bluuebunny/crossref_metadata_2025 huggingface dataset:
Traditional Healers as Client Advocates in the HIV-endemic Region of Maputo, Mozambique: Results from a qualitative study
Authors: Sundararajan Radhika , Langa Patrício V. , Morshed Trisha , Manuel Sandra
Published: October 2019

Traditional healers are commonly utilized throughout sub-Saharan Africa instead of – and in concert with – biomedical facilities. Traditional healers are trusted providers and prominent community members, and could be important partners in improving engagement with HIV services in endemic contexts. Our study sought to understand the roles of healers in the urban setting of Maputo, Mozambique, where HIV prevalence is high and testing rates are low. Qualitative data were gathered through minimally-structured interviews with 36 healers. Analysis followed an inductive, grounded theory approach. Data reveal three themes relevant to improving engagement with HIV services in this endemic region: 1) healers have positive attitudes towards biomedicine; 2) healers advocate for their sick clients; and 3) clients are reticent to present to biomedical facilities. Healers describe their roles as ‘cooperative’ with biomedical providers to provide healthcare for their clients. Results suggest that healers could be considered critical enablers to effective HIV programs in communities. They have social and symbolic capital that positions them to beneficially influence clients, and are natural partners for interventions to improve uptake of HIV services.
A conceptual model for pluralistic healthcare behavior: results from a qualitative study in southwestern Uganda
Authors: Sundararajan Radhika , Mwanga-Amumpaire Juliet , King Rachel , Ware Norma C
Published: October 2019

Introduction: Medical pluralism, or concurrent utilization of multiple therapeutic modalities, is common in various international contexts, and has been characterized as a factor contributing to poor health outcomes in low-resource settings. Traditional healers are ubiquitous providers in most regions, including the study site of southwestern Uganda. It is not well understood why patients in pluralistic settings continue to engage with both therapeutic healthcare modalities, rather than simply selecting one or the other. The goal of this study was to identify factors that motivate pluralistic healthcare utilization, and create a general, conceptual framework of pluralistic health behavior.

Methods: In-depth interviews were conducted between September 2017 and February 2018 with patients seeking care at traditional healers (N=30) and at an outpatient medicine clinic (N=30) in Mbarara, Uganda; the study is nested within a longitudinal project examining HIV testing engagement among traditional healer-utilizing communities. Inclusion criteria included age 18 years or older, and ability to provide informed consent. Participants were recruited from healer practices representing the range of healer specialties. Following an inductive approach, interview transcripts were reviewed and coded to identify conceptual categories explaining healthcare utilization.

Results: We identified three broad categories relevant to healthcare utilization among study participants: 1) traditional healers treat patients with “care”; 2) biomedicine uses “modern” technologies; and 3) peer “testimony” influences healthcare engagement. These categories describe variables at the healthcare provider, healthcare system, and peer levels that interrelate to motivate individual engagement in pluralistic health resources.

Conclusions: Patients perceive clear advantages and disadvantages to biomedical and traditional care in medically pluralistic settings. We identified factors at the healthcare provider, healthcare system, and peer levels which influence patients' therapeutic itineraries. Our findings provide a basis to improve health outcomes in medically pluralistic settings, and underscore the importance of recognizing traditional healers as important stakeholders in community health.
Alpha-ketoglutarate, an endogenous metabolite, extends lifespan and compresses morbidity in aging mice
Authors: Shahmirzadi Azar Asadi , Edgar Daniel , Liao Chen-Yu , Hsu Yueh-Mei , Lucanic Mark , Shahmirzadi Arash Asadi , Wiley Christopher , Riley Rebeccah , Kaplowitz Brian , Gan Garbo , Kuehnemann Chisaka , Bhaumik Dipa , Campisi Judith , Kennedy Brian K , Lithgow Gordon J.
Published: October 2019

The decline in early life mortality since the 1950s has resulted in dramatic demographic shift towards aged population. Aging manifests as a decline in health, multiple organ dysfunction and increased vulnerability to diseases, which degrades quality of life. A verity of genetic and pharmacological interventions, mostly from non-vertebrate models, have been identified that can enhance lifespan. Whether these interventions extend healthspan, the disease free and functional period of life, has only sometimes been tested and is often a matter of debate. Human aging indices have been developed to assess elements of functional decline with aging (e.g. sarcopenia, cognitive function). However, corresponding comprehensive indices in mice are seldom applied to aging studies. To probe the relationship between healthspan and lifespan extension in mammals, we performed a series of longitudinal, clinically-relevant healthspan measurements. Metabolism and aging are tightly connected and specific perturbations of nutrient-sensing pathways can enhance longevity in laboratory animals. Here we show that alpha-ketoglutarate (delivered in the form of a Calcium salt, CaAKG), a key metabolite in tricarboxylic (TCA) cycle that is reported to extend lifespan in worms, can significantly extend lifespan and healthspan in mice. AKG is involved in various fundamental processes including collagen synthesis and epigenetic changes. Due to its broad roles in multiple biological processes, AKG has been a subject of interest for researchers in various fields. AKG also influences several age-related processes, including stem cell proliferation and osteoporosis. To determine its role in mammalian aging, we administered CaAKG in 18 months old mice and determined its effect on the onset of frailty and survival, discovering that the metabolite promotes longer, healthier life associated with a decrease in levels of inflammatory factors. Interestingly the reduction in frailty was more dramatic than the increase in lifespan, leading us to propose that CaAKG compresses morbidity.
Policy should change to improve invited speaker diversity and reflect trainee diversity
Authors: Hagan Ada K. , Pollet Rebecca M. , Libertucci Josie
Published: October 2019

