bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frustraevo: A Web Server To Localize And Quantify The Conservation Of Local Energetic Frustration In Protein Families
Authors: Parra R. Gonzalo , Freiberger Maria I. , Poley-Gil Miriam , Fernandez-Martin Miguel , Radusky Leandro G. , Wolynes Peter G. , Ferreiro Diego U. , Valencia Alfonso 
Published: December 2023

ABSTRACTAccording to the Principle of Minimal Frustration, folded proteins can have only a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.The webserver is freely available at URL:https://frustraevo.qb.fcen.uba.ar
Increased multiplexity in optical tissue clearing-based 3D immunofluorescence microscopy of the tumor microenvironment by LED photobleaching
Authors: Zheng Jingtian , Wu Yi-Chien , Phillips Evan H. , Wang Xu , Lee Steve Seung-Young 
Published: December 2023

AbstractOptical tissue clearing and three-dimensional (3D) immunofluorescence (IF) microscopy have been transforming imaging of the complex tumor microenvironment (TME). However, current 3D IF microscopy has restricted multiplexity; only three or four cellular and non-cellular TME components can be localized in a cleared tumor tissue. Here we report a LED photobleaching method and its application for 3D multiplexed optical mapping of the TME. We built a high-power LED light irradiation device and temperature-controlled chamber for completely bleaching fluorescent signals throughout optically cleared tumor tissues without compromise of tissue and protein antigen integrity. With newly developed tissue mounting and selected region-tracking methods, we established a cyclic workflow involving IF staining, tissue clearing, 3D confocal microscopy, and LED photobleaching. By registering microscope channel images generated through three work cycles, we produced 8-plex image data from individual 400 μm-thick tumor macrosections that visualize various vascular, immune, and cancer cells in the same TME at tissue-wide and cellular levels in 3D. Our method was also validated for quantitative 3D spatial analysis of cellular remodeling in the TME after immunotherapy. These results demonstrate that our LED photobleaching system and its workflow offer a novel approach to increase the multiplexing power of 3D IF microscopy for studying tumor heterogeneity and response to therapy.
Barcode 100K Specimens: In a Single Nanopore Run
Authors: Hebert Paul DN , Floyd Robin , Jafarpour Saeideh , Prosser Sean WJ 
Published: December 2023

ABSTRACTIt is a global priority to better manage the biosphere, but action needs to be informed by monitoring shifts in the abundance and distribution of species across the domains of life. The acquisition of such information is currently constrained by the limited knowledge of biodiversity. Among the 20 million or more species of eukaryotes, just a tenth have scientific names. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive analytical protocols are critical as the census of all animal species will require processing a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By recovering barcodes from highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until now, kept analytical cost above Sequel. However, the improved performance of its latest flow cells (R10.4.1) might erase this differential. This study demonstrates that a regular MinION flow cell can characterize an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow. By coupling simplified protocols for DNA extraction with ultra-low volume PCRs, it will be possible to move from specimen to DNA barcode for $0.10, a price point that will enable the census of all species within two decades.
Heterogeneity in lung macrophage control ofMycobacterium tuberculosisis determined by T cells
Authors: Lai Rocky , Williams Travis , Rakib Tasfia , Lee Jinhee , Behar Samuel M. 
Published: December 2023

AbstractFollowingMycobacterium tuberculosisinfection, alveolar macrophages are initially infected but ineffectively restrict bacterial replication. The distribution ofM. tuberculosisamong different cell types in the lung changes with the onset of T cell immunity when the dominant infected cellular niche shifts from alveolar to monocyte-derived macrophages (MDM). We hypothesize that changes in bacterial distribution among different cell types is driven by differences in T cell recognition of infected cells and their subsequent activation of antimicrobial effector mechanisms. We show that CD4 and CD8 T cells efficiently eliminateM. tuberculosisinfection in alveolar macrophages, but they have less impact on suppressing infection in MDM, which may be a bacterial niche. Importantly, CD4 T cell responses enhance MDM recruitment to the lung. Thus, the outcome of infection depends on the interaction between the T cell subset and the infected cell; both contribute to the resolution and persistence of the infection.
DISRUPTION OF THE ENDOGENOUS INDOLE GLUCOSINOLATE PATHWAY IMPACTS THEARABIDOPSIS THALIANAROOT EXUDATION PROFILE AND RHIZOBACTERIAL COMMUNITY
Authors: Acuña Daniel , Bletz Molly C , Sasse Joelle , Micallef Shirley A , Kosina Suzanne , Bowen Benjamin P , Northen Trent R , Colón-Carmona Adán 
Published: December 2023

