bluuebunny/crossref_metadata_2025 huggingface dataset:
Skill acquisition and gaze behavior during laparoscopic surgical simulation
Authors: Liu Sicong , Donaldson Rachel , Subramaniam Ashwin , Palmer Hannah , Champion Cosette , Cox Morgan L. , Appelbaum L. Gregory
Published: July 2020

Background

Experts consistently exhibit more efficient gaze behaviors than non-experts during motor tasks. In surgery, experts have been shown to gaze more at surgical targets than surgical tools during simple simulations and when watching surgical recordings, suggesting a proactive control strategy with greater use of feedforward visual sampling. To investigate such expert gaze behaviors in a more dynamic and complex laparoscopic surgery simulation, the current study measured and compared gaze patterns between surgeons and novices who practiced extensively with laparoscopic simulation.

Methods

Three surgeons were assessed in a testing visit and five novices were trained and assessed (at pre-, mid-, and post-training points) in a 5-visit protocol on the Fundamentals of Laparoscopic Surgery peg transfer task. The task was adjusted to have a fixed action sequence to allow recordings of dwell durations based on pre-defined areas of interest (AOIs). Novices’ individualized learning curves were analyzed using an inverse function model, and group-level differences were tested using analysis of variance on both behavioral performance and dwell duration measures.

Results

Trained novices were shown to reach more than 98% (M= 98.62%,SD= 1.06%) of their behavioral learning plateaus, leading to equivalent behavioral performance to that of surgeons. Despite this equivalence in behavioral performance, surgeons continued to show significantly shorter dwell durations at visual targets of current actions and longer dwell durations at future steps in the action sequence than trained novices (ps≤ .03, Cohen’sds> 2).

Conclusion

This study demonstrates that, whereas novices can train to match surgeons on behavioral performance, their gaze pattern is still less efficient than that of surgeons, suggesting that eye-tracking metrics might be more sensitive than behavioral performance in detecting surgical expertise. Such insight can be applied to develop training protocols so non-experts can internalize experts’ “gaze templates” to accelerate learning.

Article Summary

Gaze pattern differences persist between laparoscopic surgery experts and novices who have been trained to reach over 98% of individualized behavioral learning plateaus in the Fundamentals of Laparoscopic Surgery (FLS) peg transfer task.

The importance of this finding lies in motivating the decision and method of including gaze behaviors via eyetracking technology in the present surgical training programs.
Identification of SARS-CoV-2 3CL Protease Inhibitors by a Quantitative High-throughput Screening
Authors: Zhu Wei , Xu Miao , Chen Catherine Z. , Guo Hui , Shen Min , Hu Xin , Shinn Paul , Klumpp-Thomas Carleen , Michael Samuel G. , Zheng Wei
Published: July 2020

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emphasized the urgency to develop effective therapeutics. Drug repurposing screening is regarded as one of the most practical and rapid approaches for the discovery of such therapeutics. The 3C like protease (3CLpro), or main protease (Mpro) of SARS-CoV-2 is a valid drug target as it is a specific viral enzyme and plays an essential role in viral replication. We performed a quantitative high throughput screening (qHTS) of 10,755 compounds consisting of approved and investigational drugs, and bioactive compounds using a SARS-CoV-2 3CLproassay. Twenty-three small molecule inhibitors of SARS-CoV-2 3CLprohave been identified with IC50s ranging from 0.26 to 28.85 μM. Walrycin B (IC50= 0.26 µM), Hydroxocobalamin (IC50= 3.29 µM), Suramin sodium (IC50= 6.5 µM), Z-DEVD-FMK (IC50= 6.81 µM), LLL-12 (IC50= 9.84 µM), and Z-FA-FMK (IC50= 11.39 µM) are the most potent 3CLproinhibitors. The activities of anti-SARS-CoV-2 viral infection was confirmed in 7 of 23 compounds using a SARS-CoV-2 cytopathic effect assay. The results demonstrated a set of SARS-CoV-2 3CLproinhibitors that may have potential for further clinical evaluation as part of drug combination therapies to treating COVID-19 patients, and as starting points for chemistry optimization for new drug development.
TRAF6-IRF5 kinetics, TRIF, and biophysical factors drive synergistic innate responses to particle-mediated MPLA-CpG co-presentation
Authors: Pradhan P. , Toy R. , Jhita N. , Blanchard E. L. , Atalis A. , Pandey B. , Santangelo P. J. , Shayakhmetov D. M. , Roy K.
Published: July 2020

