bluuebunny/crossref_metadata_2025 huggingface dataset:
BODY TEMPERATURE VARIATION AFTER PACKED CELL TRANSFUSION IN ADULT PATIENTS WITH SEPSIS—WHERE WILL THE PENDULUM STOP?
Authors: Klein Moti , Hassan Lior , Binyamin Yair , Frank Dmitry , Boyko Matthew , Zlotnik Alexander , Raab Tehila , Novack Victor , Frenkel Amit
Published: April 2023

Background: Critically ill patients with sepsis often require packed cell transfusions (PCTs). Packed cell transfusion causes changes in body’s core temperature. Objective: To trace the course and amplitude of body core temperature after PCT in adults with sepsis. Methods: We conducted a population-based retrospective cohort study of patients with sepsis who received one unit of PCT during their hospitalization in a general intensive care unit during 2000–2019. A control group was established by matching each of these patients to a patient who did not receive PCT. We calculated the mean values of urinary bladder temperature for the 24 h before and 24 h after PCT. To evaluate the effect of PCT on body core temperature, multivariable analyses using a mixed linear regression model were performed. Results: The study comprised 1,100 patients who received one unit of PCT and 1,100 matched patients. The mean temperature before PCT was 37.3°C. Immediately from initiation of PCT, body temperature decreased, to a minimum of 37.0°C. During the 24 subsequent hours, the temperature increased gradually and consistently, until a peak temperature of 37.4°C. In a linear regression model, body core temperature increased by a mean 0.06°C in the first 24 h after PCT and decreased by a mean 0.65°C for every 1.0°C increase before PCT. Conclusions: Among critically ill patients with sepsis, PCT itself causes only mild and clinically insignificant temperature changes. Thus, significant changes in core temperature during the 24 h after PCT may indicate an unusual clinical event that requires clinicians’ immediate attention.
DeepUMQA3: a web server for model quality assessment of protein complexes
Authors: Liu Jun , Liu Dong , Zhang Guijun
Published: April 2023

Model quality assessment is a crucial part of protein structure prediction and a gateway to proper usage of models in biomedical applications. Many methods have been proposed for assessing the quality of structural models of protein monomers, but few methods for evaluating protein complex models. As protein complex structure prediction becomes a new challenge, model quality assessment methods that can provide accurate evaluation of complex structures are urgently required. Here, we present DeepUMQA3, a web server for evaluating protein complex structures using deep neural network. For an input complex structure, features are extracted from three levels of overall complex, intra-monomer, and inter-monomer, and a improved deep residual neural network is used to predict per-residue lDDT and interface residue accuracy. DeepUMQA3 ranks first in the blind test of interface residue accuracy estimation in CASP15, with Pearson, Spearman and AUC of 0.564, 0.535 and 0.755 under the lDDT measurement, which are 18.5%, 23.6% and 10.9% higher than the second-best method, respectively. DeepUMQA3 can also accurately assess the accuracy of all residues in the entire complex and distinguish high- and low-precision residues/models. The websever of DeepUMQA3 are freely available athttp://zhanglab-bioinf.com/DeepUMQA_server/.
Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition
Authors: Wang Hanwen , Arulraj Theinmozhi , Kimko Holly , Popel Aleksander S.
Published: April 2023

Generating realistic virtual patients from a limited amount of patient data is one of the major challenges for quantitative systems pharmacology modeling in immuno-oncology. Quantitative systems pharmacology (QSP) is a mathematical modeling methodology that integrates mechanistic knowledge of biological systems to investigate dynamics in a whole system during disease progression and drug treatment. In the present analysis, we parameterized our previously published QSP model of the cancer-immunity cycle to non-small cell lung cancer (NSCLC) and generated a virtual patient cohort to predict clinical response to PD-L1 inhibition in NSCLC. The virtual patient generation was guided by immunogenomic data from iAtlas portal and population pharmacokinetic data of durvalumab, a PD-L1 inhibitor. With virtual patients generated following the immunogenomic data distribution, our model predicted a response rate of 18.6% (95% bootstrap confidence interval: 13.3-24.2%) and identified CD8/Treg ratio as a potential predictive biomarker in addition to PD-L1 expression and tumor mutational burden. We demonstrated that omics data served as a reliable resource for virtual patient generation techniques in immuno-oncology using QSP models.
African rice (Oryza glaberrima) genomic introgressions impacting upon panicle architecture in Asian rice (O. sativa) lead to the identification of key QTLs
Authors: Adam Hélène , Gutierrez Andrés , Couderc Marie , Sabot François , Ntakirutimana Fabrice , Serret Julien , Orjuela Julie , Tregear James , Jouannic Stefan , Lorieux Mathias
Published: April 2023

Background

Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativaL.) and the African rice (O. glaberrimaSteud). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, withO. sativadisplaying a highly branched panicle, which in turn produces a larger number of grains than that ofO. glaberrima. The genetic interactions that govern the diversity of panicle complexity within and between the two species are still poorly understood.

Results

To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments fromO. glaberrimacv. MG12 in the genetic background ofO. sativaTropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12 and QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand howO. glaberrimaintrogression events may lead to alterations in panicle traits.

