bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extending the dynamic range of biomarker quantification through molecular equalization
Authors: Newman Sharon S. , Wilson Brandon D. , Mamerow Daniel , Wollant Benjamin , Nyein Hnin , Rosenberg-Hasson Yael , Maecker Holden T. , Eisenstein Michael , Soh H. Tom 
Published: February 2023

AbstractPrecision medicine requires highly scalable methods of multiplexed biomarker quantification that can accurately describe patient physiology. Unfortunately, contemporary molecular detection methods are generally limited to a dynamic range of sensitivity spanning just 3–4 orders of magnitude, whereas the actual physiological dynamic range of the human plasma proteome spans more than 10 orders of magnitude. Current methods rely on sample splitting and differential dilution to compensate for this mismatch, but such measures greatly limit the reproducibility and scalability that can be achieved—in particular, the effects of non-linear dilution can greatly confound the analysis of multiplexed assays. We describe here a two- pronged strategy for equalizing the signal generated by each analyte in a multiplexed panel, thereby enabling simultaneous quantification of targets spanning a wide range of concentrations. We apply our ‘EVROS’ strategy to a proximity ligation assay and demonstrate simultaneous quantification of four analytes present at concentrations spanning from low femtomolar to mid-nanomolar levels. In this initial demonstration, we achieve a dynamic range spanning seven orders of magnitude in a single 5 µl sample of undiluted human serum, highlighting the opportunity to achieve sensitive, accurate detection of diverse analytes in a highly multiplexed fashion.
Paracrine enhancement of tumor cell proliferation provides indirect stroma-mediated chemoresistance via acceleration of tumor recovery between chemotherapy cycles
Authors: Miroshnychenko Daria , Miti Tatiana , Kumar Pragya , Miller Anna , Laurie Mark , Giraldo Nathalia , Bui Marilyn M. , Altrock Philipp M. , Basanta David , Marusyk Andriy 
Published: February 2023

AbstractThe ability of tumors to survive therapy reflects both cell-intrinsic and microenvironmental mechanisms. Across many cancers, including triple-negative breast cancer (TNBC), a high stroma/tumor ratio correlates with poor survival. In many contexts, this correlation can be explained by the direct reduction of therapy sensitivity by stroma-produced paracrine factors. We sought to explore whether this direct effect contributes to the link between stroma and poor responses to chemotherapies. Ourin vitrostudies with panels of TNBC cell line models and stromal isolates failed to detect a direct modulation of chemoresistance. At the same time, consistent with prior studies, we observed treatment-independent enhancement of tumor cell proliferation by fibroblast-produced secreted factors. Using spatial statistics analyses, we found that proximity to stroma is often associated with enhanced tumor cell proliferationin vivo. Based on these observations, we hypothesized an indirect link between stroma and chemoresistance, where stroma-augmented proliferation potentiates the recovery of residual tumors between chemotherapy cycles. To evaluate the feasibility of this hypothesis, we developed a spatial agent-based model of stroma impact on proliferation/death dynamics. The model was quantitatively parameterized using inferences from histological analyses and experimental studies. We found that the observed enhancement of tumor cell proliferation within stroma-proximal niches can enable tumors to avoid elimination over multiple chemotherapy cycles. Therefore, our study supports the existence of a novel, indirect mechanism of environment-mediated chemoresistance that might contribute to the negative correlation between stromal content and poor therapy outcomes.
Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT)
Authors: Ansari Saad , Gergely Zachary R. , Flynn Patrick , Li Gabriella , Moore Jeffrey K. , Betterton Meredith D. 
Published: February 2023

AbstractFluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non-linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite development of automated microtubule analysis tools forin vitrostudies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that is solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes severalS. pombemutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work, and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules inS. cerevisiae, with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells.
Shared evolutionary processes shape landscapes of genomic variation in the great apes
Authors: Rodrigues Murillo F. , Kern Andrew D. , Ralph Peter L. 
Published: February 2023

