bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein intake per day and at each daily meal and skeletal muscle mass declines among older community dwellers in Japan
Authors: Otsuka Rei , Kato Yuki , Tange Chikako , Nishita Yukiko , Tomida Makiko , Imai Tomoko , Ando Fujiko , Shimokata Hiroshi , Arai Hidenori 
Published: October 2019

AbstractObjective:To examine associations between protein intake per day and at different meals and skeletal muscle mass declines.Design:Two-year prospective cohort study among older community dwellers.Setting:National Institute for Longevity Sciences–Longitudinal Study of Aging (NILS-LSA) in Japan.Participants:Older men (n 292) and women (n 363) aged 60–87 years who participated in the baseline (2006–2008) and follow-up studies (2008–2010) of NILS-LSA and did not exhibit low skeletal muscle mass at baseline. Muscle mass was assessed using dual-energy X-ray absorptiometry at baseline and follow-up. Low muscle mass was defined as skeletal muscle mass index <7·0 kg/m2 for men and <5·4 kg/m2 for women at follow-up. Daily protein intake and protein intake at each meal were calculated from 3 d dietary records at baseline and sex-stratified tertiles were determined.Results:Mean (sd) protein intake at breakfast, lunch and dinner was 22·7 (7·8), 26·7 (9·3) and 37·4 (10·5) g for men and 19·3 (6·3), 23·2 (7·3) and 28·5 (7·0) g for women, respectively. After adjusting for age, baseline skeletal muscle mass and other confounders in logistic modelling, greater total protein intake was associated with lower prevalence of skeletal muscle mass decline among men at follow-up (P = 0·024). Particularly, the OR (95 % CI) for high lunchtime protein intake was low (0·11 (0·02, 0·61); P = 0·01). No significant association between total protein intake and prevalence of skeletal muscle mass decline was found among women.Conclusions:High total protein intake, particularly at lunchtime, is associated with retention of skeletal muscle mass in men.
3‐D Modeling of Vertical Gravity Gradients and the Delimitation of Tectonic Boundaries: The Caribbean Oceanic Domain as a Case Study
Authors: Gómez‐García Ángela María , Meeßen Christian , Scheck‐Wenderoth Magdalena , Monsalve Gaspar , Bott Judith , Bernhardt Anne , Bernal Gladys 
Published: October 2019

AbstractGeophysical data acquisition in oceanic domains is challenging, implying measurements with low and/or nonhomogeneous spatial resolution. The evolution of satellite gravimetry and altimetry techniques allows testing 3‐D density models of the lithosphere, taking advantage of the high spatial resolution and homogeneous coverage of satellites. However, it is not trivial to discretise the source of the gravity field at different depths. Here, we propose a new method for inferring tectonic boundaries at the crustal level. As a novelty, instead of modeling the gravity anomalies and assuming a flat Earth approximation, we model the vertical gravity gradients (VGG) in spherical coordinates, which are especially sensitive to density contrasts in the upper layers of the Earth. To validate the methodology, the complex oceanic domain of the Caribbean region is studied, which includes different crustal domains with a tectonic history since Late Jurassic time. After defining a lithospheric starting model constrained by up‐to‐date geophysical data sets, we tested several a‐priory density distributions and selected the model with the minimum misfits with respect to the VGG calculated from the EIGEN‐6C4 data set. Additionally, the density of the crystalline crust was inferred by inverting the VGG field. Our methodology enabled us not only to refine, confirm, and/or propose tectonic boundaries in the study area but also to identify a new anomalous buoyant body, located in the South Lesser Antilles subduction zone, and high‐density bodies along the Greater, Lesser, and Leeward Antilles forearcs.
Magnetic Pore Fabrics: The Role of Shape and Distribution Anisotropy in Defining the Magnetic Anisotropy of Ferrofluid‐Impregnated Samples
Authors: Biedermann Andrea R. 
Published: October 2019

