bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic modifiers of Huntington’s disease differentially influence motor and cognitive domains
Authors: Lee Jong-Min , Huang Yuan , Orth Michael , Gillis Tammy , Siciliano Jacqueline , Hong Eunpyo , Mysore Jayalakshmi Srinidhi , Lucente Diane , Wheeler Vanessa C. , Seong Ihn Sik , McLean Zachariah L. , Mills James A. , McAllister Branduff , Lobanov Sergey V. , Massey Thomas H. , Ciosi Marc , Landwehrmeyer G. Bernhard , Paulsen Jane S. , Dorsey E. Ray , Shoulson Ira , Sampaio Cristina , Monckton Darren G. , Kwak Seung , Holmans Peter , Jones Lesley , MacDonald Marcy E. , Long Jeffrey D. , Gusella James F.
Published: January 2022

Genome-wide association studies (GWAS) of Huntington’s disease (HD) have identified six DNA maintenance gene loci (among others) as modifiers and implicated a two step-mechanism of pathogenesis: somatic instability of the causative HTT CAG repeat with subsequent triggering of neuronal damage. The largest studies have been limited to HD individuals with a rater-estimated age at motor onset. To capitalize on the wealth of phenotypic data in several large HD natural history studies, we have performed algorithmic prediction using common motor and cognitive measures to predict age at other disease landmarks as additional phenotypes for GWAS. Combined with imputation using the Trans-Omics for Precision Medicine reference panel, predictions using integrated measures provided objective landmark phenotypes with greater power to detect most modifier loci. Importantly, substantial differences in the relative modifier signal across loci, highlighted by comparing common modifiers at MSH3 and FAN1, revealed that individual modifier effects can act preferentially in the motor or cognitive domains. Individual components of the DNA maintenance modifier mechanisms may therefore act differentially on the neuronal circuits underlying the corresponding clinical measures. In addition, we identified new modifier effects at the PMS1 and PMS2 loci and implicated a potential new locus on chromosome 7. These findings indicate that broadened discovery and characterization of HD genetic modifiers based on additional quantitative or qualitative phenotypes offers not only the promise of in-human validated therapeutic targets, but also a route to dissecting the mechanisms and cell types involved in both the somatic instability and toxicity components of HD pathogenesis.
Convolution Neural Networks for Point-of-Care Diagnostics of Bacterial Infections in Blood
Authors: Hegde Omkar , Chatterjee Ritika , Roy Durbar , Jaiswal Vivek , Chakravortty Dipshikha , Basu Saptarshi
Published: January 2022

A droplet of blood, when evaporated on a surface, leaves dried residue—the fractal patterns formed on the dried residues can act as markers for infection present in the blood. Exploiting the unique patterns found in the residues of a naturally dried droplet of blood, we propose a Point-of-Care (POC) diagnostic tool for detecting broad-spectrum of bacterial infections (such asEnterobacter aerogenes, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, Salmonella Typhi) in blood. The diagnosis process we propose is straightforward and can be performed with the following steps: A droplet of blood (healthy or infected) of volume range 0.5 to 2μlis allowed to dry on a clean glass surface and is imaged using a conventional optical microscope. A computer algorithm based on the framework of convolution neural network (CNN) is used to classify the captured images of dried blood droplets according to the bacterial infection. In total, our multiclass model reports an accuracy of 92% for detecting six bacterial species infections in the blood (with control being the uninfected or healthy blood). The high accuracy of detecting bacteria in the blood reported in this article is commensurate with the standard bacteriological tests. Thus, this article presents a proof-of-concept of a potential futuristic tool for a rapid and low-cost diagnosis of bacterial infection in the blood.
Performance evaluation of novel fluorescent-based lateral immune flow assay (LIFA) for rapid detection and quantitation of total anti-SARS-CoV-2 S-RBD binding antibodies in infected individuals
Authors: Shurrab Farah M. , Younes Nadin , Al-Sadeq Duaa W. , Qotba Hamda , Abu-Raddad Laith J. , Nasrallah Gheyath K.
Published: January 2022

1.

Background

The vast majority of the commercially available LFIA is used to detect SARS-CoV-2 antibodies qualitatively. Recently, a novel fluorescence-based LIFA test was developed for quantitative measurement of the total binding antibody units (BAU/mL) against the receptor-binding domain of the SARS-CoV-2 spike protein (S-RBD).

Aim

To evaluate the performance of the fluorescence LIFA Finecare™ 2019-nCoV S-RBD test along with its reader (Model No.: FS-113).

Methods

Plasma from 150 RT-PCR confirmed-positive individuals and 100 pre-pandemic samples were tested by FinCare™ to access sensitivity and specificity. For qualitative and quantitative validation of the FinCar™ measurements, the BAU/mL results of FinCare™ were compared with results of two reference assays: the surrogate virus-neutralizing test (sVNT, GenScript, USA), and the VIDAS®3 automated assay (BioMérieux, France).

