bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a Multifaceted Antimicrobial Stewardship Curriculum for Undergraduate Medical Education: The Antibiotic Stewardship, Safety, Utilization, Resistance, and Evaluation (ASSURE) Elective
Authors: Wang Rebecca , Degnan Kathleen O , Luther Vera P , Szymczak Julia E , Goren Eric N , Logan Ashleigh , Shnekendorf Rachel , Hamilton Keith W
Published: May 2021

To address the growing need for dedicated stewardship training in undergraduate medical education, we developed an antimicrobial stewardship curriculum for medical students with the objectives of increasing expertise in antimicrobial prescribing, introducing antimicrobial stewardship fundamentals, and enhancing comfort with engagement in interprofessional antimicrobial stewardship activities.
Intestinal Infection Is Associated With Impaired Lung Innate Immunity to Secondary Respiratory Infection
Authors: Trivedi Shubhanshi , Grossmann Allie H , Jensen Owen , Cody Mark J , Wahlig Taylor A , Hayakawa Serpa Paula , Langelier Charles , Warren Kristi J , Yost Christian C , Leung Daniel T
Published: May 2021

Background

Pneumonia and diarrhea are among the leading causes of death worldwide, and epidemiological studies have demonstrated that diarrhea is associated with an increased risk of subsequent pneumonia. Our aim was to determine the impact of intestinal infection on innate immune responses in the lung.

Methods

Using a mouse model of intestinal infection by Salmonella enterica serovar Typhimurium (S. Typhimurium [ST]), we investigated associations between gastrointestinal infections and lung innate immune responses to bacterial (Klebsiella pneumoniae) challenge.

Results

We found alterations in frequencies of innate immune cells in the lungs of intestinally infected mice compared with uninfected mice. On subsequent challenge with K. pneumoniae, we found that mice with prior intestinal infection have higher lung bacterial burden and inflammation, increased neutrophil margination, and neutrophil extracellular traps, but lower overall numbers of neutrophils, compared with mice without prior intestinal infection. Total numbers of dendritic cells, innate-like T cells, and natural killer cells were not different between mice with and without prior intestinal infection.

Conclusions

Together, these results suggest that intestinal infection impacts lung innate immune responses, most notably neutrophil characteristics, potentially resulting in increased susceptibility to secondary pneumonia.
Herb and conifer roots show similar high sensitivity to water deficit
Authors: Bourbia Ibrahim , Pritzkow Carola , Brodribb Timothy J
Published: May 2021

Root systems play a major role in supplying the canopy with water, enabling photosynthesis and growth. Yet, much of the dynamic response of root hydraulics and its influence on gas exchange during soil drying and recovery remains uncertain. We examined the decline and recovery of the whole root hydraulic conductance (Kr) and canopy diffusive conductance (gc) during exposure to moderate water stress in two species with contrasting root systems: Tanacetum cinerariifolium (herbaceous Asteraceae) and Callitris rhomboidea (woody conifer). Optical dendrometers were used to record stem water potential at high temporal resolution and enabled non-invasive measurements of Kr calculated from the rapid relaxation kinetics of water potential in hydrating roots. We observed parallel declines in Kr and gc to <20% of unstressed levels during the early stages of water stress in both species. The recovery of Kr after rewatering differed between species. T. cinerariifolium recovered quickly, with 60% of Kr recovered within 2 h, while C. rhomboidea was much slower to return to its original Kr. Recovery of gc followed a similar trend to Kr in both species, with C. rhomboidea slower to recover. Our findings suggest that the pronounced sensitivity of Kr to drought is a common feature among different plant species, but recovery may vary depending on root type and water stress severity. Kr dynamics are proposed to modulate gc response during and following drought.
High-throughput genotype-based population structure analysis of selected buffalo breeds
Authors: Thakor Prakash B , Hinsu Ankit T , Bhatia Dhruv R , Shah Tejas M , Nayee Nilesh , Sudhakar A , Rank Dharamshibhai N , Joshi Chaitanya G
Published: May 2021

India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.
Nutrient intake and influence on markers of oxidative stress in zoo-managed male snow leopards (Uncia uncia)
Authors: Iske Cayla J , Herrick Jason R , Morris Cheryl L
Published: May 2021

