bluuebunny/crossref_metadata_2025 huggingface dataset:
Systems-level identification of key transcription factors in immune cell specification
Authors: Liu Cong , Omilusik Kyla , Toma Clara , Kurd Nadia S. , Chang John T. , Goldrath Ananda W. , Wang Wei
Published: May 2022

Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
Great tits differ in glucocorticoid plasticity in response to spring temperature
Authors: Hau Michaela , Deimel Caroline , Moiron Maria
Published: May 2022

Fluctuations in environmental temperature affect energy metabolism, stimulating the expression of phenotypic plasticity in behavioral and physiological traits. Vertebrate hormonal signals like glucocorticoids underpin environmentally-induced phenotypic plasticity, with changes in circulating concentrations orchestrating plastic changes in diverse traits. Climate change is predicted to alter temperature variation globally, making it imperative to evaluate whether free-living animal populations can cope adaptively. To evaluate their potential to respond to ongoing global change, we quantified individual variation in glucocorticoid plasticity to ambient temperature in wild great tits (Parus major). Using a reaction norm approach, we repeatedly sampled individuals for circulating glucocorticoid concentrations across five years. As expected, baseline and stress-induced glucocorticoid concentrations increased with lower ambient temperatures at the population and within-individual level. Moreover, we provide unique evidence that free-living individuals differ significantly in their plastic responses to temperature variation for both glucocorticoid traits, with some displaying greater plasticity than others. Average concentrations and degree of plasticity covaried for baseline glucocorticoids, indicating that these two reaction norm components are linked. Hence, individual variation in glucocorticoid plasticity to an important environmental factor exists in a wild population, representing a crucial step to assess the adaptive potential of vertebrates to endure current temperature fluctuations.
OptoRheo: Simultaneousin situmicro-mechanical sensing and imaging of live 3D biological systems
Authors: Mendonca Tania , Lis-Slimak Katarzyna , Matheson Andrew B. , Smith Matthew G. , Anane-Adjei Akosua B. , Ashworth Jennifer C. , Cavanagh Robert , Paterson Lynn , Dalgarno Paul A. , Alexander Cameron , Tassieri Manlio , Merry Catherine L. R. , Wright Amanda J.
Published: May 2022

Biomechanical cues from the extracellular matrix (ECM) are essential for directing many cellular processes, from normal development and repair, to disease progression. To better understand cell-matrix interactions, we have developed a new instrument named ‘OptoRheo’ that combines light sheet fluorescence microscopy with particle tracking microrheology. OptoRheo lets us image cells in 3D as they proliferate over several days while simultaneously sensing the mechanical properties of the surrounding extracellular and pericellular matrix at a sub-cellular length scale. OptoRheo can be used in two operational modalities (with and without an optical trap) to extend the dynamic range of microrheology measurements. We corroborated this by characterising the ECM surrounding live breast cancer cells in two distinct culture systems, cell clusters in 3D hydrogels and spheroids in suspension culture. This cutting-edge instrument will transform the exploration of drug transport through complex cell culture matrices and optimise the design of the next-generation of disease models.
Human pancreatic islet microRNAs implicated in diabetes and related traits by large-scale genetic analysis
Authors: Taylor Henry J. , Hung Yu-Han , Narisu Narisu , Erdos Michael R. , Kanke Matthew , Yan Tingfen , Grenko Caleb M. , Swift Amy J. , Bonnycastle Lori L. , Sethupathy Praveen , Collins Francis S. , Taylor D. Leland
Published: May 2022

Genetic studies have identified ≥240 loci associated with risk of type 2 diabetes (T2D), yet most of these loci lie in non-coding regions, masking the underlying molecular mechanisms. Recent studies investigating mRNA expression in human pancreatic islets have yielded important insights into the molecular drivers of normal islet function and T2D pathophysiology. However, similar studies investigating microRNA (miRNA) expression remain limited. Here, we present data from 63 individuals, representing the largest sequencing-based analysis of miRNA expression in human islets to date. We characterize the genetic regulation of miRNA expression by decomposing the expression of highly heritable miRNAs into cis- and trans-acting genetic components and mapping cis-acting loci associated with miRNA expression (miRNA-eQTLs). We find (i) 81 heritable miRNAs, primarily regulated by trans-acting genetic effects, and (ii) 5 miRNA-eQTLs. We also use several different strategies to identify T2D-associated miRNAs. First, we colocalize miRNA-eQTLs with genetic loci associated with T2D and multiple glycemic traits, identifying one miRNA, miR-1908, that shares genetic signals for blood glucose and glycated hemoglobin (HbA1c). Next, we intersect miRNA seed regions and predicted target sites with credible set SNPs associated with T2D and glycemic traits and find 32 miRNAs that may have altered binding and function due to disrupted seed regions. Finally, we perform differential expression analysis and identify 13 miRNAs associated with T2D status—including miR-187-3p, miR-21-5p, miR-668, and miR-199b-5p—and 4 miRNAs associated with a polygenic score for HbA1c levels—miR-216a, miR-25, miR-30a-3p, and miR-30a-5p.
Upregulated Ca2+ release from the endoplasmic reticulum leads to impaired presynaptic function in Alzheimer’s disease
Authors: Adeoye Temitope , Shah Syed I , Demuro Angelo , Rabson David A , Ullah Ghanim
Published: May 2022

