bluuebunny/crossref_metadata_2025 huggingface dataset:
Enthalpic and Entropic Contributions to Interleaflet Coupling Drive Domain Registration and Anti-registration in Biological Membrane
Authors: Sharma Akshara , Seal Aniruddha , Iyer Sahithya S. , Srivastava Anand
Published: October 2021

Biological membrane is a complex self-assembly of lipids, sterols and proteins organized as a fluid bilayer of two closely stacked lipid leaflets. Differential molecular interactions among its diverse constituents give rise to heterogeneities in the membrane lateral organization. Under certain conditions, heterogeneities in the two leaflets can be spatially synchronised and exist as registered domains across the bilayer. Several contrasting theories behind mechanisms that induce registration of nanoscale domains have been suggested[1–3]. Following a recent study[4] showing the effect of position of lipid tail unsaturation on domain registration behavior, we decided to develop an analytical theory to elucidate the driving forces that create and maintain domain registry across leaflets. Towards this, we formulated a Hamiltonian for a stacked lattice system where site variables capture the lipid molecular properties such as the position of unsaturation and various other interactions that could drive phase separation and interleaflet coupling. We solve the Hamiltonian using Monte Carlo simulations and create a complete phase diagram that reports the presence or absence of registered domains as a function of various Hamiltonian parameters. We find that the interleaflet coupling should be described as a competing enthalpic contribution due to interaction of lipid tail termini, primarily due to saturated-saturated interactions, and an interleaflet entropic contribution from overlap of unsaturated tail termini. A higher position of unsaturation is seen to provide weaker interleaflet coupling. Thermodynamically stable nanodomains could also be observed for certain points in the parameter space in our bilayer model, which were further verified by carrying out extended Monte Carlo simulations. These persistent non-coalescing registered nanodomains close to the lower end of the accepted nanodomain size range also point towards a possible “nanoscale” emulsion description of lateral heterogeneities in biological membrane leaflets.
Tumor cell intrinsic and extrinsic features predicts prognosis in estrogen receptor positive breast cancer
Authors: Yao Kevin , Schaafsma Evelien , Zhang Baoyi , Cheng Chao
Published: October 2021

Although estrogen-receptor-positive (ER+) breast cancer is generally associated with favorable prognosis, clinical outcome varies substantially among patients. Genomic assays have been developed and applied to predict patient prognosis for personalized treatment. We hypothesize that the recurrence risk of ER+ breast cancer patients is determined by both genomic mutations intrinsic to tumor cells and extrinsic immunological features in the tumor microenvironment. Based on the Cancer Genome Atlas (TCGA) breast cancer data, we identified the 72 most common genomic aberrations (including gene mutations and indels) in ER+ breast cancer and defined sample-specific scores that systematically characterized the deregulated pathways intrinsic to tumor cells. To further consider tumor cell extrinsic features, we calculated immune infiltration scores for six major immune cell types. Many individual intrinsic features are predictive of patient prognosis in ER+ breast cancer, and some of them achieved comparable accuracy with the Oncotype DX assay. In addition, statistical learning models that integrated these features predicts the recurrence risk of patients with significantly better performance than the Oncotype DX assay. As a proof-of-concept, our study indicates the great potential of genomic and immunological features in prognostic prediction for improving breast cancer precision medicine. The framework introduced in this work can be readily applied to other cancers.

Author Summary

Many genomic biomarker tests such as Oncotype DX have been developed for breast cancer and have helped guide clinical decisions. We have developed gene signatures to integrate cancer genomic and transcriptomic data to characterize the downstream effect of driver genomic events. These signatures recapitulate the de-regulated pathways underlying the corresponding driver genomic events and are more correlated with clinical phenotypes such as recurrence free survival than mutation status alone. We apply this framework to ER+ breast cancer and define gene signatures for a total of 72 most commonly observed genomic events including gene mutations, amplifications and deletions. We find that many of these gene signatures are predictive of patient prognosis in ER+ breast cancer, and some of them achieved comparable accuracy with the Oncotype DX assay. We combine these tumor-intrinsic signatures with infiltration signatures for major immune cell types (tumor-extrinsic features) to construct integrative models for prognosis prediction. The models predicts the recurrence risk of patients with significantly better performance than the Oncotype DX assay.
Predicting Knee Adduction Moment Response to Gait Retraining with Minimal Clinical Data
Authors: Rokhmanova Nataliya , Kuchenbecker Katherine J. , Shull Peter B. , Ferber Reed , Halilaj Eni
Published: October 2021

Knee osteoarthritis is a progressive disease mediated by high joint loads. Foot progression angle modifications that reduce the knee adduction moment (KAM), a surrogate of knee loading, have demonstrated efficacy in alleviating pain and improving function. Although changes to the foot progression angle are overall beneficial, KAM reductions are not consistent across patients. Moreover, customized interventions are time-consuming and require instrumentation not commonly available in the clinic. We present a model that uses minimal clinical data to predict the extent of first peak KAM reduction after toe-in gait retraining. For such a model to generalize, the training data must be large and variable. Given the lack of large public datasets that contain different gaits for the same patient, we generated this dataset synthetically. Insights learned from ground-truth datasets with both baseline and toe-in gait trials (N=12) enabled the creation of a large (N=138) synthetic dataset for training the predictive model. On a test set of data collected by a separate research group (N=15), the first peak KAM reduction was predicted with a mean absolute error of 0.134% body weight * height (%BW*HT). This error is smaller than the test set’s subject average standard deviation of the first peak during baseline walking (0.306 %BW*HT). This work demonstrates the feasibility of training predictive models with synthetic data and may provide clinicians with a streamlined pathway to identify a patient-specific gait retraining outcome without requiring gait lab instrumentation.