Oxidative stress (OS) results from the overproduction of reactive species. Nutrient intake can contribute positively or negatively to OS, and the lack of established nutrient requirements for most of the exotic species managed in zoos exacerbates the possibilities for nutrient imbalances that potentially could lead to reactive species production. The objective of this study was to evaluate the influence of nutrient intake and nutritional husbandry on markers of OS in male snow leopards (n = 14) maintained in U.S. facilities (n = 12). Diet samples and husbandry information were obtained and snow leopards were immobilized once for collection of blood. Samples were analyzed for chemical composition (diet and blood), antioxidant capacity (blood), and markers of OS (blood). Correlations between weekly nutrient intakes and markers of OS were analyzed by linear regression. Analyzed markers of OS included antioxidant enzymes (superoxide dismutase [SOD] and glutathione peroxidase [GPx]) and ferric reducing antioxidant potential that are protective against OS, and protein carbonyls, thiobarbituric acid reactive substances, and DNA/RNA damage that are indicative of oxidative damage. Weekly copper intake (10.1 to 80.2 mg) was negatively correlated with DNA/RNA damage (R2 = 0.44; P = 0.01). Weekly sodium intake (4.4 to 12.7 g) was positively correlated with GPx activity (R2 = 0.43; P = 0.04). More frequent feeding of whole prey (0.3 to 3 times/wk) was correlated with increased blood SOD activity (R2 = 0.55; P < 0.01). In conclusion, greater dietary copper intake and more frequent feeding of whole prey may reduce OS in snow leopards. Dietary sodium intake and relationship with GPx activity should be further evaluated to determine benefit or detriment. No cause and effect can be inferred from our results, but our data suggest altering dietary form and nutrient concentrations may influence OS in snow leopards.
Fitness facility staff demonstrate high fidelity when implementing an evidence-based diabetes prevention program
Authors: Dineen Tineke E , Banser Tekarra , Bean Corliss , Jung Mary E
Published: May 2021

Translating evidence-based diabetes prevention programs into the community is needed to make promising interventions accessible to individuals at-risk of type 2 diabetes. To increase the likelihood of successful translation, implementation evaluations should be conducted to understand program outcomes and provide feedback for future scale-up sites. The purpose of this research was to examine the delivery of, and engagement with, an evidence-based diet and exercise diabetes prevention program when delivered by fitness facility staff within a community organization. Ten staff from a community organization were trained to deliver the diabetes prevention program. Between August 2019–March 2020, 26 clients enrolled in the program and were assigned to one of the ten staff. Three fidelity components were accessed. First, staff completed session-specific fidelity checklists (n = 156). Second, two audio-recorded counseling sessions from all clients underwent an independent coder fidelity check (n = 49). Third, staff recorded client goals on session-specific fidelity checklists and all goals were independently assessed for (a) staff goal-setting fidelity, (b) client intervention receipt, and (c) client goal enactment by two coders (n = 285). Average self-reported fidelity was 90% for all six sessions. Independent coder scores for both counseling sessions were 83% and 81%. Overall staff helped clients create goals in line with program content and had a goal achievement of 78%. The program was implemented with high fidelity by staff at a community organization and clients engaged with the program. Findings increase confidence that program effects are due to the intervention itself and provide feedback to refine implementation strategies to support future scale-up efforts.
Precision Health Diagnostic and Surveillance Network uses S Gene Target Failure (SGTF) combined with sequencing technologies to identify emerging SARS-CoV-2 variants
Authors: Guerrero-Preston Rafael , Rivera-Amill Vanessa , Caraballo Karem , García Andrea Arias , Sánchez Torres Raphael , Zamuner Fernando Tadeu , Zanettini Claudio , MacKay Matthew J. , Baits Rachet , Beaubier Nike , Khullar Gaurav , Metti Jessica , Pipic Una , Purcell-Wiltz Ana , Vale Keilyn , Pérez Gabriela , De Jesus Lorena , Miranda Yaima , Ortiz Denise , García Negrón Amanda , Viera Liliana , Ortiz Alberto , Acevedo Jorge , Romaguera Josefina , Jiménez-Velazquez Ivonne , Marchionni Luigi , Rodríguez-Orengo José , Baez Adriana , Mason Christopher E. , Sidransky David
Published: May 2021

Several genomic epidemiology tools have been developed to track the public and population health impact of SARS-CoV-2 community spread worldwide. A SARS-CoV-2 Variant of Concern (VOC) B.1.1.7, known as 501Y.V1, which shows increased transmissibility, has rapidly become the dominant VOC in the United States (US). Our objective was to develop an evidenced-based genomic surveillance algorithm that combines RT-PCR and sequencing technologies to identify VOCs. Deidentified data were obtained from 508,969 patients tested for COVID-19 with the TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) in four CLIA certified clinical laboratories in Puerto Rico (n=86,639) and in three CLIA certified clinical laboratories in the US (n=422,330). TaqPath data revealed a frequency of S Gene Target Failure (SGTF) >47% for the last week of March 2021, in both Puerto Rico and US laboratories. The monthly frequency of SGTF in Puerto Rico steadily increased exponentially from 4% in November 2020 to 47% in March 2021.The weekly SGTF rate in US samples was high (>8%) from late December to early January, and then also increased exponentially through April (48%). The exponential increase in SGFT prevalence in Puerto Rico is concurrent with a sharp increase in VOCs among all SARS-CoV-2 sequences from Puerto Rico uploaded to GISAID (n=461). B.1.1.7 frequency increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021. The exponential increase in SGTF and B.1.1.7 prevalence in Puerto Rico and US requires an urgent response. According to the proposed evidence-based algorithm, approximately 50% of all positive samples should be managed as potential B.1.1.7 carriers with VOC quarantine and contact tracing protocols while their lineage is confirmed by WGS in surveillance laboratories. Patients infected with VOCs should be effectively triaged for isolation, contact tracing and follow-up treatment purposes.
Visual field improvement in neglect after virtual reality intervention: a case study
Authors: Leitner Michael Christian , Hawelka Stefan
Published: May 2021

