bluuebunny/crossref_metadata_2025 huggingface dataset:
N-terminal modification of actin by acetylation and arginylation determines the architecture and assembly rate of linear and branched actin networks
Authors: Chin Samantha M. , Hatano Tomoyuki , Sivashanmugam Lavanya , Suchenko Andrejus , Kashina Anna S. , Balasubramanian Mohan K. , Jansen Silvia
Published: June 2020

The great diversity in actin network architectures and dynamics is exploited by cells to drive fundamental biological processes, including cell migration, endocytosis and cell division. While it is known that this versatility is the result of the many actin-remodeling activities of actin-binding proteins, recent work implicates post-translational modification of the actin N-terminus by either acetylation or arginylation itself as an equally important regulatory mechanism. However, the molecular mechanisms by which acetylation and arginylation alter the properties of actin are not well understood. Here, we directly compare how processing, and modification of the N-terminus of actin affects its intrinsic polymerization dynamics and its remodeling by actin-binding proteins that are essential for cell migration. We find that in comparison to acetylated actin, arginylated actin reduces intrinsic as well as formin-mediated elongation and Arp2/3-mediated nucleation. By contrast, there are no significant differences in Cofilin-mediated severing. Taken together, these results suggest that cells can employ the differently modified actins to precisely regulate actin dynamics. In addition, unprocessed, or non-acetylated actin show very different effects on formin-mediated-elongation, Arp2/3-mediated nucleation, and severing by Cofilin. Altogether, this study shows that the nature of the N-terminus of actin can induce distinct actin network dynamics, which can be differentially used by cells to locally finetune actin dynamics at distinct cellular locations, such as at the leading edge.
An unbiased, quantitative and versatile method for determining misaligned and lagging chromosome during mitosis
Authors: Braga Luciano Gama , Prifti Diogjena Katerina , Garand Chantal , Saini Pawan Kumar , Elowe Sabine
Published: June 2020

Accurate chromosome alignment at metaphase facilitates the equal segregation of sister chromatids to each of the nascent daughter cells. Lack of proper metaphase alignment is an indicator of defective chromosome congression and aberrant kinetochore-microtubule attachments which in turn promotes chromosome missegregation and aneuploidy, hallmarks of cancer. Therefore, tools to sensitively and quantitatively measure chromosome alignment at metaphase will facilitate understanding of how changes in the composition and regulation of the microtubule attachment machinery impinge on this process. In this work, we have developed and validated a method based on analytical geometry to measure several indicators of chromosome misalignment. We generated semi-automated and flexible ImageJ2/Fiji pipelines to quantify kinetochore misalignment at metaphase plates as well as lagging chromosomes at anaphase. These tools will ultimately allow sensitive, unbiased, and systematic quantitation of these chromosome segregation defects in cells undergoing mitosis.
Resource optimization in COVID-19 diagnosis
Authors: Taniwaki S.A , Silva S.O.S , Santana-Clavijo N.F , Conselheiro J. A , Barone G.T , Menezes A.A.R , Pereira E.S , Brandão P.E
Published: June 2020

Abtsract

The emergence and rapid dissemination worldwide of a novelCoronavirus(SARS-CoV-2) results in decrease of swabs availability for clinical samples collection, as well as, reagents for RT-qPCR diagnostic kits considered a confirmatory test for COVID-19 infection. This scenario, showed the requirement of improve de diagnostic capacity, so the aim of this study were to verify the possibility of reducing the reaction volume of RT-qPCR and to test cotton swabs as alternative for sample collection. RT-qPCR volumes and RNA sample concentration were optimized without affecting the sensitivity of assays, using both probe-based and intercalation dyes methods. Although rayon swabs showed better performance, cotton swabs could be used as alternative type for clinical sample collection. COVID-19 laboratory diagnosis is important to isolate and restrict the dissemination of virus, so seek for alternatives to decrease the coast of assays improve the control of disease.
Myristoylation alone is sufficient for PKA catalytic subunits to fractionally associate with the plasma membrane to regulate neuronal functions
Authors: Xiong Wei-Hong , Qin Maozhen , Zhong Haining
Published: June 2020

Myristoylation is a post-translational modification that plays diverse functional roles in many protein species. The myristate moiety is considered insufficient for protein-membrane associations unless additional membrane-affinity motifs, such as a stretch of positively charged residues, are present. Here, we report that the electrically neutral N-terminal fragment of the protein kinase A catalytic subunit (PKA-C), in which myristoylation is the only functional motif, is sufficient for membrane association. This myristoylation can associate a fraction of PKA-C molecules or fluorescent proteins (FPs) to the plasma membrane in neuronal dendrites. The net neutral charge of PKA-C is evolutionally conserved, even though its membrane affinity can be readily tuned by changing charges near the myristoylation site. The observed membrane association, while moderate, is sufficient to concentrate PKA activity at the membrane by nearly 20-fold, and is required for PKA regulation of AMPA receptors at neuronal synapses. Our results indicate that myristoylation alone may be sufficient to drive functionally significant membrane association in the absence of assisting motifs. This provides a revised foundation for the understanding of how myristoylation regulates protein functions.
Abnormalities of the rib growth plate and the periphysis of previously healthy infants and toddlers dying suddenly and unexpectedly
Authors: Groff Elisa , Uday Suma , Zapata Vázquez Rita , Zainun Khairul , Cohen Marta C
Published: June 2020