Author Summary

Gait retraining as a conservative intervention for knee osteoarthritis shows great promise in extending pain-free mobility and preserving joint health. Although customizing a treatment plan for each patient may help to ensure a therapeutic response, this procedure cannot yet be performed outside of the gait laboratory, preventing research advances from becoming a part of clinical practice. Our work aims to predict the extent to which a patient with knee osteoarthritis will benefit from a non-invasive gait retraining therapy using measures that can be easily collected in the clinic. To overcome a lack of normative databases for gait retraining, we generated data synthetically based on limited ground-truth examples, and provided experimental evidence for the model’s ability to generalize to new subjects by evaluating on data collected by a separate research group. Our results can contribute to a future in which predicting the therapeutic benefit of a potential treatment can determine a custom treatment path for any patient.
The European Prevention of Alzheimer’s Dementia (EPAD) MRI Dataset and Processing Workflow
Authors: Lorenzini Luigi , Ingala Silvia , Wink Alle Meije , Kuijer Joost PA , Wottschel Viktor , Dijsselhof Mathijs , Sudre Carole H , Haller Sven , Molinuevo José Luis , Gispert Juan Domingo , Cash David M , Thomas David L , Vos Sjoerd B , Prados Ferran , Petr Jan , Wolz Robin , Palombit Alessandro , Schwarz Adam J , Gael Chételat , Payoux Pierre , Di Perri Carol , Wardlaw Joanna , Frisoni Giovanni B , Foley Christopher , Fox Nick C , Ritchie Craig , Pernet Cyril , Waldman Adam , Barkhof Frederik , Mutsaerts Henk JMM ,   for the EPAD consortium
Published: October 2021

The European Prevention of Alzheimer Dementia (EPAD) is a multi-center study that aims to characterize the preclinical and prodromal stages of Alzheimer’s Disease. The EPAD imaging dataset includes core (3D T1w, 3D FLAIR) and advanced (ASL, diffusion MRI, and resting-state fMRI) MRI sequences.

Here, we give an overview of the semi-automatic multimodal and multisite pipeline that we developed to curate, preprocess, quality control (QC), and compute image-derived phenotypes (IDPs) from the EPAD MRI dataset. This pipeline harmonizes DICOM data structure across sites and performs standardized MRI preprocessing steps. A semi-automated MRI QC procedure was implemented to visualize and flag MRI images next to site-specific distributions of QC features — i.e. metrics that represent image quality. The value of each of these QC features was evaluated through comparison with visual assessment and step-wise parameter selection based on logistic regression. IDPs were computed from 5 different MRI modalities and their sanity and potential clinical relevance were ascertained by assessing their relationship with biological markers of aging and dementia.

The EPAD v1500.0 data release encompassed core structural scans from 1356 participants 842 fMRI, 831 dMRI, and 858 ASL scans. From 1356 3D T1w images, we identified 17 images with poor quality and 61 with moderate quality. Five QC features — Signal to Noise Ratio (SNR), Contrast to Noise Ratio (CNR), Coefficient of Joint Variation (CJV), Foreground-Background energy Ratio (FBER), and Image Quality Rate (IQR) — were selected as the most informative on image quality by comparison with visual assessment. The multimodal IDPs showed greater impairment in associations with age and dementia biomarkers, demonstrating the potential of the dataset for future clinical analyses.
Plasticity in female timing may explain current shifts in breeding phenology of a North American songbird
Authors: Kimmitt Abigail A. , Becker Daniel J. , Diller Sara N. , Gerlach Nicole M. , Rosvall Kimberly A. , Ketterson Ellen D.
Published: October 2021

Climate change has driven changes in breeding phenology. Identifying the magnitude of phenological shifts and whether selection in response to climate change drives these shifts is key for determining species’ reproductive success and persistence in a changing world.

We investigated reproductive timing in a primarily sedentary population of the dark-eyed junco (Junco hyemalis) over 32 years. We predicted that juncos would breed earlier in warmer springs in response to selection favouring earlier breeding.

To test this prediction, we compared the annual median date for reproductive onset (i.e., egg one date) to monthly spring temperatures and examined evidence for selection favouring earlier breeding and for plasticity in timing.

Egg one dates occurred earlier over time, with the timing of breeding advancing up to 24 days over the 32-year period. Breeding timing also strongly covaried with maximum April temperature. We found significant overall selection favouring earlier breeding (i.e., higher relative fitness with earlier egg one dates) that became stronger over time, but strength of selection was not predicted by temperature. Lastly, individual females exhibited plastic responses to temperature across years.

