bluuebunny/crossref_metadata_2025 huggingface dataset:
The accuracy of machine learning models using ultrasound images in prostate cancer diagnosis: A systematic review
Authors: Sihotang Retta C , Agustino Claudio , Huang Ficky , Parikesit Dyandra , Rahman Fakhri , Hamid Agus Rizal AH
Published: February 2022

Prostate Cancer (PCa) is the third most commonly diagnosed cancer worldwide, and its diagnosis requires many medical examinations, including imaging. Ultrasound offers a practical and cost-effective method for prostate imaging due to its real-time availability at the bedside. Nowadays, various Artificial Intelligence (AI) models, including Machine learning (ML) with neural networks, have been developed to make an accurate diagnosis. In PCa diagnosis, there have been many developed models of ML and the model algorithm using ultrasound images shows good accuracy. This study aims to analyse the accuracy of neural network machine learning models in prostate cancer diagnosis using ultrasound images. The protocol was registered with PROSPERO registration number CRD42021277309. Three reviewers independently conduct a literature search in five online databases (MEDLINE, EBSCO, Proquest, Sciencedirect, and Scopus). We screened a total of 132 titles and abstracts that meet our inclusion and exclusion criteria. We included articles published in English, using human subjects, using neural networks machine learning models, and using prostate biopsy as a standard diagnosis. Non relevant studies and review articles were excluded. After screening, we found six articles relevant to our study. Risk of bias analysis was conducted using QUADAS-2 tool. Of the six articles, four articles used Artificial Neural Network (ANN), one article used Recurrent Neural Network (RNN), and one article used Deep Learning (DL). All articles suggest a positive result of ultrasound in the diagnosis of prostate cancer with a varied ROC curve of 0.76-0.98. Several factors affect AI accuracy, including the model of AI, mode and type of transrectal sonography, Gleason grading, and PSA level. Although there was only limited and low-moderate quality evidence, we managed to analyse the predominant findings comprehensively. In conclusion, machine learning with neural network models is a potential technology in prostate cancer diagnosis that could provide instant information for further workup with relatively high accuracy above 70% of sensitivity/specificity and above 0.5 of ROC-AUC value. Image-based machine learning models would be helpful for doctors to decide whether or not to perform a prostate biopsy.
The HR concerns and coping mechanisms for enhancing workplace flexibility in the healthcare sector during the COVID-19 Pandemic: A systematic review.
Authors: Kerketta Ajit , B. Sathiyaseelan
Published: February 2022

Abstract The COVID-19 pandemic devastated the globe, claimed billions of lives, and hampered trade and regular activities. Safety against the COVID-19 pandemic was the priority of the whole human species in society, the workplace, the family, and personal life. All sectors have been working responsibly to adjust to the new normal. The government is doing its best to implement the best laws and regulations to support and protect livelihood and industry. Healthcare professionals were at risk, and HR employees found it difficult to ensure effective and efficient business operations. The purpose of the study was to examine the role of HR professionals and investigate problems encountered in confronting the COVID-19 pandemic to improve workplace flexibility in the healthcare sector. The study used an evidence-based technique reproducible from previous research on HR issues in the health industry during the COVID-19 era. Such methodology assisted in producing a wide range of results from within and outside India. The population was selected with the health-related articles published between April 2020 to November 2021 during the COVID-19 era. The findings showed that redesigning the systems posed the biggest challenge for HR employees and required significant financial commitment, skilled human resources, cutting-edge technology, and an adequate supply of PPE. Thus, the HR managers were tasked with safeguarding a favourable environment by prioritising adequate, efficient, and workplace flexibility.
Vitamin D and acute respiratory infection: secondary analysis of a previous randomised controlled trial and updated meta-analyses
Authors: Bolland Mark J , Avenell Alison , Grey Andrew , Gamble Greg
Published: February 2022

Background

Recent meta-analyses concluded that vitamin D supplementation can prevent acute respiratory infection (ARI). However, the findings were heavily influenced by results from two arms of a six-arm cluster-randomised trial that were analysed without accounting for the cluster trial design. We have used publicly available data to provide results from the remaining four unpublished trial arms and to reanalyse the meta-analyses, accounting for the cluster trial design.

Methods

The intracluster correlation co-efficient (ICC) and design effect were estimated. We then calculated the risk reduction (RR) of ARI from summary statistics, adjusting for the design effect, individually for the five different vitamin D treatment groups (four previously unpublished) and for all the vitamin D groups pooled. For this trial, individual patient data were used to estimate the effect of vitamin D on ARI risk and number of ARIs, adjusting for the cluster trial design, using random-effects models. Finally, we reanalysed the most recent trial-level meta-analysis, including the trial data generated by the correct analysis of the cluster randomized trial.

