bluuebunny/crossref_metadata_2025 huggingface dataset:
PepCleav: a classification method for evaluating the cleavability of peptide fragments presented by MHC class I
Authors: Jiang Dawei , Zhu Wenxin , Xi Binbin , Du Hongli
Published: July 2024

Neoantigens, due to their tumor specificity and lack of central tolerance, are promising targets for cancer immunotherapy. Evaluating the cleavability of peptide fragments generated by proteasomes and aminopeptidases is crucial for neoantigen identification, but tools for this purpose are scarce. To address this, we developed PepCleav, a method for evaluating peptide cleavability by classifying the amino acids at the proteasome and aminopeptidase recognition sites of the C- and N-termini. By integrating C- and N-terminal cleavability, PepCleav accurately predicted the overall cleavability of peptide fragments in test datasets, correctly identifying 84-89% of cleavable peptides and 63-92% of non-cleavable peptides. We also found that highly cleavable peptides have a higher likelihood of being effective neoantigens, highlighting PepCleav’s potential to improve neoantigen identification. PepCleav’s source code is publicly available athttps://github.com/Dulab2020/PepCleav.
Metabolomic differentiation of amino acid profiles in adult deltamethrin-resistantAedes albopictus(L.)
Authors: Ong Song-Quan , Ishak Intan H , Nair Gomesh , Paulous Rolinus
Published: July 2024

Understanding the susceptibility status of mosquitoes to insecticides is critical for effective decision making regarding the use or rotation of insecticides in control programs. In this study, we demonstrated the use of amino acid profiling for the detection of deltamethrin-resistantAedes albopictus(L.). Mosquitoes collected in the field were first tested with WHO adulticide bioassay kits, and the amino acid profiles of the resistant mosquitoes were compared with the susceptible strain ofAe. albopictus. Samples were lyophilized and derived by silylation and then analyzed by gas chromatography-mass spectrometry (GC-MS). Using standardized, known concentrations of amino acids, we quantified the amino acids in both resistant and susceptible strains. An independent t-test was performed to compare the concentrations of each amino acid between strains. Logistic regression was then performed to assess the relationship between amino acid concentrations and susceptibility status of the mosquitoes. Our results showed that the amino acids in resistant mosquitoes differed significantly from those in susceptible mosquitoes, with the exception of serine. Further regression analysis showed that seven amino acids significantly predicted susceptibility, suggesting that they are suitable as biological indicators for rapid assessment of resistance status in field mosquitoes.

Graphic abstract

Identification of deltamethrin-resistant mosquitoes based on differences in the amino acid profile: Deltamethrin-susceptible and -resistant mosquito strains were lyophilised and converted into esters by silylation, which were then analysed using a gas chromatography-mass spectrometer (GC-MS). The difference between susceptible and resistant could be classified by developing a classification model with logistic regression.
The guardians of mitochondrial dynamics: a novel role for intermediate filament proteins
Authors: Hemel Irene MGM , Steen Carlijn , Denil Simon LIJ , Ertaylan Gökhan , Kutmon Martina , Adriaens Michiel , Gerards Mike
Published: July 2024

Mitochondria are dynamic organelles and the main source of cellular energy. Their dynamic nature is crucial to meet cellular requirements. However, the processes and proteins involved in mitochondrial dynamics are not fully understood. Using a computational protein-protein interaction approach, we identified ITPRIPL2, which caused mitochondrial elongation upon knockdown. ITPRIPL2 co-localizes with the intermediate filament protein vimentin and interacts with vimentin according to protein simulations. ITPRIPL2 knockdown alters vimentin processing, disrupts intermediate filaments and transcriptomics analysis revealed changes in vimentin-related pathways. Our data illustrates that ITPRIPL2 is essential for vimentin related intermediate filament structure. Interestingly, like ITPRIPL2 knockdown, vimentin knockdown results in mitochondrial elongation. Our data highlights ITPRIPL2 as a vimentin-associated protein and reveals a role for intermediate filaments in mitochondrial dynamics, improving our understanding of mitochondrial dynamics regulators. Moreover, our study demonstrates that protein- protein interaction analysis is a powerful approach for identifying novel mitochondrial dynamics proteins.
In the AlphaFold era, when is experimental phasing of protein crystals still required?
Authors: Keegan Ronan M. , Simpkin Adam J. , Rigden Daniel J.
Published: July 2024

The availability of highly accurate protein structure predictions from AlphaFold 2 (AF2) and similar tools has hugely expanded the applicability of Molecular Replacement (MR) for crystal structure solution. Many structures solve routinely using raw models, structures processed to remove unreliable parts or models split into distinct structural units. There is therefore an open question around how many and which cases still require experimental phasing methods such as single-wavelength anomalous diffraction (SAD). Here we address the question using a large set of PDB deposits that were solved by SAD. A large majority (87%) solve using unedited or minimally edited AF2 predictions. A further 17 (4%) yield straightforwardly to MR after splitting of the AF2 prediction using Slice’N’Dice, although different splitting methods succeed on slightly different sets of cases. We also find that further unique targets can be solved by alternative modelling approaches such as ESMFold (four cases), alternative MR approaches such as ARCIMBOLDO and AMPLE (two cases each), and multimeric model building with AlphaFold-Multimer or UniFold (three cases). Ultimately, only 12 cases, or 3% of the SAD-phased set did not yield to any form of MR tested here, offering valuable hints as to the number and characteristics of cases where experimental phasing remains essential for macromolecular structure solution.
Design principles of small intestinal crypt maintenance
Authors: Banjac Isidora , Maimets Martti , Tsang Ingrid , Dioli Marius , Hansen Stine Lind , Krizic Kata , Bressan Raul Bardini , Lövkvist Cecilia , Jensen Kim B.
Published: July 2024