Objective

Studies on neuropsychological rehabilitation of visual field defects provide an inconsistent picture regarding the effectiveness of so-called “restorative approaches” in visual field recovery (VFR). During a current research project on the clinical evaluation of VFR - in combination with head mounted virtual reality displays (HMD) - a patient (“Patient 7”) suffering from visual neglect was investigated. Although the concept of VFR is originally not intended for patients suffering from higher cortical regions (as in neglect), we hypothesized that due to the strong attention-demanding training situation in HMDs, neglect patients might benefit from these intervention procedures based on restorative approaches.

Methods and Analysis

Patient 7 was examined perimetrically using a “Humphrey Field Analyzer”, “Goldmann Perimetry” and our newly developed and validated eye-tracking supported perimetric methodology “Eye tracking based visual field analysis” (EFA). Based on these high resolution results from the EFA, the exact location of the transition area between intact and defect visual field of Patient 7 was assessed. Next, bright light stimuli were placed along this area in our newly developed HMD “Salzburg Visual Field Trainer” (SVFT). The aim was to stimulate neuroplasticity - according to the concept of restitutive approaches - in the corresponding cortical areas of the patient. Patient 7 trained with the SVFT for a time period of 254 days. In 6 appointments the objective and subjective rehabilitation progress was assessed.

Results

Perimetric assessment with the EFA shows an expansion of Patient 7’s visual field of 48.8% (left eye) and 36.8% (right eye) after 254 days of training with the SVFT. Individual areas in the patient’s visual field show a visual improvement of approximately 5.5° to 10.5° of visual angle. Subjective self-report of Patient 7 additionally shows improvements in self-evaluation of up to 317% in visual field functionality compared to self-evaluation on the first assessment date.

Conclusions

The results from Patient 7 indicate that patients suffering from visual neglect potentially benefit from a neuropsychological intervention with HMD based on the restorative concept of visual field recovery. However, further studies with large case numbers and a focus both on daily-life improvements and on a clear distinction between patients with lesions in earlier and higher cortical areas are needed to make empirically valid and generalizing statements about our findings.
Impact of Asian and black donor and recipient ethnicity on the outcomes after deceased donor kidney transplantation in the United Kingdom
Authors: Hakeem Abdul R , Asthana Sonal , Johnson Rachel J , Brown Chloe , Ahmad Niaz
Published: May 2021

Background

Patients of Asian and black ethnicity face disadvantage on the renal transplant waiting list in the United Kingdom, because of lack of HLA and blood group matched donors from an overwhelmingly white deceased donor pool. This study evaluates outcomes of renal allografts arising from Asian and black donors.

Methods

The UK Transplant Registry was analysed for adult deceased donor kidney only transplants performed during January 2001-December 2015.

Results

Asian and black ethnicity patients constituted 12.4% and 6.7% of all deceased donor recipients but only 1.6% and 1.2% of all deceased donors, respectively. Across all recipients, and unsurprisingly given the predominantly white recipient pool, HLA matching was superior for grafts from white donors than from Asian and black donors (p<0.0001). Unadjusted survival analysis demonstrated significantly inferior long-term allograft outcomes associated with Asian and black donors, compared to white donors (7-year graft survival 71.9%, 74.0% and 80.5%; log-rank p=0.0007, respectively). On Cox regression analysis, Asian donor (HR 1.37 for Asian donors vs. white donors as baseline) and black recipient (HR 1.21 for black recipients vs. white recipient as baseline) ethnicities were associated with poorer outcomes than white counterparts, and on ethnicity matching, compared with the white donor–white recipient baseline group and adjusting for other donor and recipient factors, 5-year graft outcomes were significantly poorer for black donor-black [HR 1.92 (1.11-3.32), p=0.02], Asian donor-white recipient [HR 1.56 (1.09-2.24), p=0.016] and white donor-black recipient [HR 1.22 (1.05-1.42), p=0.011] combinations in decreasing order of worse unadjusted 5-year graft survival.