Neurotransmitter release from presynaptic terminals is primarily regulated by rapid Ca2+ influx through membrane-resident voltage-gated Ca2+ channels (VGCCs). Also, accumulating evidence indicates that the endoplasmic reticulum (ER) is extensively present in axonal terminals of neurons and plays a modulatory role in synaptic transmission by regulating Ca2+ levels. Alzheimer’s disease (AD) is marked by enhanced Ca2+ release from the ER and downregulation of Ca2+ buffering proteins. However, the precise consequence of impaired Ca2+ signalling within the vicinity of VGCCs (active zone (AZ)) on exocytosis is poorly understood. Here, we perform in-silico experiments of intracellular Ca2+ signalling and exocytosis in a detailed biophysical model of hippocampal synapses to investigate the effect of aberrant Ca2+ signalling on neurotransmitter release in AD. Our model predicts that enhanced Ca2+ release from the ER increases the probability of neurotransmitter release in AD. Moreover, over very short timescales (30-60 msec), the model exhibits activity-dependent and enhanced short-term plasticity in AD, indicating neuronal hyperactivity—a hallmark of the disease. Similar to previous observations in AD animal models, our model reveals that during prolonged stimulation (~450 msec), pathological Ca2+ signalling increases depression and desynchronization with stimulus, causing affected synapses to operate unreliably. Overall, our work provides direct evidence in support of a crucial role played by altered Ca2+ homeostasis mediated by intracellular stores in AD.
Asymmetric dysregulation of glutamate dynamics across the synaptic cleft in a mouse model of Alzheimer disease
Authors: Brymer Kyle J , Hurley Emily P , Barron Jessica C , Mukherjee Bandhan , Barnes Jocelyn R , Nafar Firoozeh , Parsons Matthew P
Published: May 2022

Most research on glutamate spillover focuses on the deleterious consequences of postsynaptic glutamate receptor overactivation. However, two decades ago, it was noted that the glial coverage of hippocampal synapses is asymmetric: astrocytic coverage of postsynaptic sites exceeds coverage of presynaptic sites by a factor of four. The fundamental relevance of this glial asymmetry remains poorly understood. Here, we used the glutamate biosensor iGluSnFR, and restricted its expression to either CA3 or CA1 neurons to visualize glutamate dynamics at pre- and postsynaptic microenvironments, respectively. We demonstrate that inhibition of the primarily astrocytic glutamate transporter-1 (GLT-1) slows glutamate clearance to a greater extent at presynaptic compared to postsynaptic membranes. GLT-1 expression was reduced early in a mouse model of AD, resulting in slower glutamate clearance rates at presynaptic but not postsynaptic membranes that opposed presynaptic short-term plasticity. Overall, our data demonstrate that the presynapse is particularly vulnerable to GLT-1 dysfunction and may have implications for presynaptic impairments in a variety of brain diseases.
Landscape change and alien invasions drive shifts in native lady beetle communities over a century
Authors: Perry Kayla I , Bahlai Christie A , Assal Timothy J , Riley Christopher B , Turo Katherine J , Taylor Leo , Radl James , Delgado de la flor Yvan A , Sivakoff Frances S , Gardiner Mary M
Published: May 2022

Aim

Understanding drivers of insect population declines is essential for the development of successful conservation plans, but data limitations restrict assessment across spatial and temporal scales. Museum records represent a unique source of historical data that can be leveraged to investigate temporal trends in insect communities. Native lady beetle decline has been attributed to competition with established alien species and landscape change, but the relative importance of these drivers is difficult to measure with short-term field-based studies. Here we assessed distribution patterns for native lady beetle species over 12 decades using museum records and evaluated the relative importance of alien species and landscape change as long-term drivers contributing to changes in lady beetle communities.

Location

Ohio, USA.

Methods

We compiled occurrence records for 28 lady beetle species collected in Ohio, USA from 1900-2018. Incidence-based measures of taxonomic beta-diversity were used to evaluate changes in lady beetle community composition over time. To evaluate the relative influence of temporal, spatial, landscape, and community drivers on the captures of native lady beetles, we constructed negative binomial generalized additive models.

