bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired succinate oxidation prevents growth and influences drug susceptibility in Mycobacterium tuberculosis
Authors: Adolph Cara , McNeil Matthew B. , Cook Gregory M.
Published: June 2021

Succinate is a major focal point in mycobacterial metabolism and respiration, serving as both an intermediate of the TCA cycle and a direct electron donor for the respiratory chain. Mycobacterium tuberculosis encodes multiple enzymes predicted to be capable of catalyzing the oxidation of succinate to fumarate, including two different succinate dehydrogenases (Sdh1 and Sdh2) and a separate fumarate reductase (Frd) with possible bi-directional behavior. Previous attempts to investigate the essentiality of succinate oxidation in M. tuberculosis have relied on the use of single-gene deletion mutants, raising the possibility that the remaining enzymes could catalyze succinate oxidation in the absence of the other. To address this, we report on the use of mycobacterial CRISPR interference (CRISPRi) to construct single, double, and triple transcriptional knockdowns of sdhA1, sdhA2, and frdA in M. tuberculosis. We show that the simultaneous knockdown of sdhA1 + sdhA2 is required to prevent succinate oxidation and overcome the functional redundancy within these enzymes. Succinate oxidation was demonstrated to be essential for the optimal growth of M. tuberculosis, with the combined knockdown of sdhA1 + sdhA2 significantly impairing the activity of the respiratory chain and preventing growth on a range of carbon sources. Moreover, impaired succinate oxidation was shown to influence the activity of several antitubercular drugs against M. tuberculosis, including potentiating the activity of bioenergetic inhibitors and attenuating the activity of cell wall inhibitors. Together, these data provide fundamental insights into mycobacterial physiology, energy metabolism, and antimicrobial susceptibility.

Importance

New drugs are urgently required to combat the tuberculosis epidemic that claims 1.5 million lives annually. Inhibitors of mycobacterial energy metabolism have shown significant promise clinically; however, further advancing this nascent target space requires a more fundamental understanding of the respiratory enzymes and pathways used by Mycobacterium tuberculosis. Succinate is a major focal point in mycobacterial metabolism and respiration; yet the essentiality of succinate oxidation, and the consequences of inhibiting this process, are poorly defined. In this study, we demonstrate that impaired succinate oxidation prevents the optimal growth of M. tuberculosis on a range of carbon sources and significantly reduces the activity of the electron transport chain. Moreover, we show that impaired succinate oxidation both positively and negatively influences the activity of a variety of anti-tuberculosis drugs. Combined, these findings provide fundamental insights into mycobacterial physiology and drug susceptibility that will be useful in the continued development of bioenergetic inhibitors.
Pickering stabilization of a dynamic intracellular emulsion
Authors: Folkmann Andrew W. , Putnam Andrea , Lee Chiu Fan , Seydoux Geraldine
Published: June 2021

Biomolecular condensates are cellular compartments that form by phase separation in the absence of limiting membranes. Studying the P granules of C. elegans, we find that condensate dynamics are regulated by protein clusters that adsorb to the condensate interface. Using in vitro reconstitution, live observations and theory, we demonstrate that localized assembly of P granules is controlled by MEG-3, an intrinsically disordered protein that forms low dynamic assemblies on P granules. Following classic Pickering emulsion theory, MEG-3 clusters lower surface tension and slow down coarsening. During zygote polarization, MEG-3 recruits DYRK/MBK-2 kinase to accelerate localized growth of the P granule emulsion. By tuning condensate-cytoplasm exchange, interfacial clusters regulate the structural integrity of biomolecular condensates, reminiscent of the role of lipid bilayers in membrane-bound organelles.

One Sentence Summary

Biomolecular condensates are stabilized by interfacial nanoscale protein clusters.
H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate
Authors: Dubois A. , Vincenti L. , Chervova A. , Vandormael-Pournin S. , Cohen-Tannoudji M. , Navarro P.
Published: June 2021

Mouse Embryonic Stem (ES) cells have an inherent propensity to explore distinct gene-regulatory states associated with either self-renewal or differentiation. This property is largely dependent on ERK activity, which promotes silencing of pluripotency genes, most notably of the transcription factor Nanog. Here, we aimed at identifying repressive histone modifications that would mark the Nanog locus for inactivation in response to ERK activity. We found histone H3 lysine 9 tri-methylation (H3K9me3) focally enriched between the Nanog promoter and its −5kb enhancer. While in undifferentiated ES cells H3K9me3 at Nanog depends on ERK activity, in somatic cells it becomes ERK-independent. Moreover, upon deletion of the region harbouring H3K9me3, ES cells display reduced heterogeneity of NANOG expression, delayed commitment into differentiation and impaired ability to acquire a primitive endoderm fate. We suggest that establishment of irreversible H3K9me3 at specific master regulators allows the acquisition of particular cell fates during differentiation.
Design, Mutate, Screen: High-throughput creation of genetic clocks with different period-amplitude characteristics
Authors: Lezia Andrew , Csicsery Nicholas , Hasty Jeff
Published: June 2021

