bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family
Authors: Guo Xiaohu , Söderholm Annika , Kanchugal P Sandesh , Isaksen Geir Villy , Warsi Omar , Eckhard Ulrich , Trigüis Silvia , Gogoll Adolf , Jerlström-Hultqvist Jon , Åqvist Johan , Andersson Dan I. , Selmer Maria
Published: August 2020

The first SAM degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as an S-adenosyl-L-methionine (SAM) hydrolase forming 5’-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha-beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography and NMR spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis,in vitroandin vivomutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.
Structural defects caused by Acrodermatitis Enteropathica mutations in the extracellular domain account for mistrafficking and malfunction of ZIP4
Authors: Kuliyev Eziz , Zhang Chi , Sui Dexin , Hu Jian
Published: August 2020

ZIP4 is a representative member of the Zrt-/Irt-like protein (ZIP) transporter family and responsible for zinc uptake from diet. Loss-of-function mutations of human ZIP4 (hZIP4) drastically reduce zinc absorption, causing a life-threatening autosomal recessive disorder, Acrodermatitis Enteropathica (AE). Although the zinc transport machinery is located in the transmembrane domain conserved in the entire ZIP family, half of the missense mutations occur in the extracellular domain (ECD) of hZIP4, which is only present in a fraction of mammalian ZIPs. How the AE-causing mutations in the ECD lead to ZIP4 malfunction has not be fully clarified. In this work, we characterized all the seven confirmed AE-causing missense mutations in hZIP4-ECD and found that the variants exhibited completely abolished zinc transport activity measured in a cell-based transport assay. Although the variants were able to be expressed in HEK293T cells, they failed to traffic to cell surface and were largely retained in the ER with immature glycosylation. When the corresponding mutations were introduced in the ECD of ZIP4 from Pteropus Alecto, a close homolog of hZIP4, the variants exhibited impaired protein folding and reduced thermal stability, which likely account for intracellular mistrafficking of the AE-associated variants and as such a total loss of zinc uptake in cells. This work provides a molecular pathogenic mechanism for AE, which lays out a basis for potential therapy using small molecular chaperones.
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Authors: Wang Jerry C. , Ramaswami Gokul , Geschwind Daniel H.
Published: August 2020

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.
Transcriptome-wide Association Study of Circulating IgE Levels Identifies Novel Targets for Asthma and Allergic Diseases
Authors: Kathryn Recto , Tianxiao Huan , Heon Lee Dong , Young Lee Gha , Jessica Gereige , Chen Yao , Shih-Jen Hwang , Roby Joehanes , Kelly Rachel S , Jessica Lasky-Su , George O’Connor , Daniel Levy
Published: August 2020

Measurement of circulating immunoglobulin E (IgE) concentration is helpful for diagnosing and treating asthma and allergic diseases. Identifying gene expression signatures associated with IgE might elucidate novel pathways for IgE regulation. To this end, we performed a discovery transcriptome-wide association study (TWAS) to identify differentially expressed genes associated with circulating IgE levels in whole-blood derived RNA from 5,345 participants in the Framingham Heart Study (FHS) across 17,873 mRNA gene-level transcripts. We identified 216 significant transcripts at a false discovery rate (FDR)< 0.05. We conducted replication using the meta-analysis of two independent external studies: the Childhood Asthma Management Program (n = 610) and the Genetic Epidemiology of Asthma in Costa Rica Study (n = 326); we then reversed the discovery and replication cohorts, which revealed 59 significant genes that bidirectionally replicated. Gene ontology analysis revealed that many of these genes were implicated in immune function pathways, including defense response, inflammatory response, and cytokine production. Mendelian randomization (MR) analysis revealed four genes (CLC, CCDC21, S100A13, andGCNT1) as putatively causal (p< 0.05) regulators of IgE levels.GCNT1(beta = 1.5, p = 0.01)—which is a top result in the MR analysis of expression in relation to asthma and allergic diseases—plays a role in regulating T helper type 1 (Th1) cell homing, lymphocyte trafficking, and B cell differentiation. Our findings build upon prior knowledge of IgE regulation and provide a deeper understanding of underlying molecular mechanisms. The IgE-associated genes that we identified—particularly those implicated in MR analysis—can be explored as promising therapeutic targets for asthma and IgE-related diseases.
Risk factors associated with morbidity and mortality outcomes of COVID-19 patients on the 14th and 28th day of the disease course: a retrospective cohort study in Bangladesh
Authors: Islam M.Z. , Riaz B.K. , Islam ANMS , Khanam F. , Akhter J. , Choudhury R. , Farhana N. , Jahan N.A. , Uddin M.J. , Efa S.S.
Published: August 2020