AbstractRoot exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. We usedArabidopsis thalianamutant lines with disruptions in the indole glucosinolate pathway, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how disrupting this pathway affects the root exudate profile ofArabidopsis thaliana, and in turn, impacts the rhizosphere microbial community. Chemical analysis of the root exudates from the wild-type Columbia (Col-0), a mutant plant line overexpressing the MYB transcription factorATR1(atr1D)which increases glucosinolate production, and the loss-of-functioncyp79B2cyp79B3double mutant line with low levels of glucosinolates confirmed that alterations to the indole glucosinolate biosynthetic pathway shifts the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. This work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria (PGPR). Our results suggest that genetic alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.
Trojan horse virus delivering CRISPR-AsCas12f1 controls plant bacterial wilt caused byRalstonia solanacearum
Authors: Peng Shiwen , Xu Yanan , Qu Hao , Nong Fushang , Shu Fangling , Yuan Gaoqing , Ruan Lifang , Zheng Dehong 
Published: December 2023

AbstractPlant bacterial wilt caused by theRalstonia solanacearumspecies complex results in huge food and economic losses. Accordingly, the development of an effective control method for this disease is urgently required. Traditional lytic phage biocontrol methods have inherent limitations. However, filamentous phages, which do not lyse host bacteria and exert minimal burden, offer a potential solution. A filamentous phage RSCq that infectsR. solanacearumwas isolated in this study through genome mining. We constructed engineered filamentous phages based on RSCq by employing our proposed approach with a wide applicability to non-model phages, enabling the infection ofR. solanacearumin medium and soil and delivering exogenous genes into bacterial cells. Similar to the Greek soldiers hidden within the Trojan horse, CRISPR-AsCas12f1 gene editing system that targets the key virulence regulator genehrpBwas implanted into the engineered phage, generating the engineered phage RSCqCRISPR-Cas. Our findings demonstrated that RSCqCRISPR-Cas could disarm the key “weapon”,hrpB, ofR. solanacearum, in medium and in plants. Remarkably, pretreatment with RSCqCRISPR-Cas significantly controlled tobacco bacterial wilt, highlighting the potential of engineered filamentous phages as promising biocontrol agents against plant bacterial wilt and other bacterial diseases.
Extreme miniaturization in plasmid design: generation of the 903 bp cloning vector pICOt2
Authors: Staal Jens , Beyaert Rudi 
Published: December 2023

AbstractInspired by the size optimizations in the recently published pUdO series of plasmids, we set out to break our previous world record (pICOz, 1185 bp) in designing the smallest possible self-replicating high copy cloning vector. By replacing the zeocin resistance marker with trimethoprim resistance, deleting the parts upstream of -35 in the ampicilin resistance promoter and replacing the extended multiple cloning site with a single SpeI site, we managed to reduce the plasmid size to 903 bp, almost a 24% reduction in size compared to our previous accomplishments.
metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis
Authors: Sun Yingying , Xing Ziyuan , Liang Shuang , Miao Zelei , Zhuo Lai-bao , Jiang Wenhao , Zhao Hui , Gao Huanhuan , Xie Yuting , Zhou Yan , Yue Liang , Cai Xue , Chen Yu-ming , Zheng Ju-Sheng , Guo Tiannan 
Published: December 2023

AbstractBackgroundAnalysis of mass spectrometry-based metaproteomic data, in particular large-scale data-independent acquisition MS (DIA-MS) data, remains a computational challenge. Here, we aim to develop a software tool for efficiently constructing spectral libraries and analyzing extensive datasets of DIA-based metaproteomics.ResultsWe present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS (DDA-MS), protein identification and quantification using DIA-MS, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. To enhance accessibility and ease of use, all modules and dependencies are encapsulated within a Docker container.By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap-based and PASEF-based DDA and DIA data. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples demonstrated that metaExpertPro quantified an average of 45,000 peptides in a 60-minute diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual False Discovery Rate (FDR) of less than 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67–0.90) in genus diversity and demonstrated a high correlation (rSpearman= 0.73–0.82) between the measured and true genus relative abundance in benchmark tests.Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.ConclusionsmetaExpertPro presents a robust one-stop computational solution for constructing metaproteomics spectral libraries, analyzing DIA-MS data, and annotating taxonomic as well as functional data.
Autoantibodies to truncated GAD(96-585) antigen stratify risk of early insulin requirement in adult-onset diabetes
Authors: Grace Sian L. , Gillespie Kathleen M. , Williams Claire L. , Lampasona Vito , Achenbach Peter , Pearson Ewan R. , Williams Alistair J.K. , Long Anna E. , McDonald Timothy J. , Jones Angus G. 
Published: December 2023