Results

We report evidence of declines in captures for several native species, includingAdalia bipunctata, Coccinella novemnotata, Hippodamia convergens, andColeomegilla maculata. Importantly, the timing, severity, and drivers of these documented declines were species-specific. Changes in lady beetle species composition began in the 1980s, when processes of species loss/gain and turnover shifted communities towards dominance by a few alien lady beetle species. Land cover change also was associated with declines in captures, particularly forC. novemnotatawhich declined prior to the arrival of alien species in the state.

Main conclusions

Our study documented shifts in Ohio’s lady beetle communities beginning in the 1980s as alien species supplanted natives. Drivers of declines in captures of native lady beetle species were highly species-specific, emphasizing that mechanisms driving population losses cannot be generalized even among closely related species. These findings also indicate the importance of museum holdings and the analysis of species-level data when studying temporal trends in insect populations.
Impaired immune response drives age-dependent severity of COVID-19
Authors: Beer Julius , Crotta Stefania , Breithaupt Angele , Ohnemus Annette , Becker Jan , Sachs Benedikt , Kern Lisa , Llorian Miriam , Ebert Nadine , Labroussaa Fabien , Thao Tran Thi Nhu , Trueeb Bettina Salome , Jores Joerg , Thiel Volker , Beer Martin , Fuchs Jonas , Kochs Georg , Wack Andreas , Schwemmle Martin , Schnepf Daniel
Published: May 2022

SARS-CoV-2 is a highly contagious respiratory virus and the causative agent for COVID-19. The severity of disease varies from mildly symptomatic to lethal and shows an extraordinary correlation with increasing age, which represents the major risk factor for severe COVID-191. However, the precise pathomechanisms leading to aggravated disease in the elderly are currently unknown. Delayed and insufficient antiviral immune responses early after infection as well as dysregulated and overshooting immunopathological processes late during disease were suggested as possible mechanisms. Here we show that the age-dependent increase of COVID-19 severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) responses. To overcome the limitations of mechanistic studies in humans, we generated a mouse model for severe COVID-19 and compared the kinetics of the immune responses in adult and aged mice at different time points after infection. Aggravated disease in aged mice was characterized by a diminished IFN-γ response and excessive virus replication. Accordingly, adult IFN-γ receptor-deficient mice phenocopied the age-related disease severity and supplementation of IFN-γ reversed the increased disease susceptibility of aged mice.

Mimicking impaired type I IFN immunity in adult and aged mice, a second major risk factor for severe COVID-192–4, we found that therapeutic treatment with IFN-λ in adult and a combinatorial treatment with IFN-γ and IFN-λ in aged Ifnar1-/-mice was highly efficient in protecting against severe disease.

Our findings provide an explanation for the age-dependent disease severity of COVID-19 and clarify the nonredundant antiviral functions of type I, II and III IFNs during SARS-CoV-2 infection in an age-dependent manner. Based on our data, we suggest that highly vulnerable individuals combining both risk factors, advanced age and an impaired type I IFN immunity, may greatly benefit from immunotherapy combining IFN-γ and IFN-λ.
Increased spinal excitation causes decreased locomotor complexity
Authors: de Graaf Myriam Lauren , Mochizuki Luis , Wagner Heiko , Le Mouel Charlotte
Published: May 2022

Animals display rich and coordinated motor patterns during walking and running, that are generated and controlled within the central nervous system. Previous computational and experimental results suggest that the balance between excitation and inhibition in neural circuits may be critical for generating such structured motor patterns. In this paper, we explore the influence of this balance on the ability of a reservoir computing artificial neural network to learn human locomotor patterns, using mean-field theory analysis and simulations. We varied the numbers of neurons, connection percentages and connection strengths of excitatory and inhibitory neuron populations, and introduced the anatomicalimbalancethat quantifies their combined overall effect. Our results indicate that network dynamics and performance depend critically on the anatomical imbalance in the network. Inhibition-dominated networks work well, displaying balanced input to the neurons and good firing rate variability. Excitation-dominated networks, however, lead to saturated firing rates, thereby reducing the effective dimensionality of the networks and leading to simplified motor output patterns. This suggests that motor pattern generation may be robust to increased inhibition but not increased excitation in neural networks.
scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments
Authors: Ebrahimi Ghazal , Orabi Baraa , Robinson Meghan , Chauve Cedric , Flannigan Ryan , Hach Faraz
Published: May 2022

Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as alternative splicing. New library preparation techniques attempt to extend single-cell sequencing by utilizing both long-and short-reads. These techniques split the library material, after it is tagged with cellular barcodes, into two pools: one for short-read sequencing and one for long-read sequencing. However, the challenge of utilizing these techniques is that they require matching the cellular barcodes sequenced by the erroneous long-reads to the cellular barcodes detected by the short-reads. To overcome this challenge, we introduce scTagger, a computational method to match cellular barcodes data from long-and short-reads. We tested scTagger against another state-of-the-art tool on both real and simulated datasets and we demonstrate that scTagger has both significantly better accuracy and time efficiency.
A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and cellular senescence
Authors: Kang Taekyu , Moore Emily C. , Kopania Emily E. K. , King Christina D. , Schilling Birgit , Campisi Judith , Good Jeffrey M. , Brem Rachel B.
Published: May 2022

Cellular senescence is a program of cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in metazoan cells. Landmark studies in laboratory mice have characterized a number of master senescence regulators, including p16INK4a, p21, NF-kB, p53, and C/EBPβ. To discover other molecular players in senescence, we developed a screening approach to harness the evolutionary divergence between mouse species. We found that primary cells from the Mediterranean mouseMus spretus, when treated with DNA damage to induce senescence, produced less cytokine and had less-active lysosomes than cells from laboratoryM. musculus. We used allele-specific expression profiling to catalog senescence-dependentcis-regulatory variation between the species at thousands of genes. We then tested for correlation between these expression changes and interspecies sequence variants in the binding sites of transcription factors. Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, USF2, for molecular validation. In acute irradiation experiments, cells lacking USF2 had compromised DNA damage repair and response. Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program—shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type. We interpret these findings under a model of pro-repair, anti-senescence regulatory function by USF2. Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens.
Synaptotagmin 7 docks synaptic vesicles to support facilitation and Doc2α-triggered asynchronous release
Authors: Wu Zhenyong , Kusick Grant F. , Berns Manon M. M. , Raychaudhuri Sumana , Itoh Kie , Walter Alexander M. , Chapman Edwin R. , Watanabe Shigeki
Published: May 2022

Despite decades of intense study, the molecular basis of asynchronous neurotransmitter release remains enigmatic. Synaptotagmin (syt) 7 and Doc2 have both been proposed as Ca2+sensors that trigger this mode of exocytosis, but conflicting findings have led to controversy. Here, we demonstrate that at excitatory mouse hippocampal synapses, Doc2α is the major Ca2+sensor for asynchronous release, while syt7 supports this process through activity-dependent docking of synaptic vesicles. In synapses lacking Doc2α, asynchronous release after single action potentials is strongly reduced, while deleting syt7 has no effect. However, in the absence of syt7, docked vesicles cannot be replenished on millisecond timescales. Consequently, both synchronous and asynchronous release depress from the second pulse onward during repetitive activity. By contrast, synapses lacking Doc2α have normal activity-dependent docking, but continue to exhibit decreased asynchronous release after multiple stimuli. Moreover, disruption of both Ca2+sensors is non-additive. These findings result in a new model whereby syt7 drives activity-dependent docking, thus providing synaptic vesicles for synchronous (syt1) and asynchronous (Doc2 and other unidentified sensors) release during ongoing transmission.
Does fatigue influence joint-specific work and ground force production during the first steps of maximal accelerative running?
Authors: Vial Shayne , Wilkie Jodie Cochrane , Turner Mitchell , Scanlan Mark , Blazevich Anthony J.
Published: May 2022

The rate of initial acceleration during the first steps of a maximal-effort (sprint) run often determines success or failure in prey capture and predator evasion, and is a vital factor of success in many modern sports. However, accelerative events are commonly performed after having already run considerable distances, and the associated fatigue should impair muscle force production and thus reduce acceleration rate. Despite this, the effects of running-induced fatigue on our ability to accelerate as well as the running technique used to achieve it has been incompletely studied. We recorded 3-D kinematics and ground reaction forces during the first three steps of the acceleration phase from a standing start before and after performing a high-speed, multi-directional, fatiguing run-walk protocol in well-trained running athletes who were habituated to accelerative sprinting. We found that the athletes were able to maintain their rate of initial acceleration despite changing running technique, which was associated with use of a more upright posture, longer ground contact time, increased vertical ground reaction impulse, decreased hip flexion and extension velocities, and a shift in peak joint moments, power, and positive work from the hip to the knee joint; no changes were detected in ankle joint function. Thus, a compensatory increase in knee joint function alleviated the reduction in hip flexor-extensor capacity. These acute adaptations may indicate that the hip extensors (gluteal and hamstring muscle groups) were more susceptible to fatigue than the ankle and knee musculature, and may thus be a primary target for interventions promoting fatigue resistance.
Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory
Authors: Katriel Guy , Mahanaymi Udi , Koutschan Christoph , Zeilberger Doron , Steel Mike , Snir Sagi
Published: May 2022

The genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analysing the point mutations of standard markers is too crude and slow for fine-scale phylogenetics. Nevertheless, genome dynamics events provide far richer information. The synteny index (SI) between a pair of genomes combines gene order and gene content information, allowing the comparison of genomes of unequal gene content, together with order considerations of their common genes. Recently, genome dynamics has been modelled as a continuous-time Markov process, and gene distance in the genome as a birth–death–immigration process. Nevertheless, due to complexities arising in this setting such as overlapping neighbourhoods and other confounding factors, no precise and provably consistent estimators could be derived.