Directed evolution has become an invaluable tool in protein engineering and has also greatly influenced the construction of synthetic gene circuits. The ability to generate diversity at precise targets for directed evolution approaches has improved vastly, allowing researchers to create large, specific mutant libraries with relative ease. Screening approaches for large mutant libraries have similarly come a long way, especially when the desired behavior can easily be tested for with static, single time-point assays. For more complex gene circuits with dynamic phenotypes that change over time, directed evolution approaches to controlling and tuning circuit behavior have been hindered by the lack of sufficiently high-throughput screening methods to isolate variants with desired characteristics. Here we utilize directed mutagenesis and multiplexed microfluidics to develop a workflow for creating, screening and tuning dynamic gene circuits that operate at the population level. Specifically, we create a mutant library of an existing oscillator, the synchronized lysis circuit, and tune its dynamics while uncovering principles regarding its behavior. Lastly, we utilize this directed evolution workflow to construct a new synchronized genetic oscillator that exhibits robust dynamics over long time scales.
A mechanistic density functional theory for ecology across scales
Authors: Trappe Martin-I. , Chisholm Ryan A.
Published: June 2021

Our ability to predict the properties of a system typically diminishes as the number of its interacting constituents rises. This poses major challenges for understanding natural ecosystems, and humanity’s effects on them. How do macroecological patterns emerge from the interplay between species and their environment? What is the impact on complex ecological systems of human interventions, such as extermination of large predators, deforestation, and climate change? The resolution of such questions is hampered in part by the lack of a holistic approach that unifies ecology across temporal and spatial scales. Here we use density functional theory, a computational method for many-body problems in physics, to develop a novel computational framework for ecosystem modelling. Our methods accurately fit experimental and synthetic data of interacting multi-species communities across spatial scales and can project to unseen data. Our mechanistic framework provides a promising new avenue for understanding how ecosystems operate and facilitates quantitative assessment of interventions.
Task complexity temporally extends the causal requirement for visual cortex in perception
Authors: Oude Lohuis Matthijs N. , Pie Jean L. , Marchesi Pietro , Montijn Jorrit S. , de Kock Christiaan P.J. , Pennartz Cyriel M. A. , Olcese Umberto
Published: June 2021

The transformation of sensory inputs into behavioral outputs is characterized by an interplay between feedforward and feedback operations in cortical hierarchies. Even in simple sensorimotor transformations, recurrent processing is often expressed in primary cortices in a late phase of the cortical response to sensory stimuli. This late phase is engaged by attention and stimulus complexity, and also encodes sensory-independent factors, including movement and report-related variables. However, despite its pervasiveness, the nature and function of late activity in perceptual decision-making remain unclear. We tested whether the function of late activity depends on the complexity of a sensory change-detection task. Complexity was based on increasing processing requirements for the same sensory stimuli. We found that the temporal window in which V1 is necessary for perceptual decision-making was extended when we increased task complexity, independently of the presented visual stimulus. This window overlapped with the emergence of report-related activity and decreased noise correlations in V1. The onset of these co-occurring activity patterns was time-locked to and preceded reaction time, and predicted the reduction in behavioral performance obtained by optogenetically silencing late V1 activity (>200 ms after stimulus onset), a result confirmed by a second multisensory task with different requirements. Thus, although early visual response components encode all sensory information necessary to solve the task, V1 is not simply relaying information to higher-order areas transforming it into behavioral responses. Rather, task complexity determines the temporal extension of a loop of recurrent activity, which overlaps with report-related activity and determines how perceptual decisions are built.
Known mechanisms cannot account for at least one third of reduced susceptibility in a diverse collection of non-aureusstaphylococci
Authors: Felgate Heather , Crossman Lisa C. , Gray Elizabeth , Clifford Rebecca , Wain John , Langridge Gemma C.
Published: June 2021

Introduction

Non-aureusstaphylococci (NAS) are implicated in many healthcare-acquired infections and an understanding of the genetics of antimicrobial resistance in NAS is important in relation to both clinical intervention and the role of NAS as a reservoir of resistance genes.

Gap statement

The burden of antimicrobial resistance in NAS, particularly to clinically relevant antimicrobials, is under recognised.

Methodology

We sourced 394 NAS isolates from clinical samples, healthy human volunteers, animals and type cultures and subjected them to agar dilution susceptibility testing against eight antimicrobials. Cefoxitin was used to screen for methicillin resistance inS. aureus, as it stimulates expression ofmecA. We performed whole genome sequencing on 366 isolates and analysed these genotypically for the presence of genetic mechanisms responsible for the phenotypic levels of reduced antimicrobial susceptibility.