Aims

Histological examination of the rib is of critical value in perinatal pathology and points to the health of the child preceding death. The rib is considered ideal because it is the most rapidly growing long bone in infants and demonstrates growth arrest at onset of the insult. We aimed to identify: 1: changes in the perichondrial ring in the rib of infants and children up to 16 months of age dying suddenly at our institution and 2: any association with presence of histological changes of vitamin D deficiency (VDD) /metabolic bone disease (MBD) in the growth plate.

Methods

Retrospective review of the perichondrial rib histology and comparison with the presence or absence of histological features of VDD in the growth plate of 167 cases. The cases were anonymised and divided in six age/sex categories.

Results

Periphyseal abnormalities were only seen in 38% of the cases; of whom 33% had established and 67% had mild changes. Only 14.5% of cases with established histological appearance of VDD at the growth plate had significant PR abnormality; of whom majority (83%) were ≤3 months of age and none ≥9 months old, reflecting a temporal relation with birth and beyond the perinatal period.

Conclusion

The histological changes in the perichondrial ring are significantly associated with histological changes of VDD /MBD at the rib growth plate with an Odds Ratio of 3.04.
Evaluation on the diagnostic efficiency of different methods in detecting COVID-19
Authors: Yang Haitao , Lan Yuzhu , Yao Xiujuan , Lin Sheng , Xie Baosong
Published: June 2020

Objective

To evaluate the diagnostic efficiency of different methods in detecting COVID-19 to provide preliminary evidence on choosing favourable method for COVID-19 detection.

Methods

PubMed, Web of Science and Embase databases were searched for identifing eligible articles. All data were calculated utilizing Meta Disc 1.4, Revman 5.3.2 and Stata 12. The diagnostic efficiency was assessed via these indicators including summary sensitivity and specificity, positive likelihood ratio (PLR), negative LR (NLR), diagnostic odds ratio (DOR), summary receiver operating characteristic curve (sROC) and calculate the AUC.

Results

18 articles (3648 cases) were included. The results showed no significant threshold exist. EPlex: pooled sensitivity was 0.94; specificity was 1.0; PLR was 90.91; NLR was 0.07; DOR was 1409.49; AUC=0.9979, Q*=0.9840. Panther Fusion: pooled sensitivity was 0.99; specificity was 0.98; PLR was 42.46; NLR was 0.02; DOR was 2300.38; AUC=0.9970, Q*=0.9799. Simplexa: pooled sensitivity was 1.0; specificity was 0.97; PLR was 26.67; NLR was 0.01; DOR was 3100.93; AUC=0.9970, Q*=0.9800. Cobas®: pooled sensitivity was 0.99; specificity was 0.96; PLR was 37.82; NLR was 0.02; DOR was 3754.05; AUC=0.9973, Q*=0.9810. RT-LAMP: pooled sensitivity was 0.98; specificity was 0.99; PLR was 36.22; NLR was 0.04; DOR was 751.24; AUC=0.9905, Q*=0.9596. Xpert Xpress: pooled sensitivity was 0.99; specificity was 0.97; PLR was 27.44; NLR was 0.01; DOR was 3488.15; AUC=0.9977, Q*=0.9829.

Conclusions

These methods (ePlex, Panther Fusion, Simplexa, Cobas®, RT-LAMP and Xpert Xpress) bear higher sensitivity and specificity, and might be efficient methods complement to the gold standard.
COVID-19 Confirmed Cases and Fatalities in 883 U.S. Counties with a Population of 50,000 or More: Predictions Based on Social, Economic, Demographic Factors and Shutdown Days
Authors: Robertson Leon S.
Published: June 2020

The spread of the COVID-19 virus is highly variable among U.S. counties. Seventeen factors known or thought to be related to spread of the COVID-19 virus were studied by Poisson regression analysis of confirmed cases and deaths in 883 U.S. counties with a population of 50,000 or more as of May 31, 2020. With little exception, each factor was predictive of incidence and mortality. The regression equation can be used to identify priority locations for preventive efforts and preparation for medical care caseloads when prevention is unsuccessful. Based on the correlation of cases and deaths to days since stay-at-home orders were issued, the orders reduced the cases about 48 percent and deaths about 50 percent. Focusing preventive efforts on the more vulnerable counties may be more effective and less economically damaging than statewide shutdowns.
Sex influences the effects of APOE genotype and Alzheimer’s diagnosis on neuropathology and memory
Authors: Duarte-Guterman Paula , Albert Arianne Y. , Barha Cindy K. , Galea Liisa A.M.
Published: June 2020

