bluuebunny/crossref_metadata_2025 huggingface dataset:
fruitlessmutant male mosquitoes gain attraction to human odor
Authors: Basrur Nipun S. , De Obaldia Maria Elena , Morita Takeshi , Herre Margaret , von Heynitz Ricarda K. , Tsitohay Yael N. , Vosshall Leslie B.
Published: September 2020

While sexual dimorphism in courtship and copulation behavior is common in the animal kingdom, sexual dimorphism in feeding behavior is rare. TheAedes aegyptimosquito provides an example of extreme sexual dimorphism in feeding, because only the females show strong attraction to humans, and bite them to obtain a blood-meal necessary to stimulate egg production1-8. The genetic basis of this complex, modular, and sexually dimorphic feeding behavior is unknown. Thefruitlessgene is sex-specifically spliced in the brain of multiple insect species including mosquitoes9-11and encodes a BTB zinc-finger transcription factor that has been proposed to be a master regulator of male courtship and mating behavior across insects12-17. Here we use CRISPR-Cas9 to mutate thefruitlessgene in male mosquitoes.fruitlessmutant males fail to mate, confirming the ancestral function of this gene in male sexual behavior. Remarkably,fruitlessmutant males also gain strong attraction to a live human host, a behavior that wild-type males never display. Humans produce multiple sensory cues that attract mosquitoes and we show thatfruitlessspecifically controls hostseeking in response to human odor. These results suggest that male mosquitoes possess the neural circuits required to host-seek and that removingfruitlessreveals this latent behavior in males. Our results highlight an unexpected repurposing of a master regulator of male-specific sexual behavior to control one module of female-specific blood-feeding behavior in a deadly vector of infectious diseases.
Whole-Genome Enrichment and Sequencing ofChlamydia trachomatisDirectly from Patient Clinical Vaginal and Rectal Swabs
Authors: Bowden Katherine E. , Joseph Sandeep J. , Cartee John , Ziklo Noa , Danavall Damien , Raphael Brian H. , Read Timothy D. , Dean Deborah
Published: September 2020

Chlamydia trachomatisis the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. U.S. cases have been steadily increasing for more than a decade in both the urogenital tract and rectum.C. trachomatisis an obligate intracellular bacterium that is not easily cultured, limiting the capacity for genome studies to understand strain diversity and emergence among various patient populations globally. While Agilent SureSelectXTtarget-enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing ofC. trachomatisdirectly from clinical urine, vaginal, conjunctival and rectal samples, efficiencies are only 60-80% for ≥95-100% genome coverage. We therefore re-designed and expanded the RNA bait library to augment enrichment of the organism from clinical samples to improve efficiency. We describe the expanded library, the limit of detection forC. trachomatisgenome copy input, and the 100% efficiency and high-resolution of generated genomes where genomic recombination among paired vaginal and rectal specimens from four patients was identified. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporaryC. trachomatisSTIs across sample types, among geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.

Importance

Chlamydia trachomatisis an obligate intracellular bacterium that is not easily cultured, and there is limited information on rectalC. trachomatistransmission and its impact on morbidity. To improve efficiency of previous studies involving whole genome target enrichment and sequencing ofC. trachomatisdirectly from clinical urine, vaginal, conjunctival, and rectal specimens, we expanded the RNA bait library to augment enrichment of the organism from clinical samples. We demonstrate an increased efficiency in the percentage of reads mapping toC. trachomatis. We show the new system is sensitive for near identical genomes ofC. trachomatisfrom two body sites in four women. Further, we provide a robust genomic epidemiologic approach to advance our understanding ofC. trachomatisstrains causing ocular, urogenital and rectal infections, and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.
In situstructure determination using single particle cryo-electron microscopy images
Authors: Cheng Jing , Li Bufan , Si Long , Zhang Xinzheng
Published: September 2020

Cryo-electron microscopy (cryo-EM) tomography is a powerful tool forin situstructure determination. However, this method requires the acquisition of tilt series, and its time consuming throughput of acquiring tilt series severely slows determination ofin situstructures. By treating the electron densities of non-target protein as non-Gaussian distributed noise, we developed a new target function that greatly improves the efficiency of the recognition of the target protein in a single cryo-EM image without acquiring tilt series. Moreover, we developed a sorting function that effectively eliminates the false positive detection, which not only improves the resolution during the subsequent structure refinement procedure but also allows using homolog proteins as models to recognize the target protein. Together, we developed anin situsingle particle analysis (isSPA) method. Our isSPA method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. The cryo-EM data from both samples were collected within 24 hours, thus allowing fast and simple structural determinationin situ.
Single-cell RNA-seq reveals early heterogeneity during ageing in yeast
Authors: Zhang Yi , Wang Jincheng , Sang Yuchen , Jin Shengxian , Wang Xuezheng , Azad Gajendra Kumar , McCormick Mark A. , Kennedy Brian K. , Li Qing , Wang Jianbin , Zhang Xiannian , Huang Yanyi
Published: September 2020

