bluuebunny/crossref_metadata_2025 huggingface dataset:
A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells
Authors: Rees Jenaid M. , Kirk Katie , Gattoni Giacomo , Hockman Dorit , Ritter Dylan J. , Benito-Gutierrez Èlia , Knapik Ela W. , Crump J. Gage , Fabian Peter , Gillis J. Andrew
Published: February 2024

Vertebrate calcitonin-producing cells (C-cells) are neuroendocrine cells that secrete the small peptide hormone calcitonin in response to elevated blood calcium levels. C-cells are crucial for maintenance of calcium homeostasis, yet the embryonic and evolutionary origins of this cell type remain contentious. Whereas mouse C-cells reside within the thyroid gland and derive from pharyngeal endoderm, avian C-cells are located within ultimobranchial glands and were reported to derive from the neural crest. We use a comparative cell lineage tracing approach in a range of vertebrate model systems to resolve the ancestral embryonic origin of vertebrate C-cells. We find, contrary to previous studies, that chick C-cells derive from pharyngeal endoderm, with neural crest-derived cells instead contributing to connective tissue intimately associated with C-cells in the ultimobranchial gland. This endodermal origin of C-cells is conserved in a ray-finned bony fish (zebrafish) and a cartilaginous fish (the little skate,Leucoraja erinacea). Furthermore, we discover putative C-cell homologues within the endodermally-derived pharyngeal epithelium of the ascidianCiona intestinalisand the amphioxusBranchiostoma lanceolatum, two invertebrate chordates that lack neural crest cells. Our findings point to a conserved endodermal origin of C-cells across vertebrates and to a pre-vertebrate origin of this cell type along the chordate stem.
Social-ecological models with social hierarchy and spatial structure applied to small scale fisheries
Authors: Wulfing Sophie , White Easton R.
Published: February 2024

1

Socio-ecological models combine ecological systems with human social dynamics in order to better understand human interactions with the environment. To model human behavior, replicator dynamics can be used to model how societal influence and financial costs can change opinions about resource extraction. Previous research on replicator dynamics has shown how evolving opinions on conservation can change how humans interact with their environment and therefore change population dynamics of the harvested species. However, social-ecological models often assume that human societies are homogeneous with no social structure. Building on previous work on social-ecological models, we develop a two-patch socio-ecological model with social hierarchy in order to study the interactions between spatial dynamics an social inequity. We found that fish movement between patches is a major driver of model dynamics, especially when the two patches exhibit different social equality and fishing practices. Further, we found that the societal influence between groups of harvesters was essential to ensuring stable fishery dynamics. Next, we developed a case-study of a co-managed fishery where one group fishes sustainably while another was over-harvests, resulting in a fishery collapse of both patches. We also found that because social influence only included number of fishers and not effective strategies, increased social pressure actually decreased the sustainability of the fishery. The findings of this study indicate the importance of including spatial components to socio-ecological models and highlights the importance of understanding species movements when making conservation decisions. Further, we demonstrate how incorporating fishing methods from outside sources can result in higher stability of the harvested population, indicating a need for diversified information when managing resources.
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
Authors: Shahneh Mohammad Reza Zare , Strobel Michael , Vitale Giovanni Andrea , Geibel Christian , Abiead Yasin El , Garg Neha , Aron Allegra T , Phelan Vanessa V , Petras Daniel , Wang Mingxun
Published: February 2024

Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the re-identification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder that leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes these information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.
Retrotransposon-mediated variation of a chitin synthase gene confers insect resistance toBacillus thuringiensisVip3Aa toxin
Authors: Liu Zhenxing , Liao Chongyu , Zou Luming , Jin Minghui , Shan Yinxue , Quan Yudong , Yao Hui , Zhang Lei , Wang Peng , Liu Zhuangzhuang , Wang Na , Li Anjing , Liu Kaiyu , Heckel David G. , Wu Kongming , Xiao Yutao
Published: February 2024

Bacillus thuringiensis(Bt) crops expressing Vip3Aa are highly efficacious in controlling major lepidopteran pests and delaying evolution of pest resistance. Although practical resistance to Vip3Aa in the field has not been reported, to proactively manage the pest resistance, there is an urgent need to better understand the genetic basis of resistance to Vip3Aa. This is particularly important for the fall armyworm (Spodoptera frugiperda), one of the most destructive pests around the world, which has evolved practical resistance toBtcrystal (Cry) toxins. Here, a highly Vip3Aa-resistant (resistance ratio: 5,562-fold) strain ofS. frugiperdawas selected in the laboratory. Results from bulked segregant analysis, fine-scale mapping, and genetic linkage analysis indicate that a mutation in the midgut-specific chitin synthase gene,SfCHS2, is strongly associated with high-level resistance to Vip3Aa. The resistance is ascribed to the transcriptional variation caused by retrotransposon insertion. The same variation ofSfCHS2was also detected in a field population. Importantly, knockout ofSfCHS2via CRISPR/Cas9 in susceptibleS. frugiperdaconfers its complete resistance (>10,000-fold) to Vip3Aa. Also, we demonstrate that knockout ofCHS2can result in complete resistance to Vip3Aa in additional lepidopteran species, suggesting a general role of this gene in Vip3Aa resistance among lepidopteran pests. These results reported here would contribute to monitor and management of pest resistance to Vip3Aa.
Mimicking Human EED Variants in Drosophila: A Promising Strategy to Analyse Human EED Variant Function
Authors: Cyrus Sharri S. , Giró Sònia Medina , Lian Tianshun , Allan Douglas W. , Gibson William T.
Published: February 2024