Results

We observed 175 sequenced isolates with a minimum inhibitory concentration (MIC) of at least 4 μg/ml to cefoxitin, of which 50% (87/175) did not harbour a knownmechomologue. Eight clinical NAS isolates displayed high daptomycin MICs (>4 μg/ml), with no known mechanism identified. Differences in MICs against erythromycin were attributable to the presence of different resistance genes (msrAandermC). In total, 49% (193 /394) of isolates displayed reduced susceptibility to three or more of the antimicrobials tested.

Conclusions

The widespread presence of reduced antimicrobial susceptibility in NAS is a concern, with an increased likelihood of (1) harder to treat infections caused directly by NAS, and (2) resistance genes being passed on to other bacteria via horizontal gene transfer, both of which have clinical implications for treatment and management of patients.
Genomic sequencing of Lowe syndrome trios reveal a mechanism for the heterogeneity of neurodevelopmental phenotypes
Authors: Pallikonda Husayn Ahmed , Singh Pramod , Thakur Rajan , Kumari Aastha , Krishnan Harini , Philip Ron George , Vasudevan Anil , Raghu Padinjat
Published: June 2021

Lowe syndrome is an X-linked recessive monogenic disorder resulting from mutations in theOCRLgene that encodes a phosphatidylinositol 4,5 bisphosphate 5-phosphatase. The disease affects three organs-the kidney, brain and eye and clinically manifests as proximal renal tubule dysfunction, neurodevelopmental delay and congenital cataract. Although Lowe syndrome is a monogenic disorder, there is considerable heterogeneity in clinical presentation; some individuals show primarily renal symptoms with minimal neurodevelopmental impact whereas others show neurodevelopmental defect with minimal renal symptoms. However, the molecular and cellular mechanisms underlying this clinical heterogeneity remain unknown. Here we analyze a Lowe syndrome family in whom affected members show clinical heterogeneity with respect to the neurodevelopmental phenotype despite carrying an identical mutation in theOCRLgene. Genome sequencing and variant analysis in this family identified a large number of damaging variants in each patient. Using novel analytical pipelines and segregation analysis we prioritize variants uniquely present in the patient with the severe neurodevelopmental phenotype compared to those with milder clinical features. The identity of genes carrying such variants underscore the role of additional gene products enriched in the brain or highly expressed during brain development that may be determinants of the neurodevelopmental phenotype in Lowe syndrome. We also identify a heterozygous variant inCEP290, previously implicated in ciliopathies that underscores the potential role ofOCRLin regulating ciliary function that may impact brain development. More generally, our findings demonstrate analytic approaches to identify high-confidence genetic variants that could underpin the phenotypic heterogeneity observed in monogenic disorders.
Integrated gene landscapes uncover multi-layered roles of repressive histone marks during mouse CNS development
Authors: Mora Ariane , Rakar Jonathan , Cobeta Ignacio Monedero , Salmani Behzad Yaghmaeian , Starkenberg Annika , Thor Stefan , Bodén Mikael
Published: June 2021

A prominent aspect of most, if not all, central nervous systems (CNSs) is that anterior regions (brain) are larger than posterior ones (spinal cord). Studies inDrosophilaand mouse have revealed that the Polycomb Repressor Complex 2 (PRC2), a protein complex responsible for applying key repressive histone modifications, acts by several mechanisms to promote anterior CNS expansion. However, it is unclear what the full spectrum of PRC2 action is during embryonic CNS development and how PRC2 integrates with the epigenetic landscape. We removed PRC2 function from the developing mouse CNS, by mutating the key geneEed, and generated spatio-temporal transcriptomic data. To decode the role of PRC2, we developed a method that incorporates standard statistical analyses with probabilistic deep learning to integrate the transcriptomic response to PRC2 inactivation with epigenetic information from ENCODE. This multi-variate analysis corroborates the central involvement of PRC2 in anterior CNS expansion, and reveals layered regulation via PRC2. These findings uncover a differential logic for the role of PRC2 upon functionally distinct gene categories that drive CNS anterior expansion. To support the analysis of emerging multi-modal datasets, we provide a novel bioinformatics package that integrates transcriptomic and epigenetic datasets to identify regulatory underpinnings of heterogeneous biological processes.
A combined test for feature selection on sparse metaproteomics data - an alternative to missing value imputation
Authors: Plancade Sandra , Berland Magali , Blein-Nicolas Melisande , Langella Olivier , Bassignani Ariane , Juste Catherine
Published: June 2021

One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely “at random” or “not at random”. To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential missingness). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.
The RNA-binding protein RBP45D of Arabidopis plays a role in epigenetic control of flowering time and DCL3-independent RNA-directed DNA methylation
Authors: Wang Liangsheng , Xu Duorong , Habermann Kristin , Frank Wolfgang , Leister Dario , Kleine Tatjana
Published: June 2021

