinbao Liu

An increase of phosphatidylcholines in follicular fluid implies attenuation of embryo quality on day 3 post-fertilization

Although oocyte quality is the dominant factor determining embryo quality, few studies have been conducted to evaluate embryo quality based on the metabolites related to the oocyte. With quantification of the ...

Authors: Ju Wang, Wei Zheng, Shuoping Zhang, Keqiang Yan, Miao Jin, Huiling Hu, Zhen Ma, Fei Gong, Guangxiu Lu, Yan Ren, Liang Lin, Ge Lin, Liang Hu and Siqi Liu

Pathologic tau conformer ensembles induce dynamic, liquid-liquid phase separation events at the nuclear envelope

The microtubule-associated protein tau forms aggregates in different neurodegenerative diseases called tauopathies. Prior work has shown that a single P301L mutation in tau gene, MAPT, can promote alternative tau...

Authors: Sang-Gyun Kang, Zhuang Zhuang Han, Nathalie Daude, Emily McNamara, Serene Wohlgemuth, Laura Molina-Porcel, Jiri G. Safar, Sue-Ann Mok and David Westaway

Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis

Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Functions of the noncodi...

Authors: Hemakumar M. Reddy, Rupa Bhattacharya, Shrish Tiwari, Kankadeb Mishra, Pranatharthi Annapurna, Zeenath Jehan, Nissankararao Mary Praveena, Jomini Liza Alex, Vishnu M. Dhople, Lalji Singh, Mahadevan Sivaramakrishnan, Anurag Chaturvedi, Nandini Rangaraj, Thomas Michael Shiju, Badanapuram Sreedevi, Sachin Kumar…

Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep

Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Me...

Authors: Bingru Zhao, Hanpeng Luo, Junmin He, Xixia Huang, Siqian Chen, Xuefeng Fu, Weidan Zeng, Yuezhen Tian, Shuli Liu, Cong-jun Li, George E. Liu, Lingzhao Fang, Shengli Zhang and Kechuan Tian

Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection

The biophysics of an organism span multiple scales from subcellular to organismal and include processes characterized by spatial properties, such as the diffusion of molecules, cell migration, and flow of intr...

Authors: T. J. Sego, Josua O. Aponte-Serrano, Juliano F. Gianlupi and James A. Glazier

Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins

QconCATs are quantitative concatamers for proteomic applications that yield stoichiometric quantities of sets of stable isotope-labelled internal standards. However, changing a QconCAT design, for example, to ...

Authors: James Johnson, Victoria M. Harman, Catarina Franco, Edward Emmott, Nichola Rockliffe, Yaqi Sun, Lu-Ning Liu, Ayako Takemori, Nobuaki Takemori and Robert J. Beynon

ACBD3 modulates KDEL receptor interaction with PKA for its trafficking via tubulovesicular carrier

KDEL receptor helps establish cellular equilibrium in the early secretory pathway by recycling leaked ER-chaperones to the ER during secretion of newly synthesized proteins. Studies have also shown that KDEL r...

Authors: Xihua Yue, Yi Qian, Lianhui Zhu, Bopil Gim, Mengjing Bao, Jie Jia, Shuaiyang Jing, Yijing Wang, Chuanting Tan, Francesca Bottanelli, Pascal Ziltener, Sunkyu Choi, Piliang Hao and Intaek Lee

Inheritance of the reduced mitochondria of Giardia intestinalis is coupled to the flagellar maturation cycle

The presence of mitochondria is a distinguishing feature between prokaryotic and eukaryotic cells. It is currently accepted that the evolutionary origin of mitochondria coincided with the formation of eukaryot...

Authors: Pavla Tůmová, Luboš Voleman, Andreas Klingl, Eva Nohýnková, Gerhard Wanner and Pavel Doležal

A pair of long intergenic non-coding RNA LINC00887 variants act antagonistically to control Carbonic Anhydrase IX transcription upon hypoxia in tongue squamous carcinoma progression

Long noncoding RNAs (lncRNAs) are important regulators in tumor progression. However, their biological functions and underlying mechanisms in hypoxia adaptation remain largely unclear.

Authors: Tao Shen, Wangxiao Xia, Sainan Min, Zixuan Yang, Lehua Cheng, Wei Wang, Qianxi Zhan, Fanghong Shao, Xuehan Zhang, Zhiyu Wang, Yan Zhang, Guodong Shen, Huafeng Zhang, Li-Ling Wu, Guang-Yan Yu, Qing-Peng Kong…

Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis

Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct ef...

