bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation of Sensory perception at different body parts with BMI using Two Point Discrimination
Authors: Desai Dev Himanshubhai , Dave Prahasth , Mahajan Neeraj , Verma Anita
Published: March 2023

Purpose

Two-point discrimination (2PD) is the ability to discern that two nearby objects touching the skin are truly two distinct points, not one. It is often tested with two sharp points during a neurological examination and is assumed to reflect how finely innervated an area of skin is. objective was to find out the normal value of Two Point Discrimination on the Back, Finger, Forehead & Sole and to Correlate values of Two Point Discrimination on Back, Finger, Forehead & Sole with corresponding BMI according to Gender.

Methods

Two point discrimination test is a part of practical course of Physiology Department of the teaching institute. Here, the students perform the practical under strict supervision of professors, the data of the students’ practical is recorded for department’s personal use.

This data was collected with the permission from the head of the department and then analyzed to see the normal values of two-point discrimination and also to assess the correlation between Gender, BMI, & Two-point Discrimination(TPD). Pearson Correlation, T-test, SEM, CI95, Scatter diagrams were used to analyze and understand the data.

Results

Values of Two-Point-Discrimination(TPD) Average(in mm), SD, and Pearson Correlation(with BMI) at Back (Males=32.19 ± 4.94,r=0.808 & Females=29.38 ±5.29,r=0.848), Fingertips (Males=3.43 ± 1.52,r=0.0344 & Females=3.47 ± 1.52,r=0.0141), Forehead (Males=13.53 ± 2.36,r=0.0223 & Females=12.25 ± 2.61,r=0.198), Sole (Males=14.69 ± 3.54,r=0.00493 & Females=13.87 ± 3.36, r=0.0234)

Conclusion

The results depict the normal values of Two-point discrimination at the respective location. The normal values at a particular location in Males and Females are almost the same Strong Correlation of TPD value at Back with BMI can be justified as fat Accumulation increases in Skin with increasing BMI.

Fat mainly accumulates on the abdomen, thighs, and back and neck but not on Forehead, Fingertips & soles.

Fat accumulation hypothetically leads to increase skin surface leading to virtually variable per area relative decreased skin innervation resulting in higher TPD values and Strong Positive Correlation.

TPD values at Forehead, Fingertips & soles do not correlate with BMI.
The Zero-Corrected, Gravity-Model Estimator (ZERO-G): A novel method to create high-quality, continuous incidence estimates at the community-scale from passive surveillance data
Authors: Evans Michelle V , Ihantamalala Felana A , Randriamihaja Mauricianot , Aina Andritiana Tsirinomen’ny , Bonds Matthew H , Finnegan Karen E , Rakotonanahary Rado JL , Raza-Fanomezanjanahary Mbolatiana , Razafinjato Bénédicte , Raobela Oméga , Raholiarimanana Sahondraritera Herimamy , Randrianavalona Tiana Harimisa , Garchitorena Andres
Published: March 2023

Data on population health are vital to evidence-based decision making but are rarely adequately localized or updated in continuous time. They also suffer from low ascertainment rates, particularly in rural areas where barriers to healthcare can cause infrequent touch points with the health system. Here, we demonstrate a novel statistical method to estimate the incidence of endemic diseases at the community level from passive surveillance data collected at primary health centers. The zero-corrected, gravity-based (ZERO-G) estimator explicitly models sampling intensity as a function of health facility characteristics and statistically accounts for extremely low rates of ascertainment. The result is a standardized, real-time estimate of disease incidence at a spatial resolution nearly ten times finer than typically reported by facility-based passive surveillance systems. We assessed the robustness of this method by applying it to a case study of field-collected malaria incidence rates from a rural health district in southeastern Madagascar. The ZERO-G estimator decreased geographic and financial bias in the dataset by over 90% and doubled the agreement rate between spatial patterns in malaria incidence and incidence estimates derived from prevalence surveys. The ZERO-G estimator is a promising method for adjusting passive surveillance data of common, endemic diseases, increasing the availability of continuously updated, high quality surveillance datasets at the community scale.
High-throughput splicing assays identify known and novelWT1exon 9 variants in nephrotic syndrome
Authors: Smith Cathy , Burugula Bala Bharathi , Dunn Ian , Aradhya Swaroop , Kitzman Jacob O. , Yee Jennifer Lai
Published: March 2023