The Polycomb Repressive Complex 2 is an epigenetic reader/writer that methylates histone H3K27. Rare germline partial loss of function (pLoF) variants in core members of the complex (EZH2, EED, SUZ12) cause overgrowth and intellectual disability syndromes, whereas somatic variants are implicated in cancer. However, up to 1% of the general population will have a rare variant in one of these genes, most of which would be classified as variants of uncertain significance (VoUS). Towards screening these VoUS for partial LoF alleles that may contribute to disease, here we report functional assays inDrosophilato interrogateEEDmissense variants. We mimicked the amino acid change(s) ofEEDvariants into itsDrosophilaortholog,esc, and tested their function. Known likely benign variants functioned wildtype and known pathogenic variants were LoF. We further demonstrate the utility of this calibrated assay as a scalable approach to assist clinical interpretation of humanEEDVoUS.
Leveraging the Red List of Ecosystems for national action on coral reefs through the Kunming-Montreal Global Biodiversity Framework
Authors: Gudka Mishal , Obura David , Treml Eric , Samoilys Melita , Aboud Swaleh , Osuka Kennedy , Mbugua James , Mwaura Jelvas , Karisa Juliet , Knoester Ewout , Musila Peter , Omar Mohamed , Nicholson Emily
Published: February 2024

Countries have committed to conserving and restoring ecosystems after signing the Kunming-Montreal Global Biodiversity Framework (GBF). The IUCN Red List of Ecosystems (RLE) will serve as a headline indicator to track progress of countries towards achieving this goal, and to guide action across the GBF’s targets. Using Kenyan coral reefs, we demonstrate how nations implementing the GBF, can use standardised estimates of ecosystem degradation from RLE assessments to support site-specific management decisions. We undertook a reef-by-reef analysis to evaluate the relative severity of decline of four key ecosystem components over the past 50-years: hard corals, macroalgae, parrotfish and groupers. Using the two benthic indicators, we also calculated standardised estimates of state to identify reef sites which maintain a better condition through time relative to adjacent sites. Over the past 50 years, Kenya’s coral reefs have degraded across all four ecosystem components. At more than half the monitored sites both parrotfish and grouper abundance declined by more than 50%, while coral cover and macroalgae-coral ratio declined by at least 30%. This resulted in a Vulnerable threat status for coral reefs in Kenya based on degradation (under criterion D of the RLE). The temporal trends in coral cover revealed four sites which maintained an above average condition over their monitoring history (15-25 years). The results can guide management actions to contribute to at least nine of the 23 GBF targets. For example, we identified several sites with relatively healthy benthic and fish communities as candidate areas for protection measures under Target 3. We also found that Marine Protected Areas and Locally Managed Marine Areas, which restrict fishing and control gears, had lower declines in groupers compared to unmanaged areas, providing further evidence for their expansion. The RLE has a key role to play in monitoring and meeting the goals and targets of the Global Biodiversity Framework, and our work demonstrates how using the wealth of data within these assessments can inform local-scale ecosystem management and amplify the GBF’s impact.
POMC neurons control fertility through differential signaling of MC4R in Kisspeptin neurons
Authors: Talbi Rajae , Stincic Todd L. , Ferrari Kaitlin , Ji Hae Choi , Walec Karol , Medve Elizabeth , Gerutshang Achi , León Silvia , McCarthy Elizabeth A. , Rønnekleiv Oline K. , Kelly Martin J. , Navarro Víctor M.
Published: February 2024