Authors: Nazreen F. Hadjirin, Eric L. Miller, Gemma G. R. Murray, Phung L. K. Yen, Ho D. Phuc, Thomas M. Wileman, Juan Hernandez-Garcia, Susanna M. Williamson, Julian Parkhill, Duncan J. Maskell, Rui Zhou, Nahuel Fittipaldi, Marcelo Gottschalk, A. W. ( Dan) Tucker, Ngo Thi Hoa, John J. Welch…

Urban bat pups take after their mothers and are bolder and faster learners than rural pups

Urbanization is rapidly changing our planet and animals that live in urban environments must quickly adjust their behavior. One of the most prevalent behavioral characteristics of urban dwelling animals is an ...

Authors: Lee Harten, Nesim Gonceer, Michal Handel, Orit Dash, H. Bobby Fokidis and Yossi Yovel

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species

The identification of open chromatin regions and transcription factor binding sites (TFBs) is an important step in understanding the regulation of gene expression in diverse species. ATAC-seq is a technique us...

Authors: Lianggang Huang, Xuejie Li, Liangbo Dong, Bin Wang and Li Pan

Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

A number of cellular processes have evolved in metazoans that increase the proteome repertoire in relation to the genome, such as alternative splicing and translation recoding. Another such process, translatio...

Authors: Yunpo Zhao, Bo Gustav Lindberg, Shiva Seyedoleslami Esfahani, Xiongzhuo Tang, Stefano Piazza and Ylva Engström

The ATPase SRCAP is associated with the mitotic apparatus, uncovering novel molecular aspects of Floating-Harbor syndrome

A variety of human genetic diseases is known to be caused by mutations in genes encoding chromatin factors and epigenetic regulators, such as DNA or histone modifying enzymes and members of ATP-dependent chrom...

Authors: Giovanni Messina, Yuri Prozzillo, Francesca Delle Monache, Maria Virginia Santopietro, Maria Teresa Atterrato and Patrizio Dimitri

Transcription-dependent confined diffusion of enzymes within subcellular spaces of the bacterial cytoplasm

Knowledge on the localization and mobility of enzymes inside bacterial cells is scarce, but important for understanding spatial regulation of metabolism. The four central enzymes (Rib enzymes) of the riboflavi...

Authors: Daniel A. O. Rotter, Christoph Heger, Luis M. Oviedo-Bocanegra and Peter L. Graumann

Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

Speed and trajectory of locomotion are the characteristic traits of individual species. Locomotion kinematics may have been shaped during evolution towards increased survival in the habitats of each species. A...

Authors: Yuji Matsuo, Akinao Nose and Hiroshi Kohsaka

Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular di...

Authors: Charles Ross Lindsey, Frank Rosenzweig and Matthew D. Herron

Asymmetric expansions of FT and TFL1 lineages characterize differential evolution of the EuPEBP family in the major angiosperm lineages

In flowering plants, precise timing of the floral transition is crucial to maximize chances of reproductive success, and as such, this process has been intensively studied. FLOWERING LOCUS T (FT) and TERMINAL ...

Authors: Tom Bennett and Laura E. Dixon

Single-cell analysis of cell fate bifurcation in the chordate Ciona

Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted ...

Authors: Konner M. Winkley, Wendy M. Reeves and Michael T. Veeman

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding

The L-arginine/agmatine transporter AdiC is part of the arginine-dependent extreme acid resistance system of the bacterium Escherichia coli and its pathogenic varieties such as strain E. coli O157:H7. At the pres...

Authors: Hüseyin Ilgü, Jean-Marc Jeckelmann, David Kalbermatter, Zöhre Ucurum, Thomas Lemmin and Dimitrios Fotiadis

Genus-level evolutionary relationships of FAR proteins reflect the diversity of lifestyles of free-living and parasitic nematodes

Nematodes are a widespread and diverse group comprising free-living and parasitic species, some of which have major detrimental effects on crops, animals, and human health. Genomic comparisons of nematodes may...

Authors: Dongjuan Yuan, Song Li, Ziyu Shang, Muchun Wan, Yu Lin, Yanhua Zhang, Yaoyu Feng, Lian Xu and Lihua Xiao

Apomixis and genetic background affect distinct traits in Hieracium pilosella L. grown under competition

Apomixis, the asexual reproduction through seeds, occurs in over 40 plant families and avoids the hidden cost of sex. Apomictic plants are thought to have an advantage in sparse populations and when colonizing...

Authors: Christian Sailer, Simone Tiberi, Bernhard Schmid, Jürg Stöcklin and Ueli Grossniklaus

Molecular and morphological analysis of the developing nemertean brain indicates convergent evolution of complex brains in Spiralia

The brain anatomy in the clade Spiralia can vary from simple, commissural brains (e.g., gastrotrichs, rotifers) to rather complex, partitioned structures (e.g., in cephalopods and annelids). How often and in w...

