bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of lactate, super-GDF9 and low oxygen tension during biphasic in vitro maturation on the bioenergetic profiles of mouse cumulus-oocyte-complex
Authors: Akin Nazli , Ates Gamze , Mengden Lucia von , Herta Anamaria-Cristina , Meriggioli Cecilia , Billooye Katy , Stocker William A. , Ghesquiere Brecht , Harrison Craig A. , Cools Wilfried , Klamt Fabio , Massie Ann , Smitz Johan , Anckaert Ellen 
Published: November 2022

ABSTRACTIn vitro maturation (IVM) is an alternative assisted reproductive technology (ART) with reduced hormone related side-effects and treatment burden compared to conventional IVF. Capacitation (CAPA)-IVM is a biphasic IVM system with improved clinical outcomes compared to standard monophasic IVM. Yet, CAPA-IVM efficiency compared to conventional IVF is still suboptimal in terms of producing utilizable blastocysts. Previously we have shown that CAPA-IVM leads to a precocious increase in cumulus cell (CC) glycolytic activity during cytoplasmic maturation. In the current study, considering the fundamental importance of CCs for oocyte maturation and cumulus-oocyte complex (COC) microenvironment, we further analyzed the bioenergetic profiles of maturing CAPA-IVM COCs. Through a multi-step approach, we (i) explored mitochondrial function of the in vivo and CAPA-IVM matured COCs through real-time metabolic analysis with Seahorse analyzer; and to improve COC metabolism (ii) supplemented the culture media with lactate and/or super-GDF9 (an engineered form of growth differentiation factor 9) and (iii) reduced culture oxygen tension. Our results indicated that the pre-IVM step is delicate and prone to culture related disruptions. Lactate and/or super-GDF9 supplementations failed to eliminate pre-IVM induced stress on COC glucose metabolism and mitochondrial respiration. However, when performing pre-IVM culture under 5% oxygen tension, CAPA-IVM COCs showed a similar bioenergetic profiles compared to in vivo matured counterparts. This is the first study providing real-time metabolic analysis of the COCs from a biphasic IVM system. The currently used analytical approach provides the quantitative measures and the rational basis to further improve IVM culture requirements.
Plant secondary metabolite-dependent plant-soil feedbacks can improve crop yield in the field
Authors: Gfeller Valentin , Waelchli Jan , Pfister Stephanie , Deslandes-Hérold Gabriel , Mascher Fabio , Glauser Gaétan , Aeby Yvo , Mestrot Adrien , Robert Christelle A.M. , Schlaeppi Klaus , Erb Matthias 
Published: November 2022

AbstractPlant secondary metabolites that are released into the rhizosphere alter biotic and abiotic soil properties, which in turn affect the performance of other plants. How such plant-soil feedbacks affect agricultural productivity and food quality in crop rotations is unknown. Here, we assessed the impact of maize benzoxazinoids on the performance, yield and food quality of three winter wheat varieties in a two-year field experiment. Following maize cultivation, we detected benzoxazinoid-dependent chemical and microbial fingerprints in the soil. The chemical fingerprint was still visible during wheat growth, while the microbial fingerprint was no longer detected. Benzoxazinoid soil conditioning by wild-type maize led to increased wheat emergence, tillering, growth and biomass compared to soil conditioning bybx1mutant plants. Weed cover remained unaffected, while insect damage decreased in a subset of varieties. Wheat yield was increased by over 4% without a reduction in grain quality across varieties. This improvement was directly associated with increased germination and tillering. Taken together, our experiments demonstrate that plant secondary metabolites can increase yield via plant-soil feedbacks under agronomically realistic conditions. If this phenomenon holds across different soils and environmental conditions, optimizing plant root exudation could be a powerful, genetically tractable strategy to enhance crop yields without additional inputs.
Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogenCampylobacter jejuni
Authors: Froschauer Kathrin , Svensson Sarah L. , Gelhausen Rick , Fiore Elisabetta , Kible Philipp , Klaude Alicia , Kucklick Martin , Fuchs Stephan , Eggenhofer Florian , Engelmann Susanne , Backofen Rolf , Sharma Cynthia M. 
Published: November 2022

