bluuebunny/crossref_metadata_2025 huggingface dataset:
Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during algal blooms
Authors: Vincent Flora , Gralka Matti , Schleyer Guy , Schatz Daniella , Cabrera-Brufau Miguel , Kuhlisch Constanze , Sichert Andreas , Vidal-Melgosa Silvia , Mayers Kyle , Barak-Gavish Noa , Flores J.Michel , Masdeu-Navarro Marta , Egge Jorun Karin , Larsen Aud , Heheman Jan-Hendrik , Marrasé Celia , Simó Rafel , Cordero Otto X. , Vardi Assaf
Published: October 2021

Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global nutrient cycling. When blooms collapse, organic carbon is transferred to higher trophic levels, microbial respiration or sinking in proportions that depend on the dominant mortality agent. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains an open question. Here, we characterized the consequences of viral infection on the microbiome composition and biogeochemical landscape of marine ecosystems by conducting a large-scale mesocosm experiment. Moniroting of seven induced coccolithophore blooms, which showed different degrees of viral infection, revealed that only high levels of viral infection caused significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, viral infection favored the growth of eukaryotic heterotrophs (thraustochytrids) over bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection can increase per-cell rates of extracellular carbon release by 2-4.5 fold. This happened via production of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain
Authors: Jibiki Kazuya , Liu Mo-yan , Lei Chao-sen , Kodama Takashi S. , Kojima Chojiro , Fujiwara Toshimichi , Yasuhara Noriko
Published: October 2021

Importin α has been described as a nuclear protein transport receptor that enables proteins synthesized in the cytoplasm to translocate into the nucleus. Besides its function in nuclear transport, an increasing number of studies have examined its non-nuclear transport functions. In both nuclear transport and non-nuclear transport, a functional domain called the IBB domain (importin β binding domain) plays a key role in regulating importin α behavior, and is a common interacting domain for multiple binding partners. However, it is not yet fully understood how the IBB domain interacts with multiple binding partners, which leads to the switching of importin α function. In this study, we have distinguished the location and propensities of amino acids important for each function of the importin α IBB domain by mapping the biochemical/physicochemical propensities of evolutionarily conserved amino acids of the IBB domain onto the structure associated with each function. We found important residues that are universally conserved for IBB functions across organisms and families, in addition to those previously known, as well as residues that are presumed to be responsible for the differences in complex-forming ability between families and for functional switching.
AT-752, a double prodrug of a guanosine nucleotide analog, inhibits yellow fever virus in a hamster model
Authors: Lin Kai , Good Steven S. , Julander Justin G. , Weight Abbie , Moussa Adel , Sommadossi Jean-Pierre
Published: October 2021

Yellow fever virus (YFV) is a zoonotic pathogen re-emerging in parts of the world, causing a viral hemorrhagic fever associated with high mortality rates. While an effective vaccine is available, having an effective antiviral against YFV is critical against unexpected outbreaks, or when vaccination is not recommended. We have previously identified AT-281, the free base of AT-752, an orally available double prodrug of a guanosine nucleotide analog, as a potent inhibitor of YFV in vitro, with a 50% effective concentration (EC50) of 0.31 μM. In hamsters infected with YFV (Jimenez strain), viremia rose about 4 log10-fold and serum alanine aminotransferase (ALT) 2-fold compared to sham-infected animals. Treatment with 1000 mg/kg AT-752 for 7 days, initiated 4 h prior to viral challenge, reduced viremia to below the limit of detection by day 4 post infection (pi) and returned ALT to normal levels by day 6 pi. When treatment with AT-752 was initiated 2 days pi, the virus titer and ALT dropped >2 log10 and 53% by day 4 and 6 pi, respectively. In addition, at 21 days pi, 70 – 100% of the infected animals in the treatment groups survived compared to 0% of the untreated group (p<0.001). Moreover, in vivo formation of the active triphosphate metabolite AT-9010 was measured in the animal tissues, with the highest concentrations in liver and kidney, organs that are vulnerable to the virus. The demonstrated in vivo activity of AT-752 suggests that it is a promising compound for clinical development in the treatment of YFV infection.

Author summary

Yellow fever virus (YFV) is transmitted by mosquitoes, and its infection can lead to a lethal viral hemorrhagic fever associated with liver damage. While an effective vaccine is available, in places where the vaccination rate is low, in the event of an unexpected outbreak, or where vaccination is not recommended individually, having an effective antiviral treatment is critical. We previously reported that the nucleotide analog prodrug AT-752 potently inhibited the YFV in cultured cells. Here we showed that in hamsters infected with YFV, oral treatment with 1000 mg/kg AT-752 for 7 days reduced the production of infectious virus particles in the blood, and decreased serum alanine aminotransferase, a marker of liver damage, to levels measured in uninfected animals. In addition, at 21 days after infection, 70 – 100% of the infected animals in the treatment groups survived compared to 0% in the untreated group. Moreover, the amount of the active metabolite formed from AT-752 was highest in the livers and kidneys of the treated animals, organs that are targeted by the virus. These results suggest that AT-752 is a promising compound to develop for the treatment of YFV infection.
The pre-existing human antibody repertoire to computationally optimized influenza H1 hemagglutinin vaccines
Authors: Nagashima Kaito , Dzimianski John V. , Han Julianna , Abbadi Nada , Gingerich Aaron D. , Royer Fredejah , O’Rourke Sara , Sautto Giuseppe A. , Ross Ted M. , Ward Andrew B. , DuBois Rebecca M. , Mousa Jarrod J.
Published: October 2021

