bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of a Symptom-triggered Protocol for Alcohol Withdrawal for Use in the Emergency Department, General Medical Wards, and Intensive Care Unit
Authors: RICHMAN LISA S. , GARCIA CAROLYN , BOUCHARD NICOLE , MUSKIN PHILIP R. , DZIERBA AMY L.
Published: January 2019

Background:

Alcohol withdrawal is common in hospitalized patients and symptom-triggered guidelines have been shown to reduce treatment duration, length of stay, and need for mechanical ventilation.

Objectives:

To assess the feasibility of incorporating symptom-triggered alcohol withdrawal guidelines early in the hospital course and to evaluate outcomes of patients before and after implementation of the guidelines.

Methods:

This was a retrospective pre-post study of adult patients admitted from the emergency department to an urban, academic, tertiary care center. Subjects in the preguideline (PRE) group were given benzodiazepines in a nonprotocolized manner at the discretion of the treating physician, whereas subjects in the postguideline (POST) group were treated according to the alcohol withdrawal guidelines with treatment beginning in the emergency department.

Results:

The PRE group involved 113 admissions for severe alcohol withdrawal and the POST group involved 103 admissions for severe alcohol withdrawal. The median benzodiazepine dose per day, in milligrams of chlordiazepoxide, was higher in the POST group (100 mg in the PRE group vs. 141 mg in the POST group; P<0.02). A higher percentage of patients in the POST group were admitted to the intensive care unit (4.4% in the PRE group vs. 12.6% in the POST group; P=0.05); however, more patients in the PRE group than in the POST group received continuous intravenous sedation and mechanical ventilation, although the difference was not statistically significant (P=0.37 for both variables). There was no difference between the 2 groups in length of stay in the intensive care unit or hospital or discharge disposition.

Conclusions:

Incorporating symptom-triggered guidelines for alcohol withdrawal early in the hospital course at a large medical center is feasible. This approach may result in increased benzodiazepine use, but it seems that it is safe and does not result in adverse outcomes.
IL-10-producing B cells are enriched in murine pericardial adipose tissues and ameliorate the outcome of acute myocardial infarction
Authors: Wu Lan , Dalal Rajeev , Cao Connie , Postoak J. Luke , Zhang Qinkun , Wang Zhizhang , Lal Hind , Kaer Luc Van
Published: January 2019

Acute myocardial infarction (MI) provokes an inflammatory response in the heart that removes damaged tissues to facilitate repair. However, exaggerated and/or persistent inflammation compromises healing, which may be counteracted by regulatory immune mechanisms. A key regulatory factor in an inflammatory response is the anti-inflammatory cytokine IL-10, which can be produced by a number of immune cells including subsets of B lymphocytes. Here, we investigated IL-10-producing B cells in pericardial adipose tissues (PATs) and their role in the healing process following acute MI in mice. We found abundant IL-10-producing B cells in PATs under homeostatic conditions, with the majority of them bearing cell surface CD5 (CD5+B cells). These cells were detected early in life, maintained a steady presence during adulthood, and resided in fat-associated lymphoid clusters (FALCs). The cytokine IL-33 was preferentially expressed in PATs under homeostatic conditions and contributed to enrichment of IL-10-producing CD5+B cells in PATs. CD5+B cells expanded in PATs following MI, and accumulated in the infarcted heart during the resolution of MI-induced inflammation. B cell-specific deletion of IL-10 worsened cardiac function after MI, exacerbated myocardial injury, and delayed resolution of inflammation. These findings reveal a significant contribution of IL-10-producing B cells to the anti-inflammatory mechanism that terminates MI-induced inflammation, and identify these cells as novel therapeutic targets to improve the outcome of MI.

Significance Statement

Myocardial infarction (MI) remains a leading cause of mortality and morbidity worldwide. Although it is now recognized that a balanced and timely terminated pro-inflammatory response following acute MI is essential in promoting tissue repair, the underlying regulatory mechanisms are poorly defined. In this report, we show that IL-10-producing B cells in mice 1) are enriched in pericardial adipose tissues (PATs) and influenced by cytokine IL-33 under homeostatic conditions; 2) expand in PATs following MI and accumulate in the infarcted heart during the resolution of MI-induced inflammation; and 3) facilitate resolution of inflammation and reduce myocardial injury to preserve cardiac function after MI. These findings identify IL-10-producing B cells as novel therapeutic targets to improve the outcome of MI.
Multiple quantitative trait loci contribute tolerance to bacterial canker incited byPseudomonas syringaepv.actinidiaein kiwifruit (Actinidia chinensis)
Authors: Tahir Jibran , Hoyte Stephen , Bassett Heather , Brendolise Cyril , Chatterjee Abhishek , Templeton Kerry , Deng Cecilia , Crowhurst Ross , Montefiori Mirco , Morgan Ed , Wotton Andrew , Funnell Keith , Wiedow Claudia , Knaebel Mareike , Hedderley Duncan , Vanneste Joel , McCallum John , Hoeata Kirsten , Chagné David , Gea Luis , Gardiner Susan E.
Published: January 2019