Frasier Syndrome (FS) is a rare Mendelian form of nephrotic syndrome caused by variants which disrupt the proper splicing ofWT1. This key transcription factor gene is alternatively spliced at exon 9 to produce two isoforms (“KTS+” and “KTS-”), which are normally expressed in the kidney at a ∼2:1 (KTS+:KTS-) ratio. FS results from variants that reduce this ratio by disrupting the splice donor of the KTS+ isoform. FS is extremely rare, and it is unclear whether any variants beyond the eight already known could cause FS. To prospectively identify other splicing-disruptive variants, we leveraged a massively parallel splicing assay. We tested every possible single nucleotide variant (n=519) in and aroundWT1exon 9 for effects upon exon inclusion and KTS+/- ratio. Splice disruptive variants made up 11% of the tested point variants overall, and were tightly concentrated near the canonical acceptor and the KTS+/- alternate donors. Our map successfully identified all eight known FS or focal segmental glomerulosclerosis variants and 16 additional novel variants which were comparably disruptive to these known pathogenic variants. We also identified 19 variants that, conversely, increased the KTS+/KTS- ratio, of which two are observed in unrelated individuals with 46,XX ovotesticular disorder of sex development (46,XX OTDSD). This splicing effect map can serve as functional evidence to guide the clinical interpretation of newly observed variants in and aroundWT1exon 9.
First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody
Authors: Omidvari Negar , Jones Terry , Price Pat M , Ferre April L , Lu Jacqueline , Abdelhafez Yasser G , Sen Fatma , Cohen Stuart H , Schmiedehausen Kristin , Badawi Ramsey D , Shacklett Barbara L , Wilson Ian , Cherry Simon R
Published: March 2023

With the majority of CD8+T cells residing and functioning in tissue, not blood, developing noninvasive methods forin vivoquantification of their biodistribution and kinetics in humans offers the means for studying their key role in adaptive immune response and memory. This study is the first report on using positron emission tomography (PET) dynamic imaging and compartmental kinetic modeling forin vivomeasurement of whole-body biodistribution of CD8+T cells in human subjects. For this, a89Zr-labeled minibody with high affinity for human CD8 (89Zr-Df-Crefmirlimab) was used with total-body PET in healthy subjects (N=3) and in COVID-19 convalescent patients (N=5). The high detection sensitivity, total-body coverage, and the use of dynamic scans enabled the study of kinetics simultaneously in spleen, bone marrow, liver, lungs, thymus, lymph nodes, and tonsils, at reduced radiation doses compared to prior studies. Analysis and modeling of the kinetics was consistent with T cell trafficking effects expected from immunobiology of lymphoid organs, suggesting early uptake in spleen and bone marrow followed by redistribution and delayed increasing uptake in lymph nodes, tonsils, and thymus. Tissue-to-blood ratios from the first 7 h of CD8-targeted imaging showed significantly higher values in the bone marrow of COVID-19 patients compared to controls, with an increasing trend between 2 and 6 months post-infection, consistent with net influx rates obtained by kinetic modeling and flow cytometry analysis of peripheral blood samples. These results provide the platform for using dynamic PET scans and kinetic modelling to study total-body immunological response and memory.
Leveraging Electronic Medical Records and Knowledge Networks to Predict Disease Onset and Gain Biological Insight Into Alzheimer’s Disease
Authors: Tang Alice , Rankin Katherine P. , Cerono Gabriel , Miramontes Silvia , Mills Hunter , Roger Jacquelyn , Zeng Billy , Nelson Charlotte , Soman Karthik , Woldemariam Sarah , Li Yaqiao , Lee Albert , Bove Riley , Glymour Maria , Oskotsky Tomiko , Miller Zachary , Allen Isabel , Sanders Stephan J. , Baranzini Sergio , Sirota Marina
Published: March 2023

Early identification of Alzheimer’s Disease (AD) risk can aid in interventions before disease progression. We demonstrate that electronic health records (EHRs) combined with heterogeneous knowledge networks (e.g., SPOKE) allow for (1) prediction of AD onset and (2) generation of biological hypotheses linking phenotypes with AD. We trained random forest models that predict AD onset with mean AUROC of 0.72 (-7 years) to .81 (-1 day). Top identified conditions from matched cohort trained models include phenotypes with importance across time, early in time, or closer to AD onset. SPOKE networks highlight shared genes between top predictors and AD (e.g., APOE, IL6, TNF, and INS). Survival analysis of top predictors (hyperlipidemia and osteoporosis) in external EHRs validates an increased risk of AD. Genetic colocalization confirms hyperlipidemia and AD association at the APOE locus, and AD with osteoporosis colocalize at a locus close to MS4A6A with a stronger female association.
Plasma Plasmin Generation and its Determinants in Third Trimester of Pregnancy
Authors: Okoye Helen Chioma , Nwagha Theresa Ukamaka , Enebe Joseph Tochukwu , Efobi Chilota , Nnachi Oluomachi Charity , Okwor Chikaodili J
Published: March 2023

Background

Pregnancy, especially in the third trimester, is associated with changes in the fibrinolytic system that supports clot formation and reduces hemorrhagic risk. Imbalance in the system may occur and can be assessed by plasmin generation (PG). Certain factors are known to affect PG.

Aim

To assess PG and its determinants during pregnancy using plasma D-dimer and plasmin-antiplasmin (PAP) complex levels.

Methods

Healthy pregnant women in the third trimester of pregnancy were systematically recruited. Using the ELISA method, venous blood samples were taken to assess D-Dimer and PAP complex plasma levels. IBM Statistical Package for Social Sciences (SPSS) version 21 was used for statistical analysis.