Diverse risk factors intercede the outcomes of COVID-19. We conducted this retrospective cohort study to identify the risk factors associated with morbidity and mortality outcomes with a cohort of 1016 COVID-19 patients diagnosed in May 2020. Data were collected by telephone-interview and reviewing records using a questionnaire and checklist. Morbidity (64.4% Vs. 6.0%) and mortality (2.3% Vs. 2.5%) outcomes varied between the 14th and 28th day. Morbidity risk factors included chronic obstructive pulmonary disease (COPD) (RR=1.19, RR=2.68) both on the 14th and 18th day while elderly (AOR=2.56) and smokeless tobacco (SLT) (AOR=2.17) on the 28th day. Mortality risk factors included elderly (AOR=10.14), COPD (RR=5.93), and SLT (AOR=2.25) on the 14th day, and elderly (AOR=24.37) and COPD (RR=2.72) on the 28th day. The morbidity risk was higher with chronic kidney disease (CKD) (RR=3.33) and chronic liver disease (CLD) (RR=3.99) on the 28th day. The mortality risk was higher with coronary heart disease (RR=4.54) and CLD (RR=9.66) on the 14th while with diabetes mellitus (RR=3.08, RR=2.08), hypertension (RR=3.14, RR=2.30), CKD (RR=8.97, RR=2.71), and malignant diseases (RR=10.29) on both 14th and 28th day. We must espouse program interventions considering the morbidity and mortality risk factors to condense the aggressive outcomes of COVID-19.
Evidence and magnitude of seasonality in SARS-CoV-2 transmission: Penny wise, pandemic foolish?
Authors: Kaplin Adam , Junker Caesar , Kumar Anupama , de Amorim Ribeiro Mary Anne , Yu Eileen , Wang Michael , Smith Ted , Rai Shesh N , Bhatnagar Aruni
Published: August 2020

Importance

Intensity and duration of the COVID-19 pandemic, and planning required to balance concerns of saving lives and avoiding economic collapse, could depend significantly on whether SARS-CoV-2 transmission is sensitive to seasonal changes.

Objective

Hypothesis is that increasing temperature results in reduced SARS CoV-2 transmission and may help slow the increase of cases over time.

Setting

Fifty representative Northern Hemisphere countries meeting specific criteria had sufficient COVID-19 case and meteorological data for analysis.

Methods

Regression was used to find relationship between the log of number of COVID-19 cases and temperature over time in 50 representative countries. To summarize the day-day variability, and reduce dimensionality, we selected a robust measure, Coefficient of Time (CT), for each location. The resulting regression coefficients were then used in a multivariable regression against meteorological, country-level and demographic covariates.

Results

Median minimum daily temperature showed the strongest correlation with the reciprocal of CT (which can be considered as a rate associated with doubling time) for confirmed cases (adjusted R2 = 0.610, p = 1.45E-06). A similar correlation was found using median daily dewpoint, which was highly colinear with temperature, and therefore was not used in the analysis. The correlation between minimum median temperature and the rate of increase of the log of confirmed cases was 47% and 45% greater than for cases of death and recovered cases of COVID-19, respectively. This suggests the primary influence of temperature on SARS-CoV2 transmission more than COVID-19 morbidity. Based on the correlation between temperature and the rate of increase in COVID-19, it can be estimated that, between the range of 30 to 100 degrees Fahrenheit, a one degree increase leads to a 1% decrease--and a one degree decrease leads to a 3.7% increase--in the rate of increase of the log of daily confirmed cases.

Conclusion

The results suggest that boreal summer months are associated with slower rates of COVID-19 transmission, with the reverse true in winter months. Knowledge of COVID-19 seasonality could prove useful in local planning for phased reductions social interventions and help to prepare for the timing of possible pandemic resurgence during cooler months.
PROFILING OF Y1 CELLS TREATED WITH FGF-2 REVEALS PARALLELS WITH ONCOGENE-INDUCED SENESCENCE
Authors: Lund Peder J. , Lopes Mariana , Sidoli Simone , Coradin Mariel , de Luna Vitorino Francisca Nathália , da Cunha Julia Pinheiro Chagas , Garcia Benjamin Aaron
Published: August 2020

Paradoxically, oncogenes that drive cell cycle progression may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Along these lines, Y1 cells, which carry an amplification of Ras, become senescent after treatment with the mitogen FGF-2. To understand how FGF-2 promotes senescence, we profiled the epigenome, transcriptome, proteome, and phospho-proteome of Y1 cells stimulated with FGF-2. FGF-2 caused delayed acetylation of histone H4 and higher levels of H3K27me3. Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac. In contrast, FGF-2 promoted the expression of p21, various cytokines, and MAPK-related genes. Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2. Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle. Altogether, the response of Y1 cells to FGF-2 is consistent with oncogene-induced senescence. We propose that Y1 cells enter senescence due to deficient cyclin expression and high levels of p21, which may stem from DNA damage or TGFb signaling.
Oxylipin metabolism is controlled by mitochondrial β-oxidation during bacterial inflammation
Authors: Misheva Mariya , Kotzamanis Konstantinos , Davies Luke C , Tyrrell Victoria J , Rodrigues Patricia R S , Benavides Gloria A , Hinz Christine , Murphy Robert C , Kennedy Paul , Taylor Philip R , Rosas Marcela , Jones Simon A , McLaren James E , Deshpande Sumukh , Andrews Robert , Schebb Nils Helge , Czubala Magdalena A , Gurney Mark , Aldrovandi Maceler , Meckelmann Sven W , Ghazal Peter , Darley-Usmar Victor , White Daniel A , O’Donnell Valerie B
Published: August 2020

