bluuebunny/crossref_metadata_2025 huggingface dataset:
Craniofacial Dysmorphology in Infants With Non-Syndromic Unilateral Coronal Craniosynostosis
Authors: Bellaire Christopher P. , Devarajan Alex , Napoli James G. , Rutland John W. , Liu Helen , Jacob Laya , Mandelbaum Max , Sayegh Farah , Margulies Ilana G. , Goel Pedram , Delman Bradley N. , Urata Mark M. , Taub Peter J.
Published: January 2022

Background:

Unilateral coronal craniosynostosis (UCS) is a congenital disorder resulting from the premature suture fusion, leading to complex primary and compensatory morphologic changes in the shape of not only the calvarium and but also into the skull base. This deformity typically requires surgery to correct the shape of the skull and prevent neurologic sequelae, including increased intracranial pressure, sensory deficits, and cognitive impairment.

Methods:

The present multicenter study sought to reverse-engineer the bone dysmorphogenesis seen in non-syndromic UCS using a geometric morphometric approach. Computed tomography scans for 26 non-syndromic UCS patients were converted to three-dimensional mesh models. Two hundred thirty-six unique anatomical landmarks and semi-landmarked curves were then plotted on each model, creating wireframe representations of the Patients’ skulls.

Results:

Generalized Procrustes superimposition, Principal Component Analysis, and heatmaps identified significant superior displacement of the ipsilateral orbit (“harlequin” eye deformity), anterior displacement of the ear ipsilateral to the fused coronal suture, acute deviation of midline skull base structures ipsilateral to the fused coronal suture and flattening of the parietal bone and associated failure to expand superiorly.

Conclusions:

The described technique illustrates the impact of premature coronal suture fusion on the development of the entire skull and proposes how bone dysmorphology contributes to the Patients’ neurologic sequelae. By bridging novel basic science methodologies with clinical research, the present study quantitatively describes craniofacial development and bone dysmorphogenesis.
Selection and T-cell antigenicity of synthetic long peptides derived from SARS-CoV-2
Authors: Piadel Katarzyna , Haybatollahi Amin , Dalgleish Angus George , Smith Peter Lawrence
Published: January 2022

The pandemic caused by SARS-CoV-2 has led to the successful development of effective vaccines however the prospect of variants of SARS-CoV-2 and future coronavirus outbreaks necessitates the investigation of other vaccine strategies capable of broadening vaccine mediated T-cell responses and potentially providing cross-immunity. In this study the SARS-CoV-2 proteome was assessed for clusters of immunogenic epitopes restricted to diverse human leucocyte antigen. These regions were then assessed for their conservation amongst other coronaviruses representative of different alpha and beta coronavirus genera. Sixteen highly conserved peptides containing numerous HLA class I and II restricted epitopes were synthesized from these regions and assessed in vitro for their antigenicity against T-cells from individuals with previous SARS-CoV-2 infection. Monocyte derived dendritic cells were generated from these peripheral blood mononuclear cells (PBMC), loaded with SARS-CoV-2 peptides, and used to induce autologous CD4+ and CD8+ T cell activation. The SARS-CoV-2 peptides demonstrated antigenicity against the T-cells from individuals with previous SARS-CoV-2 infection indicating that this approach holds promise as a method to activate anti-SAR-CoV-2 T-cell responses from conserved regions of the virus which are not included in vaccines utilising the Spike protein.
Thalamo-Prefrontal Connectivity Correlates with Early Command Following After Severe Traumatic Brain Injury
Authors: Cosgrove Megan E. , Saadon Jordan R. , Mikell Charles B. , Stefancin Patricia L. , Alkadaa Leor , Wang Zhe , Saluja Sabir , Servider John , Razzaq Bayan , Huang Chuan , Mofakham Sima
Published: January 2022

Recovery of consciousness after traumatic brain injury (TBI) is heterogeneous and difficult to predict. Structures such as the thalamus and prefrontal cortex are thought to be important in facilitating consciousness. We sought to investigate whether the integrity of thalamo-prefrontal circuits, assessed via diffusion tensor imaging (DTI), was associated with the return of goal-directed behavior after severe TBI. We classified a cohort of severe TBI patients (N = 25, 20 males) into Early and Late/Never outcome groups based on their ability to follow commands within 30 days post-injury. We assessed connectivity between whole thalamus, and mediodorsal thalamus (MD), to prefrontal cortex (PFC) subregions including dorsolateral PFC (dlPFC), medial PFC (mPFC), anterior cingulate (ACC), and orbitofrontal (OFC) cortices. We found that the integrity of thalamic projections to PFC subregions (L OFC, L and R ACC, and R mPFC) was significantly associated with Early command-following. This association persisted when the analysis was restricted to prefrontal-mediodorsal (MD) thalamus connectivity. In contrast, dlPFC connectivity to thalamus was not significantly associated with command-following. Using the integrity of thalamo-prefrontal connections, we created a linear regression model that demonstrated 72% accuracy in predicting command-following after a leave-one-out analysis. Together, these data support a role for thalamo-prefrontal connectivity in the return of goal-directed behavior following TBI.
Can single-neuron frequency tuning in human auditory cortex be quantified through fMRI adaptation?
Authors: Besle Julien , Sánchez-Panchuelo Rosa-María , Francis Susan , Krumbholz Katrin
Published: January 2022

