bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel function of transcription factor Uga3 as an activator of branched-chain amino acid permease BAP2 gene expression
Authors: Muñoz Sebastián A. , Gulias Juan F. , Valencia-Guillén Jenniffer , Correa-García Susana , Bermúdez-Moretti Mariana
Published: October 2019

Gene regulation in yeast occurs at the transcription level, i.e. the basal level of expression is very low and increased transcription requires gene-specific transcription factors allowing the recruitment of basal transcriptional machinery. Saccharomyces cerevisiae BAP2 gene encodes the permease responsible for most uptake of leucine, valine and isoleucine, amino acids that this yeast can use as nitrogen sources. Moreover, BAP2 expression is known to be induced by the presence of amino acids such as leucine. In this context, the results presented in this paper show that BAP2 is an inducible gene in the presence of nitrogen-non-preferred source proline but exhibits high constitutive non-inducible expression in nitrogen-preferred source ammonium. BAP2 expression is regulated by the SPS sensor system and transcription factors Leu3, Gcn4 and Dal81. This can be achieved or not through a direct binding to the promoter depending on the quality of the nitrogen source. We further demonstrate here that an interaction occurs in vivo between Uga3 ‒ the transcriptional activator responsible for γ-aminobutyric acid (GABA)-dependent induction of the GABA genes ‒ and the regulatory region of the BAP2 gene, which leads to an increase in BAP2 transcription.
Reorganization of nurse scheduling reduces the risk of healthcare associated infections
Authors: Valdano Eugenio , Poletto Chiara , Boëlle Pierre-Yves , Colizza Vittoria
Published: October 2019

Background

Efficient prevention and control of healthcare associated infections (HAIs) is still an open problem.

Objective

To design efficient hospital infection control strategies by reorganizing nurse scheduling.

Design, setting, and participants

Proof-of-concept modeling study based on high-resolution contact data from wearable sensors between patients, nurses, doctors, and administrative staff at a short-stay geriatric ward of a University hospital.

Methods

We considered isolation and contact removal to identify the most important class of individuals for HAI dissemination. We introduced a novel intervention based on the reorganization of nurse scheduling. This strategy switches and reassigns nurses’ tasks through the optimization of shift timelines, while respecting feasibility constraints and satisfying patient-care requirements. We evaluated the impact of interventions through a Susceptible-Colonized-Susceptible transmission model on the empirical and reorganized contacts.

Results

Isolation and contact removal produced the largest risk reduction when acting on nurses. Reorganizing their schedules reduced HAI risk by 27% (95% confidence interval [24,29]%) while preserving the timeliness, number, and duration of contacts. More than 30% nurse-nurse contacts should be avoided to achieve an equivalent reduction through simple contact removal. No overall change in the number of nurses per patient resulted from the intervention.

Conclusions

Reorganization of nurse scheduling offers an alternative change of practice that substantially limits HAI risk in the ward while ensuring the timeliness and quality of healthcare services. This calls for including optimization of nurse scheduling practices in programs for better infection control in hospitals.
Sugar or Salt (“SOS”): a protocol for a UK multicentre randomised trial of mannitol and hypertonic saline in severe traumatic brain injury and intracranial hypertension
Authors: Rowland MJ , Veenith T , Scomparin C , Wilson MH , Hutchinson PJ , Kolias AG , Lall R , Regan S , Mason J , Andrews PJD , Horner D , Naisbitt J , Devrell A , Malins A , Dark P , McAuley DF , Perkins GD
Published: October 2019

Hyperosmolar solutions are widely used to treat raised intracranial pressure (ICP) following severe traumatic brain injury (TBI). Although mannitol has historically been the most frequently administered, hypertonic saline (HTS) solutions are increasingly being used. However, definitive evidence regarding their comparative effectiveness is lacking. The Sugar or Salt (SOS) Trial is a UK randomised, allocation concealed open label multicentre pragmatic trial designed to determine the clinical and cost-effectiveness of hypertonic saline (HTS) compared with mannitol in the management of patients with severe TBI. Patients requiring intensive care unit admission and intracranial pressure (ICP) monitoring post-TBI will be allocated at random to receive equi-osmolar boluses of either mannitol or HTS following failure of routine first line measures to control ICP. The primary outcome for the study will be the Extended Glasgow Outcome Scale (GOS-E) assessed at 6 months after randomisation. Results will inform current clinical practice in the routine use of hyperosmolar therapy as well as assess the impact of potential side effects. Pre-planned longer term clinical and cost effectiveness analyses will further inform the use of these treatments.
Phase I assessments of first-in-human administration of a novel malaria anti-sporozoite vaccine candidate, R21 in matrix-M adjuvant, in UK and Burkinabe volunteers
Authors: Venkatraman Navin , Tiono Alfred B. , Bowyer Georgina , Powlson Jonathan , Collins Katharine A. , Coulibaly Sam , Datoo Mehreen , Silman Daniel , Ouedraogo Alphonse , Nébié Issa , Imoukhuede Egeruan , Brod Florian , Folegatti Pedro , Dickinson Emma , Jamieson Sophie , Bougouma Edith C. , Wright Daniel , Bellamy Duncan , Diarra Amidou , Bliss Carly M. , Morter Richard , Glenn Greg , Fries Louis F. , Reimer Jenny , Lovgren-Bengtsson Karin , Baker Megan , Poulton Ian , Moyle Sarah , Berrie Eleanor , Green Nicola , Mukhopadhyay Ekta , Viebig Nicola , Angus Brian , Lawrie Alison , Roberts Rachel , Gilbert Sarah C. , Lewis David J.M. , Sirima Sodiomon B. , Ewer Katie J. , Hill Adrian V. S.
Published: October 2019