The intestinal epithelium has a remarkably high turnover in homeostasis. It remains unresolved how turnover is orchestrated at the cellular level and how the behaviour of stem and progenitor cells ensures tissue maintenance. To address this, we combined quantitative fate mapping in three complementary mouse models with mathematical modelling and single-cell RNA sequencing. Our integrated approach generated a spatially and temporally defined model of crypt maintenance that is based on two cycling populations: crypt-based columnar (CBC) and transit amplifying (TA) cells. Validation experiments substantiated the predictions from the model revealing TA cells as the major contributor to the absorptive lineage, while balanced CBC cell fate choices controlled the numbers of cells in the secretory lineage. By unravelling these mechanisms, we gain insights into the process of tissue turnover and provide direct evidence to support the notion of CBC cells as the major driver of the intestinal epithelium replenishment.

Highlights

Spatially and temporally resolved cellular model of small intestinal crypt maintenance.

Stem cells exhibit predisposition towards secretory fate.

Secretory lineage has a limited contribution to the high turnover of intestinal epithelium.

Cellular differentiation within the crypt occurs rapidly within 72 hours.
Test of a conservation intervention highlights temporal variability in hybridization dynamics inCatostomusfishes
Authors: Campbell Jillian N. , Hooley-Underwood Zachary E. , Mandeville Elizabeth G.
Published: July 2024

Non-native species are a leading threat to fish biodiversity. They pose risks to native populations through human-mediated introductions resulting in hybridization events, which could result in demographic or genetic swamping.Catostomusfishes in the Upper Colorado River Basin are an example of this. Extensive hybridization occurs between non-native white suckers (C. commersonii) and native flannelmouth and bluehead suckers (C. latipinnisandC. discobolus). This system provides a suitable model for using genomic analyses to test the efficacy of an intervention to reduce the abundance of non-native species and production of hybrid offspring. This study implemented a Resistance Board Weir (RBW) as a fish barrier across Roubideau Creek, a tributary of the Gunnison River in Colorado (USA), to restrict non-native sucker participation in spawning events. Conducted over four years, the study gathered genomic data from larval fish samples, pre- and post-implementation of the RBW. We used genomic data to determine the efficacy of a RBW at limiting non-native and hybridized sucker larval production. We found no significant effect of the weir on the proportion of white sucker ancestry in larval fish across the four years of the study, which included three years of weir usage when access was successfully controlled for variable amounts of time. Overall, this work provides insight into the efficacy of a resistance board weir as a management tool for non-native suckers, and highlights interannual variability. This work contributes valuable information for policy and fisheries management in Colorado.
Cryopreservation Enables Long-Term Studies ofOctopus vulgarisHemocyte Immune Functions
Authors: Costa MM , Paredes E , Peleteiro M , Gambón F , Dios S , Gestal C
Published: July 2024

As with their nervous system and other physiological traits, the immune system of cephalopods, in general, and of the common octopus, Octopus vulgaris, in particular, could also present highly evolved characteristics compared to other classes of molluscs. However, to date, there is not much information about it, and studying the defense mechanisms is a key step in understanding their response system to external aggressions and, thus, having the tools to anticipate animal health problems and ensure their welfare.

The lack of cell cultures in molluscs is a major problem when carrying outin vitroassays that help to deepen the knowledge of the main immune cells of this species. Cryopreservation becomes an alternative to maintain viable and functional cells after freezing/thawing processes, allowing a larger repertoire of studies to be performed with the same sample or to perform time courses.

Having access to good quality cells for long periods will allow to cover a larger repertoire of studies with the same sample or to perform time courses, avoiding logistic bottlenecks that could arise due to the loss of viability and/or functionality of the cells on the lab bench, the lack of time to develop all the desired assays in the same day or the possible losses derived from transporting the samples between different laboratories. Additionally, high-quality suspensions of viable and functional cells are required for successful massive sequencing studies, such as single-cell analysis, where these aspects are the key to an optimal identification.

We show here the first functional results from cryopreserved octopus hemocytes, where the cells were able to maintain viability above 80% after two months post cryopreservation and storage at −80°C and their functional ability to phagocytose bacteria similar to fresh cells. Our data revealed that the acclimation process after thawing was essential to recovering the functional activity of the cells.

