bluuebunny/crossref_metadata_2025 huggingface dataset:
Re-analysis of lipidomic data reveals Specialised Pro-Resolution Lipid Mediators (SPMs) to be lower than quantifiable limits of assay in a human model of resolving inflammation
Authors: Homer Natalie ZM , Andrew Ruth , Gilroy Derek W
Published: March 2023

Using a model of UV-killedE. colidriven dermal inflammation in healthy human volunteers we originally reported that following inflammatory resolution there was the infiltration of macrophages, which, through prostanoids including prostaglandin (PG)E2, imprints long-term tissue immunity. In addition to the prostanoids, we also presented data on levels ofSpecialisedPro-Resolution LipidMediators (SPMs) throughout inflammatory onset, resolution and post-resolution phases of this model. However, our collaborators who carried out the lipidomic analysis received a complaint concerning how they generally present SPM data in their publications, namely their use of graphical illustrations to depict data. Importantly, such lipidomic illustrations were used in our human UV-killedE. colistudy. Therefore, in the interest of transparency and to replace these illustrations with more meaningful images, the original data from our human UV-killedE. colimodel were re-analysed by two independent experts. It transpires that the integrated areas of the chromatographic peaks of the SPM lipid mediators were below the amounts that could be reliably either detected and/or quantified using community standards for quantitation. Here we show the outcome of this reanalysis. Importantly, with prostanoids including PGE2being robustly detected, this re-analysis does not alter the original report that post-resolution PGs imprint tissue immunity.
Molecular Consequences of Peripheral Influenza A Infection on Cell Populations in the Murine Hypothalamus
Authors: Lemcke René , Egebjerg Christine , Berendtsen Nicolai T. , Egerod Kristoffer L. , Thomsen Allan R. , Pers Tune H. , Christensen Jan P. , Kornum Birgitte R.
Published: March 2023

Infection with Influenza A virus (IAV) causes the well-known symptoms of the flu, including fever, loss of appetite and excessive sleepiness. These responses, mediated by the brain, will normally disappear once the virus is cleared from the system, but a severe respiratory virus infection may cause long-lasting neurological disturbances. These include encephalitis lethargica and narcolepsy. The mechanisms behind such long lasting changes are unknown. The hypothalamus is a central regulator of the homeostatic response during a viral challenge. To gain insight into the neuronal and non-neuronal molecular changes during an IAV infection, we intranasally infected mice with an H1N1 virus and extracted the brain at different time points. Using single-nucleus RNA sequencing (snRNA-seq) of the hypothalamus, we identify transcriptional effects in all identified cell populations. The snRNA-seq data showed the most pronounced transcriptional response at 3 days past infection, with a strong downregulation of genes across all cell types. General immune processes were mainly impacted in microglia, the brain resident immune cells, where we found increased numbers of cells expressing pro-inflammatory gene networks. In addition, we found that most neuronal cell populations downregulated genes contributing to the energy homeostasis in mitochondria and protein translation in the cytosol, indicating potential reduced cellular and neuronal activity. This might be a preventive mechanism in neuronal cells to avoid intracellular viral replication and attack by phagocytosing cells. The change of microglia gene activity suggest that this is complemented by a shift in microglia activity to provide increased surveillance of their surroundings.
Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma
Authors: Samuel Ryan M. , Navickas Albertas , Maynard Ashley , Gaylord Eliza A. , Garcia Kristle , Bhat Samyukta , Majd Homa , Richter Mikayla N. , Elder Nicholas , Le Daniel , Nguyen Phi , Shibata Bradley , Llabata Marta Losa , Selleri Licia , Laird Diana J. , Darmanis Spyros , Goodarzi Hani , Fattahi Faranak
Published: March 2023

Summary/Abstract

The neural crest (NC) is highly multipotent and generates diverse lineages in the developing embryo. However, spatiotemporally distinct NC populations display differences in fate potential, such as increased gliogenic and parasympathetic potential from later migrating, nerve-associated Schwann cell precursors (SCPs). Interestingly, while melanogenic potential is shared by both early migrating NC and SCPs, differences in melanocyte identity resulting from differentiation through these temporally distinct progenitors have not been determined. Here, we leverage a human pluripotent stem cell (hPSC) model of NC temporal patterning to comprehensively characterize human NC heterogeneity, fate bias, and lineage development. We captured the transition of NC differentiation between temporally and transcriptionally distinct melanogenic progenitors and identified modules of candidate transcription factor and signaling activity associated with this transition. For the first time, we established a protocol for the directed differentiation of melanocytes from hPSCs through a SCP intermediate, termed trajectory 2 (T2) melanocytes. Leveraging an existing protocol for differentiating early NC-derived melanocytes, termed trajectory 1 (T1), we performed the first comprehensive comparison of transcriptional and functional differences between these distinct melanocyte populations, revealing differences in pigmentation and unique expression of transcription factors, ligands, receptors and surface markers. We found a significant link between the T2 melanocyte transcriptional signature and decreased survival in melanoma patients in the cancer genome atlas (TCGA). We performed anin vivoCRISPRi screen of T1 and T2 melanocyte signature genes in a human melanoma cell line and discovered several T2-specific markers that promote lung metastasis in mice. We further demonstrated that one of these factors, SNRPB, regulates the splicing of transcripts involved in metastasis relevant functions such as migration, cell adhesion and proliferation. Overall, this study identifies distinct developmental trajectories as a source of diversity in melanocytes and implicates the unique molecular signature of SCP-derived melanocytes in metastatic melanoma.
Species Delimitation Under Allopatry: Genomic Divergences Within and Across Continents in Lepidoptera
Authors: Joshi Mukta , Espeland Marianne , Huemer Peter , deWaard Jeremy , Mutanen Marko
Published: March 2023