AbstractFor at least the past five decades population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modelling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways. In this paper, we describe how diversity and divergence between closely related species change with time, using correlations between landscapes of genetic variation as a tool to understand the interplay between evolutionary processes. We find strong correlations between landscapes of diversity and divergence in a well sampled set of great ape genomes, and explore how various processes such as incomplete lineage sorting, mutation rate variation, GC-biased gene conversion and selection contribute to these correlations. Through highly realistic, chromosome-scale, forward-in-time simulations we show that the landscapes of diversity and divergence in the great apes are too well correlated to be explained via strictly neutral processes alone. Our best fitting simulation includes both deleterious and beneficial mutations in functional portions of the genome, in which 9% of fixations within those regions is driven by positive selection. This study provides a framework for modelling genetic variation in closely related species, an approach which can shed light on the complex balance of forces that have shaped genetic variation.
Separation of function mutations in microcephaly protein CPAP/CENPJ, reveal its role in regulating centriole number and length
Authors: Jaiswal Sonal , Sanghi Srishti , Singh Priyanka 
Published: February 2023

ABSTRACTCentriole are microtubule-based cylindrical structures characterized by their definite size, and stable, slow growing microtubules. The centriole core protein CPAP/CENPJ is known to act as a molecular cap regulating centriole length by interacting with microtubule/tubulinviathe conserved microtubule destabilizing, PN2-3, and microtubule stabilizing, A5N, domains. The C-terminus of CPAP has a conserved glycine-rich G-box/TCP domain (1050-1338 amino acids). This region is involved in centriole cartwheel assembly by interacting with the cartwheel protein STIL. However, previously reported primary microcephaly mutation mapped in the G-box of CPAP, i.e., E1235V (MCPH6) affects centriole lengthviaan unknown mechanism. Recently, another primary microcephaly mutation has been mapped to this region of CPAP, i.e., D1196N. However, the effect of D1196N on CPAP functioning is not known. We simultaneously characterized these two MCPH mutations in the G-box of CPAP. We identified that despite affecting the same domain of CPAP, they affect distinct CPAP functions at the centriole. The E1235V mutation caused an overly long centriole, and the D1196N mutation increased the centriole number. Interestingly, both these mutations affect CPAP direct interaction with the cartwheel protein STIL, which is involved in CPAP recruitment to the centriole. Accordingly, the CPAP E1235V centriole localization is significantly affected at the centriole. However, CPAP D1196N can still localize to centriole at levels comparable to the wild-type CPAP. We show that CPAP utilizes an alternate CEP152-dependent route for centriole recruitment. Importantly, our work highlights the importance of the CPAP region outside direct microtubule/tubulin interacting domains in influencing CPAP activity in cartwheel assembly and centriole length. Perhaps, this is why deleterious naturally occurring missense mutations are frequently occurring in this particular region of CPAP in primary microcephaly.
The Limits of Touch: Spatial acuity for frequency-resolved air-borne ultrasound vibrotactile stimuli
Authors: Cataldo Antonio , Frier William , Haggard Patrick 
Published: February 2023

SummarySpatial acuity is a fundamental property of any sensory system. In the case of the somatosensory system, the two-point discrimination (2PD) test has long been used to investigate the spatial resolution of tactile perception. The somatosensory system comprises multiple mechanoreceptive channels, each tuned to specific vibrotactile frequencies. In particular, the rapidly adapting channel (RA) responds to low-frequency vibration and is thought to have high spatial acuity. The Pacinian channel (PC) responds to high-frequency vibration and is thought to convey little or no spatial information. However, the mechanical stimulations used in most 2PD tests make it difficult to disentangle the contribution of each mechanoreceptive channel to spatial tactile perception. Here we developed a novel 2PD test based on ultrasound stimulation to deliver frequency-resolved vibrotactile stimuli designed to preferentially activate specific tactile channels. Across four experiments, we systematically investigated the spatial resolution of the two main vibrotactile channels. Contrary to the textbook view of poor spatial resolution for PC-like stimuli, we found that high-frequency vibration produced surprisingly good spatial acuity. This effect remained after controlling for differences between the channels in stimulus detectability and perceived intensity. Laser doppler vibrometry experiments confirmed that the acuity of the PC channel was not simply an artifact of the skin’s resonance to high-frequency mechanical stimulation. Thus, PC receptors may transmit substantial spatial information, despite their sparse distribution, deep location, and large receptive fields.
Mass spectrometric analysis and biostimulatory effects of boar seminal gel, saliva and semen in pigs
Authors: Kumar Sunil , Islam Rafiqul , Chanda Anesha , Das Pranab Jyoti , Banik Santanu , Barman Keshab , Pegu Seema Rani , Rajkhowa Swaraj , Gupta Vivek Kumar 
Published: February 2023

