bluuebunny/crossref_metadata_2025 huggingface dataset:
Superresolution microscopy reveals photoreceptor-specific subciliary location and function of Cep290
Authors: Potter Valencia L. , Moye Abigail R. , Robichaux Michael A. , Wensel Theodore G.
Published: October 2020

Mutations in the cilium-associated protein CEP290 cause retinal degeneration as part of multi-organ syndromic ciliopathies or as retina-specific diseases. The precise location and the functional roles of CEP290 within cilia and, specifically, the connecting cilia (CC) of photoreceptors, remain unclear. We used superresolution fluorescence microscopy and electron microscopy (TEM) to localize CEP290 in the CC and in primary cilia of cultured cells with sub-diffraction resolution, and to determine effects of CEP290 deficiency. Radially, CEP290 co-localizes with the microtubule doublets and extends beyond them. Longitudinally, it is distributed throughout the length of the CC but is strictly confined to the very base of primary cilia in hRPE-1 cells. We found Y-shaped links, the ciliary sub-structures between microtubules and membrane, at the base of the transition zone in primary cilia of epithelial cells and throughout the length of the CC. Severe CEP290 deficiencies in mouse models did not prevent assembly of cilia or cause obvious mislocalization of ciliary components in early stages of degeneration. They did not lead to loss of the Y-shaped links but caused changes in their structures. These results point to photoreceptor-specific functions of CEP290 essential for CC maturation and stability following the earliest stages of ciliogenesis.
Genetic ancestry predicts male-female affiliation in a natural baboon hybrid zone
Authors: Fogel Arielle S. , McLean Emily M. , Gordon Jacob B. , Archie Elizabeth A. , Tung Jenny , Alberts Susan C.
Published: October 2020

Opposite-sex social relationships are important predictors of fitness in many animals, including several group-living mammals. Consequently, understanding sources of variance in the tendency to form opposite-sex relationships is important for understanding social evolution. Genetic contributions are of particular interest due to their importance in long-term evolutionary change, but little is known about genetic effects on male-female relationships in social mammals, especially outside of the mating context. Here, we investigate the effects of genetic ancestry on male-female affiliative behavior in a hybrid zone between the yellow baboon (Papio cynocephalus) and the anubis baboon (P. anubis), in a population in which male-female social bonds are known predictors of lifespan. We place our analysis within the context of other social and demographic predictors of affiliative behavior in baboons. Genetic ancestry was the most consistent predictor of opposite-sex affiliative behavior we observed, with the exception of strong effects of dominance rank. Our results show that increased anubis genetic ancestry is associated with subtly, but significantly higher rates of opposite-sex affiliative behavior, in both males and females. Additionally, pairs of anubis-like males and anubis-like females were the most likely to socially affiliate, resulting in moderate assortativity in grooming and proximity behavior as a function of genetic ancestry. Our findings indicate that opposite-sex affiliative behavior partially diverged during baboon evolution to differentiate yellow and anubis baboons, despite overall similarities in their social structures and mating systems. Further, they suggest that affiliative behavior may simultaneously promote and constrain baboon admixture, through additive and assortative effects of ancestry, respectively.

HIGHLIGHTS

Opposite-sex social relationships can have important fitness consequences.

In hybrid baboons, genetic ancestry predicted male-female affiliative behavior.

Both an individual’s genetic ancestry and that of its social partner mattered.

Male-female affiliation was assortative with respect to genetic ancestry.

Dominance rank and group demography also influenced male-female social affiliation.
High dose IFN-βactivates GAF to enhance expression of ISGF3 target genes in epithelial cells
Authors: Kishimoto Kensei , Wilder Catera , Buchanan Justin , Nguyen Minh , Okeke Chidera , Hoffmann Alexander , Cheng Quen J.
Published: October 2020

Interferonβ(IFN-β) signaling activates the transcription factor complex ISGF3 to induce gene expression programs critical for antiviral defense and host immune responses. It has also been observed that IFN-βactivates a second transcription factor, γ-activated factor (GAF), but the significance of this coordinated activation is unclear. We report that in respiratory epithelial cells high doses of IFN-βindeed activate both ISGF3 and GAF, which bind to distinct genomic locations defined by their respective DNA sequence motifs. In contrast, low doses of IFN-βpreferentially activate ISGF3 but not GAF. Surprisingly, in epithelial cells GAF binding does not induce nearby gene expression even when strongly bound to the promoter. Yet expression of interferon stimulated genes is enhanced when GAF and ISGF3 are both active compared to ISGF3 alone. Our data suggest that GAF enhances ISGF3 target gene expression by co-localizing with ISGF3 at some promoters and facilitating chromosome looping between distal enhancers and other promoters. We propose that GAF may function as a dose-sensitive amplifier of ISG expression to enhance antiviral immunity and establish pro-inflammatory states in respiratory epithelial cells.