Background

Improvements in malaria control have stalled recently and new tools are needed. The R21 vaccine is comprised of the malaria circumsporozoite protein fused to hepatitis B surface antigen (HBsAg). It forms particles that lack the excess HBsAg in the frequently tested malaria vaccine candidate, RTS,S/AS01B.

Methods

We conducted an open-label, first-in-human, Phase Ia study evaluating safety and immunogenicity of R21 administered alone and with the saponin-based adjuvant, Matrix-M™ (MM). Twenty-eight healthy adults received three doses of R21 given intramuscularly 4 weeks apart. We subsequently conducted a Phase Ib randomised, controlled trial in West African adults.

Findings

Vaccinations were well tolerated, and the majority of local and systemic adverse events were mild. Reactogenicity was significantly lower in Burkinabe than UK vaccinees (p<0.0001). Antibody responses increased significantly 28 days after the 2nd vaccination in UK volunteers. Antibody responses to R21 in all dose groups (2μg, 10μg and 50μg) were comparable to those of 50μg RTS,S/AS01B in malaria-naïve adults at 28 days after final vaccination. The 10μg dose induced more durable responses, with 2-fold higher NANP-specific IgG titres at 6 months compared with the 2μg and 50μg dose groups. R21 also boosted baseline humoral responses in Burkinabe adults with well-maintained responses suggesting natural boosting.

Interpretation

R21 adjuvanted with MM is safe and has comparable immunogenicity to RTS,S/AS01B, even when administered at a five-fold lower 10μg dose in UK and African populations. This forms the basis for efficacy testing of this vaccine which could prove to be particularly cost-effective to manufacture and deploy.
Olanzapine Combined with 5-HT3 RA Plus Dexamethasone for Prevention and Treatment of Chemotherapy-Induced Nausea and Vomiting in High and Moderate Emetogenic Chemotherapy: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Zhou jianguo , HUang Lang , Jin Su-Han , Xc Cheng , Ma Hu
Published: October 2019

Objectives: We performed a pooled analysis to evaluate the efficacy and adverse events (AEs) of olanzapine combined with dexamethasone plus compared with 5 HT3 RA plus dexamethasone for the prevention and treatment of chemotherapy-induced nausea and vomiting (CINV) in high and moderate emetogenic chemotherapy based on randomized controlled trials (RCTs).
Methods: PubMed, EMBASE, Web of Science, the Cochrane Library, China Biomedical Literature database (CBM), WanFang Database, China National Knowledge Infrastructure (CNKI), and Chinese Science and Technology Periodical Database (VIP) (from their inception to April 2019) were searched to capture relevant articles. Relative risk (RR) with 95% confidence intervals (CIs) for CINV and AEs were all extracted or calculated.
Result: Eleven studies with 1107 cancer patients were involved in this review. The pooled RR of delayed CINV (RR=0.50, 95%CI: 0.38 0.66, P<0.01) were significant decreased in olanzapine group. Besides, the occurrence of insomnia was statistically decreased. The rate of acute CINV (RR=0.60, 95%CI: 0.48 0.75, P<0.01) was also significant decreased. However only the percent of CINV III and CINV IV were significant deceased in acute and delayed phase. Subgroup analysis demonstrated that the efficacy was no statistically significant difference between 5mg and 10mg for olanzapine.
Conclusion: Olanzapine significant decreased the occurrence of CINV III and CINV IV and insomnia in high and moderately emetogenic chemotherapy. Compared with 10mg per day, 5mg oral may be more appropriate for patients with cancer.
Immune response and endocytosis pathways are associated with the resilience against Alzheimer’s Disease
Authors: Tesi Niccolò , van der Lee Sven J. , Hulsman Marc , Jansen Iris E. , Stringa Najada , van Schoor Natasja M. , Scheltens Philip , van der Flier Wiesje M. , Huisman Martijn , Reinders Marcel J. T. , Holstege Henne
Published: October 2019