AbstractPore fabrics define physical properties of a rock, such as permeability and elasticity, both of which are important to many geological, hydrological, and environmental applications. Minerals and hence pores are often preferentially aligned, leading to anisotropy of physical properties and preferred flow directions. Preferred flow paths are defined by the shape and arrangement of pores, and a characterization of this pore fabric forms the basis for prediction of fluid flow directions. Magnetic pore fabrics (MPFs), that is, magnetic anisotropy measurements on ferrofluid‐impregnated samples, are a promising and fast way to characterize the pore fabric of connected pores in 3‐D, while analyzing a large number of pores with sizes down to 10 nm, without the need for any a priori knowledge about fabric orientation. Empirical relationships suggest that the MPF is related to the pore shape and orientation and approximates permeability anisotropy. This study uses models including shape and distribution anisotropy to better understand and quantify MPFs, using simple pore shapes and pore assemblies measured in previous studies. The results obtained in this study show that (1) shape anisotropy reliably predicts the MPF of single pores, (2) both shape and distribution anisotropy are needed to predict MPFs of pore assemblies, and (3) the anisotropy parameters P, L, and F are affected by the intrinsic susceptibility of the ferrofluid in addition to pore geometry. These findings can help explain some of the variability in empirical relationships and are an important step toward a quantitative understanding and application of MPFs in geological and environmental studies.
IRF2 is a master regulator of human keratinocyte stem cell fate
Authors: Mercado Nicolas , Schutzius Gabi , Kolter Christian , Estoppey David , Bergling Sebastian , Roma Guglielmo , Gubser Keller Caroline , Nigsch Florian , Salathe Adrian , Terranova Remi , Reece-Hoyes John , Alford John , Russ Carsten , Knehr Judith , Hoepfner Dominic , Aebi Alexandra , Ruffner Heinz , Beck Tanner C. , Jagannathan Sajjeev , Olson Calla M. , Sheppard Hadley E. , Elsarrag Selma Z. , Bouwmeester Tewis , Frederiksen Mathias , Lohmann Felix , Lin Charles Y. , Kirkland Susan 
Published: October 2019

AbstractResident adult epithelial stem cells maintain tissue homeostasis by balancing self-renewal and differentiation. The stem cell potential of human epidermal keratinocytes is retained in vitro but lost over time suggesting extrinsic and intrinsic regulation. Transcription factor-controlled regulatory circuitries govern cell identity, are sufficient to induce pluripotency and transdifferentiate cells. We investigate whether transcriptional circuitry also governs phenotypic changes within a given cell type by comparing human primary keratinocytes with intrinsically high versus low stem cell potential. Using integrated chromatin and transcriptional profiling, we implicate IRF2 as antagonistic to stemness and show that it binds and regulates active cis-regulatory elements at interferon response and antigen presentation genes. CRISPR-KD of IRF2 in keratinocytes with low stem cell potential increases self-renewal, migration and epidermis formation. These data demonstrate that transcription factor regulatory circuitries, in addition to maintaining cell identity, control plasticity within cell types and offer potential for therapeutic modulation of cell function.
Detecting changes at the leading edge of an interface between oceanic water layers
Authors: Tang Qunshu , Tong Vincent C. H. , Hobbs Richard W. , Morales Maqueda Miguel Ángel 
Published: October 2019

AbstractMany physical phenomena in the ocean involve interactions between water masses of different temperatures and salinities at boundaries. Of particular interest is the characterisation of finescale structure at the marginal interaction zones of these boundaries, where the structure is either destroyed by mixing or formed by stratification. Using high-resolution seismic reflection imaging, we present observations of temporal changes at the leading edge of an interface between sub-thermocline layers in the Panama Basin. By studying time-lapse images of a seismic reflector between two water boundaries with subtle differences, we provide empirical constraints on how stratified layers evolve. The leading edge of this reflector, which is characterised by a gradual lateral decrease in vertical temperature contrast ($$|\Delta T|$$
∣
Δ
T
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), increases in length over ~3 days coupled with an increase in $$|\Delta T|$$
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Δ
T
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. A critical mixing state, in which turbulent diffusion is gradually replaced by double-diffusion as the dominant mixing process, is thus revealed.
A new species in the major malaria vector complex sheds light on reticulated species evolution
Authors: Barrón Maite G. , Paupy Christophe , Rahola Nil , Akone-Ella Ousman , Ngangue Marc F. , Wilson-Bahun Theodel A. , Pombi Marco , Kengne Pierre , Costantini Carlo , Simard Frédéric , González Josefa , Ayala Diego 
Published: October 2019

AbstractComplexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studiedAnopheles fontenilleisp.n., a new species in theAnopheles gambiaecomplex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of theAn.gambiaecomplex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, withAnopheles gambiaeandAnopheles coluzzii, of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species allowed us to clarify the evolutionary history of the 3La inversion. Overall,An.fontenilleisp.n. analysis improved our understanding of the relationship between species within theAn.gambiaecomplex, and provided insight into the evolution of vectorial capacity traits that are relevant for the successful control of malaria in Africa.
Experimental challenge with bovine respiratory syncytial virus in dairy calves: bronchial lymph node transcriptome response
Authors: Johnston Dayle , Earley Bernadette , McCabe Matthew S. , Lemon Ken , Duffy Catherine , McMenamy Michael , Cosby S. Louise , Kim JaeWoo , Blackshields Gordon , Taylor Jeremy F. , Waters Sinead M. 
Published: October 2019

AbstractBovine Respiratory Disease (BRD) is the leading cause of mortality in calves. The objective of this study was to examine the response of the host’s bronchial lymph node transcriptome to Bovine Respiratory Syncytial Virus (BRSV) in a controlled viral challenge. Holstein-Friesian calves were either inoculated with virus (103.5 TCID50/ml × 15 ml) (n = 12) or mock challenged with phosphate buffered saline (n = 6). Clinical signs were scored daily and blood was collected for haematology counts, until euthanasia at day 7 post-challenge. RNA was extracted and sequenced (75 bp paired-end) from bronchial lymph nodes. Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. There was a clear separation between BRSV challenged and control calves based on gene expression changes, despite an observed mild clinical manifestation of the disease. Therefore, measuring host gene expression levels may be beneficial for the diagnosis of subclinical BRD. There were 934 differentially expressed genes (DEG) (p < 0.05, FDR <0.1, fold change >2) between the BRSV challenged and control calves. Over-represented gene ontology terms, pathways and molecular functions, among the DEG, were associated with immune responses. The top enriched pathways included interferon signaling, granzyme B signaling and pathogen pattern recognition receptors, which are responsible for the cytotoxic responses necessary to eliminate the virus.
The link between yeast cell wall porosity and plasma membrane permeability after PEF treatment
Authors: Stirke Arunas , Celiesiute-Germaniene Raimonda , Zimkus Aurelijus , Zurauskiene Nerija , Simonis Povilas , Dervinis Aldas , Ramanavicius Arunas , Balevicius Saulius 
Published: October 2019

AbstractAn investigation of the yeast cell resealing process was performed by studying the absorption of the tetraphenylphosphonium (TPP+) ion by the yeast Saccharomyces cerevisiae. It was shown that the main barrier for the uptake of such TPP+ ions is the cell wall. An increased rate of TPP+ absorption after treatment of such cells with a pulsed electric field (PEF) was observed only in intact cells, but not in spheroplasts. The investigation of the uptake of TPP+ in PEF treated cells exposed to TPP+ for different time intervals also showed the dependence of the absorption rate on the PEF strength. The modelling of the TPP+ uptake recovery has also shown that the characteristic decay time of the non-equilibrium (PEF induced) pores was approximately a few tens of seconds and this did not depend on the PEF strength. A further investigation of such cell membrane recovery process using a florescent SYTOX Green nucleic acid stain dye also showed that such membrane resealing takes place over a time that is like that occurring in the cell wall. It was thus concluded that the similar characteristic lifetimes of the non-equilibrium pores in the cell wall and membrane after exposure to PEF indicate a strong coupling between these parts of the cell.
Adipocyte PU.1 knockout promotes insulin sensitivity in HFD-fed obese mice
Authors: Lackey Denise E. , Reis Felipe C. G. , Isaac Roi , Zapata Rizaldy C. , El Ouarrat Dalila , Lee Yun Sok , Bandyopadhyay Gautam , Ofrecio Jachelle M. , Oh Da Young , Osborn Olivia 
Published: October 2019