RNA-directed DNA methylation (RdDM) helps to defend plants against invasive nucleic acids. In the canonical form of RdDM, 24-nt small interfering RNAs (siRNAs) are produced by DICER-LIKE 3 (DCL3). Here, we describe the Arabidopsis thaliana prors1 (LUC) transgenic system, in which transcriptional gene silencing (TGS) is independent of DLC3. A forward genetics screen performed with this system identified both known components of RdDM, and the RNA-binding protein RBP45D. RBP45D promotes DNA methylation, and its loss delays flowering, especially at high temperature, presumably mediated by elevated FLC levels. RBP45D is localized to the nucleus, where it is associated with snRNAs and snoRNAs. RBP45D maintains siRNA production originating from the LUC transgene, but does not alter mRNA levels or affect processing of transcripts of known RdDM genes. We suggest that RBPD45 facilitates DCL3-independent siRNA production by stabilising either the precursor RNA or the – as yet unidentified – slicer protein.
Electrophysiological correlates of perceptual prediction error are attenuated in dyslexia
Authors: Beach Sara D. , Lim Sung-Joo , Cardenas-Iniguez Carlos , Eddy Marianna D. , Gabrieli John D. E. , Perrachione Tyler K.
Published: June 2021

A perceptual adaptation deficit often accompanies reading difficulty in dyslexia, manifesting in poor perceptual learning of consistent stimuli and reduced neurophysiological adaptation to stimulus repetition. However, it is not known how adaptation deficits relate to differences in feedforward or feedback processes in the brain. Here we used electroencephalography (EEG) to interrogate the feedforward and feedback contributions to neural adaptation as adults with and without dyslexia viewed pairs of faces and words in a paradigm that manipulated whether there was a high probability of stimulus repetition versus a high probability of stimulus change. We measured three neural dependent variables:expectation(the difference between prestimulus EEG power with and without the expectation of stimulus repetition), feedforwardrepetition(the difference between event-related potentials (ERPs) evoked by an expected change and an unexpected repetition), and feedback-mediatedprediction error(the difference between ERPs evoked by an unexpected change and an expected repetition). Expectation significantly modulated prestimulus theta- and alpha-band EEG in both groups. Unexpected repetitions of words, but not faces, also led to significant feedforward repetition effects in the ERPs of both groups. However, neural prediction error when an unexpected change occurred instead of an expected repetition was significantly weaker in dyslexia than the control group for both faces and words. These results suggest that the neural and perceptual adaptation deficits observed in dyslexia reflect the failure to effectively integrate perceptual predictions with feedforward sensory processing. In addition to reducing perceptual efficiency, the attenuation of neural prediction error signals would also be deleterious to the wide range of perceptual and procedural learning abilities that are critical for developing accurate and fluent reading skills.
Computational neural network provides naturalistic solution for recovery of finger dexterity after stroke
Authors: Kadry Ashraf , Norman Sumner L. , Xu Jing , Solomonow-Avnon Deborah , Mawase Firas
Published: June 2021

Finger dexterity is a fundamental movement skill of humans and the ability to individuate fingers imparts high motor flexibility. Disruption of dexterity due to brain injury reduces quality of life. Thus, understanding the neurological mechanisms responsible for recovery is critical to effective neurorehabilitation. Two neuronal pathways have been proposed to play crucial roles in finger individuation: thecorticospinaltract, originating from primary motor cortex and premotor areas, and the subcorticalreticulospinaltract, originating from the reticular formation in the brainstem. Finger individuation in patients with lesions to these pathways may recover. However, it remains an open question how the cortical-reticular network reorganizes and contributes to this recovery following a stroke. We hypothesized that interactive connections between cortical and subcortical neurons reflect dynamics appropriate for generating outgoing commands for finger movement. To test this hypothesis, we developed an Artificial Neural Network (ANN) representing a premotor planning input layer, a cortical layer including excitatory and inhibitory neurons and, a reticular layer that control motoneurons eliciting unilateral flexion of two fingers. The ANN was trained to reproduce “normal” activity of finger individuation and strength. Analysis of the trained ANN revealed that the natural dynamical solution was a near-linear relationship between the force of the instructed and uninstructed finger, resembling individuation patterns in humans. A simulated stroke lesion was then applied to the ANN and the resulting finger dexterity was assessed at multiple stages post stroke. Analysis revealed: (1) increased unintended force produced by uninstructed fingers (i.e., enslaving) and (2) weakening of the force in the instructed finger immediately after stroke, (3) improved finger control during recovery that typically occurs early after stroke, and (4) association of this behavior with increased neural plasticity of the residual neurons, as reflected by strengthening of connectivity weights between premotor and focal cortical excitatory and inhibitory neurons, but reduction in connectivity in shared cortical neurons. Interestingly, the network solution predicted that the reticulospinal pathway also contributed to the improved behavior. Lastly, the ANN also predicts the effect of cortical lesion size on finger individuation. Our model provides a framework by which to understand a number of experimental findings. The model solution suggests that a key mechanism of finger individuation is establishment of an interactive relationship between cortical and subcortical regions, appropriate to produce desired finger movement.
A Thioredoxin reductive mechanism balances the oxidative protein import pathway in the intermembrane space of mitochondria
Authors: Cardenas-Rodriguez Mauricio , Manganas Phanee , Kallergi Emmanouela , Edwards Ruairidh , Chatzi Afroditi , Lacko Erik , Tokatlidis Kostas
Published: June 2021