Conclusions

Increased deceased donation among ethnic minority communities would benefit the entire recipient pool by increasing the numbers of available organs and may specifically benefit the Asian and black recipients by increasing the numbers of blood group and HLA-compatible grafts for allocation but may not improve allograft outcomes.
Multi-omics signatures of the human early life exposome
Authors: Maitre Léa , Bustamante Mariona , Hernández-Ferrer Carles , Thiel Denise , Lau Chung-Ho , Siskos Alexandros , Vives-Usano Marta , Ruiz-Arenas Carlos , Robinson Oliver , Mason Dan , Wright John , Cadiou Solène , Slama Rémy , Heude Barbara , Gallego-Paüls Marta , Casas Maribel , Sunyer Jordi , Papadopoulou Eleni Z. , Gutzkow Kristine B. , Andrusaityte Sandra , Grazuleviciene Regina , Vafeiadi Marina , Chatzi Leda , Sakhi Amrit K. , Thomsen Cathrine , Tamayo Ibon , Nieuwenhuijsen Mark , Urquiza Jose , Borràs Eva , Sabidó Eduard , Quintela Inés , Carracedo Ángel , Estivill Xavier , Coen Muireann , González Juan R. , Keun Hector C. , Vrijheid Martine
Published: May 2021

Environmental exposures during early life play a critical role in life-course health, yet the molecular phenotypes underlying environmental effects on health are poorly understood. In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1,301 mother-child pairs, we associated individual exposomes consisting of >100 chemical, physical and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, metabolome and proteins) in childhood. We identified 1,170 associations, 249 in pregnancy and 921 in childhood, which revealed potential biological responses and sources of exposure. The methylome best captures the persistent influence of pregnancy exposures, including maternal smoking; while childhood exposures were associated with features from all omics layers, revealing novel signatures for indoor air quality, essential trace elements, endocrine disruptors and weather conditions. This study provides a unique resource (https://helixomics.isglobal.org/) to guide future investigation on the biological effects of the early life exposome.
Study of PLEKHA1 gene polymorphism and their association with age related macular degeneration in Indian patients
Authors: Gupta Divya , Chawla Shobhit , Phadke Shubha R.
Published: May 2021

Background

Age-related macular degeneration (AMD) is an important cause of visual impairment in elderly people. AMD is a multifactorial disease in which both environmental and genetic factors have been implicated. Various single nucleotide polymorphisms (SNPs) have been found to be associated with AMD.

Aim

This study was aimed to investigate the association of polymorphisms in PLEKHA1 rs4146894 (G>A) gene with age related macular degeneration (AMD) in Indian patients.

Method

Genotyping for the PLEKHA1 rs4146894 (G>A) polymorphism performed in 121 AMD patients and 100 controls by polymerase chain reaction (PCR) and sequencing method.

Results

This is the first study from India on PLEKHA1 rs4146894 (G>A) polymorphism. In this study, we did not get any change in DNA sequence by sequencing method. So, we can say that the risk allele of PLEKHA1 rs4146894 (G>A) polymorphism is not find in Indian population. On the other hand in Indian population the risk of A allele is not present, and this gene is not playing any significant contribution with AMD in Indian population.

Conclusion

Very limited literatures are available for PLEKHA1 polymorphism in AMD patients, though, it is quite possible that the variation in the data shows population based differences. So, the present study raises the possibility that PLEKHA1 rs4146894 (G>A) polymorphism may not have a significant association with AMD in Indian patients.
EPHX1mutations cause a lipoatrophic diabetes syndrome due to impaired epoxide hydrolysis and increased cellular senescence
Authors: Gautheron Jérémie , Morisseau Christophe , Chung Wendy K. , Zammouri Jamila , Auclair Martine , Baujat Geneviève , Capel Emilie , Moulin Célia , Wang Yuxin , Yang Jun , Hammock Bruce D , Cerame Barbara , Phan Franck , Fève Bruno , Vigouroux Corinne , Andreelli Fabrizio , Jéru Isabelle
Published: May 2021

Epoxide hydrolases (EHs) regulate cellular homeostasis through hydrolysis of epoxides to less reactive diols. The first discovered EH was EPHX1, also known as mEH. EH functions remains partly unknown and no pathogenic variants have been reported in humans. We identified twode novovariants located in EPHX1 catalytic site in patients with a lipoatrophic diabetes characterized by loss of adipose tissue, insulin resistance, and multiple organ dysfunction. Functional analyses revealed that these variants led to the protein aggregation within the endoplasmic reticulum and to a loss of its hydrolysis activity. CRISPR-Cas9-mediatedEphx1knockout (KO) abolished adipocyte differentiation and decreased insulin response. This KO also promoted oxidative stress and cellular senescence, an observation confirmed in patient-derived fibroblasts. A major beneficial effect of metreleptin therapy was observed. This translational study highlights the importance of epoxide regulation for adipocyte function, and provides new insights into the physiological roles of EHs in humans.
Behavioral, Demographic, and Clinical determinants of HIV Status in Zambian Women
Authors: Gebreyohannes Debebe , Shen Ji , Sams Kelley
Published: May 2021

The rate of human immunodeficiency virus (HIV) infection shows a diminishing trend globally while increasing in intensity of mortality, morbidity, and burden of HIV in Sub-Saharan Africa. The intertwined behavioral, demographic, and clinical determinants fueled the incidence of infections in Zambian women. This study aimed to determine the association between demographic, behavioral, and clinical determinants with HIV serostatus in Zambian women. With the conceptual framework of the World Health Organization’s Commission for Social Determinants of Health (CSDH) and the quantitative method of MANOVA, this study examined Zambian Demographic Health Survey data for Zambian women of two ages groups (adolescent and adult). The findings showed statistically significant results in the association between HIV serostatus and self-perceived HIV risk for both groups and in the association between education and HIV serostatus among women in both groups. However, there was no statistically significant association between behavioral, demographic, and clinical determinants of HIV serostatus. These findings imply the need to conduct prospective studies on such determinants to curb HIV and improve women’s community health in Africa.