Our findings provide further evidence that phenotypic plasticity plays a crucial role in driving phenological shifts in response to climate change. For multi-brooded bird populations, a warming climate might extend the breeding season and provide more opportunities to re-nest rather than drive earlier breeding in response to potential phenological mismatches. However, as plasticity will likely be insufficient for long-term survival in the face of climate change, further research in understanding the mechanisms of female reproductive timing will be essential for forecasting the effects of climate change on population persistence.
The evolutionary trajectory of drosophilid walking
Authors: York Ryan A. , Brezovec Luke , Coughlan Jenn , Herbst Steven , Krieger Avery , Lee Su-Yee , Pratt Brandon , Smart Ashley , Song Eugene , Suvorov Anton , Matute Daniel R. , Tuthill John C. , Clandinin Thomas R.
Published: October 2021

Neural circuits must both execute the behavioral repertoire of individuals and account for behavioral variation across species. Understanding how this variation emerges over evolutionary time requires large-scale phylogenetic comparisons of behavioral repertoires. Here, we describe the evolution of walking in fruit flies by capturing high-resolution, unconstrained movement from 13 species and 15 strains of drosophilids. We find that walking can be captured in a universal behavior space, the structure of which is evolutionarily conserved. However, the occurrence of, and transitions between, specific movements have evolved rapidly, resulting in repeated convergent evolution in the temporal structure of locomotion. Moreover, a meta-analysis demonstrates that many behaviors evolve more rapidly than other traits. Thus, the architecture and physiology of locomotor circuits can both execute precise individual movements in one species and simultaneously support rapid evolutionary changes in the temporal ordering of these modular elements across clades.
Genomics Characterization of an engineered Corynebacterium glutamicum in Bioreactor Cultivation under Ionic Liquid Stress
Authors: Banerjee Deepanwita , Eng Thomas , Sasaki Yusuke , Srinivasan Aparajitha , Oka Asun , Herbert Robin A. , Trinh Jessica , Singan Vasanth R. , Sun Ning , Putnam Dan , Scown Corinne D. , Simmons Blake , Mukhopadhyay Aindrila
Published: October 2021

Corynebacterium glutamicum is an ideal microbial chassis for the production of valuable bioproducts including amino acids and next-generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs. absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of a C. glutamicum strain engineered to produce IP.
Distance estimation from monocular cues in an ethological visuomotor task
Authors: Parker Philip R. L. , Abe Elliott T. T. , Beatie Natalie T. , Leonard Emmalyn S. P. , Martins Dylan M. , Sharp Shelby L. , Wyrick David G. , Mazzucato Luca , Niell Cristopher M.
Published: October 2021

In natural contexts, sensory processing and motor output are closely coupled, which is reflected in the fact that many brain areas contain both sensory and movement signals. However, standard reductionist paradigms decouple sensory decisions from their natural motor consequences, and head-fixation prevents the natural sensory consequences of self-motion. In particular, movement through the environment provides a number of depth cues beyond stereo vision that are poorly understood. To study the integration of visual processing and motor output in a naturalistic task, we investigated distance estimation in freely moving mice. We found that mice use vision to accurately jump across a variable gap, thus directly coupling a visual computation to its corresponding ethological motor output. Monocular eyelid suture did not affect gap jumping success, thus mice can use cues that do not depend on binocular disparity and stereo vision. Under monocular conditions, mice altered their head positioning and performed more vertical head movements, consistent with a shift from using stereopsis to other monocular cues, such as motion or position parallax. Finally, optogenetic suppression of primary visual cortex impaired task performance under both binocular and monocular conditions when optical fiber placement was localized to binocular or monocular zone V1, respectively. Together, these results show that mice can use monocular cues, relying on visual cortex, to accurately judge distance. Furthermore, this behavioral paradigm provides a foundation for studying how neural circuits convert sensory information into ethological motor output.
KRAB Zinc Finger protein Znf684 interacts with Nxf1 to regulate mRNA export
Authors: Nitoiu Alexandra , Nabeel-Shah Syed , Farhangmehr Shaghayegh , Pu Shuye , Braunschweig Ulrich , Blencowe Benjamin J. , Greenblatt Jack F.
Published: October 2021

Cys2His2 (C2H2) type zinc finger (ZnF) proteins constitute a large class of proteins that are generally considered to be DNA-binding transcription factors. Using affinity purification followed by mass spectrometry, as well as reciprocal co-immunoprecipitation experiments, we determined that the C2H2-ZnF protein Znf684 interacts physically with several proteins involved in mRNA export, including Nxf1 and Alyref. We utilized individual nucleotide resolution cross-linking immunoprecipitation followed by high throughput sequencing (iCLIP-seq) experiments to show that Znf684 binds directly to specific mRNAs in vivo and has an RNA-binding profile similar to those of Nxf1 and Alyref, suggesting a role in mRNA export regulation. Immunofluorescence microscopy (IF) experiments revealed that Znf684 localizes to both the nucleus and cytoplasm. Using cellular fractionation experiments, we demonstrate that overexpression of Znf684 negatively impacts the export of SMAD3 and other target mRNAs. Taken together, our results suggest that Znf684 regulates the export of a subset of transcripts through physical interactions with Nxf1 and specific target mRNAs.
Biophysical characterization of the oligomeric states of recombinant Immunoglobulins type-M and their C1q binding kinetics by Biolayer Interferometry
Authors: Chouquet Anne , Pinto Andrea J. , Hennicke Julia , Ling Wai Li , Bally Isabelle , Schwaigerlehner Linda , Thielens Nicole M. , Kunert Renate , Reiser Jean-Baptiste
Published: October 2021