Delimitation of allopatric populations into species remains subjective and largely arbitrary. Many cold-adapted species from the subarctic and Central and Southern European Mountain systems display frequent allopatry with disjunct distributions of their populations. The same concerns Holarctic species which are many and which almost regularly show various degrees of differentiation between the continents. In this study, we analyze high- throughput target enrichment data for ten groups of arctic-alpine and Holarctic lepidopteran species sampled from four main regions across the Holarctic realm – Fennoscandia, North America, Alps and Altai. We first aimed to assess whether the genetic differences in the nuclear genome reflect observed DNA barcode divergences and second, whether the gap between population and species-level differences can be dissected using genomic data. We compared the phylogenetic trees and uncorrected pairwise genetic distances obtained from target enrichment and the mitochondrial cytochrome oxidase I (COI) barcodes for each of the study species. Additionally, we also performed a suite of population genetic and species delimitation analyses to further shed light on patterns of intraspecific variation using a large number of nuclear markers. We observed that in about one half of the cases, DNA barcodes tended to show phylogenetic relationships similar to the target enrichment markers. We report varying levels of nuclear genetic differentiation among the populations analyzed, starting from low differentiation of geographically separated populations to the deeper separation of some Nearctic population and further arctic-alpine disjunction. Given that no single consistent pattern emerged across different case studies, we demonstrate that the delimitation of allopatric populations into species could be done much more efficiently and in a consistent manner if based on a large set of universal genetic loci, which would help in reaching standards for taxonomic delimitation of allopatric populations.
Application of fuzzy measures to move towards the cyber-taxonomy
Authors: Ciguene Richardson , Mozziconacci Julien , Clément Francis , Miralles Aurélien
Published: March 2023

The species inventory of global biodiversity is constantly revised and refined by taxonomic research, through the addition of newly discovered species. This almost three century old project provide a knowledge foundation essential for humankind, and notably to develop appropriate conservation strategies. This task relies on the study of millions of specimens housed all around the world in natural history collections. Since two decades, taxonomy generates a plethoric amount of numeric data every year, and notably through the digitization of collection specimens, gradually transforms into a big data science. In this line, the French National Museum of Natural History (MNHN) has embarked into a major research and engineering challenge within its information system, in order to facilitate the transition towards cyber-taxonomic practices which require a facilitated access to data on reference collection specimens housed all over the world. To this end, a first mandatory step is to automatically complete classification data usually associated to collection specimens found in multiple databases. We use here fuzzy approaches to connect one database with other databases and match identical specimens found in each databases together.
Urban living can rescue Darwin’s finches from the lethal effects of invasive vampire flies
Authors: Knutie Sarah A. , Webster Cynthia N. , Vaziri Grace J. , Albert Lauren , Harvey Johanna A. , LaRue Michelle , Verrett Taylor B. , Soldo Alexandria , Koop Jennifer A.H. , Chaves Jaime A. , Wegrzyn Jill L.
Published: March 2023

Human activity changes multiple factors in the environment, which can have additive or neutralizing effects on organisms. However, few studies have explored the causal effects of multiple anthropogenic factors, such as urbanization and invasive species, on animals, and the mechanisms that mediate these interactions. This study examines the influence of urbanization on the detrimental effect of invasive avian vampire flies (Philornis downsi) on endemic Darwin’s finches in the Galápagos Islands. We experimentally manipulated nest fly abundance in an urban and non-urban area and then characterized nestling health, survival, diet, and gene expression patterns related to host defense. Survival of fumigated nestlings from urban and non-urban nests did not differ significantly. However, sham-fumigated, non-urban nestlings lost more blood and few nestlings survived compared to urban nestlings. Stable isotopic values (δ15N) from urban nestling feces were higher than non-urban nestlings, suggesting that urban nestlings are consuming more protein. δ15N values correlated negatively with parasite abundance, which suggests that diet might influence host defenses (e.g., tolerance and resistance). Parasitized urban nestlings differentially expressed genes within pathways associated with red blood cell production (tolerance) and pro-inflammatory response (innate immunological resistance), compared to sham-fumigated non-urban nestlings. In contrast, sham-fumigated non-urban nestlings differentially expressed genes within pathways associated with immunoglobulin production (adaptive immunological resistance). Our results suggest that urban nestlings are investing more in pro-inflammatory responses to resist parasites, but also recovering more blood cells to tolerate blood loss. Although non-urban nestlings are mounting an adaptive immune response, it is likely a last effort by the immune system rather than an effective defense against avian vampire flies since few nestlings survived.
Cytotoxic CD4+T cells eliminate senescent cells by targeting cytomegalovirus antigen
Authors: Hasegawa Tatsuya , Oka Tomonori , Son Heehwa G. , Oliver-García Valeria S. , Azin Marjan , Eisenhaure Thomas M. , Lieb David J. , Hacohen Nir , Demehri Shadmehr
Published: March 2023