Alzheimer’s disease (AD) is characterised by severe cognitive decline and pathological changes in the brain (brain atrophy, hyperphosphorylation of tau, and deposition of toxic amyloid-beta protein). Females have greater neuropathology (AD biomarkers and brain atrophy rates) and cognitive decline than males, however these effects can depend on diagnosis (amnestic mild cognitive impairment (aMCI) or AD) and APOE genotype (presence of ε4 alleles). Using the ADNI database (N=630 females, N=830 males), we analysed the effect of sex, APOE genotype (non-carriers or carriers of APOEε4 alleles), and diagnosis (cognitively normal (CN), early aMCI (EMCI), late aMCI (LMCI), probable AD) on cognition (memory and executive function), hippocampal volume, and AD biomarkers (CSF levels of amyloid beta, tau and ptau). Regardless of APOE genotype, memory scores were higher in CN, EMCI, and LMCI females compared to males but this sex difference was absent in probable AD, which may suggest a delay in the onset of cognitive decline or diagnosis and/or a faster trajectory of cognitive decline in females. We found that, regardless of diagnosis, CSF tau-pathology was disproportionately elevated in female carriers of APOEε4 alleles compared to males. In contrast, male carriers of APOEε4 alleles had reduced levels of CSF amyloid beta compared to females, irrespective of diagnosis. We also detected sex differences in hippocampal volume but the direction was dependent on the method of correction. Altogether results suggest that across diagnosis females show greater memory decline compared to males and APOE genotype affects AD neuropathology differently in males and females which may influence sex differences in incidence and progression of aMCI and AD.
Transgender fathering: children’s psychological and family outcomes
Authors: Condat Agnès , Mamou Grégor , Lagrange Chrystelle , Mendes Nicolas , Wielart Joy , Poirier Fanny , Medjkane François , Brunelle Julie , Drouineaud Véronique , Rosenblum Ouriel , Gründler Nouria , Ansermet François , Wolf Jean-Philippe , Falissard Bruno , Cohen David
Published: June 2020

Medical advances in assisted reproductive technology have created new ways for transgender persons to become parents outside the context of adoption. The paucity of empirical data does not support the idea that trans-parenthood negatively impacts children’s development. However, the question has led to lively societal debates making the need for evidence-based studies urgent.

We aimed to compare cognitive development, mental health, gender identity, quality of life and family dynamics using standardized instruments and experimental protocols in 32 children who were conceived by donor sperm insemination (DSI) in couples with a cisgender woman and a transgender man, the transition occurring before conception. We constituted two control groups matched for age, gender and family status.

We found no significant difference between groups regarding cognitive development, mental health, and gender identity, meaning that neither the trans factor nor the use of DSI had any impact on these characteristics. The results of the descriptive analysis showed positive psycho-emotional development. Additionally, when we asked raters to differentiate the family drawings of the group of children of trans-fathers from those who were naturally conceived, no rater was able to differentiate the groups above chance levels, meaning that what children expressed through family drawing did not indicate cues related to trans-fatherhood. However, when we assessed mothers and fathers with the Five-Minute Speech Sample, we found that the emotions expressed by transgender fathers were higher than those of cisgender fathers who conceived by sex or by DSI.

We conclude that the first empirical data regarding child development in the context of trans-parenthood are reassuring. We believe that this research will also improve transgender couple care and that of their children in a society where access to care remains difficult in this population. However, further research is needed with adolescents and young adults.
BATF3-dependent induction of IL-27 in B cells bridges the innate and adaptive stages of the antibody response
Authors: Yan Hui , Wang Rui , Wang Jingwei , Wu Shuai , Fernandez Maria , Rivera Carlos E. , Cervantes Christian , Moroney Justin B. , Li Xiao-Dong , Zhang Nu , Zan Hong , Meng Xiangzhi , Zhang Fushun , Zheng Siyuan , Chen Yidong , Yin Zhinan , Kedl Ross , Min Booki , Hunter Christopher A. , Xiang Yan , Casali Paolo , Xu Zhenming
Published: June 2020

B cells are exposed to innate and T cell stimuli during the antibody response, although whether and how they functionally integrate such signals are unclear. Here we have identified IL-27 as the cytokine specifically produced by murine B cells upon sequential stimulation by TLR ligands and then CD154 and IL-21, the hallmark factors of T follicular helper cells, and during the T-dependent antibody response to a conjugated hapten or virus infection. B-cellIl27p28transcription is concomitant with increased locus accessibility and depends on newly induced BATF3 transcription factor. IL-27-producing B cells are inefficient in antibody secretion, but cooperate with IFNγ to promote proliferation, survival, class-switching and plasma cell differentiation of CD40-activated B cells, leading to optimal IgG2a and IgG1 responses. Overall, IL-27-producing B cells function as “helper” B cells that integrate the innate and adaptive stages of the antibody response.