Innate immune responses to pathogens are driven by co-presentation of multiple pathogen-associated molecular patterns (PAMPs). PAMPs and PAMP-analogs are also used as immune-adjuvants to enhance vaccine efficacy by activating various Pattern Recognition Receptors (PRRs), like Toll-like receptors (TLRs). Various combinations of PAMP adjuvants can trigger synergistic immune responses, but the underlying molecular mechanisms driving that synergy are poorly understood. Here, we used synthetic particulate carriers co-loaded with MPLA (TLR4-adjuvant) and CpG (TLR9-adjuvant) as pathogen-like particles (PLPs) to dissect the signaling pathways responsible for the integrated, dual-adjuvant immune response. PLP-based co-presentation of MPLA and CpG to mouse bone marrow derived antigen-presenting cells (BM-APCs) elicited synergistic Type-I Interferon (IFN-β) and IL-12p70 responses, which were strongly influenced by the biophysical properties of PLPs. Mechanistically, we found that the adapter protein MyD88 and the Interferon-Regulatory-Factor-5 (IRF-5), but not the canonical factors IRF-3 or IRF-7, were necessary for production of both IFN-β and IL12p70. TRIF signaling was required to elicit the synergistic response; the absence of TRIF abolished synergy. Importantly, both the kinetics and magnitude of downstream TRAF6 and IRF5 signaling (TRIF-TRAF-IRF5 pathway kinetics) drove the observed synergy. These results identify not only the key signaling mechanism that cooperates to generate a combinatorial response to MPLA-CpG dual engagement in BM-APCs, but they also underscore the critical role that signaling kinetics and biophysical presentation plays in integrated responses to combination adjuvants.
Actin bundle architecture and mechanics regulate myosin II force generation
Authors: Weirich Kimberly L. , Stam Samantha , Munro Ed , Gardel Margaret L.
Published: July 2020

The actin cytoskeleton is a soft, structural material that underlies biological processes such as cell division, motility, and cargo transport. The cross-linked actin filaments self-organize into a myriad of architectures, from disordered meshworks to ordered bundles, which are hypothesized to control the actomyosin force generation that regulates cell migration, shape, and adhesion. Here, we use fluorescence microscopy and simulations to investigate how actin bundle architectures with varying polarity, spacing, and rigidity impact myosin II dynamics and force generation. Microscopy reveals that mixed polarity bundles formed by rigid cross-linkers support slow, bidirectional myosin II filament motion, punctuated by periods of stalled motion. Simulations reveal that these locations of stalled myosin motion correspond to sustained, high forces in regions of balanced actin filament polarity. By contrast, mixed polarity bundles formed by compliant, large cross-linkers support fast, bidirectional motion with no traps. Simulations indicate that trap duration is directly related to force magnitude, and that the observed increased velocity corresponds to lower forces resulting from both the increased bundle compliance and filament spacing. Our results indicate that the properties of actin structures regulate the dynamics and magnitude of myosin II forces, highlighting the importance of architecture and mechanics in regulating forces in biological materials.
TLR7 and RIG-I dual-adjuvant loaded nanoparticles drive broadened and synergistic responses in dendritic cellsin vitroand generate unique cellular immune responses in influenza vaccination
Authors: Toy Randall , Keenum M. Cole , Pradhan Pallab , Phang Katelynn , Chen Patrick , Chukwu Chinwendu , Nguyen Anh , Liu Jiaying , Jain Sambhav , Kozlowski Gabrielle , Hosten Justin , Suthar Mehul S. , Roy Krishnendu
Published: July 2020

Although the existing flu vaccines elicit strong antigen-specific antibody responses, they fail to provide effective, long term protection – partly due to the absence of robust cellular memory immunity. We hypothesized that co-administration of combination adjuvants, mirroring the flu-virus related innate signaling pathways, could elicit strong cellular immunity. Here, we show that the small molecule adjuvant R848 and the RNA adjuvant PUUC, targeting endosomal TLR7s and cytoplasmic RLRs respectively, when delivered together in polymer nanoparticles (NP), elicits a broadened immune responses in mouse bone marrow-derived dendritic cells (mBMDCs) and a synergistic response in both mouse and human plasmacytoid dendritic cells (pDCs). In mBMDCs, NP-R848-PUUC induced both NF-κB and interferon signaling. Interferon responses to co-delivered R848 and PUUC were additive in human peripheral blood mononuclear cells (PBMCs) and synergistic in human FLT3-differentiated mBMDCs and CAL-1 pDCs. Vaccination with NPs loaded with H1N1 Flu antigen, R848, and PUUC increased percentage of CD8+ T-cells in the lungs, percentage of antigen-specific CD4+T-cells in the spleen, and enhanced overall cytokine-secreting T cell percentages upon antigen restimulation. Also in the spleen, T lymphopenia, especially after in vitro restimulation, was observed. Our results demonstrate that simultaneous engagement of TLR7 and RIG-I pathways using particulate carriers is a potential approach to improve cellular immunity in flu vaccination.

GRAPHICAL ABSTRACT
Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in theSORL1gene implicated in early onset familial Alzheimer’s disease
Authors: Barthelson Karissa , Pederson Stephen Martin , Newman Morgan , Lardelli Michael
Published: July 2020

Background

To prevent or delay the onset of Alzheimer’s disease (AD), we must understand its molecular basis. The great majority of AD cases arise sporadically with a late onset after 65 years of age (LOAD). However, rare familial cases of AD can occur due to dominant mutations in a small number of genes that cause an early onset prior to 65 years of age (EOfAD). As EOfAD and LOAD share similar pathologies and disease progression, analysis of EOfAD genetic models may give insight into both subtypes of AD. Sortilin-related receptor 1 (SORL1) is genetically associated with both EOfAD and LOAD and provides a unique opportunity to investigate the relationships between both forms of AD. Currently, the role ofSORL1mutations in AD pathogenesis is unclear.