Conclusion

Our analysis led to the detection of genomic variations betweenO. sativacv. Caiapó andO. glaberrimacv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development inO. sativaand their interspecific genomic variations may explain the phenotypic effects observed.
A Ray of Light Against Age Related Neurodegeneration
Authors: Fear Elizabeth J. , Torkelsen Frida H. , Chen Kuan-Ju , Scott Martin , Jeffery Glenn , Baseler Heidi , Kennerley Aneurin J.
Published: April 2023

Mitochondrial function declines with age and many pathological processes of neurodegenerative diseases stem from this dysfunction when mitochondria fail to produce the necessary energy required. Photobiomodulation (PBM), long-wavelength light therapy, has been shown to rescue mitochondrial function in animal models and improve human health, but clinical uptake is limited due to uncertainty around efficacy and the mechanisms responsible. Through combined theoretical Monte Carlo light modelling and practical31P Magnetisation Transfer Magnetic Resonance Spectroscopy (MT-MRS) we quantify the effects of 670 nm PBM treatment on healthy aging brains.31P MT-MRS revealed a significant increase in the rate of ATP flux after PBM in a sample of older adults. Light modelling shows 1% absorption in grey matter and confirms absorption peaks at 670 and 820 nm. Our study provides evidence of PBM therapeutic efficacy and strengthens confidence in PBM as an acceptable healthcare technology to improve mitochondrial function and human health.
A brain model of altered self-appraisal in social anxiety disorder
Authors: Jamieson Alec J. , Harrison Ben J. , Delahoy Rebekah , Schmaal Lianne , Felmingham Kim L. , Phillips Lisa , Davey Christopher G.
Published: April 2023

The brain’s default mode network has a central role in the processing of information concerning oneself. Dysfunction in this self-referential processing represents a key component of multiple mental health conditions, including social anxiety disorder (SAD). This case-control study aimed to clarify alterations to network dynamics present during self-appraisal in SAD participants. A total of 38 adolescents and young adults with SAD and 72 healthy control participants underwent a self-referential processing fMRI task. The task involved two primary conditions of interest:direct self-appraisal(thinking about oneself) andreflected self-appraisal(thinking about how others might think about oneself). Dynamic causal modelling and parametric empirical Bayes were then used to explore differences in the effective connectivity of the default mode network between groups. We observed connectivity differences between SAD and healthy control participants in the reflected self-appraisal but not the direct self-appraisal condition. Specifically, SAD participants exhibited greater excitatory connectivity from the posterior cingulate cortex (PCC) to medial prefrontal cortex (MPFC) and greater inhibitory connectivity from the inferior parietal lobule (IPL) to MPFC. In contrast, in the absence of task modulation, SAD participants exhibited reduced intrinsic connectivity, with reduced excitatory connectivity from the PCC to MPFC and reduced inhibitory connectivity from the IPL to MPFC. As such, participants with SAD showed changes to afferent connections to the MPFC which occurred during both reflected self-appraisal as well as intrinsically. The presence of connectivity differences in reflected and not direct self-appraisal is consistent with the characteristic fear of negative social evaluation that is experienced by people with SAD.
Two distinct mechanisms lead to either oocyte or spermatocyte decrease inC. elegansafter whole developmental exposure to γ-rays
Authors: Dufourcq Sekatcheff E. , Godon C. , Bailly A. , Quevarec L. , Camilleri V. , Galas S. , Frelon S.
Published: April 2023

Wildlife is subject to various sources of pollution, including ionizing radiation. Adverse effects can impact organisms’ survival, growth, or reproduction, later affecting population dynamics. In invertebrates, reproduction, which directly impacts population dynamics, has been found to be the most radiosensitive endpoint. Understanding the underlying molecular pathways inducing this reproduction decrease can help to comprehend species-specific differences in radiosensitivity. In line with previous studies, we used a life stage dependent approach to better understand the molecular determinants of reproduction decrease, especially of gamete decrease, in the hermaphrodite roundwormCaenorhabditis elegans. Worms were chronically exposed to 50 mGy·h−1external gamma ionizing radiations throughout different developmental periods (namely embryogenesis, gametogenesis, and full development). Conserved molecular pathways across invertebrates and vertebrates involved in reproduction processes and stress response were analyzed: apoptosis and MAP kinase Ras/ERK (MPK-1). Our results showed that these pathways are life-stage dependant, resulting from an accumulation of damages upon chronic exposure to IR throughout the whole development. The Ras/ERK pathway was found to be activated in our conditions in the pachytene region of the gonad where it induces the apoptotic pathway, but not in the ovulation zone, showing no incidence on oocyte maturation and ovulation. Additionally, no effect on germ cell proliferation was found, meaning that Ras/ERK pathway is probably not involved in this process in our conditions. Finally, a functional analysis of apoptosis revealed that the decrease of ovulation rate is due to DNA-damaged induced apoptosis which does not occur in spermatocytes. Thus, sperm decrease seem to be mediated via another mechanism, probably a decrease in germ cells proliferation speed that needs further investigation to better characterize sex-specific responses to IR exposure.
Reproductive success mediates the effects of climate change and grassland management on plant populations dynamics
Authors: Andrzejak Martin , Knight Tiffany M. , Plos Carolin , Korell Lotte
Published: April 2023