Author Summary

Zambia is a country in the Sub-Saharan region of Africa, which is disproportionately facing the risk of HIV increase in infection rate and the number of people impacted. HIV exposure shows an extraordinary rise for women aged 18–49 years old. The behavioral, demographic, and clinical determinants of HIV serostatus form an intricate web that snares adolescent and adult women, deteriorating their quality of life and their mental and emotional well-being.
Independent dynamics of slow, intermediate, and fast intracranial EEG spectral activities during human memory formation
Authors: Marks Victoria S. , Saboo Krishnakant V. , Topçu Çağdaş , Thayib Theodore P. , Nejedly Petr , Kremen Vaclav , Worrell Gregory A. , Kucewicz Michal T.
Published: May 2021

A wide spectrum of brain rhythms are engaged throughout the human cortex in cognitive functions. How the rhythms of various low and high frequencies are spatiotemporally coordinated across the human brain during memory processing is inconclusive. They can either be coordinated together across a wide range of the frequency spectrum or induced in specific bands. We used a large dataset of human intracranial electroencephalography (iEEG) to parse the spatiotemporal dynamics of spectral activities induced during formation of verbal memories. Encoding of words for subsequent free recall activated slow theta, intermediate alpha and beta, and fast gamma frequency power in discrete cortical sites. A majority of the electrode sites recorded activity in only one of these frequencies, except for the visual cortex where spectral power was induced across multiple bands. Each frequency band showed characteristic dynamics of the induced power specific to cortical area and hemisphere. The power of the low, intermediate, and fast activities propagated in distinct spatiotemporal patterns across the visual, temporal and prefrontal cortical areas as the words were presented for encoding. Our results suggest anatomically and temporally distributed spectral activities in the formation of human memory.
Generic solving of one-compartment toxicokinetic models
Authors: Charles Sandrine , Ratier Aude , Lopes Christelle
Published: May 2021

This paper gives the full analytical solution of the generic set of ordinary differential equations that define one-compartment toxicokinetic models. These models describe uptake and elimination processes taking place within living organisms when exposed to chemical substances. The models solved in this paper consider living organisms as a unique compartment, into which a parent compound enters via several possible exposure routes and from which it is eliminated as well as its potential metabolites. Benefiting from generic solutions of one-compartment toxicokinetic models is particularly useful when fitting them to experimental data, facilitating the writing of the inference algorithms leading to parameter estimates. Additionally, these models are of crucial interest in environmental risk assessment for the calculation of bioaccumulation metrics as required by regulators in support of decision making when they evaluate dossiers for marketing authorisation of active substances.

Abstract Figure

Graphical abstract
Role of hypocretin in the medial preoptic area in the regulation of sleep, maternal behavior and body temperature of lactating rats
Authors: Rivas Mayda , Serantes Diego , Peña Florencia , González Joaquín , Ferreira Annabel , Torterolo Pablo , Benedetto Luciana
Published: May 2021

The hypocretins (HCRT), also known as orexin, includes two neuroexcitatory peptides, HCRT-1 and HCRT-2 (orexin A y B, respectively), synthesized by neurons located in the postero-lateral hypothalamus, whose projections and receptors are widely distributed throughout the brain, including the medial preoptic area (mPOA). HCRT have been associated with a wide range of physiological functions including sleep-wake cycle, maternal behavior and body temperature, all regulated by the mPOA. Previously we showed that HCRT in the mPOA facilitates certain active maternal behaviors, while the blockade of HCRT-R1 increased the time spent in nursing. As mother rats mainly sleep while they nurse, we hypothesize that HCRT in the mPOA of lactating rats reduce sleep and nursing, while the intra-mPOA administration of the dual orexin receptor antagonist (DORA) would generate the opposite effect. Therefore, the aim of this study was to determine the role of HCRT within the mPOA, in the regulation and integration of the sleep-wake cycle, maternal behavior and body temperature of lactating rats. To evaluate this idea, we assessed the sleep-wake states, maternal behavior and body temperature of lactating rats following microinjections of HCRT-1 (100 and 200 μM) and DORA (5mM) into the mPOA. As expected, our data shows that HCRT-1 in mPOA promoted wakefulness and a slightly increase in body temperature, whereas DORA increased both NREM and REM sleep along with nursing and milk ejection. Taken together, our results strongly suggest that the reduction of the endogenous HCRT within the mPOA of lactating rats is important to promote sleep, nursing and milk ejection.
NERD-seq: A novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs
Authors: Saville Luke , Cheng Yubo , Gollen Babita , Mitchell Liam , Stuart-Edwards Matthew , Haight Travis , Mohajerani Majid , Zovoilis Athanasios
Published: May 2021

