bluuebunny/crossref_metadata_2025 huggingface dataset:
Unique and Common Agonists Activate the Insect Juvenile Hormone Receptor and the Human AHR
Authors: Sedlak David , Tuma Roman , Kolla Jayaprakash Narayana , Mokhamatam Raveendra Babu , Bahrova Liliia , Lisova Michaela , Bittova Lenka , Jindra Marek
Published: January 2024

Abstract

Transcription factors of the bHLH-PAS family play vital roles in animal development, physiology, and disease. Two members of the family require binding of low-molecular weight ligands for their activity: the vertebrate aryl hydrocarbon receptor (AHR) and the insect juvenile hormone receptor (JHR). In the flyDrosophila melanogaster, the paralogous proteins GCE and MET constitute the ligand-binding component of JHR complexes. Whilst GCE/MET and AHR are phylogenetically heterologous, their mode of action is similar. JHR is targeted by several synthetic agonists that serve as insecticides disrupting the insect endocrine system. AHR is an important regulator of human endocrine homeostasis and it responds to environmental pollutants and endocrine disruptors. Whether AHR signaling is affected by compounds that can activate JHR has not been reported. To address this question, we screened a chemical library of 50,000 compounds to identify 93 novel JHR agonists in a reporter system based onDrosophilacells. Of these compounds, 26% modulated AHR signaling in an analogous reporter assay in a human cell line, indicating a significant overlap in the agonist repertoires of the two receptors. To explore the structural features of agonist-dependent activation of JHR and AHR, we compared the ligand-binding cavities and their interactions with selective and common ligands of AHR and GCE. Molecular dynamics modeling revealed ligand-specific as well as conserved side chains within the respective cavities. Significance of predicted interactions was supported through site-directed mutagenesis. The results have indicated that synthetic insect juvenile hormone agonists might interfere with AHR signaling in human cells.
PredictingAluexonization in the human genome with a deep learning model
Authors: He Zitong , Chen Ou , Phillips Noelani , Pasquesi Giulia Irene Maria , Sabunciyan Sarven , Florea Liliana
Published: January 2024

Aluexonization, or the recruitment of intronicAluelements into gene sequences, has contributed to functional diversification; however, its extent and the ways in which it influences gene regulation are not fully understood. We developed an unbiased approach to predictAluexonization events from genomic sequences implemented in a deep learning model, eXAlu, that overcomes the limitations of tissue or condition specificity and the computational burden of RNA-seq analysis. The model captures previously reported characteristics of exonizedAlusequences and can predict sequence elements important forAluexonization. Using eXAlu, we estimate the number ofAluelements in the human genome undergoing exonization to be between 55-110K, 11-21 fold more than represented in the GENCODE gene database. Using RT-PCR we were able to validate selected predictedAluexonization events, supporting the accuracy of our method. Lastly, we highlight a potential application of our method to identify polymorphicAluinsertion exonizations in individuals and in the population from whole genome sequencing data.
Hidden route of protein damage through confined oxygen gas
Authors: Kim Seoyoon , Kim Eojin , Park Mingyu , Kim Seong Ho , Kim Byung-Gyu , Sadongo Victor W. , Wijesinghe W.C. Bhashini , Eom Yu-Gon , Yoon Gwangsu , Lee Chaiheon , Jeong Hannah , Kim Chae Un , Myung Kyungjae , Choi Jeong-Mo , Min Seung Kyu , Kwon Tae-Hyuk , Min Duyoung
Published: January 2024

Oxidative modifications can severely impair protein structure, fold, and function, closely linked to human aging and diseases. Conventional oxidation pathways typically involve the free diffusion of reactive oxygen species (ROS), followed by chemical attacks on the protein surface. Here, we report a hidden route of protein oxidative damage, which we refer to as O2-confinement oxidation pathway. This pathway starts with the initial trapping of dissolved molecular oxygen (O2) within protein cavity spaces, followed by interaction with photosensitizing tryptophan residues. The trapped O2is then converted to singlet oxygen (1O2), a powerful ROS, through spin-flip electron transfer mechanism under blue light. The generated1O2within the protein ultimately attacks the protein core residues through constrained diffusion, accelerating the oxidative damage. This alternative photooxidation pathway through the initial O2trapping would bypass the antioxidant defense systems which target freely-diffusing ROS, constituting an additional layer of protein oxidative damage in cells and tissues.
SEX-SPECIFIC IMPACTS OF EARLY LIFE SLEEP DISRUPTION: ETHANOL SEEKING, SOCIAL INTERACTION, AND ANXIETY ARE DIFFERENTIALLY ALTERED IN ADOLESCENT PRAIRIE VOLES
Authors: Ginder Darren E. , Tinsley Carolyn E. , Kaiser Mara E. , Lim Miranda M.
Published: January 2024