The budding yeastSaccharomyces cerevisiaehas relatively short lifespan and is genetically tractable, making it a widely used model organism in ageing research. Here, we carried out a systematic and quantitative investigation of yeast ageing with single-cell resolution through transcriptomic sequencing. We optimized a single-cell RNA sequencing (scRNA-seq) protocol to quantitatively study the whole transcriptome profiles of single yeast cells at different ages, finding increased cell-to-cell transcriptional variability during ageing. The single-cell transcriptome analysis also highlighted key biological processes or cellular components, including oxidation-reduction process, oxidative stress response (OSR), translation, ribosome biogenesis and mitochondrion that underlie ageing in yeast. Remarkably, we uncovered a molecular marker,FIT3, that was linked to mitochondrial DNA loss and indicated the early heterogeneity during ageing in yeast. We also analyzed the regulation of transcription factors and further characterized the distinctive temporal regulation of the OSR byYAP1and proteasome activity byRPN4during ageing in yeast. Overall, our data profoundly reveal early heterogeneity during ageing in yeast and shed light on the ageing dynamics at the single cell level.
The oriental fruit moth genome provides insights into evolutionary adaptation of tortricid pests
Authors: Song Wei , Cao Li-Jun , Yue Lei , Guo Shao-Kun , Chen Jin-Cui , Gong Ya-Jun , Fan Xu-Lei , Wei Shu-Jun
Published: September 2020

Moths of the family Tortricidae (Insecta: Lepidoptera) usually distribute in temperate and tropical high upland regions. The oriental fruit moth (OFM)Grapholita molestais a globally important pest of stone and pome fruit from this family. In this study, we assembled a chromosome-level genome for the OFM and conducted a comparative genomic analysis with other lepidopterans. This genome was assembled to 28 chromosomes with a size of 517.71 Mb, an N50 of 19.5 Mb, and a BUSCO completeness of 97.1%. In total, 19968 protein-coding genes were predicted, among which 15269 were functionally annotated. We manually annotated ten gene families for 13 representative genomes from the Lepidopteran. In general, two tortricid moths have a moderate number of detoxification and receptor genes and the lowest number of HSP genes, congruent with their polyphagous dietary and pattern of distribution. However, the OFM has the highest number of P450, I Rs and ORs among all species. Compared to the other tortricid species of the codling mothCydia pomonella, the OFM has more genes in all gene families. Our results indicate that the high number of some detoxification and receptor genes may be related to the strong adaptation of OFM as a global pest. The high-quality genome of OFM provides an invaluable resource for understanding the ecology, genetics, and evolution of tortricid moths.
No evidence for cross-contextual consistency in spatial learning and behavioural flexibility in a passerine
Authors: Troisi CA , Cooke AC , Davidson GL , de la Hera I , Reichert MS , Quinn JL
Published: September 2020

Although the evolution of cognitive differences among species has long been of interest in ecology, whether natural selection acts on cognitive processes within populations has only begun to receive similar attention. One of the key challenges is to understand how consistently cognitive traits within any one domain are expressed over time and across different contexts, as this has direct implications for the way in which selection might act on this variation. Animal studies typically measure a cognitive domain using only one task in one context, and assume that this captures the likely expression of that domain in different contexts. This deficit is not surprising because, from an ecologist’s perspective, cognitive tasks are notoriously laborious to employ, and for design reasons most tasks can only be deployed in a specific context. Thus our knowledge of whether individual differences in cognitive abilities are consistent across contexts is limited. Using a wild population of great tits (Parus major) we characterised consistency of two cognitive abilities, each in two different contexts: 1) spatial learning at two different spatial scales, and 2) behavioural flexibility as both performance in a detour reaching task and reversal learning in a spatial task. We found no evidence of a correlation between the two spatial learning speeds, or between the two measures of behavioural flexibility. This suggests that cognitive performance is highly plastic and sensitive to differences across tasks, or that variants of these well-known tasks may tap into different combinations of both cognitive and non-cognitive mechanisms, or that they simply do not adequately measure each putative cognitive domain. Our results highlight the challenges of developing standardised cognitive assays to explain natural behaviour and to understand the selective consequences of that variation.
Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients
Authors: Levasseur Anthony , Delerce Jeremy , Caputo Aurelia , Brechard Ludivine , Colson Philippe , Lagier Jean-Christophe , Fournier Pierre-Edouard , Raoult Didier
Published: September 2020

