bluuebunny/crossref_metadata_2025 huggingface dataset:
Determinants of self-reported health status during COVID-19 lockdown among surveyed Ecuadorian population: a cross sectional study
Authors: Dueñas-Espín Iván , Jacques-Aviñó Constanza , Egas-Reyes Verónica , Larrea Sara , Torres-Castillo Ana Lucía , Trujillo Patricio , Peralta Andrés
Published: September 2022

Objective

To examine the associations of sociodemographic, socioeconomic, and behavioral factors with depression, anxiety, and self-reported health status during the COVID-19 lockdown in Ecuador. We also assessed the differences in these associations between women and men.

Design, setting, and participants

We conducted a cross-sectional study of adults living in Ecuador between July and October 2020. All data were collected through an online survey. We ran descriptive and bivariate analyses and fitted sex-stratified multivariate logistic regression models to assess the association between explanatory variables and self-reported health status.

Results

1801 women and 1123 men completed the survey. Their median (IQR) age was 34 (27–44) years, most participants had a university education (84%) and a full-time public or private job (63%); 16% of participants had poor health self-perception. Poor self-perceived health was associated with severe depression, COVID-19 infection, and chronic diseases. For women, and self-employment, having cohabitants requiring care, having COVID-19 and having a chronic disease increased the likelihood of having poor self-reported health status. For men, poor self-reported health status was associated with perceived poor or inadequate housing and depression.

Conclusion

Being female, having solely public healthcare system access, perceiving housing conditions as inadequate, living with cohabitants requiring care, perceiving difficulties in coping with work or managing household chores, COVID-19 infection, chronic disease, and depression symptoms were significantly and independently associated with poor self-reported health status in Ecuadorian population.
The impact of COVID-19 vaccination in the US: averted burden of SARS-COV-2-related cases, hospitalizations and deaths
Authors: Yamana Teresa K. , Galanti Marta , Pei Sen , Di Fusco Manuela , Angulo Frederick J. , Moran Mary M. , Khan Farid , Swerdlow David L. , Shaman Jeffrey
Published: September 2022

By August 1, 2022, the SARS-CoV-2 virus had caused over 90 million cases of COVID-19 and one million deaths in the United States. Since December 2020, SARS-CoV-2 vaccines have been a key component of US pandemic response; however, the impacts of vaccination are not easily quantified. Here, we use a dynamic county-scale metapopulation model to estimate the number of cases, hospitalizations, and deaths averted due to vaccination during the first six months of vaccine availability. We estimate that COVID-19 vaccination was associated with over 8 million fewer confirmed cases, over 120 thousand fewer deaths, and 700 thousand fewer hospitalizations during the first six months of the campaign.
Associations of ABO and Rhesus D Blood Groups with Phenome-Wide Disease Incidence: A 41-year Retrospective Cohort Study of 482,914 Patients
Authors: Bruun-Rasmussen Peter , Dziegiel Morten Hanefeld , Banasik Karina , Johansson Pär Ingemar , Brunak Søren
Published: September 2022

Background

The natural selection responsible for the observed blood group frequency differences between populations remains debatable. The ABO system has been associated with several diseases and recently also with susceptibility to COVID-19 infection. Associative studies of the RhD system and diseases are sparser. A large disease-wide risk analysis may further elucidate the relationship between the ABO/RhD blood groups and disease incidence.

Methods

We performed a systematic log-linear quasi-Poisson regression analysis of the ABO/RhD blood groups across 1,312 phecode diagnoses. Unlike prior studies, we determined the uniqueness of each individual ABO blood group as opposed to using blood group O as the reference. Moreover, we used up to 41-years of nationwide Danish follow-up data, and a disease categorization scheme specifically developed for diagnosis-wide analysis. Further, we determined associations between the ABO/RhD blood groups and the age at the first diagnosis. Estimates were adjusted for multiple testing.

Results

The retrospective cohort included 482,914 Danish patients (60.4% females). The incidence rate ratios (IRRs) of 101 phecodes were found statistically significant between the ABO blood groups, while the IRRs of 28 phecodes were found statistically significant for the RhD blood group. The associations included cancers and musculoskeletal-, genitourinary-, endocrinal-, infectious-, cardiovascular-, and gastrointestinal diseases.

Conclusions

We found associations of disease-wide susceptibility differences between the blood groups of the ABO and RhD systems, including cancer of the tongue, monocytic leukemia, cervical cancer, osteoarthrosis, asthma, and HIV- and hepatitis B infection. This may indicate that the ABO/RhD blood groups are the results of a selective pressure driven partly by robustness to disease. We found marginal evidence of associations between the blood groups and disease onset.