Early life sleep is important for neuronal development and maturation. Using the highly social prairie vole rodent model, we have previously reported that early-life sleep disruption (ELSD) during the pre-weaning period postnatal day (P)14 to 21 results in adult interference with social bonding and increases ethanol consumption following a stressor. Furthermore, we have reported increased parvalbumin expression and reduced glutamatergic neurotransmission in cortical regions in adult prairie voles that experienced this paradigm. To understand the impact of ELSD on the lifespan, examination of an earlier time in life is necessary. Thus, the aim of the present study was to examine the behavioral outcomes of ELSD on adolescent prairie voles. Here we hypothesized that anxiety and reward related behaviors, as measured by light/dark box, 2-bottle choice and social interactions, would be negatively impacted by ELSD in adolescent male and female prairie voles. Male ELSD voles were no different from control voles in measures of anxiety and ethanol preference or consumption, but affiliative social interactions were significantly reduced. ELSD differentially impacted female prairie voles, with increased anxiety-like behavior and reductions in ethanol consumption compared to Controls, but no impact on ethanol preference or social interactions. Together, these results suggest both male and female prairie voles experience differential changes to reward seeking behaviors, but only female prairie voles showed increases in anxiety-like behavior. These results further suggest that early-life sleep is critically important for neurotypical behaviors in adolescence, a time where reward-seeking and risky behaviors are adaptive for learning and promoting survival.
Leveraging Soil Mapping and Machine Learning to Improve Spatial Adjustments in Plant Breeding Trials
Authors: Carroll Matthew E. , Riera Luis G. , Miller Bradley A. , Dixon Philip M. , Ganapathysubramanian Baskar , Sarkar Soumik , Singh Asheesh K.
Published: January 2024

Spatial adjustments are used to improve the estimate of plot seed yield across crops and geographies. Moving mean and P-Spline are examples of spatial adjustment methods used in plant breeding trials to deal with field heterogeneity. Within trial spatial variability primarily comes from soil feature gradients, such as nutrients, but study of the importance of various soil factors including nutrients is lacking. We analyzed plant breeding progeny row and preliminary yield trial data of a public soybean breeding program across three years consisting of 43,545 plots. We compared several spatial adjustment methods: unadjusted (as a control), moving means adjustment, P-spline adjustment, and a machine learning based method called XGBoost. XGBoost modeled soil features at (a) local field scale for each generation and per year, and (b) all inclusive field scale spanning all generations and years. We report the usefulness of spatial adjustments at both progeny row and preliminary yield trial stages of field testing, and additionally provide ways to utilize interpretability insights of soil features in spatial adjustments. These results empower breeders to further refine selection criteria to make more accurate selections, and furthermore include soil variables to select for macro– and micro-nutrients stress tolerance.
TEMINET: A Co-Informative and Trustworthy Multi-Omics Integration Network for Diagnostic Prediction
Authors: Luo Haoran , Liang Hong , Liu Hongwei , Fan Zhoujie , Wei Yanhui , Yao Xiaohui , Cong Shan
Published: January 2024

Advancing the domain of biomedical investigation, integrated multi-omics data have shown exceptional performance in elucidating complex human diseases. However, as the variety of omics information expands, precisely perceiving the informativeness of intra- and inter-omics becomes challenging due to the intricate interrelations, thus posing significant obstacles in multi-omics data integration. To address this, we introduce a novel multi-omics integration approach, referred to as TEMINET. This approach enhances diagnostic prediction by leveraging an intra-omics co-informative representation method and a trustworthy learning strategy used to address inter-omics fusion. Considering the multifactorial nature of complex diseases, TEMINET utilizes intra-omics features to construct disease-specific networks, then applies graph attention networks and a multi-level framework to capture more collective informativeness than pairwise relations. To perceive the contribution of co-informative representations within intra-omics, we design a trustworthy learning strategy to identify the reliability of each omics in integration. To integrate inter-omics information, a combined beliefs fusion approach is deployed to harmonize the trustworthy representations of different omics types effectively. Our experiments across four different diseases using mRNA, methylation, and miRNA data demonstrate that TEMINET achieves advanced performance and robustness in classification tasks.
Soil respiration is correlated with rainfall and soil moisture at multiple temporal scales in a seasonal wet tropical forest
Authors: Chakravarthy Dayani , Raghavendra H. V. , Ratnam Jayashree , Sankaran Mahesh
Published: January 2024

Soil respiration is the second largest natural flux of carbon (C) between terrestrial ecosystems and the atmosphere, with tropical forests amongst the largest contributors of such soil-derived carbon efflux. With climate change expected to drive changes in both temperature and rainfall, our ability to predict responses of the carbon cycle in the future hinges upon an understanding of how these factors influence soil respiration (Rs). However, these relationships remain poorly characterised across the seasonal tropics, especially south Asia. Here, for two seasonal tropical sites in the Western Ghats of India, we characterised annual, seasonal and temporal variation in Rs and assessed its temperature and moisture sensitivity over 6 years. At both sites, Rs was positively correlated with temperature at the instantaneous scale, but showed no relationship with temperature at seasonal or annual scales. In contrast, Rs showed significant relationships with rainfall and soil moisture at all temporal scales. At the annual scale, respiration was negatively correlated with total annual rainfall. At the seasonal scale, wet season Rs was significantly lower than in the dry season. At the instantaneous scale, Rs showed a parabolic relationship with soil moisture, where soil respiration increased with soil moisture up to ∼21% and decreased beyond that point. Our results suggest that future responses of soil respiration in this seasonal tropical forest will largely be driven by changes in the Indian Summer Monsoon, not only mean annual precipitation, but also the frequency and intensity of extreme rainfall events.
The clade-specific target recognition mechanisms of plant RISCs
Authors: Iwakawa Hiro-oki
Published: January 2024