Senescent cell accumulation has been implicated in the pathogenesis of aging-associated diseases including cancer. The mechanism that prevents the accumulation of senescent cells in aging human organs is unclear. Here, we demonstrate that a virus-immune axis controls the senescent fibroblast accumulation in the human skin. Senescent fibroblasts increased in old compared with young skin. However, they did not increase with advancing age in the elderly. Increased CXCL9 and cytotoxic CD4+T cell (CD4 CTL) recruitment were significantly associated with reduced senescent fibroblasts in the old skin. Senescent fibroblasts expressed human leukocyte antigen class II (HLA-II) and human cytomegalovirus glycoprotein B (HCMV-gB), becoming direct CD4 CTL targets. Skin-resident CD4 CTL eliminated HCMV-gB+senescent fibroblasts in an HLA-II-dependent manner, and HCMV-gB activated CD4 CTL from the human skin. Collectively, our findings demonstrate HCMV reactivation in senescent cells, which can be directly eliminated by CD4 CTL through the recognition of the HCMV-gB antigen.
Modulation of locus coeruleus neurons and strong release of noradrenaline during acute hippocampal seizures in rats
Authors: Larsen Lars Emil , Caestecker Sielke , Stevens Latoya , van Mierlo Pieter , Carrette Evelien , Boon Paul , Vonck Kristl , Raedt Robrecht
Published: March 2023

The locus coeruleus (LC), a brainstem nucleus, is the sole source of noradrenaline in the neocortex, hippocampus and cerebellum. Noradrenaline is a powerful neuromodulator involved in the regulation of excitability and plasticity of large-scale brain networks. In this study, we assessed the activity of locus coeruleus neurons and changes in noradrenergic transmission during acute hippocampal seizures evoked with perforant path stimulation. LC neurons were recorded in anesthetized rats using a multichannel electrophysiology probe and were identified based on electrophysiological characteristics or optogenetic tagging. The majority of LC neurons (55%) were inhibited during seizures, while only a subset of LC neurons (28%) was excited during seizures. Topographic analysis of multi-unit activity showed anatomical separation of neurons that were excited and inhibited during seizures. Changes in hippocampal noradrenaline transmission during seizures were assessed using a fluorescent biosensor for noradrenaline, GRABNE2m, in combination with fiber photometry in both anesthetized and awake rats. Our results indicate that acute electrically evoked hippocampal seizures are associated with strong changes in LC unit activity and strong and consistent time-locked release of noradrenaline. Understanding the role of mass release of noradrenaline during hippocampal seizures is likely to be important to understand seizure pathophysiology.
Challenging popular belief, mosquito larvae breathe underwater
Authors: Alvarez-Costa Agustin , Leonardi Maria Soledad , Giraud Silvère , Schilman Pablo E. , Lazzari Claudio R.
Published: March 2023

It is taken for granted that immature mosquito only breathe atmospheric air through their siphons. However, there is no quantitative study that demonstrated it. We analysed the survival of the last instar larvae ofAedes aegyptifully submerged at different temperatures, and measured oxygen consumption from air and dissolved in water, of larvae and pupae of this species under different conditions. Results revealed that under water, larvae survived much longer than expected, reaching 50% mortality only after 58, 10, and 5 days at 15°, 25° and 35°C, respectively. Interestingly, whereas we registered moults to pupae in larvae with access to air, individuals kept submerged never moulted. When remaining at the water surface, larvae obtained 12.72% of O2from the water, while pupae only 5.32%. When completely submerged, larvae consumed less oxygen than in contact with the surface, but enough for surviving, while pupae did not. At both media, temperature affected larvae respiration rate, with relatively close Q10values. In the related species,Ae. albopictus, a similar pattern of O2consumption were observed. Larvae got 12.14% of their oxygen from the water. Interestingly, no significant differences in total O2consumption were found between water O2consumption, whenAe. albopictuslarvae were submerged, or when they also have access to air (dual O2consumption). Our findings not only challenge the classical idea that mosquito larvae only breathe atmospheric O2, but also force us to reconsider the potential effectiveness of control methods based on asphyxiating larvae by detaching from water surface.