Climate change is one of the largest threats to grassland plant species, which can be modified by land management. Although climate change and land management can separately and interactively influence plant demography this has been rarely considered within one experimental set-up. We used a large-scale experiment to quantify the effects of grassland management, climate change and their joint effect on the demography and population growth rate of 11 native plant species. We parameterized integral projection models with four years of demographic data to project the population growth rate. We hypothesized, plants would perform better in ambient than in the future climate treatment that creates hotter and drier summer conditions and that plant performance in grazing vs. mowing would vary across species and depend on their traits. Due to extreme drought events, over half of our study species went quasi extinct, which highlights how extreme climate events can influence long term experimental results. Of the persistent species, only one supported our expectations, and the rest either had higher population growth rates in the future climate treatment or showed no significant difference in population growth between climate treatments. Species with shorter flowering durations performed better in the mowing treatment while those with longer flowering durations performed better in the grazing treatment. The population growth rates of these species were sensitive to changes in vital rates related to reproduction and recruitment. Depending on the species we found effects of land management and climate change on population growth rates but we did not find strong support for interactive effects among both factors. Experiments combined with measuring plant demographic responses provide a way to isolate the effects of different drivers on the long-term persistence of species, and to identify the demographic vital rates that are critical to manage in the future. Our study suggests that it will become increasingly difficult to maintain species with preferences for moister soil conditions, that traits such as flowering duration might predict responses to management, and that vital rates such as reproduction and recruitment are disproportionately important.
Rit2 silencing in dopamine neurons drives a Parkinsonian phenotype
Authors: Kearney Patrick J. , Zhang Yuanxi , Tan Yanglan , Kahuno Elizabeth , Conklin Tucker L. , Fagan Rita R. , Pavchinskiy Rebecca G. , Shafer Scott A. , Yue Zhenyu , Melikian Haley E.
Published: April 2023

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease and arises from dopamine (DA) neuron death selectively in the substantia nigra pars compacta (SNc). Rit2 is a reported PD risk allele, and recent single cell transcriptomic studies identified a major RIT2 cluster in PD DA neurons, potentially linking Rit2 expression loss to a PD patient cohort. However, it is still unknown whether Rit2 loss itself is causative for PD or PD-like symptoms. Here we report that conditional Rit2 silencing in mouse DA neurons drove motor dysfunction that occurred earlier in males than females and was rescued at early stages by either inhibiting the DA transporter (DAT) or with L-DOPA treatment. Motor dysfunction was accompanied by decreased DA release, striatal DA content, phenotypic DAergic markers, DA neurons, and DAergic terminals, with increased pSer129-alpha synuclein and pSer935-LRRK2 expression. These results provide the first evidence that Rit2 loss is causal for SNc cell death and a PD-like phenotype, and reveal key sex-specific differences in the response to Rit2 loss.
Rapid cold hardening modifies mechanisms of ion regulation to delay anoxia-induced spreading depolarization in the CNS ofLocusta migratoria
Authors: Srithiphaphirom Phinyaphat , Wang Yuyang , Aristizabal Maria J. , Robertson R. Meldrum
Published: April 2023

Insects live in varied habitats and experience different kinds of environmental stresses. These stresses can impair neural performance, leading to spreading depolarization (SD) of nerve cells and neural shutdown underlying coma. The sensitivity of an insect’s nervous system to stress (e.g., anoxia) can be modulated by acute pre-treatment. Rapid cold hardening (RCH) is a form of preconditioning, in which a brief exposure to low temperature can enhance the stress tolerance of insects. SD is associated with a sudden loss of ion, notably K+, homeostasis. We used a pharmacological approach to investigate whether RCH affects anoxia-induced SD in the locust,L. migratoria, via one or more of the following homeostatic mechanisms: (1) Na+/K+-ATPase (NKA), (2) Na+/K+/2Cl-co-transporter (NKCC), and (3) voltage-gated K+(Kv) channels. We also assessed abundance and phosphorylation of NKCC using immunoblotting. We found that inhibition of NKA or Kvchannels delayed the onset of anoxia-induced SD in both control and RCH preparations. However, NKCC inhibition preferentially abrogated the effect of RCH. Additionally, we observed a higher abundance of NKCC in RCH preps but no statistical difference in its phosphorylation level, indicating the involvement of NKCC expression or degradation as part of the RCH mechanism.
Social aging trajectories are sex-specific, sensitive to adolescent stress, and most robustly revealed during social tests with familiar stimuli
Authors: Figueroa Christopher , Edgar Erin L. , Kirkland J. M. , Patel Ishan , King’uyu David N. , Kopec Ashley M.
Published: April 2023