Eukaryotic Argonaut proteins (AGOs) assemble RNA-induced silencing complexes (RISCs) with guide RNAs that allow binding to complementary RNA sequences and subsequent silencing of target genes. The model plantArabidopsis thalianaencodes 10 different AGOs, categorized into three distinct clades based on amino acid sequence similarity. While clade 1 and 2 RISCs are known for their roles in post-transcriptional gene silencing, and clade 3 RISCs are associated with transcriptional gene silencing in the nucleus, the specific mechanisms of how RISCs from each clade recognize their targets remain unclear. In this study, I conducted quantitative binding analyses between RISCs and target nucleic acids with mismatches at various positions, unveiling distinct target binding characteristics unique to each clade. Clade 1 and 2 RISCs require base pairing not only in the seed region but also in the 3′ supplementary region for stable target RNA binding, with clade 1 exhibiting a higher stringency. Conversely, clade 3 RISCs tolerate dinucleotide mismatches beyond the seed region. Strikingly, they bind to DNA targets with an affinity equal to or surpassing that of RNA, like prokaryotic AGO complexes. These insights challenge existing views on plant RNA silencing and open avenues for exploring new functions of eukaryotic AGOs.
Compact RNA sensors for increasingly complex functions of multiple inputs
Authors: Choe Christian , Andreasson Johan O. L. , Melaine Feriel , Kladwang Wipapat , Wu Michelle J. , Portela Fernando , Wellington-Oguri Roger , Nicol John J. , Wayment-Steele Hannah K. , Gotrik Michael , Participants Eterna , Khatri Purvesh , Greenleaf William J. , Das Rhiju
Published: January 2024

Designing single molecules that compute general functions of input molecular partners represents a major unsolved challenge in molecular design. Here, we demonstrate that high-throughput, iterative experimental testing of diverse RNA designs crowdsourced from Eterna yields sensors of increasingly complex functions of input oligonucleotide concentrations. After designing single-input RNA sensors with activation ratios beyond our detection limits, we created logic gates, including challenging XOR and XNOR gates, and sensors that respond to the ratio of two inputs. Finally, we describe the OpenTB challenge, which elicited 85-nucleotide sensors that compute a score for diagnosing active tuberculosis, based on the ratio of products of three gene segments. Building on OpenTB design strategies, we created an algorithm Nucleologic that produces similarly compact sensors for the three-gene score based on RNA and DNA. These results open new avenues for diverse applications of compact, single molecule sensors previously limited by design complexity.
DeepRod: A human-in-the-loop system for automatic rodent behavior analysis
Authors: Loy A. , Garafolj M. , Schauerte H. , Behnke H. , Charnier C. , Schwarz P. , Rast G. , Wollmann T.
Published: January 2024

We present a human-in-the-loop system for efficient rodent behavior analysis in drug development. Addressing the time-consuming and labor-intensive nature of manual behavior categorization, this UX-optimized platform integrates AI for complex behavior prediction and active learning to identify rare events. The proposed solution leverages a cloud-native data processing pipeline, AI-based novelty behavior recognition and multi-class classification, demonstrating significant improvements in behavior labeling and discovery.
The vast majority of somatic mutations in plants are layer-specific
Authors: Goel Manish , Campoy Jose A. , Krause Kristin , Baus Lisa C. , Sahu Anshupa , Sun Hequan , Walkemeier Birgit , Marek Magdalena , Beaudry Randy , Ruiz David , Huettel Bruno , Schneeberger Korbinian
Published: January 2024

Background All plant tissues and organs develop from meristems. Plant meristems are structured organs consisting of distinct layers of stem cells. Somatic mutations occurring in one of these layers can propagate into large sectors of the plant. However, the frequency and characteristics of meristematic mutations that form the basis of somaclonal phenotypic variation remain unclear. Results Here, we analysed the frequency and distribution of somatic mutations in an individual Apricot tree. For this, we sequenced the genomes of fruit samples corresponding to distinct meristematic cell layers selected across the entire tree. Most somatic mutations (>90%) were specific to individual layers. Genotyping the somatic mutations in leaves sampled next to the fruits confirmed their meristematic origin. Interestingly, layer 1 (epidermis) had a higher mutation load than layer 2 (mesocarp), implying differential mutational dynamics between the layers. The somatic mutations followed the branching pattern of the tree. These factors led to the unexpected observation that the layer 1 samples from different branches were more similar to each other than to layer 2 samples of the same branch. Further, using single-cell RNA sequencing, we demonstrated that the layer-specific mutant alleles could only be found in the transcripts of the respective, layer-specific cell clusters and could form the basis for somaclonal phenotypic variation. Conclusions Here, we analyzed the prevalence and distribution of somatic mutations with meristematic origin. Our insights into the yet unexplored layer-specificity of such somatic mutations outlined how they can be identified and how they impact the breeding of clonally propagated crops.
Impaired Visuospatial Working Memory but Preserved Attentional Control in Bipolar Disorder
Authors: Barnes-Scheufler Catherine V. , Rösler Lara , Schiweck Carmen , Peters Benjamin , Matura Silke , Mayer Jutta S. , Kittel-Schneider Sarah , Schaum Michael , Reif Andreas , Wibral Michael , Bittner Robert A.
Published: January 2024

