bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of expression of genes encoding glycogen degrading enzymes inGardnerella swidsinskiiand identification of reference genes for quantitative real-time PCR
Authors: Kim Andy , Fernando Champika , Kularatne Divanthika , Hill Janet E.
Published: March 2024

Gardnerellaspp. express and export enzymes for the breakdown of glycogen into glucose, maltose, and malto-oligosaccharides for consumption by the vaginal microbiota but how the expression of these “public goods” is affected by substrate and product levels in the environment is not known. Accurate measurement of relative gene expression using real-time quantitative PCR relies on the identification of appropriate reference genes whose expression levels remain constant under the conditions of the study. Currently, no reference genes have been identified for gene expression analysis ofGardnerellaspp. The objectives of this study were to identify reference genes and apply them in determining the relative gene expression levels of genes encoding α-amylase and α-amylase-pullulanase in media supplemented with substrate (glycogen) or a preferred product (maltotriose). Ten candidate reference genes were evaluated and analysis of Cq values from qPCR using multiple algorithms identifieduppS(encoding polyprenyl diphosphate synthase) as the top comprehensively ranked reference gene followed bygatA(encoding Asp-tRNA/Glu-tRNA amidotransferase subunit gatA). Interpretation of the Cq values for α-amylase and α-amylase-pullulanase was performed by applying these two reference genes in the calculation of relative gene expression levels. α-amylase-pullulanase gene expression was upregulated in media supplemented with 1% glycogen in comparison to media supplemented with 1% maltotriose suggesting a regulatory mechanism inG. swidsinskiithat responds to nutrient availability. No significant difference in gene expression of α-amylase was observed suggesting expression is not influenced by substrate availability. The RNA purification protocol and reference genes validated in this study will be useful in future studies of gene expression inGardnerella.

Importance

Knowledge of the factors affecting growth of vaginal microbiota is critical to understanding how vaginal dysbiosis is initiated and maintained. Overgrowth ofGardnerellaspecies includingG. swidsinskiiis a hallmark of bacterial vaginosis. These organisms break down vaginal glycogen and the products become available for uptake byGardnerellaand other microbiota. Measuring how expression of genes encoding glycogen degrading enzymes relates to relative abundance of substrate and products in the environment requires development of protocols for RNA purification and identification of reference genes for RT-qPCR.
Spatial attention alters visual cortical representation during target anticipation
Authors: Tünçok Ekin , Carrasco Marisa , Winawer Jonathan
Published: March 2024

Attention enables us to efficiently and flexibly interact with the environment by prioritizing some image features in preparation for responding to a stimulus. Using a concurrent psychophysics– fMRI experiment, we investigated how covert spatial attention affects responses in human visual cortex prior to target onset, and how it affects subsequent behavioral performance. Performance improved at cued locations and worsened at uncued locations, relative to distributed attention, demonstrating a selective tradeoff in processing. Pre-target BOLD responses in cortical visual field maps changed in two ways: First, there was a stimulus-independent baseline shift, positive in map locations near the cued location and negative elsewhere, paralleling the behavioral results. Second, population receptive field centers shifted toward the attended location. Both effects increased in higher visual areas. Together, the results show that spatial attention has large effects on visual cortex prior to target appearance, altering neural response properties throughout and across multiple visual field maps.
Investigating the mode of action for liver toxicity and wasting-like responses produced by high dose exposures to longer chain perfluoroacid substances (PFAS) using high throughput transcriptomics
Authors: Barutcu A. Rasim , Black Michael B. , Andersen Melvin E.
Published: March 2024

Single doses of perfluoro-n-decanoic acid (PFDA) cause wasting, a progressive loss of 30 to 50% body weight, increasing liver/body weight ratios, and death within several weeks (Olson and Andersen, 1983). Repeat high doses of perfluorooctane sulfonate (PFOS) produce a subset of these responses in rats and monkeys. The mode of action (MOA) of these wasting-like syndromes is not clear, nor is it understood if these responses are limited to a subset of perfluoroacid substances (PFAS) or a common response to high dose exposure with a larger number of PFAS. To identify pathway perturbations in liver caused by PFAS, we analyzed publishedin vitrogene expression studies from human primary liver spheroids treated with various PFAS for treatment times up to 14 days (Rowan-Carrollet al., 2021). With treatment times of 10 to 14 days, longer-chain PFAS compounds, specifically PFOS, perfluorodecane sulfonate (PFDS) and higher doses of perfluorooctanoic acid (PFOA), downregulated large numbers of genes in pathways for steroid metabolism, fatty acid metabolism and biological oxidations. Shorter chain PFAS compounds upregulated genes in pathways for fatty acid metabolism. Although PFDA was more toxic and could only be examined at 1-day of treatment, it also downregulated genes for lipid metabolism, steroid metabolism, and biological oxidations. Shorter chain PFAS, both carboxylic and sulfonic acids, did not lead to downregulation of pathways for fatty acid or steroid metabolism. TCDD is also known to cause wasting responses in rodents and humans. In intact rats, high dose responses of longer chain PFAS produce downregulation of batteries of genes associated with fatty acid oxidation and lipogenesis similar to those seen with TCDD. Based on our results, when combined with other literature, we propose that the longer-chain PFAS impair lipogenic pathways through inhibitory interactions between PPARβ, PPARα and PPARγ.
Individualized fMRI neuromodulation enhances visuospatial perception: a guided approach targeted towards the neuro-rehabilitation of cortical blindness and deceleration of subjective cognitive impairment
Authors: Allam Anthony , Allam Vincent , Reddy Sandy , Patel Ankit , Froudarakis Emmanouil , Rohren Eric M. , Sheth Sameer A. , Papageorgiou T. Dorina
Published: March 2024