Pseudomonas syringaepv.actinidiae(Psa) Biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidiaspp.) industry worldwide. The commercially grown diploid (2x)A. chinensisvar.chinensisis more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulatingPsaresistance in kiwifruit is not available. Here we report mapping of quantitative trait loci (QTLs) regulating tolerance to Psa in a diploid kiwifruit population, derived from a cross between an elite Psa-susceptible ‘Hort16A’ and a tolerant male breeding parent P1. Using high-density genetic maps and intensive phenotyping, we identified a single QTL for Psa tolerance on Linkage Group (LG) 27 of ‘Hort16A’ revealing 16-19% phenotypic variance and candidate alleles for susceptibility and tolerance at this loci. In addition, six minor QTLs were identified in P1 on distinct LGs, exerting 4-9% variance. Complete tolerance in the F1 population is attained by additive effects from ‘Hort16A’ and P1 QTLs providing evidence that divergent genetic pathways fend-off virulent Psa strain. Two different bioassays further identified new QTLs for tissue-specific responses to Psa. Transcriptome analysis of Psa-tolerant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening Psa tolerance.
Hybrid optical gating for long-term 3D time-lapse imaging of the beating embryonic zebrafish heart
Authors: Taylor Jonathan M. , Nelson Carl J. , Bruton Finnius A. , Baghbadrani Aryan K. , Buckley Charlotte , Tucker Carl S. , Mullins John J. , Denvir Martin A.
Published: January 2019

Three-dimensional fluorescence time-lapse imaging of structural, cellular and sub-cellular processes in the beating heart is an increasingly achievable goal using the latest imaging and computational techniques. However, previous approaches have had significant limitations. Temporarily arresting the heart using drugs disrupts the heart’s physiological state, and the use of ultra-high frame-rates for fluorescence image acquisition causes phototoxic cell damage. Real-time triggered imaging, synchronized to a specific phase in the cardiac-cycle, can computationally “freeze” the heart to acquire the minimal number of fluorescence images required for 3D time-lapse imaging. However, until now no solution has been able to maintain phase-lock to the same point in the cardiac cycle for more than about one hour. Our new hybrid optical gating system maintains phase-lock for up to 24 h, acquiring synchronized 3D+time video stacks of the unperturbed heartin vivo. This approach has enabled us to observe detailed developmental, structural, cellular and subcellular processes, including live cell division and cell fate tracking, in the embryonic zebrafish heart using transgenic fish lines expressing cell-specific fluorophores. We show that our approach not only provides high spatial and temporal resolution 3D-imaging, but also avoids phototoxic injury, where alternative approaches induce measurable harm. This provides superb cellular and subcellular imaging of the heart while it is beating in its normal physiological state, and opens up new and exciting opportunities for further study in the heart and other moving cellular and subcellular structuresin vivo.
CHAP: A versatile tool for the structural and functional annotation of ion channel pores
Authors: Klesse Gianni , Rao Shanlin , Sansom Mark S.P. , Tucker Stephen J.
Published: January 2019

The regulation of ion channel and transporter function requires the modulation of energetic barriers or ‘gates’ within their transmembrane pathways. However, despite the ever-increasing number of available structures, our understanding of these barriers is often simply determined from calculating the physical dimensions of the pore. Such approaches (e.g. the HOLE program) have worked very well in the past, but there is now considerable evidence that the unusual behaviour of water within the narrow hydrophobic spaces found within many ion channel pores can also produce energetic barriers to ion conduction without requiring physical occlusion of the permeation pathway. Several different classes of ion channels have now been shown to exploit this principle of ‘hydrophobic gating’ to regulate ion flow. However, measurement of pore radius alone is unable to identify such barriers and new tools are required for more accurate functional annotation of an exponentially increasing number of ion channel structures. We have previously shown how molecular dynamics simulations of water behaviour can be used as a proxy to accurately predict hydrophobic gates. Here we now present a new and highly versatile computational tool, the Channel Annotation Package (CHAP) that implements this methodology to predict the conductive status of new ion channel structures.
A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease
Authors: Vieira Braga F.A. , Kar G. , Berg M. , Carpaij O.A. , Polanski K. , Simon L.M. , Brouwer S. , Gomes T. , Hesse L. , Jiang J. , Fasouli E.S. , Efremova M. , Vento-Tormo R. , Affleck K. , Palit S. , Strzelecka P. , Firth H.V. , Mahbubani K.T.A. , Cvejic A. , Meyer K.B. , Saeb-Parsy K. , Luinge M. , Brandsma C.-A. , Timens W. , Angelidis I. , Strunz M. , Koppelman G.H. , van Oosterhout A.J. , Schiller H.B. , Theis F.J. , van den Berge M. , Nawijn M.C. , Teichmann S.A.
Published: January 2019