Measuring neuronal frequency selectivity in human auditory cortex may be crucial for understanding common auditory deficits such as speech-in-noise difficulty. Non-invasive methods measure aggregate responses of large populations of neurons and therefore overestimate single-neuron tuning selectivity. Here we explore whether cortical frequency selectivity can be estimated through fMRI adaptation. Using ultra-high-field (7T) BOLD-fMRI and individualized functional parcellation of auditory cortex, we measured the suppression (or adaptation) of primary and non-primary cortical responses to a high-frequency (3.8 kHz) probe sound as a function of the frequency of a preceding adaptor sound (ranging from 0.5 to 3.8 kHz). The degree of frequency tuning of the adaptation effect strongly depended on the temporal structure of the adaptor. Suppression by a single 200-ms adaptor showed little or no tuning, despite clear frequency tuning of the responses to the different adaptors. In contrast, suppression by multiple (four) 50-ms adaptor bursts was clearly tuned, with greater frequency selectivity than the adaptor response tuning, suggesting that fMRI adaption to multiple adaptors may reflect the frequency tuning of the underlying neuronal response. Importantly, adaptation tuning differed between primary and non-primary regions, suggesting a local suppression effect, rather than inheritance from upstream subcortical structures. Using a computational model of fMRI adaptation in a tonotopically-organized neuronal array, we identify key factors determining the relationship between observed fMRI adaptation tuning and the frequency selectivity of the underlying neuronal response. Using this model, we derive a plausible range for the frequency selectivity of individual neurons in each region of auditory cortex.
Diversity of cave Phlebotomines (Diptera: Psychodidae) from a Colombian cave
Authors: Velazquez Manuela , Stuckert Adam M. M. , Vivero Rafael J. , Matute Daniel R.
Published: January 2022

Sandflies are vector species ofLeishmania, among many other pathogens, with a global distribution and a variety of ecological niches. Previous samplings have found that karstic formations (i.e., caves and folds formed by the erosion of limestone) serve as a natural habitat to sandfly species. The majority of samplings of cave sandfly diversity have occurred in Brazil and to date none have studied the species composition in a cave in the Northern Andes. We collected sandflies in the Cave “Los Guácharos”, in the state of Antioquia, Colombia. The sampling was carried out during two consecutive nights in September 2019. CDC-type light traps were installed inside the cavern and in other surrounding karst systems (caves and folds). In total, we identified 18 species of sandfly from the cave and surrounding karst systems, including three new records for Colombia (Bichromomyia olmeca nociva, Brumptomyia brumpti, andWarileya leponti), and provide the first karstic reports for four other species (Lutzomyia gomezi, Lutzomyia hartmanni, Pintomyia ovallesi, andPsychodopygus panamensis). We then used the results of our survey and published literature to test two hypotheses. First, that sandfly diversity in Neotropical caves is richest nearer to the equator and second that there is a phylogenetic signal of karstic habitat use in sandflies. Counter to our predictions, we found no evidence that diversity follows a latitudinal gradient. Further, we find no evidence of a phylogenetic signal of karstic habitat use, instead finding that the use of caves likely evolved multiple times across several genera. Our results highlight the importance of a wide sampling to understand the natural habitat of sandflies and other disease vectors.
Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2
Authors: Saunders Nell , Planas Delphine , Bolland William , Rodriguez Christophe , Fourati Slim , Buchrieser Julian , Planchais Cyril , Prot Matthieu , Staropoli Isabelle , Guivel-Benhassine Florence , Porrot Françoise , Veyer David , Péré Hélène , Robillard Nicolas , Saliba Madelina , Baidaliuk Artem , Seve Aymeric , Hocqueloux Laurent , Prazuck Thierry , Mouquet Hugo , Simon-Lorière Etienne , Bruel Timothée , Pawlotsky Jean-Michel , Schwartz Olivier
Published: January 2022