Neuromodulation is a growing precision-medicine approach to modulating neural activity that can be used to treat neuropsychiatric, and general pathophysiologic conditions. We developed individualized fMRI neuromodulation (iNM) to study the mechanisms of visuospatial perception modulation with the long-term goal of applying it in low-vision patient populations having cortical blindness or visuospatial impairment preceding subjective cognitive impairment. To determine these mechanisms, we developed a direction and coherence discrimination task to engage visual perception (VP), visual imagery (VI), selective extero-intero-ceptive attention (SEIA), and motor planning (MP) networks. Participants discriminated up and down direction, at full and subthreshold coherence under iNM or control (no iNM). We determined the blood-oxygen-level-dependent (BOLD) magnitude as area under the curve (AUC) for VI, SEIA, and MP encoded networks and used a decoder to predict the stimulus from brain maps. The increased AUC BOLD magnitude under iNM across directions and coherences ranged from: 48-76% for SEIA, 26-59% for MP, 20-47% for VI, and 100% for strong VP coherences, but decreased for weak coherences. iNM increased classification performance. Our results imply a causal role of iNM-induced visuospatial mechanisms in strengthening these networks and provide a pathway for more accurate encoding models and effective treatment.
Closed-loop auditory stimulation targeting alpha and theta oscillations during REM sleep induces phase-dependent power and frequency changes
Authors: Jaramillo Valeria , Hebron Henry , Wong Sara , Atzori Giuseppe , Bartsch Ullrich , Dijk Derk-Jan , Violante Ines R.
Published: March 2024

Background

Alpha and theta oscillations characterize the waking human electroencephalogram (EEG) and can be modulated by closed-loop auditory stimulation (CLAS). These oscillations also occur during rapid eye movement (REM) sleep, but whether they can be modulated by CLAS is not known.

Objective

Investigate whether CLAS can modulate alpha and theta oscillations during REM sleep in a targeted phase-dependent manner.

Methods

We recorded high-density EEG during an extended overnight sleep period in 18 healthy young adults. Auditory stimulation was delivered during both phasic and tonic REM sleep in alternating 6 s ON and 6 s OFF windows. During the ON windows, stimuli were phase-locked to four orthogonal phases of ongoing alpha or theta oscillations detected in a frontal electrode (Fz).

Results

During ON windows, the four orthogonal phases of ongoing alpha and theta oscillations were targeted with high accuracy. Alpha and theta CLAS induced phase-dependent changes in power and frequency at the target location. Frequency-specific effects were observed for alpha trough (speeding up) and rising (slowing down) and theta trough (speeding up) conditions. These phase-dependent changes of CLAS were observed during both REM sleep substages, even though the amplitude evoked by auditory stimuli which were not phase-locked was very much reduced in phasic compared to tonic REM sleep.

Conclusions

This study provides evidence that faster REM sleep rhythms can be modulated by CLAS in a phase-dependent manner. This offers a new approach to investigate how modulation of REM sleep oscillations affects the contribution of this vigilance state to brain function.

Highlights

- REM sleep alpha and theta oscillations can be modulated using phase-locked CLAS

- Phase-dependent changes in power and frequency are observed in the target area

- Phase-dependent modulation occurs in phasic and tonic REM sleep

Graphical Abstract
Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits
Authors: Wu Hui , Luo Ling-Yun , Zhang Ya-Hui , Zhang Chong-Yan , Huang Jia-Hui , Mo Dong-Xin , Zhao Li-Ming , Wang Zhi-Xin , Wang Yi-Chuan , EEr He-Hua , Bai Wen-Lin , Han Di , Dou Xing-Tang , Ren Yan-Ling , Dingkao Renqing , Chen Hai-Liang , Ye Yong , Du Hai-Dong , Zhao Zhan-Qiang , Wang Xi-Jun , Jia Shan-Gang , Liu Zhihong , Li Meng-Hua
Published: March 2024