Mitochondria biogenesis crucially depends on the oxidative folding system in the mitochondrial intermembrane space. The oxidative capacity needs however to be balanced by a reductive pathway for optimal mitochondrial fitness. Here we report that the cytosolic thioredoxin machinery fulfils this critical reductive function by dual localisation in the mitochondrial intermembrane space (IMS) via an unconventional import pathway. We show that the presence of the Thioredoxin system in the IMS mediates a hitherto unknown communication between mitochondria biogenesis and the metabolic state of the cell via the cytosolic pool of NADPH. By a combination of complete in vitro reconstitution with purified components, import assays and protein interaction analysis we find that the IMS-localised thioredoxin machinery critically controls the redox state of Mia40, the key player in the MIA pathway in mitochondria thereby ensuring optimal mitochondria biogenesis. Intriguingly, we find that the IMS thioredoxin system fulfils a previously unknown role in the retrograde release of structurally destabilised proteins into the cytosol and protection against oxidative damage, both of which serve as critical mechanisms of mitochondrial surveillance and quality control.
The effects of long duration spaceflight on sensorimotor control and cognition
Authors: Tays GD , Hupfeld KE , McGregor HR , Salazar AP , De Dios YE , Beltran NE , Reuter-Lorenz PA , Kofman IG , Wood SJ , Bloomberg JJ , Mulavara AP , Seidler RD
Published: June 2021

Astronauts returning from spaceflight typically show transient declines in mobility and balance. These whole-body postural control behaviors have been investigated thoroughly, while study of the effects of spaceflight on other sensorimotor behaviors is prevalent. Here, we tested the effects of the spaceflight environment of microgravity on various sensorimotor and cognitive tasks during and after missions to the International Space Station (ISS). We obtained mobility (Functional Mobility Test), balance (Sensory Organization Test-5), bimanual coordination (bimanual Purdue Pegboard), cognitive-motor dual-tasking and various cognitive measures (Digit Symbol Substitution Test, Cube Rotation, Card Rotation, Rod and Frame Test) before, during and after 15 astronauts completed 6+ month missions aboard the ISS. We used linear mixed effect models to analyze performance changes due to entering the microgravity environment, behavioral adaptations aboard the ISS and subsequent recovery from microgravity. We identified declines in mobility and balance from pre- to post-flight, suggesting possible disruption and/or downweighting of vestibular inputs; these behaviors recovered to baseline levels within 30 days post-flight. We also identified bimanual coordination declines from pre- to post-flight and recovery to baseline levels within 30 days post-flight. There were no changes in dual-task performance during or following spaceflight. Cube rotation response time significantly improved from pre- to post-flight, suggestive of practice effects. There was a trend for better in-flight cube rotation performance on the ISS when crewmembers had their feet in foot loops on the “floor” throughout the task. This suggests that tactile inputs to the foot sole aided orientation. Overall, these results suggest that sensory reweighting due to the microgravity environment of spaceflight affected sensorimotor performance, while cognitive performance was maintained. A shift from exocentric (gravity) spatial references on Earth towards an egocentric spatial reference may also occur aboard the ISS. Upon return to Earth, microgravity adaptions become maladaptive for certain postural tasks, resulting in transient sensorimotor performance declines that recover within 30 days.
Striatonigrostriatal Circuit Architecture for Disinhibition of Dopamine Signaling
Authors: Ambrosi Priscilla , Lerner Talia N.
Published: June 2021

SUMMARY/ABSTRACT

The basal ganglia operate largely in closed parallel loops, including an associative circuit for goal-directed behavior originating from the dorsomedial striatum (DMS) and a somatosensory circuit important for habit formation originating from the dorsolateral striatum (DLS). An exception to this parallel circuit organization has been proposed to explain how information might be transferred between striatal subregions, for example from DMS to DLS during habit formation. The “ascending spiral hypothesis” proposes that DMS disinhibits dopamine signaling in DLS through a tri-synaptic, open-loop striato-nigro-striatal circuit. Here, we used transsynaptic and intersectional genetic tools to investigate both closed- and open-loop striato-nigro-striatal circuits. We found strong evidence for closed loops, which would allow striatal subregions to regulate their own dopamine release. We also found evidence for functional synapses in open loops. However, these synapses were unable to modulate tonic dopamine neuron firing, questioning the prominence of their role in mediating crosstalk between striatal subregions.
MONTE enables serial immunopeptidome, ubiquitylome, proteome, phosphoproteome, acetylome analyses of sample-limited tissues
Authors: Abelin Jennifer G. , Bergstrom Erik J. , Taylor Hannah B. , Rivera Keith D. , Klaeger Susan , Xu Charles , White C. Jackson , Olive Meagan E. , Maynard Myranda , Kane M. Harry , Rachimi Suzanna , Mani D.R. , Gillette Michael A. , Clauser Karl R. , Udeshi Namrata D. , Carr Steven A.
Published: June 2021