The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.
Method comparison studies of telomere length measurement using qPCR approaches: a critical appraisal of the literature
Authors: Lindrose Alyssa R. , McLester-Davis Lauren W. Y. , Tristano Renee I. , Kataria Leila , Gadalla Shahinaz M. , Eisenberg Dan T. A. , Verhulst Simon , Drury Stacy
Published: September 2020

Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. PCR-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.
Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study
Authors: Salim Khan S Muhammad , Qurieshi Mariya Amin , Haq Inaamul , Majid Sabhiya , Bhat Arif Akbar , Nabi Sahila , Ganai Nisar Ahmad , Zahoor Nazia , Nisar Auqfeen , Chowdri Iqra Nisar , Qazi Tanzeela Bashir , Kousar Rafiya , Lone Abdul Aziz , Sabah Iram , Nabi Shahroz , Sumji Ishtiyaq Ahmad , Kawoosa Misbah Ferooz , Ayoub Shifana
Published: September 2020

Background

Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. We estimate the seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar.

Methods

2906 persons >18 years of age selected from hospital visitors across District Srinagar participated in the study. We tested samples for the presence of SARS-CoV-2 specific IgG antibodies using a chemiluminescent microparticle immunoassay-based serologic test.

Results

Age- and gender-standardized seroprevalence was 3.6% (95% CI 2.9% to 4.3%). Age 30-69 years, a recent history of symptoms of an influenza-like-illness, and a history of being placed under quarantine were significantly related to higher odds of the presence of SARS-CoV-2 specific IgG antibodies. The estimated number of SARS-CoV-2 infections during the two weeks preceding the study, adjusted for test performance, was 32602 with an estimated (median) infection-to-known-case ratio of 46 (95% CI 36 to 57).

Conclusions

The seroprevalence of SARS-CoV-2 specific IgG antibodies is low in the District. A large proportion of the population is still susceptible to the infection. A sizeable number of infections remain undetected, and a substantial proportion of people with symptoms compatible with COVID-19 are not tested.
Phasic modulation of visual representations during sustained attention
Authors: van Es Mats W.J. , Marshall Tom R. , Spaak Eelke , Jensen Ole , Schoffelen Jan-Mathijs
Published: September 2020

Sustained attention has long been thought to benefit perception in a continuous fashion, but recent evidence suggests that it affects perception in a discrete, rhythmic way. Periodic fluctuations in behavioral performance over time, and modulations of behavioral performance by the phase of spontaneous oscillatory brain activity point to an attentional sampling rate in the theta or alpha frequency range. We investigated whether such discrete sampling by attention is reflected in periodic fluctuations in the decodability of visual stimulus orientation from magnetoencephalographic (MEG) brain signals.

In this exploratory study, human subjects attended one of two grating stimuli while MEG was being recorded. We assessed the strength of the visual representation of the attended stimulus using a support vector machine (SVM) to decode the orientation of the grating (clockwise vs. counterclockwise) from the MEG signal. We tested whether decoder performance depended on the theta/alpha phase of local brain activity. While the phase of ongoing activity in visual cortex did not modulate decoding performance, theta/alpha phase of activity in the FEF and parietal cortex, contralateral to the attended stimulus did modulate decoding performance. These findings suggest that phasic modulations of visual stimulus representations in the brain are caused by frequency- specific top-down activity in the fronto-parietal attention network.
Proteome dynamics during antibiotic persistence and resuscitation
Authors: Semanjski Maja , Gratani Fabio , Englert Till , Nashier Payal , Beke Viktor , Nalpas Nicolas , Germain Elsa , George Shilpa , Wolz Christiane , Gerdes Kenn , Macek Boris
Published: September 2020