Social networks and support are integral to health and wellness across the lifespan, and social engagement may be particularly important during aging. However, social behavior and social cognition decline naturally during aging across species. Social behaviors are in part supported by the ‘reward’ circuitry, a network of brain regions that develops during adolescence. We published that male and female rats undergo adolescent social development during sex-specific periods, pre-early adolescence in females and early-mid adolescence males. Although males and females have highly dimorphic development, expression, and valuation of social behaviors, there is relatively little data indicating whether social aging is the same or different between the sexes. Thus, we sought to test two hypotheses: (1) natural social aging will be sex-speciifc, and (2) social isolation stress restricted to sex-specific adolescent critical periods for social development would impact social aging in sex-specific ways. To do this, we bred male and female rats in-house, and divided them randomly to receive either social isolation for one week during each sex’s respective critical period, or no manipulation. We followed their social aging trajectory with a battery of five tests at 3, 7, and 11 months of age. We observed clear social aging signatures in all tests administered, but sex differences in natural social aging were most robustly observed when a familiar social stimulus was included in the test. We also observed that adolescent isolation did impact social behavior, in both age-independent and age-dependent ways, that were entirely sex-specific. Please note, this preprint will not be pushed further to publication (by me, AMK), as I am leaving academia. So, it’s going to be written more conversationally.
Molecular cloning and characterization of an AP2/ERF protein gene in cotton (Gossypium hirsutumL.)
Authors: Wu Chaofeng , Ma Xuemei , Li Shuyan
Published: April 2023

Upland cotton (Gossypium hirsutumL.) is one of the most economically important crops worldwide due to the significant source of natural fiber, feed, oil and biofuel products. Cottonseed can also serve as an excellent source of edible protein and oil. However,the presence of gossypol in pigment gland has limited it utilization In the past few decades, some progress has been made in the understanding molecular mechanism of the formation of the pigment gland. However, little is known about the specific mechanism of pigment gland formation in cotton. In this study, the cDNA sequence of a ethylene transcription factor gene, designated GhERF105a, was cloned from upland cotton CCRI12. Sequence alignment revealed that GhERF105a gene contained a typical AP2/ERF domain of 61 amino acids, and belonged to the ERF subgroup of the ERF supfamily. It was highly expressed in the leaves and stems of glanded plants but had substantially lower expression of the glandless plants. GhERF105a, localized to the nucleus, could bind to GCC-box and DRE. Some development, phytohormone and stress related cis-elements were enriched in the promoters ofGhERF105a/d. Split ubiquitin assays in yeast and BiFC experiments showed extensive interactions between GhERF105a and Gh_A07G1044. In addition,GhERF105awas highly similar withGhERF105din the gene length, molecular weight, protein molecule, gene structure and expression pattern. The overall results suggested thatGhERF105amight participate in the pigment gland formation and stree-response processes.
Identification of the alternative sigma factor regulons ofChlamydia trachomatisusing multiplexed CRISPR interference
Authors: Hatch Nathan D. , Ouellette Scot P.
Published: April 2023

C. trachomatisis a developmentally regulated, obligate intracellular bacterium that encodes three sigma factors: σ66, σ54, and σ28. σ66 is the major sigma factor controlling most transcription initiation during early and mid-cycle development as the infectious EB transitions to the non-infectious RB that replicates within an inclusion inside the cell. The roles of the minor sigma factors, σ54 and σ28, have not been well characterized to date – however, there are data to suggest each functions in late-stage development and secondary differentiation as RBs transition to EBs. As the process of secondary differentiation itself is poorly characterized, clarifying the function of these alternative sigma factors by identifying the genes regulated by them will further our understanding of chlamydial differentiation. We hypothesize that σ54 and σ28 have non-redundant and essential functions for initiating late gene transcription thus mediating secondary differentiation inChlamydia. Here, we demonstrate the necessity of each minor sigma factor in successfully completing the developmental cycle. We have implemented and validated multiplexed CRISPRi techniques novel to the chlamydial field to examine effects of knocking down each alternative sigma factor individually and simultaneously. In parallel, we also overexpressed each sigma factor. Altering transcript levels for either or both alternative sigma factors resulted in a severe defect in EB production as compared to controls. Furthermore, RNA sequencing identified differentially expressed genes during alternative sigma factor dysregulation, indicating the putative regulons of each. These data demonstrate the levels of alternative sigma factors must be carefully regulated to facilitate chlamydial growth and differentiation.

Importance

Chlamydia trachomatisis a significant human pathogen in both developed and developing nations. Due to the organism’s unique developmental cycle and intracellular niche, basic research has been slow and arduous. However, recent advances in chlamydial genetics have allowed the field to make significant progress in experimentally interrogating the basic physiology ofChlamydia. Broadly speaking, the driving factors of chlamydial development are poorly understood, particularly regarding how the later stages of development are regulated. Here, we employ a novel genetic tool for use inChlamydiawhile investigating the effects of dysregulating the two alternative sigma factors in the organism that help control transcription initiation. We provide further evidence for both sigma factors’ essential roles in late-stage development and their potential regulons, laying the foundation for deeper experimentation to uncover the molecular pathways involved in chlamydial differentiation.
Deletion of the gene for the African swine fever virus BCL-2 family member A179L increases virus uptake and apoptosis, but decreases virus spread in macrophages and reduces virulence in pigs
Authors: Reis Ana Luisa , Rathakrishnan Anusyah , Goulding Leah V. , Barber Claire , Goatley Lynnette C. , Dixon Linda K.
Published: April 2023