ABSTRACTThe present study aimed to identify novel biostimulatory compounds in boar seminal gel (SG), saliva and semen using Gas chromatography-mass spectrometry (GC-MS). SG alone and its combined application with saliva (SG+saliva) and semen (SG+semen) also studied to train young boars. SG alone and SG+Saliva investigated for estrus induction in gilts and sows. Distilled water (DW) exposure was kept as control. SG, saliva and semen screened for total 105, 96 and 89 compounds. The highest concentration was of alkanes followed by sugar alcohols, then hydrocarbons, amino acids and fatty acids. Elaidic acid is the novel compound identified in pigs. Other compounds were tridecenol, undecane, hexadecone, eicosane, tetracosane etc. Further, young males (64.86%) were able to get trained. Significant higher (p<0.05) number of males got trained in exposure to SG (80%), SG+saliva (75%) and SG+semen (75%) than control. The time (hrs) taken by young boars to get trained on exposure to combination of SG+saliva (244±22.19) and SG+semen (216±13.14) was lesser (p<0.05) than SG (356±61.85) alone. Interval (hrs) for exhibition of different sexual behaviour by males on exposure to SG, saliva and semen was lesser (p<0.05) than control. Estrus was induced in 61.25% of females. Significant (p<0.05) higher number of females showed estrus response to exposure of SG (72.72%) and SG+saliva (69.23%) than control. Interval taken to exhibit estrus was lesser (p<0.05) in females exposed to SG+saliva (201.88±12.66) than SG (262.14±20.06) alone. Interval (hrs) for exhibition of different sexual behaviour by females on exposure to SG+saliva was lesser (p<0.05) than control. In conclusion, novel compounds with biostimulatory properties have been identified in boar SG, saliva and semen. The combined exposure of SG with saliva and semen have more intense biostimulation effect than SG alone. Such compounds and biostimulatory effects can be exploited for augmenting reproductive efficiency in pigs.
RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy
Authors: Ugrina Marijana , Burkhart Ines , Müller Diana , Schwalbe Harald , Schwierz Nadine 
Published: February 2023

ABSTRACTThe kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates.We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno
Authors: Shi Xingjie , Yang Yi , Ma Xiaohui , Zhou Yong , Guo Zhenxing , Wang Chaolong , Liu Jin 
Published: February 2023

AbstractIn the analysis of both single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data, classifying cells/spots into cell/domain types is an essential analytic step for many secondary analyses. Most of the existing annotation methods have been developed for scRNA-seq datasets without any consideration of spatial information. Here, we present SpatialAnno, an efficient and accurate annotation method for spatial transcriptomics datasets, with the capability to effectively leverage a large number of non-marker genes as well as “qualitative” information about marker genes without using a reference dataset. Uniquely, SpatialAnno estimates low-dimensional embeddings for a large number of non-marker genes via a factor model while promoting spatial smoothness among neighboring spots via a Potts model. Using both simulated and four real spatial transcriptomics datasets from the 10x Visium, ST, Slide-seqV1/2, and seqFISH platforms, we showcase the method’s improved spatial annotation accuracy, including its robustness to the inclusion of marker genes for irrelevant cell/domain types and to various degrees of marker gene misspecification. SpatialAnno is computationally scalable and applicable to SRT datasets from different platforms. Furthermore, the estimated embeddings for cellular biological effects facilitate many downstream analyses.
Metabolization of α-D-carba-glucosamine in vivo generates antimetabolites of cell wall precursors
Authors: Mund Milena , Friz Simon , Esser Anna , Matzner Daniel , Babczyk Alexander , Menche Dirk , Brötz-Oesterhelt Heike , Mayer Christoph , Mayer Günter 
Published: February 2023

ABSTRACTα-D-Carba-glucosamine (CGlcN) is a carbocyclic analog of α-D-glucosamine that inhibits growth ofBacillus subtilisandStaphylococcus aureus. CGlcN is internalized and concomitantly phosphorylated via the phosphotransferase system yielding α-D-carba-glucosamine-6-phosphate (CGlcN6P), which interferes with expression of the glutamine-fructose-6-phosphate amidotransferase (GlmS; glucosamine synthase) by activating theglmSriboswitch. Herein, we report that CGlcN6P is efficiently metabolized to carbasugar nucleotides along the peptidoglycan biosynthetic route. Mass spectrometric analysis confirmed the occurrence of carbocyclic peptidoglycan nucleotides UDP-carba-D-N-acetyl-glucosamine (UDP-CGlcNAc) and UDP-carba-D-N-acetylmuramic acid-pentapeptide (UDP-CMurNAc-5P) in the presence of CGlcN and revealed accumulation of these carba-metabolites upon antibiotic treatment interfering with biosynthetic enzyme functions. Thus, carbocyclic carbohydrates and nucleotide analogs are generated by the promiscuous bacterial cell wall biosynthetic enzymes and act as antimetabolites, causing bacterial growth inhibition by interference with cell wall synthesis. Our findings reveal CGlcN not only as putative antibiotic molecule with previously unknown antimetabolite mode of action, but also as tool to study the bacterial cell wall metabolism, e.g., in synergy with other antibiotics.
Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but partially conserved gut microbiomes
Authors: Methou Pierre , Cueff-Gauchard Valérie , Michel Loïc N. , Gayet Nicolas , Pradillon Florence , Cambon-Bonavita Marie-Anne 
Published: February 2023