Oxylipins are potent biological mediators requiring strict control, but how they are removed en masse during infection and inflammation is unknown. Here we show that lipopolysaccharide (LPS) dynamically enhances oxylipin removal via mitochondrial β-oxidation. Specifically, genetic or pharmacological targeting of carnitine palmitoyl transferase 1 (CPT1), a mitochondrial importer of fatty acids, reveal that many oxylipins are removed by this protein during inflammation in vitro and in vivo. Using stable isotope-tracing lipidomics, we find secretion-reuptake recycling for 12-HETE and its intermediate metabolites. Meanwhile, oxylipin β-oxidation is uncoupled from oxidative phosphorylation, thus not contributing to energy generation. Testing for genetic control checkpoints, transcriptional interrogation of human neonatal sepsis finds upregulation of many genes involved in mitochondrial removal of long-chain fatty acyls, such asACSL1,3,4, ACADVL, CPT1B, CPT2 and HADHB. Also,ACSL1/Acsl1upregulation is consistently observed following the treatment of human/murine macrophages with LPS and IFN-γ. Last, dampening oxylipin levels by β-oxidation is suggested to impact on their regulation of leukocyte functions. In summary, we propose mitochondrial β-oxidation as a regulatory metabolic checkpoint for oxylipins during inflammation.
A workflow for sizing oligomeric biomolecules based on cryo single molecule localization microscopy
Authors: Schneider Magdalena C. , Telschow Roger , Mercier Gwenael , López-Martinez Montserrat , Scherzer Otmar , Schütz Gerhard J.
Published: August 2020

Single molecule localization microscopy (SMLM) has enormous potential for resolving subcellular structures below the diffraction limit of light microscopy: Localization precision in the low digit nanometer regime has been shown to be achievable. In order to record localization microscopy data, however, sample fixation is inevitable to prevent molecular motion during the rather long recording times of minutes up to hours. Eventually, it turns out that preservation of the sample’s ultrastructure during fixation becomes the limiting factor. We propose here a workflow for data analysis, which is based on SMLM performed at cryogenic temperatures. Since molecular dipoles of the fluorophores are fixed at low temperatures, such an approach offers the possibility to use the orientation of the dipole as an additional information for image analysis. In particular, assignment of localizations to individual dye molecules becomes possible with high reliability. We quantitatively characterized the new approach based on the analysis of simulated oligomeric structures. Side lengths can be determined with a relative error of less than 1% for tetramers with a nominal side length of 5 nm, even if the assumed localization precision for single molecules is more than 2 nm.
Synthesis and in vitro Activity of Eugenyl Benzoate Derivatives as BCL-2 Inhibitor in Colorectal Cancer with QSAR and Molecular Docking Approach
Authors: Fadilah Fadilah , Andrajati Retnosari , Arsianti Ade , Paramita Rafika Indah , Erlina Linda , Yanuar Arry
Published: August 2020

Eugenol derivatives can inhibit BCL-2 in HT29 colorectal cancer cells. This study is aimed to acquiring new compounds of Eugenyl benzoate (2-methoxy-4-(prop-2-en-1-yl)phenyl benzoate) derivatives that can inhibit HT29 colorectal cancer cells. In this research, we used several chemical reactions to synthesize novel compounds, such as Esterification, Demethylation, Halohydrin, and Sharpless reaction. Cytotoxicity assays were performed to test the inhibitory activity of compounds against HT29 colon cancer cells. QSAR analysis were carried out to analyse the relationship of chemical structure of the novel compounds with their cytotoxic activity. Ten novel compounds were successfully synthesized and testedin vitroagainst the HT29 cell. The IC50of the novel compounds were between 26.56 μmol/ml - 286.81 μmol/ml which compound 4-[(2S)-2,3-dihydroxypropyl]-2-methoxyphenyl 2-hydroxybenzoate(9)showed as best active compound as BCL-2 inhibitors better than other synthesized compounds and Eugenol as well. QSAR analysis of thein vitroresults gave a Log equation: 1/IC50= −0.865-0.210 (LogP)2+ 1,264 (logP)-0.994 CMR (n = 10; r = 0.706; SE: 0.21; F = 0.497, sig = 7.86). The equation shows the log variable P and CMR affect IC50. The properties of hydrophobicity (log P) are more instrumental than the ones of steric (CMR).
The impact of intravenous dodecafluoropentane on a murine model of acute lung injury
Authors: Mosier Jarrod M , Sammani Saad , Kempf Carrie , Unger Evan , Garcia Joe GN
Published: August 2020