African swine fever virus encodes proteins that inhibit apoptosis including one member of the BCL-2 family, A179L. Deletion of the A179L gene from the virulent genotype I isolate Benin 97/1 compared to Benin 97/1 expressing A179L or mock-infected macrophages, resulted in increased Caspase 3 and 7 activity, annexin V binding to surface phosphatidyl serine and DNA fragmentation, measured by terminal deoxynucleotidyl transferase nick-end labelling. These results confirmed that apoptosis was induced earlier in macrophages infected with the BeninΔA179L virus. Increased cell entry of the A179L gene-deleted virus was indicated at early times since up to double the numbers of cells expressed fluorescent protein from the virus genome. Yields of infectious virus were similar over a single cycle but were significantly lower for the A179L gene-deleted virus over a multi-step growth cycle. Pigs immunised and boosted with the BeninΔA179L virus showed no clinical signs, although a weak cellular response to ASFV was observed showing that the virus had replicated. The immunised pigs were not protected against challenge with the virulent parental virus Benin 97/1 although viremia was lower at 3 days post-challenge compared to the control non-immune pigs. The reduced levels of virus replication in macrophages probably limited induction of a protective immune response. The results show an important role for the A179L protein in virus replication in macrophages and virulence in pigs.

IMPORTANCE

African swine fever virus (ASFV) causes a lethal disease of pigs that has spread extensively in Africa, Europe and Asia. The virus codes for more than 150 proteins, many of which help the virus to evade the host’s defences following infection. We investigated the effect of deleting one of these genes, A179L, from the genome of an ASFV isolate that causes death of infected pigs. A179L belongs to the BCL-2 protein family, consisting of members which promote or inhibit apoptosis with A179L belonging to the latter. Deleting the A179L gene reduced ASFV replication and spread between macrophages, its main target cells. This was correlated with an increase in cell death. Pigs infected with the virus with A179L gene deleted did not show signs of disease and no virus replication was detected in blood. A low immune response was generated but the immunised pigs were not protected when challenged with the parental deadly virus. The results show that the A179L gene is important for ASFV to replicate efficiently in cells and in animals.
Integrated Spatial Transcriptomic and Proteomic Analysis of Fresh Frozen Tissue Based on Stereo-seq
Authors: Liao Sha , Heng Yang , Liu Weiqing , Xiang Jinqiong , Ma Yong , Chen Ligen , Feng Xiuwen , Jia Dongmei , Liang Diyan , Huang Caili , Zhang Jiajun , Jian Min , Su Kui , Li Mei , Loh Yuin Han , Chen Ao , Xu Xun
Published: April 2023

To simultaneously detect whole transcriptomes and protein markers on the same tissue section, we combined Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Stereo-seq to develop the Stereo-CITE-seq workflow. Here, we demonstrated that Stereo-CITE-seq can co-detect mRNAs and proteins in immune organs with high spatial resolution, reproducibility and accuracy.
Development of two mouse strains conditionally expressing bright luciferases with distinct emission spectra as new tools for in vivo imaging
Authors: Nakashiba Toshiaki , Ogoh Katsunori , Iwano Satoshi , Sugiyama Takashi , Mizuno-Iijima Saori , Nakashima Kenichi , Mizuno Seiya , Sugiyama Fumihiro , Yoshiki Atsushi , Miyawaki Atsushi , Abe Kuniya
Published: April 2023

In vivo bioluminescence imaging (BLI) has been an invaluable noninvasive method to visualize molecular and cellular behaviors in laboratory animals. Bioluminescent reporter mice possessing luciferases for general use have been limited to a classical luciferase, Luc2, fromPhotinus pyralis, and have been extremely powerful for various in vivo studies. However, applicability of reporter mice for in vivo BLI could be further accelerated by increasing light intensity using other luciferases and/or improving the biodistribution of their substrates in animal body. Here, we created two Cre-dependent reporter mice incorporating luciferases: oFluc derived fromPyrocoeli matsumuraiand Akaluc, both of which had been reported previously to be brighter than Luc2 when using appropriate substrates; we then tested their bioluminescence in neural tissues and other organs in living mice. When expressed throughout the body, both luciferases emitted an intense yellow (oFluc) or far-red (Akaluc) light easily visible to the naked eye. Moreover, oFluc and Akaluc were similarly bright in the pancreas for in vivo BLI. However, Akaluc was superior to oFluc for brain imaging, because its substrate, AkaLumine-HCl, was distributed to the brain more efficiently than the oFluc substrate, D-luciferin. We also demonstrated that the light produced by oFluc and Akaluc was sufficiently spectrally distinct for dual-color imaging in a single living mouse. Taken together, these novel bioluminescent reporter mice are an ideal source of cells with bright bioluminescence and may facilitate the in vivo BLI of various tissues/organs for preclinical and biomedical research in combination with a wide variety of Cre-driver mice.
Synthetic neuromelanin as a trigger of inflammation in the brain – new mouse model of Parkinson’s disease
Authors: Tejchman-Skrzyszewska Anna , Strzelec Martyna , Kot Marta , Chlebanowska Paula , Badyra Bogna , Sobocińska Małgorzata , Zecca Luigi , Majka Marcin
Published: April 2023