Funding

Novo Nordisk Foundation and the Innovation Fund Denmark
Genetic Analysis of Activin/Inhibin β Subunits in Zebrafish Development and Reproduction
Authors: Zhao Cheng , Zhai Yue , Geng Ruijing , Wu Kun , Song Weiyi , Ai Nana , Ge Wei
Published: September 2022

Activin and inhibin are both dimeric proteins sharing the same β subunits that belong to the TGF-β superfamily. They are well known for stimulating and inhibiting pituitary FSH secretion, respectively, in mammals. In addition, activin also acts as a mesoderm-inducing factor in frogs. However, their functions in development and reproduction of other species are poorly defined. In this study, we disrupted all three activin/inhibin β subunits (βAa,inhbaa; βAb,inhbab; and βB,inhbb) in zebrafish using CRISPR/Cas9. The loss of βAa/b but not βB led to a high mortality rate in the post-hatching stage. Surprisingly, the expression offshbbut notlhbin the pituitary increased in the female βA mutant together with aromatase (cyp19a1a) in the ovary. The single mutant of βAa/b showed normal folliculogenesis in young females; however, their double mutant (inhbaa−/−;inhbab−/−) showed delayed follicle activation, granulosa cell hypertrophy, stromal cell accumulation and tissue fibrosis. The ovary ofinhbaa−/−deteriorated progressively after 180 dpf with reduced fecundity and the folliculogenesis ceased completely around 540 dpf. In addition, tumor- or cyst-like tissues started to appear in theinhbaa−/−ovary after about one year. In contrast to females, activin βAa/b mutant males showed normal spermatogenesis and fertility. As for activin βB subunit, theinhbb−/−mutant exhibited normal folliculogenesis, spermatogenesis and fertility in both sexes; however, the fecundity of mutant females decreased dramatically at 270 dpf with accumulation of early follicles. In summary, the activin-inhibin system plays an indispensable role in fish reproduction, in particular folliculogenesis and ovarian homeostasis.
A glimpse of the paleome in endolithic microbial communities
Authors: Wegner Carl-Eric , Stahl Raphaela , Velsko Irina , Hübner Alex , Fagernäs Zandra , Warinner Christina , Lehmann Robert , Ritschel Thomas , Totsche Kai U. , Küsel Kirsten
Published: September 2022

The terrestrial subsurface houses a significant proportion of the Earth’s microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments. To obtain more insights about endolithic microbiomes and their metabolic status, we investigated rock samples from the vadose zone, fractured aquifers, and deep aquitards. Using methods from paleogenomics, we recovered sufficient DNA for metagenomics from rock specimens independent of porosity, lithology, and depth. We estimated between 2.81 and 4.25 × 105 cells × g−1 rock. DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens from the vadose zone. The taxonomy and functional potential of paleome communities revealed increased abundances of chemolithoautotrophs, and a broader metabolic potential for aromatic hydrocarbon breakdown. Our study suggests that limestones represent ideal archives for genetic records of past microbial communities, due to their specific conditions facilitating long-term DNA preservation.
Genome-wide association studies of seed metabolites identify loci controlling specialized metabolites in Arabidopsis thaliana
Authors: Naake Thomas , Scossa Federico , de Souza Leonardo Perez , Borghi Monica , Brotman Yariv , Mori Tetsuya , Nakabayashi Ryo , Tohge Takayuki , Fernie Alisdair R.
Published: September 2022

Plants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential to synthesize these metabolites. Quantitative differences in metabolite levels of natural Arabidopsis thaliana accessions can be employed to unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed metabolic GWAS (mGWAS) on seeds of a panel of 315 A. thaliana natural accessions, including the reference genotypes C24 and Col-0, for polar and semi-polar seed metabolites using untargeted ultra-performance liquid chromatography-mass spectrometry. As a complementary approach, we performed quantitative trait locus (QTL) mapping of near-isogenic introgression lines between C24 and Col-0 for specific seed specialized metabolites. Besides common QTL between seeds and leaves, GWAS revealed seed-specific QTL for specialized metabolites indicating differences in the genetic architecture of seeds and leaves. In seeds, aliphatic methylsulfinylalkyl and methylthioalkyl glucosinolates associated with the GS-ALK and GS-OHP locus on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) and/or with the GS-ELONG locus on chromosome 5 containing methylthioalkyl malate synthase (MAM1) and MAM3. We detected two unknown sulfur-containing compounds that were also mapped to these loci. In GWAS, some of the annotated flavonoids (kaempferol 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-rhamnoside-7-O-rhamnoside) were mapped to transparent testa 7 (AT5G07990), encoding a cytochrome P450 75B1 monooxygenase. Three additional mass signals corresponding to quercetin-containing flavonols were mapped to UGT78D2 (AT5G17050). The association of the loci and associating metabolic features were functionally verified in knockdown mutant lines. By performing GWAS and QTL mapping, we were able to leverage variation of natural populations and parental lines to study seed specialized metabolism. The GWAS data set generated here is a high-quality resource that can be interrogated in further studies.
Tug-of-peace: Visual Rivalry and Atypical Visual Motion Processing in MECP2 duplication Syndrome of Autism
Authors: Bogatova Daria , Smirnakis Stelios M. , Palagina Ganna
Published: September 2022

Extracting common patterns of neural circuit computations in the autism spectrum and confirming them as a cause of specific core traits of autism is the first step towards identifying cell- and circuit-level targets for effective clinical intervention. Studies in human subjects with autism have identified functional links and common anatomical substrates between core restricted behavioral repertoire, cognitive rigidity, and over-stability of visual percepts during visual rivalry. To be able to study these processes with single-cell precision and comprehensive neuronal population coverage, we developed the visual bi-stable perception paradigm for mice. Our task is based on plaid patterns consisting of two transparent gratings drifting at an angle of 120° relative to each other. This results in spontaneous reversals of the perception between local component motion (motion of the plaid perceived as two separate moving grating components) and integrated global pattern motion (motion of the plaid perceived as a fused moving texture). Furthermore, this robust paradigm does not depend on the explicit report of the mouse, since the direction of the optokinetic nystagmus (OKN, rapid eye movements driven by either pattern or component motion) is used to infer the dominant percept. Using this paradigm, we found that the rate of perceptual reversals between global and local motion interpretations of the stimulus is reduced in the MECP2 duplication mouse model of autism.