SARS-CoV-2 lineages are continuously evolving. As of December 2021, the AY.4.2 Delta sub-lineage represented 20 % of sequenced strains in UK and has been detected in dozens of countries. It has since then been supplanted by the Omicron variant. AY.4.2 displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain (NTD) of the spike when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. Here, we analyzed the fusogenicity of the AY.4.2 spike and the sensitivity of an authentic AY.4.2 isolate to neutralizing antibodies. The AY.4.2 spike exhibited similar fusogenicity and binding to ACE2 than Delta. The sensitivity of infectious AY.4.2 to a panel of monoclonal neutralizing antibodies was similar to Delta, except for the anti-RBD Imdevimab, which showed incomplete neutralization. Sensitivity of AY.4.2 to sera from individuals having received two or three doses of Pfizer or two doses of AstraZeneca vaccines was reduced by 1.7 to 2.1 fold, when compared to Delta. Our results suggest that mutations in the NTD remotely impair the efficacy of anti-RBD antibodies. The temporary spread of AY.4.2 was not associated with major changes in spike function but rather to a partially reduced neutralization sensitivity.
Functionally distinct BMP1 isoforms show an opposite pattern of abundance in plasma from non-small cell lung cancer subjects and controls
Authors: Donovan Margaret K. R. , Huang Yingxiang , Blume John E. , Wang Jian , Hornburg Daniel , Ferdosi Shadi , Mohtashemi Iman , Kim Sangtae , Ko Marwin , Benz Ryan W. , Platt Theodore L. , Batzoglou Serafim , Diaz Luis A. , Farokhzad Omid C. , Siddiqui Asim
Published: January 2022

Advancements in deep plasma proteomics are enabling high-resolution measurement of plasma proteoforms, which may reveal a rich source of novel biomarkers previously concealed by aggregated protein methods. Here, we analyze 188 plasma proteomes from non-small cell lung cancer subjects (NSCLC) and controls to identify NSCLC-associated protein isoforms by examining differentially abundant peptides as a proxy for isoform-specific exon usage. We find four proteins comprised of peptides with opposite patterns of abundance between cancer and control subjects. One of these proteins, BMP1, has known isoforms that can explain this differential pattern, for which the abundance of the NSCLC-associated isoform increases with stage of NSCLC progression. The presence of cancer and control-associated isoforms suggests differential regulation of BMP1 isoforms. The identified BMP1 isoforms have known functional differences, which may reveal insights into mechanisms impacting NSCLC disease progression.
Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses
Authors: Rodríguez-Rodríguez Juanita C. , Bergeron Yves , Kembel Steven W. , Fenton Nicole J.
Published: January 2022

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species, but may also be shaped by environmental conditions related with tree-canopy dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree-canopy dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberiandPtilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. Forest type, not host species, was the main factor affecting moss phyllosphere bacterial community composition, though the interaction of both variables was significant. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β- diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the bacterial family Nostocaceae (Cyanobacteria) differing the most between both forest types. Our results suggest that the increasing change in dominance from coniferous to broadleaf trees due to natural and anthropic disturbances is likely to affect the composition of moss-associated bacteria in boreal forests.
Molecular Structure Study on the Polyelectrolyte Properties of Actin Filaments
Authors: Manrique-Bedoya Santiago , Marucho Marcelo
Published: January 2022

An accurate characterization of the polyelectrolyte properties of actin filaments might provide a deeper understanding of the fundamental mechanisms governing the intracellular ionic wave packet propagation in neurons. Infinitely long cylindrical models for actin filaments and approximate electrochemical theories for the electrolyte solutions were recently used to characterize these properties in in vitro and intracellular conditions. This article uses a molecular structure model for actin filaments to investigate the impact of roughness and finite size on the mean electrical potential, ionic density distributions, currents, and conductivities. We solved the electrochemical theories numerically without further approximations. Our findings bring new insights into the electrochemical interactions between a filament’s irregular surface charge density and the surrounding medium. The irregular shape of the filament structure model generated pockets, or hot spots, where the current density reached higher or lower magnitudes than those in neighboring areas throughout the filament surface. It also revealed the formation of a well-defined asymmetric electrical double layer with a thickness larger than that commonly used for symmetric models.
An NMR fingerprint matching approach for the identification and structural re-evaluation ofPseudomonaslipopeptides
Authors: De Roo Vic , Verleysen Yentl , Kovács Benjámin , Matthias De Vleeschouwer , Girard Léa , Höfte Monica , De Mot René , Madder Annemieke , Geudens Niels , Martins José C.
Published: January 2022

Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs fromPseudomonasin particular display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity and stereochemistry (e.g. D- vs. L-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. UsingPseudomonasCLiPs from the Bananamide, Orfamide and Xantholysin groups as test cases, we demonstrate and validate that1H and13C NMR chemical shifts of CLiPs are sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single D/L configuration. Rapid screening, involving simple comparison of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, NMR fingerprinting still allows verifying whether a CLiP from a novel source is already present in the reference collection, thus contributing to dereplication. To benefit research involving CLiPs, we have made a publicly available ‘knowledge base’ athttps://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures.