Inactivating mutations in the melanocortin 4 receptor (MC4R) gene cause monogenic obesity. Interestingly, female patients also display various degrees of reproductive disorders, in line with the subfertile phenotype of MC4RKO female mice. However, the cellular mechanisms by which MC4R regulates reproduction are unknown. Kiss1 neurons directly stimulate gonadotropin-releasing hormone (GnRH) release through two distinct populations; the Kiss1ARHneurons, controlling GnRH pulses, and the sexually dimorphic Kiss1AVPV/PeNneurons controlling the preovulatory LH surge. Here, we show thatMc4rexpressed in Kiss1 neurons regulates fertility in females.In vivo, deletion ofMc4rfrom Kiss1 neurons in female mice replicates the reproductive impairments of MC4RKO mice without inducing obesity. Conversely, reinsertion ofMc4rin Kiss1 neurons of MC4R null mice restores estrous cyclicity and LH pulsatility without reducing their obese phenotype.In vitro, we dissect the specific action of MC4R on Kiss1ARHvs Kiss1AVPV/PeNneurons and show that MC4R activation excites Kiss1ARHneurons through direct synaptic actions. In contrast, Kiss1AVPV/PeNneurons are normally inhibited by MC4R activation except under elevated estradiol levels, thus facilitating the activation of Kiss1AVPV/PeNneurons to induce the LH surge driving ovulation in females. Our findings demonstrate that POMCARHneurons acting through MC4R, directly regulate reproductive function in females by stimulating the “pulse generator” activity of Kiss1ARHneurons and restricting the activation of Kiss1AVPV/PeNneurons to the time of the estradiol-dependent LH surge, and thus unveil a novel pathway of the metabolic regulation of fertility by the melanocortin system.
PCNA unloading is crucial for the bypass of DNA lesions by homologous recombination
Authors: Arbel-Groissman Matan , Liefshitz Batia , Katz Nir , Kuryachiy Maxim , Kupiec Martin
Published: February 2024

The DNA Damage Tolerance (DDT) mechanisms allow cells to bypass lesions in the DNA during replication. This allows the cells progress normally through the cell cycle in face of abnormalities in their DNA. PCNA, a homotrimeric sliding clamp complex plays a central role in the coordination of various processes during DNA replication, including the choice of mechanism used during DNA damage bypass. Mono-or poly-ubiquitination of PCNA facilitate an error-prone or an error-free bypass mechanism, respectively. In contrast, SUMOylation recruits the Srs2 helicase, which prevents local homologous recombination. The Elg1 RFC-like complex plays an important role in unloading PCNA from the chromatin. We analyse the interaction of mutations that destabilize PCNA with mutations in the Elg1 clamp unloader and the Srs2 helicase. Our results suggest that in addition to its role as a coordinator of bypass mechanisms, the very presence of PCNA on the chromatin prevents homologous recombination, even in the absence of the Srs2 helicase. Thus, PCNA unloading seems to be a pre-requisite for recombinational repair.
Unveiling chemotherapy-induced immune landscape remodeling and metabolic reprogramming in lung adenocarcinoma by scRNA-sequencing
Authors: Huang Yiwei , Wu Gujie , Bi Guoshu , Cheng Lin , Liang Jiaqi , Li Ming , Zhang Huan , Shan Guangyao , Hu Zhengyang , Chen Zhencong , Lin Zongwu , Jiang Wei , Wang Qun , Xi Junjie , Yin Shanye , Zhan Cheng
Published: February 2024

Background

Chemotherapy is widely used to treat lung adenocarcinoma (LUAD) patients comprehensively. Considering the limitations of chemotherapy due to drug resistance and other issues, it is crucial to explore the impact of chemotherapy and immunotherapy on these aspects.

Methods and Materials

Tumor samples from nine LUAD patients, of which four only received surgery and five received neoadjuvant chemotherapy, were subjected to scRNA-seq analysis. In vitro and in vivo assays, including flow cytometry, immunofluorescence, Seahorse assay, and tumor xenograft models, were carried out to validate our findings.

Results

A total of 83,622 cells were enrolled for subsequent analyses. The composition of cell types exhibited high heterogeneity across different groups. Functional enrichment analysis revealed that chemotherapy drove significant metabolic reprogramming in tumor cells and macrophages. We identified two subtypes of macrophages: Anti-mac cells (CD45+CD11b+CD86+) and Pro-mac cells (CD45+CD11b+ARG+) and sorted them by flow cytometry. The proportion of Pro-mac cells in lung adenocarcinoma tissues increased significantly after neoadjuvant chemotherapy. Pro-mac cells promote tumor growth and angiogenesis and also suppress tumor immunity. Moreover, through analyzing the remodeling of T and B cells induced by neoadjuvant therapy, we noted that chemotherapy ignited a relatively more robust immune cytotoxic response towards tumor cells.

Conclusion

Our study demonstrates that chemotherapy induces metabolic reprogramming within the TME of LUAD, particularly affecting the function and composition of immune cells such as macrophages and T cells. We believe our findings will offer insight into the mechanisms of drug resistance and provide novel therapeutic targets for LUAD in the future.
The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird
Authors: Cloutier Alison , Chan David Tsz Chung , Poon Emily Shui Kei , Sin Simon Yung Wa
Published: February 2024

Studies of widely distributed species can offer insight regarding how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). In contrast to the low variation in mitochondrial genomes, a genome-wide panel of >4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling indicated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are indicative of multiple, isolated glacial refugia that coincide with present-day population structure. This study highlights the power of genome-level sequencing approaches to deepen our understanding of evolutionary processes in nonmodel wild species and to contribute to efforts assessing how historic demographic events and contemporary factors might influence biodiversity.
Combining radio-telemetry and radar measurements to test optimal foraging in an aerial insectivore bird
Authors: Bloch Itai , Troupin David , Toledo Sivan , Nathan Ran , Sapir Nir
Published: February 2024

