bluuebunny/crossref_metadata_2025 huggingface dataset:
Lonely in the dark: trauma memory and sex-specific dysregulation of amygdala reactivity to fear signals
Authors: Morr Mitjan , Noell Jeanine , Sassin Daphne , Daniels Jule , Philipsen Alexandra , Becker Benjamin , Stoffel-Wagner Birgit , Hurlemann René , Scheele Dirk
Published: November 2021

Loneliness exacerbates psychological distress and increases the risk of psychopathology after trauma exposure. The prevalence of trauma-associated disorders varies substantially between sexes, and accumulating evidence indicates sex-specific effects of loneliness. However, it is still unclear whether a lack of social connectedness affects trauma-induced intrusions and the neural processing of fear signals. Moreover, it is uncertain, whether loneliness plays a different role in women and men. We used a prestratification strategy and recruited n=47 (n=20 women) healthy individuals with high loneliness and n=35 controls (n=18 women). Participants were exposed to an experimental trauma and evoked intrusive thoughts in daily life were monitored for three consecutive days. Functional magnetic resonance imaging was used to assess neural habituation to fearful faces and fear learning (conditioning and extinction) prior to trauma exposure. The total number of intrusions and amygdala reactivity in neural fear processing served as the primary study outcomes. Our results revealed a significant interaction between loneliness and sex such that loneliness was associated with more intrusions in men, but not in women. A similar pattern emerged at the neural level, with both reduced amygdala habituation to repeated fearful faces and amygdala hyperreactivity during the conditioning of fear signals in lonely men, but not in women. Our findings indicate that loneliness may confer vulnerability to intrusive memories after trauma exposure in healthy men and that this phenotype relates to altered limbic processing of fear signals. Collectively, interventions targeting social connectedness may mitigate the sequelae of traumatic experiences.
Marker-free characterization of single live circulating tumor cell full-length transcriptomes
Authors: Poonia Sarita , Goel Anurag , Chawla Smriti , Bhattacharya Namrata , Rai Priyadarshini , Lee Yi Fang , Yap Yoon Sim , West Jay , Bhagat Ali Asgar , Tayal Juhi , Mehta Anurag , Ahuja Gaurav , Majumdar Angshul , Ramalingam Naveen , Sengupta Debarka
Published: November 2021

The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor that hinders enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypic traits relative to the tumor of origin. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from the peripheral blood. Most CTC detection methods use a mix of size selection, immune marker based white blood cells (WBC) depletion, and positive enrichment antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. Single-cell RNA sequencing (scRNA-Seq) of CTCs provides a wealth of information about their tumors of origin as well as their fate and is a potent method of enabling unbiased identification of CTCs. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analysis tasks. These include a novel method of scRNA-Seq clustering, namedDeepDictionaryLearning usingK-means clustering cost (DDLK), expression based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-Seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell®FX and PolarisTMworkflow that works by the principles of size-based separation of CTCs and marker based WBC depletion.
Highly variable response of hard coral taxa to successive coral bleaching events (2019-2020) and rising ocean temperatures in Northeast Peninsular Malaysia
Authors: Szereday Sebastian , Amri Affendi Yang
Published: November 2021

Due to current greenhouse gas emissions, Malaysian coral reefs are predicted to experience severe annual coral bleaching events by 2043, threatening the survival of coral reefs within this century. However, there is no field data on how Malaysian coral reefs respond to successive events of coral bleaching. Despite the notion that many scleractinian taxa exhibit increased thermal tolerance over the last decade, it remains unresolved whether these changes are a result of ‘weeding out’ thermally susceptible species and actually ameliorate accelerating warming rates and increasing frequencies of heat disturbances. Moreover, complex interaction of environmental and biological factors that underlie differences in the bleaching response necessitate conducting studies at the within-reef scale (i.e., leeward shallow, windward shallow). Here, we studied two successive thermal stress events starting during the 2019 El Niño Southern Oscillation (ENSO), and determined bleaching trajectories of 29 hard coral taxa across fine spatio-temporal gradients in Northeast Peninsular Malaysia. Analysis of climate trajectories affirms accelerating warming rates (0.17°C per decade) and higher return-frequency of heat disturbance. Despite high annual maximum temperatures above the putative bleaching threshold (31.07°C and 31.74°C, respectively), accumulated thermal stress was low during both bleaching episodes (Degree Heating Weeks of 1.05°C-weeks and 0.18°C-weeks, respectively), suggesting widespread thermal sensitivity of hard coral taxa (55.21% and 26.63% bleaching incidence in 2019 and 2020, respectively). However, significant discrepancies between satellite and in-situ temperature data were found (0.63°C; SD±0.26). Bleaching severity was highly taxon-specific, varied across and within reef scales due to wind exposure and depth (e.g., less bleaching at shallow windward sites), and partially contrasted historical bleaching observations (e.g., Acropora and Montipora were less susceptible, Cyphastrea, Echinopora, Goniastrea, Heliopora and Porites were highly susceptible). While bleaching severity was higher in 2019, Galaxea and Leptastrea were bleaching more in 2020 despite lower heat stress, suggesting negative legacy effects of the 2019 bleaching event on these taxa. In conclusion, hard corals were subjected to more frequent heat stress during the last decade and remain highly vulnerable to marine heatwaves across all biophysical reef scales. Annual coral bleaching impacted all hard coral taxa and reduced thermal tolerance in at least two taxa.
Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations
Authors: Simola Jaana , Siebenhühner Felix , Myrov Vladislav , Kantojärvi Katri , Paunio Tiina , Palva J. Matias , Brattico Elvira , Palva Satu
Published: November 2021