Results

Finecare™ showed 92% sensitivity and 100% specificity compared to PCR. Cohen’s Kappa statistic denoted moderate and excellent agreement with sVNT and VIDAS®3, ranging from 0.557 (95% CI: 0.32-0.78) to 0.731 (95% CI: 0.51-0.95), respectively. A strong correlation was observed between Finecare™/sVNT (r=0.7, p<0.0001) and Finecare™/VIDAS®3 (r=0.8, p<0.0001).

Conclusion

Finecare™ is a reliable assay and can be used as a surrogate to assess binding and neutralizing antibody response post-infection or vaccination, particularly in none or small laboratory settings.
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
Authors: Stervander Martin , Melo Martim , Jones Peter , Hansson Bengt
Published: January 2022

Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.

Abstract Figure
Resolution and b value dependent Structural Connectome in ex vivo Mouse Brain
Authors: Crater Stephanie , Maharjan Surendra , Qi Yi , Zhao Qi , Cofer Gary , Cook James J. , Johnson G. Allan , Wang Nian
Published: January 2022

Diffusion magnetic resonance imaging has been widely used in both clinical and preclinical studies to characterize tissue microstructure and structural connectivity. The diffusion MRI protocol for the Human Connectome Project (HCP) has been developed and optimized to obtain high-quality, high-resolution diffusion MRI (dMRI) datasets. However, such efforts have not been fully explored in preclinical studies, especially for rodents. In this study, high quality dMRI datasets of mouse brains were acquired at 9.4T system from two vendors. In particular, we acquired a high-spatial resolution dMRI dataset (25 μm isotropic with 126 diffusion encoding directions), which we believe to be the highest spatial resolution yet obtained; and a high-angular resolution dMRI dataset (50 μm isotropic with 384 diffusion encoding directions), which we believe to be the highest angular resolution compared to the dMRI datasets at the microscopic resolution. We systematically investigated the effects of three important parameters that affect the final outcome of the connectome: b value (1000 s/mm2to 8000 s/mm2), angular resolution (10 to 126), and spatial resolution (25 µm to 200 µm). The stability of tractography and connectome increase with the angular resolution, where more than 50 angles are necessary to achieve consistent results. The connectome and quantitative parameters derived from graph theory exhibit a linear relationship to the b value (R2> 0.99); a single-shell acquisition with b value of 3000 s/mm2shows comparable results to the multi-shell high angular resolution dataset. The dice coefficient decreases and both false positive rate and false negative rate gradually increase with coarser spatial resolution. Our study provides guidelines and foundations for exploration of tradeoffs among acquisition parameters for the structural connectome in ex vivo mouse brain.
Chronic Cognitive and Cerebrovascular Function Following Mild Traumatic Brain Injury in Rats
Authors: Griffiths Daniel R. , Law L. Matthew , Young Conor , Fuentes Alberto , Truran Seth , Karamanova Nina , Bell Laura C. , Turner Gregory , Emerson Hannah , Mastroeni Diego , Gonzales Rayna , Reaven Peter D. , Quarles Chad C. , Migrino Raymond Q. , Lifshitz Jonathan
Published: January 2022

Severe traumatic brain injury results in cognitive dysfunction in part due to vascular perturbations. In contrast, the long-term vasculo-cognitive pathophysiology of mild TBI (mTBI) remains unknown. We evaluated mTBI effects on chronic cognitive and cerebrovascular function and assessed their interrelationships. Sprague-Dawley rats received midline fluid percussion injury (N=20) or sham (N=21). Cognitive function was assessed (3- and 6-month novel object recognition (NOR), novel object location (NOL) and temporal order object recognition (TOR)). 6-month cerebral blood flow (CBF) and blood volume (CBV) using contrast MRI and ex vivo pial artery endothelial and smooth muscle-dependent function were measured. mTBI rats showed impaired NOR, with similar (non-significant) trends in NOL/TOR. Regional CBF and CBV were similar in sham and mTBI. NOR correlated with CBF in lateral hippocampus, medial hippocampus and primary somatosensory barrel cortex while inversely correlating with arterial smooth muscle-dependent dilation. 6-month baseline endothelial and smooth muscle-dependent arterial function were similar among mTBI and sham, but post-angiotensin II stimulation, mTBI showed no change in smooth muscle-dependent dilation from baseline response, unlike the reduction in sham. mTBI led to chronic cognitive dysfunction and altered angiotensin II-stimulated smooth muscle-dependent vasoreactivity, a paradigm that could advance understanding of the long-term sequelae of human mild TBI.
Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland
Authors: Hou Huayun , Chan Cadia , Yuki Kyoko E. , Sokolowski Dustin , Roy Anna , Qu Rihao , Uusküla-Reimand Liis , Faykoo-Martinez Mariela , Hudson Matt , Corre Christina , Goldenberg Anna , Zhang Zhaolei , Palmert Mark R. , Wilson Michael D.
Published: January 2022

