Articles

Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models

Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TN...

Authors: Charlène Roussel, Kim De Paepe, Wessam Galia, Jana De Bodt, Sandrine Chalancon, Françoise Leriche, Nathalie Ballet, Sylvain Denis, Monique Alric, Tom Van de Wiele and Stéphanie Blanquet-Diot

Population structure and pharmacogenomic risk stratification in the United States

Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized that genetic...

Authors: Shashwat Deepali Nagar, Andrew B. Conley and I. King Jordan

Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate

Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Our understanding of dinoflagellate toxin biosynthesis has been h...

Authors: Girish Beedessee, Takaaki Kubota, Asuka Arimoto, Koki Nishitsuji, Ross F. Waller, Kanako Hisata, Shinichi Yamasaki, Noriyuki Satoh, Jun’ichi Kobayashi and Eiichi Shoguchi

Importance of scientific collaboration in contemporary drug discovery and development: a detailed network analysis

Growing evidence shows that scientific collaboration plays a crucial role in transformative innovation in the life sciences. For example, contemporary drug discovery and development reflects the work of teams ...

Authors: Feixiong Cheng, Yifang Ma, Brian Uzzi and Joseph Loscalzo

Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus’ evolution

African swine fever virus (ASFV) is a most devastating pathogen affecting swine. In 2007, ASFV was introduced into Eastern Europe where it continuously circulates and recently reached Western Europe and Asia, ...

Authors: Jan H. Forth, Leonie F. Forth, Samantha Lycett, Lesley Bell-Sakyi, Günther M. Keil, Sandra Blome, Sébastien Calvignac-Spencer, Antje Wissgott, Johannes Krause, Dirk Höper, Helge Kampen and Martin Beer

Effects of immune challenge on expression of life-history and immune trait expression in sexually reproducing metazoans—a meta-analysis

Life-history theory predicts a trade-off between investment into immune defence and other fitness-related traits. Accordingly, individuals are expected to upregulate their immune response when subjected to imm...

Authors: M. Nystrand and D. K. Dowling

Suprachiasmatic nucleus-dependent and independent outputs driving rhythmic activity in hypothalamic and thalamic neurons

Daily variations in mammalian physiology are under control of a central clock in the suprachiasmatic nucleus (SCN). SCN timing signals are essential for coordinating cellular clocks and associated circadian va...

Authors: Court Harding, David A. Bechtold and Timothy M. Brown

Deleterious mutations show increasing negative effects with age in Drosophila melanogaster

In order for aging to evolve in response to a declining strength of selection with age, a genetic architecture that allows for mutations with age-specific effects on organismal performance is required. Our und...

Authors: Martin I. Brengdahl, Christopher M. Kimber, Phoebe Elias, Josephine Thompson and Urban Friberg

Retargeting azithromycin analogues to have dual-modality antimalarial activity

Resistance to front-line antimalarials (artemisinin combination therapies) is spreading, and development of new drug treatment strategies to rapidly kill Plasmodium spp. malaria parasites is urgently needed. Azit...

Authors: Amy L. Burns, Brad E. Sleebs, Ghizal Siddiqui, Amanda E. De Paoli, Dovile Anderson, Benjamin Liffner, Richard Harvey, James G. Beeson, Darren J. Creek, Christopher D. Goodman, Geoffrey I. McFadden and Danny W. Wilson

Functional signatures of evolutionarily young CTCF binding sites

The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. The exact mechanism and...

Authors: Dhoyazan Azazi, Jonathan M. Mudge, Duncan T. Odom and Paul Flicek

ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems

Many favorable traits of crops and livestock and human genetic diseases arise from multiple single nucleotide polymorphisms or multiple point mutations with heterogeneous base substitutions at the same locus. ...

Authors: Jingke Xie, Xingyun Huang, Xia Wang, Shixue Gou, Yanhui Liang, Fangbing Chen, Nan Li, Zhen Ouyang, Quanjun Zhang, Weikai Ge, Qin Jin, Hui Shi, Zhenpeng Zhuang, Xiaozhu Zhao, Meng Lian, Jiaowei Wang…

Deep learning-enabled analysis reveals distinct neuronal phenotypes induced by aging and cold-shock

Access to quantitative information is crucial to obtain a deeper understanding of biological systems. In addition to being low-throughput, traditional image-based analysis is mostly limited to error-prone qual...

Authors: Sahand Saberi-Bosari, Kevin B. Flores and Adriana San-Miguel

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages ...