Parkinson’s disease (PD) is a neurodegenerative disease that is an increasing threat to an aging society. The idiopathic form of PD accounts for over 90% of all cases, and the current etiology is still unknown. One of the reasons hindering research on this form of PD is the lack of an appropriate animal models. Among mouse models of the disease, those based on the administration of neurotoxins such as 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine (MPTP) or 6-hydroxydopamine (6-OHDA) to the substantia nigra pars compacta (SNpc) or striatum are predominantly used. In these models, there are metabolic disturbances causing oxidative stress in the SNpc or striatum, which ultimately leads to the death of dopaminergic neurons. However, the models used so far have serious limitations, most of all they do not fully reflect the processes occurring in the course of the disease and do not consider the involvement of inflammation in the etiology and pathogenesis of PD. In this study we show that the administration of synthetic neuromelanin, which activates astrocytes and microglia, induces the inflammation and may be involved in degeneration of dopaminergic neurons. Neuromelanin under physiological conditions acts as a neuroprotector, however, released from dying dopaminergic neurons is an important factor activating astrocytes, microglia and causing neuroinflammation. Since one of the causes of Parkinson’s appear to be the death of dopaminergic neurons overloaded with neuromelanin and consequent pathological activation of microglia, the use of synthetic neuromelanin reflect the natural pathological processes occurring during the development of the disease.
CyAbrB2 is a nucleoid-associated protein inSynechocystiscontrolling hydrogenase expression during fermentation
Authors: Kariyazono Ryo , Osanai Takashi
Published: April 2023

Thehoxoperon inSynechocystissp. PCC 6803, encoding bidirectional hydrogenase responsible for H2production, is transcriptionally upregulated under microoxic conditions. Although several regulators forhoxtranscription have been identified, their dynamics and higher-order DNA structure ofhoxregion in microoxic conditions remain elusive. We focused on key regulators for thehoxoperon: cyAbrB2, a conserved regulator in cyanobacteria, and SigE, an alternative sigma factor. Chromatin immunoprecipitation-sequencing revealed that cyAbrB2 binds to thehoxpromoter region under aerobic conditions, with its binding being flattened in microoxic conditions. Concurrently, SigE exhibited increased localization to thehoxpromoter under microoxic conditions. Genome-wide analysis revealed that cyAbrB2 binds broadly to AT-rich genome regions and represses gene expression. Moreover, we demonstrated the physical interactions of thehoxpromoter region with its distal genomic loci. Both the transition to microoxic conditions and the absence of cyAbrB2 influenced the chromosomal interaction. From these results, we propose that cyAbrB2 is a cyanobacterial nucleoid-associated protein (NAP), modulating chromosomal conformation, which blocks RNA polymerase from thehoxpromoter in aerobic conditions. We further infer that cyAbrB2, with altered localization pattern upon microoxic conditions, modifies chromosomal conformation in microoxic conditions, which allows SigE-containing RNA polymerase to access thehoxpromoter. The coordinated actions of this NAP and the alternative sigma factor are crucial for the properhoxexpression in microoxic conditions. Our results highlight the impact of cyanobacterial chromosome conformation and NAPs on transcription, which have been insufficiently investigated.
Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data
Authors: Maity Alok K. , Teschendorff Andrew E.
Published: April 2023

Variations of cell-type proportions within tissues could be informative of biological aging and disease risk. Single-cell RNA-sequencing offers the opportunity to detect such differential abundance (DA) patterns, yet this task can be statistically challenging due to the noise in single-cell data, inter-sample variability and because DA patterns are often of small effect size. Here we present a DA-testing paradigm called ELVAR that uses cell attribute aware clustering when inferring differentially enriched communities within the single-cell manifold. Using simulated and real single-cell and single-nucleus RNA-Seq datasets, we benchmark ELVAR against an analogous DA algorithm that uses Louvain for clustering, as well as local neighborhood-based DA-testing methods, demonstrating that ELVAR improves the sensitivity to detect DA-shifts in relation to aging, precancerous states and Covid-19 phenotypes. In effect, leveraging cell attribute information when inferring cell communities can denoise single-cell data, avoid the need for batch correction and help retrieve more robust cell states for subsequent DA-testing. ELVAR is available as an open-source R-package.
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
Authors: Ding Ruofan , Zou Xudong , Qin Yangmei , Chen Hui , Ma Xuelian , Yu Chen , Wang Gao , Li Lei
Published: April 2023

Genome-wide association studies (GWAS) have identified thousands of disease-associated non-coding variants, posing urgent needs for functional interpretation. Molecular quantitative trait loci (xQTLs) such as eQTLs serve as an essential intermediate link between these non-coding variants and disease phenotypes and have been widely used to discover disease-risk genes from many population-scale studies. However, mining and analyzing the xQTLs data presents several significant bioinformatics challenges, particularly when it comes to integration with GWAS data. Here, we developed xQTLbiolinks as the first comprehensive and scalable tool for xQTLs data retrieval, quality controls, and pre-processing from 75 human tissues and cell types. In addition, xQTLbiolinks provided a robust colocalization module through integration with GWAS data. The result generated by xQTLbiolinks can be flexibly visualized or stored in standard R objects that can easily be integrated with other R packages and custom pipelines. We applied xQTLbiolinks to cancer GWAS summary statistics as case studies and demonstrated its robust utility and reproducibility. xQTLbiolinks will profoundly accelerate the interpretation of disease-associated variants, thus promoting a better understanding of disease etiologies. xQTLbiolinks is available athttps://github.com/lilab-bioinfo/xQTLbiolinks.
An ancient ecospecies ofHelicobacter pylorifound in Indigenous populations and animal adapted lineages
Authors: Tourrette Elise , Torres Roberto C. , Svensson Sarah L. , Matsumoto Takashi , Miftahussurur Muhammad , Fauzia Kartika Afrida , Alfaray Ricky Indra , Vilaichone Ratha-Korn , Tuan Vo Phuoc ,   HelicobacterGenomicsConsortium, Wang Difei , Yadegar Abbas , Olsson Lisa M. , Zhou Zhemin , Yamaoka Yoshio , Thorell Kaisa , Falush Daniel
Published: April 2023