The computationally optimized broadly reactive antigen (COBRA) approach has previously been used to generate hemagglutinin (HA) immunogens for several influenza subtypes that expand vaccine-elicited antibody breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA antigens. Cross-reactivity between wild type HA and H1 COBRA HA proteins were observed at both the oligoclonal B cell level and for a subset of isolated monoclonal antibodies (mAbs). The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 head and stem domains, and the majority of the mAbs had HAI and neutralizing activity against pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had HAI and neutralizing activity against a pre-pandemic H1 strain. One mAb, P1-05, targets the stem region of H1 HA proteins, but does not compete with known stem-targeting H1 mAbs. We determined that mAb P1-05 recognizes a recently discovered membrane proximal epitope on HA, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by P1-05. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA- reactive B cells that target head, central stalk, and anchor epitopes, and demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes.

Significance

Influenza imposes significant human and economic costs every year. The current seasonal vaccine elicits primarily strain-specific antibodies, and year to year vaccine effectiveness is variable. The COBRA approach could provide longer protection and obviate the requirement for annual vaccination. Whereas COBRA HAs have previously been evaluated in animal models, the pre-existing COBRA HA-reactive human B cell population has yet to be elucidated, and is important to identify specific B cells that may be recalled by H1 HA COBRA vaccination. This work demonstrates that seasonally vaccinated individuals possess a functional B cell population targeting both head and stem domains that could be recalled with COBRA HA immunogens.
Intestinal Gluconeogenesis Regulates Brown and White Adipose Tissues Functions in mice
Authors: Vily-Petit Justine , Soty-Roca Maud , Silva Marine , Micoud Manon , Bron Clara , Raffin Margaux , Beiroa Daniel , Nogueiras Rubén , Roussel Damien , Gautier-Stein Amandine , Rajas Fabienne , Cota Daniela , Mithieux Gilles
Published: October 2021

Objective

Intestinal gluconeogenesis, via the initiation of a gut-brain nervous circuit, accounts for the metabolic benefits linked to dietary proteins or fermentable fibre in rodents and has been positively correlated with the rapid amelioration of body weight after gastric bypass surgery in obese humans. In particular, the activation of intestinal gluconeogenesis moderates the development of hepatic steatosis accompanying obesity. In this study, we investigated the specific effects of intestinal gluconeogenesis on adipose tissue metabolism, independently of its induction by nutritional manipulation.

Methods

We used two transgenic mouse models of suppression or overexpression of G6PC, the catalytic subunit of glucose-6 phosphatase, the key enzyme of endogenous glucose production, specifically in the intestine.

Results

Under a hypercaloric diet, mice with a genetic overexpression of intestinal gluconeogenesis showed a lower adiposity and higher thermogenic capacities than wild-type mice, featuring marked browning of white adipose tissue and prevention of the whitening of brown adipose tissue. Suppression of sympathetic nervous signalling in brown adipose tissue impairs the activation of thermogenesis. Conversely, mice with genetic suppression of intestinal gluconeogenesis exhibit an increase in adiposity under standard diet, associated with a decreased expression of markers of thermogenesis in both the brown and white adipose tissues.

Conclusion

Intestinal gluconeogenesis is sufficient in itself to activate the sympathetic nervous system and prevent the expansion and the metabolic alterations of brown and white adipose tissues metabolism under high calorie diet, thus preventing the development of obesity. These data increase knowledge of the mechanisms of weight reduction in gastric bypass surgery and pave the way of new approaches to prevent or cure obesity.
A MademoiseLLE domain binding platform links the key RNA transporter to endosomes
Authors: Devan Senthil-Kumar , Schott-Verdugo Stephan , Müntjes Kira , Bismar Lilli , Reiners Jens , Hachani Eymen , Schmitt Lutz , Höppner Astrid , Smits Sander HJ , Gohlke Holger , Feldbrügge Michael
Published: October 2021

Spatiotemporal expression can be achieved by transport and translation of mRNAs at defined subcellular sites. An emerging mechanism mediating mRNA trafficking is microtubule- dependent co-transport on shuttling endosomes. Although progress has been made in identifying various components of the endosomal mRNA transport machinery, a mechanistic understanding of how these RNA-binding proteins are connected to endosomes is still lacking. Here, we demonstrate that a flexible MademoiseLLE (MLLE) domain platform within RNA- binding protein Rrm4 ofUstilago maydisis crucial for endosomal attachment. Our structure/function analysis uncovered three MLLE domains at the C-terminus of Rrm4 with a functionally defined hierarchy. MLLE3 recognises two PAM2-like sequences of the adaptor protein Upa1 and is essential for endosomal shuttling of Rrm4. MLLE1 and MLLE2 are most likely accessory domains exhibiting a variable binding mode for interaction with currently unknown partners. Thus, endosomal attachment of the mRNA transporter is orchestrated by a sophisticated MLLE domain binding platform.
CircSry regulates spermatogenesis by enhancing γH2AX expression via sponging miR-138-5p
Authors: Song Yanze , Chen Min , Zhang Yingfan , Li Na , Chen Min , Qiao Miaomiao , Cao Yuanwei , Chen Jian , Gao Fei , Wang Haoyi
Published: October 2021