Developing Alzheimer’s disease (AD) is influenced by multiple genetic variants that are involved in five major AD-pathways. Per individual, these pathways may differentially contribute to the modification of the AD-risk. The pathways involved in the resilience against AD have thus far been poorly addressed. Here, we investigated to what extent each molecular mechanism associates with (i) the increased risk of AD and (ii) the resilience against AD until extreme old age, by comparing pathway-specific polygenic risk scores (pathway-PRS). We used 29 genetic variants associated with AD to develop pathway-PRS for five major pathways involved in AD. We developed an integrative framework that allows multiple genes to associate with a variant, and multiple pathways to associate with a gene. We studied pathway-PRS in the Amsterdam Dementia Cohort of well-phenotyped AD patients (N=1,895), Dutch population controls from the Longitudinal Aging Study Amsterdam (N=1,654) and our unique 100-plus Study cohort of cognitively healthy centenarians who avoided AD (N=293). Last, we estimated the contribution of each pathway to the genetic risk of AD in the general population. All pathway-PRS significantly associated with increased AD-risk and (in the opposite direction) with resilience against AD (except for angiogenesis, p<0.05). The pathway that contributed most to the overall modulation of AD-risk was β-amyloid metabolism (29.6%), which was driven mainly by APOE-variants. After excluding APOE variants, all pathway-PRS associated with increased AD-risk (except for angiogenesis, p<0.05), while specifically immune response (p=0.003) and endocytosis (p=0.0003) associated with resilience against AD. Indeed, the variants in these latter two pathways became the main contributors to the overall modulation of genetic risk of AD (45.5% and 19.2%, respectively). The genetic variants associated with the resilience against AD indicate which pathways are involved with maintained cognitive functioning until extreme ages. Our work suggests that a favorable immune response and a maintained endocytosis pathway might be involved in general neuro-protection, which highlight the need to investigate these pathways, next to β-amyloid metabolism.
Matching the forecast horizon with the relevant spatial and temporal processes and data sources
Authors: Adler Peter B. , White Ethan P. , Cortez Michael H.
Published: October 2019

Most phenomenological, statistical models used to generate ecological forecasts take either a time-series approach, based on long-term data from one location, or a space-for-time approach, based on data describing spatial patterns across environmental gradients. Here we consider how the forecast horizon determines whether more accurate predictions come from the time-series approach, the space-for-time approach, or a combination of the two. We use two simulated case studies to show that forecasts for short and long forecast horizons need to focus on different ecological processes, which are reflected in different kinds of data. In the short-term, dynamics reflect initial conditions and fast processes such as birth and death, and the time-series approach makes the best predictions. In the long-term, dynamics reflect the additional influence of slower processes such as evolutionary and ecological selection, colonization and extinction, which the space-for-time approach can effectively capture. At intermediate time-scales, a weighted average of the two approaches shows promise. However, making this weighted model operational will require new research to predict the rate at which slow processes begin to influence dynamics.
Systematic Identification of Novel Cancer Genes through Analysis of Deep shRNA Perturbation Screens
Authors: Montazeri Hesam , Coto-Llerena Mairene , Bianco Gaia , Zangene Ehsan , Taha-Mehlitz Stephanie , Paradiso Viola , Srivatsa Sumana , de Weck Antoine , Roma Guglielmo , Lanzafame Manuela , Bolli Martin , Beerenwinkel Niko , von Flüe Markus , Terracciano Luigi M. , Piscuoglio Salvatore , Ng Charlotte K. Y.
Published: October 2019

Background

Systematic perturbation screens provide comprehensive resources for the elucidation of cancer driver genes, including rarely mutated genes that are missed by approaches focused on frequently mutated genes and driver genes for which the basis for oncogenicity is non-genetic. The perturbation of many genes in relatively few cell lines in such functional screens necessitates the development of specialized computational tools with sufficient statistical power.

Results

Here we developed APSiC (Analysis ofPerturbationScreens foridentifying novelCancer genes) that can identify genetic and non-genetic drivers even with a limited number of samples. Applying APSiC to the large-scale deep shRNA screen Project DRIVE, APSiC identified well-known, pan-cancer genetic drivers, novel putative genetic drivers known to be dysregulated in specific cancer types and the context dependency of mRNA-splicing between cancer types. Additionally, APSiC discovered a median of 28 and 35 putative non-genetic oncogenes and tumor suppressor genes, respectively, for individual cancer types, including genes involved in genome stability maintenance and cell cycle. We functionally demonstrated thatLRRC4B, a putative non-genetic tumor suppressor gene that has not previously been associated with carcinogenesis, suppresses proliferation by delaying cell cycle and modulates apoptosis in breast cancer.

Conclusion

We demonstrate APSiC is a robust statistical framework for discovery of novel cancer genes through analysis of large-scale perturbation screens. The analysis of DRIVE using APSiC is provided as a web portal and represents a valuable resource for the discovery of novel cancer genes.
Multi-taxon inventory reveals highly consistent biodiversity responses to ecospace variation
Authors: Brunbjerg Ane Kirstine , Bruun Hans Henrik , Dalby Lars , Classen Aimée T. , Fløjgaard Camilla , Frøslev Tobias G. , Hansen Oskar Liset Pryds , Høye Toke Thomas , Moeslund Jesper Erenskjold , Svenning Jens-Christian , Ejrnæs Rasmus
Published: October 2019