Here, we extend this modelling approach by using techniques from birth–death theory to derive explicit expressions of the system’s probabilistic dynamics in the form of rational functions of the model parameters. This, in turn, allows us to infer analytically the expected distances between organisms based on a transformation of their SI. Despite the complexity of the expressions obtained, we establish additivity of this estimated evolutionary distance (a desirable property yielding phylogenetic consistency).

Applying the new measure in simulation studies shows that it attains very accurate results in realistic settings and even under model extensions. In the real-data realm, we applied the new formulation to unique data structure that we constructed - the ordered orthology DB - based on a new version of the EggNOG database, to construct a tree with more than 4.5K taxa. The resulted tree was compared it with a NCBI taxonomy for these organisms. To the best of our knowledge, this is the largest gene-order-based tree constructed and it overcomes flaws found in previous approaches.
Predicting past and future SARS-CoV-2-related sick leave using discrete time Markov modelling
Authors: Lei Jiayao , Clements Mark , Elfström Miriam , Lundgren Kalle Conneryd , Dillner Joakim
Published: May 2022

Background

Prediction of SARS-CoV-2-induced sick leave among healthcare workers (HCWs) is essential for being able to plan the healthcare response to the epidemic.

Methods

During first wave of the SARS-Cov-2 epidemic (April 23rd to June 24th, 2020), the HCWs in the greater Stockholm region in Sweden were invited to a study of past or present SARS-CoV-2 infection. We develop a discrete time Markov model using a cohort of 9449 healthcare workers (HCWs) who had complete data on SARS-CoV-2 RNA and antibodies as well as sick leave data for the calendar year 2020. The one-week and standardized longer term transition probabilities of sick leave and the ratios of the standardized probabilities for the baseline covariate distribution were compared with the referent period (an independent period when there were no SARS-CoV-2 infections) in relation to PCR results, serology results and gender.

Results

The one-week probabilities of transitioning from healthy to partial sick leave or full sick leave during the outbreak as compared to after the outbreak were highest for healthy HCWs testing positive for large amounts of virus (3.69, (95% confidence interval, CI: 2.44-5.59) and 6.67 (95% CI: 1.58-28.13), respectively). The proportion of all sick leaves attributed to COVID-19 during outbreak was at most 55% (95% CI: 50%-59%).

Conclusions

A robust Markov model enabled use of simple SARS-CoV-2 testing data for quantifying past and future COVID-related sick leave among HCWs, which can serve as a basis for planning of healthcare during outbreaks.
Will The Grass Be Greener On The Other Side Of Climate Change?
Authors: Morris Craig D , Kirkman Kevin P , Zacharias Pete JK
Published: May 2022

Increasing atmospheric [CO2] is stimulating photosynthesis and plant production, increasing the demand for nitrogen relative to soil supply with declining global foliar nitrogen concentrations as a consequence. The effect of such oligotrophication on the forage quality of sweetveld, mixedveld, and sourveld grasslands in South Africa, which support livestock production and native ungulates, are unknown. Soil characteristics and the herbage quality of an abundant grass are described from baseline historical (mid 1980s) data collected across a sweet-mixed-sour grassland gradient in KwaZulu-Natal. Sourveld occurred on the most acidic, dystrophic soils and exhibited a pronounced decline in leaf N, digestibility, and other macronutrients during winter, in sharp contrast to sweetveld, on nutrient-rich soils, where forage quality varied little seasonally. In a carbon enriched, warmer, and most likely drier future climate, we predict that forage quality will be little altered in sweetveld where soil nutrients and temperature are not limiting but that sourveld could become ‘sourer’ because soil nutrients will be inadequate to match higher plant production promoted by elevated [CO2] and warmer and longer growing seasons. Reassessing historical data and seasonal and spatial monitoring of forage quality will enable past and future impacts of climate change on grassland forage quality to be assessed.

Significance

Grassland forage quality will likely decline with elevated [CO2] and warming, particularly in sourveld.