Summary statement

We present the first quantitative analysis of mosquito larvae respiration in air and water, unravelling the unknown capacity of larvae of the most cosmopolitan disease vector of breathing underwater.
Cryo-electron tomography sheds light on the elastic nature of theTrypanosoma bruceitripartite attachment complex
Authors: Bregy Irina , Radecke Julika , Noga Akira , van den Hoek Hugo , Kern Mara , Haenni Beat , Engel Benjamin D. , Siebert C. Alistair , Ishikawa Takashi , Zuber Benoît , Ochsenreiter Torsten
Published: March 2023

In contrast to many eukaryotic organisms, trypanosomes only contain a single mitochondrion per cell. Within that singular mitochondrion, the protist carries a single mitochondrial genome that consists of a complex DNA network, the kinetoplast DNA (kDNA). Segregation of the replicated kDNA is coordinated by the basal body of the cell’s single flagellum. The tripartite attachment complex (TAC) forms a physical connection between the proximal end of the basal body and the kDNA. This allows anchoring of the kDNA throughout the cell cycle and couples kDNA segregation with the separation of the basal bodies prior to cell division. Over the past years, several components of the TAC have been identified. To shed light on the structure of the cytoplasmic part of the TAC (known as the exclusion zone), we performed cryo-electron tomography on whole cells. This allowed us to acquire three-dimensional high-resolution images of the exclusion zonein situ. We observed that the exclusion zone filaments offer great mechanical flexibility for basal body movement. We measured the dimensions of the individual structural elements of the area, as well as the overall orientation and positioning of the basal bodies towards the mitochondrial kDNA pocket. Using a combination of experimental data and modelling, we generated a structural model of the exclusion zone protein p197. Our findings suggest that the majority of p197 consists of a string of spectrin-like repeats. We propose that these structural units provide the architecture of a molecular spring and that they are required in the TAC to withstand the mechanical forces generated through basal body repositioning events during kDNA segregation and motility of the organism.
Variation in female-biased sexual size dimorphism of Northern Pike (Esox lucius) associated with environment and life history
Authors: Kennedy P.J. , Rennie M.D.
Published: March 2023

Background

Sexual size dimorphism (SSD) is a widespread phenomenon in the animal world resulting from differential selection on the sexes. The Northern Pike (Esox lucius) is a freshwater apex predatory fish species that exhibits female-biased SSD, but the degree to which SSD varies among populations and what variables might dictate variation in SSD in this species remain poorly understood.

Aim

We sought to quantify the degree of variation in SSD among Northern Pike populations across a large portion of their North American range, as well as evaluate associations between the magnitude of SSD in Northern Pike populations with environmental variables and life history traits of populations.

Methods

We quantified SSD in 102 populations of Northern Pike across the province of Ontario, Canada, using a standardized gillnetting database. We further investigated the degree to which both environmental variables (Cisco abundance as catch-per-unit-effort, lake surface area, and latitude) and Northern Pike life-history traits (early growth and mortality rates) explained variation in female-biased SSD using linear models.

Results

Female-biased SSD in mean weight of Northern Pike increased with increasing Cisco (Coregonus artedi) abundance, and the difference in female and male mean age increased with increasing latitude. Furthermore, SSD was greater in populations with lower female mortality and early growth rates.

Conclusion

This study indicates that slow-growing, long-lived populations of Northern Pike should exhibit greater female-biased SSD, and that these conditions may be facilitated by the availability of large, energy-dense prey and cooler temperatures at northern latitudes.
Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of anti-malarial drug resistance
Authors: He Qixin , Chaillet John K. , Labbé Frédéric
Published: March 2023

The establishment and spread of anti-malarial drug resistance vary drastically across different biogeographic regions. Though most infections occur in Sub-Saharan Africa, resistant strains often emerge in low-transmission regions. Existing models on resistance evolution lack consensus on the relationship between transmission intensity and drug resistance, possibly due to overlooking the feedback between antigenic diversity, host immunity, and selection for resistance. To address this, we developed a novel compartmental model that tracks sensitive and resistant parasite strains, as well as the host dynamics of generalized and antigen-specific immunity. Our results show a negative correlation between parasite prevalence and resistance frequency, regardless of resistance cost or efficacy. Validation using chloroquine-resistant marker data supports this trend. Post discontinuation of drugs, resistance remains high in low-diversity, low-transmission regions, while it steadily decreases in high-diversity, high-transmission regions. Our study underscores the critical role of malaria strain diversity in the biogeographic patterns of resistance evolution.
A molecularly defined and spatially resolved cell atlas of the whole mouse brain
Authors: Zhang Meng , Pan Xingjie , Jung Won , Halpern Aaron , Eichhorn Stephen W. , Lei Zhiyun , Cohen Limor , Smith Kimberly A. , Tasic Bosiljka , Yao Zizhen , Zeng Hongkui , Zhuang Xiaowei
Published: March 2023