Neuronal oscillations, their inter-areal synchronization, and scale-free dynamics constitute fundamental mechanisms for cognition by regulating communication in neuronal networks. These oscillatory dynamics have large inter-individual variability that is partly heritable. However, the genetic underpinnings of oscillatory dynamics have remained poorly understood. We recorded resting-state magnetoencephalography (MEG) from 82 healthy participants and investigated whether oscillation dynamics were influenced by genetic polymorphisms in Catechol-O-methyltransferase (COMT) Val158Met and brain-derived neurotrophic factor (BDNF) Val66Met. Both COMT and BDNF polymorphisms influenced local oscillation amplitudes and their long-range temporal correlations (LRTCs), while only BDNF polymorphism affected the strength of large-scale synchronization. Our findings demonstrate that COMT and BDNF genetic polymorphisms contribute to inter-individual variability in local and large-scale synchronization dynamics of neuronal oscillations. Comparison of these results to computational modelling of near-critical synchronization dynamics further suggested that COMT and BDNF polymorphisms influenced local oscillations by modulating the excitation-inhibition balance according to the brain criticality framework.
Reversible inactivation of ferret auditory cortex impairs spatial and non-spatial hearing
Authors: Town Stephen M. , Poole Katarina C. , Wood Katherine C. , Bizley Jennifer K.
Published: November 2021

A key question in auditory neuroscience is to what extent are brain regions functionally specialized for processing specific sound features such as sound location and identity. In auditory cortex, correlations between neural activity and sounds support both the specialization of distinct cortical subfields, and encoding of multiple sound features within individual cortical areas. However, few studies have tested the contribution of auditory cortex to hearing in multiple contexts. Here we determined the role of ferret primary auditory cortex in both spatial and non-spatial hearing by reversibly inactivating the middle ectosylvian gyrus during behavior using cooling (n=2) or optogenetics (n=1). In optogenetic experiments, we utilized the mDLx promoter to express Channelrhodopsin 2 in GABAergic interneurons and confirmed both viral expression (n=2) and light-driven suppression of spiking activity in auditory cortex, recorded using Neuropixels under anesthesia (n=465 units from 2 additional untrained ferrets). Cortical inactivation impaired vowel discrimination in co-located noise, but not in clean conditions, or when the temporally coincident vowel and noise were spatially separated by 180°. Testing the ferrets implanted with cooling loops in a sound localization task confirmed that deficits in spatial hearing arose from inactivation of the same region of auditory cortex that was implicated in vowel discrimination in noise. Our results are consistent with single unit recordings in primary auditory cortex showing mixed selectivity for spatial and non-spatial features of sound and suggest a contribution of this region to multiple forms of hearing necessary for auditory scene analysis.

Significance Statement

Neurons in primary auditory cortex are often sensitive to the location and identity of sounds. Here we inactivated auditory cortex during spatial and non- spatial listening tasks using cooling, or optogenetics. Auditory cortical inactivation impaired multiple behaviors, demonstrating a role in both the analysis of sound location and identity and confirming a functional contribution of mixed selectivity observed in neural activity. Parallel optogenetic experiments in two additional untrained ferrets linked behavior to physiology by demonstrating that expression of Channelrhodopsin 2 permitted rapid light-driven suppression of auditory cortical activity recorded under anesthesia.
Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines
Authors: Coombes Benedict , Fellers John P. , Grewal Surbhi , Rusholme-Pilcher Rachel , Hubbart-Edwards Stella , Yang Caiyun , Joynson Ryan , King Ian P. , King Julie , Hall Anthony
Published: November 2021

Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat’s wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterise introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilisation of introgression pre-breeding material in wheat breeding programmes.
Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus
Authors: Bird Kevin A. , Pires J. Chris , VanBuren Robert , Xiong Zhiyong , Edger Patrick P.
Published: November 2021

The Gene Balance Hypothesis (GBH) proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges (HEs) that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the GBH makes predictions about the expression response to HEs, they have not been empirically tested. We used genomic and transcriptomic data from six resynthesized, isogenicBrassica napuslines over ten generations to identify HEs, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to HEs than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the BnA subgenome. Finally, the expression response to HEs was more variable than the response to WGD, suggesting HEs create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time; from homoeolog expression bias to duplicate gene retention.
The Prevalence of Litter Foraging Among UK Birds Lessons Learned From A Citizen Science Project
Authors: Schalz Sabrina , Horrod-Wilson Warren D. , Chauhan Keir
Published: November 2021

1.