Amidst the global biodiversity crisis, identifying drivers of biodiversity variation remains a key challenge. Scientific consensus is limited to a few macroecological rules, such as species richness increasing with area, which provide limited guidance for conservation. In fact, few agreed ecological principles apply at the scale of sites or reserve management, partly because most community-level studies are restricted to single habitat types and species groups. We used the recently proposedecospaceframework and a comprehensive data set for aggregating environmental variation to predict multi-taxon diversity. We studied richness of plants, fungi, and arthropods in 130 sites representing the major terrestrial habitat types in Denmark. We found the abiotic environment (ecospace position) to be pivotal for the richness of primary producers (vascular plants, mosses, and lichens) and, more surprisingly, little support for ecospace continuity as a driver. A peak in richness at intermediate productivity adds new empirical evidence to a long-standing debate over biodiversity responses to productivity. Finally, we discovered a dominant and positive response of fungi and insect richness to organic matter accumulation and diversification (ecospace expansion). Two simple models of producer and consumer richness accounted for 77 % of the variation in multi-taxon species richness suggesting a significant potential for generalization beyond individual species responses. Our study widens the traditional conservation focus on vegetation and vertebrate populations unravelling the importance of diversification of carbon resources for diverse heterotrophs, such as fungi and insects.
manta- a clustering algorithm for weighted ecological networks
Authors: Röttjers Lisa , Faust Karoline
Published: October 2019

Microbial network inference and analysis has become a successful approach to generate biological hypotheses from microbial sequencing data. Network clustering is a crucial step in this analysis. Here, we present a novel heuristic flow-based network clustering algorithm, which equals or outperforms existing algorithms on noise-free synthetic data.mantacomes with unique strengths such as the ability to identify nodes that represent an intermediate between clusters, to exploit negative edges and to assess the robustness of cluster membership.mantadoes not require parameter tuning, is straightforward to install and run, and can easily be combined with existing microbial network inference tools.
Mitochondrial-Y chromosome epistasis inDrosophila melanogaster
Authors: Ågren J. Arvid , Munasinghe Manisha , Clark Andrew G.
Published: October 2019

The coordination between mitochondrial and nuclear genes is crucial to eukaryotic organisms. Predicting the nature of these epistatic interactions can be difficult because of the transmission asymmetry of the genes involved. While autosomes and X-linked genes are transmitted through both sexes, genes on the Y chromosome and in the mitochondrial genome are uniparentally transmitted through males and females respectively. Here, we generate 36 otherwise isogenicDrosophila melanogasterstrains differing only in the geographical origin of their mitochondrial genome and Y chromosome to experimentally examine the effects of the uniparentally inherited parts of the genome, as well as their interaction, in males. We assay longevity and gene expression through RNA-sequencing. We detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis, in both traits. In particular, genes involved in male reproduction appear to be especially sensitive. Despite these interactions, we find no evidence that the mitochondrial genome and Y chromosome are co-adapted within a geographic region. Overall, our study demonstrates a key role for the uniparentally inherited parts of the genome for male biology, but also that mito-nuclear interactions are complex and not easily predicted from simple transmission asymmetries.
Reliability of single-subject neural activation patterns in speech production tasks
Authors: Frankford Saul A. , Nieto-Castañón Alfonso , Tourville Jason A. , Guenther Frank H.
Published: October 2019

Speech neuroimaging research targeting individual speakers could help elucidate differences that may be crucial to understanding speech disorders. However, this research necessitates reliable brain activation across multiple speech production sessions. In the present study, we evaluated the reliability of speech-related brain activity measured by functional magnetic resonance imaging data from twenty neuro-typical subjects who participated in two experiments involving reading aloud simple speech stimuli. Using traditional methods like the Dice and intraclass correlation coefficients, we found that most individuals displayed moderate to high reliability. We also found that a novel machine-learning subject classifier could identify these individuals by their speech activation patterns with 97% accuracy from among a dataset of seventy-five subjects. These results suggest that single-subject speech research would yield valid results and that investigations into the reliability of speech activation in people with speech disorders are warranted.
Topography, Spectral Characteristics, and Extra-to-Intracranial Propagation Pathways of EMG
Authors: Lahr J. , Fiederer L.D.J. , Glanz O. , Schulze-Bonhage A. , Ball T.
Published: October 2019

Objective

Intracranial EEG (iEEG) plays an increasingly important role in neuroscientific research and can provide informative control signal for brain-machine interfaces (BMI). While it is clear that electromyographic (EMG) activity of extracranial origin reaches intracranial recordings, the topographic and spectral characteristics of intracranial EMG have been scarcely investigated. It is currently unclear how these characteristics compare to those of physiological brain activity. Little is also known about the exact pathways of extra- to intracranial volume conduction, including the role of craniotomy defects.

Methods

In 5 epilepsy patients under invasive pre-neurosurgical EEG monitoring, we examined chewing-related effects (ChREs) as a source of intracranial EMG activity and compared those effects with physiological brain activity of 9 patients during several behavioural tasks. These included speech production, finger movements, and music perception. Further, we analyzed the association of craniotomy defects (burr-holes and saw-lines) and the intracranial EMG-effects based on the individual post-operative images.

Results

ChRE presented with a spatially smooth distribution across almost all intracranial electrodes with the maximum below the temporal muscle. In contrast, the responses of neural origin were spatially more focalized. ChREs were broad-banded and had a higher spectral power and affected higher frequencies than event-related neural activity. ChRE were largely independent of the individual configuration of craniotomy defects. However, we found indications that the silicone sheet, in which electrocorticography (ECoG) electrodes are embedded, attenuates EMG influences, when sufficiently large.