Moreover, the stability of local motion percepts is greatly increased in MECP2 duplication mice at the expense of global motion percepts. Thus, our model reproduces a subclass of the core features in human autism (reduced rate of visual rivalry and atypical perception of visual motion). This further offers a well-controlled approach for dissecting neuronal circuits underlying these core features.
Using genomic scars to select immunotherapy beneficiaries in advanced non-small cell lung cancer
Authors: Donker H. C. , van Es B. , Tamminga M. , Lunter G. A. , van Kempen L. C. L. T. , Schuuring E. , Hiltermann T. J. N. , Groen H. J. M.
Published: September 2022

In advanced non-small cell lung cancer (NSCLC), response to immunotherapy is difficult to predict from pre-treatment information. Given the toxicity of immunotherapy and its financial burden on the healthcare system, we set out to identify patients for whom treatment is effective. To this end, we used mutational signatures from DNA mutations in pre-treatment tissue. Single base substitutions, doublet base substitutions, indels, and copy number alteration signatures were analysed inm= 101 patients (the discovery set). We found that tobacco smoking signature (SBS4) and thiopurine chemotherapy exposure-associated signature (SBS87) were linked to durable benefit. Combining both signatures in a machine learning model separated patients with a progression-free survival hazard ratio ofon the cross-validated discovery set andon an independent external validation set (m= 56). This paper demonstrates that the fingerprints of mutagenesis, codified through mutational signatures, select advanced NSCLC patients who may benefit from immunotherapy, thus potentially reducing unnecessary patient burden.
Resolving chaperone-assisted protein folding on the ribosome at the peptide level
Authors: Wales Thomas E. , Pajak Aleksandra , Roeselová Alžběta , Shivakumaraswamy Santosh , Howell Steven , Hartl F. Ulrich , Engen John R. , Balchin David
Published: September 2022

The cellular environment is critical for efficient protein maturation, but how proteins fold during biogenesis remains poorly understood. We used hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to define, at peptide resolution, the cotranslational chaperone-assisted folding pathway ofEscherichia colidihydrofolate reductase. On the ribosome, the nascent polypeptide folds via structured intermediates not populated during refolding from denaturant. Association with the ribosome allows these intermediates to form, as otherwise destabilizing C-terminal sequences remain confined in the ribosome exit tunnel. We find that partially-folded nascent chains recruit the chaperone Trigger factor, which uses a large composite hydrophobic/hydrophilic interface to engage folding intermediates without disrupting their structure. In addition, we comprehensively mapped dynamic interactions between the nascent chain and ribosomal proteins, tracing the path of the emerging polypeptide during synthesis. Our work provides a high-resolution description ofde novoprotein folding dynamics, thereby revealing new mechanisms by which cellular factors shape the conformational search for the native state.
Bill shape imposes biomechanical tradeoffs in cavity-excavating birds
Authors: Chhaya Vaibhav , Reddy Sushma , Krishnan Anand
Published: September 2022

Organisms are subject to a host of physical forces that influence morphological evolution. Birds, for instance, use their bills as implements to perform various functions, each exerting unique physical demands and selective influences on bill morphology. For example, birds that use their bills to excavate nesting or roosting cavities must resist a range of mechanical stresses to prevent fracture. However, the contribution of bill geometry and material composition to excavation stress resistance remains poorly understood. Here, we study the biomechanical consequences of bill diversification in two clades of cavity-excavating, frugivorous birds, the paleotropical barbets. Using multilayered finite element models and beam theory, we compare the excavation performance of different maxillary geometries for two loading regimes experienced by barbet bills during cavity excavation-dorsoventral impact and torsion. We find that deeper and wider maxillae perform better for impact loads than for torsional loads, with the converse for narrower maxillae. This results in a tradeoff between impact and torsion resistance imposed by bill geometry. Analytical beam models validate this prediction, showing that this relationship holds even when maxillae are simplified to solid elliptical beams. Finally, we find that composite bill structures broadly exhibit lower stresses than homogenous structures of the same geometry, indicating a functional synergy between the keratinous rhamphotheca and bony layers of the bill. Overall, our findings demonstrate the strong link between morphological evolution, behavior, and functional performance in organisms.
Rapid expansion and visual specialization of learning and memory centers in Heliconiini butterflies
Authors: Couto Antoine , Young Fletcher J , Atzeni Daniele , Marty Simon , Melo-Flórez Lina , Hebberecht Laura , Monllor Monica , Neal Chris , Cicconardi Francesco , McMillan W Owen , Montgomery Stephen H.
Published: September 2022

How do neural systems evolve to support new behaviors? Changes in the abundance and diversity of neural cell types, and their connectivity, shape brain composition and provide the substrate for behavioral variation. We describe a striking example of neural elaboration in an ecologically diverse tribe of Heliconiini butterflies. By building extensive new datasets of neural traits across the tribe, we identify major bursts in the size and cellular composition of the mushroom bodies, central brain structures essential for learning and memory. These expansion events are associated with increased innervation form visual centers and coincide with enhanced performance in multiple cognitive assays. This suite of neural and cognitive changes is likely tied to the emergence of derived foraging behaviors, facilitated by localized specialization of neural networks.