One sentence summary

GAF is transcriptionally inactive in epithelial cells but enhances expression of ISGF3 target genes, thus functioning as a dose-sensitive amplifier of the IFN-βresponse.
Emergent collective organization of bone cells in complex curvature fields
Authors: Callens Sebastien J.P. , Fan Daniel , van Hengel Ingmar A.J. , Minneboo Michelle , Fratila-Apachitei Lidy E. , Zadpoor Amir A.
Published: October 2020

Abstract

Individual cells and multicellular systems have been shown to respond to cell-scale curvatures in their environments, guiding migration, orientation, and tissue formation. However, it remains unclear how cells collectively explore and pattern complex landscapes with curvature gradients across the Euclidean and non-Euclidean spectra, partly owing to fabrication limitations and the lack of formal geometric considerations. Here, we show that micro-engineered substrates with controlled curvature variations induce the collective spatiotemporal organization of preosteoblasts. By leveraging mathematical surface design and a high-resolution free-form fabrication process, we exposed cells to a broad yet controlled, heterogeneous spectrum of curvature fields. We quantified curvature-induced spatial patterning at different time points and found that cells generally prefer regions with at least one negative principal curvature. We also show that multicellular cooperation enables cells to venture into unfavourably-curved territories, bridging large portions of the substrates, and collectively aligning their stress fibres. We demonstrate that this behaviour is partly regulated by cellular contractility and extracellular matrix development, underscoring the mechanical nature of curvature guidance. Our findings offer unifying perspectives on cell-geometry interactions that could be harnessed in the design of micro-engineered biomaterials, for example, for tissue engineering applications.
Automated Detection and Diameter Estimation for Mouse Mesenteric Artery using Semantic Segmentation
Authors: Higaki Akinori , Mahmoud Ahmad U. M. , Paradis Pierre , Schiffrin Ernesto L.
Published: October 2020

Background

Pressurized myography is useful for the assessment of small artery structure and function, and widely used in the field of cardiovascular research. However, this procedure requires technical expertise for the sample preparation and effort to choose an appropriate size of artery. In this study we sought to develop an automatic artery-vein differentiation and size measurement system utilizing the U-Net-based machine learning algorithms.

Methods and Results

We used 654 independent mesenteric artery images from 59 mice for the model training and validation. Our segmentation model yielded 0.744 ±0.031 in IoU and 0.881 ±0.016 in Dice coefficient with 5-fold cross validation. The vessel size and the lumen size calculated from the predicted vessel contours demonstrated a strong linear correlation with the manually determined vessel sizes (R = 0.722 ±0.048, p<0.001 for vessel size and R = 0.908 ±0.027, p<0.001 for lumen size). Lastly, we assessed the relation between the vessel size before and after dissection using pressurized myography system. We observed a strong positive correlation between the wall/lumen ratio before dissection and the lumen expansion ratio (R2= 0.671, p<0.01). Using multivariate binary logistic regression, two models estimating whether the vessel met the size criteria (lumen size of 160 to 240 μm) were generated with area under the ROC curve of 0.761 for the upper limit and 0.747 for the lower limit.

Conclusion

Our novel image analysis method with U-Net could streamline the experimental approach and may facilitate cardiovascular research.
Neuromuscular control of gait stability in older adults is adapted to environmental demands but not improved after standing balance training
Authors: Alizadehsaravi Leila , Bruijn Sjoerd M. , Muijres Wouter , Koster Ruud A.J. , van Dieën Jaap H.
Published: October 2020

Balance training aims to improve balance and transfer acquired skills to real-life tasks and conditions. How older adults adapt gait control to different conditions, and whether these adaptations are altered by balance training remains unclear. We investigated adaptations in neuromuscular control of gait in twenty-two older adults (72.6 ± 4.2 years) between normal (NW) and narrow-base walking (NBW), and the effects of a standing balance training program shown to enhance unipedal balance control in the same participants. At baseline, after one session and after 3-weeks of training, kinematics and EMG of NW and NBW on a treadmill were measured. Gait parameters and temporal activation profiles of five synergies extracted from 11 muscles were compared between time-points and gait conditions. No effects of balance training or interactions between training and walking condition on gait parameters or synergies were found. Trunk center of mass (CoM) displacement and velocity (vCoM), and the local divergence exponent (LDE), were lower in NBW compared to NW. For synergies associated with stance of the non-dominant leg and weight acceptance of the dominant leg, full width at half maximum (FWHM) of the activation profiles was smaller in NBW compared to NW. For the synergy associated with non-dominant heel strike, FWHM was greater in NBW compared to NW. The Center of Activation (CoA) of the activation profile associated with dominant leg stance occurred earlier in NBW compared to NW. CoAs of activation profile associated with non-dominant stance and non-dominant and dominant heel strikes were delayed in NBW compared to NW. The adaptations of synergies to NBW can be interpreted as related to a more cautious weight transfer to the new stance leg and enhanced control over CoM movement in the stance phase. However, control of mediolateral gait stability and these adaptations were not affected by balance training.
Inhibition of USP4 attenuates epithelial-mesenchymal transition of renal tubular epithelial cells by TβRI
Authors: Pu Jin-yun , Zhang Yu , Wang Li-xia , Wang Jie , Zhou Jian-hua
Published: October 2020