Human lungs enable efficient gas exchange, and form an interface with the environment which depends on mucosal immunity for protection against infectious agents. Tightly controlled interactions between structural and immune cells are required to maintain lung homeostasis. Here, we use single cell transcriptomics to chart the cellular landscape of upper and lower airways and lung parenchyma in health. We report location-dependent airway epithelial cell states, and a novel subset of tissue-resident memory T cells. In lower airways of asthma patients, mucous cell hyperplasia is shown to stem from a novel mucous ciliated cell state, as well as goblet cell hyperplasia. We report presence of pathogenic effector Th2 cells in asthma, and find evidence for type-2 cytokines in maintaining the altered epithelial cell states. Unbiased analysis of cell-cell interactions identify a shift from airway structural cell communication in health to a Th2-dominated interactome in asthma.
Wikipedia network analysis of cancer interactions and world influence
Authors: Rollin Guillaume , Lages José , Shepelyansky Dima L.
Published: January 2019

We apply the Google matrix algorithms for analysis of interactions and influence of 37 cancer types, 203 cancer drugs and 195 world countries using the network of 5 416 537 English Wikipedia articles with all their directed hyperlinks. The PageRank algorithm provides the importance order of cancers which has 60% and 70% overlaps with the top 10 cancers extracted from World Health Organization GLOBOCAN 2018 and Global Burden of Diseases Study 2017, respectively. The recently developed reduced Google matrix algorithm gives networks of interactions between cancers, drugs and countries taking into account all direct and indirect links between these selected 435 entities. These reduced networks allow to obtain sensitivity of countries to specific cancers and drugs. The strongest links between cancers and drugs are in good agreement with the approved medical prescriptions of specific drugs to specific cancers. We argue that this analysis of knowledge accumulated in Wikipedia provides useful complementary global information about interdependencies between cancers, drugs and world countries.
MPRAnalyze - A statistical framework for Massively Parallel Reporter Assays
Authors: Ashuach Tal , Fischer David Sebastian , Kreimer Anat , Ahituv Nadav , Theis Fabian , Yosef Nir
Published: January 2019

Massively parallel reporter assays (MPRAs) are a technique that enables testing thousands of regulatory DNA sequences and their variants in a single, quantitative experiment. Despite growing popularity, there is lack of statistical methods that account for the different sources of uncertainty inherent to these assays, thus effectively leveraging their promise. Development of such methods could help enhance our ability to identify regulatory sequences in the genome, understand their function under various setting, and ultimately gain a better understanding of how the regulatory code and its alteration lead to phenotypic consequence.

Here we present MPRAnalyze: a statistical framework dedicated to analyzing MPRA count data. MPRAnalyze addresses the major questions that are posed in the context of MPRA experiments: estimating the magnitude of the effect of a regulatory sequence in a single condition setting, and comparing differential activity of regulatory sequences across multiple conditions. The framework uses a nested construction of generalized linear models to account for uncertainty in both DNA and RNA observations, controls for various sources of unwanted variation, and incorporates negative controls for robust hypothesis testing, thereby providing clear quantitative answers in complex experimental settings.

We demonstrate the robustness, accuracy and applicability of MPR-Analyze on simulated data and published data sets and compare it against the existing analysis methodologies. MPRAnalyze is implemented as an R package and is publicly available through Bioconductor [1].
A metabolic dependency for host isoprenoids in the obligate intracellular pathogenRickettsia parkeriunderlies a sensitivity for the statin class of host-targeted therapeutics
Authors: Ahyong Vida , Berdan Charles A. , Nomura Daniel K. , Welch Matthew D.
Published: January 2019

Gram-negative bacteria in the order Rickettsiales are obligate intracellular parasites that cause human diseases such typhus and spotted fever. They have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome streamlining. However, it remains largely unknown which nutrients they require and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. We further investigated whether the spotted fever groupRickettsiaspeciesRickettsia parkeriscavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry in uninfected and infected cells, we found decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that bacterial growth is prohibited by inhibition of the host isoprenoid pathway with the statins class of drugs. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting statins inhibit cell wall synthesis. Altogether, our results describe an Achilles’ heel of obligate intracellular pathogens that can be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth.

Importance

Obligate intracellular parasites, which include viruses as well as certain bacteria and eukaryotes, extract essential nutrients and metabolites from their host cell. As a result, these pathogens have often lost essential biosynthetic pathways and are metabolically dependent on the host. In this study, we describe a metabolic dependency of the bacterial pathogenRickettsia parkerion host isoprenoid molecules that are used in the biosynthesis of downstream products including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent an Achilles’ heel, and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work highlights a potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism.
Reactive Dicarbonyl Scavenging Effectively Reduces MPO-Mediated Oxidation of HDL and Preserves HDL Atheroprotective Functions
Authors: Huang Jiansheng , Yancey Patricia G. , Tao Huan , Borja Mark , Smith Loren , Kon Valentina , Davies Sean S. , Linton MacRae F.
Published: January 2019