One-Sentence Summary

Major shifts in brain composition and behavior in butterflies with unique foraging and dietary behaviors.
Odor-gated oviposition behavior in an ecological specialist
Authors: Álvarez-Ocaña Raquel , Shahandeh Michael P. , Ray Vijayaditya , Auer Thomas O. , Gompel Nicolas , Benton Richard
Published: September 2022

Colonization of a novel ecological niche can require, or be driven by, evolution of an animal’s behaviors promoting their reproductive success in the new environment. Little is known about the underlying mechanisms. We have exploited an emerging genetic model for behavioral neuroecology, Drosophila sechellia – a close relative of Drosophila melanogaster that exhibits extreme specialism for Morinda citrifolia noni fruit – to study the evolution and sensory basis of oviposition. D. sechellia produces fewer eggs compared to other drosophilids, but lays these almost exclusively on noni substrates, contrasting with avoidance or indifference of noni by generalist species. Visual, textural and social cues do not explain the species-specificity of this preference. By contrast, loss of olfactory input in D. sechellia, but not D. melanogaster, essentially abolishes egg-laying, suggesting that this sensory modality gates gustatory-driven noni preference. We find the noni bouquet is detected by redundant olfactory pathways. By parsing the fruit’s volatile chemicals and genetic perturbation of individual olfactory pathways in D. sechellia, we discover a key role for hexanoic acid and its cognate receptor, the Ionotropic receptor Ir75b, in odor-evoked oviposition. Through receptor exchange in D. melanogaster, we provide evidence for a causal contribution of odor-tuning changes in Ir75b to the evolution of oviposition behavior during D. sechellia’s host specialization.
Multimodal system for recording individual-level behaviors in songbird groups
Authors: Rüttimann L. , Wang Y. , Rychen J. , Tomka T. , Hörster H. , Hahnloser R.H.R.
Published: September 2022

The implicit goal of longitudinal observations of animal groups is to identify individuals and to reliably detect their behaviors, including their vocalizations. Yet, to segment fast behaviors and to extract individual vocalizations from sound mixtures remain challenging problems. Promising approaches are multimodal systems that record behaviors with multiple cameras, microphones, and animal-borne wireless sensors. The instrumentation of these systems must be optimized for multimodal signal integration, which is an overlooked steppingstone to successful behavioral tracking.

We designed a modular system (BirdPark) for simultaneously recording small animals wearing custom low-power frequency-modulated radio transmitters. Our custom software-defined radio receiver makes use of a multi-antenna demodulation technique that eliminates data losses due to radio signal fading and that increases the signal-to-noise ratio of the received radio signals by 6.5 dB compared to best single-antenna approaches. Digital acquisition relies on a single clock, allowing us to exploit cross-modal redundancies for dissecting rapid behaviors on time scales well below the video frame period, which we demonstrate by reconstructing the wing stroke phases of free-flying songbirds. By separating the vocalizations among up to eight vocally interacting birds, our work paves the way for dissecting complex social behaviors.
Comparative Study between In-silico and Clinical Works on the Control of Blood Glucose Level in People with Type 1 Diabetes using Improved Hovorka Equations
Authors: Mohd Sohadi Nur Amanina , Som Ayub Md , Mohd Nor Noor Shafina , Ali Sherif Abdulbari , Ahmad Mohd Aizad
Published: September 2022

Background

Hovorka model is one of the diabetic models which is widely used in the artificial pancreas device (APD) also known as closed loop system, meant for people with type 1 diabetes (T1D). Previous workers had modified some equations in the sub-sections of the Hovorka model, which is also known as improved Hovorka equations, in regulating the blood glucose level (BGL) within normoglycemic range (4.0 to 7.0 mmol/L). However, the improved Hovorka equations have not been tested yet in terms of its usability to regulate and control the BGL in safe range for two or more people with T1D. This study aims to simulate their BGL with meal disturbances for 24 hours using the improved Hovorka equations.

Methods

Data for people with T1D were obtained from Clinic 1, Clinical Training Centre (CTC), UiTM Medical Specialist Centre, Sungai Buloh, Selangor. Data collected include gender, age, body weight, mealtimes, meal amount, and duration. Three patients whose ages range from 11 to 14 years old were selected. All patients consumed three meals daily: breakfast, lunch, and dinner. The simulation (in-silico work) was done using MATLAB software, and the BGL profile from both in-silico and clinical works were compared and analysed.

Results

It was revealed that the BGLs for all three people with T1D were far better in the in-silico work compared to the clinical work. The BGL for patient 1 was able to achieve normoglycaemia 73% of the time in the in-silico work. Meanwhile, patient 2 managed to stay in the normoglycemic range for 85% of the time in the in-silico work compared to clinical work, which was merely 31%. For Patient 3, the time duration spent in the normoglycemic range was only 16% in the in-silico work compared to none as in the clinical work. The p-values obtained in the study were less than 0.05, indicating that the in-silico work using the improved Hovorka equations was acceptable for predicting the BGL for people with T1D.