The process of epithelial-mesenchymal transition (EMT) is required for the progression of renal interstitial fibrosis (RIF). Ubiquitin-specific protease 4 (USP4) can facilitate development of transforming growth factor, beta 1 (TGF-β1) induced EMT in some cancer cells. However, the role of USP4 in EMT during RIF remains unknown. We aimed to explore the effect of USP4 on the EMT induced by TGF-β1 of renal tubular epithelial cells and involved mechanism in RIF. In vivo, on the 7th and 14th day after unilateral ureteral obstruction (UUO), the expression of USP4 protein in the obstructed kidneys was detected by immunohistochemistry and Western blot assay. In vitro, NRK-52E cells were stimulated with TGF-β1 10ng/ml. The protein expressions of USP4, E-cadherin and alpha smooth muscle actin (α-SMA) were detected at different time points by Western blot. After transfected with USP4 siRNA, the cells were cultured with TGF-β1 for additional 24 hours. The expressions of E-cadherin, α-SMA, and TGFβ receptor type I (TβRI) were detected by immunofluorescence. And the protein expressions of USP4, E-cadherin, α-SMA and TβRI were detected by Western blot assay. Compared with sham operation group, the expression of USP4 in UUO model group increased significantly with the prolongation of obstruction time. After NRK-52E was stimulated by TGF-β1, the expression of USP4 protein increased gradually. At 6h, 12h, and 24h, the difference between the experimental group and the control group was statistically significant. At the same time, E-cadherin decreased significantly, while α-SMA increased significantly. Compared with the TGF-β1 group, the cells in USP4 siRNA transfection group restored E-cadherin and weakened α-SMA expression. At the same time, protein expressions of USP4 and TβRI were also significantly decreased. These data imply that USP4 is a harmful molecule induced by TGF-β1, which plays an important role by upregulating the expression of TβRI and promoting EMT of renal tubular epithelial cells, thereby facilitating renal interstitial fibrosis.
Sirt1 overexpression attenuates high-fat diet induced aortic stiffening
Authors: Gogulamudi Venkateswara R. , Machin Daniel R. , Henson Grant , Donato Anthony J. , Lesniewski Lisa A.
Published: October 2020

Increased arterial stiffness is a cardiovascular disease risk factor in the setting of advancing age and high-fat (HF) diet induced obesity. Increases in large artery stiffness, as measured by pulse wave velocity (PWV), occur within 8 weeks of HF feeding in mice. Sirtuin-1 (Sirt1), a NAD-dependent deacetylase, regulates cellular metabolic activity and activation of this protein has been associated with vasoprotection in aged mice. The aim of the present study was to elucidate the effect of global Sirt1 overexpression (Sirttg) on HF diet-induced arterial stiffening. Sirt1 overexpression did not influence PWV in normal chow (NC) fed mice (Sirttg: 263 ± 6 vs WT: 274 ± 7, p=0.28). However, PWV was higher in wild-type (WT) mice (376 ± 22, p<0.04), but not Sirttg(304 ± 2 cm/s, p=0.07), after 12 weeks of HF diet. Despite no effect of Sirt1 overexpression on aortic collagen content in NC (p=0.71), aortic elastin content was higher in Sirttgmice compared with WT mice fed NC diet (P<0.05). Surprisingly, despite increased arterial stiffness, collagen content was lower (p<0.02) and elastin content was unchanged (p=0.05) in the aortas of WT mice after HF. Neither collagen (p=0.18) nor elastin content (p=0.56) were impacted by HF diet in the Sirttgmice. Likewise, there was no difference in wall thickness in NC (Sirttg: 40.7 ± 2 vs WT: 41.6 ± 2, p= 0.78). However, wall thickness was higher in mice WT mice fed a HF diet (51.7 ± 2, p<0.01) and there was no difference in Sirttgmice after HF diet (p=0.66). Similarly, there was no difference in wall-to-lumen ratio in mice fed NC diet (Sirttg: 0.08 vs WT: 0.08, p=0.48) was higher in HF diet fed WT mice (p<0.01), though, HF diet was associated with a higher wall-to-lumen ratio in WT (0.11, p<0.01), but not different in Sirttgmice fed HF diet (0.08, p=0.59). These findings demonstrate a vasoprotective effect of Sirt1 overexpression that limits increases in arterial stiffness and protects against alterations in vessel morphology in response to HF feeding. As such, activation of Sirt1 may be a novel therapeutic target to prevent elevated CVD risk associated with HF-induced aortic stiffening.
Ethacridine inhibits SARS-CoV-2 by inactivating viral particles in cellular models
Authors: Li Xiaoquan , Lidsky Peter , Xiao Yinghong , Wu Chien-Ting , Garcia-Knight Miguel , Yang Junjiao , Nakayama Tsuguhisa , Nayak Jayakar V. , Jackson Peter K. , Andino Raul , Shu Xiaokun
Published: October 2020