The Immunoglobulins type-M (IgMs) are one of the first antibody classes mobilized during immune responses against pathogens and tumor cells. Binding to specific target antigens enables the interaction with the C1 complex which strongly activates the classical complement pathway. This biological function is the basis for the huge therapeutic potential of IgMs but due to their high oligomeric complexity,in vitroproduction, biochemical and biophysical characterizations are challenging. In the present study, we present recombinant production of two IgM models (IgM617 and IgM012) in pentameric and hexameric states and the evaluation of their polymer distribution using different biophysical methods (AUC, SEC-MALLS, Mass Photometry and Transmission Electron Microscopy). Each IgM oligomer has individual specific expression pattern and yield with different protein quality likely due to intrinsic IgM properties and patterning. Nevertheless, the purified recombinant IgMs retain their ability to activate complement in a C1q dependent manner. And more importantly, a new method to evaluate their functional quality attribute by characterizing the kinetics of C1q binding to recombinant IgM has been developed using BioLayer Interferometry (BLI). We show that recombinant IgMs possess similar C1q binding properties as IgMs purified from human plasma.
Durability of immune responses to the BNT162b2 mRNA vaccine
Authors: Suthar Mehul S. , Arunachalam Prabhu S. , Hu Mengyun , Reis Noah , Trisal Meera , Raeber Olivia , Chinthrajah Sharon , Davis-Gardner Meredith E. , Manning Kelly , Mudvari Prakriti , Boritz Eli , Godbole Sucheta , Henry Amy R. , Douek Daniel C. , Halfmann Peter , Kawaoka Yoshihiro , Zarnitsyna Veronika I. , Nadeau Kari , Pulendran Bali
Published: October 2021

The development of the highly efficacious mRNA vaccines in less than a year since the emergence of SARS-CoV-2 represents a landmark in vaccinology. However, reports of waning vaccine efficacy, coupled with the emergence of variants of concern that are resistant to antibody neutralization, have raised concerns about the potential lack of durability of immunity to vaccination. We recently reported findings from a comprehensive analysis of innate and adaptive immune responses in 56 healthy volunteers who received two doses of the BNT162b2 vaccination. Here, we analyzed antibody responses to the homologous Wu strain as well as several variants of concern, including the emerging Mu (B.1.621) variant, and T cell responses in a subset of these volunteers at six months (day 210 post-primary vaccination) after the second dose. Our data demonstrate a substantial waning of antibody responses and T cell immunity to SARS-CoV-2 and its variants, at 6 months following the second immunization with the BNT162b2 vaccine. Notably, a significant proportion of vaccinees have neutralizing titers below the detection limit, and suggest a 3rd booster immunization might be warranted to enhance the antibody titers and T cell responses.
In Vivo Generation of Bone Marrow from Embryonic Stem Cells in Interspecies Chimeras
Authors: Wen Bingqiang , Wang Guolun , Li Enhong , Kolesnichenko Olena A. , Tu Zhaowei , Divanovic Senad , Kalin Tanya V. , Kalinichenko Vladimir V.
Published: October 2021

Generation of bone marrow (BM) from embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) promises to accelerate the development of future cell therapies for life-threatening disorders. However, such approach is limited by technical challenges to produce a mixture of functional BM progenitor cells able to replace all hematopoietic cell lineages. Herein, we used blastocyst complementation to simultaneously produce all BM hematopoietic cell lineages from mouse ESCs in a rat. Based on FACS analysis and single-cell RNA sequencing, mouse ESCs differentiated into hematopoietic progenitor cells and multiple hematopoietic cell types that were indistinguishable from normal mouse BM cells based on gene expression signatures and cell surface markers. Transplantation of ESC-derived BM cells from mouse-rat chimeras rescued lethally-irradiated syngeneic mice and resulted in long-term contribution of donor cells to hematopoietic cell lineages. Altogether, a fully functional bone marrow was generated from mouse ESCs using rat embryos as “bioreactors”.

KEY POINTS

- We used blastocyst complementation to simultaneously produce all bone marrow hematopoietic cell lineages from mouse ESCs in a rat.

