bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluoroquinolone-Specific Resistance Trajectories inE. coliand their Dependence on the SOS-Response
Authors: Teichmann Lisa , Luitwieler Sam , Bengtsson-Palme Johan , ter Kuile Benno
Published: June 2024

Fluoroquinolones are essential for treating bacterial infections in both human and veterinary medicine. This study investigates the mechanisms behind acquired resistance to fluoroquinolones with a specific focus on the SOS response - a critical cellular pathway activated by DNA damage. Utilizing an experimental evolution approach, we exposedEscherichia colito four fluoroquinolones and monitored the adaptation process. ArecAknock-out mutant deficient in the SOS response was used as biological control. The emergence of resistance was accompanied by numerous DNA mutations, consisting of some observed often and others that infrequently appeared. Our findings indicate that the development of resistance depends in varying degrees on the SOS response among the tested fluoroquinolones, with notable dissimilarities in clinical resistance development. Resistance developed slowest to ciprofloxacin, then levofloxacin, followed by enrofloxacin, and fastest to moxifloxacin. Genomic analysis revealed distinct mutation profiles in cultures exposed to the tested antimicrobials, emphasizing the unique adaptation strategies of bacteria. This research underscores the importance of recognizing the differences among fluoroquinolones in scientific research and clinical practice.
Policy perspectives on the sustainable introduction of pneumococcal conjugate vaccines in middle-income countries
Authors: Weeks Rose , Dhaliwal Baldeep K. , Huber Jasmine , Nabia Sarah , Al-Shaikh Ala’a F. , Chokephaibulkit Kulkanya , Fernando LaKKumar , Baghagho Ehssan , Shet Anita
Published: June 2024

Abstract

Despite the well-documented life-saving potential of pneumococcal conjugate vaccines (PCV) and global efforts to widen vaccine availability, access to PCV in middle-income countries (MICs) has remained suboptimal due, in part, to vaccine pricing and limited external funding opportunities. To understand gaps and opportunities for improving vaccine equality, this qualitative study engaged government policymakers and program leaders from MICs that do not currently have PCV in their national immunization programs to explore their perspectives on decision-making contexts and constraints related to PCV introduction. In-depth interviews with 17 participants from Egypt, Jordan, Sri Lanka, and Thailand in 2023 documented that, despite high routine immunization coverage and commitment toward building equitable health systems, implementing new vaccines such as PCV has remained challenging. Among the six thematic areas that emerged, two were strong enablers to vaccine implementation: 1) the existence of strong primary healthcare systems; and 2) established policy processes for vaccine decision-making. Three themes that emerged have historically hindered PCV introduction, including; 1) limited information on disease burden and available vaccine products; 2) competing country health priorities; and 3) financing challenges. The interplay of these thematic areas has documented a paradox unique to MICs, further contributing to inequalities in vaccine access. While a subset of MICs recently became eligible for support from Gavi, the Vaccine Alliance for introducing new vaccines, the marketplace has historically lacked tiered vaccine pricing that MICs could sustain for the long term. This is despite the great need with existing inequities and a substantial proportion of the world’s low-income and displaced populations. Finally, participants pointed to opportunities to address barriers through support from global and regional actors providing technical capacity-strengthening, advocacy, and strategic financial support. These findings are informative for strengthening equality in access to vaccines and developing sustainable strategies to introduce and sustain life-saving childhood vaccines, including PCV.
Characterizing Genetic Pathways Unique to Autism Spectrum Disorder at Multiple Levels of Biological Analysis
Authors: Schaffer Lukas S. , Breunig Sophie , Lawrence Jeremy M. , Foote Isabelle F. , Grotzinger Andrew D.
Published: June 2024

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by atypical patterns of social functioning and repetitive/restricted behaviors. ASD commonly co-occurs with ADHD and, despite their clinical distinctiveness, the two share considerable genetic overlap. Given their shared genetic liability, it is unclear which genetic pathways confer unique risk for ASD independent of ADHD. We applied Genomic Structural Equation Modeling (SEM) to GWAS summary statistics for ASD and ADHD, decomposing the genetic signal for ASD into that which is unique to ASD (uASD)and that which is shared with ADHD. We computed genetic correlations betweenuASDand 75 external traits to estimate genetic overlap betweenuASDand other clinically relevant phenotypes. We went on to apply Stratified Genomic SEM to identify classes of genes enriched foruASD. Finally, we implemented Transcriptome-Wide SEM (T-SEM) to explore patterns of gene-expression associated withuASD. We observed positive genetic correlations betweenuASDand several external traits, most notably those relating to cognitive/educational outcomes and internalizing psychiatric traits. Stratified Genomic SEM showed that heritability foruASDwas significantly enriched in genes involved in evolutionarily conserved processes, as well as for a histone mark in the germinal matrix. T-SEM revealed 83 unique genes with expression associated withuASD,many of which were novel. These findings delineate the unique biological underpinnings of ASD which exist independent of ADHD and demonstrate the utility of Genomic SEM and its extensions for disambiguating shared and unique risk pathways for genetically overlapping traits.
Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA
Authors: Mahajan Mayank , Hemberg Martin
Published: June 2024