Methods

To understand the molecular consequences ofSORL1mutation, we performed targeted mutagenesis of the orthologous gene in zebrafish. We generated an EOfAD-like mutation, V1482Afs, and a putatively null mutation, to investigate whether EOfAD-like mutations insorl1display haploinsufficiency by acting through loss-of-function mechanisms. We performed mRNA-sequencing on whole brains comparing normal (wild type) fish with their siblings heterozygous for EOfAD-like or complete loss-of-function mutations insorl1or transheterozygous for these mutations. Differential gene expression and gene set enrichment analyses identified, respectively, changes in young adult zebrafish brain transcriptomes, and putative effects on neural subcellular functions.

Results

We identified subtle effects on expression of genes involved in energy production, mRNA translation and mTORC1 signalling in both the EOfAD-like and null mutant brains, implying that these effects are due tosorl1haploinsufficiency. Surprisingly, we also observed changes to expression of genes occurring only in the EOfAD-mutation carrier brains, suggesting gain-of-function effects. Transheterozygosity for the EOfAD-like and null mutations (i.e. lacking wild typesorl1), caused apparent effects on iron homeostasis and other transcriptome changes distinct from the single-mutation heterozygous fish.

Conclusions

Our results provide insight into the possible early brain molecular effects of an EOfAD mutation in humanSORL1. Differential effects of heterozygosity and complete loss of normalSORL1expression are revealed.
Fibroblast growth factor 9 stimulates neurite outgrowth through NF-kB signaling in striatal cell Huntington’s disease models
Authors: Yusuf Issa Olakunle , Chen Hsiu-Mei , Cheng Pei-Hsun , Chang Chih-Yi , Tsai Shaw-Jenq , Chuang Jih-Ing , Wu Chia-Ching , Huang Bu-Miin , Sun H. Sunny , Chen Chuan-Mu , Yang Shang-Hsun
Published: July 2020

Proper development of neuronal cells is important for brain functions, and impairment of neuronal development may lead to neuronal disorders, implying that improvement in neuronal development may be a therapeutic direction for these diseases. Huntington’s disease (HD) is a neurodegenerative disease characterized by impairment of neuronal structures, ultimately leading to neuronal death and dysfunctions of the central nervous system. Based on previous studies, fibroblast growth factor 9 (FGF9) may provide neuroprotective functions in HD, and FGFs may enhance neuronal development and neurite outgrowth. However, whether FGF9 can provide neuronal protective functions through improvement of neuronal morphology in HD is still unclear. Here, we study the effects of FGF9 on neuronal morphology in HD and attempt to understand the related working mechanisms. Taking advantage of striatal cell lines from HD knock-in mice, we found that FGF9 increases neurite outgrowth and upregulates several structural and synaptic proteins under HD conditions. In addition, activation of nuclear factor kappa B (NF-kB) signaling by FGF9 was observed to be significant in HD cells, and blockage of NF-kB leads to suppression of these structural and synaptic proteins induced by FGF9, suggesting the involvement of NF-kB signaling in these effects of FGF9. Taken these results together, FGF9 may enhance neurite outgrowth through upregulation of NF-kB signaling, and this mechanism could serve as an important mechanism for neuroprotective functions of FGF9 in HD.
Constancy and Change in the 5’UTR of Yellow Fever Virus
Authors: Seligman Stephen J.
Published: July 2020

The nucleotide composition of the 5’UTR of the yellow fever virus (YFV) has been reported to be the most constant sequence in the viral genome, but a comprehensive analysis of this constancy has not been presented. The current report is an analysis of the 5’UTRs from 48 sequences deposited in GenBank representing the seven described genotypes, five in Africa and two in the Americas. The YFV 5’UTRs consist of 118-120 nucleotides, 92% (110/119) of which are constant in all sequences. The constancy is impressive and suggests that many participate in significant viral functions. Remarkably, analysis of the non-constant nucleotides revealed that in some instances the non-constant nucleotide changes persisted in one or a restricted number of related genotypes and were from sequences isolated over a considerable span of years. This constant feature of non-constant nucleotides is consistent with the concept that the changes were in response to different environmental features such as changes in mosquito hosts or animal reservoirs, particularly as a consequence of spread of YFV from Africa to the New World. Constancy of 5’UTR in general may be helpful in distinction of viral species. Lastly, the presence of sequences of constant nucleotides greater than 19 nucleotides suggests regions of the 5’UTR that may be exploited for use as non-codon RNA as treatment and diagnostic agents in a variety of viral diseases.