Anthropogenic food sources, such as litter, are readily available to birds in urban areas. As an overly anthropogenic diet can have negative health consequences for wildlife, monitoring the frequency of foraging in litter compared to natural food resources can be an important component of wildlife conservation efforts. To understand how common litter foraging is among different bird species, we conducted a citizen science project with volunteers across the UK. Through this project, we also tried to engage people in birdwatching and bird surveys who would not normally participate in these activities. A particular focus was on recruiting respondents from underrepresented groups, and the methodology was designed to accommodate people without any background knowledge of birds. While we did not receive enough observations to draw conclusions about the litter foraging rates of different bird species across the UK, we report the submissions we received, as well as the demographic composition of the volunteer group. We successfully reached volunteers who did not participate in birdwatching or BTO bird surveys before, as well as some young volunteers, but were unsuccessful in reaching respondents from diverse socioeconomic backgrounds. We hope that the successes and failures of our methods reported here can be useful to others designing citizen science studies, so that birdwatching and volunteering for bird surveys will be equally accessible to all in the future.
Stimulus-induced narrow-band gamma oscillations in humans can be recorded using open-hardware low-cost EEG amplifier
Authors: Pattisapu Srividya , Ray Supratim
Published: November 2021

Stimulus-induced narrow-band gamma oscillations (30–70 Hz) in human electro - encephalograph (EEG) have been linked to attentional and memory mechanisms and are abnormal in mental health conditions such as autism, schizophrenia and Alzheimer’s Disease. This suggests that gamma oscillations could be valuable both as a research tool and an inexpensive, non-invasive biomarker for disease evaluation. However, since the absolute power in EEG decreases rapidly with increasing frequency following a “1/f” power law, and the gamma band includes line noise frequency, these oscillations are highly susceptible to instrument noise. Previous studies that recorded stimulus-induced gamma oscillations used expensive research-grade EEG amplifiers to address this issue. While low-cost EEG amplifiers have become popular in Brain Computer Interface applications that mainly rely on low-frequency oscillations (< 30 Hz) or steady-state-visually-evoked-potentials, whether they can also be used to measure stimulus-induced gamma oscillations is unknown. We recorded EEG signals using a low-cost, open-source amplifier (OpenBCI) and a traditional, research-grade amplifier (Brain Products GmbH) in male (N = 6) and female (N = 5) subjects (22–29 years) while they viewed full-screen static gratings that are known to induce gamma oscillations. OpenBCI recordings showed gamma response in almost all the subjects who showed a gamma response in Brain Products recordings, and the spectral and temporal profiles of these responses in alpha (8–13 Hz) and gamma bands were highly correlated between OpenBCI and Brain Products recordings. These results suggest that low-cost amplifiers can potentially be used in stimulus induced gamma response detection, making its research, and application in medicine more accessible.
Malathion-resistant Tribolium castaneum has enhanced response to oxidative stress, immunity, and fitness
Authors: Rauf Abdur , Wilkins Richard Michael
Published: November 2021

Many cases of insecticide resistance in insect pests give resulting no-cost strains that retain the resistance genes even in the absence of the toxic stressor. Malathion has been widely used against the red flour beetle, Tribolium castaneum Herbst. in stored products although no longer used. Malathion specific resistance in this pest has provided resistance that is long lasting and widely distributed. To understand this resistance a malathion resistant strain was challenged with a range of stressors including starvation, hyperoxia, malathion and a pathogen and the antioxidant responses and some lifecycle parameters were determined. Adult life span of malathion-specific resistant strain of T. castaneum was significantly shorter than the susceptible. Starvation and/or high oxygen reduced adult life span of both strains. Starving with and without 100% oxygen gave longer lifespan for the resistant strain, but for oxygen alone there was no difference. Under oxygen the proportional survival of the resistant strain to the adult stage was significantly higher, for both larvae and pupae, than the susceptible. The resistant strain when stressed with malathion and/or oxygen significantly increased catalase activity, but the susceptible did not. The resistant strain stressed with Paranosema whitei infection had significantly higher survival compared to the susceptible, and with almost no mortality. The malathion resistant strain of T. castaneum showed greater vigour than the susceptible in most oxidative stress situations and especially where stressors were combined. The induction of the antioxidant enzyme catalase could have helped the resistant strain to withstand oxidative stresses, including insecticidal and importantly those from pathogens. These adaptations, in the absence of insecticide, seem to support the increased immunity of host insects to pathogens seen in other insect species, such as mosquitoes. By increasing the responses to a range of stressors the resistant strain could be considered as having enhanced fitness.
Localized delivery of β-NGF via injectable microrods accelerates endochondral fracture repair
Authors: Rivera Kevin O. , Cuylear Darnell L. , Duke Victoria , O’Hara Kelsey Marie , Kharbikar Bhushan N. , Kryger Alex N. , Miclau Theodore , Bahney Chelsea S. , Desai Tejal A.
Published: November 2021