The pituitary gland regulates essential physiological processes such as growth, pubertal onset, stress response, metabolism, reproduction, and lactation. While sex biases in these functions and hormone production have been described, the underlying identity, temporal deployment, and cell-type specificity of sex-biased pituitary gene regulatory networks are not fully understood. To capture sex differences in pituitary gene regulation dynamics during postnatal development, we performed 3’ untranslated region sequencing and small RNA sequencing to ascertain gene and microRNA expression respectively across five postnatal ages (postnatal days 12, 22, 27, 32, 37) that span the pubertal transition in female and male C57BL/6J mouse pituitaries (n=5-6 biological replicates for each sex at each age). We observed over 900 instances of sex-biased gene expression and 17 sex-biased microRNAs, with the majority of sex differences occurring with puberty. Using miRNA-gene target interaction databases, we identified 18 sex-biased genes that were putative targets of 5 sex-biased microRNAs. In addition, by combining our bulk RNA-seq with publicly available male and female mouse pituitary single-nuclei RNA-seq data, we obtained evidence that cell-type proportion sex differences exist prior to puberty and persist post-puberty for three major hormone-producing cell types: somatotropes, lactotropes, and gonadotropes. Finally, we predicted sex-biased genes in these three pituitary cell types after accounting for cell-type proportion differences between sexes. Our study reveals the identity and postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary. This work also highlights the importance of considering sex biases in cell-type composition when understanding sex differences in the processes regulated by the pituitary gland.

Highlights

Male and female mouse pituitary gland gene and miRNA expression was profiled across five postnatal ages spanning pubertal development

Abundant sex differences in pituitary gene expression exist prior to puberty and become more prominent upon puberty

Combining expression data from genes and miRNAs revealed 18 putative sex-biased gene targets of 5 sex-biased miRNAs

Sex differences in the proportions of somatotropes, lactotropes, and gonadotropes are predicted to occur prior to puberty
Disruption of natural killer cell homing as a biomarker in persons aging with or without HIV
Authors: Kroll Kyle W. , Shah Spandan V. , Lucar Olivier A. , Premeaux Thomas A. , Shikuma Cecilia M. , Corley Michael J. , Mosher Matthew , Bowler Scott , Ndhlovu Lishomwa C. , Reeves R. Keith
Published: January 2022

Natural killer (NK) cells are critical modulators of HIV transmission and disease. While recent evidence suggests a loss of NK cell cytotoxicity during aging, a compound analysis of NK cell biology and aging in persons with HIV (PWH) is lacking. We set out to perform one of the first large comprehensive analyses of people aging with and without HIV to determine NK phenotypic changes during aging and how these changes are modulated while aging with HIV. Utilizing high-dimensional polychromatic flow cytometry we analyzed 30 immune-related proteins spanning broad functions such as trafficking, activation/inhibition, NK specific receptors, and memory/checkpoint receptors on peripheral NK cells from health donors, PWH with viral suppression, and viremic PWH. NK cell phenotypes are dynamic across the age span but are significantly altered in HIV and ART and with co-factors such as CMV. Specifically, NK cells in healthy aging show increasing levels of ⍰4β7 and decreasing CCR7 expression during aging, a phenomenon nearly perfectly reversed in PWH. These HIV-associated trafficking changes could be in part due to NK cell recruitment to HIV reservoir formation in lymphoid tissue or failed mucosal signaling in the HIV-infected gut, but regardless appear to be tight biomarkers of age-related NK cell changes.
Treatment of wound infections in a mouse model using Zn2+-releasing phage bound to gold nanorods
Authors: Peng Huan , Rossetto Daniele , Mansy Sheref S. , Jordan Maria C. , Roos Kenneth P. , Chen Irene A.
Published: January 2022

Infections caused by drug-resistant bacteria, particularly gram-negative organisms, are increasingly difficult to treat using antibiotics. A potential alternative is ‘phage therapy’, in which phages infect and lyse the bacterial host. However, phage therapy poses serious drawbacks and safety concerns, such as the risk of genetic transduction of antibiotic resistance genes, inconsistent pharmacokinetics, and unknown evolutionary potential. In contrast, metallic nanoparticles possess precise, tunable properties, including efficient conversion of electronic excitation into heat. In this work, we demonstrate that engineered phage-nanomaterial conjugates that target the gram-negative pathogen P. aeruginosa, are highly effective as a treatment of infected wounds in mice. Photothermal heating, performed as a single treatment (15 min) or as two treatments on consecutive days, rapidly reduced the bacterial load and released Zn2+ to promote wound healing. The phage-nanomaterial treatment was significantly more effective than systemic fluoroquinolone antibiotics in reducing both bacterial load and wound size, and was notably effective against a P. aeruginosa strain resistant to polymyxins, a last-line antibiotic therapy. Unlike these antibiotics, the phage-nanomaterial showed no detectable toxicity or systemic effects in mice, consistent with the short duration and localized nature of phage- nanomaterial treatment. Our results demonstrate that phage therapy controlled by inorganic nanomaterials can be a safe and effective antimicrobial strategy in vivo.
Redirecting RiPP biosynthetic enzymes to proteins and backbone-modified substrates
Authors: Walker Joshua A. , Hamlish Noah , Tytla Avery , Brauer Daniel D. , Francis Matthew B. , Schepartz Alanna
Published: January 2022