Conclusions

It can be concluded that the improved Hovorka equations are reliable in simulating the meal disturbances effect on BGL and increasing people in T1D times’ duration in the normoglycemic range compared to the clinical work.
Allele-specific expression reveals genetic drivers of tissue regeneration in mice
Authors: Talbott Heather E. , Mack Katya L. , Griffin Michelle , Guardino Nicholas J. , Parker Jennifer B.L. , Spielman Amanda F. , Davitt Michael F. , Mascharak Shamik , Berger Mark J. , Wan Derrick C. , Fraser Hunter B. , Longaker Michael T.
Published: September 2022

In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, “super-healer” MRL mice have the unusual ability to regenerate ear punch wounds, yet the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we use allele-specific gene expression to identifycis-regulatory variation associated with ear regeneration. Analyzing three major wound cell populations, we identified extensive strain- and tissue- specificcis-regulatory divergence associated with differences in healing outcomes. Genes withcis-regulatory differences specifically in fibroblasts were associated with wound healing phenotypes and pathways, and were enriched near genetic markers associated with ear-healing in a genetic cross. Finally, we demonstrated that one of these genes,Cfh, could be applied ectopically to accelerate wound repair and induce regeneration in typically fibrotic wounds. Overall, our results provide insight into the molecular drivers of regeneration in MRL mice with potential clinical implications.
Whole Plant Transpiration Responses of Common Bean (Phaseolus vulgarisL.) to Drying Soil: Water Channels and Transcription Factors
Authors: Cordoba-Novoa H. , Zhang B. , Guo Y. , Aslam M.M. , Fristchi F.B. , Hoyos-Villegas V.
Published: September 2022

Common bean (Phaseolus vulgarisL.) is the main legume crop for direct human consumption worldwide. Among abiotic factors affecting common bean, drought is the most limiting. This study aimed at characterizing genetic variability and architecture of transpiration, stomatal regulation and whole plant water use within the Mesoamerican germplasm. A critical fraction of transpirable soil water (FTSWc) was estimated as the inflection point at which NTR starts decreasing linearly. Genome-wide association (GWA) analyses for mean NTR and FTSWc were performed. High variation on mean NTR and FTSWc was found among genotypes. Genomic signals controlling the variation of these traits were identified onPv01 andPv07 some located in intergenic, intronic and exonic regions. A set of novel candidate genes and putative regulatory elements located in these QTL were identified. Some of the genes have been previously reported to be involved in abiotic tolerance in model species, including some of the five transcription factors (TF) identified. Four candidate genes, one with potential water transportation activity and three TFs were validated. The genePhvul.001G108800,an aquaporin SIP2-1 related gene, showed water channel activity through oocyte water assays. MutantArabidopsis thaliana(Ath) lines for the homologous genes of common bean were evaluated in transpiration experiments. Two of the three evaluated TFs, UPBEAT1 and C2H2-type ZN finger protein, were involved in the control of transpiration responses to drying soil. Our results provide evidence of novel genes to accelerate the drought tolerance improvement in the crop and study the physiological basis of drought response in plants.
Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner
Authors: Kompotis Konstantinos , Mang Géraldine M. , Hubbard Jeffrey , Jimenez Sonia , Emmenegger Yann , Polysopoulos Christos , Hor Charlotte N. , Wigger Leonore , Hébert Sébastien S. , Mongrain Valérie , Franken Paul
Published: September 2022

MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression that have been implicated in a plethora of neuronal processes. Nevertheless, their role in regulating brain activity in the context of sleep has so far received little attention. To test their involvement, we deleted mature miRNAs in post-mitotic neurons at two developmental ages, i.e., in early adulthood using conditionalDicerknockout (cKO) mice and in adult mice using an inducible conditionalDicercKO (icKO) line. In both models, electroencephalographic (EEG) activity was affected and the response to sleep deprivation (SD), altered; while rapid-eye-movement sleep (REMS) rebound was compromised in both, EEG delta (1-4 Hz) power during non-REM sleep (NREMS) was reduced in cKO mice and increased in icKO mice. We subsequently investigated the effects of SD on the miRNA transcriptome and found that the expression of 48 forebrain miRNAs was affected, in particular, the activity-dependent miRNA miR-709.In vivoinhibition of miR-709 in the brain increased EEG power during NREMS in the slow-delta (0.75-1.75 Hz) range, particularly after periods of prolonged wakefulness. Transcriptome analysis of primary cortical neuronsin vitrorevealed that miR-709 regulates endosomal trafficking and glutamatergic receptor activity. A subset of the genes involved in glutamatergic transmission was affected also in the cortices of sleep-deprived, miR-709-inhibited mice. Our data implicate miRNAs in the regulation of EEG activity and indicate that miR-709 links neuronal excitability during wakefulness to brain synchrony during sleep, likely through the regulation of endosomal trafficking and glutamatergic signaling.