Sry on the Y chromosome is the master switch in sex determination in mammals. It has been well established that Sry encodes a transcription factor that is transiently expressed in somatic cells of male gonad, inducing a series of events that lead to the formation of testes. In the testis of adult mice, Sry is expressed as a circular RNA (circRNA) transcript, a type of noncoding RNA that forms a covalently linked continuous loop. However, the physiological function of this Sry circRNA (circSry) remains unknown since its discovery in 1993. Here we show that circSry is mainly expressed in the spermatocytes, but not in mature sperms and Sertoli cells. Loss of circSry led to the reduction of sperm number and the defect of germ cell development. The expression of γH2AX was decreased and failure of XY body formation was noted in circSry KO germ cells. Further study demonstrates that circSry regulates H2AX mRNA indirectly in pachytene spermatocytes through sponging miR-138-5p. Our study demonstrates that, in addition to its well-known sex-determination function, Sry also plays important role in spermatogenesis as a circRNA.
Activation of transient receptor potential vanilloid 4 is involved in pressure overload-induced cardiac hypertrophy
Authors: Zou Yan , Zhang Miaomiao , Wu Qiongfeng , Zhao Ning , Chen Minwei , yang Cui , Du Yimei , Han Bing
Published: October 2021

Previous studies, including our own, have demonstrated that transient receptor potential vanilloid 4 (TRPV4) is expressed in hearts and implicated in cardiac remodeling and cardiac dysfunction. However, the effects of TRPV4 on pressure overload-induced cardiac hypertrophy remain unclear. In this study, we found that TRPV4 expression was significantly increased in mouse hypertrophic hearts, human failing hearts, and neurohormone-induced hypertrophic cardiomyocytes. Deletion of TRPV4 attenuated transverse aortic constriction (TAC)-induced cardiac hypertrophy, cardiac dysfunction, fibrosis, inflammation, and the activation of NFκB - NOD-like receptor pyrin domain-containing protein 3 (NLRP3) in mice. In vitro, TRPV4 inhibition decreased the neurohormone-induced cardiomyocyte hypertrophy and the increase of intracellular Ca2+ concentration. TRPV4 agonist triggered Ca2+ influx and evoked the phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) but these effects were abolished by removing extracellular Ca2+ or TRPV4 inhibition. More importantly, TAC or neurohormone stimulation-induced CaMKII phosphorylation was significantly blocked by TRPV4 inhibition. Finally, we showed that CaMKII inhibition significantly inhibited the phosphorylation of NFκB induced by TRPV4 activation. Our results suggest that TRPV4 activation contributed to pressure overload-induced cardiac hypertrophy. This effect was associated with upregulated Ca2+/ CaMKII mediated the activation of NFκB-NLRP3. Thus, TRPV4 may represent a potential therapeutic drug target for cardiac hypertrophy.
A generalizable deep learning framework for inferring fine-scale germline mutation rate maps
Authors: Fang Yiyuan , Deng Shuyi , Li Cai
Published: October 2021

Germline mutation rates are essential for genetic and evolutionary analyses. Yet, estimating accurate fine-scale mutation rates across the genome is a great challenge, due to relatively few observed mutations and intricate relationships between predictors and mutation rates. Here we present MuRaL (Mutation Rate Learner), a deep learning framework to predict mutation rates at the nucleotide level using only genomic sequences as input. Harnessing human germline variants for comprehensive assessment, we show that MuRaL achieves better predictive performance than current state-of-the-art methods. Moreover, MuRaL can build models with relatively few training mutations and a moderate number of sequenced individuals, and can leverage transfer learning to further reduce data and time demands. We apply MuRaL to produce genome-wide mutation rate maps for four representative species - Homo sapiens, Macaca mulatta, Arabidopsis thaliana and Drosophila melanogaster, demonstrating its high applicability. As an example, we use improved mutation rate estimates to stratify human genes into distinct groups which are enriched for different functions, and highlight that many developmental genes are subject to high mutational burden. The open-source software and generated mutation rate maps can greatly facilitate related research.
MDA-LDL vaccination induces athero-protective germinal center-derived antibody responses
Authors: Martos-Folgado Inmaculada , Lorenzo Cristina , Busse Christian E. , Delgado Pilar , Mur Sonia , Cobos Laura , Martín-Ventura Jose Luis , Escolà-Gil Joan Carles , Wardemann Hedda , Ramiro Almudena R
Published: October 2021