- ESC-derived cells from mouse-rat chimeras were fully functional and exhibited normal gene expression signatures and cell surface markers.
Bayesian machine learning analysis of single-molecule fluorescence colocalization images
Authors: Ordabayev Yerdos A. , Friedman Larry J. , Gelles Jeff , Theobald Douglas L.
Published: October 2021

Multi-wavelength single-molecule fluorescence colocalization (CoSMoS) methods allow elucidation of complex biochemical reaction mechanisms. However, analysis of CoSMoS data is intrinsically challenging because of low image signal-to-noise ratios, non-specific surface binding of the fluorescent molecules, and analysis methods that require subjective inputs to achieve accurate results. Here, we use Bayesian probabilistic programming to implement Tapqir, an unsupervised machine learning method that incorporates a holistic, physics-based causal model of CoSMoS data. This method accounts for uncertainties in image analysis due to photon and camera noise, optical non-uniformities, non-specific binding, and spot detection. Rather than merely producing a binary “spot/no spot” classification of unspecified reliability, Tapqir objectively assigns spot classification probabilities that allow accurate downstream analysis of molecular dynamics, thermodynamics, and kinetics. We both quantitatively validate Tapqir performance against simulated CoSMoS image data with known properties and also demonstrate that it implements fully objective, automated analysis of experiment-derived data sets with a wide range of signal, noise, and non-specific binding characteristics.
Structure and function of N-acetylglucosamine kinase illuminates the catalytic mechanism of ROK kinases
Authors: Roy Sumita , Vega Mirella Vivoli , Ames Jessica R. , Britten Nicole , Kent Amy , Evans Kim , Isupov Michail N. , Harmer Nicholas J.
Published: October 2021

N-acetyl-D-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolise environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase NagK performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analogue AMP-PNP. Surprisingly, PsNagK showed two conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Molecular dynamics modelling of catalytic ion binding confirmed the location of the essential catalytic metal. Site-directed mutagenesis confirmed the catalytic base, and that the metal coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.
Multiphoton microscopy for label-free multicolor imaging of peripheral nerve
Authors: Rishøj Lars , Hernández Iván Coto , Ramachandran Siddharth , Jowett Nate
Published: October 2021

Conventional histomorphometry of peripheral nerve entails lengthy chemical processing, ultrathin sectioning in resin, and imaging by light or electron microscopy. Multiphoton microscopy techniques exist enabling label-free and in vivo imaging of histological samples. Third-harmonic-generation microscopy has recently been demonstrated effective for imaging the myelin sheath of peripheral nerve axons in animal models. Herein, we characterize use of second and third harmonic generation microscopy for label-free imaging of murine and human peripheral nerve via a novel multicolor multiphoton microscope based on a single excitation wavelength at 1300 nm. Second harmonic generation signal from collagen centered about 650 nm delineates neural connective tissue, while third harmonic general signal centered about 433 nm delineates myelin and other lipids. In transgenic mice expressing yellow fluorescent protein linked to the thy1 promoter, three-photon-excitation with emission peak at 527 nm delineates axoplasm. We compare label-free multiphoton imaging of murine and human peripheral nerve against conventional chemical stains and discuss clinical implications of this approach in guiding intraoperative decision making in nerve transfer procedures.
Association between Cognitive Function and Large Optic Nerve Cupping, Accounting for Cup-Disc-Ratio Genetic Risk Score
Authors: Kravets Sasha , Rupnow Rawan Allozi , Sethi Abhishek , Espeland Mark A. , Pasquale Louis R. , Rapp Stephen R. , Klein Barbara E. , Meuer Stacy M. , Haan Mary N. , Maki Pauline M. , Hallak Joelle A. , Vajaranant Thasarat Sutabutr
Published: October 2021

Purpose

To investigate if accounting for a cup-to-disc ratio (CDR) genetic risk score (GRS) modified the association between large CDR and cognitive function among women.

Design

This was a retrospective study using data from the Women’s Health Initiative.

Methods

Patients with glaucoma or ocular hypertension were excluded. Large CDR was defined as ≥ 0.6 in either eye. Cognitive function was measured by the Modified Mini-Mental State Examination (3MSE). We used the combined effects from 13 single nucleotide polymorphisms (SNPs) to formulate the GRS for CDR. We used logistic regression to investigate associations between weighted GRS and large CDR, then a linear regression to assess the association between weighted GRS and 3MSE scores, and between weighted GRS, CDR, and 3MSE scores, adjusted for demographic and clinical characteristics.

Results

Final analyses included 1,196 White women with mean age of 69.60 ± 3.62 years and 7.27% with large CDR. Mean GRS in women with and without large CDR was 1.51 ± 0.31 vs. 1.41 ± 0.36, respectively (p = 0.004). The odds of large CDR for a one unit increase in GRS was 2.30 (95% CI: (1.22, 4.36), p = 0.011). Adding the CDR GRS in the model with CDR and 3MSE, women with large CDR still had statistically significantly lower 3MSE scores than those without large CDR, yielding a predicted mean difference in 3MSE scores of 0.84 (p = 0.007).

Conclusions

Independent of the CDR GRS, women with large CDR had a lower cognitive function.
A gut commensal niche regulates stable association of a multispecies microbiota
Authors: Dodge Ren , Jones Eric W. , Zhu Haolong , Obadia Benjamin , Martinez Daniel J. , Wang Chenhui , Aranda-Díaz Andrés , Aumiller Kevin , Liu Zhexian , Voltolini Marco , Brodie Eoin L. , Huang Kerwyn Casey , Carlson Jean M. , Sivak David A. , Spradling Allan C. , Ludington William B.
Published: October 2021

The intestines of animals are typically colonized by a complex, relatively stable microbiota that influences health and fitness, but the underlying mechanisms of colonization remain poorly understood. As a typical animal, the fruit fly, Drosophila melanogaster, is associated with a consistent set of commensal bacterial species, yet the reason for this consistency is unknown. Here, we use gnotobiotic flies, microscopy, and microbial pulse-chase protocols to show that a commensal niche exists within the proventriculus region of the Drosophila foregut that selectively binds bacteria with exquisite strain-level specificity. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus physically remodels the niche to favor secondary colonization by Acetobacter. Our results provide a mechanistic framework for understanding the establishment and stability of an intestinal microbiome.