The biomedical sciences have a problem retaining white women and underrepresented minorities in academia. Despite increases in the representation of these groups in faculty candidate pools, they are still underrepresented at the faculty level, particularly at the Full Professor level. The lack of diverse individuals at the Full Professor level contributes to the attrition of women and under-represented minorities, as it confirms unconscious biases. The presence of unconscious biases contribute to feelings of not belonging by trainees and are amplified by visual representation of who is presented as the “top scientist in their field”. Top scientists are not only defined by the attainment of Full Professorships, but also through invited seminar series. Invitations for faculty to present their research at other university departments is highly valued offer that provides an opportunity for collaborations and networking. However, if invited speakers do not represent the demographics of current trainees, these visual representations of successful scientists may contribute to decreased attitudes of self-identification as a scientist, ultimately resulting in trainees leaving the field or the academy. In this study, we compare invited-speaker demographics to the current trainee demographics in one microbiology and immunology department and find that trainees are not proportionally represented by speakers invited to the department. Our investigation prompted changes in policy for how invited speakers are selected in the future to invite a more diverse group of scientists. To facilitate this process, we developed a set of tips and a web-based resource that allows scientists, committees, and moderators to identify members of under-served groups. These resources can be easily adapted by other fields or sub-fields to promote inclusion and diversity at seminar series’, conferences, and colloquia.
Salt Inducible Kinases as Novel Notch Interactors in the DevelopingDrosophilaRetina
Authors: Şahin H. Bahar , Sayın Sercan , Buğra Kuyaş , Çelik Arzu
Published: October 2019

Developmental processes require strict regulation of proliferation, differentiation and patterning for the generation of final organ size. Aberrations in these fundamental events are critically important in understanding tumorigenesis and cancer progression. Salt inducible kinases (Siks) are evolutionarily conserved genes involved in diverse biological processes, including salt sensing, metabolism, muscle and skeletal development. Recent findings implicate SIKs in tumor suppression or progression. However, their role in development remains largely unknown.

Using a sensitized tumor model in theDrosophilaeye, we show that perturbations of Sik function exacerbates tumor-like tissue overgrowth and metastasis. Furthermore, we show that bothDrosophila Sikgenes,Sik2andSik3, are required for proper eye development. We propose that an important target of Siks may be the Notch pathway, as we demonstrate epistasis between Siks and Notch pathway members and identify putative phosphorylation motifs on Notch, Delta and Fringe. Finally, we investigate Sik expression in the developing retina and show that Sik2 is expressed in all photoreceptors in close proximity to cell junctions, while Sik3 appears to be expressed specifically in R3/R4 cells in the developing eye. Combined, our data suggest thatSikgenes are important in tissue specification, growth, and that their dysregulation may contribute to tumor formation.
Structure-Based Protein Function Prediction using Graph Convolutional Networks
Authors: Gligorijevic Vladimir , Renfrew P. Douglas , Kosciolek Tomasz , Leman Julia Koehler , Berenberg Daniel , Vatanen Tommi , Chandler Chris , Taylor Bryn C. , Fisk Ian M. , Vlamakis Hera , Xavier Ramnik J. , Knight Rob , Cho Kyunghyun , Bonneau Richard
Published: October 2019

The large number of available sequences and the diversity of protein functions challenge current experimental and computational approaches to determining and predicting protein function. We present a deep learning Graph Convolutional Network (GCN) for predicting protein functions and concurrently identifying functionally important residues. This model is initially trained using experimentally determined structures from the Protein Data Bank (PDB) but has significant de-noising capability, with only a minor drop in performance observed when structure predictions are used. We take advantage of this denoising property to train the model on > 200,000 protein structures, including many homology-predicted structures, greatly expanding the reach and applications of the method. Our model learns general structure-function relationships by robustly predicting functions of proteins with ≤ 40% sequence identity to the training set. We show that our GCN architecture predicts functions more accurately than Convolutional Neural Networks trained on sequence data alone and previous competing methods. Using class activation mapping, we automatically identify structural regions at the residue-level that lead to each function prediction for every confidently predicted protein, advancing site-specific function prediction. We use our method to annotate PDB and SWISS-MODEL proteins, making several new confident function predictions spanning both fold and function classifications.
Antiviral signalling in human IPSC-derived neurons recapitulates neurodevelopmental disorder phenotypes
Authors: Warre-Cornish Katherine , Perfect Leo , Nagy Roland , Reid Matthew J. , Mueller Annett , Evans Amanda L. , Ghevaert Cédric , McAlonan Grainne , Loth Eva , Murphy Declan , Srivastava Deepak P. , Price Jack
Published: October 2019