Results

We studied a total of 41 subjects with a mean age ±SD and gestational age ±SD of 30.68±4.69years and 34.78±3.34weeks, respectively. The mean ± SD values of the D-Dimer and PAP complex were 194 ± 24 ng/mL and 175 ± 11 ng/mL, respectively. D-Dimer and PAP complex positively correlated with age, GA, and BMI classification. However, only age was statistically significant (p-value 0.032 and 0.016, respectively). In addition, the multiple linear regression model showed that with every unit increase in age, D-Dimer and PAP complex increased by 2.0 (95% CI 0.4 – 3.6) ng/mL and 0.8 (95% CI 0.1 – 1.5) ng/mL respectively, after controlling for GA and BMI.

Conclusion

D-Dimer and PAP levels increased with increasing age during the third trimester of pregnancy, showing that the woman’s age is an independent determinant of PG in the third trimester.
A methodology of phenotyping ICU patients from EHR data: high-fidelity, personalized, and interpretable phenotypes estimation
Authors: Wang Yanran , Stroh J.N. , Hripcsak George , Low Wang Cecilia C. , Bennett Tellen D. , Wrobel Julia , Der Nigoghossian Caroline , Mueller Scott , Claassen Jan , Albers D.J.
Published: March 2023

Objective

Computing phenotypes that provide high-fidelity, time-dependent characterizations and yield personalized interpretations is challenging, especially given the complexity of physiological and healthcare systems and clinical data quality. This paper develops a methodological pipeline to estimate unmeasured physiological parameters and produce high-fidelity, personalized phenotypes anchored to physiological mechanics from electronic health record (EHR).

Methods

A methodological phenotyping pipeline is developed that computes new phenotypes defined with unmeasurable computational biomarkers quantifying specific physiological properties in real time. Working within the inverse problem framework, this pipeline is applied to the glucose-insulin system for ICU patients using data assimilation to estimate an established mathematical physiological model with stochastic optimization. This produces physiological model parameter vectors of clinically unmeasured endocrine properties, here insulin secretion, clearance, and resistance, estimated for individual patient. These physiological parameter vectors are used as inputs to unsupervised machine learning methods to produce phenotypic labels and discrete physiological phenotypes. These phenotypes are inherently interpretable because they are based on parametric physiological descriptors. To establish potential clinical utility, the computed phenotypes are evaluated with external EHR data for consistency and reliability and with clinician face validation.

Results

The phenotype computation was performed on a cohort of 109 ICU patients who received no or short-acting insulin therapy, rendering continuous and discrete physiological phenotypes as specific computational biomarkers of unmeasured insulin secretion, clearance, and resistance on time windows of three days. Six, six, and five discrete phenotypes were found in the first, middle, and last three-day periods of ICU stays, respectively. Computed phenotypic labels were predictive with an average accuracy of 89%. External validation of discrete phenotypes showed coherence and consistency in clinically observable differences based on laboratory measurements and ICD 9/10 codes and clinical concordance from face validity. A particularly clinically impactful parameter, insulin secretion, had a concordance accuracy of 83%±27%.

Conclusion

The new physiological phenotypes computed with individual patient ICU data and defined by estimates of mechanistic model parameters have high physiological fidelity, are continuous, time-specific, personalized, interpretable, and predictive. This methodology is generalizable to other clinical and physiological settings and opens the door for discovering deeper physiological information to personalize medical care.
TheCucumis sativuskinome: Identification, annotation, and expression patterns in response to powdery mildew infection
Authors: Costa Francisco Cleilson Lopes , Pereira Welison Andrade
Published: March 2023

It is widely known that protein kinases (PKs) play a fundamental role in regulating various metabolic processes in plants, from development to response to the environment. However, a detailed characterization of this superfamily is still lacking for several species, such as cucumber (Cucumis sativus), especially regarding their involvement in the response to Powdery Mildew (PM) caused byPodosphaera xanthii. This study aimed to characterize the cucumber PK family, shedding light on its genomic distribution, classification, and expression patterns triggered byP. xanthii. The hidden Markov models (HMMs) analysis uncovered 835 PKs in the cucumber kinome, distributed across its seven chromosomes, and categorized into 20 distinct groups and 123 families, with the RLK group being the most abundant. Evidence of tandem duplication of PK genes was also observed, enriching our understanding of cucumber PKs. To investigate the expression profiles of PK genes in cucumber, we analyzed the transcription levels of all 835 PK genes in RNA-seq data from leaves of resistant and susceptible cultivars of cucumber toP. xanthii, which were artificially inoculated. Depending on the treatment, DEGs ranged from 319 to 1,690, with PK DEGs ranging from 8 to 105. The number of PK DEGs varied between the different contrasts analyzed. Notably, we observed a greater number of PK DEGs in susceptible genotypes when challenged by the pathogen. Our findings indicate the role of specific cucumber PKs in regulating metabolic processes in the context of plant-pathogen interactions and pave the way for further research into the intricate mechanisms underlying cucumber responses to Powdery Mildew.