AbstractObjectiveWe investigated whether further characterisation of full-length (f-) GADA responses could identify early insulin requirement in adult-onset diabetes.Research Design and MethodsIn 179 f-GADA positive participants diagnosed with type 2 diabetes, we assessed the association of truncated (t-)GADA positivity, f-GADA IgG subclasses, and f-GADA affinity with early insulin requirement (<5 years), type 1 diabetes genetic risk score (T1D GRS), and C-peptide. These characteristics were compared to f-GADA positive type 1 diabetes (n=141) and f-GADA negative type 2 diabetes (n=6420) cohorts.Resultst-GADA positivity was lower in f-GADA positive without early insulin in comparison to f-GADA positive type 2 diabetes requiring insulin within 5 years, and type 1 diabetes (75% vs. 91% and 95% respectively, p<0.0001). t-GADA positivity (in those f-GADA positive) identified a group with a higher type 1 diabetes genetic susceptibility (mean T1D GRS 0.248 vs. 0.225, p=0.003), lower C-peptide (1156 pmol/L vs. 4289 pmol/L, p=1×10-7), and increased IA-2A positivity (23% vs. 6%, p=0.03). In survival analysis, t-GADA positivity was associated with early insulin requirement compared with those only positive for f-GADA, independently from age of diagnosis, f-GADA titre and duration of diabetes [adjusted HR 5.7 (95% CI 1.4, 23.5), p=0.017]. Early insulin requirement was not associated with an IgG1-restricted f-GADA response (p=0.81) or a high affinity f-GADA response (p=0.89).ConclusionsThe testing of t-GADA in f-GADA positive individuals with type 2 diabetes identifies those who have genetic and clinical characteristics comparable to type 1 diabetes and stratifies those at higher risk of early insulin requirement.Article HighlightsProgression to insulin therapy is highly variable in adult-onset GADA positive diabetes.We further characterised GADA characteristics in adult-onset diabetes and assessed whether these are associated with early insulin requirement.Truncated GADA positivity was associated with a type 1 diabetes like phenotype and stratified risk of early insulin requirement. Those GADA positive who were negative for truncated GADA had the characteristics and progression of classical type 2 diabetes. Assessing full-length GADA IgG subclass and affinity did not further stratify risk of progression.t-GADA assessment remains underutilised in clinical practice, but could assist correct therapy allocation in adult-onset diabetes.
Approaches to improve mental health care for autistic children and young people: a systematic review and meta-analysis
Authors: Pemovska Tamara , Loizou Sofia , Appleton Rebecca , Spain Debbie , Stefanidou Theodora , Kular Ariana , Cooper Ruth , Greenburgh Anna , Griffiths Jessica , Barnett Phoebe , Foye Una , Baldwin Helen , Minchin Matilda , Brady Gráinne , Saunders Katherine R. K. , Ahmed Nafiso , Jackson Robin , Olive Rachel Rowan , Parker Jennie , Timmerman Amanda , Sapiets Suzi , Driskell Eva , Chipp Beverley , Parsons Bethany , Totsika Vaso , Mandy Will , Pender Richard , Clery Philippa , Lloyd-Evans Brynmor , Simpson Alan , Johnson Sonia 
Published: December 2023

AbstractAutistic children and young people (CYP) experience mental health difficulties but face many barriers to accessing and benefiting from mental health care. There is a need to explore strategies in mental health care for autistic CYP to guide clinical practice and future research and support their mental health needs. Our aim was to identify strategies used to improve mental health care for autistic CYP and examine evidence on their acceptability, feasibility, and effectiveness. A systematic review and meta-analysis were carried out. All study designs reporting acceptability/feasibility outcomes and empirical quantitative studies reporting effectiveness outcomes for strategies tested within mental health care were eligible. We conducted a narrative synthesis and separate meta-analyses by informant (self, parent, clinician). Fifty-seven papers were included, with most investigating cognitive behavioural therapy (CBT)-based interventions for anxiety and several exploring service-level strategies, such as autism screening tools, clinician training, adaptations regarding organisation of services. Most papers described caregiver involvement in therapy and reported adaptations to communication and intervention content; a few reported environmental adjustments. In the meta-analyses, parent- and clinician-reported outcomes, but not self-reported outcomes, showed with moderate certainty that CBT for anxiety was an effective treatment compared to any comparison condition in reducing anxiety symptoms in autistic individuals. The certainty of evidence for effectiveness, synthesised narratively, ranged from low to moderate. Evidence for feasibility and acceptability tended to be positive. Many identified strategies are simple, reasonable adjustments that can be implemented in services to enhance mental health care for autistic individuals. Notable research gaps persist, however.
“Nitrogen demand, supply, and acquisition strategy control plant responses to elevated CO2at different scales”
Authors: Perkowski Evan A. , Ezekannagha Ezinwanne , Smith Nicholas G. 
Published: December 2023