Authors: Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke and Marc Robinson-Rechavi

Genetic modifiers ameliorate endocytic and neuromuscular defects in a model of spinal muscular atrophy

Understanding the genetic modifiers of neurodegenerative diseases can provide insight into the mechanisms underlying these disorders. Here, we examine the relationship between the motor neuron disease spinal m...

Authors: Melissa B. Walsh, Eva Janzen, Emily Wingrove, Seyyedmohsen Hosseinibarkooie, Natalia Rodriguez Muela, Lance Davidow, Maria Dimitriadi, Erika M. Norabuena, Lee L. Rubin, Brunhilde Wirth and Anne C. Hart

A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems

Plastid electron transport systems are essential not only for photosynthesis but also for dissipating excess reducing power and sinking excess electrons generated by various redox reactions. Although numerous ...

Authors: Motoki Kayama, Jun-Feng Chen, Takashi Nakada, Yoshiki Nishimura, Toshiharu Shikanai, Tomonori Azuma, Hideaki Miyashita, Shinichi Takaichi, Yuichiro Kashiyama and Ryoma Kamikawa

Altered brain-wide auditory networks in a zebrafish model of fragile X syndrome

Loss or disrupted expression of the FMR1 gene causes fragile X syndrome (FXS), the most common monogenetic form of autism in humans. Although disruptions in sensory processing are core traits of FXS and autism, t...

Authors: Lena Constantin, Rebecca E. Poulsen, Leandro A. Scholz, Itia A. Favre-Bulle, Michael A. Taylor, Biao Sun, Geoffrey J. Goodhill, Gilles C. Vanwalleghem and Ethan K. Scott

Independent glial subtypes delay development and extend healthy lifespan upon reduced insulin-PI3K signalling

The increasing age of global populations highlights the urgent need to understand the biological underpinnings of ageing. To this end, inhibition of the insulin/insulin-like signalling (IIS) pathway can extend...

Authors: Nathaniel S. Woodling, Arjunan Rajasingam, Lucy J. Minkley, Alberto Rizzo and Linda Partridge

A molecular insight into the dissociable regulation of associative learning and motivation by the synaptic protein neuroligin-1

In a changing environment, a challenge for the brain is to flexibly guide adaptive behavior towards survival. Complex behavior and the underlying neural computations emerge from the structural components of th...

Authors: Jiaqi Luo, Jessica M. Tan and Jess Nithianantharajah

Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

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

Authors: Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps…

Mechanical force-induced morphology changes in a human fungal pathogen

The initial step of a number of human or plant fungal infections requires active penetration of host tissue. For example, active penetration of intestinal epithelia by Candida albicans is critical for disseminati...

Authors: Charles Puerner, Nino Kukhaleishvili, Darren Thomson, Sebastien Schaub, Xavier Noblin, Agnese Seminara, Martine Bassilana and Robert A. Arkowitz

Some like it hot: population-specific adaptations in venom production to abiotic stressors in a widely distributed cnidarian

In cnidarians, antagonistic interactions with predators and prey are mediated by their venom, whose synthesis may be metabolically expensive. The potentially high cost of venom production has been hypothesized...

Authors: Maria Y. Sachkova, Jason Macrander, Joachim M. Surm, Reuven Aharoni, Shelcie S. Menard-Harvey, Amy Klock, Whitney B. Leach, Adam M. Reitzel and Yehu Moran

Novel developmental bases for the evolution of hypobranchial muscles in vertebrates

Vertebrates are characterized by possession of hypobranchial muscles (HBMs). Cyclostomes, or modern jawless vertebrates, possess a rudimentary and superficial HBM lateral to the pharynx, whereas the HBM in jaw...

Authors: Rie Kusakabe, Shinnosuke Higuchi, Masako Tanaka, Mitsutaka Kadota, Osamu Nishimura and Shigeru Kuratani

Call order within vocal sequences of meerkats contains temporary contextual and individual information

The ability to recombine smaller units to produce infinite structures of higher-order phrases is unique to human language, yet evidence of animals to combine multiple acoustic units into meaningful combination...

Authors: Ramona Rauber, Bart Kranstauber and Marta B. Manser

Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress responses

The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport, and degradation within a cell. Failure to maintain proteostasis is associated with aging and disease, le...

Authors: Katherine E. Larrimore, Natalia S. Barattin-Voynova, David W. Reid and Davis T. W. Ng

Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression

Colorectal cancer (CRC) development is generally accepted as a sequential process, with genetic mutations determining phenotypic tumor progression. However, matching genetic profiles with histological transiti...