Atherosclerosis is a chronic inflammatory disease of the arteries that can lead to thrombosis, infarction and stroke and is the leading cause of mortality worldwide. Immunization of pro-atherogenic mice with malondialdehyde-modified low-density lipoprotein (MDA-LDL) neo-antigen is athero-protective. However, the immune response to MDA-LDL and the mechanisms responsible for this athero-protection are not completely understood. Here, we find that immunization of mice with MDA-LDL elicits memory B cells, plasma cells, and switched anti-MDA-LDL antibodies as well as clonal expansion and affinity maturation, indicating that MDA-LDL triggers a bona fide germinal center antibody response. Further, Prdm1fl/flAicda-Cre+/kiLdlr-/- pro-atherogenic chimeras, which lack germinal center-derived plasma cells, show accelerated atherosclerosis. Finally, we show that MDA-LDL immunization is not athero-protective in mice lacking germinal-center derived plasma cells. Our findings give further support to the development of MDA-LDL-based vaccines for the prevention or treatment of atherosclerosis.
Development of amyloid beta gold nanorod aggregates as optoacoustic probes
Authors: Soliman Mahmoud G , Davies Hannah A , Sharkey Jack , Lévy Raphaël , Madine Jillian
Published: October 2021

Propagation of small amyloid beta (Aβ) aggregates (or seeds) has been suggested as a potential mechanism of Alzheimer’s disease progression. Monitoring the propagation of Aβ seeds in an organism would enable testing of this hypothesis and, if confirmed, provide mechanistic insights. This requires a contrast agent for long-term tracking of the seeds. Gold nanorods combine several attractive features for this challenging task, in particular, their strong absorbance in the infrared (enabling optoacoustic imaging) and the availability of several established protocols for surface functionalization. In this work, polymer-coated gold nanorods were conjugated with anti-Aβ antibodies and specifically attached to pre-formed Aβ seeds. The resulting complexes were characterized for their optical properties by UV/Vis spectroscopy and multispectral optoacoustic tomography. The complexes retained their biophysical properties, i.e. their ability to seed Aβ fibril formation. They remained stable in biological media for at least 2 days and showed no toxicity to SH-SY5Y neuroblastoma cells up to 1.5 nM and 6 μM of gold nanorods and Aβ seeds, respectively. Taken together, this study describes the first steps in the development of probes for monitoring the spread of Aβ seeds in animal models.
Impact of Grain for Green Project on Water Resources and Ecological Water Stress in Yanhe River Basin
Authors: Han Yuping , Xia Fan , Huang Huiping , Mu Wenbin
Published: October 2021

Grain for Green project (GGP) initialed by China government since 1999 has achieved substantial achievements accompanied with surface runoff decrease in the Loess Plateau but impacts of large-scale afforestation on regional water resources are uncertain. Hence, the objective of this study is to explore the impact of land use change on generalized water resources and ecological water stress using blue and green water concept taking Yanhe River Basin as a case study. Soil and Water Assessment Tool (SWAT) is applied to quantify summary of green and blue water which is defined as generalized water resources, ecological water requirement of vegetation (forest and grass), agricultural water footprint and virtual water flow are considered as regional water requirements. Land use types of 1980 (scenario I), 2017 (scenario II) are input in SWAT model while keeps other parameters constant in order to isolate the influence of land use changes. Results show that average annual difference of blue, green and generalized water resources is −72.08 million m3, 24.34 million m3, −47.74 million m3respectively when simulation results of scenario II subtracts scenario I and it presents that land use change caused by GGP leads to decrease in blue and generalized water resources whereas increase in green water resources. SURQ in scenario I is more than that in scenario IIin all the study period from 1980-2017, green water storage in scenario I is more than that in scenario II in all the study period except in 1998; whereas LATQ in scenario I is less than that in scenario II except in 2000 and 2015, GWQ in 1992, 2000 and 2015, green water flow in 1998. Blue water, green water storage and green water flow in scenario II is less than that in scenario I in the whole basin, 12.89 percent of the basin and 99.21 percent of the basin respectively. Total WF increases from 1995 to 2010 because forest WF increases significantly in this period though agricultural WF and grass WF decreases. Ecological water stress index has no obvious temporal change trend in both land use scenarios but ecological water stress index in scenario II is more than that in scenario I which illustrates that GGP leads to increase of ecological water stress from perspective of generalized water resources
Effects of electroacupuncture on the expression of hypothalamic neuropeptide Y and ghrelin in pubertal rats with polycystic ovary syndrome
Authors: Li Yang , Zhi Wang , Haoxu Dong , Qing Wang , Ling Cheng , Ping Yi , Dongmei Huang
Published: October 2021

Background

Polycystic ovary syndrome often starts in puberty, and its pathogenesis is not clear. This study aimed to explore the pathogenesis of pubertal polycystic ovary syndrome (PCOS) and assess the therapeutic effect of electroacupuncture on pubertal PCOS.

Methods

Dihydrotestosterone (DHT) was used to induce rat models of pubertal PCOS. pubertal rats with PCOS were randomly divided into a model group (M), an electroacupuncture group (EA), and a sham acupuncture group (SA). Age-matched normal rats were regarded as normal controls (N). Rats were treated with EA or SA five times a week for 25 minutes during their 6th–7th week. At the end of the experiment, we observed any changes in ovarian morphology; detected levels of metabolic indices in serum, the hypothalamus and pancreas.