Results

There were 744 trial participants (6 treatment groups, 21 clusters, mean cluster size 35.4). The ICC was 0.08 (95% CI 0.02-0.14) and design effect 3.75. In analyses based on summary statistics, there was no statistically significant effect of vitamin D on ARI risk in any individual treatment group, or when groups were pooled (RR 0.75, 95%CI 0.50-1.13). In individual patient data analyses, there was also no statistically significant effect of vitamin D on the ARI risk or number of ARIs in any treatment group, or when pooled: odds ratio 0.58 (0.26-1.29), rate ratio 0.70 (0.44-1.12), respectively. Update of the previous meta-analysis showed no effect of vitamin D on ARI either when data from the two arms of the trial, or when all trial arms were incorporated (RR 0.98, 0.96-1.00, P=0.10 both analyses).

Conclusions

Overall, vitamin D supplementation had no effect on the risk of an ARI or on the number of ARIs in this trial or in a re-analysis of the most recent meta-analysis. The results of the updated meta-analysis do not suggest that vitamin D supplementation would reduce the risk of Covid 19.
Genome-wide identification, characterization, and comparative analysis of NLR resistance genes in Coffea spp
Authors: Santos Mariana de Lima , de Resende Mário Lúcio Vilela , Alves Gabriel Sérgio Costa , Huguet-Tapia Jose Carlos , de Resende Márcio Fernando Ribeiro , Brawner Jeremy Todd
Published: February 2022

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora, Coffea eugenioides and their interspecific hybrid Coffea arabica). A total of 1311 non-redundant NLR loci were identified in C. arabica, 927 in C. canephora, and 1079 in C. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The C. arabica genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, and C. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between C. arabica and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.
Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions
Authors: Xu Jiang , Kumar Sanjeev , Hua Nan , Kou Yi , Lei Xiao , Rout Michael P. , Aitchison John D. , Alber Frank , Chen Lin
Published: February 2022

Traditional methods used to map the three-dimensional organization of chromatin in-situ generally involve chromatin conformation capture by formaldehyde crosslinking, followed by detergent solubilization and enzymatic digestion of DNA. Ligation of proximal DNA fragments followed by next generation sequencing (NGS) generates contact information that enables a global view of the chromatin conformation. Here, we explore the use of cryomilling to physically fragmentize the cells under cryogenic conditions to probe chromatin interactions in the cryomilled cell fragments by the tethered chromatin conformation capture (TCC). Our results show that cryomilling TCC (CTCC) can generate a global contact map similar to that obtained with in-situ Hi-C. This result suggests that summation of chromatin interactions mapped in individual subcellular fragments can reconstitute the global contact map of intact cells in an ensemble manner, paving the way for chromatin conformation analyses of solid tissue by CTCC. Compared with the conventional in-situ methods such as Hi-C, CTCC shows more uniform access to different subcompartments of the folded genome. On the other hand, most inter-chromosomal (trans) contacts are diminished or lost in CTCC except for a group of unique trans contacts that remain intact throughout the cryomilling and in- vitro crosslinking steps. These apparently ultra-stable trans interactions have much enhanced signal in CTCC due to the elimination of signals of most, presumably weak and transient trans interactions. Systematic and comparative analyses between CTCC and in-situ Hi-C provide further insights into the chromatin structure organization and reveal a generally unentangled chromosome interface and the existence of stable inter-chromosomal contacts that may represent intermingled inter-chromosomal interfaces.
Scratching bouts are modeled as Bernoulli trials until successful itch-extinguishing in mice
Authors: Honda Kotaro , Tominaga Mitsutoshi , Takamori Kenji
Published: February 2022

Itching and subsequent scratching behavior have been observed in many species, including humans. The behavior was evolved to remove skin parasites. Yet, scratching is performed without reliable indicators of whether a parasite is present. We addressed this apparent paradox by studying scratching in mice. Video recordings of ~5000 scratching bouts were collected in free-moving C57BL6/J mice. The statistical properties of their temporal sequence were analyzed. Inter-bout time intervals preceding over 50% of 5000 bouts were <10 s. We hypothesized that episodes of repetitive scratching corresponded to the duration of discrete events of itch sensation and comprised bouts separated by inter-bout intervals of <10 s. The distribution of itch episodes comprising n (n = 1, 2, 3, …) scratching bouts was well-approximated by the geometric distribution with success probability = 0.5 in healthy mice and lower probability in dry skin mice. This suggests that scratching bouts are modeled by probabilistic Bernoulli trials, and their repetitive sequence in each episode continues until the itch is successfully extinguished. Accordingly, we can presume the presence of parasites from the repeat length of scratching bouts determined by the probability of successful itch-extinguishing. This may provide a promising stochastic model to assess itchy phenotypes.
Serological fingerprints link antiviral activity of therapeutic antibodies to affinity and concentration
Authors: Fiedler Sebastian , Devenish Sean R. A. , Morgunov Alexey S. , Ilsley Alison , Ricci Francesco , Emmenegger Marc , Kosmoliaptsis Vasilis , Theel Elitza S. , Mills John R. , Sholukh Anton M. , Aguzzi Adriano , Iwasaki Akiko , Lynn Andrew K. , Knowles Tuomas P. J.
Published: February 2022