During antibiotic persistence, bacterial cells become transiently tolerant to antibiotics by restraining their growth and metabolic activity. Detailed molecular characterization of antibiotic persistence is hindered by low count of persisting cells and the need for their isolation. Here we used sustained addition of stable isotope-labeled lysine to selectively label the proteome duringhipA-induced persistence andhipB-induced resuscitation ofE. colicells in minimal medium after antibiotic treatment. Time-resolved, 24-hour measurement of label incorporation allowed detection of over 500 newly synthesized proteins in viable cells, demonstrating low but widespread protein synthesis during persistance. Many essential proteins were newly synthesized and several ribosome-associated proteins, such as RaiA and Sra showed high synthesis levels, pointing to their roles in maintenance of persistence. At the onset of resuscitation, cells synthesized the ribosome-splitting GTPase HflX and various ABC transporters, restored translation machinery and resumed metabolism by inducing glycolysis and biosynthesis of amino acids.
In silicocandidate variant and gene identification using inbred mouse strains
Authors: Munz Matthias , Khodaygani Mohammad , Aherrahrou Zouhair , Busch Hauke , Wohlers Inken
Published: September 2020

Mice are the most widely used animal model to study genotype to phenotype relationships. Inbred mice are genetically identical, which eliminates genetic heterogeneity and makes them particularly useful for genetic studies. Many different strains have been bred over decades and a vast amount of phenotypic data has been generated. In addition, recently whole genome sequencing-based genome-wide genotype data for many widely used inbred strains has been released. Here, we present an approach forin silicofine-mapping that uses genotypic data of 37 inbred mouse strains together with phenotypic data provided by the user to propose candidate variants and genes for the phenotype under study. Public genome-wide genotype data covering more than 74 million variant sites is queried efficiently in real-time to provide those variants that are compatible with the observed phenotype differences between strains. Variants can be filtered by molecular consequences and by corresponding molecular impact. Candidate gene lists can be generated from variant lists on the fly. Fine-mapping together with annotation or filtering of results is provided in a Bioconductor package called MouseFM. In order to characterize candidate variant lists under various settings, MouseFM was applied to two expression data sets across 20 inbred mouse strains, one from neutrophils and one from CD4+T cells. Fine-mapping was assessed for about 10,000 genes, respectively, and identified candidate variants and haplotypes for many expression quantitative trait loci (eQTLs) reported previously based on these data. For albinism, MouseFM reports only one variant allele of moderate or high molecular impact that only albino mice share: a missense variant in theTyrgene, reported previously to be causal for this phenotype. Performingin silicofine-mapping for interfrontal bone formation in mice using four strains with and five strains without interfrontal bone results in 12 genes. Of these, three are related to skull shaping abnormality. Finally performing fine-mapping for dystrophic cardiac calcification by comparing 9 strains showing the phenotype with 8 strains lacking it, we identify only one moderate impact variant in the known causal geneAbcc6. In summary, this illustrates the benefit of using MouseFM for candidate variant and gene identification.
Evolution is in the details: Regulatory differences in modern human and Neanderthal
Authors: Barker Harlan R. , Parkkila Seppo , Tolvanen Martti E.E.
Published: September 2020

Transcription factor proteins play a critical role in the regulation of eukaryote gene expression via sequence- specific binding to genomic locations known as transcription factor binding sites.

We studied sites of genomic variation between modern human and Neanderthal promoters. We detected significant differences in the binding affinities of 110 transcription factors to the promoters of 74 target genes. The transcription factors were enriched for terms related to vision, motor neurons, homeobox, and brain, whereas the target genes and their direct interactors were enriched in terms related to autism, brain, connective tissue, trachea, prostate, skull morphology, and vision. Secondary analysis of single-cell data revealed that a subset of the identified transcription factors (CUX1, CUX2, ESRRG, FOXP1, FOXP2, MEF2C, POU6F2, PRRX1 and RORA) co-occur as marker genes in L4 glutamatergic neurons. The majority of these genes have known roles in autism and/or schizophrenia and are associated with human accelerated regions (elevated divergence in humans vs. other primates). These results support the value of gene regulation studies for the evolution of human cognitive abilities and the neuropsychiatric disorders that accompany it.
SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells
Authors: Singh Yogesh , Trautwein Christoph , Fendel Rolf , Krickeberg Naomi , Berezhnoy Georgy , Bissinger Rosi , Ossowski Stephan , Salker Madhuri S. , Casadei Nicolas , Riess Olaf ,   the Deutsche COVID-19 OMICS Initiative (DeCOI)
Published: September 2020