The results presented here will facilitate the study of the functions of the most important immune cells of this species and will provide tools for cell preservation in other molluscs species.
Effects ofBacillus thuringiensissubsp.kurstakiapplication on non-target nocturnal macromoth biodiversity in the eastern boreal forest, Canada
Authors: Young Jodi O. , Bowden Joseph J. , Moise Eric R. D. , Scott Robert , Christian Schmidt B.
Published: July 2024

Insect biodiversity is crucial for resilient ecosystems, supporting essential services. Moths play significant roles as herbivores, pollinators, decomposers, and as prey for birds, bats, and predatory invertebrates, emphasizing their conservation importance. However, large-scale studies on the non-target effects ofBacillus thuringiensissubs.kurstaki(Btk) on moth communities are limited, particularly in northern forests where diversity is lower. Btk is commonly used to control pest insect populations, with forest managers in eastern Canada applying it to manage eastern spruce budworm.

We established a replicated two-year study in the North American Boreal Forest of western Newfoundland, Canada, using paired Btk-treated and control (untreated) sites.

No significant differences in total abundance or richness were found between treated and control sites. In 2021, Hill numbers only differed between our northern treatment and control sites, which may reflect those stands having already received multiple years of treatment compared to just one year in the southern sites. In 2022, control sites showed higher diversity (Shannon and Simpson diversity metrics) compared to treated sites, extending to all locations.

Multiple years of Btk treatment led to shifts in community composition and the relative abundance of some common species, without affecting total richness or abundance. Species responses varied, likely due to Btk sensitivity, application timing, and differences in phenology and voltinism, making it difficult to generalize the effects of Btk on moth communities.
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis
Authors: Dutcher H. Auguste , Gasch Audrey P.
Published: July 2024

RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance inSaccharomyces cerevisiaebut its mechanistic role remains unclear. Here we used a network-based approach to inform on Ssd1’s role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and withoutSSD1and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/orssd1Δ cells to chromosome XII duplication, in several cases indicating genetic interactions withSSD1in the context of aneuploidy. We integrated these findings with results from a global over-expression screen that identified genes whose duplication complementsssd1Δ aneuploid sensitivity. The resulting network points to a sub-group of proteins with shared roles in translational repression and p-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.
How genotype-by-environment interactions can maintain variation in mutualisms
Authors: Carlson Christopher I. , Frederickson Megan E. , Osmond Matthew M.
Published: July 2024

Coevolution requires reciprocal genotype-by-genotype (GXG) interactions for fitness, which occur when the fitnesses of interacting species depend on the match between their genotypes. However, in mutualisms, when GXG interactions are mutually beneficial, simple models predict that positive feedbacks will erode genetic variation, weakening or eliminating the GXG interactions that fuel ongoing coevolution. This is inconsistent with the ample trait and fitness variation observed within real-world mutualisms. Here, we explore how genotype-by-environment (GXE) interactions, which occur when different genotypes respond differently to different environments, maintain variation in mutualisms. We employ a game theoretic model in which the fitnesses of two partners depend on mutually beneficial GXG and GXE interactions. Variation is maintained via migration-selection balance when GXE interactions are slightly stronger than GXG interactions or when they are much stronger than GXG interactions for just one partner. However, unexpectedly, when GXE interactions are much stronger than GXG interactions for both partners and dispersal is high, genotypically mismatched partners can fix, eroding variation and leading to apparent maladaptation between partners. We parameterize our model using data from three published reciprocal transplant experiments and find that the observed strengths of GXE interactions can maintain or erode variation in mutualisms via these mechanisms.
3D printed bioelectronic scaffolds with soft tissue-like stiffness
Authors: Okafor Somtochukwu S. , Park Jae , Liu Tianran , Goestenkors Anna P. , Alvarez Riley M. , Semar Barbara A. , Yu Justin S. , O’Hare Cayleigh P. , Montgomery Sandra K. , Friedman Lianna C. , Rutz Alexandra L.
Published: July 2024

3D printing is a leading technique for fabricating tissue engineering scaffolds that facilitate native cellular behavior. Engineering scaffolds to possess functional properties like electronic conductivity is the first step towards integrating new technological capabilities like stimulating or monitoring cellular activity beyond the traditionally presented biophysical and biochemical cues. However, these bioelectronic scaffolds have been largely underdeveloped since the majority of electrically conducting materials possess high stiffness values outside the physiological range and that may negatively impact desired cell behavior. Here, we present methods of 3D printing poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) hydrogel scaffolds and provide techniques to achieve stiffness relevant to many soft tissues (<100 kPa). Structures were confirmed as ideal tissue scaffolds by maintaining biostability and promoting high cell viability, appropriate cell morphology, and proliferation. With these findings, we contribute a customizable 3D platform that provides favorable soft cellular microenvironments and envision it to be adaptable to several bioelectronic applications.
Role of Kir4.1/Kir5.1 in mediating Angiotensin-II (Ang-II)-induced stimulation of thiazide-sensitive Na-Cl cotransporter
Authors: Duan Xin-Peng , Meng Xin-Xin , Xiao Yu , Zhang Cheng-Biao , Gu Ruimin , Lin Dao-Hong , Wang Wen-Hui
Published: July 2024

Background

Angiotensin-II (Ang-II) perfusion stimulates Kir4.1/Kir5.1 in the distal-convoluted-tubule (DCT) and thiazide-sensitive Na-Cl-cotransporter (NCC). However, the role of Kir4.1/Kir5.1 in mediating the effect of Ang-II on NCC is not understood.