In mammalian brains, tens of millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells in the brain have so far hindered our understanding of the molecular and cellular basis of its functions. Recent advances in spatially resolved single-cell transcriptomics have allowed systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1–3. However, these approaches have only been applied to a few brain regions1–11and a comprehensive cell atlas of the whole brain is still missing. Here, we imaged a panel of >1,100 genes in ∼8 million cells across the entire adult mouse brain using multiplexed error-robust fluorescence in situ hybridization (MERFISH)12and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating MERFISH and single-cell RNA-sequencing (scRNA-seq) data. Using this approach, we generated a comprehensive cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to ∼300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of the MERFISH images to the common coordinate framework (CCF) of the mouse brain further allowed systematic quantifications of the cell composition and organization in individual brain regions defined in the CCF. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes in the gene-expression profiles of cells. Finally, this high-resolution spatial map of cells, with a transcriptome-wide expression profile associated with each cell, allowed us to infer cell-type-specific interactions between several hundred pairs of molecularly defined cell types and predict potential molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a valuable resource for future functional investigations of neural circuits and their dysfunction in diseases.
Integration of Avidity and Differentiation is enabled by CD8+T-cell sensing of IFN-γ
Authors: Uhl Lion F.K. , Cai Han , Mahale Jagdish N. , MacLean Andrew J. , Mazet Julie M. , He Alexander J. , Lau Doreen , Elliott Tim , Gerard Audrey
Published: March 2023

The most effective responses to intracellular pathogens have a breadth of T-cell clones with different affinities for their cognate peptide, and a diversity of functional phenotypes, from effector to long-lived memory cells. While high- and low-affinity T-cells are inherently skewed towards becoming effector and memory, respectively, overall, both functional subsets exploit a wide range of affinities. How the breadth of affinities and functionalities are coordinated is therefore unclear. In this study, we provide evidence that direct sensing of the cytokine IFN-γ by CD8+T-cells is a factor controlling the integration of T-cell affinity and differentiation during infection. IFN-γ increases the expansion of low-affinity T-cells, allowing them to overcome the selective advantage of high-affinity T-cells. Concomitantly, IFN-γ reinforces high-affinity T-cell entry into the memory pool. As a result, direct IFN-γ sensing by CD8+T-cells increases the avidity of the memory response. This comes at the expense of the primary T-cell response, for which IFN-γ decreases the avidity, leading to sub-optimum immunity to infection. IFN-γ sensing by CD8+T-cells is paracrine, provided by a distinct subset of CD8+T-cells called Virtual Memory T-cells, an antigen inexperienced subset that harbors memory features. Overall, we propose that IFN-γ and Virtual Memory T-cells fulfil a critical immunoregulatory role by enabling the coordination of T-cell avidity and fate.
Accurate modeling of peptide-MHC structures with AlphaFold
Authors: Mikhaylov Victor , Levine Arnold J.
Published: March 2023

Major histocompatibility complex (MHC) proteins present peptides on the cell surface for T-cell surveillance. Reliablein silicoprediction of which peptides would be presented and which T-cell receptors would recognize them is an important problem in structural immunology. Here, we introduce an AlphaFold-based pipeline for predicting the three-dimensional structures of peptide-MHC complexes for class I and class II MHC molecules. Our method demonstrates high accuracy, outperforming existing tools in class I modeling precision and class II peptide register prediction. We explore applications of this method towards improving peptide-MHC binding prediction.
Quantum algorithm for position weight matrix matching
Authors: Miyamoto Koichi , Yamamoto Naoki , Sakakibara Yasubumi
Published: March 2023

We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The two proposed algorithms, the naive iteration method and the Monte-Carlo-based method, output matched segments, given the oracular accesses to the entries in the biological sequence and the PWM. The former uses quantum amplitude amplification (QAA) for sequence motif search, resulting in the query complexity scaling on the sequence lengthn, the sequence motif lengthmand the number of the PWMsKas, which means speedup over existing classical algorithms with respect tonandK. The latter also uses QAA, and further, quantum Monte Carlo integration for segment score calculation, instead of iteratively operating quantum circuits for arithmetic in the naive iteration method; then it provides the additional speedup with respect tomin some situation. As a drawback, these algorithms use quantum random access memories and their initialization takesO(n) time. Nevertheless, our algorithms keep the advantage especially when we search matches in a sequence for many PWMs in parallel.
SAKit: an all-in-one analysis pipeline for identifying novel protein caused by variant events at genomic and transcriptic level
Authors: Li Yan , Wang Boran , Wu Zengding , Xu Shi , Cui Fenglei , Fei Caiyi , Sun Qiang
Published: March 2023

Genetic modifications that cause pivotal protein inactivation or abnormal activation may lead to cell signaling pathway change or even dysfunction, resulting in cancer and other diseases. In turn, dysfunction will further produce “novel proteins” that do not exist in the canonical human proteome. Identification of novel proteins is meaningful for identifying promising drug targets and developing new therapies. In recent years, several tools have been developed for identifying DNA or RNA variants with the extensive application of nucleotide sequencing technology. However, these tools mainly focus on point mutation and have limited performance in identifying large-scale variants as well as the integration of mutations. Here we developed a hybridSequencingAnalysis bioinformatic pipeline by integrating all relevant detectionKits(SAKit): this pipeline fully integrates all variants at the genomic and transcriptomic level that may lead to the production of novel proteins defined as proteins with novel sequences compare to all reference sequences by comprehensively analyzing the long and short reads. The analysis results of SAKit demonstrate that large-scale mutations have more contribution to the production of novel proteins than point mutations, and long-read sequencing has more advantages in large-scale mutation detection.