Currently, there are no biological approaches to accelerate bone fracture repair. Osteobiologics that promote endochondral ossification are an exciting alternative to surgically implanted bone grafts, however, the translation of osteobiologics remains elusive because of the need for localized and sustained delivery that is both safe and effective. In this regard, an injectable system composed of hydrogel-based microparticles designed to release osteobiologics in a controlled and localized manner is ideal in the context of bone fracture repair. Here, we describe poly (ethylene glycol) dimethacrylate (PEGDMA)-based microparticles, in the form of microrods, engineered to be loaded with beta nerve growth factor (β-NGF) for use in a murine tibial fracture model. In-vitro studies demonstrated that protein-loading efficiency is readily altered by varying PEGDMA macromer concentration and that β-NGF loaded onto PEGDMA microrods exhibited sustained release over a period of 7 days. In-vitro bioactivity of β-NGF was confirmed using a tyrosine receptor kinase A (Trk-A) expressing cell line, TF-1. Moreover, TF-1 cell proliferation significantly increased when incubated with β-NGF loaded PEGDMA microrods versus β-NGF in media. In-vivo studies show that PEGDMA microrods injected into the fracture calluses of mice remained in the callus for over 7 days. Importantly, a single injection of β-NGF-loaded PEGDMA microrods resulted in significantly improved fracture healing as indicated by significant increases in bone volume, trabecular connective density, and bone mineral density and a significant decrease in cartilage despite a remarkably lower dose (∼111 fold) than the β-NGF in media. In conclusion, we demonstrate a novel and translational method of delivering β-NGF via injectable PEGDMA microrods to improve bone fracture repair.
Exploratory methods for high-performance EEG speech decoding
Authors: Comstock Lindy , Lainscsek Claudia , Carvalho Vinícius R. , Mendes Eduardo M. A. M. , Fallah Aria , Sejnowski Terrence J.
Published: November 2021

State-of-the-art technologies in neural speech decoding utilize data collected from microwires or microarrays implanted directly into the cerebral cortex. Yet as a tool accessible only to individuals with implanted electrodes, speech decoding from devices of this nature is severely limited in its implementation, and cannot be considered a viable solution for widespread application. Speech decoding from non-invasive EEG signals can achieve relatively high accuracy (70-80%), but only from very small classification tasks, with more complex tasks typically yielding a limited (20-50%) classification accuracy. We propose a novel combination of technologies in which transcranial magnetic stimulation (TMS) is first applied to augment the neural signals of interest, producing a greater signal-to-noise ratio in the EEG data. Next, delay differential analysis (DDA) – a cutting-edge computational method based on nonlinear dynamics – is implemented to capture the widest range of information available in the neural signal, by incorporating both linear and nonlinear dynamics.
Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments
Authors: Chen Ling-Yun , Lu Bei , Morales-Briones Diego F. , Moody Michael L. , Liu Fan , Hu Guang-Wan , Huang Chien-Hsun , Chen Jin-Ming , Wang Qing-Feng
Published: November 2021

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the backbone of the three main clades that could be explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and whole-genome duplications using phylogenomics.
A multiplexed cell-free assay to screen for antimicrobial peptides in double emulsion droplets
Authors: Nuti Nicola , Rottmann Philipp , Stucki Ariane , Koch Philipp , Panke Sven , Dittrich Petra S.
Published: November 2021

The global surge in bacterial resistance against traditional antibiotics triggered intensive research for novel compounds, with antimicrobial peptides (AMPs) identified as a promising candidate. Automated methods to systematically generate and screen AMPs according to their membrane preference, however, are still lacking. We introduce a novel microfluidic system for the simultaneous cell-free production and screening of AMPs for their membrane specificity. On our device, AMPs are cell-free produced within water-in-oil-in-water double emulsion droplets, generated at high frequency. Within each droplet, the peptides can interact with different classes of co-encapsulated liposomes, generating a membrane-specific fluorescent signal. The double emulsions can be incubated and observed in a hydrodynamic trapping array or analysed via flow cytometry. Our approach provides a valuable tool for the discovery and development of membrane-active antimicrobials.
Remodeling of dermal adipose tissue alleviates cutaneous toxicity induced by anti-EGFR therapy
Authors: Chen Leying , You Qing , Liu Min , Li Shuaihu , Wu Zhaoyu , Hu Jiajun , Xia Liangyong , Zhang Shiyi
Published: November 2021