Acute hypoxemic respiratory failure presents therapeutic challenges due to ventilation/perfusion mismatch and shunt. The goal of management strategies is to improve arterial oxygenation, however each management strategy presents risk to patients from iatrogenic injury. Intravenous oxygen therapeutics present an appealing option to improve arterial oxygenation without these risks. We used a two-hit murine model of acute lung injury to evaluate the effect of intravenous dodecafluoropentane (NanO2) on oxygen saturation and bronchoalveolar lavage cell count and protein. Mice were given intratracheal lipopolysaccharide and 20 hours later were intubated and ventilated with high tidal volumes. NanO2was given by bolus injection at the initiation of mechanical ventilation and again at 2 hours, while oxygen saturation was measured every 15 minutes. At the conclusion of the experiment (4 hours), a bronchoalveolar lavage was performed. There was no difference in mean O2saturation at time zero, however the difference between the mean O2saturation immediately prior to injection and the mean first O2saturation after injection in the control saline group were 91% and 83%, mean difference −7.5%; whereas mean O2saturation in the NanO2treated group rose from 89% to 91%, mean difference +2.5%, net difference 10% [95% CI: 2.7,17.3], p=0.01). There was a statistically significant difference in cell count, but not protein, on the bronchoalveolar lavage analysis. These data show that NanO2rapidly improves oxygen saturation in a two-hit model of acute lung injury, and shows potential as an intravenous oxygen therapeutic in the management in acute hypoxemic respiratory failure.
Transcriptomic profiling of human corona virus (HCoV)-229E -infected human cells and genomic mutational analysis of HCoV-229E and SARS-CoV-2
Authors: Friedman Nehemya , Jacob-Hirsch Jasmine , Drori Yaron , Eran Eyal , Kol Nitzan , Nayshool Omri , Mendelson Ella , Rechavi Gideon , Mandelboim Michal
Published: August 2020

Human coronaviruses (HCoVs) cause mild to severe respiratory infection. Most of the common cold illnesses are caused by one of four HCoVs, namely HCoV-229E, HCoV-NL63, HCoV-HKU1 and HCoV-OC43. Several studies have applied global transcriptomic methods to understand host responses to HCoV infection, with most studies focusing on the pandemic severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV) and the newly emerging SARS-CoV-2. In this study, Next Generation Sequencing was used to gain new insights into cellular transcriptomic changes elicited by alphacoronavirus HCoV-229E. HCoV-229E-infected MRC5 cells showed marked downregulation of superpathway of cholesterol biosynthesis and eIF2 signaling pathways. Moreover, upregulation of cyclins, cell cycle control of chromosomal replication, and the role of BRCA1 in DNA damage response, alongside downregulation of the cell cycle G1/S checkpoint, suggest that HCoV-229E favors S phase for viral infection. Intriguingly, a significant portion of key factors of cell innate immunity, interferon-stimulated genes (ISGs) and other transcripts of early antiviral response genes were downregulated early in HCoV-229E infection. On the other hand, early upregulation of the antiviral response factor Apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B)was observed. APOBEC3B cytidine deaminase signature (C-to-T) was previously observed in genomic analysis of SARS-CoV-2 but not HCoV-229E. Higher levels of C-to-T mutations were found in countries with high mortality rates caused by SARS-CoV-2. APOBEC activity could be a marker for new emerging CoVs. This study will enhance our understanding of commonly circulating HCoVs and hopefully provide critical information about still-emerging coronaviruses.

Author summary

Human coronaviruses (HCoVs) generate respiratory tract infections. HCoV-229E is one of four known HCoV strains that circulate annually in the population for several decades. Beside these, three pandemic CoV emerged since year 2002, the Severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2. These three strains attracted most attention for extensive research and less consideration has been given to the commonly infecting HCoVs. In this study we use Next generation sequencing analysis to understand global transcriptomic changes in human host cells following HCoV-229E infection. We found several cellular pathways that change during infection that involve cholesterol biosynthesis, cell cycle control, DNA replication, DNA repair, innate immune response and an interesting RNA editing enzyme which could be involve in CoVs pathogenesis.
PIE-1 promotes SUMOylation and activation of HDAC1 during theC. elegansoogenesis
Authors: Kim Heesun , Ding Yue-He , Lu Shan , Zuo Mei-Qing , Conte Darryl , Dong Meng-Qiu , Mello Craig C.
Published: August 2020