Maternal immune activation increases the risk of neurodevelopmental disorders. Elevated cytokines, such as interferon-gamma (IFNγ), in offspring’s brains play a central role. IFNγ activates an antiviral cellular state, limiting viral entry and replication. In addition, IFNγ has been implicated in brain development. Here, we hypothesise that IFNγ-induced antiviral signalling contributes to molecular and cellular phenotypes associated with neurodevelopmental disorders. We find that transient IFNγ treatment of neural progenitors derived from human induced pluripotent stem cells (hIPSCs) persistently increases neurite outgrowth, phenocopying hIPSC-neurons from autistic individuals. IFNγ upregulates antiviral PML bodies and MHC class I (MHCI) genes, which persists through neuronal differentiation. Critically, IFNγ-induced neurite outgrowth requires both PML and MHCI. We also find that IFNγ disproportionately alters expression of autism and schizophrenia risk genes, suggesting convergence between these genetic and environmental risk factors. Together, these data indicate that IFNγ-induced antiviral signalling may contribute to neurodevelopmental disorder aetiology.
Woody plants constructing tundra soils
Authors: Kemppinen Julia , Niittynen Pekka , Virkkala Anna-Maria , Happonen Konsta , Riihimäki Henri , Aalto Juha , Luoto Miska
Published: October 2019

In tundra, woody plants are expanding towards higher latitudes and altitudes due to increasingly favourable climatic conditions. Their expansion may also occur through increases in the coverage and height of the plants. These shifts may cascade further across the ecosystem, such as in the foundations of tundra: that is, in the soils. Yet, little is known about the effects woody plants have on local soil conditions. Here, we examined if the coverage and height of woody plants affect the growing-season soil moisture and temperature as well as soil organic carbon stocks. We carried out a field observation study in a dwarf shrub–dominated tundra and built a hierarchical model. We found that, after controlling for other possible factors influencing woody plants and soil conditions (namely, topography, snow, and the overall plant coverage), the coverage of woody plants inversely correlated with all three soil conditions. Yet, we found no link between the woody plant height to the soil variables. This indicates that woody plants affect local soil conditions in various ways, depending upon whether their expansion occurs though the growth of coverage or their height. Nevertheless, woody plants likely alter the very ground of the entire tundra system and feedback into the global climate system through the water, energy, and carbon cycles of tundra.
Circuit mechanisms underlying chromatic encoding in Drosophila photoreceptors
Authors: Heath Sarah L. , Christenson Matthias P. , Oriol Elie , Saavedra-Weisenhaus Maia , Kohn Jessica R. , Behnia Rudy
Published: October 2019

Spectral information is commonly processed in the brain through generation of antagonistic responses to different wavelengths. In many species, these color opponent signals arise as early as photoreceptor terminals. Here, we measure the spectral tuning of photoreceptors in Drosophila. In addition to a previously described pathway comparing wavelengths at each point in space, we find a horizontal-cell-mediated pathway similar to that found in mammals. This pathway enables additional spectral comparisons through lateral inhibition, expanding the range of chromatic encoding in the fly. Together, these two pathways enable optimal decorrelation of photoreceptor signals. A biologically constrained model accounts for our findings and predicts a spatio-chromatic receptive field for fly photoreceptor outputs, with a color opponent center and broadband surround. This dual mechanism combines motifs of both an insect-specific visual circuit and an evolutionarily convergent circuit architecture, endowing flies with the unique ability to extract chromatic information at distinct spatial resolutions.
Precise hyperacuity estimation of spike timing from calcium imaging
Authors: Hoang Huu , Sato Masa-aki , Shinomoto Shigeru , Tsutsumi Shinichiro , Hashizume Miki , Ishikawa Tomoe , Kano Masanobu , Ikegaya Yuji , Kitamura Kazuo , Kawato Mitsuo , Toyama Keisuke
Published: October 2019

Two-photon imaging is a major recording technique in neuroscience, but it suffers from several limitations, including a low sampling rate, the nonlinearity of calcium responses, the slow dynamics of calcium dyes and a low signal-to-noise ratio, all of which impose a severe limitation on the application of two-photon imaging in elucidating neuronal dynamics with high temporal resolution. Here, we developed a hyperacuity algorithm (HA_time) based on an approach combining a generative model and machine learning to improve spike detection and the precision of spike time inference. First, Bayesian inference estimates the calcium spike model by assuming the constancy of the spike shape and size. A support vector machine employs this information and detects spikes with higher temporal precision than the sampling rate. Compared with conventional thresholding, HA_time improved the precision of spike time estimation up to 20-fold for simulated calcium data. Furthermore, the benchmark analysis of experimental data from different brain regions and simulation of a broader range of experimental conditions showed that our algorithm was among the best in a class of hyperacuity algorithms. We encourage experimenters to use the proposed algorithm to precisely estimate hyperacuity spike times from two-photon imaging.
Pal stabilises the bacterial outer membrane during constriction by a mobilisation-and-capture mechanism
Authors: Szczepaniak Joanna , Holmes Peter , Rajasekar Karthik , Kaminska Renata , Samsudin Firdaus , Inns Patrick George , Rassam Patrice , Khalid Syma , Murray Seán M. , Redfield Christina , Kleanthous Colin
Published: October 2019