Authors: Soulafa Mamlouk, Tincy Simon, Laura Tomás, David C. Wedge, Alexander Arnold, Andrea Menne, David Horst, David Capper, Markus Morkel, David Posada, Christine Sers and Hendrik Bläker

CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of rRNA

Modification of RNAs, particularly at the terminals, is critical for various essential cell processes; for example, uridylation is implicated in tumorigenesis, proliferation, stem cell maintenance, and immune ...

Authors: Yun Wang, Chenchun Weng, Xiangyang Chen, Xufei Zhou, Xinya Huang, Yonghong Yan and Chengming Zhu

LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data

Bacterial resistance to antibiotics is a growing health problem that is projected to cause more deaths than cancer by 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the avai...

Authors: Benedict Hew, Qiao Wen Tan, William Goh, Jonathan Wei Xiong Ng and Marek Mutwil

Machine-learning strategies for testing patterns of morphological variation in small samples: sexual dimorphism in gray wolf (Canis lupus) crania

Studies of mammalian sexual dimorphism have traditionally involved the measurement of selected dimensions of particular skeletal elements and use of single data-analysis procedures. Consequently, such studies ...

Authors: Norman MacLeod and Liora Kolska Horwitz

Modified nucleic acids: replication, evolution, and next-generation therapeutics

Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics....

Authors: Karen Duffy, Sebastian Arangundy-Franklin and Philipp Holliger

Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions

Cytidine base editors (CBEs), composed of a cytidine deaminase fused to Cas9 nickase (nCas9), enable efficient C-to-T conversion in various organisms. However, current base editors can induce unwanted bystande...

Authors: Zhiquan Liu, Siyu Chen, Huanhuan Shan, Yingqi Jia, Mao Chen, Yuning Song, Liangxue Lai and Zhanjun Li

Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions

To successfully invade new hosts, plant viruses must break host resistance and be competent to move within and between plant cells. As a means, viral proteins known as pathogenicity determinants have evolved t...

Authors: Ashwin Nair, Kiran Sankar Chatterjee, Vikram Jha, Ranabir Das and P. V. Shivaprasad

Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes

Endocrine cells of the zebrafish digestive system play an important role in regulating metabolism and include pancreatic endocrine cells (PECs) clustered in the islets of Langerhans and the enteroendocrine cel...

Authors: Arnaud Lavergne, Estefania Tarifeño-Saldivia, Justine Pirson, Anne-Sophie Reuter, Lydie Flasse, Isabelle Manfroid, Marianne L. Voz and Bernard Peers

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals

Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiom...

Authors: Judith Neukamm, Saskia Pfrengle, Martyna Molak, Alexander Seitz, Michael Francken, Partick Eppenberger, Charlotte Avanzi, Ella Reiter, Christian Urban, Beatrix Welte, Philipp W. Stockhammer, Barbara Teßmann, Alexander Herbig, Katerina Harvati, Kay Nieselt, Johannes Krause…

Excess diacylglycerol at the endoplasmic reticulum disrupts endomembrane homeostasis and autophagy

When stressed, eukaryotic cells produce triacylglycerol (TAG) to store nutrients and mobilize autophagy to combat internal damage. We and others previously reported that in yeast, elimination of TAG synthesizi...

Authors: Dan Li, Shu-Gao Yang, Cheng-Wen He, Zheng-Tan Zhang, Yongheng Liang, Hui Li, Jing Zhu, Xiong Su, Qingqiu Gong and Zhiping Xie

Machine learning approaches identify male body size as the most accurate predictor of species richness 

A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness –the number of different species in a community or region - among comparable taxonomic...

Authors: Klemen Čandek, Urška Pristovšek Čandek and Matjaž Kuntner

Nutritional status impacts dengue virus infection in mice

Dengue virus (DENV) is estimated to infect 390 million people annually. However, few host factors that alter disease severity are known. Malnutrition, defined as both over- and undernutrition, is a growing pro...

Authors: Christina Chuong, Tyler A. Bates, Shamima Akter, Stephen R. Werre, Tanya LeRoith and James Weger-Lucarelli

Extreme mobility of the world’s largest flying mammals creates key challenges for management and conservation

Effective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. F...

Authors: Justin A. Welbergen, Jessica Meade, Hume E. Field, Daniel Edson, Lee McMichael, Luke P. Shoo, Jenny Praszczalek, Craig Smith and John M. Martin

Using spatial genetics to quantify mosquito dispersal for control programs

Hundreds of millions of people get a mosquito-borne disease every year and nearly one million die. Transmission of these infections is primarily tackled through the control of mosquito vectors. The accurate qu...