Availability and implementation

SAKit is freely available on docker image (https://hub.docker.com/repository/docker/therarna/sakit), which is mainly implemented within a Snakemake framework in Python language.
Fear-conditioning to unpredictable threats reveals sex differences in rat fear-potentiated startle (FPS)
Authors: Olivera-Pasilio Valentina , Dabrowska Joanna
Published: March 2023

Fear-potentiated startle (FPS) has been widely used to study fear processing in humans and rodents. Human studies have shown higher startle amplitudes and exaggerated fear reactivity to unpredictable vs. predictable threats in individuals suffering from post-traumatic stress disorder (PTSD). Although human FPS studies often use both sexes, a surprisingly limited number of rodent FPS studies use females. Here we investigate the effects of signal-threat contingency, signal-threat order and threat predictability on FPS in both sexes. We use a classic fear-conditioning protocol (100% contingency of cue and shock pairings, with forward conditioning such that the cue co-terminates with the shock) and compare it to modified fear-conditioning protocols (70% contingency; backward conditioning; or cue and shock unpaired). Although there are no sex differences in the startle amplitudes when corrected for body weight, females demonstrate higher shock reactivity during fear-conditioning. Both sexes demonstrate comparable levels of cued, non-cued, and contextual fear in the classic FPS but females show reduced fear discrimination vs. males. Fear-conditioning with 70% contingency or backward order (cue co-starts with shock) induces similar levels of cued, non-cued, and contextual fear in both sexes but they differ in contextual fear extinction. Lastly, a prominent sex difference is uncovered following unpredictable fear-conditioning protocol (cue and shock un-paired), with females showing significantly higher startle overall during the FPS recall, regardless of trial type, and higher contextual fear than males. This striking sex difference in processing unpredictable threats in rodent FPS might help to understand the mechanisms underlying higher incidence of PTSD in women.

Highlights

Male and female rats have comparable startle amplitudes when corrected for body weight

Female rats show higher foot-shock reactivity than males during fear-conditioning

Female rats show reduced fear discrimination vs. males in the classic FPS

Reversed signal-threat order increases contextual fear in both sexes

Exposure to unpredictable threats increases startle in general and contextual fear only in females
Laminar Specificity of the Auditory Perceptual Awareness Negativity: A Biophysical Modeling Study
Authors: Pujol Carolina Fernandez , Blundon Elizabeth G. , Dykstra Andrew R.
Published: March 2023

How perception of sensory stimuli emerges from brain activity is a fundamental question of neuroscience. To date, two disparate lines of research have examined this question. On one hand, human neuroimaging studies have helped us understand the large-scale brain dynamics of perception. On the other hand, work in animal models (mice, typically) has led to fundamental insight into the micro-scale neural circuits underlying perception. However, translating such fundamental insight from animal models to humans has been challenging. Here, using biophysical modeling, we show that the auditory awareness negativity (AAN), an evoked response associated with perception of target sounds in noise, can be accounted for by synaptic input to the supragranular layers of auditory cortex (AC) that is present when target sounds are heard but absent when they are missed. This additional input likely arises from cortico-cortical feedback and/or non-lemniscal thalamic projections and targets the apical dendrites of layer-V pyramidal neurons (PNs). In turn, this leads to increased local field potential activity, increased spiking activity in layer-V PNs, and the AAN. The results are consistent with current cellular models of conscious processing and help bridge the gap between the macro and micro levels of perception-related brain activity.

Author Summary

To date, our understanding of the brain basis of conscious perception has mostly been restricted to large-scale, network-level activity that can be measured non-invasively in human subjects. However, we lack understanding of how such network-level activity is supported by individual neurons and neural circuits. This is at least partially because conscious perception is difficult to study in experimental animals, where such detailed characterization of neural activity is possible. To address this gap, we used biophysical modeling to gain circuit-level insight into an auditory brain response known as the auditory awareness negativity (AAN). This response can be recorded non-invasively in humans and is associated with perceptual awareness of sounds of interest. Our model shows that the AAN likely arises from specific cortical layers and cell types. These data help bridge the gap between circuit- and network-level theories of consciousness, and could lead to new, targeted treatments for perceptual dysfunction and disorders of consciousness.
Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance
Authors: Shingleton Joseph W. , Lilley Chris J. , Wade Matthew J.
Published: March 2023

Background

Air travel plays an import role in the cross-border spread of infectious diseases. During the SARS-CoV-2 pandemic many countries introduced strict border testing protocols to monitor the incursion of the virus. However, the high implementation cost and significant inconvenience to passengers has led public health authorities to consider alternative methods of disease surveillance at borders. Aircraft wastewater monitoring has been proposed as one such alternative. In this paper we assess the theoretical limits of aircraft wastewater monitoring and compare its performance to post-arrival border screening approaches.