Germlines shape and balance heredity, integrating and regulating information from both parental and foreign sources. Insights into how the germline handles information have come from the identification of factors that specify or maintain the germline fate. In earlyC. elegansembryos, the CCCH zinc-finger protein PIE-1 localizes to the germline where it prevents somatic differentiation programs. Here we show that PIE-1 also functions in the meiotic ovary where it becomes SUMOylated and engages the SUMO-conjugating machinery. Using whole-proteome mass spectrometry to detect SUMO-conjugated proteins, we identify HDAC SUMOylation as a target of PIE-1. Our findings suggest that SUMOylation activates HDAC, lowering histone acetylation and enhancing Argonaute-mediated surveillance in the germline.
Nitrogen availability and plant functional composition modify biodiversity-multifunctionality relationships
Authors: Pichon Noémie A. , Cappelli Seraina L. , Soliveres Santiago , Mannall Tosca , Nwe Thu Zar , Hölzel Norbert , Klaus Valentin H. , Kleinebecker Till , Vincent Hugo , Allan Eric
Published: August 2020

The ability of an ecosystem to deliver multiple functions at high levels (multifunctionality) typically increases with biodiversity but there is substantial variation in the strength and direction of biodiversity effects, suggesting context-dependency. A better understanding of the drivers of this context dependency is essential to predict effects of global change on ecosystems. To determine how different factors modulate the effect of diversity on multifunctionality, we established a large grassland experiment with 216 communities, crossing a manipulation of plant species richness (1, 4, 8, 20 species) with manipulations of resources (nitrogen enrichment), plant functional composition (gradient in mean specific leaf area [SLA] to manipulate abundances of exploitative, fast-growing vs. conservative, slow-growing species), plant functional diversity (variance in SLA) and enemy abundance (foliar fungal pathogen removal). We measured ten above- and belowground functions, related to productivity, nutrient cycling and energy transfer between trophic levels, and calculated ecosystem multifunctionality. Plant species richness and functional diversity both increased multifunctionality, but their effects were context dependent. Species richness increased multifunctionality only when communities were assembled with fast growing (high SLA) species. This was because slow species were more redundant in their functional effects, whereas different fast species tended to promote different functions. Functional diversity also increased multifunctionality but this effect was dampened by nitrogen enrichment. However, unfertilised, functionally diverse communities still delivered more functions than low diversity, fertilised communities. Our study suggests that a shift towards fast-growing exploitative communities will not only alter ecosystem functioning but also the strength of biodiversity-functioning relationships, which highlights the potentially complex effects of global change on multifunctionality.
P-elements strengthen reproductive isolation within theDrosophila simulansspecies complex
Authors: Serrato-Capuchina Antonio , D’Agostino Emmanuel R. R. , Peede David , Roy Baylee , Isbell Kristin , Wang Jeremy , Matute Daniel R.
Published: August 2020

Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of reproductive isolation between species is poorly understood. Several species ofDrosophilahave been found to harbor P-elements (PEs), yet onlyD. simulansis known to be polymorphic for their presence in wild populations. PEs can cause reproductive isolation between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of reproductive isolation between species. Here, we use thesimulansspecies complex to assess whether differences in PE status betweenD. simulansand its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a PD. simulansfather and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an MD. simulansfather and an M sister-species mother. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that transposable elements can play a role in reproductive isolation and facilitate the process of speciation.

IMPACT SUMMARY

Transposable elements (TEs) are repetitive genetic units found across the tree of life. They play a fundamental role on the evolution of each species’ genome. TEs have been implicated in diversification, extinction, and the origin of novelty. However, their potential role in contributing to the maintenance of species boundaries remains largely understudied. Using whole genome sequences, we compared the relative content of TEs across the three species of theDrosophila simulanscomplex. We find that the presence of one TE,P-element, inD. simulans, and its absence in the sister taxa, differentiates the three species.P-elements (PEs) cause a suite of fitness defects inDrosophilapure-species individuals if their father has PEs but their mother does not, a phenomenon known as hybrid dysgenesis (HD). We thus studied the possibility that PEs enhance isolation between recently-diverged species. In particular, we studied whether the progeny from interspecific crosses were more prone to suffer from HD than pure species. We found that the presence of paternal PEs reduces hybrid female fecundity, mirroring observations of HD described within species. The effect of PEs is stronger in the interspecific hybrids than in pure species. Our results suggest that PEs can strengthen reproductive isolation in well-formed sister species that still hybridize in nature and pose the question of whether other TEs are involved in the formation of species or in their persistence over time.
Structure of the extracellular region of the bacterial type VIIb secretion system subunit EsaA
Authors: Klein Timothy A. , Grebenc Dirk W. , Gandhi Shil Y. , Shah Vraj S. , Kim Youngchang , Whitney John C.
Published: August 2020