High-density lipoprotein (HDL) is atheroprotective by mediating cholesterol efflux, anti-inflammatory, and anti-oxidation functions. Atheroprotective functions of HDL are related to the activity of HDL-associated enzymes such as paraoxonase 1 (PON1). We examined the impact of inhibition of myeloperoxidase (MPO)-mediated HDL oxidation by PON1 on HDL malondialdehyde (MDA) content and HDL function. In the presence of PON1, crosslinking of apoAI in response to MPO-mediated oxidation of HDL was abolished and MDA-HDL adduct levels were decreased. In addition, PON1 prevented the impaired cholesterol efflux capacity of MPO-oxidized HDL fromApoe-/-macrophages. Direct modification of HDL with MDA increased apoAI crosslinking and reduced the cholesterol efflux capacity in a dose dependent manner. In addition, MDA modification of HDL reduced its anti-inflammatory function compared to native HDL as the expression of IL-1β and IL6 increased by 3-(p<0.05) and 1.8-fold (p<0.05) inApoe-/-macrophages in response to LPS. MDA-HDL also had impaired ability to increase PON1 activity. Importantly, HDL from subjects with familial hypercholesterolemia (FH-HDL) versus controls had increased MDA-apoAI adducts, and normalization of the PON1 activity to PON1 mass revealed a 24 % (p<0.05) decrease in specific activity indicating that PON1 activity is also impaired in FH. Consistent with the impaired PON1 activity and increased MDA-apoAI, FH-HDL induced a pro-inflammatory response inApoe-/-macrophages compared to incubation with LPS alone. FH-HDL versus control HDL also had an impaired ability to promote cholesterol efflux fromApoe-/-macrophages. Interestingly, reactive dicarbonyl scavengers effectively abolished MPO-mediated apoAI crosslinking, MDA adduct formation, and improved cholesterol efflux capacity. Importantly, in vivo treatment of hypercholesterolemic mice with reactive dicarbonyl scavengers effectively reduced MDA-HDL adduct formation and increased PON1 activity and HDL cholesterol efflux capacity, supporting a therapeutic potential of reactive carbonyl scavenging in maintaining HDL function.
Comparative identification of microRNAs inApis cerana ceranaworkers’ midguts responding toNosema ceranaeinvasion
Authors: Chen Dafu , Du Yu , Chen Huazhi , Wang Haipeng , Xiong Cuiling , Zheng Yanzhen , Hou Chunsheng , Diao Qingyun , Guo Rui
Published: January 2019

MicroRNAs (miRNAs) are endogenous small noncoding RNAs that post transcriptionally regulate gene expression and are involved in many biological processes including host-pathogen interactions. However, the potential role of miRNAs in the responses of eastern honeybees toNosema ceranaeinvasion is completely unknown. Here, the expression profiles and differentially expressed miRNAs (DEmiRNAs) in the midguts ofApis cerana ceranaworkers 7 and 10 days post infection (dpi) withN. ceranaewere investigated via small RNA sequencing and bioinformatics. In total, 529 miRNAs highly conserved between various species and 25 novel miRNAs with varied expressions were identified for the first time. In addition, stem-loop RT-PCR confirmed the expression of 16 predicted miRNAs, validating their existence. Eight up-regulated miRNAs and six down-regulated miRNAs were detected in midguts at 7 dpi, while nine and three miRNAs were significantly up-regulated and down-regulated, respectively, in midguts at 10 dpi. In addition, Venn analysis showed that five DEmiRNAs were shared, while nine and seven DEmiRNAs were specifically expressed in midguts at 7 and 10 dpi, respectively. Gene ontology analysis suggested that a portion of the DEmiRNAs and corresponding target genes were involved in various biological processes, cellular components, and molecular functions including immune system processes and response to stimulus and signaling. Moreover, KEGG pathway analysis shed light on the potential functions of some DEmiRNAs in the regulation of target genes engaged in material and energy metabolism, cellular immunity such as endocytosis and phagosome, and the humoral immune system, including the Jak-STAT and MAPK signaling pathways. Further investigation demonstrated a complex regulation network between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x and miR-3654-y at the center of the network, implying their key parts in host responses. This comprehensive miRNA transcriptome analysis demonstrated thatN. ceranaeinvasion influenced the expression of miRNAs in the midguts ofA. c. ceranaeworkers; the results can not only facilitate future exploration of the regulatory roles and mechanisms of miRNAs in hosts’ responses, especially their immune responses toN. ceranae, but also provide potential candidates for further investigation of the molecular mechanisms underlying eastern honeybee-microsporidian interactions.
Revealing the ocean metabolome with mass spectrometry
Authors: Sogin E. Maggie , Puskas Erik , Dubilier Nicole , Liebeke Manuel
Published: January 2019