Serial multiomic analyses of proteome, phosphoproteome and acetylome provides functional insights into disease pathology and drug effects while conserving precious human material. To date, ubiquitylome and HLA peptidome analyses have required separate samples for parallel processing each using distinct protocols. Here we present MONTE, a highly-sensitive multi-omic native tissue enrichment workflow that enables serial, deepscale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome and acetylome from the same tissue samples. We demonstrate the capabilities of MONTE in a proof-of-concept study of primary patient lung adenocarcinoma(LUAD) tumors. Depth of coverage and quantitative precision at each of the ‘omes is not compromised by serialization, and the addition of HLA immunopeptidomics enables identification of putative immunotherapeutic targets such as cancer/testis antigens and neoantigens. MONTE can provide insights into disease-specific changes in antigen presentation, protein expression, protein degradation, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment.
BMI-CNV: A Bayesian framework for multiple genotyping platforms detection of copy number variation
Authors: Luo Xizhi , Cai Guoshuai , Mclain Alexander C. , Amos Christopher I. , Cai Bo , Xiao Feifei
Published: June 2021

Whole-exome sequencing (WES) enables detection of Copy number variations (CNVs) with high resolution in protein-coding regions. However, variations in the intergenic or intragenic regions are excluded from studies. Fortunately, samples have been previously sequenced by other genotyping platforms, such as SNP array. Moreover, conventional single sample-based methods suffer from high false discovery rate due to prominent data noise. Therefore, methods for integrating multiple genotyping platforms and samples are highly demanded for improved CNV detection.

We developed BMI-CNV, a Bayesian Multi-sample and Integrative CNV (BMI-CNV) profiling method with data sequenced by both WES and microarray. For the multi-sample integration, we identify the shared CNVs regions across samples using a Bayesian probit stick-breaking process model coupled with a Gaussian Mixture model estimation. With extensive simulations, BMI-CNV outperformed existing methods with remarkably improved accuracy. By applying to the matched 1000 genomes project and HapMap project data, we showed that BMI-CNV accurately detected common variants. We further applied it to The Research of International Cancer of Lung (TRICL) consortium with matched WES and OncoArray data and identified lung cancer risk associated genes in 17q11.2, 1p36.12, 8q23.1 and 5q22.2 regions, which may provide new insights into the etiology of lung cancer.
Humidity Reduces Rapid and Distant Airborne Dispersal of Viable Viral Particles in Classroom Settings
Authors: Skanata Antun , Spagnolo Fabrizio , Metz Molly , Smyth Davida S. , Dennehy John J.
Published: June 2021

The transmission of airborne pathogens via aerosols is considered to be the main route through which a number of known and emerging respiratory diseases infect their hosts. It is therefore essential to quantify airborne transmission in closed spaces and determine the recommendations that should be implemented to minimize exposure to pathogens in built environments. We have developed a method to detect viable virus particles from aerosols by using an aerosolized bacteriophage Phi6 in combination with its host Pseudomonas phaseolicola, which when seeded on agar plates acts as a virus detector that can be placed at a range of distances away from an aerosol-generating source. Based on this method we present two striking results. (1) We consistently detected viable phage particles at distances of up to 18 feet away from the source within 15-minutes of exposure in a classroom equipped with a state of the art HVAC system. (2) Increasing the relative humidity beyond 40% significantly reduces dispersal. Our method can be used to quantify the exposure to pathogens at various distances from the source for different amounts of time, data which can be used to set safety standards for room capacity and to ascertain the efficacy of interventions that aim to reduce pathogen levels in closed spaces of specified sizes and intended uses.

We present a method to experimentally determine the exposure to airborne pathogens in closed spaces.
TKGWV2: An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data
Authors: Fernandes Daniel M. , Cheronet Olivia , Gelabert Pere , Pinhasi Ron
Published: June 2021

Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1 - 1x minimum average genomic coverage per analysed pair of individuals between. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026x average coverage, or around 1.3 million aligned reads per sample - 4 times less data than 0.1x. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012x, or around 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals previously excluded from kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.
With No Lysine Kinase 1 Promotes Right Ventricular Dysfunction Via Glucotoxicity
Authors: Prisco Sasha Z. , Eklund Megan , Thenappan Thenappan , Prins Kurt W.
Published: June 2021

Objectives

Investigate how WNK1 inhibition modulates glucotoxicity, mitochondrial/peroxisomal protein regulation and metabolism, and right ventricular (RV) function in pulmonary arterial hypertension (PAH). Determine how hypochloremia impacts RV function in PAH patients.