Conclusion

The present work is the first comprehensive evaluation of topographic and spectral characteristics of EMG effects in iEEG based on a large sample of subjects. It shows that chewing-related EMG can affect iEEG recordings with higher power than typical physiological brain activity, especially in higher spectral frequencies. As the topographic pattern of ChRE is largely independent of the individual position of craniotomy defects, a direct pathway of volume conduction through the intact skull plays an important role for extra- to-intracranial signal propagation. Intracranial EMG activity related to natural behavior should be accounted for in neuroscientific and BMI applications, especially when based on high-frequency iEEG components. A detailed knowledge of EMG properties may help to design both EMG-reducing algorithms and ECoG grids with a high shielding factor.

Highlights

First comprehensive description of chewing-related EMG artifacts in iEEG recordings

EMG artifacts and brain activity have distinct topographic and spectral iEEG characteristics

Chewing EMG reaches the brain with higher spectral power than task-related brain activity

Chewing-related EMG artifacts are largely independent of the the position of craniotomy defects
Transcriptional Profiling of Primate Central Nucleus of the Amygdala Neurons to Understand the Molecular Underpinnings of Early Life Anxious Temperament
Authors: Kovner Rothem , Souaiaia Tade , Fox Andrew S. , French Delores A. , Goss Cooper. E. , Roseboom Patrick H. , Oler Jonathan A. , Riedel Marissa K. , Fekete Eva M. , Fudge Julie L. , Knowles James A. , Kalin Ned H.
Published: October 2019

Children exhibiting extreme anxious temperament (AT) are at an increased risk to develop anxiety and depression. Work in young rhesus monkeys mechanistically links the central nucleus of the amygdala (Ce) to AT. Here, we used laser capture microscopy and RNA sequencing in 47 young rhesus monkeys to investigate AT‘s molecular underpinnings by focusing on lateral Ce (CeL) neurons. We found 528 AT-related transcripts, including protein kinase C type-delta (PKCδ), a CeL microcircuit cell marker implicated in rodent threat processing. We characterized PKCδ neurons in the rhesus CeL, compared their distribution to the mouse, and demonstrated that a subset of these neurons project to the laterodorsal bed nucleus of the stria terminalis (BSTLd). These findings present evidence in the primate of a CeL to BSTLd circuit that maybe relevant to understanding human anxiety and points to specific molecules within this circuit that could serve as potential treatment targets for anxiety disorders.
Phenotypic and Genotypic Antiviral Resistance Testing of HSV-1 Causing Recurrent Cutaneous Lesions in a Patient with DOCK8 Deficiency
Authors: Casto Amanda M. , Stout Sean C. , Selvarangan Rangaraj , Freeman Alexandra F. , Newell Brandon D. , Stahl Erin D. , Greninger Alexander L. , Yin Dwight E.
Published: October 2019

Antiviral resistance frequently complicates treatment of herpes simplex virus (HSV) infections in immunocompromised patients. Here we review the case of an adolescent boy with dedicator of cytokinesis 8 (DOCK8) deficiency, who experienced recurrent infections with resistant HSV-1. We used both phenotypic and genotypic methodologies to characterize the resistance profile of HSV-1 in the patient and conclude that genotypic testing outperformed phenotypic testing. We also present the first analysis of intrahost HSV-1 evolution in an immunocompromised patient. While HSV-1 can remain static in an immunocompetent individual for decades, the virus from this patient rapidly acquired genetic changes throughout its genome.
Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly (MCIA) Complex Factors in the Biogenesis of Complex I
Authors: Formosa Luke E. , Muellner-Wong Linden , Reljic Boris , Sharpe Alice J. , Beilharz Traude H. , Lazarou Michael , Stroud David A. , Ryan Michael T.
Published: October 2019

Mitochondrial Complex I harbors 7 mitochondrial and 38 nuclear-encoded subunits. Its biogenesis requires the assembly and integration of distinct intermediate modules, mediated by numerous assembly factors. The Mitochondrial Complex I Intermediate Assembly (MCIA) complex, containing assembly factors NDUFAF1, ECSIT, ACAD9, and TMEM126B, is required for building the intermediate ND2-module. The role of the MCIA complex and the involvement of other proteins in the biogenesis of this module is unclear. Cell knockout studies reveal that while each MCIA component is critical for complex I assembly, a hierarchy of stability exists centred on ACAD9. We also identify TMEM186 and COA1 asbona fidecomponents of the MCIA complex with loss of either resulting in in MCIA complex defects and reduced complex I assembly. TMEM186 enriches with newly translated ND3, while COA1 enriches with ND2. Our findings provide new functional insights into the essential nature of the MCIA complex in complex I assembly.
A toolbox of Stable Integration Vectors (SIV) in the fission yeastSchizosaccharomyces pombe
Authors: Vještica Aleksandar , Marek Magdalena , N’kosi Pedro , Merlini Laura , Liu Gaowen , Bérard Melvin , Billault-Chaumartin Ingrid , Martin Sophie G
Published: October 2019

