bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact on Staff of Providing Non-Invasive Advanced Respiratory Support During the Covid-19 Pandemic– A Qualitative Study in an Acute Hospital
Authors: Wenzel David , Bleazard Lucy , Wilson Eleanor , Faull Christina
Published: March 2022

Objectives

To explore the experiences of healthcare workers of providing Non-Invasive Advanced Respiratory Support (NARS) to critically unwell patients with covid-19.

Design

A qualitative study drawing on a social constructionist perspective using thematic analysis of semi-structured interviews.

Setting

A single acute UK NHS Trust across two hospital sites.

Participants

Multidisciplinary team members in acute, respiratory and palliative medicine.

Results

21 nurses, doctors (juniors and consultants) and physiotherapists described the provision of NARS to critically unwell covid-19 patients as extremely challenging. The main themes were of feeling ill prepared and unsupported, a need to balance complex moral actions, a sense of duty to patients and their families. The impact on staff was profound and findings are discussed via a lens of moral injury. Injurious events included staff feeling they had acted in a way that caused harm, failed to prevent harm or had been let down by seniors or the Trust. Participants identified factors that mitigated adverse impact.

Conclusions

Although many of the issues described by participants are likely immutable components of healthcare in a pandemic there were several important protective factors that emerged from the data. Experience, debriefing and breaks from covid-19 wards were valuable to participants and successfully achieving a peaceful death for the patient was often viewed as compensation for a difficult journey. These protective factors may provide modelling for future education and support services to help prevent moral injury – or aide in its recovery.

Registration

registered on the Open Science Framework 10.17605/OSF.IO/XB8YH

Strengths and Limitations

Single Centre Study

The lead author had pre-existing relationships with study participants

The lead author, under strict supervision, practiced a reflexivity based approach to data collection and analysis with objectivity benchmarking from the second author.
The effect of Septoria glycines and fungicide application on the soybean phyllosphere mycobiome
Authors: Lin Heng-An , Mideros Santiago X.
Published: March 2022

Septoria brown spot (caused by Septoria glycines) is the most prevalent soybean disease in Illinois. It is common to use a foliar fungicide to control Septoria brown spot and other foliar diseases. The effects of fungicide on non-target organisms in the phyllosphere are unknown. To study the effect of S. glycines and fungicide application on the soybean phyllosphere mycobiome we sequenced full-length ITS and partial LSU region using oxford nanopore technologies. Sequencing produced 3,342 operational taxonomic units (OTUs). The richness of the fungal community significantly increased with the developmental stage. The soybean lines significantly affected the mycobiome diversity at the early developmental stage but not at the reproductive stages. S. glycines did not significantly affect the alpha diversity but some significant changes were observed for the beta diversity. At the R5 stage, fungicide application significantly changed the composition of the fungal community. The fungicide treatment significantly decreased the proportion of several fungal reads, but it increased the proportion of Septoria. The core microbiome in soybean leaves was composed of Gibberella, Alternaria, Didymella, Cladosporium, Plectosphaerella, Colletotrichum, and Bipolaris. Network analysis identified significant interactions between Septoria reads and Diaporthe, Bipolaris and two other taxonomic units. In this study, we set Septoria as the target organism and demonstrated that metabarcoding could be a tool to quantify the effect of multiple treatments on the fungal phyllosphere community. Better understanding the dynamics of the phyllosphere microbiome is necessary to start untangling late-season diseases of soybean.
Variants identify sarcomere inter-protein contacts distinguishing inheritable cardiac muscle diseases
Authors: Burghardt Thomas P.
Published: March 2022

Human ventriculum myosin (βmys) powers contraction sometimes while complexed with myosin binding protein C (MYBPC3) on the myosin thick filament. The latter regulates βmys activity through inter-protein contacts. Single nucleotide variants (SNVs) change protein sequence in βmys or MYBPC3. They cause inheritable heart disease. When a SNV modified domain locates to an inter-protein contact it affects complex coordination. Domains involved, one in βmys and the other in MYBPC3, form coordinated domains called co-domains. Co-domains are bilateral implying the potential for a shared impact from SNV modification in either domain suggesting their joint response to a common perturbation assigns location. Human population genetic divergence is the common systemic perturbation. A general contraction model with a neural/Bayes network design reveals SNV probabilities specifying correlations between domain members using 2D correlation genetics (2D-CG). It reveals co-domain locations in three common human heart diseases caused by SNVs, familial hypertrophic cardiomyopathy (FHC), dilated cardiomyopathy (DCM), and left ventricle non-compaction (LVN). Co-domain maps for DCM and LVN link MYBPC3 with two levels of myosin heads on the myosin thick filament surface implying these myosin dimers form the super-relaxed state (SRX). The FHC co-domain map involves just one myosin dimer implying the myosins do not form SRX. Comparing co-domain maps for FHC, DCM, and LVN phenotypes suggests SRX disruption involves a co-domain between MYBPC3 regulatory domain and the myosin regulatory light chain (RLC) N-terminus. The general contraction model scenarios, constructed from feed-forward neural networks, were explored with the purpose to understand how to interpret them mechanistically with basic natural language characteristics. These characteristics emerge from dependencies among inputs coded in hidden layer width and depth when they are deciphered using 2D-CG. In this application, the thick filament structural states emerge for FHC, DCM, and LVN phenotypes defining thick filament structural state joining the other standard characteristics of phenotype and pathogenicity. Emergent natural language interpretations for general network contraction models are on the horizon.
Differentiation of airway cholinergic neurons from human pluripotent stem cells for airway neurobiology studies
Authors: Goldsteen P.A. , Sabogal Guaqueta A.M. , Bos I.S.T. , Kistemaker L.E.M. , van der Koog L. , Eggens M. , Halayko A.J. , Dolga A.M. , Gosens R.
Published: March 2022