Cancer is the second leading cause of death worldwide, and although there have been advances in treatments, including immunotherapies, these often require biopsies which can be costly and invasive to obtain. Due to lack of pre-emptive cancer detection methods, many cases of cancer are detected at a late stage when the definitive symptoms appear. Plasma samples are relatively easy to obtain, and they can be used to monitor the molecular signatures of ongoing processes in the body. Profiling cell-free DNA is a popular method for monitoring cancer, but only a few studies have explored the use of cell-free RNA (cfRNA), which shows the recent footprint of systemic transcription. Here we developed FastNeo, a computational method for detecting known neoepitopes in human cfRNA. We show that neoepitopes and other biomarkers detected in cfRNA can discern Hepatocellular carcinoma (HCC) patients from the healthy patients with a sensitivity of 0.84 and a specificity of 0.79. For colorectal cancer we achieve a sensitivity of 0.87 and a specificity of 0.8. An important advantage of our cfRNA based approach is that it also reports putative neoepitopes which are important for therapeutic purposes.
5-axis CNC micro-milling machine for three-dimensional microfluidics
Authors: Modarelli Mitchell J. C. , Kot-Thompson Devin M. , Hoshino Kazunori
Published: June 2024

The gold standard of microfluidic fabrication techniques, SU-8 patterning, requires photolithography equipment and facilities and is not suitable for 3D microfluidics. A 3D printer is more convenient and may achieve high resolutions comparable to conventional photolithography, but only with select materials. Alternatively, 5-axis CNC micro-milling machines can efficiently prototype structures with high resolutions, high aspect ratios, and non-planar geometries from a variety of materials. These machines, however, have not been catered for laboratory-based, small-batch microfluidics development and are largely inaccessible to researchers. In this paper, we present a new 5-axis CNC micro-milling machine specifically designed for prototyping 3D microfluidic channels, made affordable for research and laboratories. The machine is assembled from commercially available products and custom-build parts, occupying 0.72 cubic meters, and operating entirely from computer aided design (CAD) and manufacturing (CAM) software. The 5-axis CNC micro-milling machine achieves sub-µm bidirectional repeatability (≤0.23 µm), machinable features <20 µm, and a work volume of 50 x 50 x 68 mm. The tool compatibility and milling parameters were designed to enable fabrication of virtually any mill-able material including metals like aluminum, brass, stainless steel, and titanium alloys. To demonstrate milling high resolution and high aspect ratios, we milled a thin wall from 360 brass with a width of 18.1 µm and an aspect ratio of ∼50:1. We also demonstrated fabricating molds from 360 brass with non-planar geometries to create PDMS microfluidic channels. These included a channel on a 90° edge and a channel on a rounded edge with a 250-µm radius of curvature. Our 5-axis CNC micro-milling machine offers the most versatility in prototyping microfluidics by enabling high resolutions, geometric complexity, a large work volume, and broad material compatibility, all within a user-friendly benchtop system.
The genetic basis of the black pupae phenotype in tephritid fruit flies
Authors: Paulo Daniel F. , Nguyen Thu N.M. , Ward Chris M. , Corpuz Renee L. , Kauwe Angela N. , Rendon Pedro , Ruano Rocio E.Y. , Cardoso Amanda A.S. , Gouvi Georgia , Fung Elisabeth , Crisp Peter , Okada Anzu , Choo Amanda , Stauffer Christian , Bourtzis Kostas , Sim Sheina B. , Baxter Simon W. , Geib Scott M.
Published: June 2024

The remarkable diversity of insect pigmentation offers a captivating avenue for exploring evolution and genetics. In tephritid fruit flies, decoding the molecular pathways underlying pigmentation traits also plays a central role in applied entomology. Mutant phenotypes like the black pupae (bp) have long been used as a component of genetic sexing strains, allowing male-only release in tephritid sterile insect technique applications. However, the genetic basis of bp remains largely unknown. Here, we present independent evidence from classical and modern genetics showing that the bp phenotype in the GUA10 strain of the Mexican fruit fly,Anastrepha ludens, is caused by a large deletion at theebonylocus resulting in the removal of the entire protein-coding region of the gene. Targeted knockout ofebonyinduced analogous bp phenotypes across six tephritid species spanning over 50 million years of divergent evolution. This functionally validated our findings and allowed for a deeper investigation into the role of Ebony in pigmentation and development in these species. Our study offers fundamental knowledge for developing new sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritid fruit flies.
Exon Nomenclature and Classification of Transcripts (ENACT): Systematic framework to annotate exon attributes
Authors: Verma Paras , Thakur Deeksha , Pandit Shashi Bhushan
Published: June 2024

Abstract

Motivation

Isoform diversity is known to enhance a gene’s functional repertoire. Despite studies on transcriptome diversifying processes (Alternate splicing/transcription), their extent and correlated impact on proteome diversity remains rudimentarily understood.

Results

The current study presents an innovative framework, “Exon Nomenclature and Annotation of Transcripts,” that centralizes exonic loci while integrating protein sequenceper entitywith tracking and assessing splice site variability. The resulting annotation from framework enables exon features to be tractable, facilitating a systematic analysis of isoform diversity. Our findings and case studies unveil systemic exon inclusion’s roles in regulating diversity in CDS region.