AbstractRimicaris exoculatashrimps from hydrothermal vent ecosystems are known to host dense epibiotic communities inside their enlarged heads and digestive systems. Conversely, other shrimps from the family, described as opportunistic feeders have received less attention. We examined the nutrition and bacterial communities colonizing “head” chambers and digestive systems of three other alvinocaridids –Rimicaris variabilis,Nautilocaris saintlaurentaeandManuscarissp. – using a combination of electron microscopy, stable isotopes and sequencing approaches. Our observations inside “head” cavities and on mouthparts showed only a really low coverage of bacterial epibionts. In addition, no clear correlation between isotopic ratios and relative abundance of epibionts on mouthparts could be established among shrimp individuals. Altogether, these results suggest that none of these alvinocaridids rely on chemosynthetic epibionts as their main source of nutrition. Our analyses also revealed a substantial presence of several Firmicutes within the foreguts and midguts of these shrimps, which closest known lineages were systematically digestive epibionts associated with alvinocaridids, and more broadly from digestive systems of other crustaceans from marine and terrestrial ecosystems. Overall, our study opens new perspectives not only about chemosynthetic symbioses of vent shrimps, but more largely about digestive microbiomes with potential ancient and evolutionarily conserved bacterial partnerships among crustaceans.
Increased endothelium activation and leakage do not promote diastolic dysfunction in mice fed with a high fat diet and treated with L-NAME
Authors: Cornuault Lauriane , Mora Pierre , Rouault Paul , Foussard Ninon , Chapouly Candice , Alzieu Pilippe , Gadeau Alain-Pierre , Couffinhal Thierry , Renault Marie-Ange 
Published: February 2023

AbstractCoronary microvascular disease has been proposed to be responsible for heart failure with preserved ejection fraction (HFpEF) about 10 years ago. However, to date the role and phenotype of the coronary microvasculature has still been poorly considered and investigated in animal models of HFpEF.ObjectiveTo determine whether endothelial dysfunction participates in the development of diastolic dysfunction in mice fed with a high fat diet (HDF) and treated with L-NAME.Approach and ResultsAt first, we thoroughly phenotyped the coronary microvasculature in this model in male, female and ovariectomized (OVX) female considering the sexual dimorphism associated with this disease. We found that both OVX and non OVX females but not males display increased endothelial activation, leakage, and arteriole constriction upon the HFD + L-NAME regimen while both male and OVX females but not non OVX females develop diastolic dysfunction. With the aim to investigate the role of endothelial dysfunction in the pathophysiology of diastolic dysfunction in OVX female mice, we used Cdon deficient mice. Indeed, we previously demonstrated that endothelium integrity, upon inflammatory conditions, is preserved in these mice. Both OVX Cdh5-Cre/ERT2-CdonFlox/Flox(CdonECKO) and CdonFlox/Flox(Ctrl) female mice were fed with the HFD + L-NAME regimen to induced diastolic dysfunction. As expected, CdonECKOmice displayed improved endothelium integrity i.e. decreased endothelium permeability, decreased ICAM-1 expression and decreased infiltration of CD45+ leukocytes in comparison to control mice. However, CdonECKOmice displayed cardiac hypertrophy, cardiac fibrosis and increased end diastolic pressure just like control mice. Moreover, we found that cardiac inflammation does not participate in the pathophysiology of HFpEF either by treating OVX female mice with colchicine.ConclusionAltogether, the data presented in this paper demonstrate that neither endothelium permeability nor endothelial activation or inflammation do participate in the pathophysiology of diastolic dysfunction in mice exposed to HFD+L-NAME.