All life exchanges molecules with its environment. While these metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats has hampered quantitative analyses of the ocean metabolome. To overcome these limitations, we developed SeaMet, a gas chromatography-mass spectrometry (GC-MS) method that detects hundreds of metabolites down to nano-molar concentrations in less than one milliliter of seawater. Using a set of metabolites dissolved in artificial seawater to benchmark our method, we show metabolite signal detection increased on average across ions by 324 fold in comparison to standard GC-MS methods. Our observed signal improvement occurred across tested metabolite classes and provides reproducible and quantifiable results. To showcase the capabilities of our method, we used SeaMet to explore the production and consumption of metabolites during culture of a heterotrophic bacteria that is widespread in the North Sea. Our approach revealed successional uptake of amino acids, while sugars were not consumed, and highlight the power of metabolomics in providing insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered a remarkable diversity and abundance of sugars and fatty acids, compounds predicted to be rapidly consumed by marine microorganisms. Our method advances marine metabolomics by enabling the unbiased, and quantitative analysis of marine metabolites, and will help provide new insights into carbon cycle dynamics and ocean biogeochemistry.

Significance

Metabolites are the chemical currency of cellular metabolism across all domains of life. However, describing metabolites that occur in the oceans is lagging behind similar studies conducted on land. The central challenge in marine metabolomics is that salt prevents the comprehensive analysis of metabolites in seawater. We developed a method, SeaMet, that overcomes the limitations of salt on metabolite detection. SeaMet provides a time and cost efficient method, using gas chromatography-mass spectrometry, for the reproducible identification and quantification of a broad range of marine compounds. Considering the oceans contain the largest organic carbon pool on Earth, describing the marine metabolome is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2storage.
A robust human norovirus replication model in zebrafish larvae
Authors: Van Dycke Jana , Ny Annelii , Conceição-Neto Nádia , Maes Jan , Hosmillo Myra , Cuvry Arno , Goodfellow Ian , Nogueira Tatiane C. , Verbeken Erik , Matthijnssens Jelle , de Witte Peter , Neyts Johan , Rocha-Pereira Joana
Published: January 2019

Human noroviruses (HuNoVs) are an important cause of epidemic and endemic acute gastroenteritis worldwide; annually about 700 million people develop a HuNoV infection resulting in ∼219,000 deaths and a societal cost estimated at 60 billion US dollars 1. The lack of robust small animal models has significantly hindered the understanding of norovirus biology and the development of effective therapeutics against HuNoV. Here we report that HuNoV GI and GII replicate to high titers in zebrafish (Danio rerio) larvae; replication peaks at day 2 post infection and is detectable for at least 6 days. HuNoV is detected in cells of the hematopoietic lineage, the intestine, liver and pancreas. Antiviral treatment reduces HuNoV replication by >2 log10, showing that this model is suited for antiviral studies. Downregulation of fucosyltransferase 8 (fut8) in the larvae reduces HuNoV replication, highlighting a common feature with infection in humans. Zebrafish larvae constitute a simple and robust replication model that will largely facilitate studies of HuNoV biology and the development of antiviral strategies.
The TRAPP complex mediates secretion arrest induced by stress granule assembly
Authors: Zappa Francesca , Wilson Cathal , Di Tullio Giuseppe , Santoro Michele , Pucci Piero , Monti Maria , D’Amico Davide , Vaquero Sandra Pisonero , De Cegli Rossella , Romano Alessia , Saleem Moin A. , Polishchuk Elena , Failli Mario , Giaquinto Laura , De Matteis Maria Antonietta
Published: January 2019

The TRAnsport-Protein-Particle (TRAPP) complex controls multiple membrane trafficking steps and is thus strategically positioned to mediate cell adaptation to diverse environmental conditions, including acute stress. We have identified TRAPP as a key component of a branch of the integrated stress response that impinges on the early secretory pathway. TRAPP associates with and drives the recruitment of the COPII coat to stress granules (SGs) leading to vesiculation of the Golgi complex and an arrest of ER export. Interestingly, the relocation of TRAPP and COPII to SGs only occurs in actively proliferating cells and is CDK1/2-dependent. We show that CDK1/2 activity controls the COPII cycle at ER exit sites (ERES) and that its inhibition prevents TRAPP/COPII relocation to SGs by stabilizing them at the ERES. Importantly, TRAPP is not just a passive constituent of SGs but controls their maturation since SGs that assemble in TRAPP-depleted cells are smaller and are no longer able to recruit RACK1 and Raptor, rendering the cells more prone to undergo apoptosis upon stress exposure.
Estimating seed dispersal distance: a comparison of methods using animal movement and plant genetic data on two primate-dispersed Neotropical plant species
Authors: Gelmi-Candusso Tiziana A. , Bialozyt Ronald , Slana Darja , Gómez Ricardo Zárate , Heymann Eckhard W. , Heer Katrin
Published: January 2019

Seed dispersal distances (SDD) critically influence the survival of seedlings, spatial patterns of genetic diversity within plant populations and gene flow among plant populations. In tropical forests, a large percentage of seeds is dispersed by animals, and their foraging behaviour and movement patterns determine SDD. Direct observations of seed dispersal events by animals in natural plant populations are mostly constrained by the high mobility and low visibility of their vectors. Therefore, diverse alternative methods are used to estimate SDD, but direct comparisons of these approaches within the same seed dispersal system are mostly missing.