BACKGROUND

Persistent deficits in working memory (WM) and attention have considerable clinical and functional impact in people with bipolar disorder (PBD). Understanding the neurocognitive underpinnings of these interacting cognitive constructs might facilitate the discovery of more effective pro-cognitive interventions. Therefore, we employed a paradigm designed for jointly studying attentional control and WM encoding.

METHODS

We used a visuospatial change-detection task using four Gabor Patches with differing orientations in 63 euthymic PBD and 76 healthy controls (HCS), which investigated attentional competition during WM encoding. To manipulate bottom-up attention using stimulus salience, two Gabor patches flickered, which were designated as either targets or distractors. To manipulate top-down attention, the Gabor patches were preceded by either a predictive or a non-predictive cue for the target locations.

RESULTS

Across all task conditions, PBD stored significantly less information in visual WM than HCS (significant effect of group). However, we observed no significant group by salience or group by cue interactions. This indicates that impaired WM was not caused by deficits in attentional control.

CONCLUSIONS

Our results imply that while WM is disturbed in PBD, attentional prioritization of salient targets and distractors as well as the utilization of external top-down cues were not compromised. Consequently, the control of attentional selection appears be intact. These findings provide important constraints for models of WM dysfunction in PBD by indicating that later stages of WM encoding are likely primarily impaired. We also demonstrate that selective attention is not among the main sources of cognitive impairment in PBD.
Insect hosts are nutritional landscapes navigated by fungal pathogens
Authors: De Fine Licht Henrik H. , Csontos Zsuzsanna , Nielsen Piet Jan Domela Nijegaard , Langkilde Enzo Buhl , Hansen August K. Kjærgård , Shik Jonathan Z.
Published: January 2024

Nutrition can mediate host-pathogen interactions indirectly when specific deficiencies (e.g. iron or glutamine) constrain host immune performance. Nutrition can also directly govern these interactions since invading pathogens colonize finite landscapes of nutritionally variable host tissues that must be optimally foraged during pathogen development. We first used a conceptual framework of nutritional niches to show that insect-pathogenicMetarhiziumfungi navigate host landscapes where different tissues vary widely in (protein (P) and carbohydrates (C)). We next tested whether host-specificMetarhiziumspecies have narrower fundamental nutritional niches (FNN) than host-generalists by measuring pathogen performance across anin vitronutritional landscape simulating a within-host foraging environment. We then tested how developing pathogens navigate nutritional landscapes by developing a liquid-media approach to track pathogen intake of P and C over time. Host-specificity did not govern FNN dimensions as three testedMetarhiziumspecies: 1) grew maximally across C treatments assuming P was present above a lower threshold, and 2) similarly initiated dispersal behaviors and sporulated when either C or P became depleted. However, specialist and generalist pathogens navigated nutritional landscapes differently. The host specialist (M. acridum) first prioritized C intake, but generalists (M. anisopliae,M. robertsii) prioritized P and C according to their availability. Numbers of known hosts may be insufficient to delimit pathogens as specialists or generalists since diverse hosts do not necessarily comprise diverse nutritional landscapes. Instead, immune responses of hosts and nutritional niche breadth of pathogens are likely co-equal evolutionary drivers of host specificity.
B-Cell Involvement in Immune Checkpoint Inhibitor-Induced Lichen Planus: A Comparative Analysis with Non-Drug-Related Lichen Planus
Authors: Tison Alice , Legoupil Delphine , Rochais Marion Le , Hémon Patrice , Foulquier Nathan , Hardy Quentin , Hillion Sophie , Uguen Arnaud , Pers Jacques-Olivier , Misery Laurent , Cornec Divi , Garaud Soizic
Published: January 2024

Background

Immune checkpoint inhibitors (ICI) have significantly improved cancer prognosis but can lead to immune-related adverse events (irAE), including cutaneous manifestations affecting 30% to 60% of ICI-treated patients. However, the physiopathology of cutaneaous irAE remains unclear.

Objective

This study investigated the immune infiltration in tissues affected by cutaneous irAE to elucidate their contribution to the pathogenesis of these toxicities.

Methods

Skin biopsies from 6 patients with ICI-induced lichenoid eruptions were compared using imaging mass cytometry to samples from 7 controls with non-drug-related lichen planus.

Results

T cells were the predominant cell type within the inflammatory infiltrate in all samples, but we observed a reduced T-cell infiltration and an increased B-cell frequency in ICI-induced lichen planus compared to non-drug related lichen planus. Among B cells, we observed a significant decrease in IgD-CD27-double-negative B cells and an increase in IgD+CD27-naïve B cells. Spatial analysis demonstrated that infiltrating B cells were organized in aggregates close to T cells in ICI-induced lichen planus.