Background

In PAH-induced RV failure, GLUT1/GLUT4 expression is elevated, which increases glucose uptake and glycolytic flux to compensate for mitochondrial dysfunction. However, the resultant consequences of the glucose-mediated post-translational modifications (PTM), protein O-GlcNAcylation/glycation in RV failure are understudied. WNK1, a chloride-sensitive kinase, increases GLUT1/GLUT4 expression in skeletal muscle, but its regulation in RV dysfunction is unexplored.

Methods

Rats were treated with WNK463 (small molecule WNK inhibitor) or vehicle starting two weeks after monocrotaline injection. Immunoblots quantified protein abundance/PTMs. Mitochondrial/peroxisomal proteomics and global metabolomics evaluated glucose metabolism and mitochondrial/peroxisomal function. Pulmonary vascular and cardiac histology, echocardiography, and pressure-volume loop analysis quantified RV function and PAH severity. Finally, the relationship between hypochloremia, a WNK1-activating state, and RV function was evaluated in 217 PAH patients.

Results

WNK463 decreased WNK1/GLUT1/GLUT4 expression, normalized glucose metabolite levels, which dampened excess protein O-GlcNAcylation/glycation. Integration of RV mitochondrial/peroxisomal proteomics and metabolomics identified fatty acid oxidation (FAO) as the most dysregulated metabolic pathway. WNK463 enhanced FAO as demonstrated by increased expression of mitochondrial FAO proteins and normalization of RV acylcarnitines. WNK463 reduced glutaminolysis induction and lipotoxicity, two secondary consequences of diminished FAO. WNK463 augmented RV systolic and diastolic function independent of pulmonary vascular disease severity. In PAH patients, hypochloremia resulted in more severe RV dysfunction.

Conclusions

WNK463 combated RV glucotoxicity and impaired FAO, which directly improved RV function.

Highlights

Small molecule inhibition of WNK1 (WNK463) signaling mitigates upregulation of the membrane glucose channels GLUT1 and GLUT4, restores levels of several glucose metabolites, and normalizes protein O-GlcNAcylation and glycation in the RV.

Quantitative proteomics of RV mitochondrial enrichments shows WNK463 treatment prevents downregulation of mitochondrial enzymes in the tricarboxylic acid cycle, fatty acid oxidation pathway, and the electron transport chain complexes.

Integration of proteomics and metabolomics analysis reveals WNK463 reduces glutaminolysis induction and lipotoxicity due to impaired fatty acid oxidation

WNK463 augments RV systolic and diastolic function independent of PAH severity.

Hypochloremia, a condition of predicted WNK1 activation, in PAH patients results in more severe RV dysfunction.
Antipsychotic prescribing for patients with intellectual disabilities and challenging behaviours
Authors: Elhusein Bushra , Eltorki Yassin , Abdallah Oraib , El Tahir Mohamed
Published: June 2021

Purpose

Review of antipsychotic prescribing practices, rationale and follow-up using an internationally standardized audit can be an effective tool to encourage and monitor best practices. The purpose of this study is to audit the current prescribing pattern for people with intellectual disabilities and challenging behaviours in Qatar.

Design/methodology/approach

This study was based on the challenging behaviour management guidelines recommended by the Royal College of Psychiatrists. All current electronic medical records in the Mental Health Service-Hamad Medical Corporation were examined to identify patients with intellectual disabilities who received antipsychotics for challenging behaviour. Demographic variables, such as age, sex and nationality, were collected. In addition, details of psychiatric diagnoses, prescribed psychotropic medications and diagnoses of epilepsy were also collected. For patients who were prescribed antipsychotic medication, the clinical rationale for such medication was collected along with evidence of side effect monitoring to allow performance against the audit standards to be measured.

Findings

This is the first audit on prescribing practices in people with intellectual disability and challenging behaviour in the state of Qatar. The results of this study regarding the pattern of prescribing practices for patients with intellectual disability and challenging behaviour reflect the limitation in knowledge and experience among non-specialist practitioners within mental health service. The result may be helpful to support the development of specialist service provision to improve the care for such vulnerable group. The result may also help other medical centres and clinicians by providing an improved understanding of possible deviations from the best medical practices.