Anti-epidermal growth factor receptor (EGFR) therapy–associated cutaneous toxicity is a syndrome characterized by papulopustular rash, local inflammation, folliculitis and microbial infection, resulting in a decrease in quality of life and dose interruption. However, no effective clinical intervention is available for this adverse effect. Here, we report the atrophy of dermal white adipose tissue (dWAT), a highly plastic adipose tissue with various skin-specific functions, correlates with rash occurrence and exacerbation in a murine model of EGFR inhibitor-induced rash. The reduction in dWAT is due to the inhibition of adipogenic differentiation by defects in peroxisome proliferator-activated receptor γ (PPARγ) signaling, and increased lipolysis by the induced expression of the lipolytic cytokine IL6. The activation of PPARγ by rosiglitazone maintains adipogenic differentiation and represses the transcription of IL6, eventually improving skin functions and ameliorating the severity of rash without altering the antitumor effects. Thus, activation of PPARγ represents a promising approach to ameliorate cutaneous toxicity in patients with cancer who receive anti-EGFR therapy.

Graphical abstract
Mapping morphological malformation to genetic dysfunction in blood vessel organoids with 22q11.2 Deletion Syndrome
Authors: He Siyu , Xu Cong , Lao Yeh-Hsing , Chauhan Shradha , Xiao Yang , Willner Moshe J. , Jin Yinuo , McElroy Shannon , Rao Sneha B. , Gogos Joseph A. , Tomer Raju , Azizi Elham , Xu Bin , Leong Kam W.
Published: November 2021

DiGeorge Syndrome, or 22q11.2 deletion syndrome (22q11.2 DS), is a genetic disorder caused by microdeletions in chromosome 22, impairing the function of endothelial cells (EC) and/or mural cells and leading to deficits in blood vessel development such as abnormal aortic arch morphology, tortuous retinal vessels, and tetralogy of Fallot. The mechanism by which dysfunctional endothelial cells and pericytes contribute to the vasculopathy, however, remains unknown. In this study, we used human blood vessel organoids (VOs) generated from iPSC of 22q11.2 DS patients to model the vascular malformations and genetic dysfunctions. We combined high-resolution lightsheet imaging and single-cell transcriptome analysis to link the genetic profile and vascular phenotype at the single-cell level. We developed a comprehensive analytical methodology by integrating deep learning-mediated blood vessel segmentation, network graph construction, and tessellation analysis for automated morphology characterization. We report that 22q11.2DS VOs demonstrate a smaller size with increased angiogenesis/sprouting, suggesting a less stable vascular network. Overall, clinical presentations of smaller vascular diameter, less connected vasculature, and increased branch points were recapitulated in 22q11.2DS VOs. Single-cell transcriptome profiling showed heterogeneity in both 22q11.2DS and control VOs, but the former demonstrated alterations in endothelial characteristics that are organ-specific and suggest a perturbation in the vascular developmental process. Intercellular communication analysis indicated that the vascular dysfunctions in 22q11.2 deletion were due to a lower cell-cell contact and upregulated extracellular matrix organization involving collagen and fibronectin. Voronoi diagram-based tessellation analysis also indicated that the colocalization of endothelial tubes and mural cells was different between control and 22q11.2 VOs, indicating that alterations in EC and mural interactions might contribute to the deficits in vascular network formation. This study illustrates the utility of VO in revealing the pathogenesis of 22q11.2DS vasculopathy.
Morpholino-mediated knockdown of the brain mineralocorticoid receptor affects glucocorticoid signaling and neuroplasticity in wild ocellated wrasse (Symphodus ocellatus)
Authors: Nugent Bridget M. , Stiver Kelly A. , Han Jiawei , Kindsvater Holly K. , Marsh-Rollo Susan E. , Hofmann Hans A. , Alonzo Suzanne H.
Published: November 2021