Airway cholinergic nerves play a key role in airway physiology and disease. In asthma and other diseases of the respiratory tract, airway cholinergic neurons undergo plasticity and contribute to airway hyperresponsiveness and mucus secretion. We currently lack mechanistic understanding of airway cholinergic neuroplasticity due to the absence of human in vitro models. Here, we developed the first human in vitro model for airway cholinergic neurons using human pluripotent stem cell (hPSC) technology. hPSCs were differentiated towards mature and functional airway cholinergic neurons via a vagal precursor. Airway cholinergic neurons were characterized by ChAT and VAChT expression, and responded to chemical stimulation with changes in Ca2+ mobilization. Co-culture of hPSC-derived airway cholinergic neurons with airway smooth muscle cells enhanced phenotypic and functional characteristics of these neurons. The differentiation protocol we developed for human airway cholinergic neurons from hPSCs allows for studies into airway neurobiology and airway neuroplasticity in disease.
Reciprocity and interaction effectiveness in generalised mutualisms among free-living species
Authors: Quintero Elena , Rodríguez-Sánchez Francisco , Jordano Pedro
Published: March 2022

Mutualistic interactions among free-living species generally involve weak links and highly asymmetric dependence among partners, yet our understanding of factors beyond their emergence is still limited. Using individual-based interactions of a super-generalist fleshy-fruited plant with its frugivore assemblage we estimate the Resource Provisioning Effectiveness (RPE) and Seed Dispersal Effectiveness (SDE) to assess the balance in the exchange of resources. Plants were highly dependent on a few super-generalist frugivore species, while these interacted with most individual plants, resulting in strong asymmetries in mutual dependence. Both RPE and SDE were mainly driven by interaction frequency. Despite highly asymmetric dependences, the strong reliance on quantity largely determined high reciprocity in rewards between partners (i.e., higher energy provided, more seedlings recruited), not obscured by minor variations in the quality of animal or plant service. We anticipate reciprocity will emerge in low-intimacy mutualisms where the mutualistic outcome largely relies upon interaction frequency.
Extraction and analysis of methylation features from Pacific Biosciences SMRT reads using MeStudio
Authors: Riccardi Christopher , Passeri Iacopo , Cangioli Lisa , Fagorzi Camilla , Mengoni Alessio , Fondi Marco
Published: March 2022

Motivation

DNA methylation is the most relevant epigenetic information, present in eukaryotes and prokaryotes, and is related to several biological phenomena, from cellular differentiation to control of gene flow, pathogenesis and virulence. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomics landscape.

Results

We introduce MeStudio, a pipeline which allows to analyse and combine genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences, noncoding sequences, intergenic sequences, and sequences upstream to CDS. We show the usage and performances of MeStudio on a set of single-molecule real time sequencing outputs from the bacterial species Sinorhizobium meliloti.

Availability and Implementation

MeStudio is written in Python, Bash and C and is freely available under an open source GPLv3 license at https://github.com/combogenomics/MeStudio

Supplementary information

Supplementary data are available at Bioinformatics online.

Contact

combo.unifi@gmail.com
A new monoclonal antibody enables BAR analysis of subcellular importin β1 interactomes
Authors: Song Didi-Andreas , Alber Stefanie , Doron-Mandel Ella , Schmid Vera , Albus Christin A. , Leitner Orith , Hamawi Hedva , Oses-Prieto Juan A. , Burlingame Alma L. , Fainzilber Mike , Rishal Ida
Published: March 2022

Importin β1 (KPNB1) is a nucleocytoplasmic transport factor with critical roles in both cytoplasmic and nucleocytoplasmic transport, hence there is keen interest in the characterization of its subcellular interactomes. We found limited efficiency of BioID in detection of importin complex cargos, and therefore generated a highly specific and sensitive anti-KPNB1 monoclonal antibody to enable Biotinylation by Antibody Recognition (BAR) analysis of importin β1 interactomes. The monoclonal antibody recognizes an epitope comprising residues 301-320 of human KPBN1, and strikingly is highly specific for cytoplasmic KPNB1 in diverse applications, with little or no reaction with KPNB1 in the nucleus. BAR with this novel antibody revealed numerous new interactors of importin β1, expanding the KPNB1 interactome to cytoplasmic and signaling complexes that highlight potential new functions for the importins complex beyond nucleocytoplasmic transport. Data are available via ProteomeXchange with identifier PXD032728.
Glioblastoma states are defined by cohabitating cellular populations with progression-, imaging- and sex-distinct patterns
Authors: Bond Kamila M. , Curtin Lee , Hawkins-Daarud Andrea , Urcuyo Javier C. , De Leon Gustavo , Sereduk Christopher , Singleton Kyle W. , Langworthy Jazlynn M. , Jackson Pamela R. , Krishna Chandan , Zimmerman Richard S. , Patra Devi Prasad , Bendok Bernard R. , Smith Kris , Nakaji Peter , Donev Kliment , Baxter Leslie , Mrugała Maciej M. , Al-Dalahmah Osama , Hu Leland S. , Tran Nhan L. , Rubin Joshua B. , Canoll Peter , Swanson Kristin R.
Published: March 2022