SARS-CoV-2 is the coronavirus that causes the respiratory disease COVID-19, which is now the third-leading cause of death in the United States. The FDA has recently approved remdesivir, an inhibitor of SARS-CoV-2 replication, to treat COVID-19, though recent data from the WHO shows little to no benefit with use of this anti-viral agent. Here we report the discovery of ethacridine, a safe antiseptic use in humans, as a potent drug for use against SARS-CoV-2 (EC50~ 0.08μM). Ethacridine was identified via high-throughput screening of an FDA-approved drug library in living cells using a fluorescent assay. Interestingly, the main mode of action of ethacridine is through inactivation of viral particles, preventing their binding to the host cells. Indeed, ethacridine is effective in various cell types, including primary human nasal epithelial cells. Taken together, these data identify a promising, potent, and new use of the old drug possessing a distinct mode of action for inhibiting SARS-CoV-2.
Structural insights into the cooperative interaction of the intrinsically disordered co-activator TIF2 with retinoic acid receptor heterodimer (RXR/RAR)
Authors: Senicourt Lucile , Maire Albane le , Allemand Frédéric , Carvalho JoÃo E. , Guee Laura , Germain Pierre , Schubert Michael , Bernadó Pau , Bourguet William , Sibille Nathalie
Published: October 2020

Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2NRID) containing three highly conserved α-helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2NRIDby integrating several experimental (NMR, SAXS, CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2NRIDin complex with RXR/RAR reveal a cooperative binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.
Innervation and Neuronal Control of the Mammalian Sinoatrial Node: A Comprehensive Atlas
Authors: Hanna Peter , Dacey Michael J. , Brennan Jaclyn , Moss Alison , Robbins Shaina , Achanta Sirisha , Biscola Natalia P. , Swid Mohammed A. , Rajendran Pradeep S. , Mori Shumpei , Hadaya Joseph E. , Smith Elizabeth H. , Peirce Stanley G. , Chen Jin , Havton Leif A. , Cheng Zixi (Jack) , Vadigepalli Rajanikanth , Schwaber James , Lux Robert L. , Efimov Igor , Tompkins John D. , Hoover Donald B. , Ardell Jeffrey L. , Shivkumar Kalyanam
Published: October 2020

Cardiac function is under exquisite intrinsic cardiac neural control. Neuroablative techniques to modulate control of cardiac function are currently being studied in patients, albeit with variable and sometimes deleterious results. Recognizing the major gaps in our understanding of cardiac neural control, we sought to evaluate neural regulation of impulse initiation in the sinoatrial node as an initial discovery step. Here, we report an in-depth, multi-scale structural and functional characterization of the innervation of the sinoatrial node (SAN) by the right atrial ganglionated plexus (RAGP) in porcine and human hearts. Combining intersectional strategies including tissue clearing, immunohistochemical and ultrastructural techniques, we have delineated a comprehensive neuroanatomic atlas of the RAGP-SAN complex. The RAGP shows significant phenotypic diversity of neurons while maintaining predominant cholinergic innervation. Cellular and tissue-level electrophysiologic mapping and ablation studies demonstrate interconnected ganglia with synaptic convergence within the RAGP to modulate SAN automaticity, atrioventricular (AV) conduction and left ventricular (LV) contractility. For the first time, we demonstrate that intrinsic cardiac neurons influence the pacemaking site in the heart. This provides an experimental demonstration of a discrete neuronal population controlling a specific geographic region of the heart (SAN) that can serve as a framework for further exploration of other parts of the intrinsic cardiac nervous system (ICNS) in mammalian hearts and for developing targeted therapies.
Pronounced proliferation of non-beta cells in response to beta-cell mitogens in isolated human islets of Langerhans
Authors: Maachi Hasna , Ghislain Julien , Tremblay Caroline , Poitout Vincent
Published: October 2020

