Journals

Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning

PLOS Biology (new articles) - Fri, 2019-05-17 23:00

by Carlos M. Guardia, Raffaella De Pace, Aritra Sen, Amra Saric, Michal Jarnik, David A. Kolin, Ambarish Kunwar, Juan S. Bonifacino

We report the development and characterization of a method, named reversible association with motor proteins (RAMP), for manipulation of organelle positioning within the cytoplasm. RAMP consists of coexpressing in cultured cells (i) an organellar protein fused to the streptavidin-binding peptide (SBP) and (ii) motor, neck, and coiled-coil domains from a plus-end–directed or minus-end–directed kinesin fused to streptavidin. The SBP–streptavidin interaction drives accumulation of organelles at the plus or minus end of microtubules, respectively. Importantly, competition of the streptavidin–SBP interaction by the addition of biotin to the culture medium rapidly dissociates the motor construct from the organelle, allowing restoration of normal patterns of organelle transport and distribution. A distinctive feature of this method is that organelles initially accumulate at either end of the microtubule network in the initial state and are subsequently released from this accumulation, allowing analyses of the movement of a synchronized population of organelles by endogenous motors.
Categories: Biology, Journals

mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels

PLOS Biology (new articles) - Fri, 2019-05-17 23:00

by Ofri Levi, Yoav Arava

Aminoacyl-tRNA synthetases (aaRSs) are well studied for their role in binding and charging tRNAs with cognate amino acids. Recent RNA interactome studies had suggested that these enzymes can also bind polyadenylated RNAs. Here, we explored the mRNA repertoire bound by several yeast aaRSs. RNA immunoprecipitation (RIP) followed by deep sequencing revealed unique sets of mRNAs bound by each aaRS. Interestingly, for every tested aaRSs, a preferential association with its own mRNA was observed, suggesting an autoregulatory process. Self-association of histidyl-tRNA synthetase (HisRS) was found to be mediated primarily through binding to a region predicted to fold into a tRNAHis anticodon-like structure. Introducing point mutations that are expected to disassemble this putative anticodon mimic alleviated self-association, concomitant with increased synthesis of the protein. Finally, we found that increased cellular levels of uncharged tRNAHis lead to reduced self-association and increased HisRS translation, in a manner that depends on the anticodon-like element. Together, these results reveal a novel post-transcriptional autoregulatory mechanism that exploits binding mimicry to control mRNA translation according to tRNA demands.
Categories: Biology, Journals

Dysfunctional peripheral T follicular helper cells dominate in people with impaired influenza vaccine responses: Results from the FLORAH study

PLOS Biology (new articles) - Fri, 2019-05-17 23:00

by Suresh Pallikkuth, Lesley R. de Armas, Stefano Rinaldi, Varghese K. George, Li Pan, Kristopher L. Arheart, Rajendra Pahwa, Savita Pahwa

Antigen-primed cluster of differentiation (CD) 4+ T follicular helper (Tfh) cells interact with B cells in the germinal centers (GCs) of lymph nodes to generate vaccine-induced antibody (Ab) responses. In the circulation, peripheral Tfh (pTfh) cells, a subset of memory CD4 T cells, serve as surrogates for GC Tfh because of several functional and phenotypic similarities between them. We investigated features of H1N1 influenza antigen-specific pTfh (Ag.pTfh) in virologically controlled HIV+ volunteers on antiretroviral therapy (ART) and healthy control (HC) participants selected from a seasonal influenza vaccine responsiveness study. Selection of the participants was made based on age, defined as young (18–40 y) and old (>60 y) and on their classification as a vaccine responder (VR) or vaccine nonresponder (VNR). VRs demonstrated expansion of CD40L+ and CD69+ Ag.pTfh, with induction of intracellular interleukin 21 (IL-21) and inducible costimulator (ICOS) post vaccination; these responses were strongest in young HC VRs and were less prominent in HIV+ individuals of all ages. Ag.pTfh in VNRs exhibited dramatically different characteristics from VRs, displaying an altered phenotype and a cytokine profile dominated by cytokines IL-2, tumor necrosis factor alpha (TNF-α), or IL-17 but lacking in IL-21. In coculture experiments, sorted pTfh did not support the B cell IgG production in VNRs and were predominantly an inflammatory T helper 1 (Th1)/T helper 17 (Th17) phenotype with lower ICOS and higher programmed cell death protein 1 (PD1) expression. IL-21 and ICOS on Ag.pTfh cells are negatively affected by both aging and HIV infection. Our findings demonstrate that dysfunctional Ag.pTfh cells with an altered IL-21/IL-2 axis contribute to inadequate vaccine responses. Approaches for targeting inflammation or expanding functional Tfh may improve vaccine responses in aging and those aging with HIV infection.
Categories: Biology, Journals

Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies

PLOS Biology (new articles) - Thu, 2019-05-16 23:00

by Yung-Heng Chang, Richard M. Keegan, Lisa Prazak, Josh Dubnau

Evidence is rapidly mounting that transposable element (TE) expression and replication may impact biology more widely than previously thought. This includes potential effects on normal physiology of somatic tissues and dysfunctional impacts in diseases associated with aging, such as cancer and neurodegeneration. Investigation of the biological impact of mobile elements in somatic cells will be greatly facilitated by the use of donor elements that are engineered to report de novo events in vivo. In multicellular organisms, reporter constructs demonstrating engineered long interspersed nuclear element (LINE-1; L1) mobilization have been in use for quite some time, and strategies similar to L1 retrotransposition reporter assays have been developed to report replication of Ty1 elements in yeast and mouse intracisternal A particle (IAP) long terminal repeat (LTR) retrotransposons in cultivated cells. We describe a novel approach termed cellular labeling of endogenous retrovirus replication (CLEVR), which reports replication of the gypsy element within specific cells in vivo in Drosophila. The gypsy-CLEVR reporter reveals gypsy replication both in cell culture and in individual neurons and glial cells of the aging adult fly. We also demonstrate that the gypsy-CLEVR replication rate is increased when the short interfering RNA (siRNA) silencing system is genetically disrupted. This CLEVR strategy makes use of universally conserved features of retroviruses and should be widely applicable to other LTR retrotransposons, endogenous retroviruses (ERVs), and exogenous retroviruses.
Categories: Biology, Journals

Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation

PLOS Biology (new articles) - Thu, 2019-05-16 23:00

by David McAdams, Kristofer Wollein Waldetoft, Christine Tedijanto, Marc Lipsitch, Sam P. Brown

Rapid point-of-care resistance diagnostics (POC-RD) are a key tool in the fight against antibiotic resistance. By tailoring drug choice to infection genotype, doctors can improve treatment efficacy while limiting costs of inappropriate antibiotic prescription. Here, we combine epidemiological theory and data to assess the potential of resistance diagnostics (RD) innovations in a public health context, as a means to limit or even reverse selection for antibiotic resistance. POC-RD can be used to impose a nonbiological fitness cost on resistant strains by enabling diagnostic-informed treatment and targeted interventions that reduce resistant strains’ opportunities for transmission. We assess this diagnostic-imposed fitness cost in the context of a spectrum of bacterial population biologies and find that POC-RD have a greater potential against obligate pathogens than opportunistic pathogens already subject to selection under “bystander” antibiotic exposure during asymptomatic carriage (e.g., the pneumococcus). We close by generalizing the notion of RD-informed strategies to incorporate carriage surveillance information and illustrate that coupling transmission-control interventions to the discovery of resistant strains in carriage can potentially select against resistance in a broad range of opportunistic pathogens.
Categories: Biology, Journals

Intact but empty forests? Patterns of hunting-induced mammal defaunation in the tropics