Optimal foraging theory posits that foragers adjust their movements based on prey abundance to optimize food intake. While extensively studied in terrestrial and marine environments, aerial foraging has remained relatively unexplored due to technological limitations. This study, uniquely combining BirdScan-MR1 radar and the ATLAS biotelemetry system, investigates the foraging dynamics of Little Swifts (Apus affinis) in response to insect movements over Israel’s Hula Valley. Insect Movement Traffic Rate (MoTR) substantially varied across days, strongly influencing swift movement. On days with high MoTR, swifts exhibited reduced flight distance, increased colony visit rate, and earlier arrivals at the breeding colony, reflecting a dynamic response to prey availability. However, no significant effects were observed in total foraging duration, flight speed, or daily route length. Notably, as insect abundance increased, inter-individual distances decreased. These findings suggest that Little Swifts optimize their foraging behavior in relation to aerial insect abundance, likely influencing reproductive success and population dynamics. The integration of radar technology and biotelemetry systems provides a unique perspective on the interactions between aerial insectivores and their prey, contributing to a comprehensive understanding of optimal foraging strategies in diverse environments.
Characterisation and comparison of semen microbiota and bacterial load in men with infertility, recurrent miscarriage, or proven fertility
Authors: Mowla Shahriar , Farahani Linda , Tharakan Tharu , Davies Rhianna , Correia Gonçalo D S , Lee Yun S , Kundu Samit , Khanjani Shirin , Sindi Emad , Rai Raj , Regan Lesley , Khalifa Dalia , Henkel Ralf , Minhas Suks , Dhillo Waljit S , Nagi Jara Ben , Bennett Phillip R , MacIntyre David A , Jayasena Channa N
Published: February 2024

Several studies have associated seminal microbiota abnormalities with male infertility but have yielded differing results owing to their limited sizes or depths of analyses. The semen microbiota during recurrent pregnancy loss (RPL) has not been investigated. Comprehensively assessing the seminal microbiota in men with reproductive disorders could elucidate its potential role in clinical management. We used semen analysis, terminal-deoxynucleotidyl-transferase-mediated-deoxyuridine-triphosphate-nick-end-labelling, Comet DNA fragmentation, luminol ROS chemiluminescence and metataxonomic profiling of semen microbiota by16S rRNA amplicon sequencing in this prospective, cross-section study to investigate composition and bacterial load of seminal bacterial genera and species, semen parameters, reactive oxidative species (ROS), and sperm DNA fragmentation in men with reproductive disorders and proven fathers. 223 men were enrolled included healthy men with proven paternity (n=63), the male partners in a couple encountering RPL (n=46), men with male factor infertility (n=58), and the male partners of couples unexplained infertility (n=56). Rates of high sperm DNA fragmentation, elevated ROS and oligospermia were more prevalent in the study group compared with control. In all groups, semen microbiota clustered into three majorgenera-dominant groups (1, Streptococcus; 2, Prevotella; 3, Lactobacillus and Gardnerella); no species clusters were identified. Group 2 had the highest microbial richness (P<0.001), alpha-diversity (P<0.001), and bacterial load (P<0.0001). Overall bacterial composition or load has not found to associate with semen analysis, ROS or DNA fragmentation. Whilst, global perturbation of the seminal microbiota is not associated with male reproductive disorders, men with unidentified seminalFlavobacteriumare more likely to have abnormal seminal analysis. Future studies may elucidate ifFlavobacteriumreduction has therapeutic potential.
Prior exposure to malaria decreases SARS-CoV-2 mediated mortality in K18-hACE2 mice without influencing viral load in lungs
Authors: Mawatwal Shradha , Mohapatra Amruta , Das Sayani , Ray Aisurya , Mukherjee Ratnadeep , Syed Gulam , Senapati Shantibushan , Ravindran Balachandran
Published: February 2024

Background

Epidemiological evidence for decreased prevalence and/or mortality due to SARS-CoV-2 infections in countries endemic for malaria have been reported. However, such associational studies in human population are limited by known and several unknown confounding factors. The current study, the first of its kind, was designed to seek experimental evidence to test the hypothesis if prior exposure to Plasmodial infections cross-protect against SARS-CoV-2 challenge infection in a murine model, K-18 human ACE2 transgenic mice.

Methods

Mice that had recovered fromPlasmodium chabaudiinfection 40 days earlier were challenged with a virulent strain of SARS-CoV-2 and viral load in lungs as well as mortality were scored and compared withK18 hACE2mice that had not experienced prior malaria.

Results

The viral load in lungs 6 days post challenge were comparable in malaria recovered mice and controls suggesting no significant generation of anti-viral immunity. However, mice with prior malaria exposure were significantly protected against SARS-CoV-2 induced mortality. Significant differences were observed in several host immune responses between the two groups when cytokines, chemokines and transcription factors were quantified in lungs. The plasma levels of several cytokines and chemokines were also significantly different between the two groups.