Glioblastomas (GBMs) are biologically heterogeneous within and between patients. Many previous attempts to characterize this heterogeneity have classified tumors according to their omics similarities. These discrete classifications have predominantly focused on characterizing malignant cells, neglecting the immune and other cell populations that are known to be present. We leverage a manifold learning algorithm to define a low-dimensional transcriptional continuum along which heterogeneous GBM samples organize. This reveals three polarized states: invasive, immune/inflammatory, and proliferative. The location of each sample along this continuum correlates with the abundance of eighteen malignant, immune, and other cell populations. We connect these cell abundances with magnetic resonance imaging and find that the relationship between contrast enhancement and tumor composition varies with patient sex and treatment status. These findings suggest that GBM transcriptional biology is a predictably constrained continuum that contains a limited spectrum of viable cell cohabitation ecologies. Since the relationships between this ecological continuum and imaging vary with patient sex and tumor treatment status, studies that integrate imaging features with tumor biology should incorporate these variables in their design.
On-farm Implementation of Midseason Drainage to Decrease Greenhouse Gas Emissions and Grain Arsenic Concentration in Rice Systems
Authors: Perry Henry , Carrijo Daniela R. , Duncan Aria H. , Fendorf Scott , Linquist Bruce
Published: March 2022

Rice (Oryza sativa L.) is an important staple crop throughout much of the world, however, it is also a significant source of agricultural methane (CH4) emissions and exposure to arsenic (As). Introduction of soil aerobic events through practices such as alternate wetting and drying or midseason drainage, in flooded rice systems can significantly decrease grain As concentration and seasonal CH4 emissions. Previous on small research plots research has shown that a single midseason drain accomplishes these goals without yield reduction, but the degree of benefit depends on soil-drying severity. A midseason drain also has the potential to fit in well within current management practices of California rice systems, however, it has not been tested across a wide range of soil types or at a scale that farmers typically manage in this region. Therefore, in this three-year study, we aimed to determine if the results from previous small plot research are similar to what can be expected on-farm. At seven on-farm trials we implemented a single midseason drain and compared the grain yields, GHG emissions, and As concentration to the traditional farmer practice (FP) practiced in an adjacent part of the field. Soil moisture parameters [perched water table, volumetric water content, gravimetric water content (GWC), and soil water potential], CH4 and nitrous oxide (N2O) emissions, grain As and cadmium concentration, and grain yield were quantified. Across site-years, midseason drainage reduced seasonal CH4 emissions by 20-77%, compared to the FP control with the magnitude of reduction related to the soil-drying severity. For every 1% reduction in soil GWC during the drainage period, CH4 emissions were reduced by approximately 3.2%, compared to 2.5% in previous on-station research using small plots. Midseason drainage increased N2O emissions (average = 0.248 kg N2O-N ha-1) compared to the control but this accounted for only 3% of the seasonal global warming potential across all drainage treatments. Drainage also decreased grain As concentration by approximately 20%, on average, but was not related to the degree of soil-drying. Importantly, midseason drainage had no significant impact on grain yields. Overall, these results confirm findings from previous on-station research, indicating that midseason drainage may be a viable on-farm management practice for GHG mitigation and for reducing grain As concentration in flooded rice fields with limited risk of yield reduction.
Microbial Energy Metabolism Fuels a CSF2-dependent Intestinal Macrophage Niche within Tertiary Lymphoid Organs
Authors: Chiaranunt Pailin , Burrows Kyle , Ngai Louis , Cao Eric Y , Tai Siu Ling , Liang Helen , Hamidzada Homaira , Wong Anthony , Kuypers Meggie , Despot Tijana , Momen Abdul , Lim Sung Min , Malleavey Thierry , Conway Tyrrell , Imamura Hiromi , Epelman Slava , Mortha Arthur
Published: March 2022

Maintaining intestinal macrophage (MP) heterogeneity is critical to ensure tissue homeostasis and host defense. The gut microbiota and host factors are thought to synergistically shape colonic MP development, although there remains a fundamental gap in our understanding of the details of such collaboration. Here, we report tertiary lymphoid organs (TLOs), enriched in group 3 innate lymphoid cells (ILC3s), as a microbiota-operated intestinal niche for the development of monocyte-derived MPs. ILC3-derived colony stimulating factor 2 (CSF2) serves as a developmental and functional determinant for MPs and required microbe-derived extracellular adenosine 5’-triphosphate (ATP) as a trigger. Microbial communities rich in extracellular ATP promoted MP turnover via ILC3 activity in an NLRP3-dependent fashion. Single cell RNA-sequencing of MPs revealed unique TLO-associated, CSF2-dependent MP populations critical for anti-microbial defense against enteric infection. Collectively, these findings describe a fundamental framework that constitutes an intestinal MP niche fueled by microbial energy metabolism.
Thiazides induce glucose intolerance through inhibition of mitochondrial carbonic anhydrase 5b in β-cells
Authors: Kucharczyk Patrycja , Albano Giuseppe , Deisl Christine , Wueest Stephan , Konrad Daniel , Fuster Daniel G.
Published: March 2022