AbstractPlants respond to elevated atmospheric CO2concentrations by reducing leaf nitrogen content and photosynthetic capacity – patterns that correspond with increased net photosynthesis rates, total leaf area, and total biomass. Nitrogen supply has been hypothesized to be the primary factor controlling these responses, as nitrogen availability limits net primary productivity globally. Recent work using evo-evolutionary optimality theory suggests that leaf photosynthetic responses to elevated CO2are independent of nitrogen supply and are instead driven by leaf nitrogen demand to build and maintain photosynthetic enzymes, which optimizes resource allocation to photosynthetic capacity and maximizes allocation to growth. Here,Glycine maxL. (Merr) seedlings were grown under two CO2concentrations, with and without inoculation withBradyrhizobium japonicum, and across nine soil nitrogen fertilization treatments in a full-factorial growth chamber experiment to reconcile the role of nitrogen supply and demand on leaf and whole-plant responses to elevated CO2. After seven weeks, elevated CO2increased net photosynthesis rates despite reduced leaf nitrogen content and maximum rates of Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) carboxylation and electron transport for RuBP regeneration. Effects of elevated CO2on net photosynthesis and indices of photosynthetic capacity were independent of nitrogen fertilization and inoculation. However, increasing nitrogen fertilization enhanced positive effects of elevated CO2on total leaf area and total biomass due to increased nitrogen uptake and reduced carbon costs to acquire nitrogen. Whole-plant responses to elevated CO2were not modified by inoculation across the nitrogen fertilization gradient, as plant investment toward symbiotic nitrogen fixation was similar between CO2treatments. These results indicate that leaf nitrogen demand to build and maintain photosynthetic enzymes drives leaf photosynthetic responses to elevated CO2, while nitrogen supply regulates whole-plant responses. Our findings build on previous work suggesting that terrestrial biosphere models may improve simulations of photosynthetic processes under future novel environments by adopting optimality principles.
Natural and age-related variation in circulating human hematopoietic stem cells
Authors: Furer N. , Rappoport N. , Milman O. , Lifshitz A. , Bercovich A. , Ben-Kiki O. , Danin A. , Kedmi M. , Shipony Z. , Lipson D. , Meiri E. , Yanai G , Shapira S. , Arber N. , Berdichevsky S. , Tavor S. , Tyner J. , Joshi S. , Landau D. , Ganesan S. , Dusaj N. , Chamely P. , Kaushansky N. , Chapal-Ilani N. , Shamir R. , Tanay A. , Shlush LI 
Published: December 2023

AbstractHematopoietic stem and progenitor cells (HSPCs) deliver life-long multi-lineage output. However, with aging, we exhibit certain characteristic blood count changes and accumulation of clonal disorders. Better understanding of inter-individual variation in HSPC behavior is needed to understand these age-related phenomena and the transition from health to chronic and acute hematological malignancies. Here we study 627K single circulating CD34+ HSPCs (cHSPCs) from 148 healthy individuals, along with their clinical information and clonal hematopoiesis (CH) profiles, to characterize population-wide and age-related hematopoietic variability. Individuals with CH were linked with reduced frequencies of lymphocyte progenitors and higher RDW. An age-related decrease in lymphoid progenitors was observed, predominantly in males. Inter-individual transcriptional variation in expression of a Lamin-A signature and stemness gene programs were linked with aging and presence of macrocytic anemia. Based on our model for healthy cHSPC variation we construct the normal reference for cHSPC subtype frequencies. We show how compositional and expression deviations from this normal reference can robustly identify myeloid malignancies and pre-malignant states. Together, our data and methodologies present a novel resource, shedding light on various age-related hematopoietic processes, and a comprehensive normal cHSPC reference, which can serve as a tool for diagnosing and characterizing hematological disorders.