Significance Statement

PseudomonasCLiPs, are ubiquitous specialized metabolites, impacting the producer’s lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as premise to their development is hindered because full structural characterization including stereochemistry requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology for structural comparison of newly isolated CLiPs to reference compounds with (un)known stereochemistry based on NMR fingerprints. The reference compound database available for the wide scientific community promises to facilitate structural assessment and dereplication of newly isolated CLiPs, and to support genome mining for novel CLiPs.
Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies
Authors: Forchielli Elena , Sher Daniel , Segrè Daniel
Published: January 2022

Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a “black box”, which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically-relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of inter-species interactions.

Importance

Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon (DOC). Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.
HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain’s allostery and unfolding upon B12 and TonB binding
Authors: Zmyslowski Adam M. , Baxa Michael C. , Gagnon Isabelle A. , Sosnick Tobin R.
Published: January 2022

To import large metabolites across the outer membrane of Gram-negative bacteria, TonB dependent transporters (TBDTs) undergo significant conformational change. After substrate binding in BtuB, the E. coli vitamin B12 TBDT, TonB binds and couples BtuB to the inner membrane proton motive force that powers transport (1). But, the role of TonB in rearranging the plug domain to form a putative pore remains enigmatic. Some studies focus on force-mediated unfolding (2) while others propose force-independent pore formation (3) by TonB binding leading to breakage of a salt bridge termed the “Ionic Lock”. Our hydrogen exchange/mass spectrometry measurements in E. coli outer membranes find that the region surrounding the Ionic Lock, far from the B12 site, is fully destabilized upon substrate binding. A comparison of the exchange between the B12 bound and the B12&TonB bound complexes indicates that B12 binding is sufficient to unfold the Ionic Lock region with the subsequent binding of a TonB fragment having much weaker effects. TonB binding accelerates exchange in the third substrate binding loop, but pore formation does not obviously occur in this or any region. This study provides a detailed structural and energetic description of the early stages of B12 passage that provides support both for and against current models of the transport process.

Significance Statement

TonB dependent transporters such as BtuB are found in the outer membranes of Gram-negative bacteria. They import scarce nutrients essential for growth, such as B12, the substrate of BtuB. Many transport steps remain enigmatic. Recent studies have emphasized force-mediated unfolding or the breakage of the “Ionic Lock”, a moiety far from the B12 binding site. A strong dependence on the membrane environment has been noted. Accordingly, we measured hydrogen exchange on BtuB still embedded in native outer membranes and found that B12 binding is sufficient to break the Ionic Lock. The amino terminus then extends into the periplasm to bind TonB. But we find no evidence of pore formation, which likely requires energy transduction from the inner membrane by TonB.
Quantification of salt stress in wheat leaves by Raman spectroscopy and machine learning
Authors: Kecoglu Ibrahim , Sirkeci Merve , Unlu Mehmet Burcin , Sen Ayse , Parlatan Ugur , Guzelcimen Feyza
Published: January 2022

The salinity level of the growing medium has diverse effects on the development of plants, including both physical and biochemical changes. To determine the salt stress level of a plant endures, one can measure these structural and chemical changes. Raman spectroscopy and biochemical analysis are some of the most common techniques in the literature. Here, we present a combination of machine learning and Raman spectroscopy with which we can both find out the biochemical change that occurs while the medium salt concentration changes and predict the level of salt stress a wheat sample experiences accurately using our trained regression models. In addition, by applying different machine learning algorithms, we compare the level of success for different algorithms and determine the best method to use in this application. Production units can take actions based on the quantitative information they get from the trained machine learning models related to salt stress, which can potentially increase efficiency and avoid the loss of crops.
A single amino acid substitution in PB1 of pandemic H1N1 with A/Ann Arbor/6/60 master donor virus mutations as a novel live-attenuated influenza virus vaccine
Authors: Nogales Aitor , Steel John , Liu Wen-Chun , Lowen Anice C. , Rodriguez Laura , Chiem Kevin , Cox Andrew , García-Sastre Adolfo , Albrecht Randy A. , Dewhurst Stephen , Martínez-Sobrido Luis
Published: January 2022

Influenza A viruses (IAV) remain emerging threats to human public health. Live-attenuated influenza vaccines (LAIV) are one of the most effective prophylactic options to prevent disease caused by influenza infections. However, licensed LAIV remain restricted for use in 2- to 49-year old healthy and non-pregnant people. Therefore, development of LAIV with increased safety, immunogenicity, and protective efficacy is highly desired. The United States (U.S.) licensed LAIV is based on the master donor virus (MDV) A/Ann Arbor/6/60 H2N2 backbone, which was generated by adaptation of the virus to growth at low temperatures. Introducing the genetic signature of the U.S. MDV into the backbone of other IAV strains resulted in varying levels of attenuation. While the U.S. MDV mutations conferred an attenuated phenotype to other IAV strains, the same amino acid changes did not significantly attenuate the pandemic A/California/04/09 H1N1 (pH1N1) strain. To attenuate pH1N1, we replaced the conserved leucine at position 319 with glutamine (L319Q) in PB1 and analyzed the in vitro and in vivo properties of pH1N1 viruses containing either PB1 L319Q alone or in combination with the U.S. MDV mutations using two animal models of influenza infection and transmission, ferrets and guinea pigs. Our results demonstrated that L319Q substitution in the pH1N1 PB1 alone or in combination with the mutations of the U.S. MDV resulted in reduced pathogenicity (ferrets) and transmission (guinea pigs), and an enhanced temperature sensitive phenotype. These results demonstrate the feasibility of generating an attenuated MDV based on the backbone of a contemporary pH1N1 IAV strain.