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are peptide-derived natural products that include the FDA-approved analgesic ziconotide1,2 as well as compounds with potent antibiotic, antiviral, and anticancer properties.3 RiPP enzymes known as cyclodehydratases and dehydrogenases represent an exceptionally well-studied enzyme class.3 These enzymes work together to catalyze intramolecular, interresidue condensation3,4 and aromatization reactions that install oxazoline/oxazole and thiazoline/thiazole heterocycles within ribosomally produced polypeptide chains. Here we show that the previously reported enzymes MicD-F and ArtGox accept backbone-modified monomers, including aramids and beta-amino acids, within leader-free polypeptides, even at positions immediately preceding or following the site of cyclization/dehydrogenation. The products are sequence-defined chemical polymers with multiple, diverse, non-alpha-amino acid subunits. We show further that MicD-F and ArtGox can install heterocyclic backbones within protein loops and linkers without disrupting the native tertiary fold. Calculations reveal the extent to which these heterocycles restrict conformational space; they also eliminate a peptide bond. Both features could improve the stability or add function to linker sequences now commonplace in emerging biotherapeutics. Moreover, as thiazoles and thiazoline heterocycles are replete in natural products,5–7 small molecule drugs,8,9 and peptide-mimetic therapeutics,10 their installation in protein-based biotherapeutics could improve or augment performance, activity, stability, and/or selectivity. This work represents a general strategy to expand the chemical diversity of the proteome beyond and in synergy with what can now be accomplished by expanding the genetic code.
Development of OPLS-AA/M Parameters for Simulations of G Protein-Coupled Receptors and Other Membrane Proteins
Authors: Robertson Michael J. , Skiniotis Georgios
Published: January 2022

G protein-coupled receptors (GPCRs) and other membrane proteins are valuable drug targets, and their dynamic nature makes them attractive systems for study with molecular dynamics simulations and free energy approaches. Here, we report the development, implementation, and validation of OPLS-AA/M force field parameters to enable simulations of these systems. These efforts include the introduction of post-translational modifications including lipidations and phosphorylation. We also modify previously reported parameters for lipids to be more consistent with the OPLS-AA force field standard and extend their coverage. These new parameters are validated on a variety of test systems, with the results compared to high-level quantum mechanics calculations, experimental data, and simulations with CHARMM36m where relevant. The results demonstrate that the new parameters reliably reproduce the behavior of membrane protein systems.
Adolescents Hospitalized with SARS-CoV-2: Analysis of Clinical Profile and Risk Factors for Severe Disease over a two-year period
Authors: Ghosh Tamoghna , Suri Tejas M , Jat Kana Ram , Gupta Aditya Kumar , Bhatnagar Sushma , Tiwari Pawan , Mittal Saurabh , Mohan Anant
Published: January 2022

Introduction

There is a lack of studies in adolescents with COVID-19 from developing countries. We aimed to describe the clinical profile and risk factors for severe disease in adolescents hospitalized with COVID-19.

Methods

A retrospective analysis of a prospectively admitted cohort of COVID-19 patients was performed at a tertiary hospital in north India. Adolescents aged 12 to 18 years who were hospitalized during the first wave (March 2020 to December 2020) and the second wave (March 2021 to June 2021) of the pandemic were included. Data on the demographic details, clinical presentation, laboratory parameters, disease severity at admission, treatments received, and in-hospital outcomes were retrieved and logistic regression was used to identify the risk factors for occurrence of moderate or severe disease.

Results

The study included 197 adolescents with median (IQR) age 15 (13-17) years, of whom 117 (59.4%) were male. Among these, 170 (86.3%) were admitted during the 1st wave. Underlying comorbidities were present in 9 (4.6%) patients. At the time of hospital admission, 60 (30.9%) patients were asymptomatic. In the severity grading, 148 (84.6%) had mild, 16 (9.1%) had moderate, and 11 (6.3%) had severe disease. Fever (14.9%) and cough (14.9%) were the most commonly encountered symptoms. The median (IQR) duration of hospital stay was 10 (8-13) days and 6 (3.1%) patients died in hospital. The odds of moderate to severe disease were 3.8 for second wave, 1.9 for fever and 1.1 for raised C reactive protein (CRP).

Conclusion

In our single-center study from northern India, adolescents admitted with COVID-19 had predominantly asymptomatic or mild disease. Admission during the second wave of COVID-19 pandemic, presence of fever and raised CRP were risk factors for moderate or severe disease.