Significance Statement

MicroRNAs (miRNAs) are key regulators of gene expression playing vital roles both in postnatal brain development and its functioning in adult organisms. Here, we highlight a fundamental role for miRNAs in shaping EEG slow waves, which reflect synchronous neuronal firing, characteristic of NREM sleep (NREMS) in the adult murine cortex. Disruption of the miRNA-biogenesis machinery affected brain synchrony differently, depending on when it occurred during development. Moreover, sleep deprivation altered the expression of several miRNAs in a brain-region specific manner. Among those, we identified miR-709 to affect the expression of genes involved in endosomal-trafficking and glutamatergic-transmission, thereby linking neuronal activity during wakefulness to slow EEG waves during subsequent sleep. The current study causally implicates this specific miRNA and the molecular pathways it targets in modifying the generation of NREMS EEG slow waves, which are important in synaptic plasticity and brain functioning.
The carnitine shuttle links mitochondrial metabolism to histone acetylation and lipogenesis
Authors: Izzo Luke , Trefely Sophie , Demetriadou Christina , Drummond Jack , Mizukami Takuya , Kuprasertkul Nina , Farria Aimee , Nguyen Phuong , Reich Lauren , Shaffer Joshua , Affronti Hayley , Carrer Alessandro , Andrews Andrew , Capell Brian C. , Snyder Nathaniel W. , Wellen Kathryn E.
Published: September 2022

Acetyl-CoA is a central metabolite used for lipid synthesis in the cytosol and histone acetylation in the nucleus, among other pathways. The two major precursors to acetyl-CoA in the nuclear-cytoplasmic compartment are citrate and acetate, which are processed to acetyl-CoA by ATP-citrate lyase (ACLY) and acyl-CoA synthetase short-chain 2 (ACSS2), respectively. While some evidence has suggested the existence of additional routes to nuclear-cytosolic acetyl-CoA, such pathways remain poorly defined. To investigate this, we generated cancer cell lines lacking both ACLY and ACSS2. Unexpectedly, and in contrast to observations in fibroblasts, ACLY and ACSS2 double knockout (DKO) cancer cells remain viable and proliferate, maintain pools of cytosolic acetyl-CoA, and are competent to acetylate proteins in both cytosolic and nuclear compartments. Using stable isotope tracing, we show that both glucose and fatty acids feed acetyl-CoA pools and histone acetylation in DKO cells. Moreover, we provide evidence for the carnitine shuttle and carnitine acetyltransferase (CrAT) as a substantial pathway to transfer two-carbon units from mitochondria to cytosol independent of ACLY. Indeed, in the absence of ACLY, glucose can feed fatty acid synthesis in a carnitine responsive and CrAT-dependent manner. This work defines a carnitine-facilitated route to produce nuclear-cytosolic acetyl-CoA, shedding light on the intricate regulation and compartmentalization of acetyl-CoA metabolism
Inter-organelle crosstalk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress
Authors: Kuna Ramya S , Kumar Avi , Galvez Hector , Wessendorf-Rodriguez Karl A , Green Courtney R , McGregor Grace H , Cordes Thekla , Shaw Reuben J , Svensson Robert U , Metallo Christian M
Published: September 2022

Proliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA flux under such stresses is critically important. To this end we applied13C isotope tracing cell lines deficient in these mitochondrial (ATP-citrate lyase; ACLY-), cytosolic, (acetyl-CoA synthetase (ACSS2-), and peroxisomal (peroxisomal biogenesis factor 5; PEX5-) dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation, highlighting a role for inter-organelle crosstalk in supporting cell survival in response to nutrient fluctuations.

Teaser

We quantify how acetyl-CoA metabolism is supported by distinct pathways spanning mitochondria, cytosol, and peroxisomes using comprehensive tracing applied to knockout cells.
Ceg1 depletion reveals mechanisms governing degradation of non-capped RNAs
Authors: Zanin Onofrio , Hebenstreit Daniel , Grzechnik Pawel
Published: September 2022

Most functional eukaryotic mRNAs contain a 7-methylguanosine (m7G) cap which serves as a platform that recruits proteins to support essential biological functions such as mRNA processing, nuclear export and translation. Although capping is accomplished during the first steps of transcription the fate and turnover of uncapped transcripts have not been studied extensively. Here, we employed fast nuclear depletion of the capping enzymes inSaccharomyces cerevisiaeto uncover the turnover of the transcripts that failed to be capped. We show that the levels of non-capped mRNAs are determined principally by the abundance of their synthesis. Nuclear depletion of the capping enzymes increases the levels of lowly expressed mRNAs and decreases mRNAs that are highly transcribed altogether mimicking the effects observed in cells lacking the predominantly cytoplasmic 5’-3’ exonuclease Xrn1. The nuclear 5’-3’ exonuclease Rat1 is not involved in the degradation of cap-defective transcripts and the lack of the capping does not affect the distribution of RNA Polymerase II on the chromatin. Our data indicate that the mRNAs that failed to be capped are not directed to a specific quality-control pathway and that the 5’ cap role is associated with the Xrn1-dependent buffering of the cellular mRNA levels, along with protecting from 5’-3’ degradation.
Viral proteins and virus-like particles of the LTR5_Hs endogenous retrovirus in human primordial germ cell-like cells
Authors: Kobayashi Mutsumi , Kobayashi Misato , Kreuzer Johannes , Zaniewski Eric , Kim Jae Jung , Shioda Keiko , Hagihara Hikari , Odajima Junko , Nakashoji Ayako , Zheng Yi , Fu Jianping , Ericsson Maria , Kawamura Kazuhiro , Stott Shannon L. , Irimia Daniel , Haas Wilhelm , Wu Chin-Lee , Tokuyama Maria , Shioda Toshi
Published: September 2022