Availability and implementation

All data generated during this study are publicly available atwww.iscbglab.in/enactdb/. Associated algorithmic procedures have been described in the methods section.

Supplementary information

PDF file enclosing supplementary data attached.
Differences in systemic immune parameters in individuals with lung cancer according to race
Authors: von Itzstein Mitchell S. , Liu Jialiang , Mu-Mosley Hong , Fattah Farjana , Park Jason Y. , SoRelle Jeffrey A. , Farrar J. David , Gwin Mary E. , Hsiehchen David , Gloria-McCutchen Yvonne , Wakeland Edward K. , Cole Suzanne , Bhalla Sheena , Kainthla Radhika , Puzanov Igor , Switzer Benjamin , Daniels Gregory A. , Zakharia Yousef , Shaheen Montaser , Zhang Jianjun , Xie Yang , Gerber David E.
Published: June 2024

Introduction

Racial and ethnic disparities in the presentation and outcomes of lung cancer are widely known. To evaluate potential factors contributing to these observations, we measured systemic immune parameters in Black and White patients with lung cancer.

Methods

Patients scheduled to receive cancer immunotherapy were enrolled in a multi-institutional prospective biospecimen collection registry. Clinical and demographic information were obtained from electronic medical records. Pre-treatment peripheral blood samples were collected and analyzed for cytokines using a multiplex panel and for immune cell populations using mass cytometry. Differences between Black and White patients were determined and corrected for multiple comparisons.

Results

A total of 187 patients with non-small cell lung cancer (Black, 19; White, 168) were included in the analysis. There were no significant differences in baseline characteristics between Black and White patients. Compared to White patients, Black patients had significantly lower levels of CCL23 and CCL27, and significantly higher levels of CCL8, CXCL1, CCL26, CCL25, CCL1, IL-1 b, CXCL16, and IFN-γ (allP<0.05, FDR<0.1). Black patients also exhibited greater populations of non-classical CD16+ monocytes, NKT-like cells, CD4+ cells, CD38+ monocytes, and CD57+ gamma delta T cells (allP<0.05).

Conclusions

Black and White patients with lung cancer exhibit several differences in immune parameters, with Black patients exhibiting greater levels of numerous pro-inflammatory cytokines and cell populations. The etiology and clinical significance of these differences warrant further evaluation.
Diminished Immune Cell Adhesion in Hypoimmune ICAM-1 Knockout Pluripotent Stem Cells
Authors: Saha Sayandeep , Haynes W. John , Del Rio Natalia M. , Young Elizabeth E. , Zhang Jue , Seo Jiwon , Huang Liupei , Holm Alexis M. , Blashka Wesley , Murphy Lydia , Scholz Merrick J. , Henrichs Abigale , Suresh Babu Jayalaxmi , Steill John , Stewart Ron , Kamp Timothy J. , Brown Matthew E.
Published: June 2024

Hypoimmune gene edited human pluripotent stem cells (hPSCs) are a promising platform for developing reparative cellular therapies that evade immune rejection. Existing first-generation hypoimmune strategies have used CRISPR/Cas9 editing to modulate genes associated with adaptive (e.g., T cell) immune responses, but have largely not addressed the innate immune cells (e.g., monocytes, neutrophils) that mediate inflammation and rejection processes occurring early after graft transplantation. We identified the adhesion molecule ICAM-1 as a novel hypoimmune target that plays multiple critical roles in both adaptive and innate immune responses post-transplantation. In a series of studies, we found that ICAM-1 blocking or knock-out (KO) in hPSC-derived cardiovascular therapies imparted significantly diminished binding of multiple immune cell types. ICAM-1 KO resulted in diminished T cell proliferation responsesin vitroand in longerin vivoretention/protection of KO grafts following immune cell encounter in NeoThy humanized mice. The ICAM-1 KO edit was also introduced into existing first-generation hypoimmune hPSCs and prevented immune cell binding, thereby enhancing the overall hypoimmune capacity of the cells. This novel hypoimmune editing strategy has the potential to improve the long-term efficacy and safety profiles of regenerative therapies for cardiovascular pathologies and a number of other diseases.

Highlights

Antibody blocking of ICAM-1 on human pluripotent stem cell-derived cells inhibits immune cell adhesion

CRISPR/Cas9 knock-out of ICAM-1 ablates surface and secreted ICAM-1 protein and inhibits immune adhesion

ICAM-1 knock-out results in decreased T cell proliferative responses to human pluripotent stem cell-derived graftsin vitro, and resistance to immune-mediated graft lossin vivo

Addition of ICAM-1 knock-out to first generation MHC knock-out human pluripotent stem cells confers protection against immune adhesion

Graphical Abstract

ICAM-1 Knock-out in Transendothelial Migration and at the Immune Synapse.