Importance

The 5’UTR is arguably the most neglected portion of the viral genome. It is frequently incomplete in the sequences deposited as otherwise complete sequences in GenBank. The current report is an analysis of complete 5’UTR sequences selected from those deposited in GenBank and indicates that the 5’UTR is 92% conserved confirming that it is a highly conserved portion of the viral genome and suggesting that each conserved nucleotide may be functionally significant. Repeated occurrences of even non-constant nucleotides belong to a restricted number of genotypes raising the possibility that adaptation to new mosquito hosts and animal reservoirs such as those that accompanied spread of yellow fever virus from Africa to the Western Hemisphere are relevant. Knowledge of prolonged strings of invariable nucleotides in the 5’UTR has been used in designing a method for detecting YFV and may also be relevant for designing sequences for viral control of a variety of viruses.
A single-cell transcriptome atlas of the aging human and macaque retina
Authors: Yi Wenyang , Lu Yufeng , Zhong Suijuan , Zhang Mei , Sun Le , Dong Hao , Wang Mengdi , Wei Min , Xie Haohuan , Qu Hongqiang , Peng Rongmei , Hong Jing , Yao Ziqin , Tong Yunyun , Wang Wei , Ma Qiang , Liu Zeyuan , Ma Yuqian , Li Shouzhen , Yin Chonghai , Liu Jianwei , Ma Chao , Wang Xiaoqun , Wu Qian , Xue Tian
Published: July 2020

The human retina is a complex neural tissue that detects light and sends visual information to the brain. However, the molecular and cellular processes that underlie aging primate retina remain unclear. Here, we provide a comprehensive transcriptomic atlas based on 119,520 single cells of the foveal and peripheral retina of humans and macaques covering different ages. The molecular features of retinal cells differed between the two species, suggesting the distinct regional and species specializations of the human and macaque retinae. In addition, human retinal aging occurred in a region- and cell-type- specific manner. Aging of human retina exhibited a foveal to peripheral gradient.MYO9A−rods and a horizontal cell subtype were greatly reduced in aging retina, indicating their vulnerability to aging. Moreover, we generated a dataset showing the cell-type- and region- specific gene expression associated with 55 types of human retinal disease, which provides a foundation to understand the molecular and cellular mechanisms underlying human retinal diseases. Together, these datasets are valuable for understanding the molecular characteristics of primate retina, as well as the molecular regulation of aging progression and related diseases.
Effect of chlorination and pressure flushing of drippers fed by reclaimed wastewater on biofouling
Authors: Lequette Kévin , Ait-Mouheb Nassim , Adam Nicolas , Muffat-Jeandet Marine , Bru-Adan Valérie , Wéry Nathalie
Published: July 2020

Dripper clogging reduces the performance and service life of a drip irrigation system. The impact of chlorination (1.5 ppm of free chlorine during 1 h application) and pressure flushing (0.18 MPa) on the biofouling of non-pressure-compensating drippers fed by real reclaimed wastewater was studied at lab scale using Optical Coherence Tomography. The effect of these treatments on microbial composition (bacteria and eukaryotes) was also investigated by High-throughput DNA sequencing. Biofouling was mainly observed in inlet, outlet and return areas of the drippers. Chlorination limited biofilm development mainly in the mainstream of the milli-labyrinth channel. It was more efficient when combined with pressure flushing. Moreover, chlorination was more efficient in maintaining the water distribution uniformity. It reduced the bacterial concentration and the diversity of the dripper biofilms compared to the pressure flushing method. This method strongly modified the microbial communities, promoting chlorine-resistant bacteria such asComamonadaceaeorAzospira. Inversely, several bacterial groups were identified as sensitive to chlorination such as Chloroflexi and Planctomycetes. Nevertheless, one month after stopping the treatments the bacterial diversity re-increased and the chlorine-sensitive bacteria such as Chloroflexi phylum and the Saprospiraceae, Spirochaetaceae, Christensenellaceae and Hydrogenophilaceae families re-emerged with the growth of biofouling, highlighting the resilience of the bacteria from drippers. Based on PCoA analyses, the structure of the communities still clustered separately from never-chlorinated drippers, showing that the effect of chlorination was still present one month after stopping the treatment.

Highlights

The fouling of drippers is a bottleneck for drip irrigation using reclaimed wastewater

Biofouling was lowest when chlorination was combined with pressure flushing

The β-Proteobacteria and Firmicutes contain chlorine resistant bacteria

The decrease of Chloroflexi by chlorination was transitory

The bacterial community was resilient after the interruption of cleaning events
Trans-synaptic assemblies link synaptic vesicles and neuroreceptors
Authors: Martinez-Sanchez Antonio , Laugks Ulrike , Kochovski Zdravko , Papantoniou Christos , Baumeister Wolfgang , Lucic Vladan
Published: July 2020

Synaptic transmission is characterized by fast, tightly coupled processes and complex signaling path-ways that require a distinctly non-random spatial organization of their components. Nanoscale organization of synaptic proteins at glutamatergic synapses was suggested to regulate synaptic plasticity, the process underlying learning and memory. Specifically, direct colocalization of pre- and postsynaptic proteins implicated that the alignment of neurotransmitter release sites with neurotransmitter receptors enables maximal synaptic response. However, direct visualization and the mechanistic understanding of this alignment is lacking. Here we used cryo-electron tomography to visualize synaptic complexes in their native environment with the full complement of their interacting partners, synaptic vesicles and plasma membranes on 2-4 nanometer scale. The application of our recent template-free detection and classification procedure showed that tripartite trans-synaptic assemblies (subcolumns) link synaptic vesicles to postsynaptic receptors, and established that a particular displacement between directly interacting complexes characterizes subcolumns. Furthermore, we obtained de novo average structures of ionotropic glutamate receptors in their physiological composition, embedded in lipid membranes. The data presented support the hypothesis that synaptic function is carried by precisely organized trans-synaptic units. It complements superresolution findings and provides a framework for further exploration of synaptic and other large molecular assemblies that link different cells or cellular regions and may require weak or transient interactions to exert their function.
The impact of age on genetic risk for common diseases
Authors: Jiang Xilin , Holmes Chris , McVean Gil
Published: July 2020

Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Recent work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the relationship between genetic risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic risk. The predominant pattern shows genetic risk factors having the greatest impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants although the magnitude and form of the decrease varies among diseases. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction.