The hominoid-specific endogenous retrovirus LTR5_Hs is transcriptionally activated in human primordial germ cell-like cells (hPGCLCs), a pluripotent stem cell-derived cell culture model of PGCs. Here, taking the unique advantage of our novel cell culture method to obtain large amounts of pure hPGCLCs, we performed proteomics profiling of hPGCLCs and detected various viral proteins produced from the LTR5_Hs RNA via ribosomal frameshifting. We also present transmission electron microscopy images of 100-nm diameter virus-like particles (VLPs) assembled at the surface of hPGCLCs. Compared to hPGCLCs, expression of LTR5_Hs RNA is far weaker in human seminomas, the germ cell tumors resembling PGCs. Re-analysis of published single cell RNA-seq data of human embryos revealed strong activation of LTR5_Hs in migrating PGCs but suppressed in PGCs upon they reach the gonadal anlagen. In the microfluidics-supported polarized embryoids mimicking peri-implantation stages of human embryos, LTR5_Hs RNA was detected by RNA in situ hybridization in NANOG+/TFAP2C+/SOX17+ cells resembling freshly emerged PGCs. These results support that human germ cells produce LTR5_Hs proteins and VLPs during their earliest stages of normal development until their settlement in the gonadal anlagen.

SUMMARY STATEMENT

The hominoid-specific endogenous retrovirus LTR5_Hs is activated in a cell culture model resembling early-stage human primordial germ cells, producing not only viral RNA but also retrovirus proteins and virus-like particles.
FLAIRR-seq: A novel method for single molecule resolution of near full-length immunoglobulin heavy chain repertoires
Authors: Ford Easton E. , Tieri David , Rodriguez Oscar , Francoeur Nancy , Soto Juan , Kos Justin , Peres Ayelet , Gibson William , Silver Catherine A. , Deikus Gintaras , Hudson Elizabeth , Woolley Cassandra R. , Beckmann Noam , Charney Alexander , Mitchell Thomas C. , Yaari Gur , Sebra Robert P. , Watson Corey T. , Smith Melissa L.
Published: September 2022

Current Adaptive Immune Receptor Repertoire Sequencing (AIRR-seq) strategies resolve expressed antibody (Ab) transcripts with limited resolution of the constant region. Here we present a novel near full-length AIRR-seq (FLAIRR-Seq) method that utilizes targeted amplification by 5’ rapid amplification of cDNA ends (RACE), combined with single molecule, real-time sequencing to generate highly accurate (>Q40, 99.99%) IG heavy chain transcripts. FLAIRR-seq was benchmarked by comparing IG heavy chain variable (IGHV), diversity (IGHD), and joining (IGHJ) gene usage, complementarity-determining region 3 (CDR3) length, and somatic hypermutation to matched datasets generated with standard 5’ RACE AIRR-seq and full-length isoform sequencing. Together these data demonstrate robust, unbiased FLAIRR-seq performance using RNA samples derived from peripheral blood mononuclear cells, purified B cells, and whole blood, which recapitulated results generated by commonly used methods, while additionally resolving novel IG heavy chain constant (IGHC) gene features. FLAIRR-seq data provides, for the first time, simultaneous, single-molecule characterization of IGHV, IGHD, IGHJ, and IGHC region genes and alleles, allele-resolved subisotype definition, and high-resolution identification of class-switch recombination within a clonal lineage. In conjunction with genomic sequencing and genotyping of IGHC genes, FLAIRR-seq of the IgM and IgG repertoires from 10 individuals resulted in the identification of 32 unique IGHC alleles, 28 (87%) of which were previously uncharacterized. Together, these data demonstrate the capabilities of FLAIRR-seq to characterize IGHV, IGHD, IGHJ, and IGHC gene diversity for the most comprehensive view of bulk expressed Ab repertoires to date.
Healthcare system overstretch and in-hospital mortality of intubated COVID-19 patients in Greece: an updated analysis, September 2020 to April 2022
Authors: Lytras Theodore
Published: September 2022

Background

Our previous analysis showed how in-hospital mortality of intubated COVID-19 patients in Greece is adversely affected by patient load and regional disparities. We aimed to update this analysis to include the large “delta” and “omicron” waves that affected Greece during 2021-2022, while also considering the effect of vaccination.

Methods

Anonymized surveillance data were analyzed from all COVID-19 patients in Greece intubated between 1 September 2020 and 4 April 2022, and followed up until 17 May 2022. Poisson regression was used to estimate the hazard of dying as a function of fixed and time-varying covariates.

Results

Mortality was significantly higher above 400 patients, with an adjusted Hazard Ratio of 1.22, 95% CI: 1.09-1.38), rising progressively up to 1.48 (95% CI: 1.31-1.69) for 800+ patients. Hospitalization away from Attica region was also independently associated with increased mortality, as was hospitalization after 1 September 2021 (HR=1.21, 95% CI: 1.09-1.36). Vaccination did not affect the mortality of these already severely ill patients.