Results

EA significantly improved estrous cycle disorders and the ovarian polycystic morphology in pubertal rats with PCOS, but SA only improved disorders of the estrous cycle. The serum levels of insulin, neuropeptide Y(NPY) and fasting blood glucose(FBG) increased significantly, while the serum levels of ghrelin(GHRL) decreased in the model group. After treatment with EA, the levels of NPY and FBG went into decrease, whereas the levels of GHRL and insulin increased. There was few differences in the hypothalamic expression of galanin (GAL), galanin-like peptide (GALP) and ghrelin receptor(GHSR) between the four groups. The upregulation of NPY mRNA and neuropeptide Y2 receptor(NPY2R) mRNA and the downregulation of GHRL protein and mRNA in the hypothalamus, and the increased expression of NPY and NPY2R as well as the decreased expression of GHRL in the arcuate nucleus (ARC) can be rescued by EA. But, surprisingly, SA seem to make no difference to the levels of FBG and insulin, and the protein expression of ghrelin in the hypothalamus and ARC. Co-expression of kisspeptin and GHSR, and co-expression of gonadotrophin releasing hormone(GnRH) and NPY2R were observed in ARC. No differences were found between groups in protein of GAL, GALP and GHRL expression in the pancreas. Neither EA nor SA can attenuate the upregulated kisspeptin protein expression in the pancreas of PCOS model rats.

Conclusions

EA and SA improved the symptoms of pubertal PCOS rats, and the mechanism might be associated with regulating hypothalamic NPY and ghrelin levels.
Estimated quantity of swine virus genomes based on quantitative PCR analysis in spray-dried porcine plasma samples collected from multiple manufacturing plants
Authors: Blázquez Elena , Pujols Joan , Segalés Joaquim , Rodríguez Carmen , Campbell Joy , Russell Louis , Polo Javier
Published: October 2021

This survey was conducted to estimate the incidence and level of potential viral contamination in commercially collected porcine plasma. Samples of spray dried porcine plasma (SDPP) were collected over a 12-month period from eight spray drying facilities in Spain, England, Northern Ireland, Brazil, Canada, and the United States. In this survey, viral load for several porcine pathogens including SVA, TGEV, PRRSV (EU and US strains), PEDV, PCV2, SIV, SDCoV and PPV were determined by qPCR. Regression of Ct on TCID50 of serial diluted stock solution of each virus allowed the estimate of potential viral level in SDPP and unprocessed liquid plasma (using typical solids content of commercially collected porcine plasma). In this survey SVA, TGEV or SDCoV were not detected in any of the SDPP samples. Brazil SDPP samples were free of PRRSV and PEDV. Samples of SDPP from North America primarily contained the PRRSV-US strain while the European samples contained the PRRSV-EU strain (except for one sample from each region containing a low estimated level of the alternative PRRSV strain). Estimated viral level tended to be low ranging from <1.0 log10TCID50to <2.5 log10TCID50. Estimated level of SIV was the exception with a very low incidence rate but higher estimated viral load <3.9 log10TCID50. In summary, the incidence of potential viral contamination in commercially collected porcine plasma was variable and estimated virus level in samples containing viral DNA/RNA was low.
MiR-30a-5p alters epidermal terminal differentiation during aging by regulating BNIP3L/NIX-dependent mitophagy
Authors: Chevalier Fabien P , Rorteau Julie , Ferraro Sandra , Martin Lisa S , Gonzalez-Torres Alejandro , Berthier Aurore , El Kholti Naima , Lamartine Jérôme
Published: October 2021

Chronological aging is characterized by an alteration of the genes regulatory network. In human skin, epidermal keratinocytes fail to differentiate properly with aging, leading to the weakening of the epidermal function. MiR-30a is particularly overexpressed with epidermal aging, but the downstream molecular mechanisms are still uncovered. The aim of this study was to decipher the effects of miR-30a overexpression in the human epidermis, with a focus on keratinocyte differentiation. We formally identified the mitophagy receptor BNIP3L as a direct target of miR-30a. Using a 3D organotypic model of reconstructed human epidermis overexpressing miR-30a, we observed a strong reduction of BNIP3L expression in the granular layer. In human epidermal sections of skin biopsies from donors of different ages, we observed a similar pattern of BNIP3L decrease with aging. Moreover, human primary keratinocytes undergoing differentiationin vitroalso showed a decreased expression ofBNIP3Lwith age, together with a retention of mitochondria. Moreover, aging is associated with altered mitochondrial metabolism in primary keratinocytes, including decreased ATP-linked respiration. Thus, miR-30a is a negative regulator of programmed mitophagy during keratinocytes terminal differentiation, impairing epidermal homeostasis with aging.
Nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants
Authors: Maeda Ryota , Fujita Junso , Konishi Yoshinobu , Kazuma Yasuhiro , Yamazaki Hiroyuki , Anzai Itsuki , Yamaguchi Keishi , Kasai Kazuki , Nagata Kayoko , Yamaoka Yutaro , Miyakawa Kei , Ryo Akihide , Shirakawa Kotaro , Makino Fumiaki , Matsuura Yoshiharu , Inoue Tsuyoshi , Imura Akihiro , Namba Keiichi , Takaori-Kondo Akifumi
Published: October 2021