One-Sentence Summary

A strain-specific set of bacteria inhabits a defined spatial region of the Drosophila gut that forms a commensal niche.
TRICLOSAN IS A KCNQ3 POTASSIUM CHANNEL ACTIVATOR
Authors: De la Rosa Victor , Guzmán-Hernández Maria Luisa , Carrillo Elisa
Published: October 2021

KCNQ channels participate in the physiology of several cell types. In neurons of the central nervous system, the primary subunits are KCNQ2, 3 and 5. Activation of these channels silence the neurons, limiting action potential duration and preventing high-frequency action potential burst. Mutation of the KCNQ genes are associated with a wide spectrum of phenotypes characterized by hyperexcitability. Activation of KCNQ channels is an attractive strategy to treat epilepsy and other hyperexcitability conditions as are the evolution of stroke and traumatic brain injury. In this work we show that triclosan, a bactericide widely used in personal care products, activates the KCNQ3 channels but not the KCNQ2. Triclosan induces a voltage shift in the activation, increases the conductance and slows the closing of the channel. The effect is independent of PIP2. The putative binding site is located in the pore region but is distinct from the binding site for retigabine. Our results indicate that triclosan is a new activator for KCNQ channels.
The paradox of the COVID-19 pandemic: the impact on patient demand in Japanese hospitals
Authors: Ii Masako , Watanabe Sachiko
Published: October 2021

Analyzing data from a large, nationally distributed group of Japanese hospitals, we found a dramatic decline in both inpatient and outpatient volumes over the three waves of the COVID-19 pandemic in Japan from February-December 2020. We identified three key reasons for this fall in patient demand. First, COVID-19-related hygiene measures and behavioral changes significantly reduced non-COVID-19 infectious diseases. Second, consultations relating to chronic diseases fell sharply. Third, certain medical investigations and interventions were postponed or cancelled. Despite the drop in hospital attendances and admissions, COVID-19 is said to have brought the Japanese health care system to the brink of collapse. In this context, we explore longstanding systematic issues, finding that Japan's abundant supply of beds and current payment system may have introduced a perverse incentive to overprovide services, creating a mismatch between patient needs and the supply of health care resources. Poor coordination among health care providers and the highly decentralized governance of the health care system have also contributed to the crisis. In order to ensure the long-term sustainability of the Japanese health care system beyond COVID-19, it is essential to promote specialization and differentiation of medical functions among hospitals, to strengthen governance, and to introduce appropriate payment reform.
Structure-selected RBM immunogens prime polyclonal memory responses that neutralize SARS-CoV-2 variants of concern
Authors: Almanza Gonzalo , Kouznetsova Valentina , Clark Alex E. , Olmedillas Eduardo , Castro Andrea , Tsigelny Igor F. , Wu Yan , Gao George F. , Saphire Erica Ollmann , Carlin Aaron F. , Zanetti Maurizio
Published: October 2021

Successful control of the COVID-19 pandemic depends on vaccines that prevent transmission. The full-length Spike protein is highly immunogenic but the majority of antibodies do not target the virus: ACE2 interface. In an effort to concentrate the antibody response to the receptor-binding motif (RBM) we generated a series of conformationally-constrained immunogens by inserting solvent-exposed RBM amino acid residues into hypervariable loops of an immunoglobulin molecule. Priming C57BL/6 mice with plasmid (p)DNA encoding these constructs yielded a rapid memory response to booster immunization with recombinant Spike protein. Immune sera antibodies bound strongly to the purified receptor-binding domain (RBD) and Spike proteins. pDNA primed for a consistent response with antibodies efficient at neutralizing authentic WA1 virus and two variants of concern (VOC), B.1.351 and B.1.617.2. These findings demonstrate that immunogens built on structure selection can focus the response to conserved sites of vulnerability shared between wildtype virus and VOCs and induce neutralizing antibodies across variants.
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion
Authors: Nussenblatt Veronique , Roder Allison E , Das Sanchita , de Wit Emmie , Youn Jung-Ho , Banakis Stephanie , Mushegian Alexandra , Mederos Christopher , Wang Wei , Chung Matthew , Pérez-Pérez Lizzette , Palmore Tara , Brudno Jennifer N. , Kochenderfer James N. , Ghedin Elodie
Published: October 2021

Background

B-cell depleting therapies may lead to protracted disease and prolonged viral shedding in individuals infected with SARS-CoV-2. Viral persistence in the setting of immunosuppression raises concern for viral evolution.

Methods

Amplification of sub-genomic transcripts for the E gene (sgE) was done on nasopharyngeal samples over the course of 355 days in a patient infected with SARS-CoV-2 who had previously undergone CAR T cell therapy and had persistently positive SARS-CoV-2 nasopharyngeal swabs. Whole genome sequencing was performed on samples from the patient’s original presentation and 10 months later.