Climate change could deepen and widen the sourveld winter forage bottleneck, necessitating greater supplementary feeding of livestock.
SMURF: embedding single-cell RNA-seq data with matrix factorization preserving self-consistency
Authors: Wang Bingchen , Pu Juhua , Chen Lingxi , Li Shuai Cheng
Published: May 2022

The advance of single-cell RNA-sequencing (scRNA-seq) sheds light on cell-specific transcriptomic studies of cell developments, complex diseases, and cancers. Nevertheless, scRNA-seq techniques suffer from “dropout” events, and imputation tools are proposed to address the sparsity. Here, rather than imputation, we propose a tool, SMURF, to embed cells and genes into their latent space vectors utilizing matrix factorization with a mixture of Poisson-Gamma divergent as objective while preserving self-consistency. As for wet lab dataset evaluation, SMURF exhibited feasible cell subpopulation discovery efficacy with the latent vectors on all the eight-cell line mixtures. Furthermore, SMURF can embed the cell latent vectors into a 1D-oval and recover the time course of the cell cycle. SMURF can also serve as an imputation tool, the in silico data assessment shows that SMURF paraded the most robust gene expression recovery power with low root mean square error and high Pearson correlation. Moreover, SMURF recovers the gene distribution for the WM989 Drop-seq data. SMURF is available at https://github.com/deepomicslab/SMURF.
Exceptional yield vesicle packaged recombinant protein production from E. coli
Authors: Eastwood Tara A. , Baker Karen , Streather Bree R. , Allen Nyasha , Wang Lin , Botchway Stanley W. , Brown Ian R. , Hiscock Jennifer R. , Lennon Christopher , Mulvihill Daniel P.
Published: May 2022

We describe a novel system that exports diverse recombinant proteins in extracellular vesicles from E. coli. The vesicles not only compartmentalise toxic, insoluble and disulphide bond containing proteins in a soluble and functional form (e.g. DNaseI, nanobodies and IgG-fusions), but the continued release of the inducible vesicle packaged proteins into the media supports continuous isolation of protein from active culture within a micro-environment allowing stable long-term storage. This technology results in unprecedented yields of vesicle packaged functional proteins for efficient downstream processing for a wide range of applications from discovery science to applied biotechnology and medicine.
A revised phylogenetic classification forViola(Violaceae)
Authors: Marcussen Thomas , Ballard Harvey E. , Danihelka Jiří , Flores Ana R. , Nicola Marcela V. , Watson John M.
Published: May 2022

The genusViola(Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then known 400 species were distributed among 14 sections and numerous unranked groups. Here we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species ofViola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We subdivide the 658 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus ofViola(subg.Neoandinium, a replacement name for the illegitimate subg.Andinium), six new sections (sect.Abyssinium, sect.Himalayum, sect.Melvio, sect.Nematocaulon, sect.Spathulidium, sect.Xanthidium), and seven new subsections (subsect.Australasiaticae, subsect.Bulbosae, subsect.Clausenianae, subsect.Cleistogamae, subsect.Dispares, subsect.Formosanae, subsect.Pseudorupestres). Evolution within the genus is discussed in light of biogeography, fossil record, morphology, and particular traits.Violais among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps forViolaconcern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent.Violahas also never been subject to comprehensive anatomical study. Study on seed anatomy and morphology is required to understand the fossil record of the genus.
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment
Authors: Ezzamouri Bouchra , Rosario Dorines , Bidkori Gholamreza , Lee Sunjae , Uhlen Mathias , Shoaie Saeed
Published: May 2022

The human gut microbiome has been associated with several metabolic disorders including type 2 diabetes. Understanding metabolic changes in the gut microbiome is important to elucidate the role of gut bacteria in regulating host metabolism. Here, we used available metagenomics data from a metformin study, together with genome-scale metabolic modelling of the key bacteria in individual and community-level to investigate the mechanistic role of the gut microbiome in response to metformin. Individual modelling predicted that species that are increased after metformin treatment have higher growth rates in comparison to species that are decreased after metformin treatment. Gut microbial enrichment analysis showed prior to metformin treatment pathways related to the hypoglycemic effect were enriched. Our observations highlight how the key bacterial species after metformin treatment have commensal and competing behavior, and how their cellular metabolism changes due to different nutritional environment. Integrating different diets showed there were specific microbial alterations between different diets. These results show the importance of the nutritional environment and how the dietary guidelines may improve drug efficiency through the gut microbiota.
A retrospective molecular investigation of selected pigeon viruses between 2018-2021 in Turkey
Authors: Sahindokuyucu Ismail , Yazici Zafer , Barry Gerald
Published: May 2022