Abbreviations: PSC-EC – pluripotent stem cell-derived endothelial cells; KO – knock-out; dSMAC – distal supramolecular activation complex; pSMAC – peripheral supramolecular activation complex; cSMAC – central supramolecular activation complex.
Adenine nucleotide translocase 2 silencing promotes metabolic adaptations and anoikis in P19 embryonal carcinoma stem cells
Authors: Oliveira Gabriela L. , Mota Sandra I. , Oliveira Paulo J. , Marques Ricardo
Published: June 2024

Cancer stem cells (CSCs) are amongst the group of cells constituting tumors, being characterized by their strong self-renewal and survival properties. Cancer cells, CSCs included, are thought to rely mostly on glycolysis, even in the presence of oxygen, which confers them adaptative advantages. Adenine nucleotide translocator 2 (ANT2), responsible for the exchange of ADP and ATP in the mitochondrial inner membrane, has been correlated with a higher glycolytic metabolism and is known to be overexpressed in cancer cells. Using P19 embryonal carcinoma stem cells (P19SCs) as a CSCs model, we inhibit ANT2 translation by using siRNA. ANT2 protein levels were shown to be overexpressed in P19SC when compared to their differentiated counterparts. Furthermore, we showed here that the OXPHOS machinery and mitochondrial membrane potential are compromised after ANT2 depletion, exhibiting a metabolic adaptation towards a less oxidative phenotype. Interestingly, hexokinase II levels were downregulated, which was also accompanied by decreased cell growth, and decreased ability to form spheroids. Our findings underscore ANT2 as a key regulator of metabolic remodeling and cell survival of CSCs, suggesting its potential as a therapeutic target for controlling CSC-driven tumor progression.

Highlights

ANT2 silencing promotes cell growth arrest and metabolic remodeling in CSCs.

ANT2 depletion modulates HKII protein levels.

ANT2 induce anoikis resistance in P19SCs
Accelerating Protein-Protein Interaction screens with reduced AlphaFold-Multimer sampling
Authors: Bellinzona G. , Sassera D. , Bonvin A.M.J.J
Published: June 2024

Motivation

Discovering new protein-protein interactions (PPIs) across entire proteomes offers vast potential for understanding novel protein functions and elucidate system properties within or between an organism. While recent advances in computational structural biology, particularly AlphaFold-Multimer, have facilitated this task, scaling for large-scale screenings remains a challenge, requiring significant computational resources.

Results

We evaluated the impact of reducing the number of models generated by AlphaFold-Multimer from five to one on the method’s ability to distinguish true PPIs from false ones. Our evaluation was conducted on a dataset containing both intra- and inter-species PPIs, which included proteins from bacterial and eukaryotic sources. We demonstrate that reducing the sampling does not compromise the accuracy of the method, offering a 5 time faster, efficient, and environmentally friendly solution for PPI predictions.

Availability

The code used in this article is available athttps://github.com/MIDIfactory/AlphaFastPPi. Note that the same can be achieved using the latest version of AlphaPulldown available athttps://github.com/KosinskiLab/AlphaPulldown.
Complex compositional and cellular response of river sediment microbiomes to multiple anthropogenic stressors
Authors: Stach Tom Lennard , Deep Aman , Madge Pimentel Iris , Buchner Dominik , Borton Mikayla A , Soares Andre , Starke Joern , Bornemann Till L.V. , Rehsen Philipp M. , Boenigk Jens , Vos Matthijs , Leese Florian , Beisser Daniela , Probst Alexander J
Published: June 2024

Rivers face constant anthropogenic stressors, resulting in significant changes in microbial community composition. What remains unclear is whether these changes render the microbiome better adapted to the stressed environment. Here, by subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to lowered flow velocity resulting in substantially altered community compositions not fully capable of compensating for the stressor effect within two weeks albeit having stable functions encoded in metagenomes. Transcriptomics revealed a systematic heat shock response in the community and a highly active, previously unknown anaerobic key stone species with great metabolic versatility. Increases in temperature (+3.5 degrees C) or salinity (+0.5 mS/cm) were outcompeted by lowered flow and elicited only minor responses at community or transcriptomic level with, e.g., upregulation of the photosystem of chloroplasts. Following a two week recovery period, transcriptomic stress responses vanished completely compared to control mesocosms, exemplifying the river microbiomes' resilience. We conclude that, given the complex community responses at both the cellular and compositional level, maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.
Marginated neutrophils in the lungs effectively compete for nanoparticles targeted to the endothelium, serving as a part of the reticuloendothelial system
Authors: Zamora Marco E. , Essien Eno-Obong , Bhamidipati Kartik , Murthy Aditi , Liu Jing , Kim Hyunjun , Patel Manthan N. , Nong Jia , Wang Zhicheng , Espy Carolann , Chaudhry Fatima N. , Ferguson Laura , Tiwari Sachchidanand , Hood Elizabeth , Marcos-Contreras Oscar A. , Omo-Lamai Serena , Shuvaeva Tea , Arguiri Evguenia , Wu Jichuan , Rauova Lubica , Poncz Mortimer , Basil Maria C. , Cantu Edward , Planer Joseph D. , Spiller Kara , Zepp Jarod , Muzykantov Vladimir , Myerson Jacob , Brenner Jacob S.
Published: June 2024