Methods

We used immunoblotting and patch-clamp-experiments to examine whether Ang-II-induced stimulation of NCC is achieved by activation of Kir4.1/Kir5.1 of the DCT using kidney-renal-tubule-specific AT1aR-knockout (Ks-AT1aR-KO), Ks-Kir4.1-knockout and the corresponding wild-type mice.

Results

Ang-II perfusion for 1, 3 and 7 days progressively increased phosphor-NCC (pNCC) and total-NCC (tNCC) expression and the effect of Ang-II-perfusion on pNCC and tNCC was abolished in Ks-AT1aR-KO. Ang-II perfusion for 1-day robustly stimulates Kir4.1/Kir5.1 in the late DCT (DCT2) and to a lesser degree in the early DCT (DCT1), an effect was absent in Ks-AT1aR-KO mice. However, Ang-II perfusion for 7-days did not further stimulate Kir4.1/Kir5.1 in the DCT2 and only modestly increased Kir4.1/Kir5.1-mediated K+currents in DCT1. Deletion of Kir4.1 not only significantly decreased the expression of pNCC and tNCC but also abolished the effect of 1-day Ang-II perfusion on the expression of phospho-with-no-lysine-kinase-4 (pWNK4), phosphor-ste-20-proline-alanine-rich-kinase (pSPAK), pNCC and tNCC. However, 7-days Ang-II perfusion was still able to significantly stimulate the expression of pSPAK, pWNK4, pNCC and tNCC, and increased thiazide-induced natriuresis in kidney-tubule-specific Kir4.1 knockout (Ks-Kir4.1 KO) mice without obvious changes in K+channel activity in the DCT.

Conclusions

Short-term Ang-II induced stimulation of pWNK4, pSPAK and pNCC depends on Kir4.1/Kir5.1 activity. However, long-term Ang-II is able to directly stimulate pWNK4, pSPAK and pNCC by a Kir4.1/Kir5.1 independent mechanism.
Axis reset is rate limiting for onset of whole-body regenerative abilities during planarian development
Authors: Booth Clare L.T. , Stevens Brian C. , Stubbert Clover A. , Kallgren Neil T. , Davies Erin L.
Published: July 2024

Few studies have investigated whether or how regenerative abilities vary across developmental stages of animal life cycles. Determining mechanisms that promote or limit regeneration in certain life cycle stages may pinpoint the most critical factors for successful regeneration and suggest strategies for reverse-engineering regenerative responses in therapeutic settings. In contrast to many mammalian systems, which typically show a loss of regenerative abilities with age, planarian flatworms remain highly regenerative throughout adulthood. The robust reproductive and regenerative capabilities of the planarianSchmidtea polychroa(Spol) make them an ideal model to determine when and how regeneration competence is established during development. We report thatSpolgradually acquires whole body regenerative abilities during late embryonic and early juvenile stages. Posterior (tail) regenerative abilities are constitutive, whereas anterior (head) regenerative abilities are dependent on developmental stage, tissue composition of the amputated fragment, and axial position of the cut plane. Stem-like cells are required, but not sufficient, for onset of head regeneration ability. We propose that regulation of main body axis reset, specifically the ability to remake an anterior organizing center, is a rate-limiting factor for establishment of whole-body regeneration competence. Supporting this hypothesis, knock-down of the canonical Wnt pathway effectorSpol β-catenin-1,a posterior determinant, induces precocious head regeneration under conditions that are normally head regeneration incompetent. Our results suggest that regeneration competence emerges through interactions between cycling stem-like cells, the cellular source of new tissue, and developing adult tissue(s) harboring axial patterning information.
In-uterorescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome
Authors: Reynisdottir Tinna , Anderson Kimberley Jade , Brinn Andrew , Franklin Katie , Ouyang Juan , Snorradottir Asbjorg Osk , Lutz Cathleen M. , Zuberi Aamir R. , DeLeon Valerie Burke , Bjornsson Hans Tomas
Published: July 2024

Wiedemann-Steiner syndrome (WDSTS) is a rare genetic cause of intellectual disability primarily caused by heterozygous loss of function variants in the gene encoding the histone methyltransferase KMT2A. Prior studies have shown successful postnatal amelioration of disease phenotypes for Rett, Rubinstein-Taybi and Kabuki syndromes, related Mendelian disorders of the epigenetic machinery. To explore whether the neurological phenotype in WDSTS is treatablein-utero, we created a novel mouse model carrying a loss of function variant in between two loxP sites.Kmt2a+/LSLmice demonstrate core features of WDSTS including growth retardation, craniofacial abnormalities, and hypertrichosis as well as hippocampal memory defects. The neurological phenotypes show rescue upon restoration ofKMT2A in-uterofollowing breeding to a nestin-Cre. Together, our data provide a novel mouse model to explore the therapeutic window in WDSTS. Our work suggests that WDSTS has a window of opportunity extending at least until the mid-point ofin-uterodevelopment, making WDSTS an ideal candidate for future therapeutic strategies.