One-sentence summary

B cells integrate innate TLR and adaptive CD40 signals to induce BATF3 transcription factor for production of IL-27, which together with INFg optimizes antibody responses.
Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction inBrassica napus
Authors: Scheben Armin , Severn-Ellis Anita , Patel Dhwani , Pradhan Aneeta , Rae Stephen , Batley Jacqueline , Edwards David
Published: June 2020

Brassica napusis an important oilseed crop cultivated worldwide. During domestication and breeding ofB. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering inB. napus. An F2mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ∼12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3,605.70 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trail locus (QTL) on chromosome C2 was detected in the vicinity of flowering time genes includingFTandFLC. These findings demonstrate the effectiveness of the ddRAD approach to sample theB. napusgenome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
An exon DNA element modulates heterochromatin spreading in the master regulator for sexual commitment in malaria parasites
Authors: Cordon-Obras Carlos , Barcons-Simon Anna , Scheidig-Benatar Christine , Claës Aurelie , Sabatet Valentin , Loew Damarys , Scherf Artur
Published: June 2020

Heterochromatin is essential in all eukaryotes to maintain genome integrity, long-term gene repression and to help chromosome segregation during mitosis. However, heterochromatin regions must be restricted by boundary elements to avoid its spreading over actively transcribed loci. InPlasmodium falciparum, facultative heterochromatin is important to regulate parasite virulence, antigenic variation and transmission. However, the underlying molecular mechanisms regulating repressive regions remain unknown. To investigate this topic, we chose theap2-ggene, which forms a strictly delimited and independent heterochromatin island. Using electrophoretic motility shift assay (EMSA) we identified anap2-gexon element at the 3’ end binding nuclear protein complexes. Upon replacement of this region by agfpgene, we observed a shift in the heterochromatin boundary resulting in HP1 (Heterochromatin Protein 1) spreading over ∼2 additional kb downstream. We used this DNA element to purify candidate proteins followed by proteomic analysis. The identified complexes were found to be enriched in RNA-binding proteins, pointing to a potential role of RNA in the regulation of theap2-g3’ heterochromatin boundary. Our results provide insight into the unexplored topic of heterochromatin biology inP. falciparumand identify a DNA element within the master regulator of sexual commitment modulating heterochromatin spreading.
Virus-host protein-protein interactions between human papillomavirus 16 E6 A1 and D2/D3 sub-lineages: variances and similarities
Authors: Dayer Guillem , Masoom Mehran L. , Togtema Melissa , Zehbe Ingeborg
Published: June 2020

High-risk strains of human papillomavirus are causative agents for cervical and other mucosal cancers with type 16 being the most frequent. Compared to the European Prototype (A1, denoted “EP”), the Asian-American (D2/D3, denoted “AA”) sub-lineage or “variant” is reported to have increased abilities to promote carcinogenesis. Few global interactome studies have looked at protein-protein interactions (PPIs) between host proteins and variants of the key transforming E6 protein. We applied a primary human foreskin keratinocyte model transduced with EP and AA variant E6 genes and co-immunoprecipitated expressed E6 proteins along with interacting cellular proteins to detect virus-host binding partners. We reasoned that, due to single nucleotide polymorphisms, AAE6 and EPE6 may have unique PPIs with host cellular proteins—conferring gain or loss of function—resulting in varied abilities to promote carcinogenesis. Using liquid chromatography-mass spectrometry and stringent interactor selection criteria based on the number of peptides, we identified 25 candidates: 6 unique to each of AAE6 and EPE6, along with 13 E6 targets common to both AAE6 and EPE6. We also applied a more inclusive process based on pathway selection and discovered 171 target proteins: 90 unique AAE6 and 61 unique EPE6 along with 20 common E6 targets between the two sub-lineages. Interpretations for both approaches were made using databases such as UniProt, BioGRID and Reactome. Detected E6 targets are implicated in important hallmarks of cancer: deregulating Notch and other signaling, energetics and hypoxia, DNA replication and repair, and immune response. Validation experiments, such as reverse co-immunoprecipitation and RNA interference, are required to substantiate these findings. Here, we provide an unprecedented resource for new research questions in HR HPV biology. The current data also underline our lab’s driving hypothesis that E6, being a “master regulator” in HPV-positive cancers, is an excellent candidate for anti-cancer treatment strategies.

Author Summary

Chronic infection with high-risk human papillomavirus (HPV) type 16 is the most prevalent cause of cervical and other mucosal cancers. The E6 oncoproteins of the European Prototype (EP) and the Asian-American (AA) HPV variants differentially promote carcinogenesis. We looked at protein-protein interactions between host proteins and two key HPV variant E6 proteins of these strains to reveal how high risk HPVs cause cancer, based on the proteins they bind to in infected cells. Our methodology combined molecular biology and data mining techniques using widely available databases. We confirmed and discovered novel virus-host associations that explained how HPV AA and EP variants differ in their carcinogenic capabilities, and confirmed the candidacy of the E6 protein as a viable target for HPV therapies.
Normal mammary epithelia accumulate DNA methylation changes with age that are consistent with breast cancer methylomes
Authors: Senapati Parijat , Miyano Masaru , Sayaman Rosalyn W. , Basam Mudaser , Trac Candi , Leung Amy , LaBarge Mark A. , Schones Dustin E.
Published: June 2020