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing novel insights into domestication and selection in goats and related species. Here, we assembled a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), which included a Y chromosome of 20.9 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrected numerous genome-wide structural and base errors in previous assemblies and added 288.5 Mb of previously unresolved regions (PURs) and 446 newly assembled genes to the reference genome. We sequenced the genomes of five representative goat breeds for PacBio reads, and used T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 SVs (7.41%) in the PURs and 507 overlapping genes significantly enriched (Padj. < 0.05) in the keratin filament pathway. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the PURs. Also, our analyses revealed a set of novel selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).
Olfactory bulb stimulation mitigates Alzheimer’s-like disease progression
Authors: Salimi Morteza , Nazari Milad , Shahsavar Payam , Dehghan Samaneh , Javan Mohammad , Mirnajafi-Zadeh Javad , Raoufy Mohammad Reza
Published: March 2024

Background

Deep brain stimulation (DBS) has demonstrated potential in mitigating Alzheimer’s disease (AD). However, the invasive nature of DBS presents challenges for its application. The olfactory bulb (OB), showing early AD-related changes and extensive connections with memory regions, offers an attractive entry point for intervention, potentially restoring normal activity in deteriorating memory circuits.

Aims

Our study examined the impact of electrically stimulating the OB on working memory as well as pathological and electrophysiological alterations in the OB, medial prefrontal cortex, hippocampus, and entorhinal cortex in amyloid beta (Aβ) AD model rats.

Methods

Male Wistar rats underwent surgery for electrode implantation in brain regions, inducing Alzheimer’s-like disease. Bilateral olfactory bulb (OB) electrical stimulation was performed for 1 hour daily to the OB of stimulation group animals for 18 consecutive days, followed by evaluations of histological, behavioral, and local field potential signal processing.

Results

OB stimulation counteracted Aβ plaque accumulation and prevented AD-induced working memory impairments. Furthermore, it prompted an increase in power across diverse frequency bands and enhanced functional connectivity, particularly in the gamma band, within the investigated regions during a working memory task.

Conclusion

This preclinical investigation highlights the potential of olfactory pathway-based brain stimulation to modulate the activity of deep-seated memory networks for AD treatment. Importantly, the accessibility of this pathway via the nasal cavity lays the groundwork for the development of minimally invasive approaches targeting the olfactory pathway for brain modulation.
A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease
Authors: Jafree Daniyal J , Perera Charith , Ball Mary , Tolomeo Daniele , Pomeranz Gideon , Wilson Laura , Davis Benjamin , Mason William J , Funk Eva Maria , Kolatsi-Joannou Maria , Polschi Radu , Malik Saif , Stewart Benjamin J , Price Karen L , Mitchell Hannah , Motallebzadeh Reza , Muto Yoshiharu , Lees Robert , Needham Sarah , Moulding Dale , Chandler Jennie C , Walsh Claire L , Woolf Adrian S , Winyard Paul J D , Scambler Peter J , Hägerling René , Clatworthy Menna R , Humphreys Benjamin D , Lythgoe Mark F , Walker-Samuel Simon , Long David A
Published: March 2024

Hallmarks of autosomal dominant polycystic kidney disease (ADPKD), the most common hereditary kidney anomaly, include expanding fluid-filled epithelial cysts, inflammation, and fibrosis. Despite previous work showing the potential of vascular-based therapies, renal microvascular alterations in ADPKD, and their timing, are poorly understood. Using single-cell transcriptomics of human kidney microvasculature, we identify a population of endothelial cells adjacent to cysts in ADPKD. This pericystic endothelium, distinguishable by its expression of osteopontin (SPP1), has a distinct molecular profile compared to the common endothelial cell injury signature in other kidney diseases. SPP1+pericystic endothelium was also present in an orthologous mouse model of ADPKD before overt kidney functional decline. By interrogating geometric, topological and fractal properties from three-dimensional imaging of early ADPKD mouse kidneys, we show that pericystic endothelium associates with disorganisation and non-uniformity of the renal cortical microvasculature. Concurrently, we detected region-specific reductions in cortical blood flow within ADPKD murine kidneys using arterial spin labelling. We conclude that ADPKD kidneys contain a unique subset of endothelium manifesting with aberrant remodelling and impaired blood perfusion. Its detection, prior to renal functional decline, advocates the vasculature as a therapeutic target to modulate or preserve renal function in early ADPKD.
Maternal cannabis use alters excitatory inputs to corticostriatal efferent neurons in rat offspring
Authors: Ginder Darren E. , Weimar Halle V. , Lindberg Jonathan E.M. , Fisher Zachary D.G. , Lim Miranda M. , Peters James H. , McLaughlin Ryan J.
Published: March 2024