IMPORTANCE

Vaccination represents the most effective strategy to reduce the impact of seasonal IAV infections. Although LAIV are superior in inducing protection and sterilizing immunity, they are not recommended for many individuals who are at high risk for severe disease. Thus, development of safer and more effective LAIV are needed. A concern with the current MDV used to generate the U.S. licensed LAIV is that it is based on a virus isolated in 1960. Moreover, mutations that confer the temperature sensitive, cold-adapted, and attenuated phenotype of the U.S. MDV resulted in low level of attenuation in the contemporary pandemic A/California/04/09 H1N1 (pH1N1). Here, we show that introduction of PB1 L319Q substitution, alone or in combination with the U.S. MDV mutations, resulted in pH1N1 attenuation. These findings support the development of a novel LAIV MDV based on a contemporary pH1N1 strain as a medical countermeasure against currently circulating H1N1 IAV.
Anterior Cingulate Metabolite Levels, Memory, and Inhibitory Control in Abstinent Men and Women with Alcohol Use Disorder
Authors: Oot Emily N. , Sawyer Kayle S. , Oscar-Berman Marlene , Luhar Riya B. , Jensen J.E. , Silveri Marisa M.
Published: January 2022

Aims

Alcohol use disorder (AUD), has been shown to have harmful cognitive and physiological effects, including altered brain chemistry. Further, although men and women may differ in vulnerability to the neurobiological effects of AUD, results of existing studies have been conflicting. Brain metabolite levels and cognitive functions were examined in a cross section of men with AUD (AUDm) and women with AUD (AUDw) to determine degree of abnormalities after extended periods of abstinence (mean, six years), and to evaluate gender differences in cognitive and metabolite measures.

Methods

Participants were 40 abstinent individuals with AUD (22 AUDw, 18 AUDm) and 50 age-equivalent non-AUD comparison participants (26 NCw, 24 NCm). Proton magnetic resonance spectroscopy (MRS) was employed at 3 Tesla to acquire metabolite spectra from the dorsal anterior cingulate cortex (dACC). Brain metabolites N-acetylaspartate (NAA), choline (Cho), myo-Inositol (mI), and glutamate & glutamine (Glx) were examined relative to measures of memory and inhibitory control.

Results

Metabolite levels in the AUD group showed no significant differences from the NC group. Memory and inhibitory-control impairments were observed in the AUD group. There also were significant group-specific associations between metabolite ratios and measures of inhibitory control. There were no Group-by-Gender interactions for the four metabolite ratios.

Conclusions

These findings demonstrate that brain metabolite levels in men and women with AUD, following long-term abstinence, do not differ from individuals without AUD. The data also provide evidence of associations between metabolite levels and measures of inhibitory control, a functional domain important for curtailing harmful drinking.
Radiofrequency ablation remodels the tumor microenvironment and promotes systemic immunomodulation in pancreatic cancer
Authors: Faraoni Erika Y. , Thosani Nirav C. , O’Brien Baylee , Strickland Lincoln N. , Mota Victoria , Chaney Jarod , Cen Putao , Rowe Julie , Cardenas Jessica , Poulsen Kyle L. , Wray Curtis J. , Bailey-Lundberg Jennifer
Published: January 2022

Background and Aims

Pancreatic ductal adenocarcinoma (PDAC) is characterized by resistance to therapy. A major contributing factor to therapeutic failure is profound desmoplasia and a well-documented hypoxic tumor microenvironment (TME). In PDAC, several therapeutic approaches, including chemotherapy and radiation alone or combined with immune checkpoint inhibitors, have shown minimal therapeutic success, placing an imperative need for the discovery and application of innovative treatments. Endoscopic ultrasound guided radiofrequency ablation (EUS-RFA) is a promising immunomodulator therapy for PDAC. In this work, we hypothesized RFA promotes local and systemic stromal and immunomodulating effects that can be identified for new combination therapeutic strategies.

Methods

To test our hypothesis, a syngeneic PDAC mouse model was performed by symmetrically injecting 100k murine KPC cells in bilateral flanks of C57BL/6 female mice. RFA treatment initiated when tumors reached 200-500 mm3 and was performed only in the right flank. The left flank tumor (non-RFA contralateral side) was used as a paired control for further analysis.