Luminal epithelial cells (LEps) are a key cell lineage implicated in age-related luminal breast cancers. Alterations to the epigenome are a hallmark of aging cells. However, the extent of age-associated DNA methylation alterations in LEps, and the corresponding functional consequences of these alterations, have remained unclear. We report here that aging leads to distinct methylation changes in LEps. Luminal lineage-specific genes gain promoter methylation, whereas myoepithelial-specific genes lose promoter methylation. Regulatory elements display methylation changes at lineage-specific TF binding sites consistent with the loss of lineage fidelity. CpG islands (CGIs) and transposable elements (TEs) have stochastic methylation gain and loss, respectively. PRC2 target genes that are hypermethylated in luminal breast cancer exhibit stochastic methylation increase with age. TEs with stochastic methylation loss are activated in breast cancer and potentially function as regulatory elements contributing to the loss of lineage fidelity with age. Each of these classes of methylation changes impact the regulation of genes associated with luminal breast cancer. Altogether, our results indicate that aging leads to DNA methylation changes that could determine breast cancer susceptibility.

Significance

Mammary luminal epithelial cells lose lineage-specific expression with age and accumulate stochastic methylation changes that lead to loss of silencing at transposable elements. These age-dependent events potentially promote breast cancer susceptibility.
Evaluation of K18-hACE2mice as a model of SARS-CoV-2 infection
Authors: Moreau G. Brett , Burgess Stacey L. , Sturek Jeffrey M. , Donlan Alexandra N. , Petri William A. , Mann Barbara J.
Published: June 2020

Abstract/Summary

Murine models of SARS-CoV-2 infection are critical for elucidating the biological pathways underlying COVID-19 disease. Because human ACE2 is the receptor for SARS-CoV-2, mice expressing the humanACE2gene have shown promise as a potential model for COVID-19. Five mice from the transgenic mouse strain K18-hACE2were intranasally inoculated with SARS-CoV-2 Hong Kong/VM20001061/2020. Mice were followed twice daily for five days and scored for weight loss and clinical symptoms. Infected mice did not exhibit any signs of infection until day four, when weight loss, but no other obvious clinical symptoms were observed. By day five all infected mice had lost around 10% of their original body weight, but exhibited variable clinical symptoms. All infected mice showed high viral titers in the lungs as well as altered lung histology associated with proteinaceous debris in the alveolar space, interstitial inflammatory cell infiltration and alveolar septal thickening. Overall, these results show that symptomatic SARS-CoV-2 infection can be established in the K18-hACE2transgenic background and should be a useful mouse model for COVID-19 disease.
Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit
Authors: Balliau Thierry , Duruflé Harold , Blanchet Nicolas , Blein-Nicolas Mélisande , Langlade Nicolas B. , Zivy Michel
Published: June 2020

This article describes how the proteomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower. They included both inbred lines and their hybrids

Water deficit was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide proteomic data from sunflower leaves corresponding to the identification of 3062 proteins and the quantification of 1211 of them in these 24 genotypes grown in two watering conditions. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the molecular basis of heterosis.
Dopachrome tautomerase variants in patients with oculocutaneous albinism
Authors: Pennamen Perrine , Tingaud-Sequeira Angèle , Gazova Iveta , Keighren Margaret , McKie Lisa , Marlin Sandrine , Halem Souad Gherbi , Kaplan Josseline , Delevoye Cédric , Lacombe Didier , Plaisant Claudio , Michaud Vincent , Lasseaux Eulalie , Javerzat Sophie , Jackson Ian , Arveiler Benoit
Published: June 2020

Purpose

Albinism is a clinically and genetically heterogeneous condition. Despite analysis of the nineteen known genes, ∼30% patients remain unsolved. We aimed to identify new genes involved in albinism.

Methods

We sequenced a panel of genes with known or predicted involvement in melanogenesis in 230 unsolved albinism patients.

Results

We identified variants in theDopachrome tautomerase(DCT) gene in two patients. One was compound heterozygous for a 14 bp deletion in exon 9 and c.118T>A p.(Cys40Ser). The second was homozygous for c.183C>G p.(Cys61Trp). Both patients had mild hair and skin hypopigmentation, and classical ocular features. CRISPR/Cas9 was used in C57BL/6J mice to create mutations identical to the missense mutations carried by the patients, along with one loss-of-function indel mutation. When bred to homozygosity the three mutations revealed hypopigmentation of the coat, milder for Cys40Ser compared to Cys61Trp or the frameshift mutation. Histological analysis identified significant hypopigmentation of the retinal pigmented epithelium (RPE) indicating that defective RPE melanogenesis could be associated with eye and vision defects.DCTloss of function in zebrafish embryos elicited hypopigmentation both in melanocytes and RPE cells.