AbstractInsulin resistance is a key feature of obesity and type 2 diabetes. PU.1 is a master transcription factor predominantly expressed in macrophages but after HFD feeding PU.1 expression is also significantly increased in adipocytes. We generated adipocyte specific PU.1 knockout mice using adiponectin cre to investigate the role of PU.1 in adipocyte biology, insulin and glucose homeostasis. In HFD-fed obese mice systemic glucose tolerance and insulin sensitivity were improved in PU.1 AKO mice and clamp studies indicated improvements in both adipose and liver insulin sensitivity. At the level of adipose tissue, macrophage infiltration and inflammation was decreased and glucose uptake was increased in PU.1 AKO mice compared with controls. While PU.1 deletion in adipocytes did not affect the gene expression of PPARg itself, we observed increased expression of PPARg target genes in eWAT from HFD fed PU.1 AKO mice compared with controls. Furthermore, we observed decreased phosphorylation at serine 273 in PU.1 AKO mice compared with fl/fl controls, indicating that PPARg is more active when PU.1 expression is reduced in adipocytes. Therefore, in obesity the increased expression of PU.1 in adipocytes modifies the adipocyte PPARg cistrome resulting in impaired glucose tolerance and insulin sensitivity.
A docking-based structural analysis of geldanamycin-derived inhibitor binding to human or Leishmania Hsp90
Authors: Palma Luana Carneiro , Ferreira Luiz Felipe Gomes Rebello , Petersen Antonio Luis de Oliveira Almeida , Dias Beatriz Rocha Simões , Menezes Juliana Perrone Bezerra de , Moreira Diogo Rodrigo de Magalhães , Hernandes Marcelo Zaldini , Veras Patricia Sampaio Tavares 
Published: October 2019

AbstractLeishmaniasis is a neglected disease that affects millions of individuals around the world. Regardless of clinical form, treatment is based primarily on the use of pentavalent antimonials. However, such treatments are prolonged and present intense side effects, which lead to patient abandonment in many cases. The search for chemotherapeutic alternatives has become a priority. Heat Shock Protein 90 (Hsp90) inhibitors have recently come under investigation due to antiparasitic activity in Plasmodium sp., Trypanosoma sp. and Leishmania sp. Some of these inhibitors, such as geldanamycin and its analogs, 17-AAG and 17-DMAG, bind directly to Hsp90, thereby inhibiting its activity. Previous studies have demonstrated that different parasite species are more susceptible to some of these inhibitors than host cells. We hypothesized that this increased susceptibility may be due to differences in binding of Hsp90 inhibitors to Leishmania protein compared to host protein. Based on the results of the in silico approach used in the present study, we propose that geldanamycin, 17-AAG and 17-DMAG present an increased tendency to bind to the N-terminal domain of Leishmania amazonensis Hsp83 in comparison to human Hsp90. This could be partially explained by differences in intermolecular interactions between each of these inhibitors and Hsp83 or Hsp90. The present findings demonstrate potential for the use of these inhibitors in the context of anti-Leishmania therapy.
Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes
Authors: Campbell Benjamin W. , Hoyle Jacob W. , Bucciarelli Bruna , Stec Adrian O. , Samac Deborah A. , Parrott Wayne A. , Stupar Robert M. 
Published: October 2019

AbstractDevelopments in genomic and genome editing technologies have facilitated the mapping, cloning, and validation of genetic variants underlying trait variation. This study combined bulked-segregant analysis, array comparative genomic hybridization, and CRISPR/Cas9 methodologies to identify a CPR5 ortholog essential for proper trichome growth in soybean (Glycine max). A fast neutron mutant line exhibited short trichomes with smaller trichome nuclei compared to its parent line. A fast neutron-induced deletion was identified within an interval on chromosome 6 that co-segregated with the trichome phenotype. The deletion encompassed six gene models including an ortholog of Arabidopsis thaliana CPR5. CRISPR/Cas9 was used to mutate the CPR5 ortholog, resulting in five plants harboring a total of four different putative knockout alleles and two in-frame alleles. Phenotypic analysis of the mutants validated the candidate gene, and included intermediate phenotypes that co-segregated with the in-frame alleles. These findings demonstrate that the CPR5 ortholog is essential for proper growth and development of soybean trichomes, similar to observations in A. thaliana. Furthermore, this work demonstrates the value of using CRISPR/Cas9 to generate an allelic series and intermediate phenotypes for functional analysis of candidate genes and/or the development of novel traits.
Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations
Authors: Maruyama Kei , Imai Hirotatsu , Kawamura Momoko , Ishino Sonoko , Ishino Yoshizumi , Ito Kosuke , Uchiumi Toshio 
Published: October 2019