Thiazides are associated with glucose intolerance and new onset diabetes mellitus, but the molecular mechanisms remain elusive. The aim of this study was to decipher the molecular basis of thiazide-induced glucose intolerance. In mice, hydrochlorothiazide induced a pathological glucose tolerance, characterized by reduced first phase insulin secretion but normal insulin sensitivity. In vitro, thiazides inhibited glucose-and sulfonylurea-stimulated insulin secretion in islets and the murine β-cell line Min6 at pharmacologically relevant concentrations. Inhibition of insulin secretion by thiazides was CO2/HCO3--dependent, not additive to unselective carbonic anhydrase (CA) inhibition with acetazolamide and independent of extracellular potassium. In contrast, insulin secretion was unaltered in islets of mice lacking the known molecular thiazide targets NCC (SLC12A3) or NDCBE (SLC4A8). CA expression profiling with subsequent knock-down of individual CA isoforms suggested mitochondrial CA5b as molecular target. In support of these findings, thiazides significantly attenuated Krebs cycle anaplerosis through reduction of mitochondrial oxalacetate synthesis. CA5b KO mice were resistant to thiazide-induced glucose intolerance, and insulin secretion of islets isolated from CA5b KO mice was unaffected by thiazides.

In summary, our study reveals attenuated insulin secretion due to inhibition of the mitochondrial CA5b isoform in β-cells as molecular mechanism of thiazide-induced glucose intolerance.
Designing Cost-Effective, Open-Source, Multi-Head Bioprinters via Conversion of Hobby-Grade 3D Printers
Authors: Chimene David , Deo Kaivalya A. , Thomas Jeremy , Gaharwar Akhilesh K.
Published: March 2022

Over the past decade, additive manufacturing has resulted in significant advances towards fabricating anatomic-size, patient-specific scaffolds for tissue models and regenerative medicine. This can be attributed to the development of advanced bioinks capable of precise deposition of cells and biomaterials. The combination of additive manufacturing with advanced bioinks is enabling researchers to fabricate intricate tissue scaffolds that recreate the complex spatial distributions of cells and bioactive cues found in the human body. However, the expansion of this promising technique has been hampered by the high cost of commercially available bioprinters and proprietary software. In contrast, conventional 3D printing has become increasingly popular with home hobbyists and caused an explosion of both low-cost thermoplastic 3D printers and open source software to control the printer. In this work, we bring these benefits into the field of bioprinting by converting widely available and cost-effective 3D printers into fully functional, open source, and customizable multi-head bioprinters. We demonstrate the practicality of this approach by designing bioprinters customized with multiple extruders, automatic bed leveling, and temperature controls for approximately $400. These bioprinters were then used for in vitro and ex vivo bioprinting to demonstrate their utility for tissue engineering.
Repositioning linifanib as a potent anti-necroptosis agent for sepsis
Authors: Yang Kai , Li Min , Yu Liang , He Xiaoyan
Published: March 2022

Background

Sepsis is a systemic inflammatory syndrome (SIRS) caused by acute microbial infection with high mortality rate. The role of tumour necrosis factor α (TNF-α)-induced necroptosis in promoting the pathophysiology of sepsis has been identified. Effective prevention of necroptosis is expected to improve the prognosis of sepsis patients.

Methods

We conducted bioinformatics prediction of candidate drugs by analyzing differentially expressed genes of sepsis patients extracted from GEO database, combining library of integrated network-based cellular signatures (LINCS) L1000 perturbation database. Biological experiments based on TNF-α-induced necroptosis in cellular and mouse model were performed to verify the protection of candidate drugs from SIRS. Cell viability was measured by CellTiter-Glo luminescent ATP assay. Effects of linifanib on necroptosis were investigated by western blotting, immunoprecipitation, and in vitro RIPK1 kinase assay. Survival curve analysis of SIRS mice treated by linifanib was performed.

Results

A total of 16 candidate drugs was screened out through bioinformatics analysis. Our experiments demonstrated that linifanib effectively protected cells from necroptosis and rescued the death of SIRS mice from shock induced by TNF-α. In vitro, linifanib directly suppressed RIPK1 kinase activity. In vivo, linifanib effectively reduced the overexpressed level of IL-6, a good marker of severity during severe sepsis, in the lung of SIRS mice.