Conclusions

DCTis the gene for a new type of oculocutaneous albinism that we propose to name OCA8.
Spatial Variation of Microtubule Depolymerization in Large Asters Suggests Regulation by MAP Depletion
Authors: Ishihara Keisuke , Decker Franziska , Caldas Paulo , Pelletier James F. , Loose Martin , Brugués Jan , Mitchison Timothy J.
Published: June 2020

Microtubule plus end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing inXenopusegg extract. We observed strong spatial regulation of depolymerization rates, which were almost two-fold higher in the aster interior compared to the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and MAPs in the interior cytosol compared to that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.
Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function
Authors: Feke Ann M. , Gendron Joshua M.
Published: June 2020

The small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain mediates interaction with the LOV domain of ZTL and the ZTL homologs LKP2 and FKF1. This suggests that the Kelch repeat domain of ZTL may mediate homo- and hetero-dimerization of the three LOV/F-box/Kelch proteins and provide added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain.
Germline gene de-silencing by a transposon insertion is triggered by an altered landscape of local piRNA biogenesis
Authors: Miller Danny E. , Van Vaerenberghe Kelley , Li Angela , Grantham Emily K. , Cummings Celeste , Barragan Marilyn , Egidy Rhonda , Scott Allison R. , Hall Kate , Perera Anoja , Gilliland William D. , Blumenstiel Justin P.
Published: June 2020

Transposable elements (TE) are selfish genetic elements that can cause harmful mutations. InDrosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes inDrosophila melanogaster, a truncatedDocretrotransposon within a neighboring gene was found to trigger the germline silencing ofald, theDrosophila Mps1homolog, a gene essential for meiosis. A subsequent screen for modifiers of this silencing identified a new insertion of aHoboDNA transposon in the same neighboring gene. Here we describe how the originalDocinsertion triggers flanking piRNA biogenesis and local gene silencing and how the additionalHoboinsertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the originalDocinsertion. These results support a model of TE-mediated silencing by piRNA biogenesis incisthat depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions.

Author Summary

Transposable elements (TEs) are selfish DNA elements that can move through genomes and cause mutation. In some species, the vast majority of DNA is composed of this form of selfish DNA. Because TEs can be harmful, systems of genome immunity based on small RNA have evolved to limit the movement of TEs. However, like all systems of immunity, it can be challenging for the host to distinguish self from non-self. Thus, TE insertions occasionally cause the small RNA silencing machinery to turn off the expression of critical genes. The rules by which this inadvertent form of autoimmunity causes gene silencing are not well understood. In this article, we describe a phenomenon whereby a TE insertion, rather than silencing a nearby gene, rescues the silencing of a gene caused by another TE insertion. This reveals a mode of TE interactionviasmall RNA silencing that may be important for understanding how TEs exert their effects on gene expression in populations and across species.
Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2
Authors: Wang Daxi , Wang Yanqun , Sun Wanying , Zhang Lu , Ji Jingkai , Zhang Zhaoyong , Cheng Xinyi , Li Yimin , Xiao Fei , Zhu Airu , Zhong Bei , Ruan Shicong , Li Jiandong , Ren Peidi , Ou Zhihua , Xiao Minfeng , Li Min , Deng Ziqing , Zhong Huanzi , Li Fuqiang , Wang Wen-jing , Zhang Yongwei , Chen Weijun , Zhu Shida , Xu Xun , Jin Xin , Zhao Jingxian , Zhong Nanshan , Zhang Wenwei , Zhao Jincun , Li Junhua , Xu Yonghao
Published: June 2020

The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.

Author summary

In this study, we compared SARS-CoV-2 populations of 13 Chinese COVID-19 patients. Those viral populations contained a considerable proportion of viral sub-genomic messenger RNAs (sgmRNA), reflecting an active viral replication activity in the respiratory tract tissues. The comparison of 66 identified intra-host variants further showed a low viral genetic distance between intra-household patients and a narrow transmission bottleneck size. Despite the co-existence of genetically distinct viruses within the same host, most intra-host minor variants were not shared between transmission pairs, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Furthermore, the narrow bottleneck and active viral activity in the respiratory tract show that the passage of a small number of virions can cause infection. Our data have therefore delivered a key genomic resource for the SARS-CoV-2 transmission research and enhanced our understanding of the evolutionary dynamics of SARS-CoV-2.
Phagocytosis and self-destruction execute dendrite degeneration of Drosophila sensory neurons at distinct levels of NAD+ reduction
Authors: Ji Hui , Sapar Maria L , Sarkar Ankita , Wang Bei , Han Chun
Published: June 2020