Conclusion

The results of the study suggest that prior exposure to malaria protects mice against viral induced mortality in K18 hACE2 transgenic mice challenged with a virulent isolate of SARS- CoV-2 in the absence of demonstrable host immunity inhibiting viral growth in lungs.
Single-particle track colocalization using CoPixie reveals the impact of cancer-associated POT1 mutations on telomerase-telomere interactions
Authors: Prince Samuel , Maguemoun Kamélia , Ferdebouh Mouna , Querido Emmanuelle , Derumier Amélie , Chartrand Pascal
Published: February 2024

Single-particle imaging and tracking can be combined with colocalization analysis to study the dynamic interactions between macromolecules in living cells. Indeed, single-particle tracking has been extensively used to study protein-DNA interactions and dynamics. Still, identification and quantification of binding events at specific genomic loci remains challenging. Herein we describe CoPixie, a new software that identifies colocalization events between a theoretically unlimited number of imaging channels, including single-particle movies. We employed CoPixie with live cell single-molecule imaging of telomerase and telomeres to test the model that cancer-associated POT1 mutations facilitate telomere accessibility. We show that OB-fold mutants POT1-ΔOB, Y223C, D224N or K90E increase telomere accessibility for telomerase interaction and the cumulative dwell-time of telomerase at telomeres. However, unlike POT1-ΔOB or D224N mutants, the POT1 Y223C and K90E mutations also increase the duration of long-lasting telomerase interactions at telomeres. Our data reveal that telomere elongation in cells expressing cancer-associated POT1 mutants arises from the dual impact of these mutations on telomeres accessibility and telomerase retention at telomeres. CoPixie can be used to explore a variety of questions involving macromolecular interactions in living cells, including between proteins and nucleic acids, from multi-color single-particles tracks.
Ensemble automated approaches for producing high quality herbarium digital records
Authors: Guralnick Robert. P. , LaFrance Raphael , Allen Julie M. , Denslow Michael W.
Published: February 2024

One of the slowest steps in digitizing natural history collections is converting labels associated with specimens into a digital data record usable for collections management and research. Recent work has shown a path for semi-automated approaches that can find labels, OCR them and convert the raw OCR text into digital data records. Here we address how raw OCR can be converted into a digital data record via extraction into standardized Darwin Core fields. We first showcase development of a rule-based approach and compare outcomes with a large language model-based approach, in particular ChatGPT4. We next quantified error rates in a set of OCRed labels, determining omission and commission errors for both approaches and documenting other issues. For example, we find that ChatGPT4 will often create field names that are not Darwin Core compliant. Our results suggest that these approaches each have different limitations. Therefore, we developed an ensemble approach that utilizes outputs from both in order to reduce problems from each individual method. An ensemble method reduces issues with field name heterogeneity and strongly reduces information extraction errors. This suggests that such an ensemble method is likely to have particular value for creating digital data records, even for complicated label content, given that longer labels, though more error prone, are still successfully extracted. While human validation is still much needed to ensure the best possible quality, we showcase working solutions to speed digitization of herbarium specimen labels that are likely usable more broadly for all natural history collection types.
RUDEUS, a machine learning classification system to study DNA-Binding proteins
Authors: Medina-Ortiz David , Cabas-Mora Gabriel , Moya-Barría Iván , Soto-Garcia Nicole , Uribe-Paredes Roberto
Published: February 2024

DNA-binding proteins are essential in different biological processes, including DNA replication, transcription, packaging, and chromatin remodelling. Exploring their characteristics and functions has become relevant in diverse scientific domains. Computational biology and bioinformatics have assisted in studying DNA-binding proteins, complementing traditional molecular biology methods. While recent advances in machine learning have enabled the integration of predictive systems with bioinformatic approaches, there still needs to be generalizable pipelines for identifying unknown proteins as DNA-binding and assessing the specific type of DNA strand they recognize. In this work, we introduce RUDEUS, a Python library featuring hierarchical classification models designed to identify DNA-binding proteins and assess the specific interaction type, whether single-stranded or double-stranded. RUDEUS has a versatile pipeline capable of training predictive models, synergizing protein language models with supervised learning algorithms, and integrating Bayesian optimization strategies. The trained models have high performance, achieving a precision rate of 95% for DNA-binding identification and 89% for discerning between single-stranded and doublestranded interactions. RUDEUS includes an exploration tool for evaluating unknown protein sequences, annotating them as DNA-binding, and determining the type of DNA strand they recognize. Moreover, a structural bioinformatic pipeline has been integrated into RUDEUS for validating the identified DNA strand through DNA-protein molecular docking. These comprehensive strategies and straightforward implementation demonstrate comparable performance to high-end models and enhance usability for integration into protein engineering pipelines.
Multi-species numerical validation of an efficient algorithm for auditory brainstem response hearing threshold estimation
Authors: Petersen Erik Alan , Shen Yi
Published: February 2024