PLOS Biology (new articles) - Tue, 2019-05-14 23:00

by Ana Benítez-López, Luca Santini, Aafke M. Schipper, Michela Busana, Mark A. J. Huijbregts

Tropical forests are increasingly degraded by industrial logging, urbanization, agriculture, and infrastructure, with only 20% of the remaining area considered intact. However, this figure does not include other, more cryptic but pervasive forms of degradation, such as overhunting. Here, we quantified and mapped the spatial patterns of mammal defaunation in the tropics using a database of 3,281 mammal abundance declines from local hunting studies. We simultaneously accounted for population abundance declines and the probability of local extirpation of a population as a function of several predictors related to human accessibility to remote areas and species’ vulnerability to hunting. We estimated an average abundance decline of 13% across all tropical mammal species, with medium-sized species being reduced by >27% and large mammals by >40%. Mammal populations are predicted to be partially defaunated (i.e., declines of 10%–100%) in ca. 50% of the pantropical forest area (14 million km2), with large declines (>70%) in West Africa. According to our projections, 52% of the intact forests (IFs) and 62% of the wilderness areas (WAs) are partially devoid of large mammals, and hunting may affect mammal populations in 20% of protected areas (PAs) in the tropics, particularly in West and Central Africa and Southeast Asia. The pervasive effects of overhunting on tropical mammal populations may have profound ramifications for ecosystem functioning and the livelihoods of wild-meat-dependent communities, and underscore that forest coverage alone is not necessarily indicative of ecosystem intactness. We call for a systematic consideration of hunting effects in (large-scale) biodiversity assessments for more representative estimates of human-induced biodiversity loss.
Categories: Biology, Journals

Simple nutrients bypass the requirement for HLH-30 in coupling lysosomal nutrient sensing to survival

PLOS Biology (new articles) - Tue, 2019-05-14 23:00

by John T. Murphy, Haiyan Liu, Xiucui Ma, Alex Shaver, Brian M. Egan, Clara Oh, Alexander Boyko, Travis Mazer, Samuel Ang, Rohan Khopkar, Ali Javaheri, Sandeep Kumar, Xuntian Jiang, Daniel Ory, Kartik Mani, Scot J. Matkovich, Kerry Kornfeld, Abhinav Diwan

Lysosomes are ubiquitous acidified organelles that degrade intracellular and extracellular material trafficked via multiple pathways. Lysosomes also sense cellular nutrient levels to regulate target of rapamycin (TOR) kinase, a signaling enzyme that drives growth and suppresses activity of the MiT/TFE family of transcription factors that control biogenesis of lysosomes. In this study, we subjected worms lacking basic helix–loop–helix transcription factor 30 (hlh-30), the Caenorhabditis elegans MiT/TFE ortholog, to starvation followed by refeeding to understand how this pathway regulates survival with variable nutrient supply. Loss of HLH-30 markedly impaired survival in starved larval worms and recovery upon refeeding bacteria. Remarkably, provision of simple nutrients in a completely defined medium (C. elegans maintenance medium [CeMM]), specifically glucose and linoleic acid, restored lysosomal acidification, TOR activation, and survival with refeeding despite the absence of HLH-30. Worms deficient in lysosomal lipase 2 (lipl-2), a lysosomal enzyme that is transcriptionally up-regulated in starvation in an HLH-30–dependent manner, also demonstrated increased mortality with starvation–refeeding that was partially rescued with glucose, suggesting a critical role for LIPL-2 in lipid metabolism under starvation. CeMM induced transcription of vacuolar proton pump subunits in hlh-30 mutant worms, and knockdown of vacuolar H+-ATPase 12 (vha-12) and its upstream regulator, nuclear hormone receptor 31 (nhr-31), abolished the rescue with CeMM. Loss of Ras-related GTP binding protein C homolog 1 RAGC-1, the ortholog for mammalian RagC/D GTPases, conferred starvation–refeeding lethality, and RAGC-1 overexpression was sufficient to rescue starved hlh-30 mutant worms, demonstrating a critical need for TOR activation with refeeding. These results show that HLH-30 activation is critical for sustaining survival during starvation–refeeding stress via regulating TOR. Glucose and linoleic acid bypass the requirement for HLH-30 in coupling lysosome nutrient sensing to survival.
Categories: Biology, Journals