With the recent surge in cannabis legalization across North America, there is legitimate concern that rates of cannabis use during pregnancy will dramatically increase in the coming years. However, the long-term impacts of prenatal cannabis exposure (PCE) on the brain and behavior remain poorly understood. Using a model of passive cannabis vapor exposure, we have previously shown that PCE impairs behavioral flexibility in an attentional set-shifting task in adult offspring, which is orchestrated in part by excitatory inputs from the medial prefrontal cortex (mPFC) to the nucleus accumbens (NAc). Given the fundamental role of these corticostriatal inputs in coordinating flexible reward-seeking strategies, we used a combination of retrograde tracing andex vivoelectrophysiology to test the hypothesis that maternal cannabis use alters the synaptic and intrinsic membrane properties of corticostriatal efferent neurons in exposed male and female rat offspring. Specifically, pregnant rat dams were trained to self-administer vaporized cannabis (69.7% THC; 150 mg/ml) twice daily throughout mating and gestation and offspring were subsequently injected with fluorescent retrobeads into the NAc core prior to conducting whole-cellexvivo recordings of spontaneous excitatory and inhibitory post-synaptic currents (EPSC and IPSC, respectively) in retrolabeled mPFC neurons in adulthood. Our results indicate that PCE increases the frequency of spontaneous glutamatergic events (EPSCs) in NAc-projecting mPFC neurons in a sex-specific manner, which drives changes in excitatory to inhibitory (EPSC/IPSC) ratio, particularly in females. Furthermore, the amplitude of phasic glutamatergic events was reduced in cannabis-exposed offspring of both sexes, suggesting changes in postsynaptic receptor function. Altogether, these data demonstrate that PCE shifts the balance of excitatory/inhibitory inputs onto NAc-projecting mPFC neurons with limited effects on membrane conductance in females, resulting in reduced sex differences following maternal cannabis self-administration. These results provide putative neurophysiological mechanisms mediating previously observed behavioral changes, and future studies will need to test if these cannabis-induced changes are causal to long-term deficits in behavioral flexibility that have been previously documented in exposed offspring.
Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors
Authors: Suazo Kiall F. , Mishra Vartika , Maity Sanjay , Auger Shelby A. , Justyna Katarzyna , Petre Alex , Ottoboni Linda , Ongaro Jessica , Corti Stefania P. , Lotti Francesco , Przedborski Serge , Distefano Mark D.
Published: March 2024

Protein prenylation is one example of a broad class of post-translational modifications where proteins are covalently linked to various hydrophobic moieties. To globally identify and monitor levels of all prenylated proteins in a cell simultaneously, our laboratory and others have developed chemical proteomic approaches that rely on the metabolic incorporation of isoprenoid analogues bearing bio-orthogonal functionality followed by enrichment and subsequent quantitative proteomic analysis. Here, several improvements in the synthesis of the alkyne-containing isoprenoid analogue C15AlkOPP are reported to improve synthetic efficiency. Next, metabolic labeling with C15AlkOPP was optimized to obtain useful levels of metabolic incorporation of the probe in several types of primary cells. Those conditions were then used to study the prenylomes of motor neurons (ES-MNs), astrocytes (ES-As), and their embryonic stem cell progenitors (ESCs), which allowed for the identification of 54 prenylated proteins from ESCs, 50 from ES-MNs and 84 from ES-As, representing all types of prenylation. Bioinformatic analysis revealed specific enriched pathways, including nervous system development, chemokine signaling, Rho GTPase signaling, and adhesion. Hierarchical clustering showed that most enriched pathways in all three cell types are related to GTPase activity and vesicular transport. In contrast, STRING analysis showed significant interactions in two populations that appear to be cell type dependent. The data provided herein demonstrates that robust incorporation of C15AlkOPP can be obtained in ES-MNs and related primary cells purified via magnetic-activated cell sorting allowing the identification and quantification of numerous prenylated proteins. These results suggest that metabolic labeling with C15AlkOPP should be an effective approach for investigating the role of prenylated proteins in primary cells in both normal cells and disease pathologies, including ALS.

Abstract Figure
EpicTope: narrating protein sequence features to identify non-disruptive epitope tagging sites
Authors: Zinski Joseph , Chung Henri , Joshi Parnal , Warrick Finn , Berg Brian D. , Glova Greg , McGrail Maura , Balciunas Darius , Friedberg Iddo , Mullins Mary
Published: March 2024

Epitope tagging is an invaluable technique enabling the identification, tracking, and purification of proteins in vivo. We developed a tool, EpicTope, to facilitate this method by identifying amino acid positions suitable for epitope insertion. Our method uses a scoring function that considers multiple protein sequence and structural features to determine locations least disruptive to the protein’s function. We validated our approach on the zebrafish Smad5 protein, showing that multiple predicted internally tagged Smad5 proteins rescue zebrafishsmad5mutant embryos, while the N- and C-terminal tagged variants do not, also as predicted. We further show that the internally tagged Smad5 proteins are accessible to antibodies in wholemount zebrafish embryo immunohistochemistry and by western blot. Our work demonstrates that EpicTope is an accessible and effective tool for designing epitope tag insertion sites. EpicTope is available under a GPL-3 license from:https://github.com/FriedbergLab/Epictope
Stress vulnerability and resilience in children facing COVID-19-related discrimination: A quasi-experimental study using polygenic, brain, and sociodemographic data
Authors: Yi Jinwoo , Lee Eunji , Kim Bo-Gyeom , Kim Gakyung , Joo Yoonjung Yoonie , Cha Jiook
Published: March 2024