The potential to treat diabetes by increasing beta-cell mass is driving a major effort to identify beta-cell mitogens. Demonstration of mitogen activity in human beta cells is frequently performed in ex vivo assays. However, reported disparities in the efficacy of beta-cell mitogens led us to investigate the sources of this variability. We studied 35 male (23) and female (12) human islet batches covering a range of donor ages and BMI. Islets were kept intact or dispersed into single cells and cultured in the presence of harmine, glucose, or heparin-binding epidermal growth factor-like growth factor (HB-EGF), and subsequently analyzed by immunohistochemistry or flow cytometry. Proliferating cells were identified by double labelling with EdU and Ki67 and glucagon, c-peptide or Nkx6.1, and cytokeratin-19 to respectively label alpha, beta, and ductal cells. Harmine and HB-EGF stimulated human beta-cell proliferation, but the effect of glucose was dependent on the assay and the donor. Harmine potently stimulated alpha-cell proliferation and both harmine and HB-EGF increased proliferation of insulin- and glucagon-negative cells, including cytokeratin 19-positive cells. Given the abundance of non-beta cells in human islet preparations, our results suggest that assessment of beta-cell mitogens requires complementary approaches and rigorous identification of cell identity using multiple markers.
Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes
Authors: Ansari-Pour Naser , Zheng Yonglan , Pitt Jason J. , Dentro Stefan , Yoshimatsu Toshio F. , Sanni Ayodele , Ajani Mustapha , Woodard Anna , Rajagopal Padma Sheila , Fitzgerald Dominic , Gruber Andreas J. , Odetunde Abayomi , Popoola Abiodun , Falusi Adeyinka G. , Babalola Chinedum Peace , Ogundiran Temidayo , Obafunwa John , Ojengbede Oladosu , Ibrahim Nasiru , Barretina Jordi , Van Loo Peter , Chen Mengjie , White Kevin P. , Huo Dezheng , Wedge David C. , Olopade Olufunmilayo I.
Published: October 2020

Black women of African ancestry experience more aggressive breast cancer with higher mortality rates than White women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast tumors, with RNA-seq in a subset, from indigenous African patients in Nigeria in comparison to The Cancer Genome Atlas (n=76) revealed a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonalGATA3mutations and a 10.5-year younger age at diagnosis. We also found evidence for non-coding mutations in two novel drivers (ZNF217andSYPL1) and a novel INDEL signature strongly associated with African ancestry proportion. This comprehensive analysis of an understudied population underscores the need to incorporate diversity of genomes as a key parameter in fundamental research with potential to tailor clinical intervention and promote equity in precision oncology care.
In vitroassessment of the virucidal activity of four mouthwashes containing Cetylpyridinium Chloride, ethanol, zinc and a mix of enzyme and proteins against a human coronavirus
Authors: Green A. , Roberts G. , Tobery T. , Vincent C. , Barili M. , Jones C.
Published: October 2020

Background

saliva is established to contain high counts SARS-CoV-2 virus and contact with saliva droplets, contaminated surfaces or airborne particles are sources of viral transmission. The generation of infective aerosols during clinical procedures is of particular concern. Therefore, a fuller understanding of the potential of mouthwash to reduce viral counts and modulate the risk of transmission in medical professional and public context is an important research topic.

Method

we determined the virucidal activity of four anti-bacterial mouthwashes against a surrogate for SARS-CoV-2, Human CoV-SARS 229E, using a standard ASTM suspension test, with dilution and contact times applicable to recommended mouthwash use.

Results

the mouthwash formulated with 0.07% Cetylpyridinium Chloride exhibited virucidal effects providing a ≥3.0 log reduction HCoV-229E viral count. Mouthwashes containing 15.7% ethanol, 0.2% zinc sulphate heptahydrate and a mix of enzymes and proteins did not demonstrate substantive virucidal activity in this test.

Conclusion

mouthwash containing 0.07% Cetylpyridinium Chloride warrants further laboratory and clinical assessment to determine their potential benefit in reducing the risk of SARS-CoV-2.

Highlights

SARS-CoV-2 can be transmitted through contact with infective saliva.

Studies are needed to understand if mouthwash can lower SARS-CoV-2 transmission risk.

0.07% Cetylpyridinium Chloride (CPC) mouthwash exhibited virucidal effects against HCoV-SARS 229E.

Further studies on potential of 0.07% CPC mouthwash against SARS-CoV-2 are warranted.
Evidence for selection in a prokaryote pangenome
Authors: Whelan Fiona J , Hall Rebecca J , McInerney James O
Published: October 2020

A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome’s accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40Pseudomonasgenomes for statistically significant coincident (i.e. co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other - but are not vertically or horizontally co-inherited - are more likely to share Gene Ontology categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into interacting sets of genes co-selected to function together within a given strain. Given the simi larity of thePseudomonaspangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.
Gene replacement of α-globin with β-globin restores hemoglobin balance in β-thalassemia-derived hematopoietic stem and progenitor cells
Authors: Cromer M. Kyle , Camarena Joab , Martin Renata M. , Lesch Benjamin J. , Vakulskas Christopher A. , Lemgart Viktor T. , Zhang Yankai , Goyal Ankush , Zhao Feifei , Ponce Ezequiel , Srifa Wai , Bak Rasmus O. , Uchida Naoya , Majeti Ravindra , Sheehan Vivien A. , Tisdale John F. , Dever Daniel P. , Porteus Matthew H.
Published: October 2020