Abstract Figure

Graphical abstract
Scorpio : Enhancing Embeddings to Improve Downstream Analysis of DNA sequences
Authors: Refahi Mohammad S. , Sokhansanj Bahrad A. , Mell Joshua C. , Brown James R. , Yoo Hyunwoo , Hearne Gavin , Rosen Gail L.
Published: July 2024

Analysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio, a versatile framework designed for nucleotide sequences that employs contrastive learning to improve embeddings. By leveraging pre-trained genomic language models and k-mer frequency embeddings, Scorpio demonstrates competitive performance in diverse applications, including taxonomic and gene classification, antimicrobial resistance (AMR) gene identification, and promoter detection. A key strength of Scorpio is its ability to generalize to novel DNA sequences and taxa, addressing a significant limitation of alignment-based methods. Scorpio has been tested on multiple datasets with DNA sequences of varying lengths (long and short) and shows robust inference capabilities. Additionally, we provide an analysis of the biological information underlying this representation, including correlations between codon adaptation index as a gene expression factor, sequence similarity, and taxonomy, as well as the functional and structural information of genes.
Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences
Authors: Fonseca Emanuel M. , Tran Linh N. , Mendoza Hannah , Gutenkunst Ryan N.
Published: July 2024

Low-pass genome sequencing is cost-effective and enables analysis of large cohorts. However, it introduces biases by reducing heterozygous genotypes and low-frequency alleles, impacting subsequent analyses such as demographic history inference. We developed a probabilistic model of low-pass biases from the Genome Analysis Toolkit (GATK) multi-sample calling pipeline, and we implemented it in the population genomic inference software dadi. We evaluated the model using simulated low-pass datasets and found that it alleviated low-pass biases in inferred demographic parameters. We further validated the model by downsampling 1000 Genomes Project data, demonstrating its effectiveness on real data. Our model is widely applicable and substantially improves model-based inferences from low-pass population genomic data.
Human iPSC-derived myelinating organoids and globoid cells to study Krabbe Disease
Authors: Evans Lisa Marie P , Gawron Joseph , Sim Fraser J , Laura Feltri M , Marziali Leandro N
Published: July 2024

Krabbe disease (Kd) is a lysosomal storage disorder (LSD) caused by the deficiency of the lysosomal galactosylceramidase (GALC) which cleaves the myelin enriched lipid galactosylceramide (GalCer). Accumulated GalCer is catabolized into the cytotoxic lipid psychosine that causes myelinating cells death and demyelination which recruits microglia/macrophages that fail to digest myelin debris and become globoid cells. Here, to understand the pathological mechanisms of Kd, we used induced pluripotent stem cells (iPSCs) from Kd patients to produce myelinating organoids and microglia. We show that Kd organoids have no obvious defects in neurogenesis, astrogenesis, and oligodendrogenesis but manifest early myelination defects. Specifically, Kd organoids showed shorter but a similar number of myelin internodes than Controls at the peak of myelination and a reduced number and shorter internodes at a later time point. Interestingly, myelin is affected in the absence of autophagy and mTOR pathway dysregulation, suggesting lack of lysosomal dysfunction which makes this organoid model a very valuable tool to study the early events that drive demyelination in Kd. Kd iPSC-derived microglia show a marginal rate of globoid cell formation under normal culture conditions that is drastically increased upon GalCer feeding. Under normal culture conditions, Kd microglia show a minor LAMP1 content decrease and a slight increase in the autophagy protein LC3B. Upon GalCer feeding, Kd cells show accumulation of autophagy proteins and strong LAMP1 reduction that at a later time point are reverted showing the compensatory capabilities of globoid cells. Altogether, this supports the value of our cultures as tools to study the mechanisms that drive globoid cell formation and the compensatory mechanism in play to overcome GalCer accumulation in Kd.
When does the probability of evolutionary rescue increase with the strength of selection?
Authors: Xu Kuangyi , Osmond Matthew M.
Published: July 2024

After an environmental change, populations may be rescued from extinction through adaptive evolution. Stronger environmental changes often cause a faster demographic decline but also more rapid adaptive evolution, with opposing effects on rescue. More generally, it is unclear if the probability of rescue increases with stronger selection, with implications for herbicide/drug resistance evolution. Here we show that, across many scenarios of rescue, stronger selection promotes rescue when: (1) the rate of evolution has a stronger response to selection and (2) the rate of population decline is more rapid. Condition (1) occurs when adaptive alleles are more dominant or the level of inbreeding is higher or, in quantitative genetic models, the genetic variance is larger and the environmental shift is more rapid. Intuitively, a stronger evolutionary response to selection increases the marginal benefit of increased selection, while a faster demographic decline lowers the marginal cost of a reduction in mean fitness.
The transcriptional landscape of the developing chick trigeminal ganglion
Authors: Leonard Carrie E. , McIntosh Alec , Sanyal Johena , Taneyhill Lisa A.
Published: July 2024