Results

RFA promoted a significant reduction in tumor growth rate 4 days after treatment in RFA treated and non-RFA side contralateral tumors from treated mice when compared to controls. Histological analysis revealed a significant increase in expression of cleaved Caspase3 in RFA treated tumors. In addition, collagen deposition and CD31+ cells were significantly elevated in RFA side and non-RFA contralateral tumors from RFA treated mice. Proteome profiling showed changes in C5a and IL-23 in RFA responsive tumors, indicating a role of RFA in modulating intratumoral inflammatory responses.

Conclusions

These data indicate RFA promotes local and systemic anti-tumor responses in a syngeneic mouse model of PDAC implicating RFA treatment for local tumors as well as metastatic disease.

Graphical Abstract
Liquid-liquid phase separation of the chromosomal passenger complex drives parallel bundling of midzone microtubules
Authors: Niedzialkowska Ewa , Truong Tan M. , Eldredge Luke A. , Redemann Stefanie , Chretien Denis , Stukenberg P. Todd
Published: January 2022

The spindle midzone is a dynamic structure that forms during anaphase, mediates chromosome segregation, and provides a signaling platform to position the cleavage furrow. The spindle midzone comprises two antiparallel bundles of microtubules (MTs) but the process of their formation is poorly understood. Here, we show that the Chromosomal Passenger Complex (CPC) undergoes liquid-liquid phase separation (LLPS) to generate parallel MT bundles in vitro when incubated with free tubulin and GTP. MT bundles emerge from CPC droplets with protruding minus-ends that then grow into long, tapered MT structures. During this growth, the CPC in condensates apparently reorganize to coat and bundle the resulting MT structures. CPC mutants attenuated for LLPS or MT binding prevented the generation of parallel MT bundles in vitro and reduced the number of MTs present at spindle midzones in HeLa cells. Our data uncovers a kinase-independent function of the CPC and provides models for how cells generate parallel-bundled MT structures that are important for the assembly of the mitotic spindle.
Enhanced competitive protein exchange at the nano-bio interface enables ultra-deep coverage of the human plasma proteome
Authors: Hornburg Daniel , Ferdosi Shadi , Hasan Moaraj , Tangeysh Behzad , Brown Tristan R. , Wang Tianyu , Elgierari Eltaher M. , Zhao Xiaoyan , Alavi Amir , Chu Jessica , Figa Mike , Tao Wei , Wang Jian , Goldberg Martin , Xia Hongwei , Stolarczyk Craig , Batzoglou Serafim , Siddiqui Asim , Farokhzad Omid C.
Published: January 2022

We have developed a scalable system that leverages protein-nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Introducing proprietary engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle-protein interface, driven by the relationship between protein-NP affinity and protein abundance. Here we demonstrate the importance of tuning the protein to NP-surface ratio (P/NP), which determines the competition between proteins for binding. We demonstrate how optimized P/NP ratio affects protein corona composition, ultimately enhancing performance of a fully automated NP-based deep proteomic workflow (Proteograph). By limiting the available binding surface of NPs and increasing the binding competition, we identify 1.2 – 1.7x more proteins with only 1% false discovery rate on the surface of each NP, and up to 3x compared to a standard neat plasma proteomics workflow. Moreover, increased competition means proteins are more consistently identified and quantified across replicates, yielding precise quantification and improved coverage of the plasma proteome when using multiple physicochemically distinct NPs. In summary, by optimizing NPs and assay conditions, we capture a larger and more diverse set of proteins, enabling deep proteomic studies at scale.
A visual atlas of genes’ tissue-specific pathological roles
Authors: Rai Priyadarshini , Jain Atishay , Jha Neha , Sharma Divya , Kumar Shivani , Raj Abhijit , Gupta Apoorva , Poonia Sarita , Chawla Smriti , Majumdar Angshul , Chakraborty Tanmoy , Ahuja Gaurav , Sengupta Debarka
Published: January 2022

Dysregulation of a gene’s function, either due to mutations or impairments in regulatory networks, often triggers pathological states in the affected tissue. Comprehensive mapping of these apparent gene-pathology relationships is an ever daunting task, primarily due to genetic pleiotropy and lack of suitable computational approaches. With the advent of high throughput genomics platforms and community scale initiatives such as the Human Cell Landscape (HCL) project [1], researchers have been able to create gene expression portraits of healthy tissues resolved at the level of single cells. However, a similar wealth of knowledge is currently not at our finger-tip when it comes to diseases. This is because the genetic manifestation of a disease is often quite heterogeneous and is confounded by several clinical and demographic covariates. To circumvent this, we mined ~18 million PubMed abstracts published till May 2019 and selected ~6.1 million of them that describe the pathological role of genes in different diseases. Further, we employed a word embedding technique from the domain of Natural Language Processing (NLP) to learn vector representation of entities such as genes, diseases, tissues, etc., in a way such that their relationship is preserved in a vector space. Notably, Pathomap, by the virtue of its underpinning theory, also learns transitive relationships. Pathomap provided a vector representation of words indicating a possible association between DNMT3A/BCOR with CYLD cutaneous syndrome (CCS). The first manuscript reporting this finding was not part of our training data.