Limitations

This is a retrospective single-center study with a relatively small sample size.

Conclusion

This study sheds light on the involvement of B cells in the pathogenesis of ICI-induced lichen planus, suggesting distinct immunological mechanisms from non-drug-related lichen planus.

CAPSULE SUMMARY

Lichenoid manifestations are a common but understudied side effect occurring in patients receiving anti-PD-1 antibodies.

ICI-induced lichen planus displays distinct physiopathology from non-drug-related lichen planus, with a decrease of T-cell infiltration concomitantly to the increase of B cells organized in aggregates.
Morphological deficits of glial cells in a transgenic mouse model for developmental stuttering
Authors: Adeck Afuh , Millwater Marissa , Bragg Camryn , Zhang Ruli , SheikhBahaei Shahriar
Published: January 2024

Vocal production involves intricate neural coordination across various brain regions. Stuttering, a common speech disorder, has genetic underpinnings, including mutations in lysosomal-targeting pathway genes. Using a Gnptab-mutant mouse model linked to stuttering, we examined neuron and glial cell morphology in vocal production circuits. Our findings revealed altered astrocyte and microglia processes in these circuits in Gnptab-mutant mice, while control regions remained unaffected. Our results shed light on the potential role of glial cells in stuttering pathophysiology and highlight their relevance in modulating vocal production behaviors.
Global spatial potential for implementing land-based climate mitigation
Authors: Beaury Evelyn M. , Smith Jeffrey , Levine Jonathan M.
Published: January 2024

Land-based mitigation strategies (LBMS) are critical to reducing climate change and will require large areas for their implementation. Yet few studies have considered how and where LBMS compete for land or are mutually compatible across Earth’s surface. We derived high resolution estimates of the spatial distribution of 19 different LBMS. We estimated 8.9 billion ha suitable for LBMS across the Earth, including 5.6 Bha suitable for only one of the studied strategies and 3.3 Bha suitable for multiple LBMS. We identified significant conflicts between better carbon management of existing land cover types, and restoration-based strategies such as reforestation. At the same time, several agricultural management LBMS were compatible over large areas, including for example, enhanced weathering and improved plantation rotations. Our analysis presents local stakeholders, communities, and governments with the range of LBMS options, and the opportunity costs associated with scaling up any given LBMS to reduce global climate change.
A polytypic species revisited: Phylogenetic and morphological variation, taxonomic status, and geographical distribution ofTrachops(Chiroptera: Phyllostomidae)
Authors: Camacho M. Alejandra , Menéndez-Guerrero Pablo A. , Horváth Balázs , Cadar Dániel , Murienne Jérôme
Published: January 2024

The taxonomic status of the neotropical bat genusTrachopshas been reevaluated through an integrated study that incorporates morphological, morphometric, and molecular data across its extensive geographic range. Our research, which included previously unexamined regions, revealed substantial insights into the diversity withinTrachops. The results support the elevation ofT. cirrhosus ehrhardtito species status, due to genetic and morphological differences in southeastern Brazil specimens. Conversely, our comprehensive analysis found insufficient evidence to maintain the subspecific distinction ofT. c. coffini, which lacks diagnosable morphological characters and is not genetically distinct fromT. c. cirrhosusacross its distribution range. Additionally, our findings challenge the previous belief of a latitudinal differentiation in body size forTrachops cirrhosus, as specimens from western South America and northeastern South America exhibit similar sizes to those from Central America. These results underscore the importance of revising the taxonomic framework for this bat genus, contributing to a more precise understanding of its evolutionary relationships, and further enhancing conservation efforts, considering the potential threats to the newly recognizedT. ehrhardtiin the imperiled Atlantic Forest of Brazil.
FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells
Authors: Cong Ke , MacGilvary Nathan , Lee Silviana , MacLeod Shannon G. , Calvo Jennifer , Peng Min , Kousholt Arne Nedergaard , Day Tovah , Cantor Sharon B.
Published: January 2024

Single-stranded DNA gaps are postulated to be fundamental to the mechanism of anti-cancer drugs. Gaining insights into their induction could therefore be pivotal for advancing therapeutic strategies. For poly (ADP-ribose) polymerase inhibitors (PARPi) to be effective, the presence of FANCJ helicase is required. However, the relationship between FANCJ dependent gaps and PARP1 catalytic inhibition or trapping—both linked to PARPi toxicity in BRCA deficient cells—is yet to be elucidated. Here, we find that the efficacy of PARPi is contingent on S-phase PARP1 activity, which is compromised in FANCJ deficient cells because PARP1, along with MSH2, is “sequestered” by G-quadruplexes. PARP1’s replication activity is also diminished in cells missing a FANCJ-MLH1 interaction, but in such cells, depleting MSH2 can release sequestered PARP1, restoring PARPi-induced gaps and sensitivity. Our observations indicate that sequestered and trapped PARP1 are different chromatin-bound forms, with FANCJ loss increasing PARPi resistance in cells susceptible to canonical PARP1 trapping. However, in BRCA1 null cells, the loss of FANCJ mirrors the effects of PARP1 loss or inhibition, with the common detrimental factor being the loss of PARP1 activity during DNA replication, not trapping. These insights underline the crucial role of PARP1 activity during DNA replication in BRCA deficient cells and emphasize the importance of understanding drug mechanisms for enhancing precision medicine.
Quantifying the Prevalence of Non-B DNA Motifs as a Marker of Non-B Burden in Cancer using NBBC
Authors: Xu Qi , Kowalski Jeanne
Published: January 2024