The SARS-CoV-2 virus is the causative agent of the global COVID-19 infectious disease outbreak, which can lead to acute respiratory distress syndrome (ARDS). However, it is still unclear how the virus interferes with immune cell and metabolic functions in the human body. In this study, we investigated the immune response in acute or convalescent COVID19 patients. We characterized the peripheral blood mononuclear cells (PBMCs) using flow cytometry and found that CD8+T cells were significantly subsided in moderate COVID-19 and convalescent patients. Furthermore, characterization of CD8+T cells suggested that patients with a mild and moderate course of the COVID-19 disease and convalescent patients have significantly diminished expression of both perforin and granzyme A in CD8+T cells. Using1H-NMR spectroscopy, we characterized the metabolic status of their autologous PBMCs. We found that fructose, lactate and taurine levels were elevated in infected (mild and moderate) patients compared with control and convalescent patients. Glucose, glutamate, formate and acetate levels were attenuated in COVID-19 (mild and moderate) patients. In summary, our report suggests that SARS-CoV-2 infection leads to disrupted CD8+T cytotoxic functions and changes the overall metabolic functions of immune cells.
EPAC regulates von Willebrand factor secretion from endothelial cells in a PI3K/eNOS-dependent manner during inflammation
Authors: Xiao Jie , Zhang Ben , Su Zhengchen , Liu Yakun , Shelite Thomas R. , Chang Qing , Wang Pingyuan , Bukreyev Alexander , Soong Lynn , Jin Yang , Ksiazek Thomas , Gaitas Angelo , Rossi Shannan L. , Zhou Jia , Laposata Michael , Saito Tais B. , Gong Bin
Published: September 2020

Coagulopathy is associated with both inflammation and infection, including infection with the novel SARS-CoV-2 (COVID-19). Endothelial cells (ECs) fine tune hemostasis via cAMP-mediated secretion of von Willebrand factor (vWF), which promote the process of clot formation. Theexchangeprotein directlyactivated bycAMP (EPAC) is a ubiquitously expressed intracellular cAMP receptor that plays a key role in stabilizing ECs and suppressing inflammation. To assess whether EPAC could regulate vWF release during inflammation, we utilized ourEPAC1-null mouse model and revealed an increased secretion of vWF in endotoxemic mice in the absence of the EPAC1 gene. Pharmacological inhibition of EPAC1in vitromimicked theEPAC1−/− phenotype. EPAC1 regulated TNFα-triggered vWF secretion from human umbilical vein endothelial cells (HUVECs) in a phosphoinositide 3-kinases (PI3K)/endothelial nitric oxide synthase (eNOS)-dependent manner. Furthermore, EPAC1 activation reduced inflammation-triggered vWF release, bothin vivoandin vitro. Our data delineate a novel regulatory role of EPAC1 in vWF secretion and shed light on potential development of new strategies to controlling thrombosis during inflammation.

Key Point

PI3K/eNOS pathway-mediated, inflammation-triggered vWF secretion is the target of the pharmacological manipulation of the cAMP-EPAC system.
Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis
Authors: Singh Meetali , Cornes Eric , Li Blaise , Quarato Piergiuseppe , Bourdon Loan , Dingli Florent , Loew Damarys , Proccacia Simone , Cecere Germano
Published: September 2020

In theCaenorhabditis elegansgermline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1, to synthesize 22G-RNAs in phase with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ granules. Moreover, codon optimality and efficient translation antagonize CSR-1 slicing and 22G-RNAs biogenesis. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.
Obesity-associated lipidomic remodeling of the adrenal gland indicates an important role of the FADS2-arachidonic acid axis in adrenocortical hormone production
Authors: Witt Anke , Mirtschink Peter , Palladini Alessandra , Mateska Ivona , Abdelmegeed Heba , Grzybek Michal , Wielockx Ben , Peitzsch Mirko , Coskun Ünal , Chavakis Triantafyllos , Alexaki Vasileia Ismini
Published: September 2020

Objective

Adrenocortical hormone levels increase in obesity, potentially contributing to development of obesity-associated pathologies. Here we explored whether lipidomic remodeling of the adrenal gland could mediate altered adrenocortical steroidogenesis during obesity.

Methods

Lipidomic analysis was performed in adrenal glands using shotgun mass spectrometry (MS), and steroid profiling of sera by liquid chromatography tandem mass spectrometry (LC-MS/MS) from lean and obese mice. Gene expression analysis was performed in adrenal glands and adrenocortical cell populations. The role of Fatty Acid Desaturase 2 (FADS2) and arachidonic acid on steroid hormone production was studied in primary adrenal gland cell cultures.

Results

Adrenal glands of obese mice displayed a distinct lipidomic profile, encompassing longer and more unsaturated storage lipids and phospholipids compared to adrenal glands of lean mice. Arachidonoyl acyl chains were abundant in the adrenal gland phospholipidome and increased upon obesity. This was accompanied by increasedFads2expression, the rate-limiting enzyme of arachidonic acid synthesis, and enhanced plasma adrenocortical hormone levels. Inhibition of FADS2 in primary adrenal gland cell cultures abolished steroidogenesis, which was restored by arachidonic acid supplementation.