Schizosaccharomyces pombeis a widely used model organism that resembles higher eukaryotes in many aspects of cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, yield unstable genomic loci. We overcome this problem by designing a new series of Stable Integration Vectors (SIV) that target four different prototrophy genes. SIV produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.
In vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
Authors: VanDusen Nathan J. , Lee Julianna Y. , Gu Weiliang , Sethi Isha , Zheng Yanjiang , King Justin S. , Zhou Ping-Zhu , Suo Shengbao , Guo Yuxuan , Ma Qing , Yuan Guo-Cheng , Pu William T.
Published: October 2019

Between birth and adulthood cardiomyocytes (CMs) undergo dramatic changes in size, ultrastructure, metabolism, and gene expression, in a process collectively referred to as CM maturation. The transcriptional network that coordinates CM maturation is poorly understood, creating a bottleneck for cardiac regenerative medicine. Forward genetic screens are a powerful, unbiased method to gain novel insights into transcriptional networks, yet this approach has rarely been used in vivo in mammals because of high resource demands. Here we utilized somatic mutagenesis to perform the first reported in vivo CRISPR genetic screen within a mammalian heart. We discovered and validated several novel transcriptional regulators of CM maturation. Among them were RNF20 and RNF40, which form a complex that monoubiquitinates H2B on lysine 120. Mechanistic studies indicated that this epigenetic mark controls dynamic changes in gene expression required for CM maturation. These insights into CM maturation will inform efforts in cardiac regenerative medicine. More broadly, our approach will enable unbiased forward genetics across mammalian organ systems.
Accurate and Complete Genomes from Metagenomes
Authors: Chen Lin-Xing , Anantharaman Karthik , Shaiber Alon , Eren A. Murat , Banfield Jillian F.
Published: October 2019

Genomes are an integral component of the biological information about an organism and, logically, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
DHHC20 palmitoyl-transferase reshapes the membrane to foster catalysis
Authors: Stix R. , Song J. , Banerjee A. , Faraldo-Gómez J.D.
Published: October 2019

Cysteine palmitoylation, a form of S-acylation, is a key post-translational modification in cellular signaling. This type of reversible lipidation is catalyzed by a family of integral membrane proteins known as DHHC acyltransferases. The first step in the S-acylation process is the recognition of free acyl-CoA from the lipid bilayer. The DHHC enzyme then becomes auto-acylated, at a site defined by a conserved Asp-His-His-Cys motif. This reaction entails ionization of the catalytic Cys. Intriguingly, in known DHHC structures this catalytic Cys appears to be exposed to the hydrophobic interior of the lipid membrane, which would be highly unfavorable for a negatively charged nucleophile, thus hindering auto-acylation. Here, we use biochemical and computational methods to reconcile these seemingly contradicting facts. First, we experimentally demonstrate that human DHHC20 is active when reconstituted in POPC nanodiscs. Microsecond-long all-atom molecular dynamics simulations are then calculated for hDHHC20 and for different acyl-CoA forms, also in POPC. Strikingly, we observe that hDHHC20 induces a drastic deformation in the membrane, particularly on the cytoplasmic side where auto-acylation occurs. As a result, the catalytic Cys becomes hydrated and optimally positioned to encounter the cleavage site in acyl-CoA. In summary, we hypothesize that DHHC enzymes locally reshape the membrane to foster a morphology that is specifically adapted for acyl-CoA recognition and auto-acylation.

Significance Statement

Palmitoylation, the most common form of S-acylation and the only reversible type of protein lipidation, is ubiquitous in eukaryotic cells. In humans, for example, it has been estimated that as much as ∼10% of the proteome becomes palmitoylated, i.e. thousands of proteins. Accordingly, protein palmitoylation touches every important aspect of human physiology, both in health and disease. Despite its biological and biomedical importance, little is known about the molecular mechanism of the enzymes that catalyze this post-translational modification, known as DHHC acyltransferases. Here, we leverage the recently-determined atomic-resolution structure of human DHHC20 to gain novel insights into the mechanism of this class of enzymes, using both experimental and computational approaches.
Antibody feedback limits the expansion of cognate memory B cells but drives the diversification of vaccine-induced antibody responses
Authors: McNamara Hayley A. , Idris Azza H. , Sutton Henry J. , Flynn Barbara J. , Cai Yeping , Wiehe Kevin , Lyke Kirsten E. , Chatterjee Deepyan , KC Natasha , Chakravarty Sumana , Sim B. Kim Lee , Hoffman Stephen L. , Bonsignori Mattia , Seder Robert A. , Cockburn Ian A.
Published: October 2019