ABSTRACTBackgroundKnowing the molecules encoded by bacterial pathogens and how their expression is regulated is essential to understand how they survive, colonize, and cause disease. RNA-seq technologies that map transcriptomes have revealed a wealth of new transcripts in bacterial pathogens. However, they do not provide direct evidence or coordinates for coding potential. In particular, they miss small proteins (≤ 50-100 amino acids) translated from small open reading frames (sORFs). However, this still poorly annotated component of bacterial genomes shows emerging roles in bacterial physiology and virulence.ResultsHere, we present an integrated approach based on complementary ribosome profiling (Ribo-seq) techniques to map the “translatome” ofCampylobacter jejuni, the most common cause of bacterial gastroenteritis. Besides conventional Ribo-seq, we employed translation initiation site (TIS) profiling to map start codons and reveal internal sORFs. We also developed a Ribo-seq approach for mapping of translation termination sites (TTS), which revealed stop codons not apparent from the reference genome in virulence-associated loci. Our translatome map confirms translation of leaderless ORFs and leader peptides, re-annotates start or stop codons of 35 genes, and reveals isoforms generated by internal start sites. It also adds 42 novel sORFs in diverse contexts to theC. jejuniannotation, such as within small RNAs, in 5′ untranslated regions (UTRs), or internal/out-of-frame/antisense in larger ORFs. Using epitope tagging/western blot and mass spectrometry we validated expression of almost 60 annotated and novel sORFs, includingcioY, which we show encodes a conserved, 34 amino acid component of the CioAB terminal oxidase.ConclusionsOverall, we provide a blueprint for integrating several Ribo-seq approaches to refine and enrich bacterial annotations.
Confocal reflectance microscopy for mapping collagen fiber organization in the vitreous gel of the eye
Authors: Hwang Eileen S. , Morgan Denise J. , Sun Jieliyue , Hartnett M. Elizabeth , Toussaint Kimani C. , Coats Brittany 
Published: November 2022

AbstractVitreous collagen structure plays an important role in ocular mechanics, but capturing this structure with existing vitreous imaging methods is hindered by loss of sample position and orientation, low resolution, or small field of view. The objective of this study was to evaluate confocal reflectance microscopy as a solution to these limitations. The use of intrinsic reflectance avoids staining and optical sectioning eliminates the requirement for thin sectioning, minimizing processing for optimal preservation of natural structure. We developed a sample preparation and imaging strategy usingex vivogrossly sectioned porcine eyes. Imaging revealed a network of uniform diameter crossing fibers (1.1 ± 0.3 μm for a typical image) with generally poor alignment (alignment coefficient = 0.40 ± 0.21 for a typical image). To test the utility of our approach for detecting differences in fiber spatial distribution, we imaged eyes every 1 mm along an anterior-posterior axis originating at the limbus and quantified the number of fibers in each image. Fiber density was higher anteriorly near the vitreous base, regardless of imaging plane. These data demonstrate that confocal reflectance microscopy addresses the previously unmet need for a robust, micron-scale technique to map features of collagen networksin situacross the vitreous.
Challenges in antibody structure prediction
Authors: Fernández-Quintero Monica L. , Kokot Janik , Waibl Franz , Fischer Anna-Lena M. , Quoika Patrick K. , Deane Charlotte M. , Liedl Klaus R. 
Published: November 2022

The tremendous advances in structural biology and the exponential increase of high-quality experimental structures available in the PDB motivated numerous studies to tackle the grand challenge of predicting protein structures. AlphaFold2 revolutionized the field of protein structure prediction, by combining artificial intelligence with evolutionary information.Antibodies are one of the most important classes of biotherapeutic proteins. Accurate structure models are a prerequisite to advance biophysical property predictions and consequently antibody design. Various specialized tools are available to predict antibody structures based on different principles and profiting from current advances in protein structure prediction based on artificial intelligence. Here, we want to emphasize the importance of reliable protein structure models and highlight the enormous advances in the field. At the same time, we want to raise the awareness that protein structure models—and in particular antibody models—may suffer from structural inaccuracies, namely incorrect cis-amid bonds, wrong stereochemistry or clashes. We show that these inaccuracies affect biophysical property predictions such as surface hydrophobicity. Thus, we stress the significance of carefully reviewing protein structure models before investing further computing power and setting up experiments. To facilitate the assessment of model quality, we provide a tool “TopModel” to validate structure models.
Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2
Authors: Nickchi Payman , Mirzaie Mehdi , Baumann Marc , Saei Amir Ata , Jafari Mohieddin 
Published: November 2022