A recent first detection of pigeon aviadenovirus-1 and pigeon circovirus co-infection associated with Young Pigeon Disease Syndrome (YPDS) in a pigeon flock in Turkey, prompted a study focused on documenting the distribution of Pigeon aviadenovirus (PiAdV-1 and PiAdV-2), Pigeon circovirus (PiCV), Columbid alphaherpesvirus 1 (pigeon herpesvirus (PiHV)) and Fowl aviadenovirus (FAdV) in the country. These viruses were selected as they are associated with severe disease in pigeons across the world. A total of 192 cloacal swabs were collected from young (<1 year old) pigeons from 16 different private pigeon flocks across Turkey, between 2018 and 2021 as part of routine diagnostic sampling. PiCV genetic material was the most frequently detected 4/16 (25%), PiAdV-1 and CoHV-1 DNA were both found in one flock each, while neither PiAdV-2 and FAdV were detected in any of the studied pigeon flocks. PiCV and PiHV genetic material were both detected in the same pigeon flock’s cloacal samples as a co-infection with the identification of PiHV being a first in Turkey.
Synapses learn to utilize pre-synaptic noise for the prediction of postsynaptic dynamics
Authors: Kappel David , Tetzlaff Christian
Published: May 2022

Synapses in the brain are highly noisy, which leads to a large trial-by-trial variability. Given how costly synapses are in terms of energy consumption these high levels of noise are surprising. Here we propose that synapses use their noise to represent uncertainties about the activity of the post-synaptic neuron. To show this we utilize the free-energy principle (FEP), a well-established theoretical framework to describe the ability of organisms to self-organize and survive in uncertain environments. This principle provides insights on multiple scales, from high-level behavioral functions such as attention or foraging, to the dynamics of single microcircuits in the brain, suggesting that the FEP can be used to describe all levels of brain function. The synapse-centric account of the FEP that is pursued here, suggests that synapses form an internal model of the somatic membrane dynamics, being updated by a synaptic learning rule that resembles experimentally well-established LTP/LTD mechanisms. This approach entails that a synapse utilizes noisy processes like stochastic synaptic release to also encode its uncertainty about the state of the somatic potential. Although each synapse strives for predicting the somatic dynamics of its neuron, we show that the emergent dynamics of many synapses in a neuronal network resolve different learning problems such as pattern classification or closed-loop control in a dynamic environment. Hereby, synapses coordinate their noise processes to represent and utilize uncertainties on the network level in behaviorally ambiguous situations.
Anatomical and Palynological Investigation within flora of Family Asteraceae
Authors: Shahzad Asim , Iqbal Shahid , Kayani Sadaf , Shafiq Tayyab , Zafar Muhammad , Naeem Muhammad , Yasmin Humaira
Published: May 2022

A comprehensive microscopic investigation of the leaf epidermis, as well as anatomical and palynological research of selected Asteraceae species from the flora of Havali (Kahutta) Azad Jammu and Kashmir (AJK) Pakistan, was carried out. This study includes 11 plant species comprising of Senecio jacobea, Leucanthemum vulgare, Halianthus annuus, Erigeron bonariensis, Achillea millifolium, Halianthus Linnaeus, Taraxacum officinale, Anaphalius nepalensis, Erigeron Canadensis, and Tagetes erecta. All the species studied were amphistomatic, with four different forms of stomata i.e tetracytic, anomocytic, anisocytic, and tricytic. The main stomatal type was tetracytic, followed by anomocytic. The abaxial epidermis has a higher stomatal density than the adaxial epidermis. Highest stomatal density was present Tagetes erecta while lowest is present in Conyza canadensis. In lower epidermis stomatal index was higher in Taraxacum officinale followed by Halianthus annuus and Tagetes erecta while in upper epidermis highest index was shown by Halianthus annuus. For this study species of family Acteraceae were properly collected. Furthermore, variation in pollen can be seen. List of palynomorph which includes family name, botanical name, local name, English name, flower colour, season and pollen description for the logical arrangement of these species. The logical ordering of these species was guided by dust characteristics such as form and pollen morphology. Palynological data has been found to be too big for taxonomists to calculate and make appropriate observations on their findings.
Dual RNA-seq reveals a type 6 secretion system-dependent blockage of TNF-α signaling and BicA as a Burkholderia pseudomallei virulence factor important during gastrointestinal infection
Authors: Sanchez-Villamil Javier I. , Tapia Daniel , Khakum Nittaya , Widen Steven G. , Torres Alfredo G.
Published: May 2022