Author summary

The genes we inherit from our parents influence our risk for almost all diseases, from cancer to severe infections. With the explosion of genomic technologies, we are now able to use an individual’s genome to make useful predictions about future disease risk. However, recent work has shown that the predictive value of genetic information varies by context, including age, sex and ethnicity. In this paper we introduce, validate and apply new statistical methods for investigating the relationship between age and genetic risk. These methods allow us to ask questions such as whether risk is constant over time, precisely how risk changes over time and whether all genetic risk factors have similar age profiles. By applying the methods to data from the UK Biobank, a prospective study of 500,000 people, we show that there is a tendency for genetic risk to decline with increasing age. We consider a series of possible explanations for the observation and conclude that there must be processes acting that we are currently unaware of, such as distinct phases of life in which genetic risk manifests itself, or interactions between genes and the environment.
Aspirin inhibition of prostaglandin synthesis impairs egg development across mosquito taxa
Authors: Al Baki Md. Abdullah , Ahmed Shabbir , Kwon Hyeogsun , Hall David R. , Smith Ryan C. , Kim Yonggyun
Published: July 2020

Several endocrine signals are known to mediate mosquito egg development including insulin-like peptide, 20-hydroxyecdysone, and juvenile hormone. The objective of this study was to determine the effects of prostaglandin E2(PGE2) as an additional mediator of oogenesis in the mosquitoes,Aedes albopictusandAnopheles gambiae. The injection of aspirin (an inhibitor of cyclooxygenase) shortly after blood-feeding significantly inhibited egg development at choriogenesis in a dose-dependent manner inAe. albopictus. Moreover, oral administration of aspirin toAn. albopictusandAn. gambiaealso inhibited egg production. The aspirin treatment suppressed expression of the genes (Yellow-gandYellow-g2) associated with exochorion darkening and led to the production of a malformed egg shell inAe. albopictus. These inhibitory effects of aspirin on egg development were rescued by the addition of PGE2, confirming the specificity of aspirin in inhibiting prostaglandin production. To validate these results, we identified a putative PGE2receptor (Aa-PGE2R) inAe. albopictus. Aa-PGE2Rexpression was highly inducible in adult ovary after blood-feeding. RNA interference ofAa-PGE2Rexpression resulted in the significant suppression of choriogenesis similar to aspirin treatment, where the addition of PGE2toAa-PGE2R-silenced females failed to rescue egg production. Together, these results suggest that PG synthesis and signaling are required for egg development across diverse mosquito taxa.

Author Summary

Progstaglandins (PGs) play crucial roles in mediating various physiological processes in insects. Aspirin (ASP) inhibits PG biosynthesis and has been used as an anti-inflammatory drug. ASP injection or feeding to mosquitoes ofAedes albopictusorAnopheles gambiaesignificantly inhibits egg production at chorion formation. This led to significant reduction in fecundity and egg hatchability. PG signal is interrupted by RNA interference (RNAi) of PGE2receptor. The RNAi treatment also gave a similar damage to females in egg production as seen in ASP treatment. Thus, PG signal is required for egg production of these mosquitoes.

Data Availability Statement

All relevant data are within the manuscript and its Supporting Information file.
Water Resource Management: IWRM strategies for Improved Water Management. A Systematic Review of Case Studies of East, West and Southern Africa
Authors: Dirwai Tinashe Lindel , Kanda Edwin Kimuta , Senzanje Aidan , Busari Toyin Isiaka
Published: July 2020

Objective

The analytical study systematically reviewed the evidence about the IWRM water strategy model. The study analysed the IWRM strategy advances and practical implications it had, since inception on effective water management in East, West and Southern Africa.

Methods

The study adopted the Preferred Reporting Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) and the scoping literature review approach. The study searched selected databases for peer-reviewed articles, books, and grey literature. DistillerSR software was used for article screening. A constructionist thematic analysis was employed to extract recurring themes amongst the regions.

Results

The systematic literature review detailed the adoption, policy revisions and growing/emerging policy trends and issues (or considerations) on IWRM in East, West and Southern Africa. Thematic analysis derived four cross-cutting themes that contributed to IWRM strategy implementation and adoption. The identified four themes were donor effect, water scarcity, transboundary water resources, and policy approach. The output further posited questions on the prospects, including whether IWRM has been a success or failure with the African water resource management fraternity.