Methods

We use an infectious disease model to simulate an unmitigated SARS-CoV-2 epidemic in a seed country. Seeding of the epidemic into the United Kingdom (UK) is simulated through daily flights between the two countries. We use a probabilistic approach to estimate the time of first detection of the disease in the UK in both aircraft wastewater and respiratory swab screening at the border.

Results

For simulations across a broad range of model parameters, our analysis indicates that the median time between the first incursion of a pathogen and its detection in wastewater would be approximately 17 days (IQR: 7 - 28 days), resulting in a median of 25 cumulative cases (IQR: 6 - 84 cases) in the UK at the point of detection. Comparisons to respiratory swab screening suggest that aircraft wastewater monitoring is as effective as screening of 20% of passengers at the border, using a test with 95% sensitivity. For testing regimes with sensitivity of 85% or less, the required coverage to outperform wastewater monitoring increases to 30%. These results demonstrate the potential use cases of aircraft wastewater monitoring and its utility in a wider system of public health surveillance.
Sparse Activations for Interpretable Disease Grading
Authors: Donteu Djoumessi Kerol R. , Ilanchezian Indu , Kühlewein Laura , Faber Hanna , Baumgartner Christian F. , Bah Bubacarr , Berens Philipp , Koch Lisa M.
Published: March 2023

Interpreting deep learning models typically relies on post-hoc saliency map techniques. However, these techniques often fail to serve as actionable feedback to clinicians, and they do not directly explain the decision mechanism. Here, we propose an inherently interpretable model that combines the feature extraction capabilities of deep neural networks with advantages of sparse linear models in interpretability. Our approach relies on straight-forward but effective changes to a deep bag-of-local-features model (BagNet). These modifications lead to fine-grained and sparse class evidence maps which, by design, correctly reflect the model’s decision mechanism. Our model is particularly suited for tasks which rely on characterising regions of interests that are very small and distributed over the image. In this paper, we focus on the detection of Diabetic Retinopathy, which is characterised by the progressive presence of small retinal lesions on fundus images. We observed good classification accuracy despite our added sparseness constraint. In addition, our model precisely highlighted retinal lesions relevant for the disease grading task and excluded irrelevant regions from the decision mechanism. The results suggest our sparse BagNet model can be a useful tool for clinicians as it allows efficient inspection of the model predictions and facilitates clinicians’ and patients’ trust.
Giving a voice to adults with COVID-19: An analysis of open-ended comments from smell longhaulers and non-longhaulers
Authors: Menger N. S. , Tognetti A. , Farruggia M. C. , Mucignat C. , Bhutani S. , Cooper K. W. , Rohlfs Dominguez P. , Heinbockel T. , Shields V. , D’Errico A. , Pereda-Loth V. , Pierron D. , Koyama S. , Croijmans I.
Published: March 2023

Smell disorders are commonly reported with COVID-19 infection. Some patients show prolonged smell-related issues, even after the respiratory symptoms are resolved. To explore the concerns of patients, and to provide an overview for each specific smell disorder, we explored the longitudinal survey that was conducted by1, and contained self-reports on the changes of smell that participants experienced at two time points. People who still suffered from smell disorders at the second time point, hence named ‘longhaulers’, were compared to those who were not, hence named ‘non-longhaulers’. Specifically, three aims were pursued in this study. First, to classify smell disorders based on the participants’ self-reports. Second, to classify the sentiment of each self-report using a machine learning approach, and third, to find specific keywords that best describe the smell dysfunction in those self-reports. We found that the prevalence of parosmia and hyposmia was higher in longhaulers than in non-longhaulers. Furthermore, the results suggest that longhaulers stated self-reports with more negative sentiment than non-longhaulers. Finally, we found specific keywords that were more typical for either longhaulers compared to non-longhaulers. Taken together, our work shows consistent findings with previous studies, while at the same time, provides new insights for future studies investigating smell disorders.
A modelled analysis of the impact of COVID-19-related disruptions to HPV vaccination analysis
Authors: Velentzis Louiza S , Smith Megan A , Killen James , Brotherton Julia , Guy Rebecca , Canfell Karen
Published: March 2023

COVID-19 disrupted school attendance in many countries, delaying routine adolescent vaccination against human papillomavirus (HPV) in some settings. We used the ‘Policy1-Cervix’HPV model (natural history/vaccination/screening/HPV-related cancers), to estimate the impact on HPV-related cancers from disruptions to HPV vaccination in a high-income setting. Compared to no disruption (nonavalent vaccine uptake, age 12 [females:82.4%; males:75.5%] as in Australia), additional lifetime HPV-related cancer cases were calculated for three disruption scenarios affecting one birth cohort (2008): i) 1-year delay (no doses missed); ii) 1 to 7-year delay (slow catch-up); iii) no catch-up (herd effects only). A fourth scenario assumed no catch-up for two cohorts (2008,2009). We found a 1-year delay could result in ≤0.3% more HPV-related cancers (n=4) but the increase would be greater if catch-up was slower (5%; n=70), and especially if there was no catch-up (49%; n=750). Additional cancers for a single missed cohort were most commonly cervical (23%), oropharyngeal (males:20%) or anal (females:16%). In the worst-case scenario of two cohorts missing vaccination, ≤62% more HPV-related cancers would be diagnosed (n=1,892). In conclusion, providing catch-up of missed HPV vaccines is conducted, short-term delays in vaccinating adolescents are unlikely to have substantial long-term effects on cancer.
Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex
Authors: Zhang Ivy , Rufa Dominic A. , Pulido Iván , Henry Michael M. , Rosen Laura E. , Hauser Kevin , Singh Sukrit , Chodera John D.
Published: March 2023