The Auditory Brainstem Response (ABR) can be used to evaluate hearing sensitivity of animals who are unable to respond to behavioral tasks. However, typical data collection methods are time consuming; decreasing the measurement time may save resources or allow researchers to spend more time on other tasks. Here, an adaptive algorithm is proposed for efficient estimation of ABR thresholds. The algorithm relies on the online update of the predicted hearing threshold from a Gaussian process model as ABR data are collected using iteratively optimized stimuli. To validate the algorithm, ABR threshold estimation is simulated by adaptively sub-sampling pre-collected ABR datasets for which the stimuli were systematically varied in frequency and level. The simulated experiment is performed on 5 datasets of Mouse (2 different datasets), Budgerigar, Gerbil, and Guinea Pig ABRs collected by different laboratories, with a total of 27 ears. The original datasets contain between 68 and 106 stimuli conditions, while the adaptive algorithm is run up to a total of 20 stimuli conditions. The adaptive algorithm ABR threshold estimate is compared against human rater estimates who view the full ABR dataset. The adaptive algorithm threshold matches the human estimates within 10 dB, averaged over frequency, for 19 out of 27 ears. The adaptive procedure is able to provide threshold estimates that are comparable to the human rater estimated thresholds while reducing the measurement time by a factor of 3 to 5. The standard deviation of threshold estimates from successive runs is smaller than the inter-human rater differences, indicating adequate test/retest reliability.
Structural evidence for two-stage binding of mitochondrial ferredoxin 2 to the core iron-sulfur cluster assembly complex
Authors: Steinhilper Ralf , Freibert Sven-A. , Kaltwasser Susann , Lill Roland , Murphy Bonnie J.
Published: February 2024

Iron-sulfur (FeS) clusters are ubiquitous metallocofactors that are essential for life. In eukaryotes, FeS cluster biosynthesis begins with thede novoassembly of a [2Fe-2S] cluster by the core iron-sulfur cluster assembly (ISC) complex in the mitochondrial matrix. This complex comprises the scaffold protein ISCU2, the cysteine desulfurase subcomplex NFS1-ISD11-ACP1, the allosteric activator frataxin (FXN) and the electron donor ferredoxin 2 (FDX2). The interaction of FDX2 with the complex remains unclear. Here, we present cryo-EM structures of the FDX2-bound core ISC complex and show that FDX2 and FXN compete for overlapping binding sites during [2Fe-2S] cluster biosynthesis. FDX2 binds in two conformations; in the ‘distal’ conformation, helix F of FDX2 shows loose electrostatic interaction with an arginine patch of NFS1, while in the ‘proximal’ conformation this interaction tightens and the FDX2-specific C terminus forms contacts with NFS1; in this conformation, the [2Fe-2S] cluster of FDX2 is close enough to the ISCU2 FeS cluster assembly site for rapid electron transfer.
Computational analysis of the effect of a binding protein (RbpA) on the dynamics ofMycobacterium tuberculosisRNA polymerase assembly
Authors: Bheemireddy Sneha , Sowdhamini Ramanathan , Srinivasan Narayanaswamy
Published: February 2024

RNA polymerase-binding protein A (RbpA) is an actinomycetes-specific protein crucial for the growth and survival of the pathogenMycobacterium tuberculosis. Its role is essential and influences the transcription and antibiotic responses. However, the regulatory mechanisms underlying RbpA-mediated transcription remain unknown. In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex.

Our analysis reveals significant structural rearrangements in RNA polymerase happen upon interaction with RbpA. Hotspot residues, crucial amino acids in the RbpA-mediated transcriptional regulation, were identified through our examination. The study elucidates the dynamic behavior within the complex, providing insights into the flexibility and functional dynamics of the RbpA-RNA polymerase interaction. Notably, potential allosteric mechanisms, involving the interface of subunitsα1 andα2 were uncovered, shedding light on how RbpA modulates transcriptional activity.

Finally, potential ligands meant for theα1-α2 binding site were identified through virtual screening. The outcomes of our computational study serve as a foundation for experimental investigations into inhibitors targeting the RbpA-regulated dynamics in RNA polymerase. Overall, this research contributes valuable information for understanding the intricate regulatory networks of RbpA in the context of transcription and suggests potential avenues for the development of RbpA-targeted therapeutics.

Author Summary

Infection studies byMycobacterium tuberculosis(Mtb) acquires primary importance due to its severe infection and antibiotic resistance. There is an open need for highly effective drugs and one needs to employ novel approaches such as detailed structural analysis and the possibility to focus on allosteric inhibitors. We have exploited the availability of cryo-EM structures of RNA polymerase of Mtb, with and without its transcription-activator protein namely RNA polymerase-binding protein A (RbpA). In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex. The assemblies were subject to molecular dynamics and perturbation scanning, followed by structural comparisons and measurement of subunit interface strength. These analyses could clearly show that α subunits, which are far away from the RbpA binding site, undergo differential structural changes. Hence, we focused on the αα’ site to recognize potential small molecule inhibitors using virtual screening. These analyses demonstrate that it is possible to perform comparative structural analysis of different forms of assemblies, which can be useful towards drug design.
Maturing neutrophils of lower density associate with thrombocytopenia in Puumala orthohantavirus-caused hemorrhagic fever with renal syndrome
Authors: Cabrera Luz E. , Tietäväinen Johanna , Jokiranta Suvi T. , Mäkelä Satu , Vaheri Antti , Mustonen Jukka , Vapalahti Olli , Kanerva Mari , Strandin Tomas
Published: February 2024