Islands of retroelements are major components of <i>Drosophila</i> centromeres

PLOS Biology (new articles) - Tue, 2019-05-14 23:00

by Ching-Ho Chang, Ankita Chavan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-Ting Wu, Amanda M. Larracuente, Barbara G. Mellone

Centromeres are essential chromosomal regions that mediate kinetochore assembly and spindle attachments during cell division. Despite their functional conservation, centromeres are among the most rapidly evolving genomic regions and can shape karyotype evolution and speciation across taxa. Although significant progress has been made in identifying centromere-associated proteins, the highly repetitive centromeres of metazoans have been refractory to DNA sequencing and assembly, leaving large gaps in our understanding of their functional organization and evolution. Here, we identify the sequence composition and organization of the centromeres of Drosophila melanogaster by combining long-read sequencing, chromatin immunoprecipitation for the centromeric histone CENP-A, and high-resolution chromatin fiber imaging. Contrary to previous models that heralded satellite repeats as the major functional components, we demonstrate that functional centromeres form on islands of complex DNA sequences enriched in retroelements that are flanked by large arrays of satellite repeats. Each centromere displays distinct size and arrangement of its DNA elements but is similar in composition overall. We discover that a specific retroelement, G2/Jockey-3, is the most highly enriched sequence in CENP-A chromatin and is the only element shared among all centromeres. G2/Jockey-3 is also associated with CENP-A in the sister species D. simulans, revealing an unexpected conservation despite the reported turnover of centromeric satellite DNA. Our work reveals the DNA sequence identity of the active centromeres of a premier model organism and implicates retroelements as conserved features of centromeric DNA.
Categories: Biology, Journals

Simu-dependent clearance of dying cells regulates macrophage function and inflammation resolution

PLOS Biology (new articles) - Tue, 2019-05-14 23:00

by Hannah Grace Roddie, Emma Louise Armitage, Jonathon Alexis Coates, Simon Andrew Johnston, Iwan Robert Evans

Macrophages encounter and clear apoptotic cells during normal development and homeostasis, including at numerous sites of pathology. Clearance of apoptotic cells has been intensively studied, but the effects of macrophage–apoptotic cell interactions on macrophage behaviour are poorly understood. Using Drosophila embryos, we have exploited the ease of manipulating cell death and apoptotic cell clearance in this model to identify that the loss of the apoptotic cell clearance receptor Six-microns-under (Simu) leads to perturbation of macrophage migration and inflammatory responses via pathological levels of apoptotic cells. Removal of apoptosis ameliorates these phenotypes, while acute induction of apoptosis phenocopies these defects and reveals that phagocytosis of apoptotic cells is not necessary for their anti-inflammatory action. Furthermore, Simu is necessary for clearance of necrotic debris and retention of macrophages at wounds. Thus, Simu is a general detector of damaged self and represents a novel molecular player regulating macrophages during resolution of inflammation.
Categories: Biology, Journals

Rapid antigen diversification through mitotic recombination in the human malaria parasite <i>Plasmodium falciparum</i>

PLOS Biology (new articles) - Mon, 2019-05-13 23:00

by Xu Zhang, Noah Alexander, Irina Leonardi, Christopher Mason, Laura A. Kirkman, Kirk W. Deitsch