Authors: Ludwik Gąsiorowski, Aina Børve, Irina A. Cherneva, Andrea Orús-Alcalde and Andreas Hejnol

The role of the odorant receptors in the formation of the sensory map

In the olfactory system, odorant receptors (ORs) expressed at the cell membrane of olfactory sensory neurons detect odorants and direct sensory axons toward precise target locations in the brain, reflected in ...

Authors: Simona Francia and Claudia Lodovichi

Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata

Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastroint...

Authors: Shweta V. Pipaliya, Rui Santos, Dayana Salas-Leiva, Erina A. Balmer, Corina D. Wirdnam, Andrew J. Roger, Adrian B. Hehl, Carmen Faso and Joel B. Dacks

FGF-2 promotes angiogenesis through a SRSF1/SRSF3/SRPK1-dependent axis that controls VEGFR1 splicing in endothelial cells

Angiogenesis is the process by which new blood vessels arise from pre-existing ones. Fibroblast growth factor-2 (FGF-2), a leading member of the FGF family of heparin-binding growth factors, contributes to nor...

Authors: Tao Jia, Thibault Jacquet, Fabien Dalonneau, Pauline Coudert, Elisabeth Vaganay, Chloé Exbrayat-Héritier, Julien Vollaire, Véronique Josserand, Florence Ruggiero, Jean-Luc Coll and Béatrice Eymin

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba

Authors: Nicole Gruenheit, Amy Baldwin, Balint Stewart, Sarah Jaques, Thomas Keller, Katie Parkinson, William Salvidge, Robert Baines, Chris Brimson, Jason B. Wolf, Rex Chisholm, Adrian J. Harwood and Christopher R. L. Thompson

A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis

Beneficial associations between plants and microbes are widespread in nature and have been studied extensively in the microbial-dominant environment of the rhizosphere. Such associations are highly advantageou...

Authors: Ena Šečić, Silvia Zanini, Daniel Wibberg, Lukas Jelonek, Tobias Busche, Jörn Kalinowski, Sabrine Nasfi, Jennifer Thielmann, Jafargholi Imani, Jens Steinbrenner and Karl-Heinz Kogel

An economical and highly adaptable optogenetics system for individual and population-level manipulation of Caenorhabditis elegans

Optogenetics allows the experimental manipulation of excitable cells by a light stimulus without the need for technically challenging and invasive procedures. The high degree of spatial, temporal, and intensit...

Authors: M. Koopman, L. Janssen and E. A. A. Nollen

Starvation-induced cell fusion and heterokaryosis frequently escape imperfect allorecognition systems in an asexual fungal pathogen

Asexual fungi include important pathogens of plants and other organisms, and their effective management requires understanding of their evolutionary dynamics. Genetic recombination is critical for adaptability...

Authors: Vasileios Vangalis, Ilya Likhotkin, Michael Knop, Milton A. Typas and Ioannis A. Papaioannou

An alternating active-dormitive strategy enables disadvantaged prey to outcompete the perennially active prey through Parrondo’s paradox

Dormancy is widespread in nature, but while it can be an effective adaptive strategy in fluctuating environments, the dormant forms are costly due to the inability to breed and the relatively high energy consu...

Authors: Tao Wen, Eugene V. Koonin and Kang Hao Cheong

Pitx controls amphioxus asymmetric morphogenesis by promoting left-side development and repressing right-side formation

Left-right (LR) asymmetry is an essential feature of bilateral animals. Studies in vertebrates show that LR asymmetry formation comprises three major steps: symmetry breaking, asymmetric gene expression, and L...

Authors: Chaofan Xing, Rongrong Pan, Guangwei Hu, Xian Liu, Yiquan Wang and Guang Li

Invasive snails, parasite spillback, and potential parasite spillover drive parasitic diseases of Hippopotamus amphibius in artificial lakes of Zimbabwe

Humans impose a significant pressure on large herbivore populations, such as hippopotami, through hunting, poaching, and habitat destruction. Anthropogenic pressures can also occur indirectly, such as artifici...

Authors: Ruben Schols, Hans Carolus, Cyril Hammoud, Kudzai C. Muzarabani, Maxwell Barson and Tine Huyse

The relationship between sternum variation and mode of locomotion in birds

The origin of powered avian flight was a locomotor innovation that expanded the ecological potential of maniraptoran dinosaurs, leading to remarkable variation in modern birds (Neornithes). The avian sternum i...

Authors: Talia M. Lowi-Merri, Roger B. J. Benson, Santiago Claramunt and David C. Evans