Conclusion

We provide preclinical evidence for the potential clinical utility of linifanib in sepsis. Study of drug repositioning using bioinformatical predictions combined with experimental validations provides novel strategies for the development of sepsis drug.
Genome-wide signatures of geographic expansion and breeding process in soybean
Authors: Li Ying-hui , Qin Chao , Wang Li , Jiao Chengzhi , Hong Huilong , Tian Yu , Li Yanfei , Xing Guangnan , Wang Jun , Gu Yongzhe , Gao Xingpeng , Li Delin , Li Hongyu , Liu Zhangxiong , Jing Xin , Feng Beibei , Zhao Tao , Guan Rongxia , Guo Yong , Liu Jun , Yan Zhe , Zhang Lijuan , Ge Tianli , Li Xiangkong , Wang Xiaobo , Qiu Hongmei , Zhang Wanhai , Luan Xiaoyan , Han Yingpeng , Han Dezhi , Chang Ruzhen , Guo Yalong , Reif Jochen C. , Jackson Scott A. , Liu Bin , Tian Shilin , Qiu Li-juan
Published: March 2022

The clarification of genomic signatures left during evolutionary histories of crops is crucial for breeding varieties adapting to changing climate. Soybean, a leguminous crop, provides both plant oil and protein. Here, we analyzed genome sequences of 2,214 soybeans and proposed its evolutionary route, which includes four geographic paths, expansion of annual wild soybean (Glycine soja Sieb. & Zucc.) from Southern China, domestication in Central China, expansion of landrace (G. max (L.) Merr.), and local breeding. We observed that local adaptation of the wild and cultivated soybeans was largely independent, and that genetic introgression was mostly derived from sympatric rather than allopatric wild populations during the range expansion of soybean landraces. Range expansion and breeding processes were accompanied with positive selection of flowering-time genes including GmSPA3c as validated by knock-out mutants. Our study shed lights on the evolutionary history of soybean and provides valuable genetic resources for future breeding.

Teaser

The expansion and selection history of soybean
Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention
Authors: Hadar Shani , Meller Anatoly , Shalgi Reut
Published: March 2022

Exposure to certain stresses leads to readthrough transcription. Here we found that readthrough transcription often proceeds into the proximal gene downstream, in a phenomenon termed “read-in”. Using polyA-selected RNA-seq data from mouse fibroblasts, we identified widespread read-in in heat shock, oxidative and osmotic stress conditions. We found that read-in genes share distinctive genomic characteristics; they are extremely short, and highly GC rich. Furthermore, using ribosome footprint profiling we found that translation of read-in genes is significantly reduced. Strikingly, read-in genes show extremely high levels of intron retention during stress, mostly in their first intron, which is not explained by features usually associated with intron retention, such as short introns and high GC content. Finally, we found that first introns in read-in genes have weaker splice sites. Our data portray a relationship between read-in and intron retention, suggesting it may have co-evolved to facilitate reduced translation of read-in genes during stress.
The actin assembly requirements of the formin Fus1 to build the fusion focus
Authors: Billault-Chaumartin Ingrid , Michon Laetitia , Anderson Caitlin A , Yde Sarah E , Suarez Cristian , Iwaszkiewicz Justyna , Zoete Vincent , Kovar David R , Martin Sophie G
Published: March 2022

Formins form the largest family of actin filament nucleators and elongators, involved in the assembly of diverse actin structures. Actin filament nucleation and elongation activities reside in the formin homology 1 (FH1) and FH2 domains, common to all formins. However, the rate of these reactions varies between formins by at least 20-fold. Typically, each cell expresses several distinct formins, each contributing to the assembly of one or several actin structures, raising the question of what confers each formin its specificity. Here, using the formin Fus1 in the fission yeast Schizosaccharomyces pombe, we systematically probed the importance of formin nucleation and elongation rates for function in vivo. Fus1 assembles the actin fusion focus, an aster-like structure of actin filaments at the contact site between gametes, necessary for the process of cell fusion to form the zygote during sexual reproduction. By constructing chimeric formins with combinations of FH1 and FH2 domains previously characterized in vitro, we establish that changes in formin nucleation and elongation rates have direct consequences on the architecture of the fusion focus, and that Fus1 native high nucleation and low elongation rates are optimal for fusion focus assembly. We further describe a point mutant in the Fus1 FH2 domain that preserves native nucleation and elongation rates in vitro but alters function in vivo, indicating an additional property of the FH2 domain. Thus, rates of actin assembly are tailored for assembly of specific actin structures.
Suboptimal foraging decisions and involvement of the ventral tegmental area in human opioid addiction
Authors: Raio Candace M. , Biernacki Kathryn , Kapoor Ananya , Wengler Kenneth , Bonagura Darla , Xue Joany , Constantino Sara M. , Horga Guillermo , Konova Anna B.
Published: March 2022

Addiction is marked by a tendency to exploit sources of reward despite diminishing returns. This behavior is aptly captured by animal patch-foraging models that have recently been extended to humans. Dopamine and norepinephrine centrally mediate addictive behavior and activity in both catecholaminergic systems is proposed to reflect the computations necessary for optimal foraging. However, the specific neural bases of excessive foraging and their role in human addiction are largely unknown. To address this gap, we studied the behavior of people with and without opioid use disorder (OUD) on a patch-foraging task in which they made serial decisions to “harvest” a depleting resource (“patch”) for reward or incur a varying cost to “travel” to a replenished patch. In a subset of participants, we used high-resolution neuromelanin-sensitive MRI to image neuromelanin concentration, a proxy for long-term catecholaminergic function, in distinct dopaminergic nuclei (ventral tegmental area, substantia nigra subregions) and the noradrenergic locus coeruleus. While all participants were sensitive to the long-run reward rates of different patch-foraging environments, OUD participants stayed in reward patches longer than optimal—markedly overharvesting a source of reward despite its declining value—and this correlated with more chronic drug use. Overharvesting was selectively associated with lower neuromelanin signal in the ventral tegmental area but not other dopaminergic nuclei, nor the locus coeruleus. Our findings suggest that foraging decisions relevant to addiction involve a ventral-tegmental-area circuit that may signal reward rates in dynamic environments and implicate this circuit in maladaptive reward pursuit in human addiction to opioids.