The colonization of our stomachs byHelicobacter pyloriis believed to predate the oldest splits between extant human populations. We identify a “Hardy” ecospecies ofH. pyloriassociated with indigenous groups, isolated from people in Siberia, Canada, USA and Chile. The ecospecies shares the ancestry of “Ubiquitous”H. pylorifrom the same geographical region in most of the genome but has nearly fixed SNP differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. For these parts of the genome, the ecospecies has a separate, independently evolving gene pool with a distinct evolutionary history.H. acinonychis, found in big cats, and a newly identified primate-associated lineage both belong to the Hardy ecospecies and both represent human to animal host jumps. Most strains from the ecospecies encode an additional iron-dependent urease that is shared byHelicobacterfrom carnivorous hosts, as well as a tandem duplication ofvacA, encoding the vacuolating toxin. We conclude thatH. pylorisplit into two highly distinct ecospecies in Africa and that both dispersed around the globe with humans, but the Hardy ecospecies has gone extinct in most parts of the world. Our analysis also pushes back the likely length of the association betweenH. pyloriand humans.
Role of the NO-GC/cGMP signaling pathway in platelet biomechanics
Authors: Rodríguez Johanna G. , Balmes Aylin , Seifert Jan , Pinto-Quintero Daniel , Khawaja Akif A. , Boffito Marta , Frye Maike , Friebe Andreas , Emerson Michael , Seta Francesca , Feil Robert , Feil Susanne , Schäffer Tilman E.
Published: April 2023

Cyclic guanosine monophosphate (cGMP) is a second messenger produced by the NO-sensitive guanylyl cyclase (NO-GC) enzyme. In platelets, the NO-GC/cGMP pathway inhibits aggregation. One aspect of the inhibitory mechanism involves changes in the cytoskeleton; however, the molecular mechanisms underlying platelet inhibition and its correlation with cytoskeletal cellular stiffness are poorly understood.

We measured the cellular stiffness of individual platelets after treatment with the NO-GC stimulator riociguat or the NO-GC activator cinaciguat, using scanning ion conductance microscopy (SICM). We quantified changes in platelet shape using deep learning-based platelet morphometry. Cytoskeletal actin polymerization and platelet activation were measured by co-immunostaining F-actin and P-selectin, respectively. To test for clinical applicability of NO-GC stimulators in the context of increased thrombogenicity risk, we investigated the effect of riociguat on platelets from human immunodeficiency virus (HIV)-positive patients taking abacavir sulphate (ABC)-containing regimens, compared with HIV-negative volunteers.

Stimulation of human and murine platelets with the NO-GC stimulator riociguat or with the NO-GC activator cinaciguat downregulated P-selectin expression, decreased F-actin polymerization, and decreased cellular stiffness by ≈50%, compared to vehicle control. In addition, platelets became more circular, indicating decreased activation. Riociguat did not cause any change in platelet aggregation or circularity in HIV-positive patients taking ABC-containing regimens.

These results corroborate a functional role of the NO-GC enzyme in platelet biomechanics (cellular stiffness) in correlation with the inhibition of platelet activation and morphological changes. The observed changes in stiffness and platelet shape therefore demonstrate the possibility of pharmacologically targeting the NO-GC/cGMP pathway.
Age-associated elevated inflammation and immune pathways in the mice heart are linked to Adiponectin-Adipor1-RelA signaling
Authors: Gupta Tinku , Gujaral Akash , Chandan Shivanshu
Published: April 2023

Inflammatory gene profiles using RNA seq analysis were studied by measuring pro-inflammatory cytokines and chemokines levels. qRT-PCR and Western blot analysis were used to validate the expression profile of these inflammatory mediators. Using flow cytometry analysis, CD11b+ monocytes and CD64+ Ly6C were quantified in the young and old hearts. The inflammatory response, Adipor1 and Adipor2 gene expression, RelA nuclear translocation and the effects of adiponectin in LPS-stimulated or Adipor1 silenced H9C2 cells were studied. Gene ontology analysis using differentially expressed genes revealed an enrichment of immune response pathways in the old mice hearts when compared to young mice hearts. Western blot analysis confirmed the down regulation of several anti-inflammatory proteins and the upregulation of pro-inflammatory proteins including CD68, NF-kB1 and Rel-A, in the old mice hearts. Flow cytometry suggested an infiltration of CD11b+monocytes and CD64+ Ly6C-high macrophages in the old mice hearts compared to younger hearts confirming an increased inflammation in the older hearts. Mechanistically, to understand if the Adiponectin-Adipor1-NFkB axis regulates inflammation in the aging heart, Adipor1 and Adipor2 genes were silenced in H9c2 cardiomyocytes. Immune response genes were elevated in the Adipor1 silenced H9c2 cells but not in Adipor2 silenced cells. Pretreatment with Adiponectin (APN) attenuated the Adipor1 silenced or lipopolysaccharides (LPS)-stimulated expression of inflammatory genes in H9c2 cardiomyocytes. APN also attenuated the nuclear translocation of RelA and induction of immune response genes in Adipor1 silenced or LPS-challenged H9c2 cardiomyocytes. APN-AdipoR1-RelA signaling might be a novel therapeutic target for the treatment of inflamed elderly hearts.
Mitochondrial fitness influences neuronal excitability of dopaminergic neurons from patients with idiopathic form of Parkinson’s disease
Authors: Chlebanowska Paula , Szlaga Agata , Tejchman-Skrzyszewska Anna , Kot Marta , Konieczny Pawel , Skrzypek Klaudia , Muszynska Agata , Sobocinska Malgorzata , Golebiowska Krystyna , Labaj Pawel , Blasiak Anna , Majka Marcin
Published: April 2023