β-thalassemia pathology is not only due to loss of β-globin (HBB), but also erythrotoxic accumulation and aggregation of the β-globin binding partner, α-globin (HBA1/2). Here we describe a Cas9/AAV6-mediated genome editing strategy that can replace the entireHBA1gene with a full-lengthHBBtransgene in β-thalassemia-derived hematopoietic stem and progenitor cells (HSPCs), which is sufficient to normalize β-globin:α-globin mRNA and protein ratios and restore functional adult hemoglobin tetramers in patient-derived red blood cells. Edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in mice, establishing proof-of-concept for replacement ofHBA1withHBBas a novel therapeutic strategy for curing β-thalassemia.
The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses
Authors: Bonaventure Boris , Rebendenne Antoine , de Gracia Francisco Garcia , McKellar Joe , Gracias Ségolène , Labaronne Emmanuel , Tauziet Marine , Valadão Ana Luiza Chaves , Bernard Eric , Briant Laurence , Gros Nathalie , Djilli Wassila , Arnaud-Arnould Mary , Courgnaud Valérie , Parrinello Hugues , Rialle Stéphanie , Ricci Emiliano , Jouvenet Nolwenn , Schulz Reiner , Moncorgé Olivier , Goujon Caroline
Published: October 2020

Genome-wide screens are powerful approaches to unravel new regulators of viral infections. Here, we used a CRISPR/Cas9 screen to reveal new HIV-1 inhibitors. This approach led us to identify the RNA helicase DDX42 as an intrinsic antiviral inhibitor. DDX42 was previously described as a non-processive helicase, able to bind RNA secondary structures such as G-quadruplexes, with no clearly defined function ascribed. Our data show that depletion of endogenous DDX42 significantly increased HIV-1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibited HIV-1, whereas a dominant-negative mutant increased infection. Importantly, DDX42 also restricted retrotransposition of LINE-1, infection with other retroviruses and positive-strand RNA viruses, including CHIKV and SARS-CoV-2. However, DDX42 did not inhibit infection with three negative-strand RNA viruses, arguing against a general, unspecific effect on target cells, which was confirmed by RNA-seq analysis. DDX42 was found in the vicinity of viral elements by proximity ligation assays, and cross-linking RNA immunoprecipitation confirmed a specific interaction of DDX42 with RNAs from sensitive viruses. This strongly suggested a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Taken together, our results show for the first time a new and important role of DDX42 in intrinsic antiviral immunity.
Multistate Ornstein-Uhlenbeck approach for practical estimation of movement and resource selection around central places
Authors: Eisaguirre Joseph M. , Booms Travis L. , Barger Christopher P. , Goddard Scott D. , Breed Greg A.
Published: October 2020

Home range dynamics and movement are central to a species’ ecology and strongly mediate both intra- and interspecific interactions. Numerous methods have been introduced to describe animal home ranges, but most lack predictive ability and cannot capture effects of dynamic environmental patterns, such as the impacts of air and water flow on movement.

Here, we develop a practical, multi-stage approach for statistical inference into the behavioral mechanisms underlying how habitat and dynamic energy landscapes—in this case how airflow increases or decreases the energetic efficiency of flight—shape animal home ranges based around central places. We validated the new approach using simulations, then applied it to a sample of 12 adult golden eaglesAquila chrysaetostracked with satellite telemetry.

The application to golden eagles revealed effects of habitat variables that align with predicted behavioral ecology. Further, we found that males and females partition their home ranges dynamically based on uplift. Specifically, changes in wind and sun angle drove differential space use between sexes, especially later in the breeding season when energetic demands of growing nestlings require both parents to forage more widely.

This method is easily implemented using widely available programming languages and is based on a hierarchical multistate Ornstein-Uhlenbeck space use process that incorporates habitat and energy landscapes. The underlying mathematical properties of the model allow straightforward computation of predicted utilization distributions, permitting estimation of home range size and visualization of space use patterns under varying conditions.
GWAS in Africans identifies novel lipids loci and demonstrates heterogenous association within Africa
Authors: Bentley Amy R. , Chen Guanjie , Doumatey Ayo P. , Shriner Daniel , Meeks Karlijn , Gouveia Mateus H. , Ekoru Kenneth , Zhou Jie ,   the Africa America Diabetes Mellitus Investigators, Adeyemo Adebowale , Rotimi Charles N.
Published: October 2020

Background

Serum lipids are biomarkers of cardiometabolic disease risk, and understanding the genomic factors contributing to their distribution has been of considerable interest. Large genome-wide association studies (GWAS) have identified over 150 lipids loci; however, GWAS of Africans (AF) are rare. Given the genomic diversity among those of African ancestry, it is expected that a GWAS in Africans could identify novel lipids loci. While GWAS have been conducted in African Americans (AA), such studies are not proxies for studies in continental Africans due to the drastically different environmental context. Therefore, we conducted a GWAS of 4,317 Africans enrolled in the Africa America Diabetes Mellitus study.

Methods and Results

We used linear mixed models of the inverse normal transformations of covariate-djusted residuals of high-density lipoprotein cholesterol (HDLC), low-density lipoprotein cholesterol (LDLC), total cholesterol (CHOL), triglycerides (TG), and TG/HDLC, with adjustment for three principal components and the random effect of relatedness. Replication of loci associated at p<5×10−8was attempted in 9,542 AA. Meta-analysis of AF and AA was also conducted. We also conducted analyses that excluded the relatively small number of East Africans. We evaluated known lipids loci in Africans using both exact replication and “local” replication, which accounts for interethnic differences in linkage disequilibrium.