Key points

We mined ~18 million PubMed abstracts to extract latent knowledge pertaining to tissue specific pathological roles of genes.

We found well-defined gene modules implicated in disease pathogenesis in anatomically proximal tissues.

We demonstrated an ahead of time discovery of the association between DNMT3A/BCOR with CYLD cutaneous syndrome (CCS), as a knowledge synthesis use-case.
Two-photon patterned photostimulation with low-power, high-efficiency and reliable single-cell optogenetic control
Authors: Wang Yifan , Zheng Yao , Xu Yongxian , Li Rongrong , Zheng Yameng , Chen Jiajia , Li Xiaoming , Hu Hailan , Duan Shumin , Gong Wei , Si Ke
Published: January 2022

Two-photon optogenetics enables selectively stimulating individual cells for manipulating neuronal ensembles. As the general photostimulation strategy, the patterned two-photon excitation has enabled millisecond-timescale activation for single or multiple neurons, but its activation efficiency is suffered from high laser power due to low beam-modulation efficiency. Here, we develop a high- efficiency beam-shaping method based on the Gerchberg-Saxton (GS) algorithm with spherical-distribution initial phase (GSSIP) to reduce the patterned two-photon excitation speckles and intensity. It can well control the phase of shaped beams to attain speckle-free accurate patterned illumination with an improvement of 44.21% in the modulation efficiency compared with that of the traditional GS algorithm. A combination of temporal focusing and the GSSIP algorithm (TF-GSSIP) achieves patterned focusing through 500-μm-thickness mouse brain slices, which is 2.5 times deeper than the penetration depth of TF-GS with the same signal-to-noise ratio (SNR). With our method, the laser power can be reduced to only 55.56% of that with traditional method (the temporal focusing with GS, TF-GS) to reliably evoke GCaMP6s response in C1V1-expressing cultured neurons with single-cell resolution. Besides, the photostimulation efficiency is remarkably increased by 80.19% at the same excitation density of 0.27 mW/μm2. This two-photon stimulation method with low-power, reliable and patterned illumination may pave the way for analyzing neural circuits and neural coding and decoding mechanism.
Validating amino acid variants in proteogenomics using sequence coverage by multiple reads
Authors: Levitsky L.I. , Kuznetsova K.G. , Kliuchnikova A.A. , Ilina I.Y. , Goncharov A.O. , Lobas A.A. , Ivanov M.V. , Lazarev V.N. , Ziganshin R.H. , Gorshkov M.V. , Moshkovskii S.A.
Published: January 2022

Mass spectrometry-based proteome analysis usually implies matching mass spectra of proteolytic peptides to amino acid sequences predicted from nucleic acid sequences. At the same time, due to the stochastic nature of the method when it comes to proteome-wide analysis, in which only a fraction of peptides are selected for sequencing, the completeness of protein sequence identification is undermined. Likewise, the reliability of peptide variant identification in proteogenomic studies is suffering. We propose a way to interpret shotgun proteomics results, specifically in data-dependent acquisition mode, as protein sequence coverage by multiple reads, just as it is done in the field of nucleic acid sequencing for the calling of single nucleotide variants. Multiple reads for each position in a sequence could be provided by overlapping distinct peptides, thus, confirming the presence of certain amino acid residues in the overlapping stretch with much lower false discovery rate than conventional 1%. The source of overlapping distinct peptides are, first, miscleaved tryptic peptides in combination with their properly cleaved counterparts, and, second, peptides generated by several proteases with different specificities after the same specimen is subject to parallel digestion and analyzed separately. We illustrate this approach using publicly available multiprotease proteomic datasets and our own data generated for HEK-293 cell line digests obtained using trypsin, LysC and GluC proteases. From 5000 to 8000 protein groups are identified for each digest corresponding to up to 30% of the whole proteome coverage. Most of this coverage was provided by a single read, while up to 7% of the observed protein sequences were covered two-fold and more. The proteogenomic analysis of HEK-293 cell line revealed 36 peptide variants associated with SNP, seven of which were supported by multiple reads. The efficiency of the multiple reads approach depends strongly on the depth of proteome analysis, the digesting features such as the level of miscleavages, and will increase with the number of different proteases used in parallel proteome digestion.