Results

Over the course of almost a year, the virus accumulated a unique in-frame deletion in the amino-terminal domain of the spike protein, and complete deletion of ORF7b and ORF8, the first report of its kind in an immunocompromised patient. Also, minority variants that were identified in the early samples—reflecting the heterogeneity of the initial infection—were found to be fixed late in the infection. Remdesivir and high-titer convalescent plasma treatment were given, and the infection was eventually cleared after 335 days of infection.

Conclusions

The unique viral mutations found in this study highlight the importance of analyzing viral evolution in protracted SARS-CoV-2 infection, especially in immunosuppressed hosts, and the implication of these mutations in the emergence of viral variants.

We report an immunocompromised patient with persistent symptomatic SARS-CoV-2 infection for 335 days. During this time, the virus accumulated a unique in-frame deletion in the spike, and a complete deletion of ORF7b and ORF8 which is the first report of its kind in an immunocompromised patient.
Acquisition and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient
Authors: Sabin Arick P. , Richmond Craig S. , Kenny Paraic A.
Published: October 2021

The implementation of monoclonal antibody therapeutics during the COVID19 pandemic has altered the selective pressures encountered by SARS-CoV-2, raising the possibility of selection for variants resistant to one or more monoclonal antibodies and subsequent transmission into the wider population. Early studies indicated that monoclonal antibody treatment in immunocompromised individuals could result in within-host viral evolution preferentially affecting epitopes recognized by these antibodies, although whether this signifies a real risk of transmissible antibody resistant virus is unclear.

In this study we have taken advantage of a regional SARS-CoV-2 genomic surveillance program encompassing regions in Wisconsin, Minnesota and Iowa to monitor the introduction or de novo emergence of SARS-Cov-2 lineages with clinically relevant variants. Here we describe a newly acquired E484K mutation in the SARS-CoV-2 spike protein detected within the B.1.311 lineage. Multiple individuals in two related households were infected. The timing and patterns of subsequent spread were consistent with de novo emergence of this E484K variant in the initially affected individual who had been treated with bamlanivimab monotherapy. The subsequent transmission to close contacts occurred several days after the resolution of symptoms and the end of this patient’s quarantine period. Our study suggests that the selective pressures introduced by the now widespread administration of these antibodies may warrant increased genomic surveillance to identify and mitigate spread of therapy-induced variants.
Humoral response to the BBIBP-CorV vaccine over time in healthcare workers with or without exposure to SARS-CoV-2
Authors: Noel Badano María , Sabbione Florencia , Keitelman Irene , Pereson Matias , Aloisi Natalia , Colado Ana , Ramos Victoria , Ortiz Wilczyñski Juan Manuel , Pozner Roberto , Castillo Luis , Wigdorovitz Georgina , de Bracco María Marta E , Fink Susana , Chuit Roberto , Baré Patricia
Published: October 2021

SARS-CoV-2-specific humoral response was analyzed over time in a group of healthcare workers with or without exposure to SARS-CoV-2, who underwent vaccination with BBIBP-CorV (Sinopharm) vaccine in Argentina.

Seroconversion rates in unexposed subjects after the first and second doses were 40% and 100%, respectively, showing a significant increase in antibody concentrations from dose 1 to dose 2 (p<0.0001).

The highest antibody concentrations were found in younger subjects and women, remaining significantly associated in a multivariable linear regression model (p=0.005).

A single dose of the BBIBP-CorV vaccine induced a strong antibody response in individuals with prior SARS-CoV-2infection, while a second dose did not increase this response. A sharp increase in antibody concentrations was observed following SARS-CoV-2 infection in those participants who became infected after the first and second doses (p=0.008).

Individuals with SARS-CoV-2 exposure prior to vaccination showed significantly higher anti-spike IgG antibody levels, at all-time points, than those not exposed (p<0.001). Higher antibody titers were induced by a single dose in previously SARS-CoV-2 infected individuals than those induced in naïve subjects by two doses of the vaccine (p<0.0001). Three months after the second dose both groups showed a decline in antibody levels, being more abrupt in unexposed subjects.

Overall, our results showed a trend towards lower antibody concentrations over time following BBIBP-CorV vaccination. Sex and age seem to influence the magnitude of the humoral response in unexposed subjects while the combination of exposure to SARS-CoV-2 plus vaccination, whatever the sequence of the events was, produced a sharp increase in antibody levels.

Evaluation of the humoral responses over time and the analysis of the induction and persistence of memory B and T cell responses, are needed to assess long-term immune protection induced by BBIBP-CorV vaccine.
DeepUMQA: Ultrafast Shape Recognition-based Protein Model Quality Assessment using Deep Learning
Authors: Guo Sai-Sai , Liu Jun , Zhou Xiao-Gen , Zhang Gui-Jun
Published: October 2021

Motivation

Protein model quality assessment is a key component of protein structure prediction. In recent research, the voxelization feature was used to characterize the local structural information of residues, but it may be insufficient for describing residue-level topological information. Design features that can further reflect residue-level topology when combined with deep learning methods are therefore crucial to improve the performance of model quality assessment.