We are in the midst of the historic coronavirus infectious disease 2019 (COVID-19) pandemic caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Although countless efforts to control the pandemic have been attempted—most successfully, vaccination1–3—imbalances in accessibility to vaccines, medicines, and diagnostics among countries, regions, and populations have been problematic. Camelid variable regions of heavy chain-only antibodies (VHHs or nanobodies)4 have unique modalities: they are smaller, more stable, easier to customize, and, importantly, less expensive to produce than conventional antibodies5, 6. We present the sequences of nine alpaca nanobodies that detect the spike proteins of four SARS-CoV-2 variants of concern (VOCs)—namely, the alpha, beta, gamma, and delta variants. We show that they can quantify or detect spike variants via ELISA and lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays7. The panel of nanobodies broadly neutralized viral infection by pseudotyped SARS-CoV-2 VOCs. Structural analyses showed that a P86 clone targeted epitopes that were conserved yet unclassified on the receptor-binding domain (RBD) and located inside the N-terminal domain (NTD). Human antibodies have hardly accessed both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins undetected by conventional antibodies and maintains activity against spike proteins carrying escape mutations.
P300 Parameters Over the Lifespan: Validating Target Ranges from an In-Clinic Platform
Authors: Oakley D. S. , Fosse K. , Gerwick E. , Joffe D. , Oakley D. A. , Prather A. , Lucini F Arese , Palermo F. X.
Published: October 2021

Background

Evoked potential (ERP) markers extracted from an EEG exam can provide novel sources of information regarding brain function allowing changes in cognition, from conditions such as concussion or unhealthy aging, to be measured and tracked over time. Age-related targets can provide useful guides for practitioners, trainers, and patients seeking to optimize and track brain function over time.

Objective 1: To compare age-related changes in auditory P300 metrics of latencies and amplitudes collected in the course of routine clinical evaluations with published trends from research.

Objective 2: To establish within-person test-retest variances for these P300 metrics.

Objective 3: To validate a method for presenting age-stratified target ranges of P300 metrics.

Participants

One thousand seven-hundred and seventy-eight reference subjects aged 13-90.

Methods

Audio P300 was measured as part of a health screening exam for studies through Colorado University, Children’s Hospital Colorado, Boone Heart Institute, WAVi Co., and various clinics alongside other clinical evaluations.

Results

The age-related trends in both the P300 latency and amplitude measured in clinic match the age-related trends from previous research. In particular, the 2 control group endpoints at 20 and 90 years match the linear slopes predicted for age-related decline from early studies, and the inclusion of all ages produces a maturation prediction of a recent meta analysis where metrics peak near 20 years of age. Large between-person variances are observed across all studies but within-person variances remain consistent with previous studies.

Conclusion

In-clinic measures of P300 latency and amplitude corroborate the age-related trends of published research taken over the last several decades. Large between-person variance remains, leaving P300 best suited for within-person comparison.
The regenerative response of cardiac interstitial cells
Authors: Rolland Laura , Harrington Alenca , Faucherre Adèle , Gangatharan Girisaran , Gamba Laurent , Severac Dany , Pratlong Marine , Moore-Morris Thomas , Jopling Chris
Published: October 2021

Understanding how certain animals are capable of regenerating their hearts will provide much needed insights into how this process can be induced in humans in order to reverse the damage caused by myocardial infarction. Currently, it is becoming increasingly evident that cardiac interstitial cells play crucial roles during cardiac regeneration. To understand how interstitial cells behave during cardiac regeneration, we performed single-cell RNA sequencing (scRNA-seq) of regenerating zebrafish hearts. Using a combination of immunohistochemistry, chemical inhibition and novel transgenic animals, we were able to investigate the role of cell type specific responses during cardiac regeneration. This approach allowed us to identify a number of important regenerative mechanisms within the interstitial cell populations. Here, we provide here a detailed insight into how interstitial cells behave during cardiac regeneration and identify a number of novel features of these cells which will serve to increase our understanding of how this process could eventually be induced in humans.
Quantifying the effect of caloric and non-caloric sweeteners in the brain response using EEG and convolutional neural network
Authors: von Atzingen Gustavo Voltani , Miñano Hubert Luzdemio Arteaga , da Silva Amanda Rodrigues , Ortega Nathalia Fontanari , Costa Ernane José Xavier , de Sousa Silva Ana Carolina
Published: October 2021

Sweetener type can influence sensory properties and consumer’s acceptance and preference for low-calorie products. An ideal sweetener does not exist, and each sweetener must be used in situations to which it is best suited. Aspartame and sucralose can be good substitutes for sucrose in passion fruit juice. Despite the interest in artificial sweeteners, little is known about how artificial sweeteners are processed in the human brain. Here, we evaluated brain signals of 11 healthy subjects when they tasted passion fruit juice equivalently sweetened with sucrose (9.4 g/100 g), sucralose (0.01593 g/100 g), or aspartame (0.05477 g/100 g). Electroencephalograms were recorded for two sites in the gustatory cortex (i.e., C3 and C4). Data with artifacts were disregarded, and the artifact-free data were used to feed a CNN. Our results indicated that the brain responses distinguish juice sweetened with different sweeteners with an average accuracy of 0.823.