Graphical abstract
RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro
Authors: Qi Shan , Mota Javier , Chan Siu-Hong , Villarreal Johanna , Dai Nan , Arya Shailee , Hromas Robert A. , Rao Manjeet K. , Corrêa Ivan R. , Gupta Yogesh K.
Published: January 2022

Methyltransferase like-3 (METTL3) and METTL14 complex transfers a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights a role of METTL3-METTL14 in the chromatin context, especially in processes where DNA and RNA are held in close proximity. However, a mechanistic framework about specificity for substrate RNA/DNA and their interrelationship remain unclear. By systematically studying methylation activity and binding affinity to a number of DNA and RNA oligos with different propensities to form inter- or intra-molecular duplexes or single-stranded molecules in vitro, we uncover an inverse relationship for substrate binding and methylation and show that METTL3-METTL14 preferentially catalyzes the formation of m6dA in single-stranded DNA (ssDNA), despite weaker binding affinity to DNA. In contrast, it binds structured RNAs with high affinity, but methylates the target adenosine in RNA (m6A) much less efficiently than it does in ssDNA. We also show that METTL3-METTL14-mediated methylation of DNA is largely regulated by structured RNA elements prevalent in long noncoding and other cellular RNAs.
Characterizing the performance of a DIY air filter
Authors: Porto Rachael Dal , Kunz Monet N. , Pistochini Theresa , Corsi Richard L. , Cappa Christopher D.
Published: January 2022

Air filtration serves to reduce concentrations of particles in indoor environments. Most standalone, also referred to as portable or in-room, air filtration systems use HEPA filters, and cost generally scales with the clean air delivery rate. A “do-it-yourself” lower-cost alternative, known as the Corsi-Rosenthal Box, that uses MERV-13 filters coupled with a box fan has been recently proposed, but lacks systematic performance characterization. We have characterized the performance of a five-panel Corsi-Rosenthal air filter. Measurements of size-resolved and overall decay rates of aerosol particles larger than 0.5 microns emitted into rooms of varying size with and without the air filter allowed for determination of the apparent clean air delivery rate—both as a function of size and integrated across particle sizes. The measurements made in the different rooms produced similar results, demonstrating the robustness of the method used. The size-integrated apparent clean air delivery rate increases with fan speed, from about 600 to 850 ft3 min−1 (1019 to 1444 m3 h−1). Overall, our results demonstrate that the Corsi-Rosenthal filter efficiently reduces suspended particle concentrations in indoor environments.

One Sentence Summary

A DIY air cleaner can effectively reduce aerosols in indoor spaces.
Transient interactions drive the lateral clustering of cadherin-23 on membrane
Authors: Srinivas Cheerneni S , Singaraju Gayathri S , Kaur Veerpal , Das Sayan , Ghosh Sanat K. , Sagar Amin , Kumar Anuj , Bhatia Tripta , Rakshit Sabyasachi
Published: January 2022

Cis and trans-interactions among cadherins secure multicellularity. While the molecular structure of trans-interactions of cadherins is well understood, identifying the molecular cues that spread the cis-interactions two-dimensionally is still ongoing. Here, we report that transient, weak, multivalent, and spatially distributed hydrophobic interactions, requisite for liquid-liquid phase separations of biomolecules in solution, alone can drive the lateral-clustering of cadherin-23 on a membrane. No specific cis-dimer interactions are required for the lateral clustering. In cellulo, the cis-clustering accelerates the cell-cell adhesion and, thus, contributes in cell-adhesion kinetics along with strengthening the junction. Although the physiological connection of cis-clustering with rapid adhesion is yet to be explored, M2-macrophages that predominantly express cadherin-23 undergo fast attachments to circulatory tumor cells during metastasis.
Long-term two-photon imaging of spinal cord in freely behaving mice
Authors: Ju Furong , Jian Wenling , Han Yaning , Huang Tianwen , Ke Jin , Liu Zhiheng , Cai Shengyuan , Liu Nan , Wang Liping , Wei Pengfei
Published: January 2022

The spinal cord is critical to the perception of peripheral information under sensory-guided motor behaviors in health and disease. However, the cellular activity underlie spinal cord function in freely behaving animals is not clear. Here, we developed a new method for imaging the spinal cord at cellular and subcellular resolution over weeks under naturalistic conditions. The method involves an improved surgery to reduce spinal movement, and the installation of a miniaturized two-photon microscope to obtain high-resolution imaging in moving mice. In vivo calcium imaging demonstrated that dorsal horn neurons show a sensorimotor program-dependent synchronization and heterogeneity under distinct cutaneous stimuli in behaving mice. The long-term imaging of sensory neurons revealed that in the spinal cord, healthy mice demonstrated stereotyped responses. However, in a neuropathic pain model, plasticity changes and neuronal sensitization were observed. We provide a practical method to study the function of spinal cord on sensory perception and disorders in freely behaving mice.