Lay Summary

From 3rd January 2022 onwards, adolescents between 15 to 18 years of age in India will be given Covaxin vaccine, as per the latest Indian government guidelines. In our study, we aimed to describe the clinical profile and risk factors for severe disease in adolescents hospitalized with COVID-19. Our study included 197 adolescents. 170 (86.3%) of them were admitted during the 1st wave and the rest 27 (13.7%) during the 2nd wave. At the time of hospital admission, 60 (30.9%) patients were asymptomatic. In the severity grading, 148 (84.6%) had mild, 16 (9.1%) had moderate, and 11 (6.3%) had severe disease. Fever (14.9%) and cough (14.9%) were the most commonly encountered symptoms. The median (IQR) duration of hospital stay was 10 (8-13) days and 6 (3.1%) patients died in hospital. 2nd wave, fever and high C reactive protein increased the odds of moderate to severe disease.
Fast event-related mapping of population fingertip tuning properties in human sensorimotor cortex at 7T
Authors: Khalife Sarah , Francis Susan T. , Schluppeck Denis , Sánchez-Panchuelo Rosa-Maria , Besle Julien
Published: January 2022

fMRI studies that investigate somatotopic tactile representations in the human cortex typically use either block or phase-encoded stimulation designs. Event-related (ER) designs allow for more flexible and unpredictable stimulation sequences than the other methods, but they are less efficient. Here we compared an efficiency-optimized fast ER design (2.8s average intertrial interval, ITI) to a conventional slow ER design (8s average ITI) for mapping voxelwise fingertip tactile tuning properties in the sensorimotor cortex of 6 participants at 7 Tesla. The fast ER design yielded more reliable responses compared to the slow ER design, but with otherwise similar tuning properties. Concatenating the fast and slow ER data, we demonstrate in each individual brain the existence of two separate somatotopically-organized tactile representations of the fingertips, one in the primary somatosensory cortex (S1) on the post-central gyrus, and the other shared across the motor and pre-motor cortices on the pre-central gyrus. In both S1 and motor representations, fingertip selectivity decreased progressively, from narrowly-tuned Brodmann areas 3b and 4a respectively, towards associative parietal and frontal regions that responded equally to all fingertips, suggesting increasing information integration along these two pathways. In addition, fingertip selectivity in S1 decreased from the cortical representation of the thumb to that of the pinky.

Significance Statement

Sensory and motor cortices in the human brain contain map-like representations of the body in which adjacent brain regions respond to adjacent body parts. The properties of these somatotopic maps provide important insight into how tactile and motor information is processed by the brain. Here, we describe an efficient mapping method using functional MRI to measure somatotopic maps and their tuning properties. We used a fast event-related sequence to map the five fingers of the left hand in six human participants, and show that this method is more efficient than a conventional, slower event-related design. Furthermore, we confirm previously-identified tuning properties of fingertip representations in somatosensory cortex, and reveal a hitherto unknown tactile fingertip map in the motor cortex.
Serine 1283 in extracellular matrix glycoprotein Reelin is crucial for Reelin’s function in brain development
Authors: Kleene Ralf , Loers Gabriele , Sharaf Ahmed , Wang Shaobo , Kataria Hardeep , Anstötz Max , Hermans-Borgmeyer Irm , Schachner Melitta
Published: January 2022

Deficiency in the extracellular matrix glycoprotein Reelin severely affects migration of neurons during development. The function of serine at position 1283 in Reelin has remained uncertain. To explore its relevance we generatedrlnA/Amice that carry alanine instead of serine at position 1283, thereby disrupting the putative casein kinase 2 (CK2) phosphorylation site S1283DGD. Mutated mice displayedreeler-like locomotor behavior, abnormal brain anatomy and decrease of Reelin RNA and protein levels during development and in adulthood. Since serine 1283 was previously proposed to mediate proteolysis of adhesion molecules, we investigated proteolysis of cell adhesion molecule L1 and found it normal inrlnA/Amice. Neuronal migration in the embryonicrlnA/Acerebral cortex was impaired, but rescued byin uteroelectroporation of the Reelin fragment N-R6 containing the putative CK2 phosphorylation site. InrlnA/Amice migration of cerebellar granule cellsin vitrowas promoted by application of wild-type but not by mutated Reelin. In cerebellar neuron cultures, Reelin expression was decreased upon inhibition of ecto-phosphorylation by CK2. Biochemically purified wild-type, but not mutated Reelin was found phosphorylated. Altogether, the results indicate that ecto-phosphorylation at serine 1283 rather than proteolytic processing of adhesion molecules by Reelin plays an important role in Reelin functions.
Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation
Authors: Krishnan Jaya , Wang Yan , Kenzior Olga , Huzaifa Hassan , Olsen Luke , Tsuchiya Dai , Wang Yongfu , Zhao Chongbei , Rohner Nicolas
Published: January 2022

Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (1). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with a comprehensive biochemical and molecular characterization of the cell lines, which reflects key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.
scRNA-sequencing reveals subtype-specific transcriptomic perturbations in DRG neurons ofPirt-EGFPfmice in neuropathic pain condition
Authors: Zhang Chi , Hu Ming-Wen , He Shao-Qiu , Wang Xue-Wei , Cao Xu , Zhou Feng-Quan , Qian Jiang , Guan Yun
Published: January 2022