Practical Applications

Finding sweeteners that best fit consumer preferences evolves understanding how the gustatory cortex processes sweeteners. Ideal equivalence will occur when the brain is no longer able to distinguish stimuli that are consciously perceived. This study presents a method of signal acquisition using a single channel and an open-source processing environment. This would allow, for example, to disregard the use of a commercial electroencephalograph and expand the studies in this area and offering to food industry additional tools in the development of products sweetened with non-caloric sweeteners.
Type S Non Ribosomal Peptide Synthetases for the rapid generation of tailor-made peptide libraries
Authors: Abbood Nadya , Vo Tien Duy , Watzel Jonas , Bozhueyuek Kenan A. J. , Bode Helge B.
Published: October 2021

Bacterial natural products in general, and non-ribosomally synthesized peptides in particular, are structurally diverse and provide us with a broad range of pharmaceutically relevant bioactivities. Yet, traditional natural product research suffers from rediscovering the same scaffolds and has been stigmatized as inefficient, time-, labour- and cost-intensive. Combinatorial chemistry, on the other hand, can produce new molecules in greater numbers, cheaper and in less time than traditional natural product discovery, but also fails to meet current medical needs due to the limited biologically relevant chemical space that can be addressed. Consequently, methods for the high throughput generation of new-to-nature natural products would offer a new approach to identifying novel bioactive chemical entities for the hit to lead phase of drug discovery programms. As a follow-up to our previously published proof-of-principle study on generating bipartite type S non-ribosomal peptide synthetases (NRPSs), we now envisaged the de novo generation of non-ribosomal peptides (NRPs) on an unreached scale. Using synthetic zippers, we split NRPS in up to three subunits and rapidly generated different bi- and tripartite NRPS libraries to produce 49 peptides, peptide derivatives, and de novo peptides at good titres up to 145 mgL-1. A further advantage of type S NRPSs not only is the possibility to easily expand the created libraries by re-using previously created type S NRPS, but that functions of individual domains as well as domain-domain interactions can be studied and assigned rapidly.
Zn2+ triggered two-step mechanism of CLIC1 membrane insertion and activation into chloride channels
Authors: Varela Lorena , Hendry Alex C. , Cassar Joseph , Martin-Escolano Ruben , Cantoni Diego , Edwards John C , Abdul-Salam Vahitha , Ortega-Roldan Jose L.
Published: October 2021

The CLIC protein family displays the unique feature of altering its structure from a soluble form to a membrane-bound chloride channel. CLIC1, a member of this family, is found in the cytoplasm or in internal and the plasma membranes, with membrane relocalisation linked to endothelial disfunction, tumour proliferation and metastasis. The molecular switch promoting CLIC1 activation remains unclear. Here, cellular chloride efflux assays and immunofluorescence microscopy studies have identified Zn2+ intracellular release as the trigger for CLIC1 activation and membrane relocalisation. Biophysical assays confirmed specific binding to Zn2+, inducing membrane association and enhancing chloride efflux in a pH dependent manner. Together, our results identify a two-step mechanism with Zn2+ binding as the molecular switch promoting CLIC1 membrane insertion, followed by pH activation of chloride efflux.
MACA: Marker-based automatic cell-type annotation for single cell expression data
Authors: Xu Yang , Baumgart Simon J. , Stegmann Christian , Hayat Sikander
Published: October 2021

Accurately identifying cell-types is a critical step in single-cell sequencing analyses. Here, we present marker-based automatic cell-type annotation (MACA), a new tool for annotating single-cell transcriptomics datasets. We developed MACA by testing 4 cell-type scoring methods with 2 public cell-marker databases as reference in 6 single-cell studies. MACA compares favorably to 4 existing marker-based cell-type annotation methods in terms of accuracy and speed. We show that MACA can annotate a large single-nuclei RNA-seq study in minutes on human hearts with ~290k cells. MACA scales easily to large datasets and can broadly help experts to annotate cell types in single-cell transcriptomics datasets, and we envision MACA provides a new opportunity for integration and standardization of cell-type annotation across multiple datasets.

Availability and implementation

MACA is written in python and released under GNU General Public License v3.0. The source code is available at https://github.com/ImXman/MACA.

Contact

Yang Xu (yxu71@vols.utk.edu), Sikander Hayat (hayat221@gmail.com)
Desire and Craving ratings vary significantly for healthy alcohol consumers: Differences in semantic interpretation?
Authors: Peterson H , Veach LJ , Simpson SL , Fanning J , Laurienti PJ , Gauvin L
Published: October 2021