During the pandemic, perceived COVID-19-related discrimination aggravated children’s stress levels. The remaining question is to evaluate the individual variability in these effects and to identify vulnerable or resilient populations and why. Using the Adolescent Brain and Cognitive Development dataset (N= 1,116) and causal machine learning approach – Generalized Random Forest, we examined the average and individual treatment effects of perceived discrimination on stress levels immediately and six months later. Their variability and key factors were also assessed. We observed significant variability in the acute effects of perceived discrimination across children and pinpointed the frontotemporal cortical volume and white matter connectivity (streamline counts) as key factors of stress resilience and vulnerability. The variability of these neurostructural factors partially originated from the environmental and genetic attributes. The finding was replicated in held-out samples (N= 2,503). Our study has the potential for personalized prescriptive modeling to prevent children’s future psychopathology after the pandemic.
High Resolution Multi-delay Arterial Spin Labeling with Transformer based Denoising for Pediatric Perfusion MRI
Authors: Shou Qinyang , Zhao Chenyang , Shao Xingfeng , Herting Megan M , Wang Danny JJ
Published: March 2024

Multi-delay arterial spin labeling (MDASL) can quantitatively measure cerebral blood flow (CBF) and arterial transit time (ATT), which is particularly suitable for pediatric perfusion imaging. Here we present a high resolution (iso-2mm) MDASL protocol and performed test-retest scans on 21 typically developing children aged 8 to 17 years. We further proposed a Transformer-based deep learning (DL) model with k-space weighted image average (KWIA) denoised images as reference for training the model. The performance of the model was evaluated by the SNR of perfusion images, as well as the SNR, bias and repeatability of the fitted CBF and ATT maps. The proposed method was compared to several benchmark methods including KWIA, joint denoising and reconstruction with total generalized variation (TGV) regularization, as well as directly applying a pretrained Transformer model on a larger dataset. The results show that the proposed Transformer model with KWIA reference can effectively denoise multi-delay ASL images, not only improving the SNR for perfusion images of each delay, but also improving the SNR for the fitted CBF and ATT maps. The proposed method also improved test-retest repeatability of whole-brain perfusion measurements. This may facilitate the use of MDASL in neurodevelopmental studies to characterize typical and aberrant brain development.
An experimental evaluation of the relationship between the induced radiofrequency heating near an implanted conductive medical device during MRI, scanner reported B1+rms, and scanner reported average transmit power
Authors: Gultekin David H. , Vaughan J. Thomas , Shrivastava Devashish
Published: March 2024

Background

Time-varying radiofrequency (RF) fields necessary to perform magnetic resonance imaging (MRI) may induce excessive heating near implanted conductive medical devices during MRI. Both time and space-averaged root mean square of the effective magnetic field (B1+rms) and whole-body average specific absorption rate (SAR) (average RF power per unit body weight) have been proposed as metrics to control the induced heating and avoid unintended thermal injury.

Purpose

To evaluate the relationship between the induced RF heating near an implanted conductive medical device, scanner-reported B1+rms, and scanner-reported RF power.

Methods

RF heating was measured near the electrodes of deep brain stimulation (DBS) lead placed in a gel phantom using fluoroptic temperature probes in a commercial 3T scanner during MRI. Four transmit and receive RF coil combinations were used, a circularly polarized head transmit and receive coil, a 20-channel head and neck, a 32-channel head, or a 64-channel head and neck receive-only coil with a whole-body transmit coil. RF heating was induced by running a 2D GRE sequence with two RF pulse types (fast and normal) with varying flip angles of 30°, 60°, and 90° and by turning the receive-only coils off and on. The scanner-reported B1+rms and RF power were recorded.

Results

Measurements show that the induced temperature change correlated linearly with both the scanner-reported B1+rms and RF power for each coil combination. However, the variation in the induced heating for various RF coil combinations appeared to be much larger for the scanner-reported B1+rms compared to the scanner-reported RF power.

Conclusion

Additional studies across other MR scanners are needed to better understand the full extent of the variation in the induced heating near implanted conductive devices as a function of the scanner-reported B1+rms and RF power to develop conservative and reliable patient labeling.
The Global Impact of COVID-19 on Tuberculosis: A Thematic Scoping Review, 2020-2023
Authors: Marco Michael H. , Ahmedov Sevim , Castro Kenneth G.
Published: March 2024

Background

This thematic scoping review of publications sought to understand the global impact of COVID-19 on tuberculosis (TB), interpret the scope of resonating themes, and offer policy recommendations to stimulate TB recovery and future pandemic preparedness.