Coordination of outer membrane constriction with septation is critical to faithful division in Gram-negative bacteria and vital to the barrier function of the membrane. Recent studies suggest this coordination is through the active accumulation of the peptidoglycan-binding outer membrane lipoprotein Pal at division sites by the Tol system, but the mechanism is unknown. Here, we show that Pal accumulation atEscherichia colidivision sites is a consequence of three key functions of the Tol system. First, Tol mobilises Pal molecules in dividing cells, which otherwise diffuse very slowly due to their binding of the cell wall. Second, Tol actively captures mobilised Pal molecules and deposits them at the division septum. Third, the active capture mechanism is analogous to that used by the inner membrane protein TonB to dislodge the plug domains of outer membrane TonB-dependent nutrient transporters. We conclude that outer membrane constriction is coordinated with cell division by active mobilisation-and-capture of Pal at division septa by the Tol system.
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
Authors: Escapa Isabel F. , Huang Yanmei , Chen Tsute , Lin Maoxuan , Kokaras Alexis , Dewhirst Floyd E. , Lemon Katherine P.
Published: October 2019

Background

The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can parse 16S rRNA gene sequences to high-resolution Amplicon Sequence Variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies.

Results

To achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interested. When used with the naïve Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are: 1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; 2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; 3) trimming the training set to match the sequenced regions, if necessary; and 4) placing species sharing closely related sequences into a supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio Single Molecule, Real-Time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets.

Conclusion

Here, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies.
Interferon-responsive genes are targeted during the establishment of human cytomegalovirus latency
Authors: Elder Elizabeth G. , Krishna Benjamin A. , Williamson James , Lim Eleanor Y. , Poole Emma , Sedikides George X. , Wills Mark , O’Connor Christine M. , Lehner Paul J. , Sinclair John
Published: October 2019

Human cytomegalovirus (HCMV) latency is an active process which remodels the latently infected cell to optimise latent carriage and reactivation. This is achieved, in part, through the expression of viral genes, including the G-protein coupled receptor US28. Here, we use an unbiased proteomic screen to assess changes in host proteins induced by US28, revealing that interferon-inducible genes are downregulated by US28. We validate that MHC Class II and two PYHIN proteins, MNDA and IFI16, are downregulated during experimental latency in primary human CD14+monocytes. We find that IFI16 is targeted rapidly during the establishment of latency in a US28-dependent manner, but only in undifferentiated myeloid cells, a natural site of latent carriage. Finally, by overexpressing IFI16, we show that IFI16 can activate the viral major immediate early promoter and immediate early gene expression during latency via NF-κB, a function which explains why downregulation of IFI16 during latency is advantageous for the virus.

Importance

Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus which infects 50-100% of humans worldwide. HCMV causes a lifelong subclinical infection in immunocompetent individuals, but is a serious cause of mortality and morbidity in the immunocompromised and in neonates. In particular, reactivation of HCMV in the transplant setting is a major cause of transplant failure and related disease. Therefore, a molecular understanding of HCMV latency and reactivation could provide insights into potential ways to target the latent viral reservoir in at-risk patient populations.
Leveraging genetic data to investigate molecular targets and drug repurposing candidates for treating alcohol use disorder and hepatotoxicity
Authors: Gray Joshua C. , Murphy Mikela , Leggio Lorenzo
Published: October 2019

Background

Novel treatments for alcohol use disorder (AUD) and alcohol-related liver disease (ALD) are greatly needed. Genetic information can improve drug discovery rates by facilitating the identification of novel biological targets and potential drugs for repurposing.

Methods

The present study utilized a recently developed Bayesian approach, Integrative Risk Gene Selector (iRIGS), to identify additional risk genes for alcohol consumption using SNPs from the largest alcohol consumption GWAS to date (N = 941,280). iRIGS incorporates several genomic features and closeness of these genes in network space to compute a posterior probability for protein coding genes near each SNP. We subsequently used the Target Central Resource Database to search for drug-protein interactions for these newly identified genes and previously identified risk genes for alcohol consumption.

Results

We identified several genes that are novel contributions to the previously published alcohol consumption GWAS. Namely, ACVR2A, which is critical for liver function and linked to anxiety and cocaine self-administration, and PRKCE, which has been linked to alcohol self-administration. Notably, only a minority of the SNPs (18.4%) were linked to genes with confidence (≥.75), underscoring the need to apply multiple methods to assign function to loci. Finally, several previously identified risk genes for alcohol consumption code for proteins that are implicated in liver function and are targeted by drugs that are promising candidates for managing hepatotoxicity (e.g., metformin).