Conclusions

Our data suggest that the FADS2 – arachidonic acid axis regulates adrenocortical hormone synthesis, while alterations in the content of arachidonoyl chains in the adrenal gland phopsholipidome could account for disturbed adrenocortical hormone production.

Highlights

The adrenal gland lipidome is remodeled in obesity.

Arachidonoyl groups are abundant in the adrenal gland phospholipidome and increase in obesity.

FADS2 is highly expressed in the adrenal gland and its expression is further increased in obesity.

FADS2 inhibition blunts adrenocortical steroidogenesis in primary adrenal gland cell cultures, while arachidonic acid supplementation restores it.
Histone tails cooperate to control the breathing of genomic nucleosomes
Authors: Huertas Jan , Schöler Hans R , Cojocaru Vlad
Published: September 2020

Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 146 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and internucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 18μs. Transitions between open and closed nucleosome conformations were driven by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics.
Evolutionarily conserved chaperone-mediated proteasomal degradation of a disease-linked aspartoacylase variant
Authors: Gersing Sarah K. , Wang Yong , Grønbæk-Thygesen Martin , Kampmeyer Caroline , Clausen Lene , Andréasson Claes , Stein Amelie , Lindorff-Larsen Kresten , Hartmann-Petersen Rasmus
Published: September 2020

Canavan disease is a severe progressive neurodegenerative disorder that is characterized by swelling and spongy degeneration of brain white matter. The disease is genetically linked to polymorphisms in the aspartoacylase (ASPA) gene, including the substitution C152W. ASPA C152W is associated with greatly reduced protein levels in cells, yet biophysical experiments suggest a wild-type like thermal stability. Here, we examine the stability and degradation pathway of ASPA C152W. When we expressed ASPA C152W inSaccharomyces cerevisiae, we found a decreased steady state compared to wild-type ASPA as a result of increased proteasomal degradation. However, molecular dynamics simulations of ASPA C152W did not substantially deviate from wild-type ASPA, indicating that the native state is structurally preserved. Instead, we suggest that the C152W substitution prevents ASPA from reaching its stable native conformation, presumably by impacting onde novofolding. Systematic mapping of the protein quality control components acting on misfolded and aggregation-prone species of C152W, revealed that the degradation is highly dependent on the molecular chaperone Hsp70, its co-chaperone Hsp110 as well as several quality control E3 ubiquitin-protein ligases, including Ubr1. In human cells, ASPA C152W displayed increased proteasomal turnover that was similarly dependent on Hsp70 and Hsp110. We propose that Hsp110 is a potential therapeutic target for misfolding ASPA variants that trigger Canavan disease due to excessive degradation.
Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
Authors: Jimeno-Martín Angela , Sousa Erick , Brocal-Ruiz Rebeca , Daroqui Noemi , Maicas Miren , Flames Nuria
Published: September 2020

To systematically investigate the complexity of neuron-specification regulatory networks we performed an RNA interference (RNAi) screen against all 875 transcription factors (TFs) encoded inCaenorhabditis elegansgenome and searched for defects in nine different neuron types of the monoaminergic (MA) superclass and two cholinergic motoneurons.

We identified 91 TF candidates to be required for correct generation of these neuron types of which 28 were confirmed by mutant analysis. We found that correct reporter expression in each individual neuron type requires at least nine different TFs. Individual neuron types do not usually share TFs involved in their specification but share a common pattern of TFs belonging to the five most common TF families: Homeodomain (HD), basic Helix Loop Helix (bHLH), Zinc Finger (ZF), Basic Leucine Zipper Domain (bZIP) and Nuclear Hormone Receptors (NHR). HD TF members are over-represented, supporting a key role for this family in the establishment of neuronal identities. These five TF families area also prevalent when considering mutant alleles with previously reported neuronal phenotypes inC. elegans,Drosophilaor mouse. In addition, we studied terminal differentiation complexity focusing on the dopaminergic terminal regulatory program. We found two HD TFs (UNC-62 and VAB-3) that work together with known dopaminergic terminal selectors (AST-1, CEH-43, CEH-20). Combined TF binding sites for these five TFs constitute a cis-regulatory signature enriched in the regulatory regions of dopaminergic effector genes. Our results provide new insights on neuron-type regulatory programs inC. elegansthat could help better understand neuron specification and evolution of neuron types.
Nanoscopy on the Chea(i)p
Authors: Diederich Benedict , Helle Øystein , Then Patrick , Carravilla Pablo , Schink Kay Oliver , Hornung Franziska , Deinhardt-Emmer Stefanie , Eggeling Christian , Ahluwalia Balpreet Singh , Heintzmann Rainer
Published: September 2020