Alternative DNA structures, such as Z-DNA, G-quadruplexes, and mirror repeats, have shown potential involvement in cancer etiology. NBBC (Non-B DNA Burden in Cancer) is a web-based tool designed for quantifying and analyzing non-B DNA motifs within a cancer context. Herein, we provide a step-by-step protocol for employing NBBC, starting with data input and proceeding through the quantification and normalization of non-B DNA motifs that result in calculation of non-B burden. With detailed instructions for performing various motif-centric analyses based on cancer gene signatures, including DNA damage repair and response pathways for exploring genomic stability, and sample-level gene mutation signatures, a user is able to explore non-B associative correlations within current cancer biology. We provide additional detail on input queries into NBBC, interpret the quantitative results, and apply normalization techniques to ensure accurate comparisons across different genomic regions and non-B DNA structures.

NBBC offers a powerful and user-friendly interface for the cancer research community. This chapter serves as an essential, enhanced instructional guide for researchers to leverage NBBC in their cancer biomarker investigations for an understanding of the potential role of non-B DNA in contributing to them.
Identification of essential genes that support fitness ofAcinetobacter baumanniiefflux pump overproducers in the presence of fluoroquinolone
Authors: Hamami Efrat , Huo Wenwen , Neal Katherine , Neisewander Isabelle , Geisinger Edward , Isberg Ralph R.
Published: January 2024

Acinetobacter baumanniiis a nosocomial pathogen often associated with multidrug resistance (MDR) infections. Fluoroquinolone resistance (FQR) due to drug target site mutations and elevated expression of RND drug transporters is common among clinical isolates. We describe here a CRISPRi platform that identifies hypomorphic mutations that preferentially altered drug sensitivity in RND pump overproducers. An sgRNA library against essential genes ofA. baumanniiwas constructed with single and double nucleotide mutations that produced titratable knockdown efficiencies and introduced into multiple strain backgrounds. Other thannusGdepletions, there were few candidates in the absence of drug treatment that showed lowered fitness specifically in strains overexpressing clinically relevant RND efflux pumps AdeAB, AdeIJK, or AdeFGH. In the presence of ciprofloxacin, the hypomorphs causing hypersensitivity were predicted to result in outer membrane dysfunction, to which the AdeFGH overproducer appeared particularly sensitive. Depletions of either the outer membrane assembly BAM complex, LOS biogenesis proteins, or Lpt proteins involved in LOS transport to the outer membrane caused drug hypersensitivity in at least two of the three pump overproducers. On the other hand, depletions of translation-associated proteins, as well as components of the proton-pumping ATP synthase pump resulted in fitness benefits for at least two pump-overproducing strains in the presence of the drug. Therefore, pump overproduction exacerbated stress caused by defective outer membrane integrity, while the efficacy of drug resistance in efflux overproducers was enhanced by slowed translation or defects in ATP synthesis linked to the control of proton movement across the bacterial membrane.
Predicting the subcellular location of prokaryotic proteins with DeepLocPro
Authors: Moreno Jaime , Nielsen Henrik , Winther Ole , Teufel Felix
Published: January 2024

Protein subcellular location prediction is a widely explored task in bioinformatics because of its importance in proteomics research. We propose DeepLocPro, an extension to the popular method DeepLoc, tailored specifically to archaeal and bacterial organisms. DeepLocPro is a multiclass subcellular location prediction tool for prokaryotic proteins, trained on experimentally verified data curated from UniProt and PSORTdb. DeepLocPro compares favorably to the PSORTb 3.0 ensemble method, surpassing its performance across multiple metrics on our benchmark experiment. The DeepLocPro prediction tool is available online athttps://ku.biolib.com/deeplocproandhttps://services.healthtech.dtu.dk/services/DeepLocPro-1.0/.
Checkpoint-independent association of Mad3BUBR1with Stu1CLASPdirects homolog alignment in meiosis I
Authors: Mukherjee Anuradha , Spanos Christos , Marston Adele L.
Published: January 2024