Gram-positive bacteria use type VII secretion systems (T7SSs) to export effector proteins that manipulate the physiology of nearby prokaryotic and eukaryotic cells. Several mycobacterial T7SSs have established roles in virulence. By contrast, recent work has demonstrated that the genetically distinct T7SSb pathway found in Firmicutes bacteria more often functions to mediate interbacterial competition. A lack of structural information on the T7SSb has limited the understanding of effector export by this protein secretion apparatus. In this work, we present the 2.4Å crystal structure of the extracellular region of the elusive T7SSb subunit EsaA fromStreptococcus gallolyticus. Our structure reveals that homodimeric EsaA is an elongated, arrow-shaped protein with a surface-accessible ‘tip’, which serves as a receptor for lytic bacteriophages in some species of bacteria. Because it is the only T7SSb subunit large enough to traverse the thick peptidoglycan layer of Firmicutes bacteria, we propose that EsaA plays a critical role in transporting effectors across the entirety of the Gram-positive cell envelope.
Causal evidence for the adaptive benefits of social foraging in the wild
Authors: Snijders Lysanne , Krause Stefan , Tump Alan N. , Breuker Michael , Ortiz Chente , Rizzi Sofia , Ramnarine Indar W. , Krause Jens , Kurvers Ralf H.J.M.
Published: August 2020

Sociality is a fundamental organizing principle across taxa, thought to come with a suite of adaptive benefits. However, making causal inferences about these adaptive benefits requires experimental manipulation of the social environment, which is rarely feasible in the field. Here we manipulated the number of conspecifics in Trinidadian guppies (Poecilia reticulata) in the wild, and quantified how this affected a key benefit of sociality, social foraging, by investigating several components of foraging success. As adaptive benefits of social foraging may differ between sexes, we studied males and females separately, expecting females, the more social and risk-averse sex, to benefit more from conspecifics than males. Conducting over 1,600 foraging trials, we found that in both sexes, increasing the number of conspecifics led to faster detection of novel food patches and a higher probability of feeding following detection of the patch, resulting in greater individual resource consumption. The slope of the latter relationship differed between the sexes, with males unexpectedly exhibiting a stronger social benefit. Our study provides rare causal evidence for the adaptive benefits of social foraging in the wild, and highlights that sex differences in sociality do not necessarily imply an unequal ability to profit from the presence of others.
Retracing the evolution of kinesin-2 deployment from mouse to worm
Authors: Cleetus Augustine , Merck Georg , Ökten Zeynep
Published: August 2020

During the course of evolution, cells have repurposed homologous motor proteins for the transport of an astonishingly diverse set of intracellular cargo. One prominent example of such diversification is the deployment of the respective kinesin-2 homologs inC. elegans(CeOSM-3) and mouse (MmKIF-17). WhileCeOSM-3 is deployed exclusively inside the cilium as a transport motor, its mouse counterpart behaves as a ciliary cargo. Instead,MmKIF-17 powers many different transport processes in the cytoplasm. Here we turned to functional reconstitution assays to uncover the molecular underpinnings of kinesin-2 deployment. Based on our findings, we propose that cells specified adaptor proteins as strictly conserved ‘on- and off-switches’, and ‘tailored’ the motors to fit the respective switches. This is exemplified by the surprising ability of the mouse adaptor to function as a ciliary on-switch for the distantly relatedCeOSM-3, but not for its ownMmKIF-17 motor. Worms, in contrast, retained ciliary on- and off-switches, and can thus deployCeOSM-3 as a regulatable transport motor inside the cilium.MmKIF-17 escaped this regulatory control by losing its interaction with the ciliary on-switch and has evidently been tailored to fit many different cytoplasmic adaptors over the course of evolution. We could further trace the robustness of an adaptor to serve as a conserved on-switch back to a few strictly conserved residues, which are also present in unicellular organisms. It is therefore conceivable that eukaryotes started to engineer dedicated on- and off-switches early in the evolution and kept their function conserved up to mammals.
Parkinson’s Disease Genetic Risk Evaluation in Microglia Highlights Autophagy and Lysosomal Genes
Authors: Booms Alix , Pierce Steven E. , Coetzee Gerhard A.
Published: August 2020

Genome-wide association studies (GWAS) have uncovered thousands of single nucleotide polymorphisms (SNPs) that are associated with Parkinson’s disease (PD) risk. The functions of most of these SNPs, including the cell type they influence, and how they affect PD etiology remain largely unknown. To identify functional SNPs, we aligned PD risk SNPs within active regulatory regions of DNA in microglia, a cell type implicated in PD development. Out of 6,749 ‘SNPs of interest’ from the most recent PD GWAS metanalysis, 73 were located in open regulatory chromatin as determined by both ATAC-seq and H3K27ac ChIP-seq. We highlight a subset of SNPs that are favorable candidates for further mechanistic studies. These SNPs are located in regulatory DNA at theSLC50A1, SNCA, BAG3, FBXL19, SETD1A, andNUCKS1loci. A network analysis of the genes with risk SNPs in their promoters, implicated substance transport, involving autophagy and lysosomal genes. Our study provides a more focused set of risk SNPs and their associated risk genes as candidates for further follow-up studies, which will help identify mechanisms in microglia that increase the risk for PD.
Vector and cell-culture passaging of dengue clinical samples for virus isolation and amplification does not significantly change genome consensus or frequencies of intra-host viral variants
Authors: Fung Christian K. , Li Tao , Pollett Simon , Alera Maria Theresa , Yoon In-Kyu , Hang Jun , Macareo Louis , Srikiatkhachorn Anon , Ellison Damon , Rothman Alan L. , Fernandez Stefan , Jarman Richard G. , Berry Irina Maljkovic
Published: August 2020

Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low passage number increases viral load, but to date, no studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence, and there is no information on the intra-host virus population changes that may result from viral isolation. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T.splendensinoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 1000x, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found that the nucleotide call concordance (including called iSNVs with variant cutoff at 5%) between direct sera sample and its cultured virus was on average 99.99%. There were a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNV frequencies were also largely preserved between the samples, with an average difference in minor variant frequency of 6.8% (95CI: 3.6%-10%) and 9.6% (95CI: 7%-12.2%) for DENV1 and DENV2, respectively. Furthermore, we found no significant differences in either DENV1 or DENV2 between the sample pairs (clinical sample and isolate) in their number of iSNV positions per genome, or in the difference in variant frequencies (p=0.36 andp=0.13, respectively, F-test). Our results show that low-passage DENV isolates may be used for identification of the majority of their human-derived within-host variant populations, which are increasingly being used for precision tracking of DENV and other RNA viruses.
HDAC1 SUMOylation promotes Argonaute directed transcriptional silencing inC. elegans
Authors: Kim Heesun , Ding Yue-He , Zhang Gangming , Yan Yong-Hong , Conte Darryl , Dong Meng-Qiu , Mello Craig C.
Published: August 2020

Eukaryotic cells use guided search to coordinately control dispersed genetic elements. The transitive effectors of these mechanisms, Argonaute proteins and their small-RNA co-factors, engage nascent RNAs and chromatin-associated proteins to direct transcriptional silencing. The small ubiquitin-like modifier (SUMO) has been shown to promote the induction and maintenance of silent chromatin (called heterochromatin) in yeast, plants, and animals. Here we show that Argonaute-directed transcriptional silencing inC. elegansrequires SUMOylation of the type 1 histone deacetylase HDA-1. SUMOylation of HDA-1 promotes interactions with components of the nucleosome remodeling and deacetylase (NuRD) complex and with the nuclear Argonaute HRDE-1/WAGO-9. Our findings suggest how HDAC1 SUMOylation promotes the association of HDAC and other chromatin remodeling factors with a nuclear Argonaute in order to initiate de novo heterochromatin silencing.
NMR unveils an N-terminal interaction interface on acetylated-α-synuclein monomers for recruitment to fibrils
Authors: Yang Xue , Wang Baifan , Hoop Cody L. , Williams Jonathan K. , Baum Jean
Published: August 2020

Amyloid fibril formation of α-synuclein (αS) is associated with multiple neurodegenerative diseases, including Parkinson’s Disease (PD). Growing evidence suggests that progression of PD is linked to cell-to-cell propagation of αS fibrils, which leads to seeding of endogenous intrinsically disordered monomer via templated elongation and secondary nucleation. A molecular understanding of the seeding mechanism and driving interactions is crucial to inhibit progression of amyloid formation. Here, using relaxation-based solution NMR experiments designed to probe large complexes, we probe weak interactions of intrinsically disordered acetylated-αS (Ac-αS) monomers with seeding-competent Ac-αS fibrils and seeding-incompetent off-pathway oligomers to identify Ac-αS monomer residues at the binding interface. Under conditions that favor fibril elongation, we determine that the first 11 N-terminal residues on the monomer form a common binding site for both fibrils and off-pathway oligomers. Additionally, the presence of off-pathway oligomers within a fibril seeding environment suppresses seeded amyloid formation, as observed through thioflavin-T fluorescence experiments. This highlights that off-pathway αS oligomers can act as an auto-inhibitor against αS fibril elongation. Based on these data taken together with previous results, we propose a model in which Ac-αS monomer recruitment to the fibril is driven by interactions between the intrinsically disordered monomer N-terminus and the intrinsically disordered flanking regions (IDR) on the fibril surface. We suggest that this monomer recruitment may play a role in the elongation of amyloid fibrils and highlight the potential of the IDRs of the fibril as important therapeutic targets against seeded amyloid formation.

Significance

Cell-to-cell spreading of αS fibrils leads to amyloid seeding of endogenous monomer. Detailed atomic-level mechanistic understanding of the fibril seeding process of αS is essential for design of therapeutic approaches against Parkinson’s disease. In light of its complexity, this process remains ill-defined at the molecular level. Using relaxation-based solution NMR experiments, we mapped a common N-terminal binding interface of the Ac-αS intrinsically disordered monomer with Ac-αS fibrils and off-pathway oligomers to elucidate critical monomer–aggregate interactions during seeded aggregation and in equilibrium with mature aggregates. From this work, we propose a new paradigm, in which Ac-αS monomer recruitment to the fibril is driven by interactions between the intrinsically disordered monomer N-terminus and the flanking IDRs on the fibril surface.
The Role of Temperature on the Development of Circadian Rhythms in Honey Bee Workers
Authors: Giannoni-Guzmán Manuel A. , Aleman-Rios Janpierre , Moreno Alexander M. Melendez , Hernandez Gabriel Diaz , Perez Melina , Loubriel Darimar , Giray Tugrul , Agosto-Rivera Jose L.
Published: August 2020