The trigeminal ganglion is a critical structure in the peripheral nervous system, responsible for transmitting sensations of touch, pain, and temperature from craniofacial regions to the brain. Trigeminal ganglion development depends upon intrinsic cellular programming as well as extrinsic signals exchanged by diverse cell populations. With its complex anatomy and dual cellular origin from cranial placodes and neural crest cells, the trigeminal ganglion offers a rich context for examining diverse biological processes, including cell migration, fate determination, adhesion, and axon guidance. Avian models have, so far, enabled key insights into craniofacial and peripheral nervous system development. Yet, the molecular mechanisms driving trigeminal ganglion formation and subsequent nerve growth remain elusive. In this study, we performed RNA-sequencing at multiple stages of chick trigeminal ganglion development and generated a novel transcriptomic dataset that has been curated to illustrate temporally dynamic gene expression patterns. This publicly available resource identifies major pathways involved in trigeminal gangliogenesis, particularly with respect to the condensation and maturation of placode-derived neurons, thus inviting new lines of research into the essential processes governing trigeminal ganglion development.
Proteome-wide neuropeptide identification using NeuroPeptide-HMMer (NP-HMMer)
Authors: Zandawala Meet , Amir Muhammad Bilal , Shin Joel , Yim Won C. , Yañez Guerra Luis Alfonso
Published: July 2024

Neuropeptides are essential neuronal signaling molecules that orchestrate animal behavior and physiology via actions within the nervous system and on peripheral tissues. Due to the small size of biologically active mature peptides, their identification on a proteome-wide scale poses a significant challenge using existing bioinformatics tools like BLAST. To address this, we have developed NeuroPeptide-HMMer (NP-HMMer), a hidden Markov model (HMM)-based tool to facilitate neuropeptide discovery, especially in underexplored invertebrates. NP-HMMer utilizes manually curated HMMs for 46 neuropeptide families, enabling rapid and accurate identification of neuropeptides. Validation of NP-HMMer onDrosophila melanogaster, Daphnia pulex, Tribolium castaneumandTenebrio molitordemonstrated its effectiveness in identifying known neuropeptides across diverse arthropods. Additionally, we showcase the utility of NP-HMMer by discovering novel neuropeptides in Priapulida and Rotifera, identifying 22 and 19 new peptides, respectively. This tool represents a significant advancement in neuropeptide research, offering a robust method for annotating neuropeptides across diverse proteomes and providing insights into the evolutionary conservation of neuropeptide signaling pathways.
predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases
Authors: Weinreich Marcel , McDonough Harry , Yacovzada Nancy , Magen Iddo , Cohen Yahel , Harvey Calum , Gornall Sarah , Boddy Sarah , Alix James , Mohseni Nima , Kurz Julian M , Kenna Kevin P , Zhang Sai , Iacoangeli Alfredo , Al-Khleifat Ahmad , Snyder Michael P , Hobson Esther , Al-Chalabi Ammar , Hornstein Eran , Elhaik Eran , Shaw Pamela J , McDermott Christopher , Cooper-Knock Johnathan
Published: July 2024

Time-to-event prediction is a key task for biological discovery, experimental medicine, and clinical care. This is particularly true for neurological diseases where development of reliable biomarkers is often limited by difficulty visualising and sampling relevant cell and molecular pathobiology. To date, much work has relied on Cox regression because of ease-of-use, despite evidence that this model includes incorrect assumptions. We have implemented a set of deep learning and spline models for time-to-event modelling within a fully customizable ‘app’ and accompanying online portal, both of which can be used for any time-to-event analysis in any disease by a non-expert user. Our online portal includes capacity for end-users including patients, Neurology clinicians, and researchers, to access and perform predictions using a trained model, and to contribute new data for model improvement, all within a data-secure environment. We demonstrate a pipeline for use of our app with three use-cases including imputation of missing data, hyperparameter tuning, model training and independent validation. We show that predictions are optimal for use in downstream applications such as genetic discovery, biomarker interpretation, and personalised choice of medication. We demonstrate the efficiency of an ensemble configuration, including focused training of a deep learning model. We have optimised a pipeline for imputation of missing data in combination with time-to-event prediction models. Overall, we provide a powerful and accessible tool to develop, access and share time-to-event prediction models; all software and tutorials are available atwww.predictte.org.
A Suite of Biochemical and Cell-Based Assays for the Characterization of KRAS Inhibitors and Degraders
Authors: Kidane Medhanie , Hoffman Rene M. , Wolfe-Demarco Jennifer K. , Huang Ting-Yu , Teng Chi-Ling , Gonzalez Lira Luis M. , Lin-Jones Jennifer , Pallares Gabriel , Lamerdin Jane E. , Servant Nicole B. , Lee Chun-Yao , Yang Chao-Tsung , Bernatchez Jean A.
Published: July 2024

KRAS is an important oncogenic driver which is mutated in numerous cancers. Recent advances in the selective targeting of KRAS mutants via small molecule inhibitors and targeted protein degraders have generated an increase in research activity in this area in recent years. As such, there is a need for new assay platforms to profile next generation inhibitors which improve on the potency and selectivity of existing drug candidates, while evading the emergence of resistance. Here, we describe the development of a new panel of biochemical and cell-based assays to evaluate the binding and function of known chemical entities targeting mutant KRAS. Our assay panels generated selectivity profiles and quantitative binding interaction dissociation constants for small molecules and degraders against wild type, G12C, G12D, and G12V KRAS, which were congruent with published data. These assays can be leveraged for additional mutants of interest beyond those described in this study, using both overexpressed cell-free systems and cell-based systems with endogenous protein levels.