We assessed the affinities of the therapeutic monoclonal antibodies (mAbs) cilgavimab, tixagevimab, sotrovimab, casirivimab, and imdevimab to the receptor binding domain (RBD) of wild type, Delta, and Omicron spike. The Omicron RBD affinities of cilgavimab, tixagevimab, casirivimab, and imdevimab decreased by at least two orders of magnitude relative to their wild type equivalents, whereas sotrovimab binding was less severely impacted. These affinity reductions correlate with reduced antiviral activities of these antibodies, suggesting that simple affinity measurements can serve as an indicator for activity before challenging and time-consuming virus neutralization assays are performed. We also compared the properties of these antibodies to serological fingerprints (affinities and concentrations) of wild type RBD specific antibodies in 74 convalescent sera. The affinities of the therapeutic mAbs to wild type and Delta RBD were in the same range as the polyclonal response in the convalescent sera indicative of their high antiviral activities against these variants. However, for Omicron RBD, only sotrovimab retained affinities that were within the range of the polyclonal response, in agreement with its high activity against Omicron. Serological fingerprints thus provide important context to affinities and antiviral activity of mAb drugs and could guide the development of new therapeutics.
Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond
Authors: Fouks Bertrand , Harrison Mark C. , Mikhailova Alina A. , Marchal Elisabeth , English Sinead , Carruthers Madeleine , Jennings Emily C. , Pippel Martin , Attardo Geoffrey M. , Benoit Joshua B. , Bornberg-Bauer Erich , Tobe Stephen S.
Published: February 2022

Insects provide an unparalleled opportunity to link genomic changes with the rise of novel phenotypes, given tremendous variation in the numerous and complex adaptations displayed across the group. Among these numerous and complex adaptations, live-birth has arisen repeatedly and independently in insects and across the tree of life, suggesting this is one of the most common types of convergent evolution among animals. We sequenced the genome and transcriptome of the Pacific beetle-mimic cockroach, the only truly viviparous cockroach, and performed comparative analyses including two other viviparous insect lineages, the tsetse and aphids, to unravel the genomic basis underlying the transition to viviparity in insects. We identified pathways experiencing adaptive evolution, common in all viviparous insects surveyed, involved in uro-genital remodeling, maternal control of embryo development, tracheal system, and heart development. Our findings suggest the essential role of those pathways for the development of placenta-like structure enabling embryo development and nutrition. Viviparous transition seems also to be accompanied by the duplication of genes involved in eggshell formation. Our findings from the viviparous cockroach and tsetse reveal that genes involved in uterine remodeling are up-regulated and immune genes are down-regulated during the course of pregnancy. These changes may facilitate structural changes to accommodate developing young and protect them from the mothers immune system. Our results denote a convergent evolution of live-bearing in insects and suggest similar adaptive mechanisms occurred in vertebrates, targeting pathways involved in eggshell formation, uro-genital remodeling, enhanced tracheal and heart development, and reduced immunity.
Interferon receptor gene dosage determines diverse hallmarks of Down syndrome
Authors: Waugh Katherine A. , Minter Ross , Baxter Jessica , Chi Congwu , Tuttle Kathryn D. , Eduthan Neetha P. , Galbraith Matthew D. , Kinning Kohl T. , Andrysik Zdenek , Araya Paula , Dougherty Hannah , Dunn Lauren N. , Ludwig Michael , Schade Kyndal A. , Tracy Dayna , Smith Keith P. , Granrath Ross E. , Busquet Nicolas , Khanal Santosh , Anderson Ryan D. , Cox Liza L. , Estrada Belinda Enriquez , Rachubinski Angela L. , Lyford Hannah R. , Britton Eleanor C. , Orlicky David J. , Matsuda Jennifer L. , Song Kunhua , Cox Timothy C. , Sullivan Kelly D. , Espinosa Joaquin M.
Published: February 2022

Trisomy 21 causes Down syndrome, a condition characterized by cognitive impairments, immune dysregulation, and atypical morphogenesis. Using whole blood transcriptome analysis, we demonstrate that specific overexpression of four interferon receptors encoded on chromosome 21 associates with chronic interferon hyperactivity and systemic inflammation in Down syndrome. To define the contribution of interferon receptor overexpression to Down syndrome phenotypes, we used genome editing to correct interferon receptor gene dosage in mice carrying triplication of a large genomic region orthologous to human chromosome 21. Normalization of interferon receptor copy number attenuated lethal antiviral responses, prevented heart malformations, decreased developmental delays, improved cognition and normalized craniofacial anomalies. Therefore, interferon receptor gene dosage determines major hallmarks of Down syndrome, indicating that trisomy 21 elicits an interferonopathy amenable to therapeutic intervention.