Super-resolution microscopy allows for stunning images with a resolution well beyond the optical diffraction limit, but the imaging techniques are demanding in terms of instrumentation and software. Using scientific-grade cameras, solid-state lasers and top-shelf microscopy objective lenses drives the price and complexity of the system, limiting its use to well-funded institutions. However, by harnessing recent developments in CMOS image sensor technology and low-cost illumination strategies, super-resolution microscopy can be made available to the mass-markets for a fraction of the price. Here, we present a 3D printed, self-contained super-resolution microscope with a price tag below 1000 $ including the objective and a cellphone. The system relies on a cellphone to both acquire and process images as well as control the hardware, and a photonic-chip enabled illumination. The system exhibits 100nmoptical resolution using single-molecule localization microscopy and can provide live super-resolution imaging using light intensity fluctuation methods. Furthermore, due to its compactness, we demonstrate its potential use inside bench-top incubators and high biological safety level environments imaging SARS-CoV-2 viroids. By the development of low-cost instrumentation and by sharing the designs and manuals, the stage for democratizing super-resolution imaging is set.
Inferring Patterns of Hybridization and Polyploidy in the Plant GenusPenstemon(Plantaginaceae)
Authors: Blischak Paul D. , Thompson Coleen E. , Waight Emiko M. , Kubatko Laura S. , Wolfe Andrea D.
Published: September 2020

Reticulate evolutionary events are hallmarks of plant phylogeny, and are increasingly recognized as common occurrences in other branches of the Tree of Life. However, inferring the evolutionary history of admixed lineages presents a difficult challenge for systematists due to genealogical discordance caused by both incomplete lineage sorting (ILS) and hybridization. Methods that accommodate both of these processes are continuing to be developed, but they often do not scale well to larger numbers of species. An additional complicating factor for many plant species is the occurrence of whole genome duplication (WGD), which can have various outcomes on the genealogical history of haplotypes sampled from the genome. In this study, we sought to investigate patterns of hybridization and WGD in two subsections from the genusPenstemon(Plantaginaceae; subsect.HumilesandProceri), a speciose group of angiosperms that has rapidly radiated across North America. Species in subsect.HumilesandProcerioccur primarily in the Pacific Northwest of the United States, occupying habitats such as mesic, subalpine meadows, as well as more well-drained substrates at varying elevations. Ploidy levels in the subsections range from diploid to hexaploid, and it is hypothesized that most of the polyploids are hybrids (i.e., allopolyploids). To estimate phylogeny in these groups, we first developed a method for estimating quartet concordance factors (QCFs) from multiple sequences sampled per lineage, allowing us to model all haplotypes from a polyploid. QCFs represent the proportion of gene trees that support a particular species quartet relationship, and are used for species network estimation in the program SNaQ (Solís-Lemus & Ané. 2016.PLoS Genet.12:e1005896). Using phased haplotypes for nuclear amplicons, we inferred species trees and networks for 38 taxa fromP. subsect.HumilesandProceri. Our phylogenetic analyses recovered two clades comprising a mix of taxa from both subsections, indicating that the current taxonomy for these groups is inconsistent with our estimates of phylogeny. In addition, there was little support for hypotheses regarding the formation of putative allopolyploid lineages. Overall, we found evidence for the effects of both ILS and admixture on the evolutionary history of these species, but were able to evaluate our taxonomic hypotheses despite high levels of gene tree discordance. Our method for estimating QCFs from multiple haplotypes also allowed us to include species of varying ploidy levels in our analyses, which we anticipate will help to facilitate estimation of species networks in other plant groups as well.
A telomere to telomere assembly ofOscheius tipulaeand the evolution of rhabditid nematode chromosomes
Authors: Gonzalez de la Rosa Pablo Manuel , Thomson Marian , Trivedi Urmi , Tracey Alan , Tandonnet Sophie , Blaxter Mark
Published: September 2020