After injury, severed dendrites and axons expose the "eat-me" signal phosphatidylserine (PS) on their surface and degenerate by disassembly. While axon degeneration is controlled by a conserved "axon-death" pathway that is thought to activate self-destruction, how PS exposure is regulated by this pathway and whether PS-induced phagocytosis contributes to neurite breakdown in vivo remain unknown. Here we show that in Drosophila sensory dendrites, PS exposure and self-destruction are triggered by two distinct levels of NAD+ reduction downstream of Sarm activation. Surprisingly, phagocytosis is the main driver of dendrite degeneration induced by both genetic NAD+ disruptions and injury. Furthermore, the axon-death factor Axed is only partially required for self-destruction of injured dendrites, acting in parallel with PS-induced phagocytosis. Lastly, injured dendrites exhibit a unique rhythmic calcium flashing that correlates with self-destruction. Therefore, a special genetic program coordinates PS exposure and self-destruction in injury-induced dendrite degeneration in vivo.
The Gb3-enriched CD59/flotillin plasma membrane domain regulates host cell invasion byPseudomonas aeruginosa
Authors: Brandel Annette , Aigal Sahaja , Lagies Simon , Schlimpert Manuel , Lehmann Anika , Hummel Daniel , Fisch Daniel , Meléndez Ana Valeria , Madl Josef , Eierhoff Thorsten , Kammerer Bernd , Römer Winfried
Published: June 2020

The opportunistic pathogenPseudomonas aeruginosais responsible for a high number of acute and chronic hospital-acquired infections. As it develops more and more resistances against existing antibiotics,P. aeruginosahas been placed highest on the global priority list of antibiotic-resistant bacteria for which alternative treatments are urgently needed. Former studies have highlighted the crucial role of the bacterial lectin LecA and the host cell glycosphingolipid globotriaosylceramide (Gb3) for the cellular uptake ofP. aeruginosainto epithelial cells via the lipid zipper mechanism. To further characterize the host cell plasma membrane domain for LecA-driven attachment and invasion, we analyzed the protein and lipid composition of pulled-down membrane domains for novel interaction partners of LecA by mass spectrometry. We unraveled a predilection of LecA for binding to saturated Gb3 species in the extracellular membrane leaflet and an induction of dynamic phosphatidylinositol (3,4,5)-trisphosphate clusters at the intracellular leaflet co-localizing with sites of LecA binding. Moreover, we identified the GPI-anchored protein CD59 and flotillins, known as cargo and eponymous component of flotillin-assisted endocytosis, as LecA interaction partners. Depletion of each of these host cell proteins resulted in more than 50% of reduction in invasiveness of theP. aeruginosastrain PAO1 highlighting the importance of this LecA-induced plasma membrane domain. Our strategy to reduce the complexity of host-pathogen interactions by first identifying interaction partners of a single virulence factor and subsequently transferring these findings to the bacterium has been proven to be a successful approach in elucidating the molecular mechanisms of bacterial infections.
The infection cushion: a fungal “weapon” of plant-biomass destruction
Authors: Choquer Mathias , Rascle Christine , Gonçalves Isabelle R , de Vallée Amélie , Ribot Cécile , Loisel Elise , Smilevski Pavlé , Ferria Jordan , Savadogo Mahamadi , Souibgui Eytham , Gagey Marie-Josèphe , Dupuy Jean-William , Rollins Jeffrey A , Marcato Riccardo , Noûs Camille , Bruel Christophe , Poussereau Nathalie
Published: June 2020

Grey mold disease affects fruits, vegetables and ornamental plants around the world, causing considerable losses every year. Its causing agent, the necrotrophic fungusBotrytis cinerea, produces infection cushions (IC) that are compound appressorial structures dedicated to the penetration of the plant tissues.

A microarray analysis was performed to identify genes up-regulated in mature IC. The expression data were supported by RT-qPCR analysis performedin vitroandin planta, proteomic analysis of the IC secretome and mutagenesis of two candidate genes.

1,231 up-regulated genes and 79 up-accumulated proteins were identified. They highlight a secretion of ROS, secondary metabolites including phytotoxins, and proteins involved in virulence: proteases, plant cell wall degrading enzymes and necrosis inducers. The role in pathogenesis was confirmed for two up-regulated fasciclin genes. DHN-melanin pathway and chitin deacetylases genes are up-regulated and the conversion of chitin into chitosan was confirmed by differential staining of the IC cell wall. In addition, up-regulation of sugar transport and sugar catabolism encoding genes was found.

These results support a role for theB. cinereaIC in plant penetration and suggest other unexpected roles for this fungal organ, in camouflage, necrotrophy or nutrition of the pathogen.
The GET pathway safeguards against non-imported mitochondrial protein stress
Authors: Xiao Tianyao , Shakya Viplendra P.S. , Hughes Adam L.
Published: June 2020