Conclusions

This study demonstrates the value of incorporating regulatory information and drug-protein interaction data to highlight additional molecular targets and drug repurposing candidates for treating AUD and ALD.
Ancient genomes reveal early Andean farmers selected common beans while preserving diversity
Authors: Emiliano Trucchi , Andrea Benazzo , Martina Lari , Alice Iob , Stefania Vai , Laura Nanni , Elisa Bellucci , Elena Bitocchi , Chunming Xu , Scott Jackson A , Verónica Lema , Pilar Babot , Nurit Oliszewski , Adolfo Gil , Gustavo Neme , Teresa Michieli Catalina , Monica De Lorenzi , Lucio Calcagnile , David Caramelli , Bastiaan Star , Hugo de Boer , Sanne Boessenkool , Roberto Papa , Giorgio Bertorelle
Published: October 2019

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations [1, 2]. Farmers selected desirable phenotypic traits, such as improved energy accumulation, palatability of seeds or reduced natural shattering [3], while leading domesticated populations through several more or less gradual demographic contractions [2, 4]. As a consequence, erosion of wild genetic variation [5] is typical of modern cultivars making them highly susceptible to pathogens, pests and environmental change [6,7]. The loss of genetic diversity hampers further crop improvement programs to increase food production in a changing world, posing serious threats to food security [8,9]. Using both ancient and modern seeds, we analyzed the temporal dynamic of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) that occurred in the Southern Andes. Here we show that most domestic traits were selected for prior to 2,500 years ago, with no or only minor loss of whole-genome variation. In fact, i) all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable - at least as variable as a modern genome from the wild; the genetic erosion that we observe in modern cultivars is therefore a recent process that occurred in the last centuries; ii) the majority of changes at coding genes that differentiate wild and domestic genomes are already present in the ancient genomes analyzed here. Considering that most desirable phenotypic traits are likely controlled by multiple polymorphic genes [10], a likely explanation of this decoupling of selection and genomic erosion is that early farmers applied a relatively weak selection pressure [2] by using many phenotypically similar but genomically diverse individuals as breeders. Selection strategies during the last few centuries were probably less sustainable and produced further improvements focusing on few plants carrying the traits of interest, at the cost of marked genetic erosion.
Chemogenetic modulation and single-photon calcium imaging in anterior cingulate cortex reveal a mechanism for effort-based decisions
Authors: Hart Evan E. , Blair Garrett J. , O’Dell Thomas J. , Blair Hugh T. , Izquierdo Alicia
Published: October 2019

The anterior cingulate cortex (ACC) is implicated in effort exertion and choices based on effort cost, but it is still unclear how it mediates this cost-benefit evaluation. Here, male rats were trained to exert effort for a high-value reward (sucrose pellets) in a progressive ratio lever pressing task. Trained rats were then tested in two conditions: a no-choice condition where lever pressing for sucrose was the only available food option, and a choice condition where a low-value reward (lab chow) was freely available as an alternative to pressing for sucrose. Disruption of ACC—via either chemogenetic inhibition or excitation—reduced lever pressing in the choice, but not in the no-choice, condition. We next looked for value coding cells in ACC during effortful behavior and reward consumption phases during choice and no-choice conditions. For this, we utilized in vivo miniaturized fluorescence microscopy to reliably track responses of the same cells and compare how ACC neurons respond during the same effortful behavior where there was a choice versus when there was no-choice. We found that lever-press and sucrose-evoked responses were significantly weaker during choice compared to no-choice sessions, which may have rendered them more susceptible to chemogenetic disruption. Taken together, findings from our interference experiments and neural recordings suggest that a mechanism by which ACC mediates effortful decisions is in the discrimination of the utility of available options. ACC regulates these choices by providing a stable population code for the relative value of different options.

Significance Statement

The anterior cingulate cortex (ACC) is implicated in effort-based decision making. Here, we used chemogenetics and in vivo calcium imaging to explore its mechanism. Rats were trained to lever press for a high-value reward and tested in two conditions: a no-choice condition where lever pressing for the high-value reward was the only option, and a choice condition where a low-value reward was also available. Inhibition or excitation of ACC reduced effort toward the high value option, but only in the choice condition. Neural responses in ACC were weaker in the choice compared to the no-choice condition. A mechanism by which ACC regulates effortful decisions is in providing a stable population code for the discrimination of the utility of available options.
Plexin-B2 is a key regulator of cell mechanics during multicellular organization
Authors: Junqueira Alves Chrystian , Dariolli Rafael , Hannah Theodore , Wiener Robert J. , Daviaud Nicolas , Tejero Rut , Gusella G. Luca , Tsankova Nadejda M. , Dias Rodrigo Alves , Furtado de Mendonça José Paulo R. , Azeloglu Evren U. , Friedel Roland H. , Zou Hongyan
Published: October 2019