Functionally distinct subtypes/clusters of dorsal root ganglion (DRG) neurons, which differ in soma size and neurochemical properties, may play different roles in nerve regeneration and pain. However, details about transcriptomic changes in different neuronal subtypes under maladaptive neuropathic pain conditions remain unclear. Chronic constriction injury (CCI) of the sciatic nerve represents a well-established model of neuropathic pain that mimics the etiology of clinical conditions. Therefore, we conducted single-cell RNA-sequencing (scRNA-seq) to characterize subtype-specific perturbations of transcriptomes in lumbar DRG neurons 7 days after sciatic CCI. By usingPirt-EGFPfmice that selectively express enhanced green fluorescent protein in DRG neurons, we established a highly efficient purification process to enrich neurons for scRNA-seq. We observed a loss of marker genes in injured neurons of 12 standard neuronal clusters, and the emergence of four prominent CCI-induced clusters at this peak-maintenance phase of neuropathic pain. Importantly, a portion of injured neurons from a subset of the 12 standard clusters (NP1, PEP5, NF1, and NF2) were spared from injury-induced identity loss, suggesting subtype-specific transcriptomic changes in injured neurons. Moreover, uninjured neurons, which are necessary for mediating the evoked pain, also demonstrated subtype-specific transcriptomic perturbations in these clusters, but not others. Notably, male and female mice showed differential transcriptomic changes in multiple neuronal clusters after CCI, suggesting transcriptomic sexual dimorphism in primary sensory neurons after nerve injury. Collectively, these findings may contribute to the identification of new target genes and development of DRG neuron subtype-specific therapies for optimizing neuropathic pain treatment and nerve regeneration.
Metastable Oscillatory Modes emerge from synchronization in the Brain Spacetime Connectome
Authors: Cabral Joana , Castaldo Francesca , Vohryzek Jakub , Litvak Vladimir , Bick Christian , Lambiotte Renaud , Friston Karl , Kringelbach Morten L. , Deco Gustavo
Published: January 2022

A rich repertoire of oscillatory signals is detected from human brains with electro- and magnetoencephalography (EEG/MEG). However, the principles underwriting coherent oscillations and their link with neural activity remain under debate. Here, we revisit the mechanistic hypothesis that transient brain rhythms are a signature of metastable synchronization, occurring at reduced collective frequencies due to delays between brain areas. We consider a system of damped oscillators in the presence of background noise – approximating the short-lived gamma-frequency oscillations generated within neuronal circuits – coupled according to the diffusion weighted tractography between brain areas. Varying the global coupling strength and conduction speed, we identify a critical regime where spatially and spectrally resolved metastable oscillatory modes (MOMs) emerge at sub-gamma frequencies, approximating the MEG power spectra from 89 healthy individuals at rest. Further, we demonstrate that the frequency, duration, and scale of MOMs – as well as the frequency-specific envelope functional connectivity – can be controlled by global parameters, while the connectome structure remains unchanged. Grounded in the physics of delay-coupled oscillators, these numerical analyses demonstrate how interactions between locally generated fast oscillations in the connectome spacetime structure can lead to the emergence of collective brain rhythms organized in space and time.
Malformations of the sacculus and the semicircular canals in spider morph pythons
Authors: Starck J. Matthias , Schrenk Fabian , Schröder Sofia , Pees Michael
Published: January 2022

Spider morph ball pythons are a frequently bred design morph with striking alterations of the skin color pattern. We created high resolution µCT-image series through the otical region of the skulls, used 3D-reconstruction software for rendering anatomical models, and compare the anatomy of the semicircular ducts, sacculus and ampullae of wildtypePython regius(ball python) with spider morph snakes. All spider morph snakes showed the wobble condition. We describe the inner ear structures in wild-type and spider-morph snakes and report a deviant morphology of semicircular canals, ampullae and sacculus in spider morph snakes. We also report about associated differences in the desmal skull bones of spider morph snakes. The spider morph snakes were characterized by wider semicircular canals, anatomically poorly defined ampulla, a deformed crus communis and a small sacculus, with a highly deviant x-ray morphology as compared to wildtype individuals. We observed considerable intra- and interindividual variability of these features. This deviant morphology of spider morph snakes can easily be associated with an impairment of sense of equilibrium and the observed neurological wobble condition. Limitations in sample size prevent statistical analyses, but the anatomical evidence is strong enough to support an association between the wobble condition in design bread spider morph snakes and a malformation of the inner ear structures. A link between artificially selected alterations in pattern and specific color design with neural-crest associated developmental malformations of the statoacoustic organ as known from other vertebrates is discussed.
A unified view of low complexity regions (LCRs) across species
Authors: Lee Byron , Jaberi-Lashkari Nima , Calo Eliezer
Published: January 2022

Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
Determinants of trafficking, conduction, and disease within a K+ channel revealed through multiparametric deep mutational scanning
Authors: Coyote-Maestas Willow , Nedrud David , He Yungui , Schmidt Daniel
Published: January 2022