Parkinson disease is the second most common neurodegenerative disease defined by presence of Lewy bodies and the loss of dopaminergic neurons in the substantia nigra pars compacta (SNc). There are three types of PD - familial, early-onset and idiopathic. Idiopathic PD (IPD) accounts for approximately 90% of all PD cases. Mitochondrial dysfunction accompanies the pathogenesis of Parkinson’s disease. Loss of mitochondrial function increases oxidative stress and calcium buffering, which in turn hinders the production of ATP and disrupts the functioning of dopaminergic neurons. The main barrier in PD research was the lack of proper human models to study the mechanisms of PD development and progression. Using induced pluripotent stem (iPS) cells we generated patient-specific dopaminergic neurons.

We observed differences in the mitochondria fitness but not differences in mitochondria mass, morphology or membrane potential. Expression of OXPHOS mitochondrial complexes were lower in PD patients in comparison to control group what resulted in changes in mitochondria respiratory status. We observed also lower expression levels of Na+/K+-ATPase subunits and ATP-sensitive K+(K-ATP) channel subunits. The lower oxygen consumption rate and extracellular acidification rate values were observed in dopaminergic progenitors and iPSC from PD patients compared to the control group. Importantly, observed decrease in the availability of ATP and in the energy consumption, as well as changes in acidification, may constitute contributing factors to the observed reduced neuronal excitability of PD patients dopaminergic neurons.
Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools
Authors: Biderman Dan , Whiteway Matthew R , Hurwitz Cole , Greenspan Nicholas , Lee Robert S , Vishnubhotla Ankit , Warren Richard , Pedraja Federico , Noone Dillon , Schartner Michael , Huntenburg Julia M , Khanal Anup , Meijer Guido T , Noel Jean-Paul , Pan-Vazquez Alejandro , Socha Karolina Z , Urai Anne E ,   The International Brain Laboratory, Cunningham John P , Sawtell Nathaniel B , Paninski Liam
Published: April 2023

Contemporary pose estimation methods enable precise measurements of behavior via supervised deep learning with hand-labeled video frames. Although effective in many cases, the supervised approach requires extensive labeling and often produces outputs that are unreliable for downstream analyses. Here, we introduce “Lightning Pose,” an efficient pose estimation package with three algorithmic contributions. First, in addition to training on a few labeled video frames, we use many unlabeled videos and penalize the network whenever its predictions violate motion continuity, multiple-view geometry, and posture plausibility (semi-supervised learning). Second, we introduce a network architecture that resolves occlusions by predicting pose on any given frame using surrounding unlabeled frames. Third, we refine the pose predictions post-hoc by combining ensembling and Kalman smoothing. Together, these components render pose trajectories more accurate and scientifically usable. We release a cloud application that allows users to label data, train networks, and predict new videos directly from the browser.
A Zika virus protein expression screen inDrosophilato investigate targeted host pathways during development
Authors: Link Nichole , Harnish J Michael , Hull Brooke , Gibson Shelley , Dietze Miranda , Mgbike Uchechukwu E. , Medina-Balcazar Silvia , Shah Priya S. , Yamamoto Shinya
Published: April 2023

In the past decade, Zika virus (ZIKV) emerged as a global public health concern. While adult infections are typically mild, maternal infection can lead to adverse fetal outcomes. Understanding how ZIKV proteins disrupt development can provide insights into the molecular mechanisms of symptoms caused by this virus including microcephaly. In this study, we generated a toolkit to ectopically express Zika viral proteinsin vivoinDrosophila melanogasterin a tissue-specific manner using the GAL4/UAS system. We use this toolkit to identify phenotypes and host pathways targeted by the virus. Our work identified that expression of most ZIKV proteins cause scorable phenotypes, such as overall lethality, gross morphological defects, reduced brain size, and neuronal function defects. We further use this system to identify strain-dependent phenotypes that may contribute to the increased pathogenesis associated with the more recent outbreak of ZIKV in the Americas. Our work demonstratesDrosophila’suse as an efficientin vivomodel to rapidly decipher how pathogens cause disease and lays the groundwork for further molecular study of ZIKV pathogenesis in flies.