One-Sentence Summary

Correction of interferon receptor gene dosage rescues multiple key phenotypes in a mouse model of trisomy 21.
Beta-cell Cre expression and reduced Ins1 gene dosage protect mice from type 1 diabetes
Authors: Skovsø Søs , Overby Peter , Memar-Zadeh Jasmine , Lee Jason T.C. , Yang Jenny C.C. , Shanina Iryna , Sidarala Vaibhav , Levi-D’Ancona Elena , Zhu Jie , Soleimanpour Scott A. , Horwitz Marc S. , Johnson James D.
Published: February 2022

A central goal of physiological research is the understanding of cell-specific roles of disease-associated genes. Cre-mediated recombineering is the tool of choice for cell type-specific analysis of gene function in pre-clinical models. In the type 1 diabetes research field, multiple lines of NOD mice have been engineered to express Cre recombinase in pancreatic β-cells using insulin promoter fragments, but tissue promiscuity remains a concern. Constitutive Ins1tm1.1(cre)Thor (Ins1Cre) mice on the C57/bl6-J background has high β-cell specificity and with no reported off-target effects. We explored if NOD:Ins1Cre mice could be used to investigate β-cell gene deletion in type 1 diabetes disease modeling. We studied wildtype (Ins1WT/WT), Ins1 heterozygous (Ins1Cre/WT or Ins1Neo/WT), and Ins1 null (Ins1Cre/Neo) littermates on a NOD background. Female Ins1Neo/WT mice exhibited significant protection from diabetes, with further near-complete protection in Ins1Cre/WT mice. The effects of combined neomycin and Cre knock-in in Ins1Neo/Cre mice were not additive to the Cre knock-in alone. In Ins1Neo/Cre mice, protection from diabetes was associated with reduced insulitis at 12 weeks of age. Collectively, these data confirm previous reports that loss of Ins1 alleles protects NOD mice from diabetes development and demonstrates, for the first time, that Cre itself may have additional protective effects. This has significant implications for the experimental design and interpretation of pre-clinical type 1 diabetes studies using β-cell-specific Cre in NOD mice.
An Inducible Cre Mouse with Preferential Activity in Vascular Smooth Muscle Evades a Previously Lethal Intestinal Phenotype
Authors: Warthi Ganesh D. , Faulkner Jessica L. , Doja Jaser , Ghanam Amr R. , Gao Pan , Yang Allison C. , Slivano Orazio J. , Barris Candee T. , Kress Taylor C. , Zawieja Scott D. , Griffin Susan H. , Xie Xiaoling , Ashworth Alan , Christie Christine K. , Bryant William B. , Kumar Ajay , Davis Michael J. , Long Xiaochun , Gan Lin , Belin de Chantemèle Eric J. , Lyu Qing , Miano Joseph M.
Published: February 2022

All smooth muscle cell (SMC) restricted Cre mice recombine floxed alleles in vascular and visceral SMCs. We generated a new tamoxifen-inducible CreERT2 mouse, Itga8-CreERT2, and compared its activity to the widely used Myh11-CreERT2 mouse. Both CreERT2 mice showed similar activity in vascular SMCs; however, Itga8-CreERT2 displayed limited activity in visceral SMC-containing tissues (e.g., intestine). Myh11-CreERT2 (but not Itga8-CreERT2) mice displayed high levels of CreERT2 protein, tamoxifen-independent activity, and an altered transcriptome. Whereas Myh11-CreERT2-mediated knockout of Srf resulted in a lethal intestinal phenotype, loss of Srf with Itga8-CreERT2 (SrfItga8) revealed viable mice with attenuated vascular SMC contractile gene expression, but no evidence of intestinal pathology. Male and female SrfItga8 mice presented with vascular contractile incompetence; however, only male SrfItga8 mice showed systemic changes in blood pressure. These results establish the Itga8-CreERT2 mouse as an alternative to existing SMC Cre strains, including Myh11-CreERT2, where SMC gene loss results in visceral myopathies that obfuscate accurate phenotyping in vascular SMCs.
In vitrophenotypic and transcriptomic variation inNeisseria musculimorphotypes correlate with colonization variability and persistencein vivo
Authors: Thapa Eliza , Lauderback Leah , Simmons Cassandra , Holzschu Donald L. , D’Mello Adonis , Ma Mancheong , So Magdalene , Tettelin Hervé , Weyand Nathan J.
Published: February 2022

Asymptomatic colonization of the upper respiratory tract is a common trait of the two human restricted pathogens,Neisseria gonorrhoeaeandNeisseria meningitidis. In vivomodels of pathogenic neisserial infections are heterologous systems that permit short-term colonization but do not fully recapitulate infections in humans. StudyingNeisseria musculi(Nmus), an oral commensal, in laboratory mice allows investigation ofNeisseria-host interactions that avoids host restriction barriers. Nmus produces smooth and rough morphotypes on solid media. We compared thein vitrophenotypes, biofilm transcriptomes,in vivocolonization patterns and burdens of the two Nmus morphotypes. We observed that the two morphotypes differ in biofilm formation, pilin production, transformation frequency, and aggregationin vitro. These phenotypes strongly correlated with differential expression of a set of genes in the Nmus biofilms including those that encoded factors for bacterial attachment.In vivo, the smooth morphotype stably colonized the oral cavities of all inoculated A/J and C57BL/6J mice at higher burdens relative to the rough. Interestingly, both morphotypes colonized the oral cavities of A/Js at higher magnitudes than in C57BL/6Js. Gut colonization by the smooth morphotype was qualitatively higher than the rough. Nasal colonization in the A/Js were transient following nasal inoculations. Collectively, our results demonstrate that colonization by Nmus can be affected by various factors including Nmus morphotypes, inoculation routes, anatomical niches, and host backgrounds. The Nmus-mouse model can use variable morphotype-host combinations to study the dynamics of neisserial asymptomatic colonization and persistence in multiple extragenital niches.