Significance statement

Patch-foraging provides a potentially important translational framework for understanding addictive behavior by revealing how maladaptive reward pursuit emerges in more ecologically valid decision contexts. Here, we show that the tendency to exploit sources of reward despite diminishing returns is associated with chronic drug use in people with opioid use disorder, a particularly devastating form of addiction. We further use neuromelanin-sensitive MRI, a neuroimaging measure of the long-term function of dopamine neurons, to reveal that variation in ventral tegmental area neuromelanin signal selectively underlies individual differences in this overharvesting bias. These findings establish a role for specific dopaminergic circuits in patch-foraging decisions and advance understanding of the neurobiology of human addiction to opioids that has so far eluded the field.
Comparative assessment of computed tomography and magnetic resonance imaging of the spider morph of Python regius and wild type Python regius to evaluate the morphological correlate of the wobble syndrome
Authors: Schrenk Fabian , Starck Matthias , Kiefer Ingmar , Flegel Thomas , Tebrün Wiebke , Pees Michael
Published: March 2022

There is general awareness of artificial selection and its potential implications on health and welfare of animals. Despite growing popularity and increasing numbers of breeds of atypical colour and pattern variants in reptiles, only few studies have investigated the appearance and cause of various diseases associated with colour morphs. Ball pythons (Python regius) are among the most frequently bred reptiles and breeders selected for a multitude of different colour and pattern morphs. Among those colour variants, the spider morph of the ball python is frequently associated with the wobble syndrome. The aim of this study was to determine, whether a morphological variant can be found and brought in association with the clinical occurrence of the wobble syndrome in spider ball pythons, using MRI and CT-imaging as intra-vitam diagnostic methods. Data from eight ball pythons including five spider ball pythons and three wild type ball pythons was assessed and evaluated comparatively. We were able to identify distinctive structural differences in inner ear morphology in spider ball pythons highly probable to relate to the wobble syndrome. To our knowledge, these anomalies are described for the first time and represent a basis for further anatomical and genetic studies and discussions regarding animal welfare in reptile breeding.
Complex developmental and transcriptional dynamics underlie pollinator-driven evolutionary transitions in nectar spur morphology in Aquilegia (columbine)
Authors: Edwards Molly B. , Ballerini Evangeline S. , Kramer Elena M.
Published: March 2022

Premise

Determining the developmental programs underlying morphological variation is key to elucidating the evolutionary processes that generated the stunning biodiversity of the angiosperms. Here, we characterize the developmental and transcriptional dynamics of the elaborate petal nectar spur of Aquilegia (columbine) in species with contrasting pollination syndromes and spur morphologies.

Methods

We collected petal epidermal cell number and length data across four Aquilegia species, two with the short, curved nectar spurs of the bee-pollination syndrome, and two with the long, straight spurs of the hummingbird syndrome. We also performed RNA-seq on A. brevistyla (bee) and A. canadensis (hummingbird) distal and proximal spur compartments at multiple developmental stages. Finally, we intersected these datasets with a previous QTL mapping study on spur length and shape to identify new candidate loci.

Results

The differential growth between the proximal and distal surfaces of curved spurs is primarily driven by differential cell division. However, independent transitions to straight spurs in the hummingbird syndrome have evolved by increasing differential cell elongation between spur surfaces. The RNA-seq data reveal these tissues to be transcriptionally distinct, and point to auxin signaling as being involved with the differential cell elongation responsible for the evolution of straight spurs. We identify several promising candidate genes for future study.

Conclusions

Our study, taken together with previous work in Aquilegia, reveals the complexity of the developmental mechanisms underlying trait variation in this system. The framework we have establish here will lead to exciting future work examining candidate genes and processes involved in the rapid radiation of the genus.
Bursts of genomic instability potentiate phenotypic and genomic diversification in Saccharomyces cerevisiae
Authors: Heasley Lydia R. , Argueso Juan Lucas
Published: March 2022