Graphical Abstract
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings
Authors: Sasse Alexander , Ng Bernard , Spiro Anna E. , Tasaki Shinya , Bennett David A. , Gaiteri Christopher , De Jager Philip L. , Chikina Maria , Mostafavi Sara
Published: March 2023

Introductory Paragraph

Deep learning methods have recently become the state-of-the-art in a variety of regulatory genomic tasks1–6including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the full spectrum of genetic variation observed in personal genomes. Previous evaluation strategies have assessed their predictions of gene expression across genomic regions, however, systematic benchmarking is lacking to assess their predictions across individuals, which would directly evaluates their utility as personal DNA interpreters. We used paired Whole Genome Sequencing and gene expression from 839 individuals in the ROSMAP study7to evaluate the ability of current methods to predict gene expression variation across individuals at varied loci. Our approach identifies a limitation of current methods to correctly predict the direction of variant effects. We show that this limitation stems from insufficiently learnt sequence motif grammar, and suggest new model training strategies to improve performance.
Conditionally deleterious mutation load accumulates in genomic islands but can be purged with sufficient genotypic redundancy
Authors: Mee Jonathan A. , Carson Bryce , Yeaman Sam
Published: March 2023

Local adaptation frequently evolves in patches or environments that are connected via migration. In these cases, genomic regions that are linked to an adaptive locus experience reduced effective migration rates. Via individual-based simulations of a two-patch system, we show that this reduced effective migration results in the accumulation of conditionally deleterious mutations, but not universally deleterious mutations, adjacent to adaptive loci. When there is redundancy in the genetic basis of local adaptation (i.e. genotypic redundancy), turnover of adaptive loci allows conditionally deleterious mutation load to be purged. The amount of mutational load that accumulates adjacent to adaptive loci is dependent on redundancy, recombination rate, migration rate, population size, strength of selection, and the phenotypic effect size of adaptive alleles. Our results highlight the need to be cautious when interpreting patterns of local adaptation at the level of phenotype or fitness, as the genetic basis of local adaptation can be transient, and evolution may confer a degree of maladaptation to non-local environments.
Characterization of popcorn temperate and tropical populations and GWAS for zeins and starch contents
Authors: Gotardi Leonardo Fioravante , Viana José Marcelo Soriano , Ribeiro Matheus Pereira , de Castro Raissa Barbosa , Ramos Humberto Josué de Oliveira , Fietto Juliana Lopes Rangel
Published: March 2023

Because measuring expansion volume (EV) is simple and inexpensive, popcorn breeders have developed high-quality single crosses ignoring the contents of zeins, starch, lipids, and cellular wall components in selection. However, some methods of quantification of these quality-related traits can be applied to popcorn breeding, increasing the selection efficacy for quality. The objectives of this study were assess methods of quantification of zeins and starch that can be used in popcorn breeding, characterize a temperate and a tropical populations for zeins and starch contents, and identify candidate genes for these quality-related traits. We genotyped and phenotyped 286 plants. For quantification of total zeins and zein subunits we choose the ‘lab-on-a-chip’ microfluidic electrophoresis. For quantification of starch and amylose/amylopectin we choose the Megazyme’s Amylose/Amylopectin kit assay. The temperate population has superior EV (+36%), a higher level (+32%) of the 19 kDa zein subunit, and lower levels of the 21, 22, and 27 kDa subunits (−1543, −40 and −47%, respectively). Although there are statistical differences between the two populations regarding starch, amylose, and amylose/amylopectin ratio, the differences are not significant (−2 to 8%). Six candidate genes were identified for the 19 and 22 kDa zeins, one for the 21 kDa zein, one for total zeins, two for starch, and four for amylose, with emphasis on three genes from the Z1C subfamily, coding for the 19 and 22 kDa alpha-zeins, located on chromosome 4. The evaluated quantification methods can be used in popcorn breeding programs, with the potential to revolutionize the breeding for quality.

Key message

The protein chip and the Amylose/Amylopectin kit assay for zein and starch quantification, respectively, can be effectively used in popcorn breeding, with the potential to revolutionize the breeding for quality.
WALLFLOWER, a RLK, simultaneously localizes to opposite sides of root hair cells & functions to position hairs
Authors: Toth Jessica N. , Rodriguez-Furlan Cecilia , Van Norman Jaimie M.
Published: March 2023

Polarized cells are frequently partitioned into subdomains with unique features or functions. As plant cells are surrounded by walls, polarized cell shape and protein polarity in the plasma membrane are particularly important for normal physiology and development. We have identified WALLFLOWER (WFL), a transmembrane receptor kinase that is asymmetrically distributed at the inner face of epidermal cells and this localization is maintained independent of cell type. In epidermal hair (H) cells in the elongation and differentiation zones, WFL exhibits a dual polar localization, accumulating at the inner domain as well as at the root hair initiation domain (RHID). Furthermore, overexpression of WFL leads to a downward shift in root hair (RH) position suggesting WFL operates in a signaling pathway that functions across H cells to inform RH position. WFL asymmetric distribution and function is affected by deletion of the intracellular domains resulting in its mislocalization to the outer polar domain of H cells and exclusion from RHIDs and bulges. Thus, our results demonstrate that in epidermal H cells the WFL intracellular domains are required to direct its dual polar localization and influence RH position.