Circadian rhythms in honey bees are involved in various processes that impact colony survival. For example, young nurses take care of the brood constantly throughout the day and lack circadian rhythms, while foragers use the circadian clock to remember and predict food availability in subsequent days. Previous studies suggested that development of circadian rhythms both in the field and the laboratory began around 7-9 days of age. However, not much is understood about the postembryonic development of circadian rhythms in honey bees. In the current study, we examine the effects of socially regulated colony temperature on the ontogeny of circadian rhythms of young workers under controlled laboratory conditions. We hypothesized that temperature plays a key role in the development of circadian rhythmicity in young workers. Our results show that young workers kept at 35°C develop circadian rhythmicity faster and in greater proportion than bees kept at 25°C. In addition, we examine if the effect of colony temperature during the first 48 hours after emergence is enough to observe effects on the rate and proportion of development of circadian rhythmicity. We observed that twice as many individuals that were exposed to 35°C during the first 48 hours develop circadian rhythms compared to individuals kept at 25°C. In addition, we observed differences in the average endogenous period length consistent with temperature compensation of the circadian rhythms between the 25°C and 35°C cohorts. We also observed differences in the degree of period length variation between the 25°C and 35°C cohorts, which combined with the proportion of arrhythmic individuals and survival data suggest that development of circadian rhythms is incomplete in individuals exposed to 25°C adult emergence. This study shows that temperature, which is socially regulated inside the hive, is a key factor that influences the ontogeny of circadian rhythmicity of workers.
Growth hormone receptor (GHR)-expressing neurons in the hypothalamic arcuate nucleus regulate glucose metabolism and energy homeostasis
Authors: de Lima Juliana Bezerra Medeiros , Debarba Lucas Kniess , Khan Manal , Ubah Chidera , Didyuk Olesya , Ayyar Iven , Koch Madelynn , Sadagurski Marianna
Published: August 2020

Growth hormone (GH) receptor (GHR), expressed in different brain regions, is known to participate in the regulation of whole-body energy homeostasis and glucose metabolism. However, GH activation of these GHR-expressing neurons is less studied. We have generated a novel GHR-driven Cre recombinase transgenic mouse line (GHRcre) in combination with the floxed tdTomato reporter mouse line we tracked and activated GHR-expressing neurons in different regions of the brain. We focused on neurons of the hypothalamic arcuate nucleus (ARC) where GHR was shown to elicit a negative feedback loop that regulates GH production. We found that ARCGHR+neurons are co-localized with AgRP, GHRH, and somatostatin neurons, which were activated by GH stimulation. Using designer receptors exclusively activated by designer drugs (DREADDs) to control GHRARCneuronal activity, we revealed that activation of GHRARCneurons was sufficient in regulating distinct aspects of energy balance and glucose metabolism. Overall, our study provides a novel mouse model to studyin vivoregulation and physiological function of GHR-expressing neurons in various brain regions. Furthermore, we identified for the first time specific neuronal population that responds to GH and directly linked it to metabolic responsesin vivo.
Harnessing population-specific protein truncating variants to improve the annotation of loss-of-function alleles
Authors: Skitchenko Rostislav K. , Kornienko Julia S. , Maksiutenko Evgeniia M. , Glotov Andrey S. , Predeus Alexander V. , Barbitoff Yury A.
Published: August 2020

Accurate annotation of putative loss-of-function (pLoF) variants is an important problem in human genomics and disease, which recently drew substantial attention. Since such variants in disease-related genes are under strong negative selection, their frequency across major ancestral groups is expected to be highly similar. In this study, we tested this assumption by systematically assessing the presence of highly population-specific protein-truncating variants (PTVs) in human genes using latest population-scale data. We discovered an unexpectedly high incidence of population-specific PTVs in all major ancestral groups. This does not conform to a recently proposed model, indicating either systemic differences in disease penetrance in different human populations, or a failure of current annotation criteria to accurately predict the loss-of-function potential of PTVs. We show that low-confidence pLoF variants are enriched in genes with non-uniform PTV count distribution, and developed a computational tool called LoFfeR that can efficiently predict tolerated pLoF variants. To evaluate the performance of LoFfeR, we use a set of known pathogenic and benign PTVs from the ClinVar database, and show that LoFfeR allows for a more accurate annotation of low-confidence pLoF variants compared to existing methods. Notably, only 4.4% of protein-truncating gnomAD SNPs in canonical transcripts can be filtered out using a recommended threshold value of the recently proposedpextscore, while up to 10.9% of such variants are filtered using LoFfeR with the same false positive rate. Hence, we believe that LoFfeR can be used for additional filtering of low-confidence pLoF variants in population genomics and medical genetics studies.