A longstanding goal in protein science and clinical genetics is to develop quantitative models of sequence, structure, and function relationships and delineate the mechanisms by which mutations cause disease. Deep Mutational Scanning (DMS) is a promising strategy to map how amino acids contribute to protein structure and function and to advance clinical variant interpretation. Here, we introduce 7,429 single residue missense mutation into the Inward Rectifier K+ channel Kir2.1 and determine how this affects folding, assembly, and trafficking, as well as regulation by allosteric ligands and ion conduction. Our data provides high-resolution information on a cotranslationally­folded biogenic unit, trafficking and quality control signals, and segregated roles of different structural elements in fold-stability and function. We show that Kir2.1 trafficking mutants are underrepresented in variant effect databases, which has implications for clinical practice. By comparing fitness scores with expert-reviewed variant effects, we can predict the pathogenicity of ‘variants of unknown significance’ and disease mechanisms of know pathogenic mutations. Our study in Kir2.1 provides a blueprint for how multiparametric DMS can help us understand the mechanistic basis of genetic disorders and the structure-function relationships of proteins.
Proteomic Dissection of a Giant Cell
Authors: Lin Athena , Piehowski Paul D. , Tsai Chia-Feng , Makushok Tatyana , Yi Lian , Diaz Ulises , Yan Connie , Summers Diana , Sood Pranidhi , Smith Richard D. , Liu Tao , Marshall Wallace F.
Published: January 2022

Many individual proteins have been identified as having defined positions relative to cell polarity axes, raising the question of what fraction of all proteins may have polarized localizations. We took advantage of the giant ciliate Stentor coeruleus to quantify the extent of polarized localization proteome-wide. This trumpet-shaped unicellular organism shows a clear morphological anterior-posterior axis defined by a circular array of cilia known as a membranellar band at one end, and a holdfast at the other end. Because individual Stentor cells are over a millimeter in length, we were able to cut the cells into three pieces along the anterior-posterior axis, followed by proteomic analysis of proteins enriched in each piece. We find that approximately 30% of all detected proteins show a polarized location relative to the anterior-posterior cell axis. Proteins with polarized enrichment include centrin-like proteins, calcium-regulated kinases, orthologs of SFI1 and GAS2, and proteases. At the organelle level, nuclear and mitochondrial proteins are enriched in the anterior half of the cell body, but not in the membranellar band itself, while ribosome related proteins are apparently uniformly distributed. RNAi of signaling proteins enriched in the membranellar band, which is the anterior-most structure in the cell, revealed a protein phosphatase 2 subunit b ortholog required for closure of the membranellar band into the ring shape characteristic of Stentor. These results suggest that a large fraction of the Stentor proteome has a polarized localization, and provide a protein-level framework for future analysis of pattern formation and regeneration in Stentor as well as defining a general strategy for subcellular spatial proteomics based on physical dissection of cells.
Modeling Cell Biological Features of Meiotic Chromosome Pairing
Authors: Navarro Erik J. , Marshall Wallace F. , Fung Jennifer C.
Published: January 2022

During meiosis, homologous chromosomes become associated side by side in a process known as homologous chromosome pairing. Pairing requires long range chromosome motion through a nucleus that is full of other chromosomes. It remains unclear how the cell manages to align each pair of chromosomes quickly while mitigating and resolving interlocks. Here, we use a coarse-grained molecular dynamics model to investigate how specific features of meiosis, including motor-driven telomere motion, nuclear envelope interactions, and increased nuclear size, affect the rate of pairing and the mitigation/resolution of interlocks. By creating in silico versions of three yeast strains and comparing the results of our model to experimental data, we find that a more distributed placement of pairing sites along the chromosome is necessary to replicate experimental findings. Active motion of the telomeric ends speeds up pairing only if binding sites are spread along the chromosome length. Adding a meiotic bouquet significantly speeds up pairing but does not significantly change the number of interlocks. An increase in nuclear size slows down pairing while greatly reducing the number of interlocks. Interestingly, active forces increase the number of interlocks, which raises the question: How do these interlocks resolve? Our model gives us detailed movies of interlock resolution events which we then analyze to build a step-by-step recipe for interlock resolution. In our model, interlocks must first translocate to the ends, where they are held in a quasi-stable state by a large number of paired sites on one side. To completely resolve an interlock, the telomeres of the involved chromosomes must come in close proximity so that the cooperativity of pairing coupled with random motion causes the telomeres to unwind. Together our results indicate that computational modeling of homolog pairing provides insight into the specific cell biological changes that occur during meiosis.

Author Summary

Early in meiosis, homologous chromosomes must find each other within the crowded nuclear space and become aligned along their entire length in a process known as homologous chromosome pairing. It remains unclear how the cell manages to align each pair of chromosomes quickly while mitigating and resolving interlocks. Here, we study this process by using a computational model. Our model attempts to capture the large-scale cell biological picture of meiotic pairing including the random initial 3D search, active motion of the chromosome ends, and meiosis specific constraints such as telomere attachment to the nuclear envelope. We use our model to study how these different features of meiosis affect the rate of pairing and the mitigation/resolution of interlocks. Importantly, our model gives us detailed movies of interlock resolution events, which we then analyze to build a step-by-step recipe for interlock resolution. We believe computational modeling of homolog pairing provides valuable insight into this complex biological process.
Multiomic characterisation of high grade serous ovarian carcinoma enables high resolution patient stratification
Authors: Hollis Robert L , Meynert Alison M , Michie Caroline O , Rye Tzyvia , Churchman Michael , Hallas-Potts Amelia , Croy Ian , McCluggage W. Glenn , Williams Alistair R W , Bartos Clare , Iida Yasushi , Okamoto Aikou , Dougherty Brian , Barrett J. Carl , March Ruth , Matakidou Athena , Roxburgh Patricia , Semple Colin A , Harkin D Paul , Kennedy Richard , Herrington C Simon , Gourley Charlie
Published: January 2022