Malaria parasites possess the remarkable ability to maintain chronic infections that fail to elicit a protective immune response, characteristics that have stymied vaccine development and cause people living in endemic regions to remain at risk of malaria despite previous exposure to the disease. These traits stem from the tremendous antigenic diversity displayed by parasites circulating in the field. For Plasmodium falciparum, the most virulent of the human malaria parasites, this diversity is exemplified by the variant gene family called var, which encodes the major surface antigen displayed on infected red blood cells (RBCs). This gene family exhibits virtually limitless diversity when var gene repertoires from different parasite isolates are compared. Previous studies indicated that this remarkable genome plasticity results from extensive ectopic recombination between var genes during mitotic replication; however, the molecular mechanisms that direct this process to antigen-encoding loci while the rest of the genome remains relatively stable were not determined. Using targeted DNA double-strand breaks (DSBs) and long-read whole-genome sequencing, we show that a single break within an antigen-encoding region of the genome can result in a cascade of recombination events leading to the generation of multiple chimeric var genes, a process that can greatly accelerate the generation of diversity within this family. We also found that recombinations did not occur randomly, but rather high-probability, specific recombination products were observed repeatedly. These results provide a molecular basis for previously described structured rearrangements that drive diversification of this highly polymorphic gene family.
Categories: Biology, Journals

Transition bias influences the evolution of antibiotic resistance in <i>Mycobacterium tuberculosis</i>

PLOS Biology (new articles) - Mon, 2019-05-13 23:00

by Joshua L. Payne, Fabrizio Menardo, Andrej Trauner, Sonia Borrell, Sebastian M. Gygli, Chloe Loiseau, Sebastien Gagneux, Alex R. Hall

Transition bias, an overabundance of transitions relative to transversions, has been widely reported among studies of the rates and spectra of spontaneous mutations. However, demonstrating the role of transition bias in adaptive evolution remains challenging. In particular, it is unclear whether such biases direct the evolution of bacterial pathogens adapting to treatment. We addressed this challenge by analyzing adaptive antibiotic-resistance mutations in the major human pathogen Mycobacterium tuberculosis (MTB). We found strong evidence for transition bias in two independently curated data sets comprising 152 and 208 antibiotic-resistance mutations. This was true at the level of mutational paths (distinct adaptive DNA sequence changes) and events (individual instances of the adaptive DNA sequence changes) and across different genes and gene promoters conferring resistance to a diversity of antibiotics. It was also true for mutations that do not code for amino acid changes (in gene promoters and the 16S ribosomal RNA gene rrs) and for mutations that are synonymous to each other and are therefore likely to have similar fitness effects, suggesting that transition bias can be caused by a bias in mutation supply. These results point to a central role for transition bias in determining which mutations drive adaptive antibiotic resistance evolution in a key pathogen.
Categories: Biology, Journals

Structures suggest a mechanism for energy coupling by a family of organic anion transporters

PLOS Biology (new articles) - Mon, 2019-05-13 23:00

by Jonathan B. Leano, Samir Batarni, Jacob Eriksen, Narinobu Juge, John E. Pak, Tomomi Kimura-Someya, Yaneth Robles-Colmenares, Yoshinori Moriyama, Robert M. Stroud, Robert H. Edwards

Members of the solute carrier 17 (SLC17) family use divergent mechanisms to concentrate organic anions. Membrane potential drives uptake of the principal excitatory neurotransmitter glutamate into synaptic vesicles, whereas closely related proteins use proton cotransport to drive efflux from the lysosome. To delineate the divergent features of ionic coupling by the SLC17 family, we determined the structure of Escherichia coli D-galactonate/H+ symporter D-galactonate transporter (DgoT) in 2 states: one open to the cytoplasmic side and the other open to the periplasmic side with substrate bound. The structures suggest a mechanism that couples H+ flux to substrate recognition. A transition in the role of H+ from flux coupling to allostery may confer regulation by trafficking to and from the plasma membrane.
Categories: Biology, Journals

Cyclic AMP signalling controls key components of malaria parasite host cell invasion machinery