AbstractPost-translational modifications (PTMs) are under significant focus in molecular biomedicine due to their importance in signal transduction in most cellular and organismal processes. Characterization of PTMs, discrimination between functional and inert PTMs, quantification of their occupancies and PTM crosstalk are demanding tasks in each biosystem. On top of that, the study of each PTM often necessitates a particular laborious experimental design. Here, we present a PTM-centric proteome informatic pipeline for prediction of relevant PTMs in mass spectrometry-based proteomics data in the absence ofa prioriinformation. Upon prediction, such PTMs can be incorporated in a refined database search. As a practical application, we showed how this pipeline suggested performing glycoproteomics in oral squamous cell carcinoma based on proteome profile of primary tumors. Subsequently, using proteome profiling of treated cells with two PTM-modulating kinase inhibitors, we experimentally identified cellular proteins that are differentially expressed in response to multikinase inhibitors dasatinib and staurosporine. Computational enrichment analysis was employed to determine the potential PTMs of protein targets for both drugs. Finally, we conducted an additional round of database search with the predicted PTMs. Our pipeline helped to analyze the enriched PTMs and even the detected proteins that were not identified in the initial search. Our findings support the idea of PTM-centric searching of MS data in proteomics based on computational enrichment analysis and we propose that this approach be integrated into future proteomics search engines.
Bell Jar: A Semi-Automated Registration and Cell Counting Tool for Mouse Neurohistology Analysis
Authors: Soronow Alec L.R. , Jacobs Matthew W. , Dickson Richard G. , Kim Euiseok J. 
Published: November 2022

AbstractTo investigate the anatomical organization of neural circuits across the whole brain, it is essential to register the experimental brain tissues to a reference atlas accurately. This procedure is also a prerequisite to quantify the locations and numbers of cells of interest in specific regions. However, it remains challenging to do registration on experimental tissue due to the intrinsic variation among the specimens, tissue deformation introduced by histological processing, and the potential inconsistency in the judgment of the experimenter during manual annotation. Here, we introduce Bell Jar, a multi-platform analysis tool with semi-automated affine warping of atlas maps onto microscopic images of brain slices and machine learning-based cell detection. Bell Jar’s intuitive GUI and internal dependency management enable users of all skill levels to obtain accurate results without programming expertise. To compare the performance of Bell Jar with previously published methods1–4, we labeled neurons in the mouse visual cortex with either an engineered rabies virus or an adeno-associated virus (AAV) for neural circuit tracing5, and quantified Bell Jar’s performance at each step of the pipeline for image alignment, segmentation, and cell counting. We demonstrated that Bell Jar’s output is as reliable as manual counting by an expert; it is more accurate than currently available techniques even with noisy data and takes less time with fewer user interventions. Bell Jar is an easy-to-navigate application that provides a reproducible, automated analysis workflow to facilitate the precise mapping of histological images of the mouse brain to the reference atlas and the quantification of cellular signals it is trained to recognize.
Energy conservation by collective movement in schooling fish
Authors: Zhang Yangfan , Lauder George V. 
Published: November 2022

AbstractMany animals moving through fluids exhibit highly coordinated group movement that is thought to reduce the cost of locomotion. However, direct energetic measurements demonstrating the energy-saving benefits of fluid-mediated collective movements remain elusive. By characterizing both aerobic and anaerobic metabolic energy contributions in schools of giant danio (Devario aequipinnatus), we discovered that fish schools have a concave upward shaped metabolism– speed curve, with a minimum metabolic cost at ∼1 body length s-1. We demonstrate that fish schools reduce total energy expenditure (TEE) per tail beat by up to 56% compared to solitary fish. When reaching their maximum sustained swimming speed, fish swimming in schools had a 44% higher maximum aerobic performance and used 65% less non-aerobic energy compared to solitary individuals, which lowered the TEE and total cost of transport by up to 53%, near the lowest recorded for any aquatic organism. Fish in schools also recovered from exercise 43% faster than solitary fish. The non-aerobic energetic savings that occur when fish in schools actively swim at high speed can considerably improve both peak and repeated performance which is likely to be beneficial for evading predators. These energetic savings may underlie the prevalence of coordinated group locomotion in fishes.One-Sentence SummaryFish schools showed aU-shaped metabolism-speed curve and reduced the energy use per tail beat up to 56% at high swimming speeds compared to solitary fish.
Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance inMycobacterium tuberculosis
Authors: Brankin Alice E. , Fowler Philip W. 
Published: November 2022