Background

High grade serous ovarian carcinoma (HGSOC) is the most common type of ovarian cancer; most patients experience disease recurrence which accumulates chemoresistance, leading to treatment failure. Previous investigations have characterised HGSOC at the genomic and transcriptomic level, identifying subtypes of patients with differential outcome and treatment response. However, the relationship between molecular events identified at the gene sequence, gene copy number and gene expression levels remains poorly defined.

Methods

We perform multi-layer molecular characterisation of a large retrospective HGSOC cohort (n=362) with detailed clinical annotation to interrogate the relationship between patient groups defined by gene mutation, copy number events, gene expression patterns and infiltrating immune cell burden. We construct a high resolution picture of the molecular landscape in HGSOC and identify features of tumours associated with distinct clinical behaviour in patients.

Results

BRCA2-mutant (BRCA2m) andEMSY-overexpressing cases demonstrated prolonged survival (multivariable hazard ratio 0.40 and 0.53) and higher chemotherapy response rates at first- and second-line treatment.CCNE1-gained (CCNE1g) cases demonstrated shorter survival (multivariable hazard ratio 1.52, 95% CI 1.10-2.10), under-representation of FIGO stage IV cases (P=0.017) and no significant difference in treatment response. We demonstrate marked overlap between the TCGA- and derived subtypes: the TCGA DIF, IMR, PRO and MES subtypes correlated with the Tothill C4, C2, C5 and C1 subtypes (P<0.001). IMR/C2 cases displayed higherBRCA1/2m frequency (25.5% and 32.5%) and significantly greater infiltration of immune cells (P<0.001), while PRO/C5 cases had the highestCCNE1g rate (23.9% and 22.2%) and were uniformly low in immune cell infiltration. The survival benefit for cases with aberrations in homologous recombination repair (HRR) genes was apparent across all transcriptomic subtypes (hazard ratio range 0.48-0.68). There was significant co-occurrence of RB loss and HRR gene aberrations (P=0.005); RB loss was further associated with favourable survival within cases harbouring HRR aberrations (multivariable hazard ratio 0.50, 95% CI 0.30-0.84).

Conclusions

These data paint a high resolution picture of the molecular landscape in HGSOC, better defining patients who may benefit most from specific molecular therapeutics and highlighting those for whom novel treatment strategies are needed to improve outcomes.
Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlormethiazide
Authors: Toro Robert A. , Dugarte-Dugarte Analio , Streek Jacco van de , Henao José Antonio , Delgado José Miguel , Díaz de Delgado Graciela
Published: January 2022

The structure of racemic (RS)-trichlormethiazide [systematic name: (RS)-6-chloro-3-(dichloromethyl)-1,1-dioxo-3,4-dihydro-2H-1λ6,2,4-benzothiadiazine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006). J. Appl. Cryst.
39, 910–915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018). J. Appl. Cryst.
51, 210–218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π–π interactions which, in turn, are connected by C—Cl...π interactions. They form chains propagating along [101], further connected by N—H...O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N—H...O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H...O and H...Cl interactions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic interactions (E
elec) to the total energy (E
tot). A comparison with the structure of S-TCMZ is also presented.
Crystal structure of a trifluoromethyl benzoato quadruple-bonded dimolybdenum complex
Authors: Aigeldinger Elisabeth , Brandao Lilliana , Powell Troy , Hartnett Alaina C. , Sun Rui , Dogutan Dilek K. , Zheng Shao-Liang
Published: January 2022

The study of quadruple bonds between transition metals, in particular those of dimolybdenum, has revealed much about the two-electron bond. The solid-state structure of the quadruple-bonded dimolybdenum(II) complex tetrakis[μ-4-(trifluoromethyl)benzoato-κ2
O:O′]bis[(tetrahydrofuran-κO)molybdenum(II)] 0.762-pentane 0.238-tetrahydrofuran solvate, [Mo2(p-O2CC6H4CF3)4·2THF]·0.762C5H12·0.238C4H8O or [Mo2(C8H4F3O2)4(C4H8O)2]·0.762C5H12·0.238C4H8O is reported. The complex crystallizes within a triclinic cell and low symmetry (P\overline{1}) results from the intercalated pentane/THF solvent molecules. The paddlewheel structure at 100 K has inversion symmetry and comprises four bridging carboxylate ligands encases the Mo2(II,II) core that is characterized by two axially coordinated THF molecules and an Mo—Mo distance of 2.1098 (7) Å.