Relative alchemical binding free energy calculations are routinely used in drug discovery projects to optimize the affinity of small molecules for their drug targets. Alchemical methods can also be used to estimate the impact of amino acid mutations on protein:protein binding affinities, but these calculations can involve sampling challenges due to the complex networks of protein and water interactions frequently present in protein:protein interfaces. We investigate these challenges by extending a GPU-accelerated open-source relative free energy calculation package (Perses) to predict the impact of amino acid mutations on protein:protein binding. Using the well-characterized model system barnase:barstar, we describe analyses for identifying and characterizing sampling problems in protein:protein relative free energy calculations. We find that mutations with sampling problems often involve charge-changes, and inadequate sampling can be attributed to slow degrees of freedom that are mutation-specific. We also explore the accuracy and efficiency of current state-of-the-art approaches—alchemical replica exchange and alchemical replica exchange with solute tempering—for overcoming relevant sampling problems. By employing sufficiently long simulations, we achieve accurate predictions (RMSE 1.61, 95% CI: [1.12, 2.11] kcal/mol), with 86% of estimates within 1 kcal/mol of the experimentally-determined relative binding free energies and 100% of predictions correctly classifying the sign of the changes in binding free energies. Ultimately, we provide a model workflow for applying protein mutation free energy calculations to protein:protein complexes, and importantly, catalog the sampling challenges associated with these types of alchemical transformations. Our free open-source package (Perses) is based on OpenMM and available athttps://github.com/choderalab/perses.
Empowering Beginners in Bioinformatics with ChatGPT
Authors: Shue Evelyn , Liu Li , Li Bingxin , Feng Zifeng , Li Xin , Hu Gangqing
Published: March 2023

The impressive conversational and programming abilities of ChatGPT make it an attractive tool for facilitating the education of bioinformatics data analysis for beginners. In this study, we proposed an iterative model to fine-tune instructions for guiding a ChatGPT in generating code for bioinformatics data analysis tasks. We demonstrated the feasibility of the model by applying it to various bioinformatics topics. Additionally, we discussed practical considerations and limitations regarding the use of the model in chatbot-aided bioinformatics education.
A sample preparation procedure enables acquisition of 2-channel super-resolution 3D STED image of an entire oocyte
Authors: Frolikova Michaela , Blazikova Michaela , Capek Martin , Chmelova Helena , Valecka Jan , Kolackova Veronika , Valaskova Eliska , Gregor Martin , Komrskova Katerina , Horvath Ondrej , Novotny Ivan
Published: March 2023

Super-resolution (SR) microscopy is a cutting-edge method that can provide detailed structural information with high resolution. However, the thickness of the specimen has been a major limitation for SR methods, and larger structures have posed a challenge. To overcome this, the key step is to optimize sample preparation to ensure optical homogeneity and clarity, which can enhance the capabilities of SR methods for the acquisition of thicker structures.

Oocytes are the largest cells in the mammalian body and are crucial objects in reproductive biology. They are especially useful for studying membrane proteins. However, oocytes are extremely fragile and sensitive to mechanical manipulation and osmotic shocks, making sample preparation a critical and challenging step.

We present an innovative, simple, and sensitive approach to oocyte sample preparation for 3D STED acquisition. This involves alcohol dehydration and mounting into a high refractive index medium. This extended preparation procedure allowed us to successfully obtain a unique 2-channel 3D STED super-resolution image of an entire mouse oocyte.

By optimizing sample preparation, we can overcome the limitations of SR methods and obtain high-resolution images of larger structures, such as oocytes, Knowledge of which are important for understanding fundamental biological processes.

RESEARCH HIGHLIGHTS

This study aimed to develop a successful sample preparation protocol for imaging mouse oocytes using 3D STED super-resolution microscopy.

The results showed that the oocyte sample was optically homogenous, enhancing the capability of the 3D STED method to capture high-resolution images throughout the full depth of the sample, resulting in highly similar SR images.

The 3D STED point spread function (PSF) pattern of the depletion laser was successfully secured throughout the entire volume of the sample, including the top and bottom.

This study presents the first-ever full volume 3D image of the mouse oocyte, which was acquired using a 2-channel 3D STED method.

GRAPHICAL ABSTRACT

Introducing an extended sample preparation procedure resulted in an outstanding optical quality sample environment pronounced by high refractive index, high transparency, and minimal spherical aberration. This procedure allowed 3D STED within the entire oocyte.