In our main analysis, we identified 23 novel associations in Africans. Of the 14 of these that were able to be tested in AA, two associations replicated (GPNMB-TG andENPP1-TG). Two additional novel loci were discovered upon meta-analysis with AA (rs138282551-TG andTLL2-CHOL). Analyses considering only those with predominantly West African ancestry (Nigeria, Ghana, and AA) yielded new insights:ORC5-LDLC and chr20:60973327-CHOL.

Conclusions

While functional work will be useful to confirm and understand the biological mechanisms underlying these associations, this study demonstrates the utility of conducting large-scale genomic analyses in Africans for discovering novel loci. The functional significance of some of these loci in relation to lipids remains to be elucidated, yet some have known connections to lipids pathways. For instance, rs147706369 (intronic,TLL2) alters a regulatory motif for sterol regulatory element-binding proteins (SREBPs), which are a family of transcription factors that control the expression of a range of enzymes involved in cholesterol, fatty acid, and triglyceride synthesis.
A systematic analysis of the beta hairpin motif in the Protein Data Bank
Authors: DuPai Cory D. , Davies Bryan W. , Wilke Claus O.
Published: October 2020

The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched inter-strand contacts. We also establish a set of broad design principles that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures.

Importance

The beta hairpin motif is a common protein structural motif that is known for its stability and varied activity in diverse proteins. Here we use nearly fifty thousand beta hairpin substructures from the Protein Data Bank to systematically analyze and identify key characteristics of the beta hairpin motif. Ultimately, we provide a set of design principles for the generation of synthetic libraries encoding proteins containing beta hairpin structures.
The effect of activity, energy use, and species identity on environmental DNA shedding of freshwater fish
Authors: Thalinger Bettina , Rieder Andreas , Teuffenbach Anna , Pütz Yannick , Schwerte Thorsten , Wanzenböck Josef , Traugott Michael
Published: October 2020

The quantitative measurement of environmental DNA (eDNA) from field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed.

In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids, and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity, and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which exhibited lower activity and higher energy use.

Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.
Developing Commotio Cordis Injury Metrics by Correlating Chest Force and Rib Deformation to Left Ventricle Strain and Pressure
Authors: Dickey Grant J. , Bian Kewei , Khan Habib R. , Mao Haojie
Published: October 2020

Commotio cordis is a sudden death mechanism that occurs when the heart is impacted during the repolarization phase of the cardiac cycle. This study aimed to investigate commotio cordis injury metrics by correlating chest force and rib deformation to left ventricle (LV) strain and pressure. We simulated 128 chest impacts using a simulation matrix which included two initial velocities, 16 impact locations spread across the transverse and sagittal plane, and four baseball stiffness levels. Results showed that an initial velocity of 17.88 m/s and an impact location over the LV was the most damaging setting across all possible settings, causing the most considerable LV strain and pressure increases. The impact force metric did not correlate with LV strain and pressure, while rib deformations located over the LV were strongly correlated to LV strain. This leads us to the recommendation of exploring new injury metrics such as the rib deformations we have highlighted for future commotio cordis safety regulations.
Oleic acid triggers hippocampal neurogenesis by binding to TLX/NR2E1
Authors: Kandel Prasanna , Semerci Fatih , Bajic Aleksandar , Baluya Dodge , Ma LiHua , Chen Kevin , Cao Austin , Phongmekhin Tipwarin , Matinyan Nick , Choi William , Jiménez-Panizo Alba , Chamakuri Srinivas , Raji Idris O. , Chang Lyra , Fuentes-Prior Pablo , MacKenzie Kevin R. , Benn Caroline L. , Estébanez-Perpiñá Eva , Venken Koen , Moore David D. , Young Damian W. , Maletic-Savatic Mirjana
Published: October 2020

Adult hippocampal neurogenesis underpins learning, memory, and mood, but diminishes with age and illness. The orphan nuclear receptor TLX/NR2E1 is known to regulate neural stem and progenitor cell self-renewal and proliferation, but the precise mechanism by which it accomplishes this is unknown. We found that neural stem and progenitor cells require monounsaturated fatty acids to survive and proliferate. Specifically, oleic acid (18:1ω9) binds to TLX to convert it from a transcriptional repressor to a transcriptional activator of cell cycle and neurogenesis genes. We propose a model in which sufficient quantities of this endogenous ligand must bind to TLX to trigger the switch to proliferation. These findings pave the way for future therapeutic manipulations to counteract pathogenic impairments of neurogenesis.
Aberrant Ca2+homeostasis in adipocytes links inflammation to metabolic dysregulation in obesity
Authors: Guney Ekin , Arruda Ana Paula , Parlakgul Gunes , Cagampan Erika , Min Nina , Lee Yankun , Greene Lily , Tsaousidou Eva , Inouye Karen , Han Myoung Sook , Davis Roger J. , Hotamisligil Gökhan S.
Published: October 2020