Puumala orthohantavirus-caused hemorrhagic fever with renal syndrome (PUUV-HFRS) is characterized by strong neutrophil activation. Neutrophils are the most abundant immune cell type in the circulation and are specially equipped to rapidly respond to infections. They are more heterogenous than previously appreciated, with specific neutrophil subsets recently implicated in inflammation and immunosuppression. Furthermore, neutrophils can be divided based on their density to either low-density granulocytes (LDGs) or “normal density” polymorphonuclear cell (PMN) fractions. In the current study we aimed to identify and characterize the different neutrophil subsets in the circulation of PUUV-HFRS patients. PMNs exhibited an activation of antiviral pathways, while circulating LDGs were increased in frequency following acute PUUV-HFRS. Furthermore, cell surface marker expression analysis revealed that PUUV-associated LDGs are primarily immature and most likely reflect an increased neutrophil production from the bone marrow. Interestingly, both the frequency of LDGs and the presence of a “left shift” in blood associated with the extent of thrombocytopenia, one of the hallmarks of severe HFRS, suggesting that immature neutrophils could play a role in disease pathogenesis. These results imply that elevated circulating LDGs might be a general finding in acute viral infections. However, in contrast to the COVID-19 associated LDGs described previously, the secretome of PUUV LDGs did not show significant immunosuppressive ability, which suggests inherent biological differences in the LDG responses that can be dependent on the causative virus or differing infection kinetics.
Schwann cells have a limited window of time in which to initiate myelination program during early migrationin vivo
Authors: El-Hage Océane , Mikdache Aya , Boueid Marie-José , Degerny Cindy , Tawk Marcel
Published: February 2024

The temporal control of mitotic exit of individual Schwann cells (SCs) is essential for radial sorting and peripheral myelination. However, it remains unknown when, during their multiple rounds of division, SCs initiate myelin signalingin vivo. By manipulating SC division during development, we report that when SCs skip their division during migration, but not during radial sorting, they fail to myelinate peripheral axons. This coincides with a sharp decrease in Laminin expression within the posterior lateral line nerve. Interestingly, elevating cAMP levels or forcing Laminin 2 expression within individual SCs restore their ability to myelinate, despite missing mitosis during migration. Our results demonstrate a limited time window during which migrating SCs initiate Laminin expression to activate the Laminin/Gpr126/cAMP signaling required for radial sorting and myelination at later stagesin vivo.
Finimizers: Variable-length bounded-frequency minimizers fork-mer sets
Authors: Alanko Jarno N. , Biagi Elena , Puglisi Simon J.
Published: February 2024

The minimizer of ak-mer is the smallestm-mer inside thek-mer according to some order relation<of them-mers. Minimizers are often used as keys in hash tables in indexing tasks in metagenomics and pangenomics. The main weakness of minimizer-based indexing is the possibility of very frequently occurring minimzers, which can slow query times down significantly. Popular minimizer alignment tools employ various and often wild heuristics as workarounds, typically by ignoring frequent minimizers or blacklisting commonly occurring patterns, to the detriment of other metrics (e.g., alignment recall, space usage, or code complexity).

In this paper, we introducefrequency-bounded minimizers, which we callfinimizers, for indexing sets ofk-mers. The idea is to use an order relation<for minimizer comparison that depends on the frequency of the minimizers within the indexedk-mers. With finimizers, the lengthmof them-mers is not fixed, but is allowed to vary depending on the context, so that the length can increase to bring the frequency down below a user-specified thresholdt. Setting a maximum frequency solves the issue of very frequent minimizers and gives us a worstcase guarantee for the query time. We show how to implement a particular finimizer scheme efficiently using the Spectral Burrows-Wheeler Transform (SBWT) (Alanko et al., Proc. SIAM ACDA, 2023) augmented with longest common suffix information. In experiments, we explore in detail the special case in which we sett= 1. This choice simplifies the index structure and makes the scheme completely parameter-free apart from the choice ofk. A prototype implementation of this scheme exhibitsk-mer localization times close to, and often faster than, stateof-the-art minimizer-based schemes. The code is available athttps://github.com/ElenaBiagi/Finito.
Annotation and visualisation of parasite, fungi and arthropod genomes with Companion
Authors: Haese-Hill William , Crouch Kathryn , Otto Thomas D.
Published: February 2024

Although sequencing genomes has become increasingly popular, there is still a bottleneck for the annotation of the resulting assemblies. Structural and functional annotation is still challenging as it includes finding the correct gene sequences, annotating other elements such as RNA and being able to submit those data to databases to share it with the community. We developed the Companion web server to allow non-experts to annotate their genome using a reference-based method, enabling them to analyse their results before submitting to public databases. In this update paper, we describe how we included novel methods for gene finding and made the server more efficient to annotate genomes of up to 1 GB in size. The reference set was increased to genomes from the fungi and arthropod kingdoms. We show that Companion outperforms existing comparable tools.