ONE SENTENCE SUMMARY

A receptor kinase with dual polar localization, to the inner polar domain and root hair initiation domain, in root epidermal cells, requires its intracellular domain for localization and function.
The first proof of concept demonstration of nanowarming in coral tissue
Authors: Daly Jonathan , Bouwmeester Jessica , Perry Riley , Page Chris , Khosla Kanav , Kangas Joseph , Lager Claire , Hardy Katherine , Bischof John C. , Hagedorn Mary
Published: March 2023

Climate change is causing ocean acidification and warming, resulting in mass bleaching and death of corals globally. Cryopreservation and biobanking to secure the genetics of threatened populations is currently limited to coral sperm and larvae, which are only available during brief annual spawning events and are impacted by ocean warming, so there is an urgent need for methods to enable biobanking activities year-round. Here, we used vitrification and nanowarming to successfully recover adult coral tissues in a novel sample type, the single-polyp microfragment (SPMF). Fluorescence and confocal microscopy showed clearly defined tissues and green fluorescent protein fluorescence around the polyp mouth post-warming in 43.3% of SPMFs at 24 hours post-warming, and 30.0% at one month. These advances provide a basis for continued research and development of a field-ready protocol for cryopreservation of adult coral tissues, to permit biobanking of threatened coral species throughout the year and support reef restoration efforts.
Identification of selective sweeps in bacteria
Authors: Avram Oren , Levy Karin Eli , Corander Jukka , Oren Yaara , Pupko Tal
Published: March 2023

Selective sweeps occur when a beneficial mutation spreads rapidly throughout the population due to natural selection. Searching for selective sweeps has proved to be one of the most fruitful ways to detect the footprints selection leaves on the genome. With a plethora of detection tools, the study of selective sweeps in eukaryotic systems is a well-established field of research. However, the search for fragment-specific selective sweeps among bacterial strains received little to no attention so far. In our work, we demonstrate that inter-strains locus-specific selective sweeps can be detected in bacteria. We introduce theSINCOPAalgorithm, the first phylogeny-based method for soft and incomplete selective sweeps detection. We useSINCOPAto explore inter-strains locus-specific selective sweeps in a dataset containing more than 500 microbial genomes. We observe strong evidence in several loci for locus-specific selective sweeps including genes involved in biofilm formation and others that are related to coping with various unfavorable environmental conditions.SINCOPAis freely accessible as a user-friendly web server application athttps://sincopa.tau.ac.il/.
NVX-CoV2373 Vaccine Efficacy Against Hospitalization: Apost hocanalysis of the PREVENT-19 phase 3, randomized, placebo-controlled trial
Authors: Marchese Anthony M. , Zhou Xiang , Kinol John , Underwood Eddie , Woo Wayne , McGarry Alice , Beyhaghi Hadi , Áñez Germán , Toback Seth , Dunkle Lisa M.
Published: March 2023

PREVENT-19, the pivotal phase 3 trial of the Novavax adjuvanted, recombinant spike protein COVID-19 vaccine (NVX-CoV2373) demonstrated that the vaccine was safe and efficacious (vaccine efficacy, VE= 90%) for the prevention of symptomatic COVID-19. In the trial, participants were randomly assigned in a 2:1 ratio to receive 2 doses of NVX-CoV2373 or placebo 21 days apart. Throughout the study, SARS-CoV-2 circulating variant was predominantly alpha, but other variants circulated (i.e., beta, gamma, epsilon, and iota). VE among the per-protocol efficacy analysis population was calculated according to pre-specified disease severity (mild, moderate, or severe) criteria, but the impact on the risk of COVID-19– associated hospitalization was not specifically investigated. During the placebo-controlled portion of the trial (January 25, 2021, to April 30, 2021), 4 hospitalizations occurred among the 77 events analyzed for the primary endpoint using the per-protocol population, 0 among vaccine recipients and 4 among placebo recipients, yielding a VE against hospitalization of 100% (95% CI: 28.8, 100). Among an expanded efficacy population, which included COVID-19–associated hospitalizations without a requirement for diagnostic polymerase chain reaction testing performed at the study central laboratory, 12 total hospitalizations were identified, 0 among vaccine recipients and 12 among placebo recipients, yielding apost hocVE against hospitalization of 100% (95% CI: 83.1, 100). These additional data from the PREVENT-19 trial provide relevant public health information concerning the attributes of NVX-CoV2373.
A first-in-human clinical study of an intranasal spray of a cocktail containing two synergetic antibodies neutralizes Omicron BA.4/5
Authors: Zhang Xinghai , Luo Feiyang , Zhang Huajun , Guo Hangtian , Zhou Junhui , Li Tingting , Chen Shaohong , Song Shuyi , Shen Meiying , Wu Yan , Gao Yan , Han Xiaojian , Wang Yingming , Hu Chao , Zhao Xiaodong , Guo Huilin , Zhang Dazhi , Lu Yuchi , Wang Wei , Wang Kai , Tang Ni , Jin Tengchuan , Ding Menglu , Luo Shuhui , Lin Cuicui , Lu Tingting , Lu Bingxia , Tian Yang , Yang Chengyong , Cheng Guofeng , Yang Haitao , Jin Aishun , Ji Xiaoyun , Gong Rui , Chiu Sandra , Huang Ailong
Published: March 2023