Craving is a central concept in alcohol, and other substance, research. Beginning in 1955 the World Health Organization outlined a working definition of the term to be used in research and clinical settings. However, the semantic interpretation of “craving” as a concept is not widely agreed upon. Since the publication of this first craving definition, a handful of studies have been conducted to investigate differences in operational definitions of “craving”, and have demonstrated a lack of agreement between studies and across research subjects. With this background as evidence, our research group investigated, when left to their own semantic understanding of the terms, if regular alcohol consumers would rate craving for alcohol and desire for alcohol in similar ways using related descriptors. Thirty-nine healthy, non-binging regular alcohol consumers were studied across periods of their typical alcohol consumption and imposed alcohol abstinence, collecting ratings of desire and craving for alcohol approximately every two hours across the two experimental periods, and during neutral and alcohol related imagery viewing. Among these non-binging regular drinkers, ratings of desire and craving for alcohol are consistently different while drinking according to a person’s typical routine or abstaining, throughout the day, and when viewing alcohol cue imagery.
A basement membrane discovery pipeline uncovers network complexity, new regulators, and human disease associations
Authors: Jayadev Ranjay , Morais Mychel RPT , Ellingford Jamie M , Srinivasan Sandhya , Naylor Richard W , Lawless Craig , Li Anna S , Ingham Jack F , Hastie Eric , Chi Qiuyi , Fresquet Maryline , Koudis Nikki-Maria , Thomas Huw B , T O’Keefe Raymond , Williams Emily , Adamson Antony , Stuart Helen M , Banka Siddharth , Smedley Damian ,   Genomics England Research Consortium, Sherwood David R , Lennon Rachel
Published: October 2021

Basement membranes (BMs) are ubiquitous extracellular matrices whose composition remains elusive, limiting our understanding of BM regulation and function. By developing a bioinformatic and in vivo discovery pipeline, we define a network of 222 human proteins localized to BMs. Network analysis and screening in C. elegans and zebrafish identified new BM regulators, including ADAMTS, ROBO, and TGFβ. More than 100 BM-network genes associate with human phenotypes and by screening 63,039 genomes from families with rare disorders, we discovered loss-of-function variants in LAMA5, MPZL2, and MATN2, and show they regulate BM composition and function. This cross-disciplinary study establishes the immense complexity and role of BMs in human health.
Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes
Authors: Allen Jacob M. , Mackos Amy R. , Jaggers Robert M. , Brewster Patricia C. , Webb Mikaela , Lin Chia-Hao , Ladaika Chris , Davies Ronald , White Peter , Loman Brett R. , Bailey Michael T.
Published: October 2021

Psychological stress alters the gut microbiota and predisposes individuals to increased risk for enteric infections and chronic bowel conditions. Intestinal epithelial cells (IECs) are responsible for maintaining homeostatic interactions between the gut microbiota and its host. In this study, we hypothesized that disruption to colonic IECs is a key factor underlying stress-induced disturbances to intestinal homeostasis. Conventionally raised (CONV-R) and germ-free (GF) mice were exposed to a social disruption stressor (Str) to ascertain how stress modifies colonic IECs, the mucosal layer, and the gut microbiota. RNA sequencing of IECs isolated from CONV-R mice revealed a robust pro-inflammatory (Saa1, Il18), pro-oxidative (Duox2, Nos2), and antimicrobial (Reg3b/g) transcriptional profile as a result of Str. This response occurred concomitant to mucus layer thinning and signs of microbial translocation. In contrast to their CONV-R counterparts, IECs from GF mice or mice treated with broad spectrum antibiotics exhibited no detectable transcriptional changes in response to Str. Nevertheless, IECs from Str-exposed GF mice exhibited an altered response to ex vivo bacterial challenge (increased dual Oxidase-2 [Duox2] and nitric oxide synthase-2 (Nos2)), indicating that STR primes host IEC pro-oxidative responses. In CONV-R mice stress-induced increases in colonic Duox2 and Nos2 (ROS generating enzymes) strongly paralleled changes to microbiome composition and function, evidencing Str-mediated ROS production as a primary factor mediating gut-microbiota dysbiosis. In conclusion, a mouse model of social stress disrupts colonic epithelial and mucosal integrity, a response dependent on an intact microbiota and host stress signals. Together these preclinical findings may provide new insight into mechanisms of stress-associated bowel pathologies in humans.
Transposable elements continuously remodel the regulatory landscape, transcriptome, and function of decidual stromal cells
Authors: Mika Katelyn , Lynch Vincent J.
Published: October 2021

Gene expression evolution underlies the origin, divergence, and conservation of biological characters including cell-types, tissues, and organ systems. Previously we showed that large-scale gene expression changes in decidual stromal cells contributed to the origins of pregnancy in eutherians and the divergence of pregnancy traits in primates, and that transposable elements likely contributed to these gene expression changes. Here we show that two large waves of TEs remodeled the transcriptome and regulatory landscape of decidual stromal cells, including a major wave in primates. Genes nearby TE-derived regulatory elements are among the most progesterone responsive in the genome and play essential roles in orchestrating progesterone responsiveness and the core function of decidual cells by donating progesterone receptor binding sites to the genome. We tested the regulatory abilities of 89 TE consensus sequences and found nearly all acted as repressors in mammalian cells, but treatment with a histone deacetylase inhibitor unmasked latent enhancer functions. These data indicate TEs have played an important role in the development, evolution, and function of primate decidual stromal cells and suggest a two-step model in which latent enhancer functions of TEs are unmasked after they lose primary repressors functions.

Significance statement

Gene expression patterns evolved very rapidly during the evolutionary origins of pregnancy in early mammals and in primates. These episodes of gene expression evolution and linked with important processes that establish and maintain pregnancy, and appear to be driven by domestication of transposable elements.