PLOS Biology (new articles) - Fri, 2019-05-10 23:00

by Avnish Patel, Abigail J. Perrin, Helen R. Flynn, Claudine Bisson, Chrislaine Withers-Martinez, Moritz Treeck, Christian Flueck, Giuseppe Nicastro, Stephen R. Martin, Andres Ramos, Tim W. Gilberger, Ambrosius P. Snijders, Michael J. Blackman, David A. Baker

Cyclic AMP (cAMP) is an important signalling molecule across evolution, but its role in malaria parasites is poorly understood. We have investigated the role of cAMP in asexual blood stage development of Plasmodium falciparum through conditional disruption of adenylyl cyclase beta (ACβ) and its downstream effector, cAMP-dependent protein kinase (PKA). We show that both production of cAMP and activity of PKA are critical for erythrocyte invasion, whilst key developmental steps that precede invasion still take place in the absence of cAMP-dependent signalling. We also show that another parasite protein with putative cyclic nucleotide binding sites, Plasmodium falciparum EPAC (PfEpac), does not play an essential role in blood stages. We identify and quantify numerous sites, phosphorylation of which is dependent on cAMP signalling, and we provide mechanistic insight as to how cAMP-dependent phosphorylation of the cytoplasmic domain of the essential invasion adhesin apical membrane antigen 1 (AMA1) regulates erythrocyte invasion.
Categories: Biology, Journals

Evolution, development, and organization of the cortical connectome

PLOS Biology (new articles) - Fri, 2019-05-10 23:00

by Miguel Ángel García-Cabezas, Basilis Zikopoulos

Hypotheses and theoretical frameworks are needed to organize and interpret the wealth of data on the organization of cortical networks in humans and animals in the light of development, evolution, and selective vulnerability to pathology. Goulas and colleagues compared several hypotheses of cortical network organization in 4 mammalian species and conclude that (1) the laminar pattern of cortico-cortical connections is better predicted by the Structural Model, which relates cytoarchitectonic differences of cortical areas to their interconnectedness, and (2) the existence of cortico-cortical connections is related to cytoarchitectonic differences and the physical distance between cortical areas. The predictions of the Structural Model can be applied to the human cortex, in which invasive studies are precluded. Goulas and colleagues advance interesting questions regarding the emergence of cortical structure and networks in development and evolution. Validated theories of cortical structure, development, and function can guide studies of cortical networks likely affected in neurodevelopmental disorders.
Categories: Biology, Journals

Regulation of membrane phospholipid asymmetry by Notch-mediated flippase expression controls the number of intraepithelial TCRαβ<sup>+</sup>CD8αα<sup>+</sup> T cells

PLOS Biology (new articles) - Thu, 2019-05-09 23:00

by Chieko Ishifune, Shin-ichi Tsukumo, Yoichi Maekawa, Katsuto Hozumi, Doo Hyun Chung, Chihiro Motozono, Sho Yamasaki, Hiroyasu Nakano, Koji Yasutomo

Intestinal intraepithelial lymphocytes (IELs) expressing CD8αα on αβ T cells (TCRαβ+CD8αα+ IELs) have suppressive capabilities in enterocolitis, but the mechanism that maintains homeostasis and cell number is not fully understood. Here, we demonstrated that the number of TCRαβ+CD8αα+ IELs was severely reduced in mice lacking recombination signal binding protein for immunoglobulin kappa J region (Rbpj) or Notch1 and Notch2 in T cells. Rbpj-deficient TCRαβ+CD8αα+ IELs expressed low levels of Atp8a2, which encodes a protein with flippase activity that regulates phospholipid asymmetry of plasma membrane such as flipping phosphatidylserine in the inner leaflet of plasma membrane. Rbpj-deficient TCRαβ+CD8αα+ IELs cannot maintain phosphatidylserine in the inner leaflet of the plasma membrane. Furthermore, depletion of intestinal macrophages restored TCRαβ+CD8αα+ IELs in Rbpj-deficient mice, suggesting that exposure of phosphatidylserine on the plasma membrane in Rbpj-deficient TCRαβ+CD8αα+ IELs acts as an “eat-me” signal. Together, these results revealed that Notch–Atp8a2 is a fundamental regulator for IELs and highlighted that membrane phospholipid asymmetry controlled by Notch-mediated flippase expression is a critical determinant in setting or balancing the number of TCRαβ+CD8αα+ IELs.
Categories: Biology, Journals