Neutralizing monoclonal antibodies (NAbs) with prophylactic and therapeutic efficacy have demonstrated fundamental importance in the control of SARS-CoV-2 transmission. However, their wide application has been largely limited by high cost and inconvenience in administration. Here, we developed an intranasal spray containing two synergetic human NAbs that could broadly neutralize the emerging Omicron variants in vitro. A unique synergetic neutralizing mechanism was identified that the two NAbs bound to exclusive epitopes on the RBD and structurally compensate each other in blocking the Spike-ACE2 interaction. Importantly, when given at low dosages for three consecutive days through the intranasal mucosal route, this cocktail showed significant improvement in the emergency preventive and therapeutic effects in hamsters challenged with authentic Omicron BA.1. Further, we performed an investigator-initiated trail in healthy volunteers (ChiCTR2200066525) to study the safety and pharmacokinetics of the antibody cocktail administrated as nasal spray. The nasal spray is generally safe and well tolerated without treatment related severe abnormal effects. The antibody cocktail nasal spray demonstrated nasal concentrations higher than the IC90of neutralization activity against Omicron BA.4/5 even at 24 hours post dosing. Furthermore, nasal samples from the study subjects demonstrated potent neutralization activity against Omicron BA.4/5 in an ex vivo pseudovirus neutralization assay. Together, we provide a novel approach for NAb regimens, a potentially highly effective product with broad applicable perspective in depressing the infection risk of new epidemic variant and ameliorating the heavy medical burden of hospital.

One Sentence Summary

An intranasal spray of two synergetic antibodies cocktail neutralizing Omicron BA.4/5 and an initial clinical evaluation in healthy volunteers.
Genetic incompatibilities and evolutionary rescue by wild relatives shaped grain amaranth domestication
Authors: Gonçalves-Dias José , Singh Akanksha , Graf Corbinian , Stetter Markus G
Published: March 2023

Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today’s crops.
A syntelog-based pan-genome provides insights into rice domestication and de-domestication
Authors: Dongya Wu , Xie Lingjuan , Sun Yanqing , Huang Yujie , Jia Lei , Dong Chenfeng , Shen Enhui , Ye Chu-Yu , Qian Qian , Fan Longjiang
Published: March 2023

Asian rice is one of the world’s most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa ofOryza sativaandOryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonicato ancient Xian/indicaor its wild ancestor, including almost all well-known domestication genes and a 4.5-Mb centromere-spanning block, supporting a single domestication event in rice. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
Molecular understanding of anthocyanin biosynthesis activated by PAP1 in engineered redArtemisia annuacells and regulation of 2, 4-dichlorophenoxyacetic acid
Authors: Dong Yilun , Li Mingzhuo , Cruz Bryanna , Ye Emily , Zhu Yue , Li Lihua , Xu Zhengjun , Xie De-Yu
Published: March 2023

Artemisia annuais an effective antimalarial medicinal crop. We have established anthocyanin-producing red cell cultures from this plant with the overexpression ofProduction of Anthocyanin Pigment 1(PAP1) encoding a R2R3MYB transcription factor. To understand the molecular mechanism by which PAP1 activated the entire anthocyanin pathway, we mined the genomic sequences ofA. annuaand obtained eight promoters of the anthocyanin pathway genes. Sequence analysis identified four types of AC cis-elements from six promoters, the MYB response elements (MRE) bound by PAP1. In addition, six promoters were determined to have at least one G-Box cis-element. Eight promoters were cloned for activity analysis. Duel luciferase assays showed that PAP1 significantly enhanced the promoting activity of seven promoters, indicating that PAP1 turned on the biosynthesis of anthocyanins via the activation of these pathway gene expression. To understand how 2,4-dichlorophenoxyacetic acid (2,4-D), an auxin, regulates the PAP1-activated anthocyanin biosynthesis, five different concentrations (0, 0.05, 0.5, 2.5, and 5 μM) were tested to characterize anthocyanin production and profiles. The resulting data showed that the concentrations tested decreased the fresh weight of callus growth, anthocyanin levels, and the production of anthocyanins per petri dish. HPLC-qTOF-MS/MS based profiling showed that these concentrations did not alter anthocyanin profiles. Real time RT-PCR was completed to characterize the expressionPAP1and four representative pathway genes. The results showed that the five concentrations reduced the expression levels of the constitutivePAP1transgene and three pathway genes significantly and eliminated chalcone synthase gene in expression either significantly or slightly. These data indicate that the constitutivePAP1expression depends on gradients added in the medium. Based on these findings, the regulation of 2,4-D is discussed for anthocyanin engineering in red cells ofA. annua.