How microbial cells leverage their phenotypic potential to survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. Stochastic phenotype switching, a particularly fascinating adaptive approach observed in numerous species across the tree of life, introduces phenotypic diversity into a population through mechanisms which have remained difficult to define. Here we describe our investigations into the mechanistic basis of colony morphology phenotype switching which occurs in populations of a pathogenic isolate of Saccharomyces cerevisiae, YJM311. We observed that clonal populations of YJM311 cells produce variant colonies that display altered morphologies and, using whole genome sequence analysis, discovered that these variant clones harbored an exceptional collection of karyotypes newly altered by de novo structural genomic variations (SVs). Overall, our analyses indicate that copy number alterations, more often than changes in allelic identity, provide the causative basis of this phenotypic variation. Individual variants carried between 1 and 16 de novo copy number variations, most of which were whole chromosomal aneuploidies. Notably, the inherent stability of the diploid YJM311 genome is comparable to that of domesticated laboratory strains, indicating that the collections of SVs harbored by variant clones did not arise by a chronic chromosomal instability (CIN) mechanism. Rather, variant clones acquired these complex karyotypic configurations simultaneously, during stochastic and transient episodes of punctuated systemic genomic instability (PSGI). Surprisingly, we found that the majority of these highly altered variant karyotypes were propagated with perfect fidelity in long-term passaging experiments, demonstrating that high aneuploidy burdens can often be conducive with prolonged genomic instability. Together, our results demonstrate that colony morphology switching in YJM311 is driven by a stochastic process in which genome stability and plasticity are integrally coupled to phenotypic heterogeneity. Consequently, this system simultaneously introduces both phenotypic and genomic variation into a population of cells, which can, in turn perpetuate population diversity for many generations thereafter.
Discordant calls across genotype discovery approaches elucidate variants with systematic errors
Authors: Atkinson Elizabeth G. , Artomov Mykyta , Karczewski Konrad J. , Loboda Alexander A. , Rehm Heidi L. , MacArthur Daniel G. , Neale Benjamin M. , Daly Mark J.
Published: March 2022

Large-scale next-generation sequencing datasets have been transformative for informing clinical variant interpretation and as reference panels for statistical and population genetic efforts. While such resources are often treated as ground truth, we find that in widely used reference datasets such as the Genome Aggregation Database (gnomAD), some variants pass gold standard filters yet are systematically different in their genotype calls across genotype discovery approaches. The inclusion of such discordant sites in study designs involving multiple genotype discovery strategies could bias results and lead to false-positive hits in association studies due to technological artifacts rather than a true relationship to the phenotype. Here, we describe this phenomenon of discordant genotype calls across genotype discovery approaches, characterize the error mode of wrong calls, provide a blacklist of discordant sites identified in gnomAD that should be treated with caution in analyses, and present a metric and machine learning classifier trained on gnomAD data to identify likely discordant variants in other datasets. We find that different genotype discovery approaches have different sets of variants at which this problem occurs but that there are characteristic variant features that can be used to predict discordant behavior. Discordant sites are largely shared across ancestry groups, though different populations are powered for discovery of different variants. We find that the most common error mode is that of a variant being heterozygous for one approach and homozygous for the other, with heterozygous in the genomes and homozygous reference in the exomes making up the majority of miscalls.
Physiological and molecular mechanisms regulated mesophyll conductance under severe drought in water-saving drought-resistant rice
Authors: He Haibing , Wang Lele , Zhang Xuelan , Zhan Li , Wang Quan , Yang Ru , You Cuicui , Ke Jian , Wu Liquan
Published: March 2022

Water-saving and drought-resistant rice (WDR) is a new type of rice varieties. It plays an important role in responding to drought with high yield and has been widely planted in central China at present. High photosynthetic production potential caused by high mesophyll conductance (gm) is the main factor promoted high yield formation in drought for WDR. But little is known about physiological and molecular mechanisms regulated gm in drought for WDR. Therefore, WDR cultivar HY73 and drought-sensitive cultivar HLY898 were used for comparative studies with three irrigation regimes before applying severe drought treatment at heading to create different differential individuals of photosynthetic potential and gm. The results showed that cultivar HY73 had lower up-regulation different expression genes (DEGs) than cultivar HLY898 in drought at transcriptional level. Conversely, DEGs of down-regulation was higher in cultivar HY73 than cultivar HLY898. In addition, 3071 DEGs were clustered in 3 modules named Midnightblue (734 DEGs), Blue (921 DEGs), and Turquoise (1416 DEGs) in severe drought merged three irrigation regimes and both cultivars, which the modules had significant correlational relationship with gm based on weighted gene co-expression network analysis (P<0.05). Only DEGs in midnightblue module were enriched in photosynthesis process and positively regulated gm (P<0.05). The main biological process were photosynthesis (GO:0015979), light harvesting in photosystem I (GO:0009768), reductive pentose-phosphate cycle (GO:0019253), protein-chromophore linkage (GO:0018298), photosynthetic electron transport in photosystem I (GO:0009773), and photosystem II repair (GO:0010206). These results indicate that gm and energy distribution in PSI and PSII systems could synergistic effect photosynthetic production potential in severe drought for rice plants. In the modules, the 18 most highly connected hub genes were screened using co-expression networks method. RT-PCR analysis indicated that CSP41B, PGLP1A, LHCA5, and GSTU6 genes had a similar variation trend with gm among treatments for both cultivar. LHCA5 and CSP41B genes were significantly up-regulated in HY73 compared with HLY898 in drought (P<0.05). And the both genes locates in thylakoid membrane in photosystems. Therefore, LHCA5 and CSP41B genes could be key genes to synergistically manage gm and energy distribution in photosystems. Our results provide some new physiological and molecular mechanisms regulated gm in severe drought for WDR.
Machine Learning Enabled Non-invasive Diagnosis of Nonalcoholic Fatty Liver Disease and Assessment of Abdominal Fat from MRI Data
Authors: Pillai Arvind , Bliznashki Kamen , Hutchison Emmette , Kumar Chanchal , Challis Benjamin , Patel Mishal
Published: March 2022