The new next-generation sequencing platforms by Oxford Nanopore Technologies for direct RNA sequencing (direct RNA-seq) allow for an in-depth and comprehensive study of the epitranscriptome by enabling direct base calling of RNA modifications. Non-coding RNAs constitute the most frequently documented targets for RNA modifications. However, the current standard direct RNA-seq approach is unable to detect many of these RNAs. Here we present NERD-seq, a sequencing approach which enables the detection of multiple classes of non-coding RNAs excluded by the current standard approach. Using total RNA from a tissue with high known transcriptional and non-coding RNA activity in mouse, the brain hippocampus, we show that, in addition to detecting polyadenylated coding and non-coding transcripts as the standard approach does, NERD-seq is able to significantly expand the representation for other classes of RNAs such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, rRFs and non-coding RNAs originating from LINE L1 elements. Thus, NERD-seq presents a new comprehensive direct RNA-seq approach for the study of epitranscriptomes in brain tissues and beyond.
Ozone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content
Authors: Nanni Adalena V. , Morse Alison M. , Newman Jeremy R. B. , Choquette Nicole E. , Wedow Jessica M. , Liu Zihao , Leakey Andrew D. B. , Conesa Ana , Ainsworth Elizabeth A. , McIntyre Lauren M
Published: May 2021

The maize pangenome has demonstrate large amounts of presence/absence variation and it has been hypothesized that presence/absence variation contributes to stress response. To uncover whether the observed genetic variation in physiological response to elevated ozone (a secondary air pollutant that causes significant crop yield losses) concentration is due to variation in genic content, and/or variation in gene expression, we examine the impact of sustained elevated ozone concentration on the leaf tissue from 5 diverse maize inbred genotypes (B73, Mo17, Hp301, C123, NC338). Analysis of long reads from the transcriptomes of the 10 conditions found expressed genes in the leaf are part of the shared genome, with 94.5% of expressed genes from syntenic loci. Quantitative analysis of short reads from 120 plants (twelve from each condition) found limited transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes), while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. The genes underpinning the divergence of B73 from the other 4 genotypes implicates ethylene signaling consistent with some findings in Arabidopsis. For the 82 of the 83 genes differentially expressed among all 5 genotypes and the 788 of 789 genes differentially expressed in 4 genotypes (excluding B73) in sensitivity to ozone is associated with oxidative stress tolerance being associated with a weaker response to a reactive oxygen species (ROS) signal and suggests that genetic variation in downstream processes is key to ozone tolerance.
Meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related knee osteoarthritis
Authors: Iijima Hirotaka , Gilmer Gabrielle , Wang Kai , Sivakumar Sruthi , Evans Christopher , Matsui Yusuke , Ambrosio Fabrisia
Published: May 2021

Increased mechanistic insight into the pathogenesis of knee osteoarthritis (KOA) is needed to develop efficacious disease-modifying treatments. Though age-related pathogenic mechanisms are most relevant to the great majority of KOA seen clinically, the bulk of our mechanistic understanding of KOA has been derived using surgically induced post-traumatic OA (PTOA) models. Here, we took an integrated approach of meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related KOA in murine model. Protein-level data together with transcriptomic profiling revealed inflammation, autophagy, and cellular senescence as primary hallmarks of age-related KOA. Importantly, the molecular profiles of aged cartilage were unique from those in PTOA, with only 1% overlap between the two. At the nexus of aging hallmarks, Advanced Glycation End-Product (AGE)/Receptor for AGE emerged as intrinsically linked to age-related KOA. This pathway was further validated by mass spectrometry. Collectively, these findings implicate dysregulation of AGE-RAGE signaling as a key driver of age-related KOA.
Isotopically Nonstationary13C Metabolic Flux Analysis in Resting and Activated Human Platelets
Authors: Sake Cara L. , Metcalf Alexander J. , Di Paola Jorge , Neeves Keith B. , Boyle Nanette R.
Published: May 2021

Platelet metabolism is linked to platelet hyper- and hypoactivity in numerous human diseases. Developing a detailed understanding of the link between metabolic shifts and platelet activation state is integral to improving human health. Here, we show the first application of isotopically nonstationary13C metabolic flux analysis to quantitatively measure carbon fluxes in both resting and thrombin activated platelets. Resting platelets primarily metabolize glucose to lactate via glycolysis, while acetate is oxidized to fuel the tricarboxylic acid cycle. Upon activation with thrombin, a potent platelet agonist, platelets increase their uptake of glucose 3-fold. This results in an absolute increase in flux throughout central metabolism, but when compared to resting platelets they redistribute carbon dramatically. Activated platelets decrease relative flux to the oxidative pentose phosphate pathway and TCA cycle from glucose and increase relative flux to lactate. These results provide the first report of reaction-level carbon fluxes in platelets and allow us to distinguish metabolic fluxes with much higher resolution than previous studies.
Bergamottin a CYP3A inhibitor found in grapefruit juice inhibits prostate cancer cell growth by downregulating androgen receptor signaling causing cell cycle block and apoptosis
Authors: Vetrichelvan Opalina , Gorjala Priyatham , Goodman Oscar , Mitra Ranjana
Published: May 2021