Nanomedicine has long pursued the goal of targeted delivery to specific organs and cell types but has not achieved this goal with the vast majority of targets. One rare example of success in this pursuit has been the 25+ years of studies targeting the lung endothelium using nanoparticles conjugated to antibodies against endothelial surface molecules. However, here we show that such “endothelial-targeted” nanocarriers also effectively target the lungs’ numerous marginated neutrophils, which reside in the pulmonary capillaries and patrol for pathogens. We show that marginated neutrophils’ uptake of many of these “endothelial-targeted” nanocarriers is on par with endothelial uptake. This generalizes across diverse nanomaterials and targeting moieties and was even found with physicochemical lung tropism (i.e., without targeting moieties). Further, we observed this inex vivohuman lungs andin vivohealthy mice, with an increase in marginated neutrophil uptake of nanoparticles caused by local or distant inflammation. These findings have implications for nanomedicine development for lung diseases. These data also suggest that marginated neutrophils, especially in the lungs, should be considered a major part of the reticuloendothelial system (RES), with a special role in clearing nanoparticles that adhere to the lumenal surfaces of blood vessels.

Graphical Abstract
Multi-objective management of naturally regenerating beech forests – An ecological-economic optimization approach
Authors: Schorn Markus E. , Quaas Martin F. , Schenk Hanna , Wirth Christian , Rüger Nadja
Published: June 2024

How can we meet economic objectives of timber harvesting while maintaining the functioning of diverse forest ecosystems? Existing forest models that address this type of question are often complex, data-intensive, challenging to couple with economic optimization models, or can not easily be generalised for uneven-aged mixed-species forests. Here, we develop an ecological-economic optimization model, which integrates a state-of-the-art demographic forest model with a continuous cover forestry harvesting model to optimise efficient and sustainable timber harvesting. As a proof-of-concept, we apply the model to a beech-dominated forest in the Hainich-Dün region in Thuringia, Germany, with the goal of optimising multiple objectives such as timber yield and the biodiversity value of the forest. The ecological module is the Perfect Plasticity Approximation (PPA) demographic forest model that simulates forest dynamics based on individual tree growth and survival rates in the canopy and understory layers, respectively, as well as recruitment rates. We used repeated forest inventory data from a 28-ha forest plot to quantify these demographic rates and validated the predictions of the ecological module against the structure of old-growth beech forests in Europe. The economic module includes the optimization of net revenues (market revenues net of harvesting cost) from harvesting timber. As an indicator of the biodiversity value of the forest, we use the number of retained habitat trees (>70 cm diameter). The forest model delivered reasonable predictions of structural attributes of unmanaged old-growth beech forests. When net revenues from timber harvest were maximised, trees were logged when they reached 55 cm in diameter. This is similar to current management practices in beech forests. We found a linear trade-off between timber net revenues and biodiversity value with about 2.5% of the maximum benefit of timber harvest being lost with each additionally retained habitat tree. We established a generic ecological-economic modelling framework that reliably represents forest dynamics as well as optimising forest management. To our knowledge, this is the first forest model for central European forests capable of identifying optimal harvesting over the full set of feasible strategies, rather than merely comparing predefined management scenarios. The framework can be extended to mixed-species forests and support forest management for diverse ecosystem services.
Strain identity effects contribute more toPseudomonascommunity functioning than strain interactions
Authors: Kramer Jos , Maréchal Simon , Figueiredo Alexandre R.T. , Kümmerli Rolf
Published: June 2024

Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of fluorescentPseudomonasbacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strains interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.
SeqLengthPlot: An easy-to-use Python-based Tool for Visualizing and Retrieving Sequence Lengths from fasta files with a Tunable Splitting Point
Authors: Domínguez-Pérez Dany , Agüero-Chapin Guillermin , Leone Serena , Modica Maria Vittoria
Published: June 2024

Motivation

Accurate sequence length profiling is essential in bioinformatics, particularly in genomics and proteomics. Existing tools like SeqKit and the Trinity toolkit, among others provide basic sequence statistics but often fall short in offering comprehensive analytics and plotting options. For instance, SeqKit is a very complete and fast tool for sequence analyses, that delivers useful metrics (e.g., number of sequences, average, minimum, maximum length), and can returns the range of sequence shorter or longer (one side, not both at once) on a given lengths. Similarly, Trinity’s utility pearl-based scripts provide detailed contig length distributions (e.g., N50, median, and average lengths) but do not encompass the total number of sequences nor offer graphical representations of data.

Results

Given that key sequence analysis tasks are distributed among separate tools, we introduce SeqLengthPlot: an easy-to-use Python-based script that fills existing gaps in bioinformatics tools on sequence length profiling, crucial. SeqLengthPlot generates comprehensive statistical summaries, filtering and automatic sequences retriving from the input FASTA (nucleotide and proteins) file into two distinct files based on a tunable, user-defined sequence length, as well as the plots or dynamic visualizations of the corresponding sequences.