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Complete enzymatic depolymerization of polyethylene terephthalate (PET) plastic using aSaccharomyces cerevisiae-based whole-cell biocatalyst
Authors: Gulati Siddhant , Sun Qing
Published: July 2024

Plastics like polyethylene terephthalate (PET) have become an integral part of everyday life, yet plastic waste management remains a significant challenge. Enzymatic biocatalysis is an eco- friendly approach for recycling and upcycling of plastic waste. PET-hydrolyzing enzymes (PHEs) such asIsPETase, along with its engineered variants like FAST-PETase, demonstrate promising PET depolymerization capabilities at ambient temperatures. Whole-cell biocatalysts, displaying PHEs on their cell surface, offer high efficiency, reusability, and stability for PET depolymerization. However, their efficacy in fully breaking down PET is hindered by the necessity of two enzymes - PETase and MHETase. Current whole-cell systems either display only one PHE or struggle with performance when displaying larger passenger proteins like the MHETase-PETase chimera. In this work, we developed aSaccharomyces cerevisiae-based whole-cell biocatalyst system for complete PET depolymerization. Leveraging a cellulosome-inspired trifunctional protein scaffoldin displayed on the yeast surface, we immobilized FAST-PETase and MHETase, forming a multi-enzyme cluster. Our whole cell biocatalyst achieved complete PET depolymerization at 30°C, yielding 4.9 mM TPA in seven days with no intermediate accumulation. Furthermore, we showed improved PET depolymerization ability by binding FAST-PETase at multiple sites on the trifunctional scaffoldin. This breakthrough in complete PET depolymerization marks an essential step towards a circular plastic economy.
Reviving the Desired Gains Index: An optimal solution for parent selection in public plant breeding programs
Authors: Werner C.R. , Gardner K.A. , Tolhurst D.J.
Published: July 2024

The Desired Gains Index is an optimal solution for parent selection in public plant breeding programs. It enables breeders to quantify their breeding objectives in terms of desired genetic gains (i.e., desired response to selection) and facilitates the efficient simultaneous improvement of multiple quantitative traits in a breeding population without the need for economic weights. We deliberately chose the term “optimal” here, which is typically associated with the profit-oriented selection indices commonly used in animal breeding, such as the Smith-Hazel Index. Our intention is to refute the perception that the Desired Gains Index is less efficient than the Smith-Hazel Index since both approaches maximise expected genetic gains in proportion to the breeding objective. To achieve this, we first review the relationship between the Desired Gains Index and the Smith-Hazel Index to show that desired gains are actually a form of economic weighting expressed as an improvement ratio for the traits under selection. We then present a general form of the Desired Gains Index to leverage best linear unbiased prediction (BLUP), which enables seamless integration of pedigree or genomic relationship information (e.g., genomic estimated breeding values) between the selection candidates and other related individuals. Finally, using stochastic simulation, we compare the performance of different parent selection strategies, including index selection for population improvement, independent culling, and selection of extreme genotypes. The objective of these demonstrations is to convey the potential impact and benefits of the Desired Gains Index to a broader audience without the need for a deep understanding of selection theory and the equations presented here.
SCAR-6elncRNA locus epigenetically regulatesPROZand modulates coagulation and vascular function
Authors: Ranjan Gyan , Sehgal Paras , Scaria Vinod , Sivasubbu Sridhar
Published: July 2024

Syntenic conservation is an effective strategy to identify evolutionarily conserved lncRNA orthologs. In this study, we identified a novel uncharacterized conserved lncRNA known asSyntenic Cardiovascular Conserved Region-Associated lncRNA-6 (scar-6)and functionally validated its role in coagulation and cardiovascular function. Precise editing of thescar-6lncRNA locus in zebrafish (scar-6gib007Δ12/Δ12) resulted in cranial hemorrhage and permeability defects. Further analysis, including overexpression, locus editing, and rescue experiments, provided compelling evidence for the critical role of thescar-6transcript in the coagulation process of zebrafish. Notably, rescue attempts were unsuccessful in mitigating cranial hemorrhage. Molecular investigation revealed that thescar-6RNA acts as an enhancer lncRNA (elncRNA), and controls the expression ofprozb, an inhibitor offactor Xa, through the enhancer element on its locus. Thescar-6locus actively suppresses the loop formation betweenprozbandscar-6sequences, facilitated by methylation of CpG island via theprdm14-PRC2complex, which is stabilized by thescar-6elncRNA transcript. Disruption of this mechanism inscar-6gib007Δ12/Δ12zebrafish led to impaired vascular function and subsequent hemorrhage. This was triggered by the activation of thePAR2receptor mediated by upregulation ofprozb, which in turn causedNF-κB-mediated endothelial cell activation. This study presents novel evidence for the multifaceted function of thescar-6locus, highlighting its crucial role in regulating the coagulation cascade geneprozband maintaining homeostasis and vascular function.