Generating sufficient antibody to block infection is a key challenge for vaccines against malaria. Here we show that antibody titres to a key target, the repeat region of thePlasmodium falciparumcircumsporozoite protein (PfCSP), plateaued after two immunizations in a clinical trial of the radiation-attenuated sporozoite vaccine. To understand the mechanisms limiting vaccine responsiveness, we developed Ig-knockin mice with elevated numbers ofPfCSP-binding B cells. We determined that recall responses were inhibited by antibody feedback via epitope masking of the immunodominantPfCSP repeat region. Importantly, the amount of antibody that prevents boosting is below the amount of antibody required for protection. Finally, while antibody feedback limited responses to thePfCSP-repeat region in vaccinated volunteers, potentially protective subdominant responses to C-terminal regions did expand with subsequent boosts. These data suggest that antibody feedback drives the diversification of immune responses and that vaccination for malaria will require the targeting of multiple antigens.
The tip of the VgrG spike is essential to functional type VI secretion assembly in Acinetobacter baumannii
Authors: Lopez Juvenal , Ly Pek Man , Feldman Mario F.
Published: October 2019

The type VI secretion system (T6SS) is a critical weapon in bacterial warfare between Gram-negative bacteria. Although invaluable for niche establishment, this machine represents an energetic burden to its host bacterium. Acinetobacter baumannii is an opportunistic pathogen that poses a serious threat to public health due to its high rates of multidrug resistance. In some A. baumannii strains, the T6SS is transcriptionally downregulated by large multidrug-resistance plasmids. Other strains, such as the clinical isolate AbCAN2, express T6SS-related genes but lack T6SS activity under laboratory conditions, despite not harboring these plasmids. This suggests that alternative mechanisms exist to repress the T6SS. Here, we employed a transposon mutagenesis approach in AbCAN2 to identify novel T6SS repressors. Our screen revealed that the T6SS of this strain is inhibited by a homolog of VgrG, an essential structural component of all T6SSs reported to date. We named this protein inhibitory VgrG (VgrGi). Biochemical and in silico analyses demonstrated that the unprecedented inhibitory capability of VgrGi is due to a single amino acid mutation in the widely conserved C-terminal domain of unknown function DUF2345. We also show that unlike in other bacteria, the C-terminus of VgrG is essential for functional T6SS assembly in A. baumannii. Our study provides insight into the architectural requirements underlying functional assembly of the T6SS of A. baumannii. We propose that T6SS-inactivating point mutations are beneficial to the host bacterium, as they eliminate the energy cost associated with maintaining a functional T6SS, which appears to be unnecessary for A. baumannii virulence.

Importance

Despite the clinical relevance of A. baumannii, little is known about its fundamental biology. Here, we show that a single amino acid mutation in VgrG, a critical T6SS structural protein, abrogates T6SS function. Given that this mutation was found in a clinical isolate, we propose that the T6SS of A. baumannii is likely not involved in virulence, an idea supported by multiple genomic analyses showing that the majority of clinical A. baumannii strains lack proteins essential to the T6SS. We also show that, unlike in other species, the C-terminus of VgrG is a unique architectural requirement for functional T6SS assembly in A. baumannii, suggesting that over evolutionary time, bacteria have developed changes to their T6SS architecture, leading to specialized systems.
Area requirements to safeguard Earth’s marine species
Authors: Jones Kendall R. , Klein Carissa , Grantham Hedley S. , Possingham Hugh P. , Halpern Benjamin S. , Burgess Neil D. , Butchart Stuart H.M. , Robinson John G. , Kingston Naomi , Watson James E.M.
Published: October 2019

Despite global policy commitments to preserve Earth’s marine biodiversity, many species are in a state of decline. Using data on 22,885 marine species, we identify 8.5 million km2 of priority areas that complement existing areas of conservation and biodiversity importance. New conservation priorities are found in over half (56%) of all coastal nations, with key priority regions in the northwest Pacific Ocean and Atlantic Ocean. We identify where different conservation actions, ranging from marine protected areas to broader policy approaches, may best overcome anthropogenic threats to these areas. This analysis shows 26-41% of the ocean (depending on targets used for species representation) needs to be effectively conserved through a combination of site-based actions and wider policy responses to achieve global conservation and sustainable development agendas.

One Sentence Summary

At least 26% of the ocean needs a combination of site-based conservation and wider policy responses to achieve global conservation goals.
Clustered Functional Domains for Curves and Corners in Cortical Area V4
Authors: Jiang Rundong , Andolina Ian M. , Li Ming , Tang Shiming
Published: October 2019

The ventral visual pathway is crucially involved in integrating low-level visual features into complex representations for objects and scenes. At an intermediate stage of the ventral visual pathway, V4 plays a crucial role in supporting this transformation. Many V4 neurons are selective for shape segments like curves and corners, however it remains unclear whether these neurons are organized into clustered functional domains, a structural motif common across other visual cortices. Using two-photon calcium imaging in awake macaques, we confirmed and localized cortical domains selective for curves or corners in V4. Single-cell resolution imaging confirmed that curve or corner selective neurons were spatially clustered into such domains. When tested with hexagonal-segment stimuli, we find that stimulus smoothness is the cardinal difference between curve and corner selectivity in V4. Combining cortical population responses with single neuron analysis, our results reveal that curves and corners are encoded by neurons clustered into functional domains in V4. This functionally-specific population architecture bridges the gap between the early and late cortices of the ventral pathway and may serve to facilitate complex object recognition.
Evaluation of Commercially Available Exosomal Isolation Kits from Human Plasma
Authors: Sun Yuzhe , Zhen Hefu , Guo Mei , Ye Jingyu , Liu Zhili , Zhang Xiuqing , Yang Yan , Nie Chao
Published: October 2019