Graphical Abstract
Novel candidates of pathogenic variants of theBRCA1andBRCA2genes in a 3,552 Japanese whole-genome sequence dataset (3.5KJPNv2)
Authors: Tokunaga Hideki , Iida Keita , Hozawa Atsushi , Ogishima Soichi , Watanabe Yoh , Shigeta Shogo , Shimada Muneaki , Yamaguchi-Kabata Yumi , Tadaka Shu , Katsuoka Fumiki , Ito Shin , Kumada Kazuki , Hamanaka Yohei , Fuse Nobuo , Kinoshita Kengo , Yamamoto Masayuki , Yaegashi Nobuo , Yasuda Jun
Published: July 2020

Identification of pathogenic germline variants yet no clinical evidence inBRCAgenes has become important in patient care of hereditary breast and ovarian cancer syndrome (HBOC). Computational scoring and prospective cohort studies may help to identify such pathogenic variants. We annotated the variants in theBRCA1andBRCA2genes from a dataset of 3,552 whole-genome sequences obtained from members of the genome cohorts by Tohoku Medical Megabank Project (TMM) with the InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAF) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar are used for filtration criteria. Familial predispositions in cancers among the 35,000 TMM genome cohort participants are analyzed to verify the pathogenicity. Seven potentially pathogenic variants were newly identified. Carriers of these potential pathogenic variants and definite P and LP variants among participants of the TMM prospective cohort show a statistically significant preponderance in cancer onset in sisters in the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potential pathogenic variants inBRCAgenes for Japanese population. These results will be helpful to follow up the carriers of variants of uncertain significance in the HBOC genes.
The human cytomegalovirus protein UL147A downregulates the most prevalent MICA allele: MICA*008, to evade NK cell-mediated killing
Authors: Seidel Einat , Dassa Liat , Oiknine-Djian Esther , Wolf Dana G. , Le-Trilling Vu Thuy Khanh , Mandelboim Ofer
Published: July 2020

Natural killer (NK) cells are innate immune lymphocytes capable of killing target cells without prior sensitization. NK cell activity is regulated by signals received from activating and inhibitory receptors. One pivotal activating NK receptor is NKG2D, which binds a family of eight ligands, including the major histocompatibility complex (MHC) class I-related chain A (MICA). Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus causing morbidity and mortality in immunosuppressed patients and congenitally infected infants. HCMV encodes multiple antagonists of NK cell activation, including many mechanisms targeting MICA. However, only one of these mechanisms counters the most prevalent MICA allele, MICA*008. Here, we discover that a hitherto uncharacterized HCMV protein, UL147A, specifically targets MICA*008 to proteasomal degradation, thus hindering the elimination of HCMV-infected cells by NK cells. Mechanistic analyses disclose that the non-canonical GPI anchoring pathway of immature MICA*008 constitutes the determinant of UL147A specificity for this MICA allele. These findings advance our understanding of the complex and rapidly evolving HCMV immune evasion mechanisms, which may facilitate the development of antiviral drugs and vaccines.

Author Summary

Human cytomegalovirus (HCMV) is a common pathogen that usually causes asymptomatic infection in the immunocompetent population, but the immunosuppressed and fetuses infectedin uterosuffer mortality and disability due to HCMV disease. Current HCMV treatments are limited and no vaccine has been approved, despite significant efforts. HCMV encodes many genes of unknown function, and virus-host interactions are only partially understood. Here, we discovered that a hitherto uncharacterized HCMV protein, UL147A, downregulates the expression of an activating immune ligand allele named MICA*008, thus hindering the elimination of HCMV-infected cells. Elucidating HCMV immune evasion mechanisms could aid in the development of novel HCMV treatments and vaccines. Furthermore, MICA*008 is a highly prevalent allele implicated in cancer immune evasion, autoimmunity and graft rejection. In this work we have shown that UL147A interferes with MICA*008’s poorly understood, nonstandard maturation pathway. Study of UL147A may enable manipulation of its expression as a therapeutic measure against HCMV.
Genome-Scale CRISPR Screening reveals novel factors regulating Wnt-dependent regeneration of mouse gastric organoids
Authors: Murakami Kazuhiro , Terakado Yumi , Saito Kikue , Jomen Yoshie , Takeda Haruna , Oshima Masanobu , Barker Nick
Published: July 2020

An ability to safely harness the powerful regenerative potential of adult stem cells for clinical applications is critically dependent on a comprehensive understanding of the underlying mechanisms regulating their activity. Epithelial organoid cultures accurately recapitulate many features ofin vivostem cell-driven epithelial regeneration, providing an excellentex vivoplatform for interrogation of key regulatory mechanisms. Here, we employed a Genome-Scale CRISPR Knock-Out (GeCKO) screening assay using mouse gastric epithelial organoids to identify novel modulators of Wnt-driven stem cell-dependent epithelial regeneration in the gastric mucosa. In addition to known Wnt pathway regulators such asApc, we found that knock-out (KO) ofAlk,Bclaf3orPrkrasupports the Wnt independent self-renewal of gastric epithelial cellsex vivo. In adult mice, expression of these factors is predominantly restricted to nonLgr5-expressing stem cell zones above the gland base, implicating a critical role for these factors in suppressing Wnt-dependent self-renewal of gastric epithelia. Furthermore, using comprehensive RNA-sequencing analysis, we found that these factors influence epithelial regeneration by regulating Wnt signalling, apoptosis and expression of Reg family genes which could contribute to the epithelial regeneration through JAK/STAT3 pathway.
Antiquity and fundamental processes of the antler cycle in Cervidae (Mammalia)
Authors: Rössner Gertrud E. , Costeur Loïc , Scheyer Torsten M.
Published: July 2020