During multicellular organization, individual cells need to constantly respond to environmental cues and adjust contractile and adhesive forces in order to maintain tissue integrity. The signaling pathways linking biochemical cues and tissue mechanics are unclear. Here, we show that Plexin-B2 regulates mechanochemical integration during multicellular organization. In human embryonic stem cells (hESCs), Plexin-B2 controls cell shape and tissue geometry in both 2D epithelial colony and 3D spheroid aggregates by regulating actomyosin contractility and junctional/cell-matrix adhesive properties. Atomic force microscopy (AFM) directly demonstrates that Plexin-B2 modulates cell stiffness in hESC colonies, which in turn impacts cell proliferation and cell fate specification through β-catenin signaling and YAP mechanosensing. YAP also functions as a mechanoregulator downstream of Plexin-B2, thus forming a mechanochemical integrative loop. In human neuroprogenitor cells (hNPCs), Plexin-B2 similarly controls cell stiffness and tensile forces, as revealed by AFM and FRET tension sensor studies. Strikingly, Plexin-B2-deficient hNPCs display accelerated neuronal differentiation. From an organogenesis perspective, Plexin-B2 maintains cytoarchitectural integrity of neuroepithelium, as modeled in cerebral organoids. On a signaling level, Plexin-B2 engages extracellular as well as intracellular Ras-GAP and RBD domains for mechanoregulation through Rap and Rac GTPases. Our data unveil a fundamental function of Plexin-B2 for mechanochemical integration during multicellular organization, and shed light on the principle of force-mediated regulation of stem cell biology and tissue morphogenesis.
Alanine, arginine, and proline but not glutamine are the feed-back regulators in the liver-alpha cell axis in mice
Authors: Galsgaard Katrine D. , Jepsen Sara Lind , Kjeldsen Sasha A.S. , Pedersen Jens , Wewer Albrechtsen Nicolai J. , Holst Jens J.
Published: October 2019

Aim

To identify the amino acids that stimulate glucagon secretion in mice and whether the metabolism of these relies on glucagon receptor signaling.

Methods

Pancreata of female C57BL/6JRj mice were perfused with 19 individual amino acids (1 mM) and secretion of glucagon was assessed using a specific glucagon radioimmunoassay. Separately, a glucagon receptor antagonist (GRA; 25-2648, 100 mg/kg) or vehicle was administered to female C57BL/6JRj mice three hours prior to an intraperitoneal injection of four different isomolar (in total 7 µmol/g body weight) amino acid mixtures; mixture 1: alanine, arginine, cysteine, and proline; mixture 2: asparatate, glutamate, histidine, and lysine; mixture 3: citrulline, methionine, serine, and threonine; and mixture 4: glutamine, leucine, isoleucine, and valine. Blood glucose, plasma glucagon, amino acid, and insulin concentrations were measured using well characterized methodologies.

Results

Alanine (P=0.03), arginine (P<0.001), and proline (P=0.03) but not glutamine (P=0.2) stimulated glucagon secretion from the perfused mouse pancreas. Cysteine had the numerically largest effect on glucagon secretion but did not reach statistical significance (P=0.08). However, when the four isomolar amino acid mixtures were administered there were no significant difference (P>0.5) in plasma concentrations of glucagon across mixture 1-4. Plasma concentrations of total amino acids were higher after administration of GRA when mixture 1 (P=0.004) or mixture 3 (P=0.04) were injected.

Conclusion

Our data suggest that alanine, arginine, and proline but not glutamine are involved in the liver-alpha cell axis in mice as they all increased glucagon secretion and their disappearance rate was altered by GRA.

Graphical abstract
Abrogation of pathogenic attributes in drug resistantCandida aurisstrains by farnesol
Authors: Srivastava Vartika , Ahmad Aijaz
Published: October 2019

Candida auris, a decade oldCandidaspecies, has been identified globally as a significant nosocomial multidrug resistant (MDR) pathogen responsible for causing invasive outbreaks. Biofilms and overexpression of efflux pumps such as Major Facilitator Superfamily and ATP Binding Cassette are known to cause multidrug resistance inCandidaspecies, includingC. auris. Therefore, targeting these factors may prove an effective approach to combat MDR inC. auris. In this study, 25 clinical isolates ofC. aurisfrom different hospitals of South Africa were used. All the isolates were found capable enough to form biofilms on 96-well microtiter plate that was further confirmed by MTT reduction assay. In addition, these strains have active drug efflux mechanism which was supported by rhodamine-6-G extracellular efflux and intracellular accumulation assays. Antifungal susceptibility profile of all the isolates against commonly used drugs was determined following CLSI recommended guidelines. We further studied the role of farnesol, an endogenous quorum sensing molecule, in modulating development of biofilms and drug efflux inC. auris. The MIC for planktonic cells ranged from 62.5-125 mM and for sessile cells was 125 mM (0 h and 4 h biofilm) and 500 mM (12 h and 24 h biofilm). Farnesol inhibited biofilm formation, blocked efflux pumps and downregulated biofilm- and efflux pump-associated genes. Modulation ofC. aurisbiofilm formation and efflux pump activity by farnesol represent a promising approach for controlling life threatening infections caused by this pathogen.
Single-cell transcriptome profiling reveals neutrophil heterogeneity and orchestrated maturation during homeostasis and bacterial infection
Authors: Xie Xuemei , Shi Qiang , Wu Peng , Zhang Xiaoyu , Kambara Hiroto , Su Jiayu , Yu Hongbo , Park Shin-Young , Guo Rongxia , Ren Qian , Zhang Sudong , Xu Yuanfu , Silberstein Leslie E. , Cheng Tao , Ma Fengxia , Li Cheng , Luo Hongbo R.
Published: October 2019