Conclusion

Promoters of eight anthocyanin pathway genes were cloned. Four types of AC cis-elements were identified from six promoters and G-Box elements were also determined from six promoters. PAP1 enhanced the activity of eight promoters. 2,4-D downregulated the expression of the constitutive PAP1 transgene leading to the decrease the biosynthesis of anthocyanins.
Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients
Authors: Abul-Husn Noura S. , Marathe Priya N. , Kelly Nicole R. , Bonini Katherine E. , Sebastin Monisha , Odgis Jacqueline A. , Abhyankar Avinash , Brown Kaitlyn , Di Biase Miranda , Gallagher Katie M. , Guha Saurav , Ioele Nicolette , Okur Volkan , Ramos Michelle A. , Rodriguez Jessica E. , Rehman Atteeq U. , Thomas-Wilson Amanda , Edelmann Lisa , Zinberg Randi E. , Diaz George A. , Greally John M. , Jobanputra Vaidehi , Suckiel Sabrina A. , Horowitz Carol R. , Wasserstein Melissa P. , Kenny Eimear E. , Gelb Bruce D.
Published: March 2023

Purpose

Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions.

Methods

Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design.

Results

645 probands (median age 9 years) underwent genetic testing, and 113 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses (P< .001). Yield was greater for GSvs. TGPs in Hispanic/Latino(a) (17.2%vs. 9.5%,P< .001) and White/European American (19.8%vs. 7.9%,P< .001), but not in Black/African American (11.5%vs. 7.7%,P= .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%)vs. White/European American (47.6%;P= .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS.

Conclusion

GS may yield up to twice as many diagnoses in pediatric patients compared to TGP testing, but not yet across all population groups.
Evidence of reduced inhibition in older adults with a history of repetitive brain trauma. A transcranial magnetic stimulation study
Authors: Pearce Alan J , Kidgell Dawson J , Fraser Ashlyn K , Rist Billymo , Tallent Jamie
Published: March 2023

International concern regarding the association between repetitive neurotrauma in sport and long term concerns with ageing continues. While previous studies have reported older (i.e. over 50 years) our study describes corticomotor changes across the lifespan between retired contact sport athletes, between the ages of 30 and 70 years. Retired athletes, minimum five years retired, (n=152; 48.6±9.0 years) and age-matched controls (n=72; 47.8±9.5 years) were assessed using single and paired-pulse transcranial magnetic stimulation (TMS) for active motor threshold (aMT), motor evoked potential and cortical silent period duration (expressed as MEP:cSP ratio), and short- and long-interval intracortical inhibition (SICI and LICI). Age-matched controls showed significant moderate correlations for MEP:cSP ratios at 130% (rho=0.48), 150% (rho=0.49)and 170% aMT (rho=0.42; allp<0.001) and significant but small negative correlation for SICI (rho=-0.27;p=0.030), and moderate negative correlation for LICI (rho=-0.43;p<0.001). Further, group-wise correlation analysis shows significant stronger corelations (allp<0.05) in the control for each variable than in the retired players. This study is the first to characterise corticomotor differences between retired athletes and age matched controls across the lifespan. in those with a history of repetitive head trauma and provides a foundation for further work to utilise TMS as a prodromal marker useful in supplementing neuropsychological assessment for traumatic encephalopathy syndrome which currently lacks physiological biomarkers.
Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding, and function
Authors: Vergara Renan , Berrocal Tania , Mejía Eva Isela Juárez , Romero-Romero Sergio , Velázquez-López Isabel , Pulido Nancy O. , López Sanchez Haven A. , Silva Daniel-Adriano , Costas Miguel , Rodríguez-Romero Adela , Rodríguez-Sotres Rogelio , Sosa-Peinado Alejandro , Fernández-Velasco D. Alejandro
Published: March 2023

Substrate-binding proteins (SBP) are used by organisms from the three domains of life for transport and signaling. SBPs are composed of two domains that collectively trap ligands with high affinity and selectivity. To explore the role of the domains and the integrity of the hinge region between them in the function and conformation of SBPs, here we describe the ligand binding, conformational stability, and folding kinetics of the Lysine Arginine Ornithine binding protein (LAO) fromSalmonella thiphimuriumand constructs corresponding to its two independent domains. LAO is a class II SBP formed by a continuous and a discontinuous domain. Contrary to the expected behavior based on their connectivity, the discontinuous domain shows a stable native-like structure that binds L-arginine with moderate affinity, whereas the continuous domain is barely stable and shows no detectable ligand binding. Regarding folding kinetics, studies of the entire protein revealed the presence of at least two intermediates. While the unfolding and refolding of the continuous domain exhibited only a single intermediate and simpler and faster kinetics than LAO, the folding mechanism of the discontinuous domain was complex and involved multiple intermediates. These findings suggest that in the complete protein the continuous domain nucleates folding and that its presence funnels the folding of the discontinuous domain avoiding nonproductive interactions. The strong dependence of the function, stability, and folding pathway of the lobes on their covalent association, is most likely the result of the coevolution of both domains as a single unit.
Non-catalytic regulation of 18SrRNA methyltransferase DIMT1 in acute myeloid leukemia
Authors: Gonskikh Yulia , Stoute Julian , Shen Hui , Budinich Krista , Pingul Bianca , Schultz Kollin , Elashal Heidi , Marmorstein Ronen , Shi Junwei , Liu Kathy Fange
Published: March 2023