Availability and implementation

The detailed SeqLengthPlot pipeline is available on GitHub athttps://github.com/danydguezperez/SeqLengthPlot, released under the GPL-3.0 license. Additional datasets used as sources or compiled as use cases are publicy available through the Mendeley Data repository:DATASET_Ss_SE.1:http://dx.doi.org/10.17632/pmxwfjyyvy.1,DATASET_Ss_SE.2:http://dx.doi.org/10.17632/3rtbr7c9s8.1,DATASET_Ss_SE.3:http://dx.doi.org/10.17632/wn5kbk5ryy.1,DATASET_Ss_SE.4:http://dx.doi.org/10.17632/sh79mdcm2c.1andDATASET_Ss_SE.5:http://dx.doi.org/10.17632/zmvvff35dx.1.
Interactive data exploration websites for large-scale electrophysiology
Authors: Birman Daniel , Chapuis Gaelle , Faulkner Mayo , Rossant Cyrille ,   the International Brain Laboratory, Benson Julius , Catarino Joana A , Churchland Anne K , Hu Fei , Huntenburg Julia M , Khanal Anup , Krasniak Christopher , Lau Petrina Y P , Meijer Guido T , Miska Nathaniel J , Noel Jean-Paul , Pan-Vazquez Alejandro , Roth Noam , Schartner Michael , Socha Karolina Z , Steinmetz Nicholas A , Urai Anne E , Wells Miles J , West Steven J , Winter Olivier
Published: June 2024

Methodological advances in neuroscience have enabled the collection of massive datasets which demand innovative approaches for scientific communication. Existing platforms for data storage lack intuitive tools for data exploration, limiting our ability to interact effectively with these brain-wide datasets. We introduce two public websites: Data and Atlas developed for the International Brain Laboratory which provide access to millions of behavioral trials and hundreds of thousands of individual neurons. These interfaces allow users to discover both the raw and processed brain-wide data released by the IBL at the scale of the whole brain, individual sessions, trials, and neurons. By hosting these data interfaces as websites they are available cross-platform with no installation. By releasing each site's code as a modular open-source framework, other researchers can easily develop their own web interfaces and explore their own data. As neuroscience datasets continue to expand, customizable web interfaces offer a glimpse into a future of streamlined data exploration and act as blueprints for future tools.
A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression inNeurospora crassa
Authors: Reckard Andrew T. , Pandeya Abhishek , Voris Jacob M. , Gonzalez Cruz Carlos G. , Oluwadare Oluwatosin , Klocko Andrew D.
Published: June 2024

Background

Organization of the eukaryotic genome is essential for proper function, including gene expression. In metazoans, chromatin loops and Topologically Associated Domains (TADs) organize genes into transcription factories, while chromosomes occupy nuclear territories in which silent heterochromatin is compartmentalized at the nuclear periphery and active euchromatin localizes to the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation typified by heterochromatic centromeres and telomeres independently clustering at the nuclear membrane, while interspersed heterochromatic loci aggregate across Megabases of linear genomic distance to loop chromatin in TAD-like structures. However, the role of individual heterochromatic loci in normal genome organization and function is unknown.

Results

We examined the genome organization of a Neurospora strain harboring a ∼47.4 kilobase deletion within a temporarily silent, facultative heterochromatic region, as well as the genome organization of a strain deleted of a 110.6 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion minimally effects local chromatin structure or telomere clustering, the constitutive heterochromatin deletion alters local chromatin structure, the predicted three-dimensional chromosome conformation, and the expression of some genes, which are qualitatively repositioned into the nucleus center, while increasing Hi-C variability.

Conclusions

Our work elucidates how an individual constitutive heterochromatic region impacts genome organization and function. Specifically, one silent region indirectly assists in the hierarchical folding of the entire Neurospora genome by aggregating into the “typical” heterochromatin bundle normally observed in wild type nuclei, which may promote normal gene expression by positioning euchromatin in the nucleus center.
α-Synuclein Overexpression and the Microbiome Shape the Gut and Brain Metabolome in Mice
Authors: Morais Livia H. , Boktor Joseph C. , MahmoudianDehkordi Siamak , Kaddurah-Daouk Rima , Mazmanian Sarkis K.
Published: June 2024

Pathological forms of the protein α-synuclein contribute to a family of disorders termed synucleinopathies, which includes Parkinson’s disease (PD). Most cases of PD are believed to arise from gene-environment interactions. Microbiome composition is altered in PD, and gut bacteria are causal to symptoms and pathology in animal models. To explore how the microbiome may impact PD-associated genetic risks, we quantitatively profiled nearly 630 metabolites from 26 biochemical classes in the gut, plasma, and brain of α-synuclein-overexpressing (ASO) mice with or without microbiota. We observe tissue-specific changes driven by genotype, microbiome, and their interaction. Many differentially expressed metabolites in ASO mice are also dysregulated in human PD patients, including amine oxides, bile acids and indoles. Notably, levels of the microbial metabolite trimethylamine N-oxide (TMAO) strongly correlate from the gut to the plasma to the brain, identifying a product of gene-environment interactions that may influence PD-like outcomes in mice. TMAO is elevated in the blood and cerebral spinal fluid of PD patients. These findings uncover broad metabolomic changes that are influenced by the intersection of host genetics and the microbiome in a mouse model of PD.
Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images
Authors: Riendeau Jeremiah M , Gillette Amani A , Guzman Emmanuel Contreras , Cruz Mario Costa , Kralovec Aleksander , Udgata Shirsa , Schmitz Alexa , Deming Dustin A , Cimini Beth A , Skala Melissa C
Published: June 2024