Results

We developed a deep-learning method, DeepUMQA, based on Ultrafast Shape Recognition (USR) for the residue-level single-model quality assessment. In the framework of the deep residual neural network, the residue-level USR feature was introduced to describe the topological relationship between the residue and overall structure by calculating the first moment of a set of residue distance sets and then combined with 1D, 2D, and voxelization features to assess the quality of the model. Experimental results on test datasets of CASP13, CASP14, and CAMEO show that USR could complement the voxelization feature to comprehensively characterize residue structure information and significantly improve the model assessment accuracy. DeepUMQA outperformed the state-of-the-art single-model quality assessment methods, including ProQ2, ProQ3, ProQ3D, Ornate, VoroMQA, and DeepAccNet.

Availability

The source code and executable are freely available athttps://github.com/iobio-zjut/DeepUMQA.

Contact

zgj@zjut.edu.cn
Mechanically active integrins direct cytotoxic secretion at the immune synapse
Authors: Wang Mitchell S. , Hu Yuesong , Sanchez Elisa E. , Xie Xihe , Roy Nathan H. , de Jesus Miguel , Jin Weiyang , Lee Joanne H. , Hong Yeonsun , Kim Minsoo , Kam Lance C. , Salaita Khalid , Huse Morgan
Published: October 2021

The secretory output of cell-cell interfaces must be tightly controlled in space and time to ensure functional efficacy. This is particularly true for the cytotoxic immune synapse (IS), the stereotyped junction formed between a cytotoxic lymphocyte and the infected or transformed target cell it aims to destroy1. Cytotoxic lymphocytes kill their targets by channeling a mixture of granzyme proteases and the pore forming protein perforin directly into the IS2, 3. The synaptic secretion of these toxic molecules constrains their deleterious effects to the target cell alone, thereby protecting innocent bystander cells in the surrounding tissue from collateral damage. Despite the importance of this process for immune specificity, the molecular and cellular mechanisms that establish secretory sites within the IS remain poorly understood. Here, we identified an essential role for integrin mechanotransduction in cytotoxic secretion using a combination of single cell biophysical measurements, ligand micropatterning, and functional assays. Upon ligand-binding, the αLβ2integrin LFA-1 functioned as a spatial cue, attracting lytic granules containing perforin and granzyme and inducing their fusion at closely adjacent sites within the synaptic membrane. LFA-1 molecules were subjected to pulling forces within these secretory domains, and genetic or pharmacological suppression of these forces abrogated cytotoxicity. We conclude that lymphocytes employ an integrin-dependent mechanical checkpoint to enhance both the potency and the security of their cytotoxic output.
Solid optical clearing agents based through-Intact-Skull (TIS) window technique for long-term observation of cortical structure and function in mice
Authors: Li Dong-Yu , Hu Zheng-Wu , Zhang Hequn , Zhu Liang , Liu Yin , Yu Ting-Ting , Zhu Jing-Tan , Xi Wang , Qian Jun , Zhu Dan
Published: October 2021

In vivo cortical optical imaging needs to overcome the scattering of skull. Compared to the traditional transcranial surgery-based open-skull glass window and thinned-skull preparation, chemical tissue optical clearing techniques can provide a skull-remained optical access to the brain while maintaining its original environment. However, previously demonstrated skull optical clearing windows could only maintain transparency for a couple of hours and hardly capable for high-resolution monitoring of awake animals. Here, we developed a convenient and easy-handling chronic skull optical clearing technique, named “Through-Intact-Skull (TIS) window”, which was compatible with long-term observation at high resolution, and yielded large imaging depth of 900 μm for cortical neurovascular visualization. In addition, our TIS window could monitor neuron activity in awake mice for a long term. Therefore, our bio-compatible and non-invasive TIS window is a new promising approach for intravital brain microscopy with great potential for basic research in neuroscience.
In VitroActivity of Cysteamine Against SARS-CoV-2 Variants
Authors: Thoene Jess , Gavin Robert F , Towne Aaron , Wattay Lauren , Ferrari Maria Grazia , Pal Ranajit
Published: October 2021

Global COVID-19 pandemic is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Continuous emergence of new variants and their rapid spread are jeopardizing vaccine countermeasures to a significant extent. While currently available vaccines are effective at preventing illness associated with SARS-CoV-2 infection, these have been shown to be less effective at preventing breakthrough infection and transmission from a vaccinated individual to others. Here we demonstrate broad antiviral activity of cysteamine HClin vitroagainst major emergent infectious variants of SARS-CoV-2 in a highly permissible Vero cell line. Cysteamine HCl inhibited infection of wild type, alpha, beta, gamma, delta, lambda, and omicron variants effectively. Cysteamine is a very well-tolerated US FDA-approved drug used chronically as a topical ophthalmic solution to treat ocular cystinosis in patients who receive it hourly or QID lifelong at concentrations 6 to 10 times higher than that required to completely inhibit SARS CoV-2 in tissue culture. Application of cysteamine as a topical nasal treatment can potentially1) mitigate existing infection 2) prevent infection in exposed individuals, and 3) limit the contagion in vulnerable populations.