Deficiencies in mitochondrial import cause the toxic accumulation of non-imported mitochondrial precursor proteins. Numerous fates for non-imported mitochondrial precursors have been identified, including proteasomal destruction, deposition into protein aggregates, and mis-targeting to other organelles. Amongst organelles, the endoplasmic reticulum (ER) has emerged as a key destination for non-imported mitochondrial proteins, but how ER-targeting of these proteins is achieved remains unclear. Here, we show that the guided entry of tail-anchored proteins (GET) complex is required for ER-targeting of endogenous mitochondrial multi-transmembrane proteins. Without a functional GET pathway, non-imported mitochondrial proteins destined for the ER are alternatively sequestered into Hsp42-dependent protein foci. The ER targeting of non-imported mitochondrial proteins by the GET complex prevents cellular toxicity and facilitates re-import of mitochondrial proteins from the ER via the recently identified ER-SURF pathway. Overall, this study outlines an important and unconventional role for the GET complex in mitigating stress associated with non-imported mitochondrial proteins.
Phosphorylation of the GARP Subunit Vps53 by Snf1 Leads to the Formation of a Golgi – Mitochondria Contact Site (GoMiCS) in Yeast
Authors: Wycislo Susanne A. , Sundag Celine , Walter Stefan , Schuck Sebastian , Fröhlich Florian
Published: June 2020

The canonical function of the Golgi-associated retrograde protein (GARP) complex is the tethering of transport carriers. GARP belongs to the complexes associated with tethering containing helical rods (CATCHR) family and is a hetero-tetrameric complex consisting of the subunits Vps51, Vps52, Vps53 and Vps54. How the activity of GARP is regulated and if it possesses other functions besides tethering remains largely unknown. Here we identify the GARP subunit Vps53 as a novel regulatory target of theS. cerevisiaeAMP kinase (AMPK) homolog Snf1. We find that Vps53 is both anin vivoandin vitrotarget of Snf1 and show that phosphorylation depends on the nature and quantity of the available carbon source. Phosphorylation of Vps53 does not affect the canonical trafficking pathway, but results in altered mitochondrial dynamics and the formation of a previously unknown contact site between the Golgi apparatus and mitochondria, termed GoMiCS. Our results provide an example of a subunit of a CATCHR complex with a constitutive function in membrane trafficking and an inducible role in organelle contact site formation. We anticipate our results to be the starting point for the characterization of this novel contact site.
Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Authors: Kim Youngchang , Wower Jacek , Maltseva Natalia , Chang Changsoo , Jedrzejczak Robert , Wilamowski Mateusz , Kang Soowon , Nicolaescu Vlad , Randall Glenn , Michalska Karolina , Joachimiak Andrzej
Published: June 2020

SARS-CoV-2 Nsp15 is a uridylate-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family. It degrades the polyuridine extensions in (−) sense strand of viral RNA and some non-translated RNA on (+) sense strand. This activity seems to be responsible for the interference with the innate immune response and evasion of host pattern recognition. Nsp15 is highly conserved in coronaviruses suggesting that its activity is important for virus replication. Here we report first structures with bound nucleotides and show that SARS-CoV-2 Nsp15 specifically recognizes U in a pattern previously predicted for EndoU. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. Inhibitors of Nsp15 have been reported but not actively pursued into therapeutics. The current COVID-19 pandemic brought to attention the repurposing of existing drugs and the rapid identification of new antiviral compounds. Tipiracil is an FDA approved drug that is used with trifluridine in the treatment of colorectal cancer. Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme’s active site, providing basis for the uracil scaffold-based drug development.
Development of a Coronavirus Disease 2019 Nonhuman Primate Model Using Airborne Exposure
Authors: Johnston Sara C. , Jay Alexandra , Raymond Jo Lynne , Rossi Franco , Zeng Xiankun , Scruggs Jennifer , Dyer David , Frick Ondraya , Moore Joshua , Berrier Kerry , Esham Heather , Shamblin Joshua , Sifford Willie , Fiallos Jimmy , Klosterman Leslie , Stevens Stephen , White Lauren , Bowling Philip , Garcia Terrence , Jensen Christopher , Ghering Jeanean , Nyakiti David , Bellanca Stephanie , Kearney Brian , Giles Wendy , Alli Nazira , Paz Fabian , Akers Kristen , Danner Denise , Barth James , Johnson Joshua A. , Durant Matthew , Kim Ruth , Pitt Margaret LM , Nalca Aysegul
Published: June 2020

Airborne transmission is predicted to be a prevalent route of human exposure with SARS-CoV-2. Aside from African green monkeys, nonhuman primate models that replicate airborne transmission of SARS-CoV-2 have not been investigated. A comprehensive and comparative evaluation of COVID-19 in African green monkeys, rhesus macaques, and cynomolgus macaques following airborne exposure to SARS-CoV-2 was performed to define parameters critical to disease progression and the extent to which they correlate with human COVID-19. Respiratory abnormalities and viral shedding were noted for all animals, indicating successful infection. Cynomolgus macaques developed fever, and thrombocytopenia was measured for African green monkeys and rhesus macaques. Type II pneumocyte hyperplasia and alveolar fibrosis were more frequently observed in lung tissue from cynomolgus macaques and African green monkeys. The data indicate that, in addition to African green monkeys, macaques can be successfully infected by airborne SARS-CoV-2, providing viable macaque natural transmission models for medical countermeasure evaluation.

One Sentence Summary

Nonhuman primates develop COVID-19 following airborne virus exposure.