Prostate cancer is the second leading cause of cancer related death in American men. Several therapies have been developed to treat advanced prostate cancer, but these therapies often have severe side effects. To improve the outcome with fewer side effects we focused on the furanocoumarin bergamottin, a natural product found in grapefruit juice and a potent CYP3A inhibitor. Our recent studies have shown that CYP3A5 inhibition can block androgen receptor (AR) signaling, critical for prostate cancer growth. We observed that bergamottin reduces prostate cancer (PC) cell growth by decreasing both total and nuclear AR (AR activation) reducing downstream AR signaling. Bergamottin’s role in reducing AR activation was confirmed by confocal microscopy studies and reduction in PSA levels. Further studies revealed that bergamottin promotes cell cycle block and accumulates G0/G1 cells. The cell cycle block was accompanied with reduction in cyclin D, cyclin B, CDK4, P-cdc2 (Y15) and P-wee1 (S642). We also observed that bergamottin triggers apoptosis in prostate cancer cell lines as evident by TUNEL staining and PARP cleavage. Our data suggest that bergamottin may be used as an adjunctive nutritional supplement to suppress prostate cancer growth and is of relevance to AA patients carrying wild type CYP3A5 often presenting aggressive disease.
Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord
Authors: Fiederling Felix , Hammond Luke A. , Ng David , Mason Carol , Dodd Jane
Published: May 2021

Spinal neurons are highly heterogeneous in location, transcriptional identity and function. To understand their contributions to sensorimotor circuits, it is essential to map the positions of identified subsets of neurons in relation to others throughout the spinal cord (SC), but we lack tools for whole SC sample preparation, imaging and in toto analysis. To overcome this problem, we have (1) designed scaffolds (SpineRacks) that facilitate efficient and ordered cryo-sectioning of the entire SC in a single block, (2) constructed a 3D reference atlas of adult mouse SC and (3) developed software (SpinalJ) to register images of sections and for standardized analysis of cells and projections in atlas space. We have verified mapping accuracies for known neurons and demonstrated the usefulness of this platform to reveal unknown neuronal distributions. Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.
Ongoing neural oscillations predict the post-stimulus outcome of closed loop auditory stimulation during slow-wave sleep
Authors: Navarrete Miguel , Arthur Steven , Treder Matthias S. , Lewis Penelope A.
Published: May 2021

The large slow oscillation (SO, 0.5-2Hz) that characterises slow-wave sleep is crucial to memory consolidation and other physiological functions. Manipulating slow oscillations can enhance sleep and memory, as well as benefitting the immune system. Closed-loop auditory stimulation (CLAS) has been demonstrated to increase the SO amplitude and to boost fast sleep spindle activity (11-16Hz). Nevertheless, not all such stimuli are effective in evoking SOs, even if they are precisely phase-locked. Here, we studied whether it is possible to use ongoing activity patterns to determine which oscillations to stimulate in order to effectively enhance SOs or SO-locked spindle activity. To this end, we trained classifiers using the morphological characteristics of the ongoing SO, as measured by electroencephalography (EEG), to predict whether stimulation would lead to a benefit in terms of the resulting SO and spindle amplitude. Separate classifiers were trained using trials from spontaneous control and stimulated datasets, and we evaluated their performance by applying them to held-out data both within and across conditions. We were able to predict both when large SOs will occur spontaneously, and whether a phase-locked auditory click will effectively enlarge them with an accuracy of ~70%. We were also able to predict when stimulation would elicit spindle activity with an accuracy of ~60%. Finally, we evaluate the importance of the various SO features used to make these predictions. Our results offer new insight into SO and spindle dynamics and provide a new method for online optimisation of stimulation.

HIGHLIGHTS

- Random forest classifiers can predict spontaneous and stimulated SOs and spindle amplitudes.

- Morphological wave features predicted the response of SOs and spindles to CLAS.

- SO amplitude during the click is the main predictor for post-stimulus SO amplitude.