AbstractTranslation elongation factor EF1A delivers aminoacyl-tRNA to the ribosome in a GTP-bound form, and is released from the ribosome in a GDP-bound form. This association/dissociation cycle proceeds efficiently via a marked conformational change in EF1A. EF1A function is dependent on the ribosomal “stalk” protein of the ribosomal large subunit, although the precise mechanism of action of the stalk on EF1A remains unclear. Here, we clarify the binding mode of archaeal stalk aP1 to GTP-bound aEF1A associated with aPelota. Intriguingly, the C-terminal domain (CTD) of aP1 binds to aEF1A•GTP with a similar affinity to aEF1A•GDP. We have also determined the crystal structure of the aP1-CTD•aEF1A•GTP•aPelota complex at 3.0 Å resolution. The structure shows that aP1-CTD binds to a space between domains 1 and 3 of aEF1A. Biochemical analyses show that this binding is crucial for protein synthesis. Comparison of the structures of aP1-CTD•aEF1A•GTP and aP1-CTD•aEF1A•GDP demonstrates that the binding mode of aP1 changes markedly upon a conformational switch between the GTP- and GDP-bound forms of aEF1A. Taking into account biochemical data, we infer that aP1 employs its structural flexibility to bind to aEF1A before and after GTP hydrolysis for efficient protein synthesis.
Characterization of biological variation of peripheral blood immune cytome in an Indian cohort
Authors: Kanodia Parna , Kaur Gurvinder , Coshic Poonam , Chatterjee Kabita , Neeman Teresa , George Anna , Rath Satyajit , Bal Vineeta , Prabhu Savit B. 
Published: October 2019

AbstractImmune parameters show characteristic normal baseline levels and variance in the population. We characterised the degree of inter-individual and within-individual variation over one-year time period in 33 immune cell subsets by flow cytometry in peripheral blood mononuclear cells from 43 healthy young adult volunteers. Our analysis revealed that immune subsets that showed low variability between individuals also showed low short-term fluctuations within-individuals, as well as concordance in siblings. However, when baseline levels and degree of fluctuation were considered together, individuals failed to cluster into discreet groups. Together, the data reveal complex inter-relationships between immune subsets in individuals, and provide insights into the observed heterogeneity between individuals and between multiple immune subsets.
Hypoxia-inducible factor-1α is the therapeutic target of the SGLT2 inhibitor for diabetic nephropathy
Authors: Bessho Ryoichi , Takiyama Yumi , Takiyama Takao , Kitsunai Hiroya , Takeda Yasutaka , Sakagami Hidemitsu , Ota Tsuguhito 
Published: October 2019

AbstractPrevious studies have demonstrated intrarenal hypoxia in patients with diabetes. Hypoxia-inducible factor (HIF)-1 plays an important role in hypoxia-induced tubulointerstitial fibrosis. Recent clinical trials have confirmed the renoprotective action of SGLT2 inhibitors in diabetic nephropathy. We explored the effects of an SGLT2 inhibitor, luseogliflozin on HIF-1α expression in human renal proximal tubular epithelial cells (HRPTECs). Luseogliflozin significantly inhibited hypoxia-induced HIF-1α protein expression in HRPTECs. In addition, luseogliflozin inhibited hypoxia-induced the expression of the HIF-1α target genes PAI-1, VEGF, GLUT1, HK2 and PKM. Although luseogliflozin increased phosphorylated-AMP-activated protein kinase α (p-AMPKα) levels, the AMPK activator AICAR did not changed hypoxia-induced HIF-1α expression. Luseogliflozin suppressed the oxygen consumption rate in HRPTECs, and subsequently decreased hypoxia-sensitive dye, pimonidazole staining under hypoxia, suggesting that luseogliflozin promoted the degradation of HIF-1α protein by redistribution of intracellular oxygen. To confirm the inhibitory effect of luseogliflozin on hypoxia-induced HIF-1α protein in vivo, we treated male diabetic db/db mice with luseogliflozin for 8 to 16 weeks. Luseogliflozin attenuated cortical tubular HIF-1α expression, tubular injury and interstitial fibronectin in db/db mice. Together, luseogliflozin inhibits hypoxia-induced HIF-1α accumulation by suppressing mitochondrial oxygen consumption. The SGLT2 inhibitors may protect diabetic kidneys by therapeutically targeting HIF-1α protein.