Fat body–specific vitellogenin expression regulates host-seeking behaviour in the mosquito <i>Aedes albopictus</i>

PLOS Biology (new articles) - Thu, 2019-05-09 23:00

by Jessica Dittmer, Ayad Alafndi, Paolo Gabrieli

The high vector competence of mosquitoes is intrinsically linked to their reproductive strategy because females need a vertebrate blood meal to develop large batches of eggs. However, the molecular mechanisms and pathways regulating mosquito host-seeking behaviour are largely unknown. Here, we test whether host-seeking behaviour may be linked to the female’s energy reserves, with low energy levels triggering the search for a nutrient-rich blood meal. Our results demonstrate that sugar feeding delays host-seeking behaviour in the invasive tiger mosquito Aedes albopictus, but the levels of energy reserves do not correlate with changes in host-seeking behaviour. Using tissue-specific gene expression analyses, we show for the first time, to our knowledge, that sugar feeding alone induces a transient up-regulation of several vitellogenesis-related genes in the female fat body, resembling the transcriptional response after a blood meal. Specifically, high expression levels of a vitellogenin gene (Vg-2) correlated with the lowest host-seeking activity of sugar-fed females. Knocking down the Vg-2 gene via RNA interference (RNAi) restored host-seeking behaviour in these females, firmly establishing that Vg-2 gene expression has a pivotal role in regulating host-seeking behaviour in young Ae. albopictus females. The identification of a molecular mechanism regulating host-seeking behaviour in mosquitoes could pave the way for novel vector control strategies aiming to reduce the biting activity of mosquitoes. From an evolutionary perspective, this is the first demonstration of vitellogenin genes controlling feeding-related behaviours in nonsocial insects, while vitellogenins are known to regulate caste-specific foraging and brood-care behaviours in eusocial insects. Hence, this work confirms the key role of vitellogenin in controlling feeding-related behaviours in distantly related insect orders, suggesting that this function could be more ubiquitous than previously thought.
Categories: Biology, Journals

Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

PLOS Biology (new articles) - Wed, 2019-05-08 23:00

by Natalya P. Degtyareva, Natalie Saini, Joan F. Sterling, Victoria C. Placentra, Leszek J. Klimczak, Dmitry A. Gordenin, Paul W. Doetsch

Redox stress is a major hallmark of cancer. Analysis of thousands of sequenced cancer exomes and whole genomes revealed distinct mutational signatures that can be attributed to specific sources of DNA lesions. Clustered mutations discovered in several cancer genomes were linked to single-strand DNA (ssDNA) intermediates in various processes of DNA metabolism. Previously, only one clustered mutational signature had been clearly associated with a subclass of ssDNA-specific apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases. Others remain to be elucidated. We report here deciphering of the mutational spectra and mutational signature of redox stress in ssDNA of budding yeast and the signature of aging in human mitochondrial DNA. We found that the predominance of C to T substitutions is a common feature of both signatures. Measurements of the frequencies of hydrogen peroxide–induced mutations in proofreading-defective yeast mutants supported the conclusion that hydrogen peroxide–induced mutagenesis is not the result of increased DNA polymerase misincorporation errors but rather is caused by direct damage to DNA. Proteins involved in modulation of chromatin status play a significant role in prevention of redox stress–induced mutagenesis, possibly by facilitating protection through modification of chromatin structure. These findings provide an opportunity for the search and identification of the mutational signature of redox stress in cancers and in other pathological conditions and could potentially be used for informing therapeutic decisions. In addition, the discovery of such signatures that may be present in related organisms should also advance our understanding of evolution.
Categories: Biology, Journals