- Prediction of spindle activity did not differ in accuracy for stimulated vs spontaneous data.
Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome
Authors: Liu Xiaomin , Tong Xin , Zhu Jie , Tian Liu , Jie Zhuye , Zou Yuanqiang , Lin Xiaoqian , Liang Hewei , Li Wenxi , Ju Yanmei , Qin Youwen , Zou Leying , Lu Haorong , Xu Xun , Yang Huanming , Wang Jian , Zong Yang , Liu Weibin , Hou Yong , Zhu Shida , Jin Xin , Jia Huijue , Zhang Tao
Published: May 2021

The oral microbiota contains billions of microbial cells, which could contribute to diseases in a number of body sites. Challenged by eating, drinking and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1,915 individuals, for both the tongue dorsum and saliva. We identified five genetic loci associated with oral microbiota at study-wide significance (p< 3.16 × 10−11). Four of the five associations were well replicated in an independent cohort of 1,439 individuals: rs1196764 atAPPL2withPrevotella jejuni, Oribacterium uSGB 3339andSolobacterium uSGB 315; rs3775944 at the serum uric acid transporterSLC2A9withOribacterium uSGB 1215, OribacteriumuSGB 489 andLachnoanaerobaculum umeaense; rs4911713 nearOR11H1with speciesF0422 uSGB 392;and rs36186689 atLOC105371703withEggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of genetic-microbiota associations including 6 genome-wide significant associations mutually validated between the two niches. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk score dominated over oral microbiome in predicting predisposing risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.
Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification
Authors: Su Emily Y. , Spangler Abby , Bian Qin , Kasamoto Jessica Y. , Cahan Patrick
Published: May 2021

Elucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. Computational gene regulatory network (GRN) reconstruction methods aim to map this control by inferring relationships from transcriptomic data. Unfortunately, existing methods are imprecise, may be computationally burdensome, and do not uncover how networks transition from one topology to another. Here we present Epoch, a computational network reconstruction tool that leverages single cell transcriptomics to infer dynamic network structures. Epoch performs favorably when benchmarked using data derived fromin vivo,in vitro,andin silicosources. To illustrate the usefulness of Epoch, we applied it to identify the dynamic networks underpinning directed differentiation of mouse embryonic stem cells (ESC) guided by multiple primitive streak induction treatments. Our analysis demonstrates that modulating signaling pathways drives topological network changes that shape cell fate potential. We also find that Peg3 is a central contributor to the rewiring of the pluripotency network to favor mesoderm specification. By integrating signaling pathways with GRN structures, we traced how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively. Finally, we compare the networks established inin vitrodirected differentiation of ESCs to those inin vivogastrulation and mesoderm specification. The methods presented here are available in the R package Epoch, and provide a foundation for future work in understanding the biological implications of dynamic regulatory structures.
Coil-to-Helix Transition at the Nup358-BicD2 Interface Activates BicD2 for Dynein Recruitment
Authors: Gibson James M. , Cui Heying , Ali M. Yusuf , Zhao Xiaoxin , Debler Erik W. , Zhao Jing , Trybus Kathleen M. , Solmaz Sozanne R. , Wang Chunyu
Published: May 2021

Nup358, a nuclear pore protein, facilitates a nuclear positioning pathway that is essential for many biological processes, including neuromuscular and brain development. Nup358 binds and activates the auto-inhibited dynein adaptor Bicaudal D2 (BicD2), which in turn recruits and activates the dynein machinery to position the nucleus. However, the molecular details of the Nup358/BicD2 interaction remain poorly understood. Here, we show that a minimal Nup358 domain activates dynein/dynactin/BicD2 for processive motility on microtubules. Using nuclear magnetic resonance (NMR) titration and chemical exchange saturation transfer (CEST), a Nup358 helix encompassing residues 2162-2184 was identified, which transitioned from random coil to an α-helix upon BicD2-binding and formed the core of the Nup358-BicD2 interface. Mutations in this region of Nup358 decreased the Nup358/BicD2 interaction, resulting in decreased dynein recruitment and impaired motility. BicD2 thus recognizes the cargo adaptor Nup358 though a “cargo recognition α-helix”, a structural feature that may stabilize BicD2 in its activated state and promote processive dynein motility.
Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function
Authors: Rajderkar Sudha , Barozzi Iros , Zhu Yiwen , Hu Rong , Zhang Yanxiao , Li Bin , Fukuda-Yuzawa Yoko , Kelman Guy , Akeza Adyam , Blow Matthew J. , Pham Quan , Harrington Anne N. , Godoy Janeth , Meky Eman M. , von Maydell Kianna , Novak Catherine S. , Plajzer-Frick Ingrid , Afzal Veena , Tran Stella , Talkowski Michael E. , Kent Lloyd K. C. , Ren Bing , Dickel Diane E. , Visel Axel , Pennacchio Len A.
Published: May 2021

Topologically associating domain (TAD) boundaries are thought to partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotype1–3, but the overall extent to which this occurs remains unknown. Here we show that TAD boundary deletions commonly disrupt normal genome functionin vivo. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80kb in size) from the genome in mice. All deletions examined resulted in at least one detectable molecular or organismal phenotype, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. For 5 of 8 (62%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion nearSmad3/Smad6caused complete embryonic lethality, while a deletion nearTbx5/Lhx5resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences forin vivogenome function and suggest that noncoding deletions affecting TAD boundaries should be carefully considered for potential pathogenicity in clinical genetics screening.