IMPORTANCE

Animal models for human adapted pathogenicNeisseriaspp. do not fully mimic human infections and are complicated by host restriction barriers that can hinder long-term persistence. Such barriers can be avoided by studyingNeisseriaspp. native to the animal host used for disease models.Neisseria musculi(Nmus) isolated from wild mice colonizes the oral cavity and gut of laboratory mice for extended periods. Nmus shares host interaction factors with species pathogenic to humans and thus provides a native system to study orthologs of factors that may facilitate asymptomatic colonization and persistence in the human upper respiratory tract. We investigated the Nmus-mouse system to comparein vitroandin vivophenotypes of two Nmus morphotypes. Our results support the hypothesis that the two morphotypes vary in different aspects ofNeisseria-host interactions. Future use of the Nmus-host system will help identify molecular mechanisms required for neisserial asymptomatic colonization, dissemination, and persistence.
In vitro effect of a non-immunosuppressive FKBP ligand, FK1706, on SARS-CoV-2 replication in combination with antivirals
Authors: Fitzsimmons William E. , Hartman Tracy L. , Mendenhall Michelle , Chen Catherine Z.
Published: February 2022

FKBP, a naturally occurring ubiquitous intracellular protein, has been proposed as a potential target for coronavirus replication. A non-immunosuppressive FKBP ligand, FK1706, was studied in vitro in a Vero cell model to assess potential activity alone and in combination with antivirals against SARS-CoV-2 replication. When combined with remdesivir, synergistic activity was seen (summary synergy score 24.7+9.56). FK1706 warrants in vivo testing as a potential new combination therapeutic for the treatment of COVID-19 infections.
The relationship of maternal gestational mass spectrometry-derived metabolites with offspring congenital heart disease: results from multivariable and Mendelian randomization analyses
Authors: Taylor Kurt , McBride Nancy , Zhao Jian , Oddie Sam , Azad Rafaq , Wright John , Andreassen Ole A. , Stewart Isobel D , Langenberg Claudia , Magnus Maria , Borges Maria Carolina , Caputo Massimo , Lawlor Deborah A
Published: February 2022

Background

It is plausible that maternal pregnancy metabolism influences risk of offspring congenital heart disease (CHD). We sought to explore this through a systematic approach using different methods and data.

Methods

We undertook multivariable logistic regression of the odds of CHD for 923 Mass Spectrometry (MS)-derived metabolites in a sub-sample of a UK birth cohort (Born in Bradford (BiB); N = 2,605, 46 CHD cases). We considered metabolites reaching a p-value threshold <0.05 to be suggestively associated with CHD. We sought validation of our findings, by repeating the multivariable regression analysis within the BiB cohort for any metabolite that was measured by nuclear magnetic resonance (NMR) or clinical chemistry (N = 7,296, 87 CHD cases), and by using genetic risk scores (GRS: weighted genetic risk scores of single nucleotide polymorphisms (SNPs) that were associated with each metabolite) in Mendelian randomization (MR) analyses. MR analyses were performed in BiB and two additional European birth cohorts (N = 38,662, 319 CHD cases).

Results

In the main multivariable analyses, we identified 44 metabolites suggestively associated with CHD, including those from the following super pathways: amino acids, lipids, co-factors and vitamins, xenobiotics, nucleotides, energy, and several unknown molecules. Of these 44, isoleucine and leucine were available in the larger BiB cohort (NMR), and for these the results were validated. MR analyses were possible for 27/44 metabolites and for 11 there was consistency with multivariable regression results.

Conclusions

In summary, we have used complimentary data sources and statistical techniques to construct layers of evidence. We found that amino acid metabolism during pregnancy, several lipids (more specifically androgenic steroids), and levels of succinylcarnitine could be important contributing factors for CHD.
Sensory Schwann cells set perceptual thresholds for touch and selectively regulate mechanical nociception
Authors: Ojeda-Alonso Julia , Calvo-Enrique Laura , Paricio-Montesinos Ricardo , Kumar Rakesh , Zhang Ming-Dong , Poulet James F.A. , Ernfors Patrik , Lewin Gary R.
Published: February 2022