Exosomes are cell-derived lipid bilayer particles which are abundant in biological fluids. Exosome is an emerging source of biomarkers to diagnose various human diseases. Sequencing based exosomal studies could provide a comprehensive view of exosomal RNA and protein. To extracted these inclusions, exosomes should be isolated from the plasma first. Several exosome isolation methods were introduced since the discover of exosome. To promote the clinical application of exosomal inclusions, different isolation methods should be compared. We isolated exosomes from human plasma by using user-friendly and commercially available kits, SBI ExoQuick and QIAGEN exoRNeasy. Subsequently, small RNA sequencing was performed with two groups of isolated exosome samples and one group of plasma samples. No fundamental differences of exRNA yield between SC and EQ were found. In RNA profile analysis, the small RNA aligned reads, miRNA pattern, sample clustering varied as a result of methodological differences. Small RNA isolated by ExoQuick presented better data quality and RNA profile than exoRNeasy. This study compared sRNA sequencing data generated from two exosome isolation kits, it provides a reference for future small RNA studies and biomarker prediction in human plasma exosome.
Harm to others acts as a cingulate dependent negative reinforcer in rat
Authors: Hernandez-Lallement Julen , Attah Augustine Triumph , Gazzola Valeria , Keysers Christian
Published: October 2019

Empathy, the ability to share another individual’s emotional state and/or experience, has been suggested to be a source of prosocial motivation by making actions that harm others aversive. The neural underpinnings and evolution of such harm aversion remain poorly understood. Here, we characterize an animal model of harm aversion in which a rat can choose between two levers providing equal amounts of food, but one additionally delivering a footshock to a neighboring rat. We find that independently of sex and familiarity, rats reduce their usage of the preferred lever when it causes harm to a conspecific, displaying an individually varying degree of harm aversion. Prior experience with pain increases this effect. In additional experiments, we show that rats reduce the usage of the harm-inducing lever when it delivers twice, but not thrice the number of pellets than the non-preferred lever, setting boundaries on the magnitude of harm aversion. Finally, we show that pharmacological deactivation of the anterior cingulate cortex, a region we have shown to be essential for emotional contagion, reduces harm aversion, while leaving behavioral flexibility unaffected. This model of harm aversion might help shed light onto the neural basis of psychiatric disorders characterized by reduced harm aversion, including psychopathy and conduct disorders with reduced empathy, and provide an assay for the development of pharmacological treatments of such disorders.
Xyloglucan remodelling defines differential tissue expansion in plants
Authors: Velasquez Silvia Melina , Guo Xiaoyuan , Gallemi Marçal , Aryal Bibek , Venhuizen Peter , Barbez Elke , Dünser Kai , Darino Martin , Pӗnčik Aleš , Novák Ondřej , Kalyna Maria , Mouille Grégory , Benkova Eva , Bhalerao Rishikesh , Mravec Jozef , Kleine-Vehn Jürgen
Published: October 2019

Size control is a fundamental question in biology, showing incremental complexity in case of plants whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Here we show that growth inducing and repressing auxin conditions correlate with reduced and enhanced complexity of extracellular xyloglucans, respectively. In agreement, genetic interference with xyloglucan complexity distinctly modulates auxin-dependent differential growth rates. Our work proposes that an auxin-dependent, spatially defined effect on xyloglucan structure and its effect on cell wall mechanics specify differential, gravitropic hypocotyl growth.
How long is long enough? Decreasing on plant extract lethal effects, over time, affectingAedes aegyptilarval mortality
Authors: Cozzer Gilberto Dinis , de Souza Rezende Renan , Lutinski Junir Antônio , Junior Walter Antônio Roman , Busato Maria Assunta , Dal Magro Jacir , Albeny-Simões Daniel
Published: October 2019

The mosquitoAedes aegyptihas overcome all kinds of human being mosquito control attempts over the last century. Strategies for vector population control resorts to the use of synthetic insecticides, which can lead to problems of intoxication in humans and environmental contamination. We evaluated the effects ofBacillus thuringiensisvar.israelensis(Bti),Ilex paraguariensis(mate-herb) andIlex theezans(caúna-herb) extracts againstA. aegyptilarvae mortality. The bioassays were conducted under controlled laboratory conditions of temperature (27±3°C) and photoperiod (12h). HydroalcoholicI. theezansleaves extract displayed better residual effect compared toI. paraguariensisfruit aqueous extract. Variation in larval mortality was also observed in the exposure periods (low after a few weeks). Low mortality after a few weeks may mean increased the food for mosquito in a oppose effect over time. The residual effect ofBtiwas observed during the 56 days of the study duration (100% of mortality). The strongest residual effect ofI. theezanswas probably due to the presence of chemical on its leaves, such coumarins, hemolytic saponins and cyanogenic glucosides, absent inI. paraguariensis. On the other hand, alternative methods to vector control present risks in a long term scale by reversal of larvicide effect into food resource. Our results contributed to the prospection of natural insecticides and open the possibility for subsequent studies of the use of plant extracts in field situations in a short time scale.