In this study, we take advantage of two plant species with different life history traits, Leonia cymosa and Parkia panurensis that are exclusively dispersed by two tamarin species, Saguinus mystax and Leontocebus nigrifrons (Callitrichidae) at our study site in the Peruvian Amazon. We compare SDD estimates obtained from direct observations, genetic identification of mother plants from seed coats, parentage analysis of seedlings, and modelling approaches, including the combination of movement data and gut passage times and individual-based modelling.

We detect differences between SDD estimates that can be linked to the processes relevant at different phases of the seed dispersal loop covered by the respective approaches. Despite these differences, SDD estimates for P. panurensis are consistently lower than for L. cymosa which is likely related to differences in fruit characteristics and fruit abundance, factors that influence gut passage time, foraging behaviour and movement patterns of the tamarins.

Our comparisons allow setting SDD estimates from studies using different methodological approaches into the seed dispersal loop context, thus improving comparability of methodologically different studies and method applicability.
The Evolution of Placental Invasion and Cancer Metastasis are Causally Linked
Authors: Kshitiz  , Afzal Junaid , Maziarz Jamie D. , Hamidzadeh Archer , Liang Cong , Erkenbrack Eric M. , Nam Hong , Haeger Jan-Dirk , Pfarrer Christiane , Hoang Thomas , Ott Troy , Spencer Thomas , Pavlicev Mihaela , Antczak Doug , Levchenko Andre , Wagner Günter P.
Published: January 2019

Among mammals, the extent of placental invasion is correlated with vulnerability to malignancy. Animals with more invasive placentation (e.g. humans) are more vulnerable to malignancy, whereas animals with a non-invasive placenta (e.g. ruminants) are less likely to develop malignant cancer. To explain this correlation, we propose the hypothesis ofEvolved Levels of Invasibility(ELI) positing that the permissiveness of stromal tissue to invasion is a unitary character affecting both placental and cancer invasion. We provide evidence for this hypothesis by contrasting invasion of human and bovine cancer and placental cells into a lawn of stromal cells from different species. We find that both bovine endometrial and skin fibroblasts are more resistant to invasion of placental and cancer cells than their human counterparts. Gene expression profiling identified genes with high expression in human but not bovine fibroblasts. Knocking down of a subset of them in human fibroblasts leads to significantly stronger resistance to cancer cell invasion. Comparative analysis of gene expression among mammals suggests that humans evolved higher vulnerability to malignancy than the eutherian ancestor, possibly as a correlate of more invasive placentation, and boroeutherians evolved to decrease stromal invasibility. Identifying the evolutionary determinants of stromal invasibility can provide significant insights to develop rational anti-metastatic therapeutics.
An integrated metagenome catalog reveals novel insights into the murine gut microbiome
Authors: Lesker Till Robin , Chakravarthy Abilash , Gálvez Eric. J.C. , Lagkouvardos Ilias , Baines John F. , Clavel Thomas , Sczyrba Alexander , McHardy Alice C. , Strowig Till
Published: January 2019

The vast complexity of host-associated microbial ecosystems requires generation of host-specific gene catalogs to survey the functions and diversity of these communities. We generated a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 high-quality metagenome-assembled genomes (MAGs) linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution, i.e. more than 89% of the identified taxa are not represented in any other databases. The tool (github.com/tillrobin/iMGMC) allowed characterizing the diversity and functions of prevalent and previously unknown microbial community members along the gastrointestinal tract. Moreover, we show that integration of MAGs and 16S rRNA gene data allows a more accurate prediction of functional profiles of communities than based on 16S rRNA amplicons alone. Integrated gene catalogs such as iMGMC are needed to enhance the resolution of numerous existing and future sequencing-based studies.
A flow extension tethered particle motion assay for single-molecule proteolysis
Authors: Drabek Andrew A. , Loparo Joseph J. , Blacklow Stephen C.
Published: January 2019

Regulated proteolysis of signaling proteins under mechanical tension enables cells to communicate with their environment in a variety of developmental and physiologic contexts. The role of force in inducing proteolytic sensitivity has been explored using magnetic tweezers at the single-molecule level with bead-tethered assays, but such efforts have been limited by challenges in ensuring that beads are not restrained by multiple tethers. Here, we describe a multiplexed assay for single-molecule proteolysis that overcomes the multiple-tether problem using a flow extension (FLEX) strategy on a microscope equipped with magnetic tweezers. Particle tracking and computational sorting of flow-induced displacements allows assignment of tethered substrates into singly-captured and multiply-tethered bins, with the fraction of fully mobile, single-tethered substrates depending inversely on the concentration of substrate loaded on the coverslip. Computational exclusion of multiply-tethered beads enables robust assessment of on-target proteolysis by the highly specific tobacco etch virus protease and the more promiscuous metalloprotease ADAM17. This method should be generally applicable to a wide range of proteases and readily extensible to robust evaluation of proteolytic sensitivity as a function of applied magnetic force.
Sex Differences in Oncogenic Mutational Processes
Authors: Li Constance H. , Prokopec Stephenie D. , Sun Ren X. , Yousif Fouad , Schmitz Nathaniel , Boutros Paul C. ,   for the PCAWG Molecular Subtypes and Clinical Correlates Working Group,   ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Published: January 2019

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here, we describe the first pan-cancer analysis of sex differences in whole genomes of 1,983 tumours of 28 subtypes from the ICGC Pan-Cancer Analysis of Whole Genomes project. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in cancer research.