That sensory neurons alone transduce mechanical stimuli was challenged by the discovery of nociceptive Schwann cells that can initiate pain. Consistent with the existence of inherently mechanosensitive sensory Schwann cells, we found that the mechanosensory function of almost all nociceptors, including those signaling fast pain, were critically dependent on sensory Schwann cells. Furthermore, in polymodal nociceptors, sensory Schwann cells signal mechanical, but not cold or heat pain. Terminal Schwann cells also surround mechanoreceptor nerve-endings within the Meissner’s corpuscle and in at hair follicle lanceolate endings that both signal vibrotactile touch. Within Meissner’s corpuscles, two molecularly and functionally distinct sensory Schwann cells positive for Sox10 and Sox2 differentially modulate rapidly adapting mechanoreceptor function. Using optogenetics we show that Meissner’s corpuscle Schwann cells are necessary for the perception of low threshold vibrotactile stimuli. These results show that sensory Schwann cells within diverse glio-neural mechanosensory end-organs are sensors for mechanical pain as well as necessary for touch perception. Thus, specialized sensory Schwann are central to the transduction of mechanical forces that underpin somatic sensation.
Single cell transcriptomic and spatial landscapes of the developing human pancreas
Authors: Olaniru Oladapo E. , Kadolsky Ulrich , Kannambath Shichina , Vaikkinen Heli , Fung Kathy , Dhami Pawan , Persaud Shanta J.
Published: February 2022

The progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas. Cell trajectory inference identified endocrine progenitor populations and novel branch-specific genes as the progenitors differentiate towards alpha or beta cells, indicating that transcriptional maturation occurred over this developmental timeframe. Spatial differentiation trajectories indicated that immature Schwann cells are spatially co-located with endocrine progenitors and contribute to beta cell maturation via the L1CAM-EPHB2 pathway. Our integrated approach enabled us to identify heterogeneity and multiple lineage dynamics within the mesenchyme, showing that it contributed to the exocrine acinar cell state. Finally, we have generated an interactive web resource for interrogating human pancreas development for the research community.
Candidate undecaprenyl phosphate translocases enable conditional microbial fitness and pathogenesis
Authors: Sit Brandon , Srisuknimit Veerasak , Hullahalli Karthik , Bueno Emilio , Cava Felipe , Waldor Matthew K.
Published: February 2022

The mechanisms that enable adaptation of peptidoglycan, the structural unit of the bacterial cell wall, to shifting extracellular conditions such as pH remain largely unknown. Here, we identify a DUF368-containing membrane protein in the cholera pathogen Vibrio cholerae that is critical for pathogenesis and alkaline fitness. V. cholerae and Staphylococcus aureus lacking their cognate DUF368-containing protein have pH-dependent cell wall defects consistent with surface accumulation of undecaprenyl phosphate (C55-P), an essential lipid carrier for the biogenesis of peptidoglycan and other key bacterial cell surface polymers. In both species, DUF368-containing proteins exhibit synthetic genetic interactions with putative transporters from the DedA family, suggesting these proteins represent complementary long-sought C55-P translocases that enable envelope maintenance functions critical for microbial fitness within and outside the host.

One-Sentence Summary

DUF368-containing and DedA-family proteins are undecaprenyl phosphate transporter candidates and are required for bacterial alkaline fitness and pathogenesis.
Evaluation of Nutritional Potential and Effect of Processing on Improving Nutrient Content of Cassava (Mannihot esculenta crantz) Root and Leaves
Authors: Lambebo Tagesse , Deme Tesfaye
Published: February 2022

Cassava (Manihot esculenta crantz) is a major food crop in Sub-Saharan Africa, Asia, the Pacific, and South America, where it feeds around 800 million people. Its roots are an excellent source of energy, and its leaves are rich in minerals, vitamins, and protein, which could substantially supplement the current starchy diets if properly detoxified since they contain some toxic anti-nutritional factors. The objective of this study was to provide information on the nutritional profile of cassava root and leaves and role of processing in enhancing and stabilizing their valuable nutrients. Two cassava varieties, kello and qulle, obtained from Areca Agricultural Research Center were used in this study. Roots and leaves were processed (fermented, boiled, and fluid bed dried), and nutritional, anti-nutritional, and functional properties were assessed using AOAC (Association of Official Analytical Chemists) standard procedures. As compared to leaves, roots had higher carbohydrate contents, ranging from 81.0 to 87.1 g/100g, whereas leaves had higher protein (21.2 to 28.4g/100g), total carotenoid (234.1 to 987.9 μg/g), fiber (16.1 to 22.9 g/100g), Ca (499.8 to 545.4 mg/100g), K (1193.4 to 1211.0 mg/100g), Mg (274.5 to 340.5 mg/100g) and Fe (129.1 to 146.1 mg/kg) contents. Anti-nutritional factors were slightly higher in the leaves than in the roots, with toxic cyanides ranging from 10.1 to 61.0 mg/kg in the leaves and from 1.8 to 47.5 mg/kg in the roots. However, the processing of leaves decreased cyanide content from 61.0 mg/kg to 10.1 mg/kg. Similarly, other anti-nutritional factors, such as condensed tannins, oxalates, and phytate were reduced from 52.0 to 21.0 mg/100g, 156.5 to 25.9 mg/100g, and 35.9 to 4.0 mg/100g), respectively. Hence, the fermentation of leaves and roots followed by boiling and drying is an interesting approach to reduce anti-nutritional factors significantly and ensure their nutritional quality. This study revealed that variety kello had a relatively better nutritional profile than variety qulle, for both root and leaves, except for total carotenoid content, which was higher in the latter. Genetic background and processing methods can greatly affect the nutritional profile of cassava varieties, so it is critical to analyze diverse cassava germplasm and refine the processing method to identify highly nutritious and healthy varieties.
Monitoring conservation effectiveness in tropical forests: bushmeat offtake parameters vary more quickly compared to parameters related to the living wildlife community
Authors: Kuenbou Jacques Keumo , Tagg Nikki , Khan Donald Mbohli , Speelman Stjin , Willie Jacob
Published: February 2022