Uncovering the genetic, physiological, and developmental mechanisms underlying phenotypic variation is necessary for understanding how genetic and genomic variation shape phenotypic variation and for discovering possible targets of selection. Although the neural and endocrine mechanisms underlying social behavior are evolutionarily ancient, we lack an understanding of the proximate causes and evolutionary consequences of variation in these mechanisms. Here, we examine in the natural environment the behavioral, neuromolecular, and fitness consequences of a morpholino-mediated knockdown of the mineralocorticoid receptor (MR) in the brain of nesting males of the ocellated wrasse, Symphodus ocellatus, a species with male alternative reproductive tactics. Even though MR knockdown did not significantly change male behavior directly, this experimental manipulation strongly altered glucocorticoid signaling and neuroplasticity in the preoptic area, the putative hippocampus homolog, and the putative basolateral amygdala homolog. We also found that individual variation in stress axis gene expression and neuroplasticity is strongly associated with variation in male behavior and fitness-related traits. The brain region-specific effects of MR knockdown on phenotypic integration in the wild reported here suggest specific neuroendocrine and neuroplasticity pathways that may be targets of selection.
2-photon-fabricated nano-fluidic traps for extended detection of single macromolecules and colloids in solution
Authors: Vanderpoorten Oliver , Babar Ali Nawaz , Krainer Georg , Jacquat Raphaёl P.B. , Challa Pavan K. , Peter Quentin , Toprakcioglu Zenon , Xu Catherine K. , Keyser Ulrich F. , Baumberg Jeremy , Kaminski Clemens F. , Knowles Tuomas P. J.
Published: November 2021

The analysis of nanoscopic species, such as proteins and colloidal assemblies, at the single-molecule level has become vital in many areas of fundamental and applied research. Approaches to increase the detection timescales for single molecules in solution without immobilising them onto a substrate surface and applying external fields are much sought after. Here we present an easy-to-implement and versatile nanofluidics-based approach that enables increased observational-timescale analysis of single biomacromolecules and nanoscale colloids in solution. We use two-photon-based hybrid lithography in conjunction with soft lithography to fabricate nanofluidic devices with nano-trapping geometries down to 100 nm in height. We provide a rigorous description and characterisation of the fabrication route that enables the writing of nanoscopic 3D structures directly in photoresist and allows for the integration of nano-trapping and nano-channel geometries within micro-channel devices. Using confocal fluorescence burst detection, we validated the functionality of particle confinement in our nano-trap geometries through measurement of particle residence times. All species under study, including nanoscale colloids, α-synuclein oligomers, and double-stranded DNA, showed a three to five-fold increase in average residence time in the detection volume of nano-traps, due to the additional local steric confinement, in comparison to free space diffusion in a nearby micro-channel. Our approach thus opens-up the possibility for single-molecule studies at prolonged observational timescales to analyse and detect nanoparticles and protein assemblies in solution without the need for surface immobilisation.
Characterizing and explaining impact of disease-associated mutations in proteins without known structures or structural homologues
Authors: Sen Neeladri , Anishchenko Ivan , Bordin Nicola , Sillitoe Ian , Velankar Sameer , Baker David , Orengo Christine
Published: November 2021

Mutations in human proteins lead to diseases. The structure of these proteins can help understand the mechanism of such diseases and develop therapeutics against them. With improved deep learning techniques such as RoseTTAFold and AlphaFold, we can predict the structure of proteins even in the absence of structural homologues. We modeled and extracted the domains from 553 disease-associated human proteins without known protein structures or close homologues in the Protein Databank (PDB). We noticed that the model quality was higher and the RMSD lower between AlphaFold and RoseTTAFold models for domains that could be assigned to CATH families as compared to those which could only be assigned to Pfam families of unknown structure or could not be assigned to either. We predicted ligand-binding sites, protein-protein interfaces, conserved residues in these predicted structures. We then explored whether the disease-associated missense mutations were in the proximity of these predicted functional sites, if they destabilized the protein structure based on ddG calculations or if they were predicted to be pathogenic. We could explain 80% of these disease-associated mutations based on proximity to functional sites, structural destabilization or pathogenicity. When compared to polymorphisms a larger percentage of disease associated missense mutations were buried, closer to predicted functional sites, predicted as destabilising and/or pathogenic. Usage of models from the two state-of-the-art techniques provide better confidence in our predictions, and we explain 93 additional mutations based on RoseTTAFold models which could not be explained based solely on AlphaFold models.
Reversible bacteriophage resistance by shedding the bacterial cell wall
Authors: Ongenae Veronique , Mabrouk Adam Sidi , Crooijmans Marjolein , Rozen Daniel , Briegel Ariane , Claessen Dennis
Published: November 2021

Phages are highly abundant in the environment and a major threat for bacteria. Therefore, bacteria have evolved sophisticated defense systems to withstand phage attacks. Here, we describe a previously unknown mechanism by which mono- and diderm bacteria survive infection with diverse lytic phages. Phage exposure leads to a rapid and near complete conversion of walled cells to a cell wall-deficient state, which remain viable in osmoprotective conditions and can revert to the walled state. While shedding the cell wall dramatically reduces the number of progeny phages produced by the host, it does not always preclude phage infection. Altogether, these results show that the formation of cell wall-deficient cells prevents complete eradication of the bacterial population and suggest that cell wall-deficiency may limit the efficacy of phage therapy, especially in highly osmotic environments or when used together with antibiotics that target the cell wall.
FDJD: RNA-Seq Based Fusion Transcript Detection Using Jaccard Distance
Authors: Mohebbi Hamidreza , Haspel Nurit
Published: November 2021