Sex disparities in cancer epidemiology include an increased overall cancer risk in males corresponding with higher incidence in most tumor types, even after adjusting for known risk factors1,2. Cancer mortality is also higher in males, due in part to better survival for female patients in many cancer types, including those of the colon and head & neck3. Interestingly, female colorectal cancer patients respond better to surgery4 and adjuvant chemotherapy, though this is partially due to biases in tumour location and microsatellite instability5. Similarly, premenopausal female nasopharyngeal cancer patients have improved survival regardless of tumour stage, radiation or chemotherapy regimen6. There is a growing body of evidence for sex differences in cancer genomics7-13, but their molecular origins and clinical implications remain largely elusive.

Previous studies have mostly focused on protein coding regions, leaving the vast majority of the genome unexplored. We hypothesized that there are uncharacterized sex differences in the non-coding regions of the genome. Using whole genome sequencing data from the Pan-cancer Analysis of Whole Genomes (PCAWG) project14, we performed a survey of sex-biased mutations in 1,983 samples (1,213 male, 770 female) from 28 tumour subtypes, excluding those of the sex organs (Supplementary Table 1). We also excluded the X and Y chromosomes to focus on autosomal sex differences in cancers affecting both men and women, but there are known to be significant X-chromosome mutational differences between tumours arising in men and women15. Our analysis revealed sex differences in both genome-wide phenomena and in specific genes. These sex-biases occur not only at the pan-cancer level across all 1,983 samples, but also in individual tumour subtypes.
Temporal inhibition of autophagy reveals segmental reversal of aging with increased cancer risk
Authors: Cassidy Liam D , Young Andrew RJ , Young Christopher NJ , Soilleux Elizabeth J , Fielder Edward , Weigand Bettina M , Brais Rebecca , Wiggins Kimberley A , Clarke Murray CH , Jurk Diana , Passos Joao F , Narita Masashi
Published: January 2019

Autophagy is an important cellular degradation pathway with a central role in metabolism as well as basic quality control, two processes inextricably linked to aging. A decrease in autophagy is associated with increasing age, yet it is unknown if this is causal in the aging process, and whether autophagy restoration can counteract these aging effects. Here we demonstrate that systemic autophagy inhibition induces the premature acquisition of age-associated phenotypes and pathologies in mammals. Remarkably, autophagy restoration provides a near complete recovery of morbidity and a significant extension of lifespan, however, at the molecular level this rescue appears incomplete. Importantly autophagy-restored mice still succumb earlier due to an increase in spontaneous tumor formation. Thus our data suggest that chronic autophagy inhibition confers an irreversible increase in cancer risk and uncovers a biphasic role of autophagy in cancer development being both tumor suppressive and oncogenic, sequentially.
CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
Authors: Zhu Qian , Liu Nan , Orkin Stuart H. , Yuan Guo-Cheng
Published: January 2019

We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.
Microbial phenotypic heterogeneity in response to a metabolic toxin: continuous, dynamically shifting distribution of formaldehyde tolerance inMethylobacterium extorquenspopulations
Authors: Lee Jessica A. , Riazi Siavash , Nemati Shahla H. , Vasdekis Andreas E. , Ridenhour Benjamin J. , Remien Christopher H. , Marx Christopher J.
Published: January 2019

While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenotypic heterogeneity has been demonstrated in a number of model systems involving binary phenotypic states (e.g., growth/non-growth); however, less is known about systems involving phenotype distributions that are continuous across an environmental gradient, and how those distributions change when the environment changes. Here, we describe a novel instance of phenotypic diversity in tolerance to a metabolic toxin within wild-type populations ofMethylobacterium extorquens, a ubiquitous phyllosphere methylotroph capable of growing on the methanol periodically released from plant leaves. The first intermediate in methanol metabolism is formaldehyde, a potent cellular toxin that is lethal in high concentrations. We have found that at moderate concentrations, formaldehyde tolerance inM. extorquensis heterogeneous, with individual cells’ minimum tolerance levels ranging between 0 mM and 8 mM. This form of heterogeneity is continuous in terms of threshold (in the range of maximum tolerances possible), yet binary in outcome (at a given formaldehyde concentration, cells either grow normally or die, with no intermediate phenotype), and it is not associated with any detectable genetic mutations. Moreover, tolerance distributions within the population are dynamic, changing over time in response to growth conditions. We characterized this phenomenon using bulk liquid culture experiments, colony growth tracking, flow cytometry, time-lapse microscopy, and genome resequencing. Finally, we used mathematical modeling to better understand the processes by which cells change phenotype, and found evidence for both stochastic, bidirectional phenotype diversification and responsive, directed phenotype shifts, depending on the growth substrate and the presence of toxin.
A pair of E3 ubiquitin ligases compete to regulate filopodial dynamics and axon guidance TRIM67 regulates filopodial stability and axon guidance
Authors: Boyer Nicholas P. , McCormick Laura E. , Urbina Fabio L. , Gupton Stephanie L.
Published: January 2019