Evaluating the effectiveness of conservation actions in tropical forests is essential. Generally based on the monitoring of living wildlife communities, combination with bushmeat extraction indicators is seldom used. It is therefore interesting to carry out a monitoring of indices related to these two categories of indicators in order to identify indices presenting more temporal variation and allowing for a rapid detection of real changes. Between 2017 and 2020, data on bushmeat offtake were recorded and surveys of wildlife and human activity signs were conducted in a conservation zone in Dja Biosphere Reserve in Cameroon. Data were collected around villages where human pressure is high. Our results show a decline in total biomass and number of animals killed. An increase in numbers of traps set was observed, but there was no notable difference in the mean biomass of a carcass and mean number of hunting trips. Overall, wildlife abundance decreased slightly in 2020, mainly reflecting changes for three species—bay duiker (Cephalophus dorsalis), yellow-backed duiker (Cephalophus sylvicultor) and red river hog (Potamocherus porcus)—which were more abundant in 2018. Regarding keystone species, we noted a slight increase in the abundance of chimpanzees. Patterns of species richness in both study years were similar. These results suggest that bushmeat offtake data may be more informative for early evaluations of the effectiveness of wildlife conservation efforts. This underlines the importance of monitoring bushmeat for the evaluation of wildlife conservation projects in contexts where hunting occurs.
AAA+ protease-adaptor structures reveal altered conformations and ring specialization
Authors: Kim Sora , Fei Xue , Sauer Robert T. , Baker Tania A.
Published: February 2022

ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here, we present high-resolution cryo-EM structures of ClpAPS complexes showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two structural classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated and tucked away from the channel, and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies demonstrate new structures and functions for key AAA+ elements. In addition to ClpAPS delivery, pore-loop tucking may be used broadly by AAA+ unfoldases, for example during enzyme pausing/unloading.
Changes in DNA double-strand break repair during aging correlate with an increase in genomic mutations
Authors: Mojumdar Aditya , Mair Nicola , Adam Nancy , Cobb Jennifer A.
Published: February 2022

A double -strand break (DSB) is one of the most deleterious forms of DNA damage. In eukaryotic cells, two main repair pathways have evolved to repair DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is the predominant pathway of repair in the unicellular eukaryotic organism, S. cerevisiae. However, during replicative aging the relative use of HR and NHEJ shifts in favor of end-joining repair. By monitoring repair events in the HO-DSB system, we find that early in replicative aging there is a decrease in the association of long-range resection factors, Dna2-Sgs1 and Exo1 at the break site and a decrease in DNA resection. Subsequently, as aging progressed, the recovery of Ku70 at DSBs decreased and the break site associated with the nuclear pore complex at the nuclear periphery, which is the location where DSB repair occurs through alternative pathways that are more mutagenic. End-bridging remained intact as HR and NHEJ declined, but eventually it too became disrupted in cells at advanced replicative age. In all, our work provides insight into the molecular changes in DSB repair pathway during replicative aging. HR first declined, resulting in a transient increase in the NHEJ. However, with increased cellular divisions, Ku70 recovery at DSBs and NHEJ subsequently declined. In wild type cells of advanced replicative age, there was a high frequency of repair products with genomic deletions and microhomologies at the break junction, events not observed in young cells which repaired primarily by HR.

Highlights

Decreased DNA resection at DSBs is an early event of replicative aging

End-joining repair increases as resection decreases at DSBs in older cells

In older cells the products of DSB repair contain deletions and microhomologies

DSBs associate with the NPC at the nuclear periphery more in older cells

Old Cell Enrichment method suitable for molecular biology approaches in budding yeast
Membrane-catalyzed aggregation of islet amyloid polypeptide is dominated by secondary nucleation
Authors: Elenbaas Barend O.W. , Khemtemourian Lucie , Killian J. Antoinette , Sinnige Tessa
Published: February 2022