Nonalcoholic fatty liver disease (NAFLD) is the most rapidly growing contributor to chronic liver disease worldwide with high disease burden and suffers from limitations in diagnosis. Inspired by recent advances in machine learning digital diagnostics, we explored the efficacy of training a neural network to classify high risk NAFLD vs. non-NAFLD patients in the UK Biobank dataset based on proton density fat fraction (PDFF). We compared the performance of several ResNet-derived architectures in the context of whole abdomen MRI, segmented liver and abdomen excluding liver (sans-liver). Non-local ResNet trained on whole abdomen MRI images yielded the highest precision (0.88 for NAFLD) and F1 (0.89 for NAFLD). Furthermore, our work on a second, larger cohort explored multi-task learning and the relationship among PDFF, visceral adipose tissue (VAT) and abdominal subcutaneous adipose tissue (ASAT). Interestingly, multi-task learning experiments found a decline in performance for PDFF when combined with VAT and ASAT. We address this deterioration using Multi-gate Mixture-of-Experts (MMoE) approaches. Our work opens the possibility for using a non-invasive deep learning-based diagnostic for NAFLD, and directly enables clinical and genomic research using a larger cohort of potential NAFLD patients in the UK Biobank study.
PLO3S : Protein LOcal Surficial Similarity Screening
Authors: Sirugue Lea , Langenfeld Florent , Lagarde Nathalie , Montes Matthieu
Published: March 2022

The study of protein molecular surfaces enable to better understand and predict protein interactions. Different methods have been developed in computer vision to compare surfaces that can be applied to protein molecular surfaces. The present work proposes a method using the the Wave Kernel Signature : Protein LOcal Surficial Similarity Screening (PLO3S). The descriptor of the PLO3S method is a local surface shape descriptor projected on a unit sphere mapped onto a 2D plane and called Surface Wave Interpolated Maps (SWIM). PLO3S allows to rapidly compare protein surface shapes through local comparisons to filter large protein surfaces datasets in protein structures virtual screening protocols.
mTORC2 coordinates the leading and trailing edge cytoskeletal programs during neutrophil migration
Authors: Saha Suvrajit , Town Jason P. , Weiner Orion D.
Published: March 2022

By acting both upstream and downstream of biochemical organizers of the cytoskeleton, physical forces function as central integrators of cell shape and movement. Here we use a combination of genetic, pharmacological, and optogenetic perturbations to probe the role of the conserved mechanoresponsive mTORC2 program in neutrophil polarity and motility. We find that the tension-based inhibition of leading edge signals (Rac, F-actin) that underlies protrusion competition is gated by the kinase-independent role of the complex, whereas the mTORC2 kinase arm is essential for regulation of Rho activity and Myosin II-based contraction at the trailing edge. Cells required mTORC2 for spatial and temporal coordination between the front and back polarity programs and persistent migration under confinement. mTORC2 is in a mechanosensory cascade, but membrane stretch did not suffice to stimulate mTORC2 unless the co-input PIP3 was also present. Our work suggests that different signalling arms of mTORC2 regulate spatially and molecularly divergent cytoskeletal programs allowing efficient coordination of neutrophil shape and movement.
Nr2f1 controls mitochondrial dynamics in mouse adult-born hippocampal neurons
Authors: Sara Bonzano , Filippo Michelon , Isabella Crisci , Ivan Molineris , Francesco Neri , Salvatore Oliviero , Ruth Beckervordersandforth , Chichung Lie Dieter , Paolo Peretto , Serena Bovetti , Michèle Studer , Silvia De Marchis
Published: March 2022

The nuclear receptor Nr2f1 plays a key role during cortical development by acting as a strong transcriptional regulator in embryonic and postnatal neural cells. In humans, its mutations cause the Bosch-Boonstra-Schaaf optic atrophy-intellectual syndrome (BBSOAS), a rare neurodevelopmental disorder characterized by multiple clinical features including optic nerve atrophy, intellectual disability, and autistic traits. In this study by genome-wide and in silico analyses we found that key factors for mitochondrial function and dynamics represent potential genomic targets under direct Nr2f1 transcriptional control in neurons. Although mitochondrial dysfunction is increasingly implicated in neurodevelopmental disorders, whether and how Nr2f1 can regulate mitochondria function in neural cells is still completely unknown. To address these questions, we have combined mouse genetics, neuroanatomical and imaging approaches. To genetically manipulate Nr2f1 function in newborn neurons we focused on the adult mouse hippocampal dentate gyrus, a site of persistent neurogenesis where Nr2f1 is highly expressed. We showed that conditional Nr2f1 loss-of-function within the hippocampal neurogenic niche lead to a reduced mitochondrial mass associated to mitochondrial fragmentation in newborn neurons, likely reflecting alteration in mitochondrial dynamics. Accordingly, we showed that the fusion factor Mfn2, which is as a putative Nr2f1 target, is downregulated following both Nr2f1 adult depletion and embryonic haploinsufficiency in mice. Overall, our study provides the first evidence of a crucial role of Nr2f1 in shaping mitochondria in neurons and opens a promising avenue for the identification of new mechanisms implicated in BBSOAS pathogenesis involving mitochondrial dysfunction.