SynopsisFluoroquinolone resistance poses a threat to the successful treatment of tuberculosis. Whole genome sequencing (WGS), and the subsequent detection of catalogued resistance-associated mutations, offers an attractive solution to fluoroquinolone susceptibility testing. However, the bioinformatic pipelines used often mask the recognition of minor alleles which are implicated in fluoroquinolone resistance. Using the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium’s (CRyPTIC) dataset of globally diverse WGSMycobacterium tuberculosisisolates, with matched minimum inhibitory concentrations for two fluoroquinolone drugs, we show that detecting minor alleles increased the sensitivity of WGS for moxifloxacin resistance prediction from 85.4% to 94.0%, without significantly reducing specificity. We also found no correlation between the proportion of anM. tuberculosispopulation containing a resistance-conferring allele and the magnitude of resistance. Together our results highlight the importance of detecting minor resistance conferring alleles when using WGS, or indeed any sequencing-based approach, to diagnose fluoroquinolone resistance.
Global analysis of suppressor mutations that rescue human genetic defects
Authors: Ünlü Betül , Pons Carles , Ho Uyen Linh , Batté Amandine , Aloy Patrick , van Leeuwen Jolanda 
Published: November 2022

ABSTRACTGenetic suppression occurs when the deleterious effects of a primary “query” mutation, such as a disease-causing mutation, are rescued by a suppressor mutation elsewhere in the genome. To capture existing knowledge on suppression relationships between human genes, we examined 2,400 published papers for potential interactions identified through either genetic modification of cultured human cells or through association studies in patients. The resulting network encompassed 476 unique suppression interactions that frequently linked genes that function in the same biological process. Suppressors were strongly enriched for genes with a role in stress response or signaling, suggesting that deleterious mutations can often be buffered by modulating signaling cascades or immune responses. Suppressor mutations tended to be deleterious when they occurred in absence of the query mutation, in apparent contrast with their protective role in the presence of the query. We formulated and quantified mechanisms of genetic suppression that could explain 71% of interactions and provided mechanistic insight into disease pathology. Finally, we used these observations to accurately predict suppressor genes in the human genome. The emerging frequency of suppression interactions and range of underlying mechanisms suggest that compensatory mutations may exist for the majority of genetic diseases.
Tailored synthetic sRNAs dynamically tune multilayer genetic circuits
Authors: Velazquez Sanchez Ana K. , Klopprogge Bjarne , Zimmermann Karl-Heinz , Ignatova Zoya 
Published: November 2022

AbstractPredictable and controllable tuning of genetic circuits to regulate gene expression, including modulation of existing circuits or constructs without the need for redesign or rebuilding, is a persistent challenge in synthetic biology. Here, we propose a rational design of de novo small RNAs (sRNAs) to dynamically modulate gene expression within a broad range, from high, medium to low repression, and implemented them inEscherichia coli. We designed multiple multilayer genetic circuits, in which the variable effector element is a transcription factor (TF) controlling downstream the production of a reporter protein. Our approach harnesses the intrinsic RNA-interference pathway inE. colito exert dynamic and modular control of the multilayer genetic circuits. The sRNAs were designed to target TFs instead of the reporter gene, which allowed for wide range of expression modulation of the reporter protein, including the most difficult to achieve dynamic switch to an OFF state. Out work provides a frame for achieving independent modulation of gene expression, by only including an independent control circuit expressing synthetic sRNAs, without altering the structure of existing genetic circuits.
Breast cancer mutations HER2V777Land PIK3CAH1047Ractivate the p21-CDK4/6 –Cyclin D1 axis driving tumorigenesis and drug resistance
Authors: Cheng Xiaoqing , Sun Yirui , Highkin Maureen , Vemalapally Nagalaxmi , Jin Xiaohua , Zhou Brandon , Prior Julie L. , Tipton Ashley R. , Li Shunqiang , Iliuk Anton , Achilefu Samuel , Hagemann Ian S. , Edwards John R. , Bose Ron 
Published: November 2022