Several rRNA modifying enzymes install rRNA modifications while participating in ribosome assembly. Here, we show that 18SrRNA methyltransferase DIMT1 is essential for acute myeloid leukemia (AML) proliferation through a non-catalytic function. We reveal that targeting a positively charged cleft of DIMT1, remote from the catalytic site, weakens the binding of DIMT1 to rRNA and mis-localizes DIMT1 to the nucleoplasm, in contrast with the primarily nucleolar localization of wild-type DIMT1. Mechanistically, rRNA binding is required for DIMT1 to undergo liquid-liquid phase separation, which explains why the distinct nucleoplasm localization of the rRNA-binding deficient DIMT1. Re-expression of wild-type or a catalytically inactive mutant E85A, but not the rRNA-binding deficient DIMT1, supports AML cell proliferation. This study provides a new strategy to target DIMT1-regulated AML proliferation via targeting this essential non-catalytic region.
Dopamine neurons govern olfactory-gated infant begging behavior
Authors: Butler Julie M. , Singh Devraj , Baker Penelope , Edwards Scott V. , Summers Kyle , O’Connell Lauren A.
Published: March 2023

Altricial young of many species beg parents for the nutrients required for healthy development. From human crying to begging chicks, young expend precious energy reserves to communicate their hunger. Despite repeated independent evolutionary origins, the neural basis of parent-directed communication by infants is unknown. Here, we examined the sensory and neural basis of begging behavior in tadpoles of the monogamous and biparental Mimetic poison frog (Ranitomeya imitator). In this species, tadpoles beg parents for egg meals by dancing. We used this robust motor display to determine that tadpoles use multimodal cues for caregiver recognition, where olfactory cues are necessary for caregiver recognition while visual cues provide an orientation goal. We found that dopamine related brain regions have higher neural activity in begging tadpoles and that dopamine signaling had opposing modulatory effects through D1 and D2 family receptors, similar to swimming behavior in other tadpole species. We then identified caudal posterior tuberculum dopamine neurons as more active during begging behavior and sensitive to caregiver olfactory cues. Projections of these dopaminergic neurons to the spinal accessory motor nucleus are required for begging displays. These findings support the idea that dopamine regulates olfactory-guided parental recognition in young and opens many avenues for studying how new communication behaviors can evolve from ancestral motor circuits.
The CARD8 inflammasome drives CD4+T-cell depletion in HIV-1 infection
Authors: Wang Qiankun , Shan Liang
Published: March 2023

CD4+T-cell depletion is the root cause of acquired immunodeficiency syndrome (AIDS). How HIV depletes CD4+T cells in humans remains unknown because vast majority of the dying CD4+T cells in patients are uninfected. Burgeoning evidence supports the hypothesis that non-productive HIV-1 infection triggers CD4+T-cell depletion in the course of pathogenic HIV and SIV infections. Here, we report that the CARD8 inflammasome is activated immediately after HIV-1 entry by the viral protease encapsulated in the incoming HIV-1 particles. Sensing of HIV-1 protease activity by the CARD8 inflammasome leads to rapid pyroptosis of quiescent CD4+T cells without productive viral infection. In humanized mice reconstituted with a CARD8-deficient immune system, CD4+T-cell loss is delayed despite increased levels of HIV-1 replication. Our study suggests that the CARD8 inflammasome drives CD4+T-cell depletion and disease progression through rapid sensing of HIV-1 particles.
Enzymatic assay for UDP-GlcNAc and its application in the parallel assessment of substrate availability and protein O-GlcNAcylation
Authors: Sunden Marc , Upadhyay Divya , Banerjee Rishi , Sipari Nina , Fellman Vineta , Kallijärvi Jukka , Purhonen Janne
Published: March 2023

O-linked N-acetylglucosaminylation (O-GlcNAcylation) is a ubiquitous and dynamic yet still relatively poorly understood non-canonical glycosylation of intracellular proteins. Several vital branches of metabolism converge at the hexosamine biosynthetic pathway (HBP) to produce the substrate for protein O-GlcNAcylation the uridine diphosphate N-acetylglucosamine (UDP-GlcNAc). Availability of this metabolite is considered a key regulator of O-GlcNAcylation. Yet UDP-GlcNAc concentrations are rarely reported in studies exploring the HBP and O-GlcNAcylation, most likely because the methods to measure it restrict to specialized chromatographic procedures. To overcome this limitation, we introduce here an enzymatic method to quantify cellular and tissue UDP-GlcNAc. The method is based on O-GlcNAcylation of a substrate peptide by recombinant O-linked N-acetylglucosamine transferase (OGT) and detection of the modification with a specific antibody. The assay can be performed in dot blot or microplate formats. The key to successful assay was the removal of strong inhibition of OGT by the reaction side product, uridine diphosphate (UDP). We applied the assay to provide the first systematic report of UDP-GlcNAc concentrations in mouse tissues and cultured cells. Furthermore, we show how changes in UDP-GlcNAc levels correlate with O-GlcNAcylation and the expression of OGT and O-GlcNAcase (OGA).