Gene fusions events, which are the result of two genes fused together to create a hybrid gene, were first described in cancer cells in the early 1980s. These events are relatively common in many cancers including prostate, lymphoid, soft tissue, and breast. Recent advances in next-generation sequencing (NGS) provide a high volume of genomic data, including cancer genomes. The detection of possible gene fusions requires fast and accurate methods. However, current methods suffer from inefficiency, lack of sufficient accuracy, and a high false-positive rate. We present an RNA-Seq fusion detection method that uses dimensionality reduction and parallel computing to speed up the computation. We convert the RNA categorical space into a compact binary array calledbinary fingerprints, which enables us to reduce the memory usage and increase efficiency. The search and detection of fusion candidates are done using the Jaccard distance. The detection of candidates is followed by refinement. We benchmarked our fusion prediction accuracy using both simulated and genuine RNA-Seq datasets. Paired-end Illumina RNA-Seq genuine data were obtained from 60 publicly available cancer cell line data sets. The results are compared against the state-of-the-art-methods such as STAR-Fusion, InFusion, and TopHat-Fusion. Our results show that FDJD exhibits superior accuracy compared to popular alternative fusion detection methods. We achieved 90% accuracy on simulated fusion transcript inputs, which is the highest among the compared methods while maintaining comparable run time.
Systems medicine dissection of chromosome 1q amplification reveals oncogenic regulatory circuits and informs targeted therapy in cancer
Authors: Trasanidis Nikolaos , Katsarou Alexia , Ponnusamy Kanagaraju , Shen Yao-An , Kostopoulos Ioannis V , Bergonia Bien , Keren Keren , Reema Paudel , Xiao Xiaolin , Szydlo Richard M , Sabbattini Pierangela MR , Roberts Irene AG , Auner Holger W , Naresh Kikkeri N , Chaidos Aristeidis , Wang Tian-Li , Magnani Luca , Caputo Valentina S , Karadimitris Anastasios
Published: November 2021

Understanding the biological and clinical impact of copy number aberrations (CNA) in cancer remains an unmet challenge. Genetic amplification of chromosome 1q (chr1q-amp) is a major CNA conferring adverse prognosis in several cancers, including the blood cancer, multiple myeloma (MM). Although several chr1q genes portend high-risk MM disease, the underpinning molecular aetiology remains elusive. Here we integrate patient multi-omics datasets with genetic variables to identify 103 adverse prognosis genes in chr1q-amp MM. Amongst these, the transcription factor PBX1 is ectopically expressed by genetic amplification and epigenetic activation of its own preserved 3D regulatory domain. By binding to reprogrammed super-enhancers, PBX1 directly regulates critical oncogenic pathways, whilst in co-operation with FOXM1, activates a proliferative gene signature which predicts adverse prognosis across multiple cancers. Notably, pharmacological disruption of the PBX1-FOXM1 axis, including with a novel PBX1 inhibitor is selectively toxic against chr1q-amp cancer cells. Overall, our systems medicine approach successfully identifies CNA-driven oncogenic circuitries, links them to clinical phenotypes and proposes novel CNA-targeted therapy strategies in cancer.

Significance

We provide a comprehensive systems medicine strategy to unveil oncogenic circuitries and inform novel precision therapy decisions against CNA in cancer. This first clinical multi-omic analysis of chr1q-amp in MM identifies a central PBX1-FOXM1 regulatory axis driving high-risk prognosis, as a novel therapeutic target against chr1q-amp in cancer.
Genome manipulation by guide-directed Argonaute cleavage
Authors: Huang Shan , Wang Kaihang , Mayo Stephen L.
Published: November 2021