Systematically improved in vitro culture conditions reveal new insights into the reproductive biology of the human parasite <i>Schistosoma mansoni</i>

PLOS Biology (new articles) - Wed, 2019-05-08 23:00

by Jipeng Wang, Rui Chen, James J. Collins III

Schistosomes infect over 200 million people. The prodigious egg output of these parasites is the sole driver of pathology due to infection, yet our understanding of sexual reproduction by schistosomes is limited because normal egg production is not sustained for more than a few days in vitro. Here, we describe culture conditions that support schistosome sexual development and sustained egg production in vitro. Female schistosomes rely on continuous pairing with male worms to fuel the maturation of their reproductive organs. Exploiting these new culture conditions, we explore the process of male-stimulated female maturation and demonstrate that physical contact with a male worm, and not insemination, is sufficient to induce female development and the production of viable parthenogenetic haploid embryos. We further report the characterization of a nuclear receptor (NR), which we call Vitellogenic Factor 1 (VF1), that is essential for female sexual development following pairing with a male worm. Taken together, these results provide a platform to study the fascinating sexual biology of these parasites on a molecular level, illuminating new strategies to control schistosome egg production.
Categories: Biology, Journals

<i>Feminizer</i> and <i>doublesex</i> knock-outs cause honey bees to switch sexes

PLOS Biology (new articles) - Mon, 2019-05-06 23:00

by Alison McAfee, Jeffery S. Pettis, David R. Tarpy, Leonard J. Foster

Honey bees are experts at refuting societal norms. Their matriarchal hives are headed by queens, backed by an all-female workforce, and males die soon after copulation. But the biochemical basis of how these distinct castes and sexes (queens, workers, and drones) arise is poorly understood, partly due to a lack of efficient tools for genetic manipulation. Now, Roth and colleagues have used clustered regularly interspaced short palindromic repeats (CRISPR) to knock out two key genes (feminizer and doublesex) that guide sexual development. Their technique yielded remarkably low rates of genetic mosaicism and offers a promising tool for engineering and phenotyping bees for diverse applications.
Categories: Biology, Journals

High-resolution mapping reveals that microniches in the gastric glands control <i>Helicobacter pylori</i> colonization of the stomach

PLOS Biology (new articles) - Thu, 2019-05-02 23:00

by Connie Fung, Shumin Tan, Mifuyu Nakajima, Emma C. Skoog, Luis Fernando Camarillo-Guerrero, Jessica A. Klein, Trevor D. Lawley, Jay V. Solnick, Tadashi Fukami, Manuel R. Amieva

Lifelong infection of the gastric mucosa by Helicobacter pylori can lead to peptic ulcers and gastric cancer. However, how the bacteria maintain chronic colonization in the face of constant mucus and epithelial cell turnover in the stomach is unclear. Here, we present a new model of how H. pylori establish and persist in stomach, which involves the colonization of a specialized microenvironment, or microniche, deep in the gastric glands. Using quantitative three-dimensional (3D) confocal microscopy and passive CLARITY technique (PACT), which renders tissues optically transparent, we analyzed intact stomachs from mice infected with a mixture of isogenic, fluorescent H. pylori strains with unprecedented spatial resolution. We discovered that a small number of bacterial founders initially establish colonies deep in the gastric glands and then expand to colonize adjacent glands, forming clonal population islands that persist over time. Gland-associated populations do not intermix with free-swimming bacteria in the surface mucus, and they compete for space and prevent newcomers from establishing in the stomach. Furthermore, bacterial mutants deficient in gland colonization are outcompeted by wild-type (WT) bacteria. Finally, we found that host factors such as the age at infection and T-cell responses control bacterial density within the glands. Collectively, our results demonstrate that microniches in the gastric glands house a persistent H. pylori reservoir, which we propose replenishes the more transient bacterial populations in the superficial mucosa.
Categories: Biology, Journals