Type II diabetes is characterized by the loss of pancreatic β-cells. This loss is thought to be a consequence of membrane disruption, caused by the aggregation of islet amyloid polypeptide (IAPP) into amyloid fibrils. However, the molecular mechanisms of IAPP aggregation in the presence of membranes have remained unclear. Here, we use kinetic analysis to elucidate the aggregation mechanism of IAPP in the presence of mixed zwitterionic and anionic lipid membranes. The results converge to a model in which aggregation on the membrane is strongly dominated by secondary nucleation, i.e. the formation of new nuclei on the surface of existing fibrils. The critical nucleus consists of a single IAPP molecule, and anionic lipids catalyze both primary and secondary nucleation, but not elongation. The fact that anionic lipids promote secondary nucleation implies that these events take place at the interface between the membrane and existing fibrils, demonstrating that fibril growth occurs at least to some extent on the membrane surface. These new insights into the mechanism of IAPP aggregation on membranes may help to understand IAPP toxicity and will be important for the development of therapeutics to prevent β-cell death in type II diabetes.
IgD+ Age-Associated B cells are the progenitors of the main T-independent B cell response to infection that generates protective Ab and can be induced by an inactivated vaccine in the aged
Authors: Kugler-Umana Olivia , Zhang Wenliang , Kuang Yi , Liang Jialing , Castonguay Catherine H. , Tonkonogy Susan L. , Marshak-Rothstein Ann , Devarajan Priyadharshini , Swain Susan L.
Published: February 2022

Age-associated B cells (ABC) accumulate with age and are associated with autoimmunity and chronic infection. However, their contributions to acute infection in the aged and their developmental pathways are unclear. We find that the response against influenza A virus infection in aged mice is dominated by a Fas+GL7- effector B cell population we call infection-induced-ABC (iABC). Most iABC express IgM and include antibody-secreting cells in the spleen, lung and bone marrow. We find that in response to influenza, IgD+CD21-CD23-ABC are the precursors of iABC. These IgD+ABC develop in germ free mice, so are independent of foreign antigen recognition, suggesting they arise from an intrinsic age-associated developmental program. The response of ABC to influenza infection, resulting in iABC, is T cell independent and requires both extrinsic TLR7 and TLR9 signals. In response to influenza infection, IgD+ABC can induce a faster recovery of weight and higher total anti-influenza IgG and IgM titers that can neutralize virus. Immunization with whole inactivated virus also generates iABC in aged mice. Thus, in unimmunized aged mice, whose other B and T cell responses have waned, IgD+ABC are likely the naïve B cells with the potential to become Ab-secreting cells and to provide protection from infection in the aged.
Cryo-EM structures reveal that RFC recognizes both the 3’- and 5’-DNA ends to load PCNA onto gaps for DNA repair
Authors: Zheng Fengwei , Georgescu Roxana E. , Yao Nina Y. , Li Huilin , O’Donnell Michael E.
Published: February 2022

RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3’ ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a 2nd DNA binding site in RFC that binds a 5’ duplex. This 5’ DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3’ and 5’ ends are present at a ssDNA gap, we propose that the 5’ site facilitates RFC’s PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5’ DNA binding domain of Rfc1. We further observe that a 5’ end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5’-DNA site in lagging strand DNA synthesis
Single-Objective Evanescent Scattering Microscopy for Imaging Single Proteins and Binding Kinetics
Authors: Zhang Pengfei , Wang Rui , Wan Zijian , Zhou Xinyu , Ma Guangzhong , Kolay Jayeeta , Jiang Jiapei , Wang Shaopeng
Published: February 2022

Plasmonic scattering microscopy has advanced the evanescent detection approaches by offering wide-field single-molecule imaging capability. However, two limitations prevent the broader application of plasmonic single-molecule imaging. One is the heating effect accompanying the plasmonic enhancement, and the other is the complicated system structure resulting from the two-objective optical arrangement. Here, we report single-objective evanescent scattering microscopy. The evanescent field is created by total internal reflection instead of the surface plasmon resonance on the gold film. As a result, the sensing substrate without gold film produces little heat, and allows excitation and observation using one objective. In addition, this system enables quantification of protein binding kinetics by simultaneously counting the binding of individual molecules and recording their binding sites with nanometer precision, providing a digital method to measure binding kinetics with high spatiotemporal resolution. This work may pave a road for label-free single protein analysis in conventional microscopy.

Teaser

Label-free single-molecule imaging on a total internal reflection fluorescence objective.
A scalable pipeline for SARS-CoV-2 replicon construction based on de-novo synthesis
Authors: Berkyurek Ahmet C. , Lee Elian , Weissbrod Omer , Rasnic Roni , Falciatori Ilaria , Chen Siyuan , Erlich Yaniv
Published: February 2022

Replicons are synthetic viral RNA molecules that recapitulate the self-replicating activities of the virus but are missing its infectivity potential. Here, we report on a scalable pipeline to generate a replicon of any SARS-CoV-2 strain using de-novo synthesis. Our pipeline relies only on publicly available sequencing data without requiring access to any material, simplifying logistical and bureaucratic issues of sample acquisition. In addition, our system retains the nucleotide sequence of most of the SARS-CoV-2 full genome and therefore better captures its underlying genomic and biological functions as compared to the popular pseudotypes or any replicon system published to-date. We utilized our system to synthesize a SARS-CoV-2 non-infectious version of the Beta strain. We then confirmed that the resulting RNA molecules are non-infectious and safe to handle in a BSL2/CL2 facility. Finally, we show that our replicon can be specifically inhibited by molnupiravir and RNAi treatments, demonstrating its utility for drug research and development.