The full neutrophil heterogeneity and differentiation landscape remains incompletely characterized. Here we profiled >25,000 differentiating and mature mouse neutrophils using single-cell RNA sequencing to provide a comprehensive transcriptional landscape of neutrophil maturation, function, and fate decision in their steady state and during bacterial infection. Eight neutrophil populations were defined by distinct molecular signatures. The three mature peripheral blood neutrophil subsets arise from distinct maturing bone marrow neutrophil subsets. Driven by both known and uncharacterized transcription factors, neutrophils gradually acquire microbicidal capability as they traverse the transcriptional landscape, representing an evolved mechanism for fine-tuned regulation of an effective but balanced neutrophil response. Bacterial infection reprograms the genetic architecture of neutrophil populations, alters dynamic transition between each subpopulation, and primes neutrophils for augmented functionality without affecting overall heterogeneity. In summary, these data establish a reference model and general framework for studying neutrophil-related disease mechanisms, biomarkers, and therapeutic targets at single-cell resolution.

Graphical Abstract

Highlights

A comprehensive single-cell resolution transcriptional landscape of mouse neutrophil maturation and fate decision under steady-state and bacterial infection conditions.

The pathogen clearance machinery in neutrophils is continuously and gradually built during neutrophil differentiation, maturation, and aging, driven by both known and uncharacterized transcription factors.

The three mature neutrophil subsets in peripheral blood, including a novel ISG-expressing subset, are derived from distinct bone marrow neutrophil precursors.

Bacterial infection reprograms the genetic architecture of neutrophil populations, alters dynamic transition between each subpopulation, and primes neutrophils for augmented functionality without affecting overall neutrophil heterogeneity.

Bacterial infection-induced emergency granulopoiesis is mediated by augmented proliferation of early stage neutrophil progenitors and accelerated post-mitotic maturation.
Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane
Authors: Banerjee Nandita , Kumar Sanjeev , Annadurai A. , Singh P. K , Singh J. , Singh R.K. , Kumar Sanjeev
Published: October 2019

Sucrose is the key economic trait in sugarcane which is a highly polyploid multi-species hybrid and shows a complex pattern of trait inheritance. The excessively large genome of sugarcane is comparatively less explored through Next Generation Sequencing tools for creating superior varieties. In this study, RNAseq libraries of two extreme bulks from a segregating full-sib population and its parents were used to identify 9905 condition-specific non-synonymous genetic variants (NSVs), out of which 43 had a very high degree of differential enrichment (Δf >0.5) for contrasting sucrose accumulating conditions. The statistical model used in this study which was able to quantify the relative effect of NSVs on the trait detected highly significant positive and negative effect NSVs located in the coding regions of genes involved in sucrose metabolism, photosynthesis, mitochondrial electron transport, glycolysis and transcription. In addition, a few differential pre-mature stop codons that could result in production of truncated proteins were also detected in genes coding for aquaporin, GAPDH, aldolase, cytochrome C-oxidase, chlorophyll synthase and plant plasma membrane intrinsic proteins. Additionally, a total of 2140 differentially expressed genes (DEGs) linked to high sucrose accumulation were identified. Among the DEGs, sucrose phosphate synthase III, genes involved in transport, auxin signal transduction, etc., were upregulated, while those involved in electron transfer, cytochrome P450, etc., were downregulated in high sucrose accumulation conditions. This study was able to give finer insights in to the role of allelic heterozygosity on sucrose accumulation and the identified NSVs and DEGs could be useful as candidate markers in marker-assisted breeding for developing high sugar varieties.
Chromosome-wide distribution and characterization of intersubspecific meiotic noncrossovers in mice
Authors: Gergelits Vaclav , Parvanov Emil , Simecek Petr , Forejt Jiri
Published: October 2019

During meiosis, the recombination-initiating DNA double-strand breaks (DSBs) are repaired by crossovers or noncrossovers (gene conversions). While crossovers are easily detectable, the noncrossover identification is hampered by the small size of their converted tracts and the necessity of sequence polymorphism to detect them. We report identification and characterization of a mouse chromosome-wide set of noncrossovers by NGS sequencing of 10 mouse chromosome substitution strains. Based on 94 identified noncrossovers we determined the mean length of a conversion tract to be 32 basepairs. The spatial chromosome-wide distribution of noncrossovers and crossovers significantly differed, though both sets overlapped the known hotspots of PRDM9-directed histone methylation and DNA DSBs, thus proving their origin in the standard DSB repair pathway. A significant deficit of noncrossovers descending from asymmetric DSBs pointed to sister chromatids as an alternative template for their repair. The finding has implications for the molecular mechanism of hybrid sterility in mice.
Dietary carotenoid supplementation facilitates egg laying in a wild passerine
Authors: García-Campa Jorge , Müller Wendt , González-Braojos Sonia , García-Juárez Emilio , Morales Judith
Published: October 2019