Eukaryotic chromosomes have phylogenetic persistence. In many taxa, the number of chromosomes is related to the number of centromeres. However, in some groups, such as rhabditid nematodes, centromeric function is distributed across multiple sites on each chromosome. These holocentric chromosomes might,a priori, be expected to be permissive of large-scale chromosomal rearrangement, as chromosomal fragments could still partition correctly and fusions would not generate lethal conflict between multiple centromeres. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematodeOscheius tipulaegenerated from nanopore long reads. The 60 MbO. tipulaegenome is resolved into six chromosomal molecules. We find evidence of specific chromatin diminution at all telomeres. Comparing this chromosomalO. tipulaeassembly with chromosomal assemblies of diverse rhabditid nematodes we identify seven ancestral chromosomal elements (Nigon elements), and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex-chromosome associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.
Surface-catalyzed SAS-6 self-assembly directs centriole formation through kinetic and structural mechanisms
Authors: Banterle Niccolò , Nievergelt Adrian P. , de Buhr Svenja , Hatzopoulos Georgios N. , Brillard Charlène , Andany Santiago , Hübscher Tania , Sorgenfrei Frieda , Schwarz Ulrich S. , Gräter Frauke , Fantner Georg E. , Gönczy Pierre
Published: September 2020

Discovering the physical principles directing organelle assembly is a fundamental pursuit in biology. Centrioles are evolutionarily conserved organelles with a 9-fold rotational symmetry of chiral microtubules imparted onto the cilia they template1. Centriole assemble from likewise symmetrical ring polymers of SAS-6 proteins, orthogonal to a toroidal surface surrounding the resident centriole2–4. How surface properties ensure ring assembly with proper symmetry and orthogonal arrangement is not known. Here, we deployed photothermally-actuated off-resonance tapping high-speed atomic force microscopy (PORT-HS-AFM) to decipher physical principles of surface-guided SAS-6 self-assembly. Using machine learning to quantify the polymerization reaction and developing a coagulation-fragmentation model, we discovered that the surface shifts the reaction equilibrium by ∼104compared to the solution situation, explaining orthogonal organelle emergence. Moreover, molecular dynamics and PORT-HS-AFM revealed that the surface converts helical SAS-6 polymers into 9-fold ring polymers with residual asymmetry, which may impart chiral features to centrioles and cilia. Overall, we discovered two fundamental physical principles directing robust centriole organelle assembly.
Capture of mouse and human stem cells with features of formative pluripotency
Authors: Kinoshita Masaki , Barber Michael , Mansfield William , Cui Yingzhi , Spindlow Daniel , Stirparo Giuliano Giuseppe , Dietmann Sabine , Nichols Jennifer , Smith Austin
Published: September 2020

Pluripotent cells emerge via a naïve founder population in the blastocyst, acquire capacity for germline and soma formation, and then undergo lineage priming. Mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) represent the initial naïve and final primed phases of pluripotency, respectively. Here we investigate the intermediate formative stage. Using minimal exposure to specification cues, we expand stem cells from formative mouse epiblast. Unlike ES cells or EpiSCs, formative stem (FS) cells respond directly to germ cell induction. They colonise chimaeras including the germline. Transcriptome analyses show retained pre-gastrulation epiblast identity. Gain of signal responsiveness and chromatin accessibility relative to ES cells reflect lineage capacitation. FS cells show distinct transcription factor dependencies from EpiSCs, relying critically on Otx2. Finally, FS cell culture conditions applied to human naïve cells or embryos support expansion of similar stem cells, consistent with a conserved attractor state on the trajectory of mammalian pluripotency.
The lysosomal TRPML1 channel promotes breast cancer survival by supporting mitochondrial function and cellular metabolism
Authors: Almasi Shekoufeh , Kennedy Barry E. , Yoast Ryan E. , Emrich Scott M. , Trebak Mohamed , Hiani Yassine El
Published: September 2020

Triple-negative breast cancer (TNBC) is an aggressive subtype representing approximately 10%-20% of breast cancers and lacking effective therapies. TRPML1, which is a lysosomal Ca2+ release channel upregulated in TNBC, promotes TNBC tumor growth. Here we show a novel crosstalk between lysosomes and mitochondria mediated by TRPML1 in TNBC. TRPML1 is required for the maintenance of mitochondrial function and reactive oxygen species (ROS) homeostasis. TRPML1 knockdown inhibits TNBC mitochondrial respiration, glycolysis and ATP production, leading to reduced proliferation, promotion of cell cycle arrest and apoptosis with enhanced global and mitochondrial ROS. Further, TRPML1 downregulation enhances the cytotoxic effect of Doxorubicin in TNBC cells. Our data reveal a hitherto unknown link between lysosomal TRPML1 channels and mitochondrial metabolism and suggest that TRPML1 inhibition in combination with established chemotherapies could be an effective strategy against TNBC tumors.