Many prokaryotic argonautes (pAgos) mediate DNA interference by using small DNA guides to cleave target DNA. A recent study shows that CbAgo, a pAgo from Clostridium butyricum, induces DNA interference between homologous sequences and generates double-stranded breaks (DSBs) in target DNAs. This mechanism enables the host to defend against invading DNAs such as plasmids and viruses. However, whether such a CbAgo-mediated DNA cleavage is mutagenic remains unexplored. Here we demonstrate that CbAgo, directed by plasmid-encoded guide sequences, can cleave genome target sites and induce chromosome recombination between downstream homologous sequences in Escherichia coli. The recombination rate correlates well with pAgo DNA cleavage activity and the mechanistic study suggests the recombination involves DSBs and RecBCD processing. In RecA-deficient E. coli strain, guide-directed CbAgo cleavage on chromosomes severely impairs cell growth, which can be utilized as counter-selection to assist Lambda-Red recombineering. These findings demonstrate the guide-directed cleavage of pAgo on the host genome is mutagenic and can lead to different outcomes according to the function of the host DNA repair machinery. We anticipate this novel DNA-guided interference to be useful in broader genetic manipulation. Our study also provides an in vivo assay to characterize or engineer pAgo DNA cleavage activity.
Interventions in sexual and reproductive health services addressing violence against women in low- and middle- income countries: a mixed-methods systematic review
Authors: Lewis Natalia V , Munas Muzrif , Colombini Manuela , d’Oliveira Ana Flavia , Pereira Stephanie , Shrestha Satya , Rajapakse Thilini , Shaheen Amira , Rishal Poonam , Alkaiyat Abdulsalam , Richards Alison , García-Moreno Claudia M , Feder Gene S , Bacchus Loraine J
Published: November 2021

Objectives

To synthesise evidence on the effectiveness, cost-effectiveness, and barriers to responding to violence against women (VAW) in sexual and reproductive health (SRH) services in low- and middle-income countries (LMICs).

Design

Mixed-methods systematic review.

Data sources

Medline, Embase, Psycinfo, Cochrane, Cinahl, IMEMR, Web of Science, Popline, Lilacs, WHO RHL,ClinicalTrials.gov, Google, Google Scholar, websites of key organisations through December 2019.

Eligibility criteria

Studies of any design that evaluated VAW interventions in SRH services in LMICs.

Data extraction and synthesis

Concurrent narrative quantitative and thematic qualitative syntheses, integration through line of argument and mapping onto a logic model. Two reviewers extracted data and appraised quality.

Results

26 studies of varied interventions using heterogeneous outcomes. Of ten interventions that strengthened health systems capacity to respond to VAW during routine SRH consultation, three reported no harm and reduction in some types of violence. Of nine interventions that strengthened health systems and communities’ capacity to respond to VAW, three reported conflicting effects on re-exposure to some types of VAW and mixed effect on SRH. The interventions increased identification of VAW but had no effect on the provision (75-100%) and uptake (0.6-53%) of referrals to VAW services. Of seven psychosocial interventions in addition to SRH consultation that strengthened women’s readiness to address VAW, four reduced re-exposure to some types of VAW and improved health. Factors that disrupted the pathway to better outcomes included accepting attitudes towards VAW, fear of consequences, and limited readiness of the society, health systems, and individuals. No study evaluated cost-effectiveness.

Conclusions

Some VAW interventions in SRH services reduced re-exposure to some types of VAW and improved some health outcomes in single studies. Future interventions should strengthen capacity to address VAW across health systems, communities, and individual women. First-line support should be better tailored to women’s needs and expectations.

PROSPERO protocol CRD42019137167.
Diagnostic signature for Heart Failure with Preserved Ejection Fraction (HFpEF): A Machine Learning Approach Using Multi-Modality Electronic Health Record Data
Authors: Farajidavar Nazli , O’Gallagher Kevin , Bean Daniel , Nabeebaccus Adam , Zakeri Rosita , Bromage Daniel , Kraljevic Zeljko , Teo James TH , Dobson Richard J , Shah Ajay M
Published: November 2021

Aims

Heart failure with preserved ejection fraction (HFpEF) is thought to be highly prevalent yet remains underdiagnosed. We sought to develop a data-driven diagnostic model to predict from electronic health records (EHR) the likelihood of HFpEF among patients with unexplained dyspnea and preserved left ventricular EF.

Methods & Results

The derivation cohort comprised patients with dyspnea and echocardiography results. Structured and unstructured data were extracted using an automated informatics pipeline. Patients were retrospectively diagnosed as HFpEF (cases), non-HF (control cohort I), or HF with reduced EF (HFrEF; control cohort II). The ability of clinical parameters and investigations to discriminate cases from controls was evaluated by extreme gradient boosting. A likelihood scoring system was developed and validated in a separate test cohort.

The derivation cohort included 1585 consecutive patients: 133 cases of HFpEF (9%), 194 non-HF cases (Control cohort I) and 1258 HFrEF cases (Control cohort II). Two HFpEF diagnostic signatures were derived, comprising symptoms, diagnoses and investigation results. A final prediction model was generated based on the averaged likelihood scores from these two models. In a validation cohort consisting of 269 consecutive patients (with 66 HFpEF cases (24.5%)), the diagnostic power of detecting HFpEF had an AUROC of 90% (P<0.001) and average precision (AP) of 74%.

Conclusion

This diagnostic signature enables discrimination of HFpEF from non-cardiac dyspnea or HFrEF from EHR and can assist in the diagnostic evaluation in patients with unexplained dyspnea.