Autofluorescence microscopy uses intrinsic sources of molecular contrast to provide cellular-level information without extrinsic labels. However, traditional cell segmentation tools are often optimized for high signal-to-noise ratio (SNR) images, such as fluorescently labeled cells, and unsurprisingly perform poorly on low SNR autofluorescence images. Therefore, new cell segmentation tools are needed for autofluorescence microscopy. Cellpose is a deep learning network that is generalizable across diverse cell microscopy images and automatically segments single cells to improve throughput and reduce inter-human biases. This study aims to validate Cellpose for autofluorescence imaging, specifically from multiphoton intensity images of NAD(P)H. Manually segmented nuclear masks of NAD(P)H images were used to train new Cellpose models. These models were applied to PANC-1 cells treated with metabolic inhibitors and patient-derived cancer organoids (across 9 patients) treated with chemotherapies. These datasets include co-registered fluorescence lifetime imaging microscopy (FLIM) of NAD(P)H and FAD, so fluorescence decay parameters and the optical redox ratio (ORR) were compared between masks generated by the new Cellpose model and manual segmentation. The Dice score between repeated manually segmented masks was significantly lower than that of repeated Cellpose masks (p<0.0001) indicating greater reproducibility between Cellpose masks. There was also a high correlation (R2>0.9) between Cellpose and manually segmented masks for the ORR, mean NAD(P)H lifetime, and mean FAD lifetime across 2D and 3D cell culture treatment conditions. Masks generated from Cellpose and manual segmentation also maintain similar means, variances, and effect sizes between treatments for the ORR and FLIM parameters. Overall, Cellpose provides a fast, reliable, reproducible, and accurate method to segment single cells in autofluorescence microscopy images such that functional changes in cells are accurately captured in both 2D and 3D culture.
Disorders in lipid metabolism, oxidative stress, and antioxidants in patients with amnestic mild cognitive impairment without major depression
Authors: Nantachai Gallayaporn , Maes Michael , Tran-Chi Vinh-Long , Amrapala Arisara , Vasupanrajit Asara , Hemrungrojn Solaphat , Tunvirachaisakul Chavit
Published: June 2024

Background

Amnestic mild cognitive impairment (aMCI) is characterized by changes in lipids and oxidative stress (OS). It is crucial to exclude patients with major depression (MDD) to accurately evaluate these biomarkers in aMCI.

Aims

To examine lipid and oxidative stress biomarkers associated with aMCI versus normal controls.

Methods

We performed a case-control analysis involving 61 individuals with aMCI (without MDD) and 60 healthy controls. We assessed the severity of aMCI, distress symptoms of old age, and lipid/OS biomarkers.

Results

The levels of serum -SH groups were significantly higher in individuals with aMCI, while the levels of malondialdehyde (MDA) were significantly lower in the same group. Serum advanced oxidation protein products, glutathione, and folic acid did not show any notable variations. In individuals with aMCI, we observed an elevated apolipoprotein B (ApoB)/ApoA ratio, as well as decreased levels of high-density lipoprotein cholesterol (HDL), ApoA, and a reverse cholesterol transport (RCT) index. The simultaneous presence of aMCI and subclinical depressive symptoms is marked by elevated levels of triglycerides and ApoB, as well as decreased levels of ApoA and HDL. A significant portion of the variability (24.9%) in a quantitative MCI severity score can be attributed to -SH groups, age (positively), MDA and education (inversely).

Discussion

The alterations in MDA and -SH levels in aMCI may potentially disrupt redox signaling, which can affect cell signaling and homeostatic setpoints. The interaction between aMCI and subclinical depressive symptoms can lead to increased atherogenicity and reduced antiatherogenic protection.
Geographic patterns of the number of root canals in permanent molars. A Systematic Review
Authors: Chaple Gil Alain Manuel , Santiesteban Velázquez Meylin , Afrashtehfar Kelvin Ian
Published: June 2024

Introduction

The variability in the distribution and number of root canals in human permanent molars makes endodontic therapy difficult if the prevalence of these patterns is not well known.

Objective

To synthesize scientific evidence on geographical variations in the number of root canals in permanent molars.

Methods

A study conducted at the University of Medical Sciences of Havana analyzed the number of root canals in permanent molars. We searched for primary studies published in English, Spanish, or Portuguese that reported the number of canals in each tooth. We excluded clinical case studies, editorials, and studies that did not provide specific information on duct anatomy. A sensitivity analysis was performed to assess the impact of the methodological quality of the studies in the two groups. The findings were synthesized by grouping the studies by geographical region and describing the prevalence of different root canal configurations.