Originality/value

This is the first audit on prescribing practices in people with intellectual disability and challenging behaviour in the state of Qatar. The study is also noteworthy as, to the best of the authors’ knowledge, it is one of only a few studies on antipsychotic prescribing for patients with intellectual disability and challenging behaviour in the Middle East; therefore, it will be useful in raising awareness and promoting the best practices in the Middle East region. This study is also among the first few studies that were designed based on the four audit standards by the Royal College of Psychiatrists in this area.
Healthassist, Inc.: leading through a pandemic
Authors: Ingols Cynthia , Eckert Devon
Published: June 2021

Case study abstract

The purpose of this case study is to illustrate how Dianne Savastano, founder and CEO of Healthassist, Inc., a US-based health-care advocacy firm, successfully led her clients and team through the COVID-19 pandemic of 2020. To gather the data for this case study, the authors interviewed the protagonists, the members of her team and two clients. The authors read Healthassist Newsletters and the firm’s documents; and in fact, they included one Newsletter and several documents in the Exhibits of the case study. The authors conducted a literature review for articles in newspapers and journals about the newly developing field of “health-care advocacy,” a field which Savastano helped to create.

Findings of the case study

The authors illustrate how Savastano, using the five practices of exemplary leadership by Kouzes and Posner, in The Leadership Challenge, led her team through the pandemic of 2020. This is a story of a woman leader, using traits such as warmth, empathy, analysis and decisiveness, keeps her small business afloat when so many other firms collapsed in 2020.

Research

The authors conducted seven interviews and literature searches on the topics of health-care advocacy; women leaders; leading through a crisis; and COVID-19.

Practical implications

The case study illustrates how a woman founder and CEO can lead her firm through a crisis.

Value of the case study

This is an example of how a woman leader managed through the 2020 pandemic.

Subject code

CSS 3: Entrepreneurship
Work experiences of qualified immigrants: a review of theoretical progress
Authors: Farashah Ali Dehghanpour , Blomquist Tomas
Published: June 2021

Purpose

Qualified immigrants (QIs) and their work experiences have been studied using a wide variety of theoretical approaches with divergent characteristics. This paper reviews theoretical progress and proposes directions for future research and practice.

Design/methodology/approach

Using relevant keywords, articles indexed by Web of Science in management, business, industrial relations and applied psychology were systematically searched for and analysed. In total, 60 theoretical articles published during 2008–2018 were included. The theoretical progress and future theoretical and practical challenges were organised based on the notions of equality, diversity and inclusion.

Findings

Eight theoretical approaches utilised to study QIs' work experiences were recognised: (1) human capital theory, (2) career capital theory, (3) theory of practice, (4) intersectionality, (5) social identity theory, (6) sensemaking, (7) cultural identity transition and (8) the career-centred approach. The contributions and limitations of each theoretical lens were then scrutinised. Overall, research on QIs still lacks a comprehensive theoretical framework. As a step towards that, the paper proposes considering the role of organisations and labour market intermediaries, strategic view over the immigrant workforce, agency–institution play, identity–capital play and host–immigrant play.

Research limitations/implications

The focus is on theory development and empirical papers with no clear theoretical foundation are excluded.

Originality/value

This review is the first attempt to summarise and direct the divergent research on the topic. The main contribution is setting an agenda for future research, particularly by proposing the elements of a comprehensive theoretical framework for studying QIs in the workplace.
Understanding the implications of pandemic outbreaks on supply chains: an exploratory study of the effects caused by the COVID-19 across four South Asian countries and steps taken by firms to address the disruptions
Authors: Butt Atif Saleem
Published: June 2021

Purpose

The purpose of this paper is to explore the disruptions caused to supply chains by COIVD-19 as well as steps/countermeasures taken by firms to address such disruptions.

Design/methodology/approach

This study employs 46 semi-structured interviews with senior managers of the three buying firms, four distribution centers and four supplying firms based in four countries (Pakistan, Sri Lanka, China and India).

Findings

Results unveil that manufacturing firms are facing limited production and delays in procuring goods and services, while distribution centres are facing inventory shortages. Furthermore, supplying firms are facing increased lead times amid the COVID-19 outbreak. In addition, each affected entity has employed specific strategies to address these disruptions. For instance, manufacturing firms are refining their production schedules based on the inventory, getting better visibility to their suppliers’ performance and developing new inbound routes to meet the production challenges. They are also assessing the tier-1 supplier’s risk and activating the relationship with secondary suppliers to address the procurement issues. Second, distributors are modifying inventory policies to meet the inventory shortage. Finally, supplying firms are developing alternative outbound logistics to meet the growing demand.

Research limitations/implications

There are some limitations to this study. First, the results of this study cannot be generalized to a wider population. Second, this study explores the interpretations of senior managers based in four Asian countries only.

Originality/value

Our study contributes to the supply chain literature by exploring the disruptions caused by COVID-19 to the supply chain operations. It also contributes to theory and practice by articulating the strategies adopted by firms to address such disruptions. Firms can use the steps highlighted in this study to mitigate the impact of COVID-19 on the supply chain disruptions.