Melioidosis is a disease caused by the Gram-negative bacillus Burkholderia pseudomallei (Bpm), commonly found in soil and water of endemic areas. Naturally acquired human melioidosis infections can result from either exposure through percutaneous inoculation, inhalation, or ingestion of soil-contaminated food or water. Our prior studies recognized Bpm as an effective enteric pathogen, capable of establishing acute or chronic gastrointestinal infections following oral inoculation. However, the specific mechanisms and virulence factors involved in the pathogenesis of Bpm during intestinal infection are unknown. In our current study, we standardized an in vitro intestinal infection model using primary intestinal epithelial cells (IECs) and demonstrated that Bpm requires a functional T6SS for full virulence. Further, we performed dual RNA-seq analysis on Bpm-infected IECs to evaluate differentially expressed host and bacterial genes in the presence or absence of a T6SS. Our results showed a dysregulation in the TNF-α signaling via NF-κB pathway in the absence of the T6SS, with some of the genes involved in inflammatory processes and cell death also affected. Analysis of the bacterial transcriptome identified virulence factors and regulatory proteins playing a role during infection, with association to the T6SS. By using a Bpm transposon mutant library and isogenic mutants, we showed that deletion of the bicA gene, encoding a putative T3SS/T6SS regulator, ablated intracellular survival and plaque formation by Bpm and impacted survival and virulence when using murine models of acute and chronic gastrointestinal infection. Overall, these results highlight the importance of the type 6 secretion system in the gastrointestinal pathogenesis of Bpm.
A revisit to universal single-copy genes in bacterial genomes
Authors: Wang Saidi , Ventolero Minerva , Hu Haiyan , Li Xiaoman
Published: May 2022

Universal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated bacterial RefSeq genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study shed new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.
Expression of the Bacillus thuringiensis vip3A insecticidal toxin gene is activated at the onset of stationary phase by VipR, an autoregulated transcription factor
Authors: Chen Haibo , Verplaetse Emilie , Slamti Leyla , Lereclus Didier
Published: May 2022

The Vegetative insecticidal protein Vip3A is produced by some Bacillus thuringiensis strains from the mid-log growth phase to sporulation. Although Vip3A is important for the entomopathogenicity of B. thuringiensis, the vip3A gene regulation is unknown. In the B. thuringiensis kurstaki HD1 strain, vip3A is carried by the pBMB299 plasmid, which is absent in the closely related strain B. thuringiensis kurstaki HD73. Using a transcriptional fusion between the vip3A promoter and lacZ, we observed that the HD73 strain is unable to express vip3A. This result suggests that a specific regulator is required for vip3A expression. Assuming that the regulator gene is located on the same plasmid as vip3A, we transferred the pBMB299 from the HD1 strain to the HD73 strain. We found that Vip3A was produced in the HD73 strain containing pBMB299, suggesting that the regulator gene is located on this plasmid. Using this heterologous host and promoter-lacZ transcription fusions, we confirmed that VipR is essential to activate vip3A expression at the onset of stationary phase. We demonstrated that vipR transcription is positively autoregulated and the determination of the vipR and vip3A promoters pinpointed a putative VipR target upstream from the Sigma A-specific −10 region of these two promoters. Surprisingly, this conserved sequence was also found upstream of cry1I and cry2 genes. Finally, we showed that vip3A and vipR expression is drastically increased in a Δspo0A mutant unable to initiate sporulation. In conclusion, we have characterized a novel regulator involved in the entomopathogenic potency of B. thuringiensis through a sporulation-independent pathway.

Importance

The insecticidal properties of Bacillus thuringiensis are mainly due to Cry toxins which form a crystalline inclusion during sporulation. However, other proteins participate in the pathogenicity of the bacterium, notably the Vip3A toxins that are produced from vegetative growth to sporulation. The VipR regulator that activates vip3A gene expression at the onset of stationary phase is positively autoregulated and analysis of the promoter region of the vip3A and vipR genes reveals the presence of a highly conserved DNA sequence. This possible VipR target sequence is also found upstream of the cry2A and cry1I genes, suggesting that Cry toxins can be produced before the bacteria enter sporulation. Such a result could allow us to better understand the role of Cry and Vip3A toxins during the B. thuringiensis infectious cycle in insects, in addition to the primary role of the Cry toxins in the toxemia caused by ingestion of crystals.
Cryo-tomography reveals rigid-body motion and organization of apicomplexan invasion machinery
Authors: Gui Long , O’Shaughnessy William J. , Cai Kai , Reetz Evan , Reese Michael L. , Nicastro Daniela
Published: May 2022

The apical complex is a specialized collection of cytoskeletal and secretory machinery in apicomplexan parasites, which include the pathogens that cause malaria and toxoplasmosis. Its structure and mechanism of motion are poorly understood. We used cryo-FIB-milling and cryo-electron tomography to visualize the 3D-structure of the apical complex in its protruded and retracted states. Averages of conoid-fibers revealed their polarity and unusual nine-protofilament arrangement with associated proteins connecting and likely stabilizing the fibers. Neither the structure of the conoidfibers nor the architecture of the spiral-shaped conoid complex change during protrusion or retraction. Thus, the conoid moves as a rigid body, and is not spring-like and compressible, as previously suggested. Instead, the apical-polar-rings (APR), previously considered rigid, dilate during conoid protrusion. We identified actin-like filaments connecting the conoid and APR during protrusion, suggesting a role during conoid movements. Furthermore, our data capture the parasites in the act of secretion during conoid protrusion.