Conclusion

Our results confirm that in-hospital mortality of severely ill COVID-19 patients is adversely affected by high patient load and regional disparities, and point to a further significant deterioration after 1 September especially away from Attica and Thessaloniki. This highlights the need for urgent strengthening of healthcare services in Greece, ensuring equitable and high-quality care for all.
A novel, ssDNA Bidnavirus in the giant freshwater prawn Macrobrachium rosenbergii
Authors: Gangnonngiw Warachin , Bunnontae Malinee , Kayansamruaj Pattanapon , Senapin Saengchan , Srisala Jiraporn , Flegel Timothy W. , Wongprasert Kanokpan
Published: September 2022

A purported parvovirus producing circular, eosinophilic inclusions in the nuclei of tubule epithelial cells of the hepatopancreas (HP) of the giant freshwater prawn Macrobrachium rosenbergii (Mr) was first reported from Malaysia in 1994. In 2009, similar inclusions in Mr from Thailand were confirmed to contain single-stranded DNA (ssDNA). In 2021, Mr samples showing similar HP inclusions were reported to give positive PCR test results for decapod Hepanhamaparvovirus (DHPV) using universal DHPV primers designed from many viral isolates of 3 penaeid shrimp species. However, the matching DNA probe revealed positive in situ hybridization (ISH) results with host HP nuclei only, and not with the intranuclear inclusions. At the time, the negative ISH result with the intranuclear inclusions has not been further elucidated. Here we describe metagenomic analysis and de novo assembly from 2016 samples of Mr with similar intranuclear inclusions that showed negative PCR test results using the DHPV universal primers. Genomes identified through metagenomics have revealed a novel ssDNA genome sequence of 6,723 bases that was confirmed by a single PCR amplicon. ISH using specific probes derived from this genome sequence demonstrated the ssDNA presented in both grossly normal nuclei and in the intranuclear inclusions. Tests with archived DNA from the samples used in the 2021 publication yielded positive PCR results for both DHPV and the novel sequence, suggesting that the shrimp had dual infections. Phylogenetic analysis of the novel sequence revealed no relationship to any known DHPV type. Instead, the sequence most closely matched the polymerase B gene in the V1 fragment from Bombyx mori bidensovirus 2 (BmBDV2) is characterized by 2 ssDNA genome fragments and has been classified in the family Bidnaviridae. The 2 BmBDV2 fragments V1 and V2 each produce their own independent capsid protein genes and virions. In contrast, the new Mr virus is independent with a single 6,723 base ssDNA genome, and we propose the name Macrobrachium hepatopancreatic bidnavirus (MHBV).
Scaffold and structural diversity of the secondary metabolite space of medicinal fungi
Authors: Vivek-Ananth R.P. , Sahoo Ajaya Kumar , Baskaran Shanmuga Priya , Samal Areejit
Published: September 2022

Medicinal fungi including mushrooms have well documented therapeutic uses. The MeFSAT database provides a curated library of more than 1800 secondary metabolites produced by medicinal fungi for potential use in high throughput screening (HTS) studies. In this study, we perform a cheminformatics based investigation of the scaffold and structural diversity of the secondary metabolite space of medicinal fungi, and moreover, perform a detailed comparison with approved drugs, other natural product libraries and semi-synthetic libraries. We find that the secondary metabolite space of MeFSAT has similar or higher scaffold diversity in comparison to other natural product libraries analysed here. Notably, 94% of the scaffolds in the secondary metabolite space of MeFSAT are not present in the approved drugs. Further, we find that the secondary metabolites of medicinal fungi, on the one hand are structurally far from the approved drugs, while on the other hand are close in terms of molecular properties to approved drugs. Lastly, chemical space visualization using dimensionality reduction methods showed that the secondary metabolite space has minimal overlap with the approved drug space. In a nutshell, our results underscore that the secondary metabolite space of medicinal fungi is a valuable resource for identifying potential lead molecules for natural product based drug discovery.
Ecological change and conflict reduction led to the evolution of a transformative social behavior in ants
Authors: Meurville Marie-Pierre , Silvestro Daniele , LeBoeuf Adria C.
Published: September 2022

Behavioral innovations can be ecologically transformative for lineages that perform them and for their associated communities. Many ecologically dominant, superorganismal, and speciose ant lineages use a mouth-to-mouth fluid exchange behavior – trophallaxis – to share both exogenously sourced and endogenously produced materials across their colonies, while lineages that are less abundant, less cooperative and less speciose tend not to perform this behavior. How and why this behavior evolved and fixed in only some ant lineages remains unclear and whether this trait enables ants’ ecological dominance is not yet understood. Here we show that trophallaxis evolved in two major events ~110 Ma in lineages that today encompass 36% of ants, and in numerous smaller and more recent events. We found that trophallaxis evolved early only in ant lineages that had reduced intra-colonial conflict by losing workers ability to reproduce. Our causal models indicate that this signature behavior of superorganismal ants required social cooperation and ecological opportunism, and likely contributed to the large colony sizes and speciation patterns of the ants that use it and dominate our landscapes today. We hypothesize that the early evolution of trophallaxis was brought about by a major shift in terrestrial ecosystems through the origin and diversification of flowering plants and the consequent opportunistic inclusion of nectar and sap-sucker honeydew in the ant diet.
RNA recoding in cephalopods tailors microtubule motor protein function
Authors: Rangan Kavita J. , Reck-Peterson Samara L.
Published: September 2022

RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed ‘recoding’. In cephalopods, recoding occurs in most proteins and is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. Using microtubule motors as a model, we found that squid rapidly employ RNA recoding to enhance kinesin function in response to cold ocean temperature. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod dynein and kinesin. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and informs the functional characterization of conserved non-cephalopod proteins.