Gametes are produced via meiosis, a specialized cell division associated with frequent errors which cause birth defects and infertility. Uniquely in meiosis I, homologous chromosomes segregate to opposite poles, usually requiring their linkage by chiasmata, the products of crossover recombination1. The spindle checkpoint delays cell cycle progression until all chromosomes are properly attached to microtubules2but the steps leading to the capture and alignment of chromosomes on the meiosis I spindle remain poorly understood. In budding yeast meiosis I, Mad2 and Mad3BUBR1are equally important for spindle checkpoint delay, but biorientation of homologs on the meiosis I spindle requires Mad2, but not Mad3BUBR13,4. Here we show that Mad3BUBR1promotes accurate meiosis I homolog segregation outside its canonical checkpoint role, independently of Mad2. We find that Mad3BUBR1associates with the TOGL1 domain of Stu1CLASP, a conserved plus-end microtubule protein which is important for chromosome capture onto the spindle. Homologous chromosome pairs that are proficient in crossover formation, but which fail to biorient, rely on Mad3BUBR1-Stu1CLASPto ensure their efficient attachment to microtubules and segregation during meiosis I. Furthermore, we show that Mad3BUBR1-Stu1CLASPare essential to rescue the segregation of mini-chromosomes lacking crossovers. Our findings define a new pathway ensuring microtubule-dependent chromosome capture and demonstrate that spindle checkpoint proteins safeguard the fidelity of chromosome segregation both by actively promoting chromosome alignment and delaying cell cycle progression until this has occurred.
A speed limit on serial strain replacement from original antigenic sin
Authors: McGough Lauren , Cobey Sarah
Published: January 2024

Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive new constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained ifR0is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a “speed limit” on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
Preclinical Development of a Stabilized RH5 Virus-Like Particle Vaccine that Induces Improved Anti-Malarial Antibodies
Authors: King Lloyd D. W. , Pulido David , Barrett Jordan R. , Davies Hannah , Quinkert Doris , Lias Amelia M. , Silk Sarah E. , Pattinson David J. , Diouf Ababacar , Williams Barnabas G. , McHugh Kirsty , Rodrigues Ana , Rigby Cassandra A. , Strazza Veronica , Suurbaar Jonathan , Rees-Spear Chloe , Dabbs Rebecca A. , Ishizuka Andrew S. , Zhou Yu , Gupta Gaurav , Jin Jing , Li Yuanyuan , Carnrot Cecilia , Minassian Angela M. , Campeotto Ivan , Fleishman Sarel J. , Noe Amy R. , MacGill Randall S. , King C. Richter , Birkett Ashley J. , Soisson Lorraine A. , Long Carole A. , Miura Kazutoyo , Ashfield Rebecca , Skinner Katherine , Howarth Mark , Biswas Sumi , Draper Simon J.
Published: January 2024

The development of a highly effective vaccine against the pathogenic blood-stage infection of human malaria will require a delivery platform that can induce an antibody response of both maximal quantity and functional quality. One strategy to achieve this includes presenting antigens to the immune system on virus-like particles (VLPs). Here we sought to improve the design and delivery of the blood-stagePlasmodium falciparumreticulocyte-binding protein homolog 5 (RH5) antigen, which is currently in a Phase 2 clinical trial as a full-length soluble protein-in-adjuvant vaccine candidate called RH5.1/Matrix-M™. We identify disordered regions of the full-length RH5 molecule induce non-growth inhibitory antibodies in human vaccinees, and a re-engineered and stabilized immunogen that includes just the alpha-helical core of RH5 induces a qualitatively superior growth-inhibitory antibody response in rats vaccinated with this protein formulated in Matrix-M™ adjuvant. In parallel, bioconjugation of this new immunogen, termed “RH5.2”, to hepatitis B surface antigen VLPs using the “plug-and-display” SpyTag-SpyCatcher platform technology also enabled superior quantitative antibody immunogenicity over soluble antigen/adjuvant in vaccinated mice and rats. These studies identify a new blood-stage malaria vaccine candidate that may improve upon the current leading soluble protein vaccine candidate RH5.1/Matrix-M™. The RH5.2-VLP/Matrix-M™ vaccine candidate is now under evaluation in Phase 1a/b clinical trials.
Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation
Authors: Minto Melyssa , Sotelo-Fonseca Jesús Emiliano , Ramesh Vijyendra , West Anne E.
Published: January 2024

Background

The Zic family of transcription factors (TFs) promote both proliferation and maturation of cerebellar granule neurons (CGNs), raising the question of how a single, constitutively expressed TF family can support distinct developmental processes. Here we use an integrative experimental and bioinformatic approach to discover the regulatory relationship between Zic TF binding and changing programs of gene transcription during CGN differentiation.

Results

We first established a bioinformatic pipeline to integrate Zic ChIP-seq data from the developing mouse cerebellum with other genomic datasets from the same tissue. In newborn CGNs, Zic TF binding predominates at active enhancers that are co-bound by developmentally-regulated TFs including Atoh1, whereas in mature CGNs, Zic TF binding consolidates toward promoters where it co-localizes with activity-regulated TFs. We then performed CUT&RUN-seq in differentiating CGNs to define both the time course of developmental shifts in Zic TF binding and their relationship to gene expression. Mapping Zic TF binding sites to genes using chromatin looping, we identified the set of Zic target genes that have altered expression in RNA-seq from Zic1 or Zic2 knockdown CGNs.