AbstractIn metastatic breast cancer, HER2 activating mutations frequently co-occur with mutations in thePIK3CA,TP53, or E-cadherin genes. Of these co-occurring mutations,HER2andPIK3CAmutations are the most prevalent gene pair, with approximately 40% ofHER2mutated breast cancers also having activating mutations inPIK3CA. To study the effects of co-occurringHER2andPIK3CAmutations, we bred genetically engineered mice with theHER2V777L;PIK3CAH1047Rtransgenes (HP mice) and studied the resulting breast cancers bothin vivoas well asex vivousing cancer organoids. HP breast cancers show accelerated tumor formationin vivoand increased invasion and migration inin vitroassays. HP breast cancers have resistance to the pan-HER tyrosine kinase inhibitor, neratinib, but are effectively treated by neratinib plus trastuzumab deruxtecan. Proteomic and RNA-Seq analysis of HP breast cancers showed increased gene expression of Cyclin D1 and p21WAF1/Cip1 and changes in cell cycle markers. Combining neratinib with CDK4/6 inhibitors was another effective strategy for HP breast cancers with neratinib plus palbociclib showing a statistically significant reduction in mouse HP tumors as compared to either drug alone. We validated both the neratinib plus trastuzumab deruxtecan and neratinib plus palbociclib combinations using a human breast cancer patient-derived xenograft that has very similar HER2 andPIK3CAmutations. Both of these drug combinations are being tested in phase 1 clinical trials and this study provides valuable preclinical evidence for them.
Microstimulation of sensory cortex engages natural sensory representations
Authors: Pancholi Ravi , Sun-Yan Andrew , Peron Simon 
Published: November 2022

SUMMARYCortical activity patterns occupy a small subset of possible network states. If this is due to intrinsic network properties, microstimulation of cortex should evoke activity patterns resembling those observed during natural sensory input. Here, we use optical microstimulation of virally transfected layer 2/3 pyramidal neurons in mouse primary vibrissal somatosensory cortex to compare artificially evoked activity with natural activity evoked by whisker touch and movement (‘whisking’). We find that photostimulation engages touch but not whisking responsive neurons more than expected by chance. Neurons that respond to photostimulation and touch or to touch alone exhibit higher spontaneous pairwise correlations than purely photoresponsive neurons. Exposure to several days of simultaneous touch and optogenetic stimulation raises both overlap and spontaneous activity correlations among touch and photoresponsive neurons. We thus find that cortical microstimulation engages existing cortical representations and that repeated co-presentation of natural and artificial stimulation enhances this effect.
Endosomal GLUT3 is essential for alternative macrophage signaling, polarization, and function
Authors: Yu Dong-Min , Zhao Jiawei , Lee Eunice E. , Rose Elysha K. , Mahapatra Ruchika , Choe Jun-Yong , Abel E Dale , Wang Richard C. 
Published: November 2022

ABSTRACTMacrophages play critical roles in both inflammation and tissue homeostasis. Classically activated (M1) macrophages promote antimicrobial and tumoricidal activity, while alternatively activated (M2) macrophages promote phagocytosis and tissue homeostasis. The facilitative GLUT1 and GLUT3 hexose transporters are expressed abundantly in different hematopoietic lineages, but their specific functions in macrophages is poorly understood. We discovered that GLUT3 expression was increased after M2-activation stimuli in macrophages. Notably, GLUT3 KO BMDM (bone marrow-derived macrophages) showed marked defects in M2, but not M1, polarization. Consistent with defects in M2 polarization, GLUT3 KO macrophages showed impaired wound healing and decreased inflammation in calcipotriol-induced, atopic dermatitislike inflammation. GLUT3 promoted IL-4/STAT6 signaling, the main signaling pathway for M2 polarization, in a glucose-transport independent manner. Unlike plasma membrane-localized GLUT1, GLUT3 and components of the IL-4 signaling pathway, localized primarily to endosomes. GLUT3, but not GLUT1, interacted with Ras through its intracytoplasmic loop, and Rac1-PAK-cofilin signaling and the endocytosis of IL4R subunits were impaired in the absence of GLUT3. Thus, GLUT3 is essential for alternative macrophage polarization and function and plays an unexpected role in the regulation of endosomal signaling.