Authors: Igor Filipović, Hapuarachchige Chanditha Hapuarachchi, Wei-Ping Tien, Muhammad Aliff Bin Abdul Razak, Caleb Lee, Cheong Huat Tan, Gregor J. Devine and Gordana Rašić

Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets

The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the functio...

Authors: Matthew J. Robertson, Katarzyna Kent, Nathan Tharp, Kaori Nozawa, Laura Dean, Michelle Mathew, Sandra L. Grimm, Zhifeng Yu, Christine Légaré, Yoshitaka Fujihara, Masahito Ikawa, Robert Sullivan, Cristian Coarfa, Martin M. Matzuk and Thomas X. Garcia

Association of Bacteroides acidifaciens relative abundance with high-fibre diet-associated radiosensitisation

Patients with pelvic malignancies often receive radiosensitising chemotherapy with radiotherapy to improve survival; however, this is at the expense of increased normal tissue toxicity, particularly in elderly...

Authors: Chee Kin Then, Salome Paillas, Xuedan Wang, Alix Hampson and Anne E. Kiltie

Reengineering anthrax toxin protective antigen for improved receptor-specific protein delivery

To increase the size of the druggable proteome, it would be highly desirable to devise efficient methods to translocate designed binding proteins to the cytosol, as they could specifically target flat and hydr...

Authors: Lukas Becker, Wouter P. R. Verdurmen and Andreas Plückthun

The role of vegetative cell fusions in the development and asexual reproduction of the wheat fungal pathogen Zymoseptoria tritici

The ability of fungal cells to undergo cell-to-cell communication and anastomosis, the process of vegetative hyphal fusion, allows them to maximize their overall fitness. Previous studies in a number of fungal...

Authors: Carolina Sardinha Francisco, Maria Manuela Zwyssig and Javier Palma-Guerrero

Modelling the suppression of a malaria vector using a CRISPR-Cas9 gene drive to reduce female fertility

Gene drives based on CRISPR-Cas9 technology are increasingly being considered as tools for reducing the capacity of mosquito populations to transmit malaria, and one of the most promising options is driving en...

Authors: Ace R. North, Austin Burt and H. Charles J. Godfray

Genome-wide pQTL analysis of protein expression regulatory networks in the human liver

Previous expression quantitative trait loci (eQTL) studies have identified thousands of genetic variants to be associated with gene expression at the mRNA level in the human liver. However, protein expression ...

Authors: Bing He, Jian Shi, Xinwen Wang, Hui Jiang and Hao-Jie Zhu

The C-terminal region of the oxidoreductase MIA40 stabilizes its cytosolic precursor during mitochondrial import

The mitochondrial intermembrane space (IMS) is home to proteins fulfilling numerous essential cellular processes, particularly in metabolism and mitochondrial function. All IMS proteins are nuclear encoded and...

Authors: Lena Maria Murschall, Anne Gerhards, Thomas MacVicar, Esra Peker, Lidwina Hasberg, Stephan Wawra, Thomas Langer and Jan Riemer

Impact of COVID-19 on early career scientists: an optimistic guide for the future

Authors: Christina M. Termini and David Traver

Genetic background mutations drive neural circuit hyperconnectivity in a fragile X syndrome model

Neural circuits are initially assembled during development when neurons synapse with potential partners and later refined as appropriate connections stabilize into mature synapses while inappropriate contacts ...

Authors: Tyler Kennedy, David Rinker and Kendal Broadie

A simple threat-detection strategy in mice

Avoiding danger and accessing environmental resources are two fundamental, yet conflicting, survival instincts across species. To maintain a balance between these instincts, animals must efficiently distinguis...

Authors: Xing Yang, Qingqing Liu, Jinling Zhong, Ru Song, Lin Zhang and Liping Wang

Correction to: Improving the usability and comprehensiveness of microbial databases

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

Authors: Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki and Serghei Mangul

Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Polydnaviruses (PDVs) are mutualistic endogenous viruses inoculated by some lineages of parasitoid wasps into their hosts, where they facilitate successful wasp development. PDVs include the ichnoviruses and b...

Authors: Fabrice Legeai, Bernardo F. Santos, Stéphanie Robin, Anthony Bretaudeau, Rebecca B. Dikow, Claire Lemaitre, Véronique Jouan, Marc Ravallec, Jean-Michel Drezen, Denis Tagu, Frédéric Baudat, Gabor Gyapay, Xin Zhou, Shanlin Liu, Bruce A. Webb, Seán G. Brady…