GRAPHICAL ABSTRACT
Impact of Triplet State Population on GFP-type Fluorescence and Photobleaching
Authors: Byrdin Martin , Byrdina Svetlana
Published: February 2024

Based on recently published parameters (Rane et al. 2023, JPCB 127, 5046-5054) for (rs)EGFP triplet state formation and decay rates and yields, we consider the power density dependence of triplet state population dynamics and its consequences for the application of green fluorescent proteins in biological single molecule fluorescence microscopy. We find that under certain conditions, the photon budget of GFP type fluorescent proteins can be linearly dependent on power density and we propose a possible explanation for such a non-Hirschfeld photobleaching behavior. Moreover, illumination with ms pulses at sub-kHz rates is shown to improve photostability. We stipulate that a judicious choice of excitation wavelength should take into account the triplet state absorption spectrum along with the singlet state absorption spectrum. Formulas are given for the estimation of the effects of such choice as function of the experimental parameters.

Abstract Figure

Hirschfeld predicted that photobleaching rates should scale with fluorescence brightness, which is obviously not the case for fluorescent proteins found in thefpbase.org. We investigate a modified theory considering the triplet state as precursor for photobleaching.
Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer
Authors: Kim Ah-Ram , Hu Yanhui , Comjean Aram , Rodiger Jonathan , Mohr Stephanie E. , Perrimon Norbert
Published: February 2024

Accurately mapping protein-protein interactions (PPIs) is critical for elucidating cellular functions and has significant implications for health and disease. Conventional experimental approaches, while foundational, often fall short in capturing direct, dynamic interactions, especially those with transient or small interfaces. Our study leverages AlphaFold-Multimer (AFM) to re-evaluate high-confidence PPI datasets fromDrosophilaand human. Our analysis uncovers a significant limitation of the AFM-derived interface pTM (ipTM) metric, which, while reflective of structural integrity, can miss physiologically relevant interactions at small interfaces or within flexible regions. To bridge this gap, we introduce the Local Interaction Score (LIS), derived from AFM’s Predicted Aligned Error (PAE), focusing on areas with low PAE values, indicative of the high confidence in interaction predictions. The LIS method demonstrates enhanced sensitivity in detecting PPIs, particularly among those that involve flexible and small interfaces. By applying LIS to large-scaleDrosophiladatasets, we enhance the detection of direct interactions. Moreover, we present FlyPredictome, an online platform that integrates our AFM-based predictions with additional information such as gene expression correlations and subcellular localization predictions. This study not only improves upon AFM’s utility in PPI prediction but also highlights the potential of computational methods to complement and enhance experimental approaches in the identification of PPI networks.
Lysis buffer selection guidance for mass spectrometry-based global proteomics including studies on the intersection of signal transduction and metabolism
Authors: Helm Barbara , Hansen Pauline , Lai Li , Schwarzmüller Luisa , Clas Simone M. , Richter Annika , Ruwolt Max , Liu Fan , Frey Dario , D’Alessandro Lorenza A. , Lehmann Wolf-Dieter , Schilling Marcel , Helm Dominic , Fiedler Dorothea , Klingmüller Ursula
Published: February 2024

Prerequisite for a successful proteomics experiment is a high-quality lysis of the sample of interest, resulting in a large number of identified proteins as well as a high coverage of protein sequences. Therefore, the choice of suitable lysis conditions is crucial. Many buffers were previously employed in proteomics studies, yet a comprehensive comparison of lysate preparation conditions was so far missing. In this study, we compared the efficiency of four commonly used lysis buffers, containing the agents NP40, SDS, urea or GdnHCl, in four different types of biological samples (suspension and adherent cell lines, primary mouse cells and mouse liver tissue). After liquid chromatography-mass spectrometry (LC-MS) measurement and MaxQuant analysis, we compared chromatograms, intensities, number of identified proteins and the localization of the identified proteins. Overall, SDS emerged as the most reliable reagent, ensuring stable performance and reproducibility across diverse samples. Furthermore, our data advocated for a dual-sample lysis approach, including that the resulting pellet is lysed again after the initial lysis with a urea lysis buffer and subsequently both lysates are combined for a single LC-MS run to maximize the proteome coverage. However, none of the investigated lysis buffers proved to be superior in every category, indicating that the lysis buffer of choice depends on the proteins of interest and on the biological question. Further, we demonstrated with our systematic studies the establishment of conditions that allows to perform global proteomics and affinity purification-based interactome characterization from the same lysate. In sum our results provide guidance for the best-suited lysis buffer for mass spectrometry-based proteomics depending on the question of interest.