Conclusion

Our data show that Zic TFs are required for both induction and repression of distinct, developmentally regulated target genes through a mechanism that is largely independent of changes in Zic TF binding. We suggest that the differential collaboration of Zic TFs with other TF families underlies the shift in their biological functions across CGN development.
Constraint on boric acid resistance and tolerance evolvability inCandida albicans
Authors: Syvolos Yana , Salama Ola E. , Gerstein Aleeza C.
Published: January 2024

Boric acid is a broad-spectrum antimicrobial used to treat vulvovaginal candidiasis when patients relapse on the primary azole drug fluconazole.Candida albicansis the most common cause of vulvovaginal candidiasis, colloquially referred to as a "vaginal yeast infection". Little is known about the propensity ofC. albicansto develop BA resistance or tolerance (the ability of a subpopulation to grow slowly in high levels of drug). We evolved 96 replicates from eight diverseC. albicansstrains to increasing BA concentrations to test the evolvability of BA resistance and tolerance. Replicate growth was individually assessed daily, with replicates passaged when they had reached an optical density consistent with exponential growth. Many replicates went extinct quickly. Although some replicates could grow in much higher levels of BA than the ancestral strains, evolved populations isolated from the highest terminal BA levels (after 11 weeks of passages) surprisingly showed only modest growth improvements and only at low levels of BA. No large increases in resistance or tolerance were observed in the evolved replicates. Overall, our findings illustrate that there may be evolutionary constraints limiting the emergence of BA resistance and tolerance, which could explain why it remains an effective treatment for recurrent yeast infections.
Disease-associated astrocyte epigenetic memory promotes CNS pathology
Authors: Lee Hong-Gyun , Rone Joseph M. , Li Zhaorong , Akl Camilo Faust , Shin Seung Won , Lee Joon-Hyuk , Flausino Lucas E. , Pernin Florian , Chao Chun-Cheih , Kleemann Kilian L. , Srun Lena , Illouz Tomer , Giovannoni Federico , Charabati Marc , Sanmarco Liliana M. , Kenison Jessica E. , Piester Gavin , Zandee Stephanie E. J. , Antel Jack , Rothhammer Veit , Wheeler Michael A. , Prat Alexandre , Clark Iain C. , Quintana Francisco J.
Published: January 2024

Astrocytes play important roles in the central nervous system (CNS) physiology and pathology. Indeed, astrocyte subsets defined by specific transcriptional activation states contribute to the pathology of neurologic diseases, including multiple sclerosis (MS) and its pre-clinical model experimental autoimmune encephalomyelitis (EAE)1–8. However, little is known about the stability of these disease-associated astrocyte subsets, their regulation, and whether they integrate past stimulation events to respond to subsequent challenges. Here, we describe the identification of an epigenetically controlled memory astrocyte subset which exhibits exacerbated pro-inflammatory responses upon re-challenge. Specifically, using a combination of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC–seq), chromatin immunoprecipitation with sequencing (ChIP–seq), focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), and cell-specificin vivoCRISPR/Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) used by the histone acetyltransferase p300 to control chromatin accessibility. ACLY+p300+memory astrocytes are increased in acute and chronic EAE models; the genetic targeting of ACLY+p300+astrocytes using CRISPR/Cas9 ameliorated EAE. We also detected responses consistent with a pro-inflammatory memory phenotype in human astrocytesin vitro; scRNA-seq and immunohistochemistry studies detected increased ACLY+p300+astrocytes in chronic MS lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, MS. These findings may guide novel therapeutic approaches for MS and other neurologic diseases.
Predicting RNA Sequence-Structure Likelihood via Structure-Aware Deep Learning
Authors: Zhou You , Pedrielli Giulia , Zhang Fei , Wu Teresa
Published: January 2024

Motivation

The active functionalities of RNA are recognized to heavily dependent on the structure and sequence. Therefore, A model that can accurately evaluate a design by giving RNA sequence-structure pairs would be a valuable tool for many researchers. Machine learning methods have been explored to develop such tools, showing promising results. However, two key issues remain. Firstly, the performance of machine learning models is affected by the features used to characterize RNA. Currently, there is no consensus on which features are the most effective for characterizing RNA sequence-structure pairs. Secondly, most existing machine learning methods extract features describing entire RNA molecule. We argue that it is essential to define additional features that characterize nucleotides and specific sections of RNA structure to enhance the overall efficacy of the RNA design process.

Results

We develop two deep learning models for evaluating RNA sequence-structure pairs. The first model, NU-ResNet, uses a convolutional neural network architecture that solves the aforementioned problems by explicitly encoding RNA sequence-structure information into a 3D matrix. Building upon NU-ResNet, our second deep learning model, NUMO-ResNet, incorporates additional information derived from the characterizations of RNA, specifically the 2D folding motifs. In this work, we introduce an automated method to extract these motifs based on fundamental secondary structure descriptions. To assess the robustness of our models, we conduct 10-fold cross validation. Furthermore, we evaluate the performance of both models on two independent testing datasets. Our proposed models demonstrate excellent performance across both datasets and surpass the performance of the ENTRNA approach.

Availability and Implementation

The corresponding source code and data for this research is available athttps://github.com/yzhou617/NU-ResNet_and_NUMO-ResNet.

Contact

Giulia.Pedrielli@asu.edu

Supplementary information

Supplementary data are available at Bioinformatics online.