During egg laying, female birds face a trade-off between self-maintenance and investment into current reproduction. Providing eggs with resources is energetically demanding, since in most species females lay one egg per day. However, the costs of egg laying not only relate to energetic requirements, but also depend on the availability of specific resources that are vital for egg production and embryonic development. One of these compounds are carotenoids, pigments with antioxidant properties and immuno-stimulatory functions, which are crucial during embryonic development. In this study, we explore how carotenoid availability alleviates this trade-off and facilitates egg laying in the blue tit. Blue tit females lay one egg per day and have the largest clutch size of all European passerines. We performed a lutein supplementation experiment, and measured potential consequences for egg laying capacity and egg quality. We found that lutein-supplemented females had less laying interruptions and thus completed their clutch faster than control females. No effects of treatment were found on the onset of egg laying or clutch size. Experimentally enhanced carotenoid availability did not elevate yolk carotenoid levels or egg mass, but negatively affected eggshell thickness. Our results provide hence evidence on the limiting role of carotenoids during egg laying, However, the benefits of laying faster following lutein supplementation were counterbalanced by a lower accumulation of calcium in the eggshell. Thus, even though single components may constrain egg laying, it is the combined availability of a range of different resources which ultimately determines egg quality and thus embryonic development.
Reducing shade avoidance can improve Arabidopsis canopy performance against competitors
Authors: Pantazopoulou Chrysoula K. , Bongers Franca J. , Pierik Ronald
Published: October 2019

The loss of crop yield due to weeds is an urgent agricultural problem. Although herbicides are an effective way to control weeds, more sustainable solutions for weed management are desirable. It has been proposed that crop plants can communally suppress weeds by shading them out. Shade avoidance responses, such as upward leaf movement (hyponasty) and stem or petiole elongation, enhance light capture of individual plants, increasing their individual fitness. The shading capacity of the entire crop community might, however, be more effective if aspects of shade avoidance are suppressed. Testing this hypothesis in crops is hampered by the lack of well-characterized mutants. We therefore investigated if Arabidopsis competitive performance at the community level against invading competitors is affected by the ability to display shade avoidance. We tested two mutants: pif4pif5 that has mildly reduced petiole elongation and hyponasty and pif7 with normal elongation but absent hyponasty in response to shade. Although pif4pif5 performed similar to wildtype, we found that pif7 showed significantly increased canopy biomass and suppression of invading competitors as compared to its wildtype. Our data thus show that modifying specific shade avoidance aspects has potential for plant community performance. This may help to suppress weeds in crop stands.

Highlight

Hyponastic response in canopies facilitates light penetration and weed growth. Inhibition of this response to neighbors increased canopy biomass, canopy closure and suppression of competitors.
Elevated CO2and warming change the nutrient status and use efficiency ofPanicum maximumJacq
Authors: Carvalho Juliana Mariano , de Mello Prado Renato , Barreto Rafael Ferreira , Habermann Eduardo , Branco Roberto Botelho Ferraz , Martinez Carlos Alberto
Published: October 2019

Panicum maximumJacq. ‘Mombaça’ (guinea grass) is a C4forage grass widely used in tropical pastures for cattle feeding. In this study, we evaluated the isolated and combined effects of warming and elevated CO2concentration [CO2] during summer on the nutrient content, nutrient accumulation, nutrient use efficiency and growth ofP. maximumunder field conditions with adequate water supply. The temperature and [CO2] in the field were controlled by temperature free-air controlled enhancement and free-air CO2enrichment systems, respectively. We tested two levels of canopy temperature: ambient temperature and 2°C above ambient temperature, as well as two levels of atmospheric [CO2]: ambient [CO2] (aCO2) and 200 ppm above ambient CO2(eCO2). The experiment was established in a completely randomised design with four replications, in a 2×2 factorial scheme. After the pasture establishment, plants were exposed to the treatments for 30 days, with evaluations at 9, 16, 23 and 30 days after the treatments started. Results were dependent on the time of the evaluation, but in the last evaluation (beginning of the grazing), contents of N, K, Mg and S did not change as a function of treatments, P decreased as a function of warming, in [aCO2] and [eCO2], and Ca increased under [eCO2] combined with warming. There was an increase in root dry mass under warming treatment. Combined treatment increased N, Ca and S accumulation without a corresponding increase in the use efficiency of these same nutrients, indicating that the fertiliser dose should increase in the next decades due to human-induced climate change. Our short-term results suggest that the combination of high [CO2] and temperature will increaseP. maximumproductivity and that the nutritional requirement for N, Ca and S will increase.