Data Sources

Publications were captured from three search engines, PubMed, EBSCO, and Google Scholar, and applicable websites written in English from January 1, 2020, to April 30, 2023.

Study Selection

Our scoping review was limited to publications detailing the impact of COVID-19 on TB. Original research, reviews, letters, and editorials describing the deleterious and harmful––yet sometimes positive–– impact of COVID-19 (sole exposure) on TB (sole outcome) were included. The objective was to methodically categorize the impacts into themes through a comprehensive review of selected studies to provide significant health policy guidance.

Data Extraction

Two authors independently screened citations and full texts, while the third arbitrated when consensus was not met. All three performed data extraction.

Data Synthesis/Results

Of 1,755 screened publications, 176 (10%) covering 39 countries over 41 months met the inclusion criteria. Ten principal themes were established, which encompassed TB’s care cascade, patient-centered care, psychosocial issues, and health services: 1) case-finding and notification (n=45; 26%); 2) diagnosis and laboratory systems (n=19; 10.7%) 3) prevention, treatment, and care (n=22; 12.2%); 4) telemedicine/telehealth (n=12; 6.8%); 5) social determinants of health (n=14; 8%); 6) airborne infection prevention and control (n=8; 4.6%); 7) health system strengthening (n=22; 13%); 8) mental health (n=13; 7.4%); 9) stigma (n=11; 6.3%); and 10) health education (n=10; 5.7%).

Limitations

Heterogeneity of publications within themes.

Conclusions

We identified ten globally generalizable themes of COVID-19’s impact on TB. These thematic areas will guide evidence-informed policies to strengthen comprehensive global responses, recovery for TB, and future airborne pandemic preparedness.

Primary Funding Source

United States Agency for International Development
Changes of urinary proteome in rats after intragastric administration of zinc gluconate
Authors: Shen Ziyun , Yang Minhui , Wang Haitong , Gao Youhe
Published: March 2024

Zinc is an essential element for maintaining normal physiological function in living organisms. In this study, the urine proteome of rats before and after short-term intragastric administration of 82 mg/kg/d zinc gluconate (equivalent to 11.7 mg/kg/d zinc) was compared and analyzed. Many differential proteins have been reported to be zinc-related, such as mucin-2 (MUC-2) (14 times before compared with after gavage, p = 0.005) and transthyretin (3.9 times after gavage compared with before gavage, p = 0.0004). Biological processes enriched in differential proteins (e.g., regulation of apoptosis process, immune system process, etc.), molecular functions (e.g., calcium binding, copper binding, signaling receptor activity, etc.), KEGG pathways (e.g., complement and coagulation cascades, PI3K-Akt signaling pathway, etc.) showed correlation with zinc. In this study, we explore the overall effect of zinc on the body from the perspective of urine proteomics, which is helpful to deeply understand the biological function of zinc and broaden the application potential of urine proteomics.
Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K
Authors: Ibrahim Mohamed , Sun Xinyuanyuan , de Oliveira Vinicius Martins , Liu Ruibin , Clayton Joseph , Kilani Haifa El , Shen Jana , Hilgenfeld Rolf
Published: March 2024

During the continuing evolution of SARS-CoV-2, the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November that year. Along with its sublineages, it has maintained a prominent role ever since. The Nsp5 main protease (Mpro) of the Omicron virus is characterized by a single dominant mutation, P132H. Here we determined the X-ray crystal structures of the P132H mutant (or O-Mpro) as free enzyme and in complex with the Mproinhibitor, the alpha-ketoamide13b-K, and we conducted enzymology, biophysical as well as theoretical studies to characterize the O-Mpro. We found that O-Mprohas a similar overall structure and binding with13b-K; however, it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro(with “WT” referring to the original Wuhan-1 strain). Intriguingly, the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here. The empirical folding free energy calculations suggest that the O-Mprodimer is destabilized relative to the WT-Mprodue to the less favorable van der Waals interactions and backbone conformation in the individual protomers. The all-atom continuous constant pH molecular dynamics (MD) simulations reveal that His132 and Glu240 display coupled titration. At pH 7, His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged. In order to examine whether the Omicron mutation eases the emergence of further Mpromutations, we also determined crystal structures of the relatively frequent P132H+T169S double mutant but found little evidence for a correlation between the two sites.
Matrix game between full siblings in Mendelian populations
Authors: Garay József , Varga Tamás , Csiszár Villő , Móri Tamás F. , Szilágyi András
Published: March 2024

We demonstrate that static evolutionary stability implies the stability of the corresponding interior equilibrium point in genotype dynamics, while a certain form of monotonicity ensures the global stability of a homozygote state.