Synopsis

ProZ-PZIis a natural inhibitor of activatedcoagulation factor X (F10)and plays a major role in maintaining hemostasis in-vivo. Here, the novel evolutionary syntenic conservedscar-6elncRNA locus is shown to regulateprozbexpression and control coagulation and vascular integrity in zebrafish.

Thescar-6acts as an enhancer lncRNA (elncRNA). It controlsprozbexpression and modulates coagulation and vascular function in zebrafish.

Thescar-6elncRNA stabilizes thePrdm14-PRC2complex binding toscar-6locus. This inhibitsprozb/scar-6looping via methylating the CpG island under wildtype conditions.

Overexpressedprozbinscar-6edited animals activatesPAR2receptor, causing endothelial cell activation and vascular dysfunction.
Telomere-to-telomere sheep genome assembly reveals new variants associated with wool fineness trait
Authors: Luo Ling-Yun , Wu Hui , Zhao Li-Ming , Zhang Ya-Hui , Huang Jia-Hui , Liu Qiu-Yue , Wang Hai-Tao , Mo Dong-Xin , EEr He-Hua , Zhang Lian-Quan , Chen Hai-Liang , Jia Shan-Gang , Wang Wei-Min , Li Meng-Hua
Published: July 2024

Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in sheep genomic studies. Here, we report a complete, gap-free telomere-to-telomere (T2T) genome of a ram (T2T-sheep1.0) with a size of 2.85 Gb, including all autosomes and chromosomes X and Y. It adds 220.05 Mb of previously unresolved regions (PURs) and 754 new genes to the most updated reference assembly,ARS-UI_Ramb_v3.0, and contains four types of repeat units (SatI, SatII, SatIII, and CenY) in the centromeric regions.T2T-sheep1.0exhibits a base accuracy of >99.999%, corrects several structural errors in previous reference assemblies, and improves structural variant (SV) detection in repetitive sequences. We identified 192,265 SVs, including 16,885 new SVs in the PURs, from the PacBio long-read sequences of 18 global representative sheep. With the whole-genome short-read sequences of 810 wild and domestic sheep representing 158 global populations and seven wild species, the use ofT2T-sheep1.0as the reference genome has improved population genetic analysis based on ∼133.31 million SNPs and 1,265,266 SVs, including 2,664,979 novel SNPs and 196,471 novel SVs.T2T-sheep1.0improves selective tests by detecting several novel genes and variants, including those associated with domestication (e.g.,ABCC4) and selection for the wool fineness trait (e.g.,FOXQ1) in tandemly duplicated regions.
Perception of audio-visual synchrony is modulated by walking speed and step-cycle phase
Authors: Clouston Gabriel , Davidson Matt , Alais David
Published: July 2024

Investigating sensory processes in active human observers is critical for a holistic understanding of perception. Recent research has demonstrated that locomotion can alter visual detection performance in a rhythmic manner, illustrating how a very frequent and natural behaviour can influence sensory performance. Here we extend this line of work to incorporate variations in walking speed, and test whether multi-sensory processing is impacted by the speed and phase of locomotion. Participants made audio-visual synchrony judgements while walking at two speeds over a range of stimulus onset asynchronies (SOAs). We find that sensitivity to multi-sensory synchrony decreases at slow walking speeds and is accompanied by an increase in reaction times, compared to when walking at a natural pace. A further analysis of the shortest SOAs was conducted to test whether subjective synchrony modulated over the step cycle. This revealed that synchrony judgements were quadratically modulated with perceived synchrony being higher in the swing phase of each step and lower when both feet were grounded during stance phase. Together, these results extend an earlier report that walking dynamically modulates visual sensitivity by contributing two new findings: first, that walking speed modulates perceived synchrony of audio-visual stimuli, and second, that modulations within the step-cycle extend to multisensory synchrony judgements which peak in the swing phase of each step.
Disposition of the chemosensory neurons in the neurotransmitter-release mutantunc-13
Authors: Bokman Eduard , Zaslaver Alon
Published: July 2024

Secretion of neurotransmitters- and neuropeptides-containing vesicles is a regulated process orchestrated by multiple proteins. Of these, mutants, defective in theunc-13andunc-31genes, responsible for neurotransmitter and neuropeptide release, respectively, are routinely used to elucidate neural and circuitry functions. While these mutants result in severe functional deficits, their neuroanatomy is assumed to be intact. Here, usingC. elegansas the model animal system, we find that the head sensory neurons show aberrant positional layout in neurotransmitter (unc-13), but not in neuropeptide (unc-31), release mutants. This finding suggests that synaptic activity may be important for proper cell migration during neurodevelopment and warrants considering possible anatomical defects when usingunc-13neurotransmitter release mutants.