The origins of the regenerative nature of antlers, being branched and deciduous apophyseal appendages of frontal bones of cervid artiodactyls, have long been associated with permanent evolutionary precursors. In this study, we provide novel insight into growth modes of evolutionary early antlers. We analysed a total of 34 early antlers affiliated to ten species, including the oldest known, dating from the early and middle Miocene (approx. 19 to 12 million years old) of Europe. Our findings provide empirical data from the fossil record to demonstrate that growth patterns and a regular cycle of necrosis, abscission and regeneration are consistent with data from modern antlers. The diverse histological analyses indicate that primary processes and mechanisms of the modern antler cycle were not gradually acquired during evolution, but were fundamental from the earliest record of antler evolution and, hence, explanations why deer shed antlers have to be rooted in basic histogenetic mechanisms.
Free fatty-acid receptor 4 inhibitory signaling in delta cells regulates islet hormone secretion in mice
Authors: Croze Marine L. , Flisher Marcus F. , Guillaume Arthur , Tremblay Caroline , Noguchi Glyn M. , Granziera Sabrina , Vivot Kevin , Castillo Vincent C. , Campbell Scott A. , Ghislain Julien , Huising Mark O. , Poitout Vincent
Published: July 2020

Objective

Maintenance of glucose homeostasis requires the precise regulation of hormone secretion from the endocrine pancreas. Free fatty-acid receptor 4 (FFAR4/GPR120) is a G protein-coupled receptor whose activation in islets of Langerhans promotes insulin and glucagon secretion and inhibits somatostatin secretion. However, the contribution of individual islet cell types (α, β, and δ cells) to the insulinotropic and glucagonotropic effects of GPR120 remains unclear. Asgpr120mRNA is enriched in somatostatin-secreting δ cells, we hypothesized that GPR120 activation stimulates insulin and glucagon secretion via inhibition of somatostatin release.

Methods

Glucose tolerance tests were performed in mice after administration of the selective GPR120 agonist Compound A. Insulin, glucagon and somatostatin secretion were measured in static incubations of isolated mouse islets in response to endogenous (ω-3 polyunsaturated fatty acids) and/or pharmacological (Compound A and AZ-13581837) GPR120 agonists. The effect of Compound A on hormone secretion was tested further in islets isolated from mice with global or somatostatin cell-specific knockout ofgpr120.Gpr120expression was assessed in pancreatic sections by RNA in situ hybridization. Cyclic AMP (cAMP) and calcium dynamics in response to pharmacological GPR120 agonists were measured specifically in α, β and δ cells in intact islets using cAMPER and GCaMP6 reporter mice, respectively.

Results

Acute exposure to Compound A increased glucose tolerance and circulating insulin and glucagon levels in vivo. Endogenous and/or pharmacological and GPR120 agonists reduced somatostatin secretion in isolated islets and concomitantly demonstrated dose-dependent potentiation of glucose-stimulated insulin secretion and arginine-stimulated glucagon secretion.Gpr120was enriched in δ cells. Pharmacological GPR120 agonists reduced cAMP and calcium levels in δ cells but increased these signals in α and β cells. Compound A-mediated inhibition of somatostatin secretion was insensitive to pertussis toxin. The effect of Compound A on hormone secretion was completely absent in islets from mice with either global or somatostatin cell-specific deletion ofgpr120and was partially reduced upon blockade of somatostatin receptor signaling by cyclosomatostatin.

Conclusions

Inhibitory GPR120 signaling in δ cells contributes to both insulin and glucagon secretion in part via mitigating somatostatin release.
Vitamin D Sufficiency Enhances Differentiation of Patient-Derived Prostate Epithelial Organoids
Authors: McCray Tara , Pacheco Julian , Baumann Bethany , Schlicht Michael J , Valyi-Nagy Klara , Nonn Larisa
Published: July 2020

Vitamin D is an essential steroid hormone that regulates systemic calcium homeostasis and cell fate decisions, including differentiation in many cell types. The prostate gland is hormonally regulated, requiring steroids for proliferation and terminal differentiation of secretory luminal cells. Vitamin D deficiency is associated with higher risk of lethal prostate cancer with an aggressive dedifferentiated pathology, linking vitamin D sufficiency to epithelial differentiation homeostasis. To determine regulation of prostate epithelial differentiation by vitamin D status, patient-derived benign prostate epithelial organoids were maintained in vitamin D deficient (vehicle) or sufficient (10 nM 1,25-dihydroxyvitamin D) conditions and assessed by phenotype and single cell RNA sequencing. Mechanistic validation demonstrated that vitamin D sufficiency promoted organoid growth and accelerated differentiation of lineage-committed cells by inhibiting canonical Wnt activity and Wnt family member DKK3. Wnt dysregulation is a known contributor to aggressive prostate cancer, thus these findings further link vitamin D deficiency to lethal disease.
Large-scale study validates that regional fungicide applications are major determinants of resistance evolution in the wheat pathogenZymoseptoria triticiin France
Authors: Garnault Maxime , Duplaix Clémentine , Leroux Pierre , Couleaud Gilles , David Olivier , Walker Anne-Sophie , Carpentier Florence
Published: July 2020

Research rationale: In modern cropping systems, the near-universal use of plant protection products selects for resistance in pest populations. The emergence and evolution of this adaptive trait threaten treatment efficacy. We identified determinants of fungicide resistance evolution and quantified their effects at a large spatiotemporal scale.