We apply our findings to familial selection in a diploid, panmictic population, where the survival rates of siblings within monogamous and exogamous families are determined by a matrix game, and the behavior is uniquely determined by an autosomal recessive-dominant or intermediate allele pair. We provide conditions for the existence of each homozygote.

In our numerical investigations of the Prisoner’s Dilemma between siblings, we distinguish two scenarios: cooperation (collaborating case) or defector-cooperator strategy pair (alternating case) that maximizes the siblings’ survival rates. Based on the stability of the pure cooperator and defector states, we provide a potential classification of genotype dynamics. We find that the pure cooperator population cannot fixate in the alternating case. However, in the collaborating case, fixation is possible but not necessary, since bistability, coexistence, moreover, the monostable fixation of pure defector state can also occur due to the interplay between the phenotypic payoff function and the genotype-phenotype mapping, which collectively determine the outcome of natural selection. In donation game, the classical Hamilton’s rule implies the fixation of the cooperation in all considered genotype-phenotype mappings.

Author Summary

In this article, we explore the dynamics among full siblings who can mutually aid each other for survival. The strategy (cooperator or defector) of each sibling is determined by Mendelian (dominant-recessive or intermediate) inheritance. The interaction between two siblings is modelled as a Prisoner’s Dilemma. We examine two scenarios: cooperation (collaborating case) and a defector-cooperator strategy pair (alternating case), aiming to maximize the combined survival rates of the interacting siblings. The endpoint of natural selection is determined by Mendelian inheritance and the two Prisoner’s dilemma scenarios. Our findings reveal the potential for the fixation of both cooperation and defection, as well as the stable coexistence of these strategies within the studied selection environment. Notably, in the alternating case, the fixation of a pure cooperating population is not achievable under the considered inheritance systems. Furthermore, when cooperation is recessive, its fixation is more likely but not guaranteed.
Knotted artifacts in predicted 3D RNA structures
Authors: Gren Bartosz A. , Antczak Maciej , Zok Tomasz , Sulkowska Joanna I. , Szachniuk Marta
Published: March 2024

Unlike proteins, RNAs deposited in the Protein Data Bank do not contain topological knots. Recently, admittedly, the first trefoil knot and some lasso-type conformations have been found in experimental RNA structures, but these are still exceptional cases. Meanwhile, algorithms predicting 3D RNA models have happened to form knotted structures not so rarely. Interestingly, machine learning-based predictors seem to be more prone to generate knotted RNA folds than traditional methods. A similar situation is observed for the entanglements of structural elements. In this paper, we analyze all models submitted to the CASP15 competition in the 3D RNA structure prediction category. We show what types of topological knots and structure element entanglements appear in the submitted models and highlight what methods are behind the generation of such conformations. We also study the structural aspect of susceptibility to entanglement. We suggest that predictors take care of an evaluation of RNA models to avoid publishing structures with artifacts, such as unusual entanglements, that result from hallucinations of predictive algorithms.

Author summary

3D RNA structure prediction contests such as CASP and RNA-Puzzles lack measures for topology-wise evaluation of predicted models. Thus, predictors happen to submit potentially inappropriate conformations, for example, containing entanglements that are prediction artifacts.

Automated identification of entanglements in 3D RNA structures is computationally hard. Distinguishing correct from incorrectly entangled conformations is not trivial and often requires expert knowledge.

We analyzed 3D RNA models submitted to CASP15 and found that all entanglements in these models are artifacts.

Compared to non-ML, machine learning-based methods are more prone to generating entanglements that are not present in natural RNAs.

To increase the reliability of 3D RNA structure prediction, it is necessary to reject abnormally entangled structures in the modeling stage.
Spatial visualization of A-to-I Editing in cells using Endonuclease V Immunostaining Assay (EndoVIA)
Authors: Quillin Alexandria L. , Arnould Benoît , Knutson Steve D. , Heemstra Jennifer M.
Published: March 2024

Adenosine-to-Inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited. Current methods rely primarily onin vitrocharacterization of extracted RNA that ultimately erases subcellular localization and cell-to-cell heterogeneity. To address these challenges, we have repurposed Endonuclease V (EndoV), a magnesium dependent ribonuclease that cleaves inosine bases in edited RNA, to selectively bind and detect A-to-I edited RNA in cells. The work herein introduces Endonuclease V Immunostaining Assay (EndoVIA), a workflow that provides spatial visualization of edited transcripts, enables rapid quantification of overall inosine abundance, and maps the landscape of A-to-I editing within the transcriptome at the nanoscopic level.
NFixDB (Nitrogen Fixation DataBase) - A Comprehensive Integrated Database for Robust ‘Omics Analysis of Diazotrophs
Authors: Bellanger Madeline , Figueroa Jose L. , Tiemann Lisa , Friesen Maren L. , White Richard Allen
Published: March 2024