Chronic metabolic inflammation is a key feature of obesity, insulin resistance and diabetes, although the initiation and propagation mechanisms of metaflammation are not fully established, particularly in the adipose tissue. Here we show that in adipocytes, altered regulation of the Ca2+channel inositol triphosphate receptor (IP3Rs) is a key, adipocyte-intrinsic, event involved in the emergence and propagation of inflammatory signaling and the resulting insulin resistance. Inflammation, either induced by cytokine exposurein vitroor by obesityin vivolead to increased expression and activity of IP3Rs in adipocytes in a JNK-dependent manner. This results in increased cytosolic Ca2+and impaired insulin action. In mice, adipocyte-specific loss of IP3R1/2 protected against adipose tissue inflammation and insulin resistance despite significant diet-induced weight gain. Thus, this work reveals that IP3R over-activation and the resulting increase in cytosolic Ca2+is a key link between obesity, inflammation and insulin resistance, and suggests that approaches to target adipocyte Ca2+homeostasis may offer new therapeutic opportunities against metabolic diseases, especially since GWAS studies also implicate this locus in human obesity.
Structural basis for a natural circular permutation in proteins
Authors: Nonis Samuel G. , Haywood Joel , Schmidberger Jason W. , Bond Charles S. , Mylne Joshua S.
Published: October 2020

Over 30 years ago, an intriguing post-translational modification was discovered to be responsible for creating concanavalin A (conA), a carbohydrate-binding protein found in the seeds of jack bean (Canavalia ensiformis) and commercially used for carbohydrate chromatography. Biosynthesis of conA involves what was then an unprecedented rearrangement in amino acid sequence, whereby the N-terminal half of the gene-encoded conA precursor is swapped to become the C-terminal half of conA. The cysteine protease, asparaginyl endopeptidase (AEP), was shown to be involved, but its mechanism was not fully elucidated. To understand the structural basis and consequences of conA circular permutation, we generated a recombinant jack bean conA precursor (pro-conA) plus jack bean AEP (CeAEP1) and solved crystal structures for each to 2.1 Å and 2.7 Å respectively. By reconstituting the biosynthesis of conAin vitro, we prove CeAEP1 alone can perform both the cleavage and cleavage-coupled transpeptidation to form conA. CeAEP1 structural analysis reveals how it is capable of carrying out both these reactions. Biophysical assays illustrated that conA is more thermally and pH stable than pro-conA, consistent with fewer intermolecular interactions between subunits in the pro-conA crystal structure. These findings elucidate the consequences of circular permutation in the only post-translation example known to occur in nature.
The fusion peptide proximal region of the HIV-1 envelope glycoproteins regulates exposure of immunogenic epitopes at the trimer base
Authors: Rojas Chávez Roberth Anthony , Boyt Devlin , Han Changze , Wu Li , Haim Hillel
Published: October 2020

The error-prone replication machinery of HIV-1 continuously generates new variants of the envelope glycoproteins (Envs). Antibody selection pressures applied in the host can limit their persistence. The target specificity of antibodies elicited in different hosts varies considerably. Whether some specificities are shared and have affected the population-level evolution of Env structure is still unclear. We examined the historical changes in amino acid sequence of the gp41 fusion peptide proximal region (FPPR), which is not exposed on the Env trimer. For three FPPR positions, the residue found in the clade B ancestor was mainly replaced by alanine. However, the changes in alanine frequency at these positions between 1979 and 2016 followed different patterns; two positions maintained a historically-constant frequency whereas the third showed a gradual increase. To understand these patterns, we introduced alanine substitutions in the FPPR of primary HIV-1 strains and examined their fitness and antigenicity relative to the clade-ancestral form. The evolutionary patterns could not be explained by effects on Env fitness. Instead, the FPPR variants with a historically-constant alanine frequency exhibited a unique open-at-the-base conformation of the trimer that exposes partially-cryptic epitopes. These Envs were modestly but significantly more sensitive to poorly-neutralizing sera from HIV-infected individuals than the clade-ancestral form. Our findings suggest that weakly-neutralizing antibodies targeting the base of the trimer are commonly elicited. Such low-level antibody pressures do not exert catastrophic effects on the emerging variants but rather determine their set-point frequency in the population and historical patterns of change.

IMPORTANCE

HIV-1 infection elicits antibodies that target the Env proteins of the virus. The specific targets of these antibodies vary between infected individuals. It is unclear whether some target specificities are shared between the antibody responses of different individuals. Our data suggest that antibodies against the base of the Env protein are commonly elicited during infection and are contained in sera with low neutralization efficacy. Such antibody pressures are weak. As a result, they do not completely eliminate the sensitive Env forms from the population, but rather maintain their frequency at a low level that has not increased during the past 40 years.