Results

Data on permanent molars were collected from 93 studies that contributed 60402 molars studied. In Africa, the first and second upper molars commonly have three root canals (45.62% and 41.31%, respectively), similar to the first and second lower molars (59.79% and 67.55%, respectively). In America, the upper first molar most frequently has four root canals (56.66%). In Asia, it is more common to find that all molar groups have three canals (51.09%– 65.58%), except for the lower thirds, which may have two or three canals (42.88% and 57.12%). In Europe, all molars are frequently present with three canals, except for the lower third. In Oceania, the first upper molars commonly have six root canals (65%).

Conclusion

Significant variations in the number of root canals in permanent molars according to geographic region were observed. Distinct patterns were observed in the Americas, Asia, Africa, Europe, and Oceania, with varying prevalences of different root canal configurations.
Large-scale generation of uniform sub-100 μm adipocyte spheroids in hydrogel microcapsules using a flow-focusing microfluidic device
Authors: Maekawa Ruri , Hattori Kazuki , Kirisako Hiromi , Iwamoto Yuichiro , Kawasaki Fumiko , Yoneshiro Takeshi , Sakai Juro , Ota Sadao
Published: June 2024

Adipocyte spheroids are a promising three-dimensional (3D) cell culture model for obesity research because they reproduce 3D adipose tissue structures and cell-cell interactions better than 2D cultures. However, current methods fail to produce uniformly sized, small adipocyte spheroids at large scales, significantly limiting their use in analysis such as large-scale drug screening. Here, we develop a scalable method that combines simple microfluidics with templated emulsification to generate small, uniformly sized adipocyte spheroids. By encapsulating preadipocytes in numerous hollow agarose microcapsules and incubating them for two days, we reproducibly produced more than 100,000 uniform spheroids with diameters of approximately 50 µm (CV: <13%); we then differentiated preadipocyte spheroids into adipocyte spheroids after an 8-day induction period. Our platform enhances large-scale 3D analysis using adipocyte spheroids for obesity research and can be adapted to generate various spheroid and organoid models, advancing biomedical research across diverse fields.
Identification of genetic modifiers of Huntington’s disease somatic CAG repeat instability by in vivo CRISPR-Cas9 genome editing
Authors: Mouro Pinto Ricardo , Murtha Ryan , Azevedo António , Douglas Cameron , Kovalenko Marina , Ulloa Jessica , Crescenti Steven , Burch Zoe , Oliver Esaria , Vitalo Antonia , Mota-Silva Eduarda , Riggs Marion J. , Correia Kevin , Elezi Emanuela , Demelo Brigitte , Carroll Jeffrey B. , Gillis Tammy , Gusella James F. , MacDonald Marcy E. , Wheeler Vanessa C.
Published: June 2024

Huntington’s disease (HD), one of >50 inherited repeat expansion disorders (Depienne and Mandel, 2021), is a dominantly-inherited neurodegenerative disease caused by a CAG expansion inHTT(The Huntington’s Disease Collaborative Research Group, 1993). Inherited CAG repeat length is the primary determinant of age of onset, with human genetic studies underscoring that the property driving disease is the CAG length-dependent propensity of the repeat to further expand in brain (Swamiet al., 2009; GeM-HD, 2015; Hensman Mosset al., 2017; Ciosiet al., 2019; GeM-HD, 2019; Honget al., 2021). Routes to slowing somatic CAG expansion therefore hold great promise for disease-modifying therapies. Several DNA repair genes, notably in the mismatch repair (MMR) pathway, modify somatic expansion in HD mouse models (Wheeler and Dion, 2021). To identify novel modifiers of somatic expansion, we have used CRISPR-Cas9 editing in HD knock-in mice to enablein vivoscreening of expansion-modifier candidates at scale. This has included testing of HD onset modifier genes emerging from human genome-wide association studies (GWAS), as well as interactions between modifier genes, thereby providing new insight into pathways underlying CAG expansion and potential therapeutic targets.
Endothelin B receptor inhibition rescues aging-dependent neuronal regenerative decline
Authors: Feng Rui , Rosen Sarah F. , Ansari Irshad , John Sebastian , Thomsen Michael B. , Geoffroy Cedric G. , Cavalli Valeria
Published: June 2024

Peripheral sensory neurons regenerate their axons after injury to regain function, but this ability declines with age. The mechanisms behind this decline are not fully understood. While excessive production of endothelin 1 (ET-1), a potent vasoconstrictor, is linked to many diseases that increase with age, the role of ET-1 and its receptors in axon regeneration is unknown. Using a single cell RNAseq approach, we reveal that in dorsal root ganglia (DRG), satellite glial cells (SGCs), which completely envelop the sensory neuron soma, express the endothelin B receptor (ETBR), while ET-1 is expressed by endothelial cells. Inhibition of ETBRex-vivoin DRG explant cultures improves axon growth in both adult and aged conditions. In vivo,treatment with the FDA- approved compound, Bosentan, improves axon regeneration and reverses the age-dependent decrease in axonal regenerative capacity. Bosentan treatment also enhances the expression of connexin 43 in SGCs after injury in adult and aged mice. These results reveal that inhibiting ETBR function enhances axon regeneration and rescues the age-dependent decrease in axonal regenerative capacity, providing a potential avenue for future therapies.

One Sentence Summary

Inhibition of endothelin signaling improves nerve regeneration after central and peripheral injuries and counters age-related regenerative decline.