Methods: We focused onZymoseptoria tritici, which causes leaf blotch in wheat. Phenotypes of qualitative or quantitative resistance to various fungicides were monitored annually, from 2004 to 2017, at about 70 sites throughout 22 regions of France (territorial units of 25 000km2on average). We modelled changes in resistance frequency with regional anti-Septoriafungicide use, yield losses due to the disease and the regional area under organic wheat.

Key results: The major driver of resistance dynamics was fungicide use at the regional scale. We estimated its effect on the increase in resistance and relative apparent fitness of each resistance phenotype. The predictions of the model replicated the spatiotemporal patterns of resistance observed in field populations (R2from 0.56 to 0.82).

Main conclusion: The evolution of fungicide resistance is mainly determined at the regional scale. This study therefore showed that collective management at the regional scale could effectively complete local actions.
The First Mitotic Division of the Human Embryo is Highly Error-prone
Authors: Ford Emma , Currie Cerys E. , Taylor Deborah M. , Erent Muriel , Marston Adele L. , Hartshorne Geraldine M. , McAinsh Andrew D.
Published: July 2020

Aneuploidy in human embryos is surprisingly prevalent and increases drastically with maternal age, resulting in miscarriages, infertility and birth defects. Frequent errors during the meiotic divisions cause this aneuploidy, while age-independent errors during the first cleavage divisions of the embryo also contribute. However, the underlying mechanisms are poorly understood, largely because these events have never been visualised in living human embryos. Here, using cell-permeable DNA dyes, we film chromosome segregation during the first and second mitotic cleavage divisions in human embryos from women undergoing assisted reproduction following ovarian stimulation. We show that the first mitotic division takes several hours to complete and is highly variable. Timings of key mitotic events were, however, largely consistent with clinical videos of embryos that gave rise to live births. Multipolar divisions and lagging chromosomes during anaphase were frequent with no maternal age association. In contrast, the second mitosis was shorter and underwent mostly bipolar divisions with no detectable lagging chromosomes. We propose that the first mitotic division in humans is a unique and highly error-prone event, which contributes to fetal aneuploidies.
Making data-driven hypotheses for gene functions by integrating dependency, expression, and literature data
Authors: Hirschey Matthew D.
Published: July 2020

Identifying the key functions of human genes is a major biomedical research goal. While some genes are well-studied, most human genes we know little about. New tools in data science -- a combination of computer programming, math & statistics, and topical expertise -- combined with the rapid adoption of open science and data sharing allow scientists to access publicly available datasets and interrogate these databeforeperforming any experiments. We present here a new research tool called data-driven hypothesis (DDH) for predicting pathways and functions for thousands of genes across the human genome. Importantly, this method integrates gene essentiality, gene expression, and literature mining to identify candidate molecular functions or pathways of known and unknown genes. Beyond single gene queries, DDH can uniquely handle queries of defined gene ontology pathways or custom gene lists containing multiple genes. The DDH project holds tremendous promise to generate hypotheses, data, and knowledge in order to provide a deep understanding of the dynamic properties of mammalian genes. We present this tool via an intuitive online interface, which will provide the scientific community a platform to query and prioritize experimental hypotheses to test in the lab.
Sex-biased gene expression in rhesus macaque and human brains
Authors: DeCasien Alex R. , Sherwood Chet C. , Higham James P.
Published: July 2020

Sexually dimorphic traits (i.e. phenotypic differences between males and females) are largely produced by sex-biased gene expression (i.e. differential expression of genes present in both sexes). These expression differences may be the result of sexual selection, although other factors (e.g., relaxed purifying selection, pleiotropy, dosage compensation) also contribute. Given that humans and other primates exhibit sex differences in cognition and neuroanatomy, this implicates sex differences in brain gene expression. Here, we compare sex-biased gene expression in humans and rhesus macaques across 16 brain regions using published RNA-Seq datasets. Our results demonstrate that most sex-biased genes are differentially expressed between species, and that overlap across species is limited. Human brains are relatively more sexually dimorphic and exhibit more male-than female-biased genes. Across species, gene expression is biased in opposite directions in some regions and in the same direction in others, suggesting that the latter may be more relevant in nonhuman primate models of neurological disorders. Finally, the brains of both species exhibit positive correlations between sex effects across regions, higher tissue specificity among sex-biased genes, enrichment of extracellular matrix among male-biased genes, and regulation of sex-biased genes by sex hormones. Taken together, our results demonstrate some conserved mechanisms underlying sex-biased brain gene expression, while also suggesting that increased neurodevelopmental plasticity and/or strong sexual selection on cognitive abilities may have played a role in shaping sex-biased brain gene expression in the human lineage.