Biological nitrogen fixation is a fundamental biogeochemical process that transforms that provides fixed biologically available nitrogen by diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which has three different gene clusters: 1) molybdenum nitrogenase (nifDHK) is the most abundant, followed by it’s alternatives 2) vanadium nitrogenase (vnfDHK), and 3) iron nitrogenase (anfDHK). Multiple databases have been constructed as resources for diazotrophic ‘omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (NitrogenFixationDataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifDHK,vnfDHK,anfDHK) and nitrogenase-like enzymes (e.g.,nflDH) linked to ribosomal operons (16S-5.8S-23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB tonifHdatabases from Buckley, Zehr, Mise, and FunGene finding extensive evidence ofnifH, in addition tovnfHandnflH. NFixDB contains more than 4,000 verifiednifHDKsequences contained on 50 unique phyla of bacteria and archaea. NFixDB offers the first comprehensive nitrogenase database available to researchers.
Improved selection of canonical proteins for reference proteomes
Authors: Insana Giuseppe , Martin Maria J. , Pearson William R.
Published: March 2024

The "canonical" protein sets distributed by UniProt are widely used for similarity searching, and functional and structural annotation. For many investigators, canonical sequences are the only version of a protein examined. However, higher eukaryotes often encode multiple isoforms of a protein from a single gene. For unreviewed (UniProtKB/TrEMBL) protein sequences, the longest sequence in a Gene-Centric group is chosen as canonical. This choice can create inconsistencies, selecting >95% identical orthologs with dramatically different lengths, which is biologically unlikely. We describe the ortho2tree pipeline, which examines Reference Proteome canonical and isoform sequences from sets of orthologous proteins, builds multiple alignments, constructs gap-distance trees, and identifies low-cost clades of isoforms with similar lengths. After examining 140,000 proteins from eight mammals in UniProtKB release 2022_05, ortho2tree proposed 7,804 canonical changes for release 2023_01, while confirming 53,434 canonicals. Gap distributions for isoforms selected by ortho2tree are similar to those in bacterial and yeast alignments, organisms unaffected by isoform selection, suggesting ortho2tree canonicals more accurately reflect genuine biological variation. 82% of ortho2tree proposed-changes agreed with MANE; for confirmed canonicals, 92% agreed with MANE. Ortho2tree can improve canonical assignment among orthologous sequences that are more than 60% identical, a group that includes vertebrates and higher plants.
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment
Authors: Zhu Bokai , Bai Yunhao , Yeo Yao Yu , Lu Xiaowei , Rovira-Clavé Xavier , Chen Han , Yeung Jason , Gerber Georg K. , Angelo Mike , Shalek Alex K. , Nolan Garry P. , Jiang Sizun
Published: March 2024

The intricate and dynamic interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited byin situapproaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduceMicrobiomeCartography (MicroCart), a framework for simultaneousin situprobing of host features and its microbiome across multiple spatial modalities. We demonstrate MicroCart by comprehensively investigating the alterations in both gut host and microbiome components in a murine model of colitis by coupling MicroCart with spatial proteomics, transcriptomics, and glycomics platforms. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, and bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multiomics.
Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation
Authors: Xu Xiaosa , Passalacqua Michael , Rice Brian , Demesa-Arevalo Edgar , Kojima Mikiko , Takebayashi Yumiko , Harris Benjamin , Sakakibara Hitoshi , Gallavotti Andrea , Gillis Jesse , Jackson David
Published: March 2024

Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators likeCLAVATA3andWUSCHEL. In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands ofCLAVATA3andWUSCHELexpressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.
Targeting dermatophyte Cdc42 and Rac GTPase signaling to hinder hyphal elongation and virulence
Authors: Ishii Masaki , Matsumoto Yasuhiko , Yamada Tsuyoshi , Uga Hideko , Katada Toshiaki , Ohata Shinya
Published: March 2024

The identification of novel molecular targets for antifungal drugs is critical due to limited treatment options and drug-resistance threats. We screened inhibitors of small GTPases, molecular switches in signal transduction, inTrichophyton rubrum, the primary cause of dermatophytosis. Our study found that chemical and genetic inhibition of Cdc42 and Rac GTPases, which are involved in cellular morphological changes, significantly impair hyphal formation, and are crucial for pathogenic fungal growth and virulence. Genetic repression of Cdc24, a guanine nucleotide exchange factor of Cdc42 and Rac, led to hyphal growth defects, abnormal cell morphology, and cell death. Chemical screening identified EHop-016 as an inhibitor of Cdc24 activity, which improved outcomes inin vitronail infection and invertible infection models ofT. rubrum. Our results suggest the Cdc24-Cdc42/Rac pathway as a promising therapeutic target for antifungal agent development, with EHop-016 as a potential lead compound.