Appropriate axon guidance is necessary to form accurate neuronal connections. Guidance cues stimulate reorganization of the cytoskeleton within the distal growth cone at the tip of the extending axon. Filopodia at the periphery of the growth cone have long been considered sensors for axon guidance cues, yet how they perceive and respond to extracellular cues remains ill-defined. Our previous work found that the filopodial actin polymerase VASP is regulated via TRIM9-dependent nondegradative ubiquitination, and that appropriate VASP ubiquitination and deubiquitination are required for axon turning in response to the guidance cue netrin-1. Here we show that the TRIM9-related protein TRIM67 antagonizes VASP ubiquitination by outcompeting the TRIM9:VASP interaction. This antagonistic role is required for netrin-1 dependent filopodial responses, axon turning and branching, and fiber tract formation. We suggest a novel model that coordinated regulation of nondegradative VASP ubiquitination by a pair of ligases is a critical element of axon guidance.
A rapid method for DNA extraction of cotton mature fiber suitable for PCR fingerprinting
Authors: Ibrahim Shafik D. , Alsamman Alsamman M. , Khalifa Kareem
Published: January 2019

Egyptian cotton with its extra-long staple fiber is the world’s finest textile crop, but it has been in a state of rapid decline for the past 20 years. One of the main problems in Egyptian cotton production that, some manufacturers are using inferior quality cotton or other cheaper cotton to cut costs. This practice impacts not only the brand owner but also the cotton farmers and producers. The ability to differentiate between different mature or processed cottons fibers according to its varietal origin is very complicated or highly expensive. We introduce the first non commercial procedure to isolate intact genomic DNA from cotton fiber with a modified CTAB protocol. This protocol was successfully used to retrieve DNA from cotton fabric and the DNA was efficient to perform PCR procedure using DNA-barcoding and SCoT assays. Additionally, we retrieved PCR markers using CAPs assay can differentiate between Egyptian and American cotton from a fiber source.
P-glycoprotein Detoxification by the Malpighian Tubules of the Desert Locust
Authors: Rossi Marta , Battisti Davide De , Niven Jeremy E.
Published: January 2019

Detoxification is essential for allowing animals to remove toxic substances present in their diet or generated as a biproduct of their metabolism. By transporting a wide range of potentially noxious substrates, active transporters of the ABC transporter family play an important role in detoxification. One such class of transporters are the multidrug resistance P-glycoprotein transporters. Here, we investigated P-glycoprotein transport in the Malpighian tubules of the desert locust (Schistocerca gregaria), a species whose diet includes plants that contain toxic secondary metabolites. To this end, we studied transporter physiology using a modified Ramsay assay in whichex vivoMalpighian tubules are incubated in different solutions containing the P-glycoprotein substrate dye rhodamine B in combination with different concentrations of the P-glycoprotein inhibitor verapamil. Our evidence shows that: (i) the Malpighian tubules contain a P-glycoprotein; (ii) tubule surface area is positively correlated with the tubule fluid secretion rate; and (iii) as the fluid secretion rate increases so too does the net extrusion of rhodamine B. We were able to quantify precisely the relationships between the fluid secretion, surface area, and net extrusion. We interpret these results in the context of the life history and foraging ecology of desert locusts. We argue that P-glycoproteins play an important role in the detoxification by contributing to the removal of xenobiotic substances from the haemolymph, thereby enabling gregarious desert locusts to maintain toxicity through the ingestion of toxic plants without suffering the deleterious effects themselves.
The structure of nano-twinned rhombohedral YCuO2.66 solved by electron crystallography
Authors: Klein Holger , Garlea V. Ovidiu , Darie Céline , Bordet Pierre
Published: January 2019

In the search for frustrated spin interactions, a YCuO2.66 phase has been synthesized by a treatment under oxygen pressure of YCuO2.5. X-ray powder diffraction and electron diffraction studies have been conducted. Electron diffraction shows that the sample is twinned on a 10 nm scale. Precession electron diffraction data obtained from a twinned crystal was treated in order to obtain intensities corresponding to only one of the orientations of the twins. From this data a structure solution was obtained where, as in YCuO2.5, the Cu atoms form triangular planes. The Cu atoms are linked in two dimensions by oxygen atoms in the present structure whereas in YCuO2.5 they are only linked in one-dimensional chains.