bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamic study of MlaC protein in Gram‐negative bacteria: conformational flexibility, solvent effect and protein‐phospholipid binding
Authors: Huang Yu‐ming M. , Miao Yinglong , Munguia Jason , Lin Leo , Nizet Victor , McCammon J. Andrew 
Published: April 2016

AbstractThe composition of the outer membrane in Gram‐negative bacteria is asymmetric, with the lipopolysaccharides found in the outer leaflet and phospholipids in the inner leaflet. The MlaC protein transfers phospholipids from the outer to inner membrane to maintain such lipid asymmetry in the Mla pathway. In this work, we have performed molecular dynamics simulations on apo and phospholipid‐bound systems to study the dynamical properties of MlaC. Our simulations show that the phospholipid forms hydrophobic interactions with the protein. Residues surrounding the entrance of the binding site exhibit correlated motions to control the site opening and closing. Lipid binding leads to increase of the binding pocket volume and precludes entry of the water molecules. However, in the absence of the phospholipid, water molecules can freely move in and out of the binding site when the pocket is open. Dehydration occurs when the pocket closes. This study provides dynamic information of the MlaC protein and may facilitate the design of antibiotics against the Mla pathway of Gram‐negative bacteria.
Implementing a screening program for acromegaly in Latin America: necessity versus feasibility
Authors: Danilowicz Karina , Day Patricia Fainstein , Manavela Marcos P. , Herrera Carlos Javier , Deheza María Laura , Isaac Gabriel , Juri Ariel , Katz Debora , Bruno Oscar D. 
Published: April 2016

Abstract

Introduction
Acromegaly is a rare disease with a large burden due its associated comorbidities and the life-long management required. Since the occurrence and severity of associated complications are related to length of exposure to the excess growth hormone seen in acromegaly, early diagnosis is imperative. The delay in diagnosis, however, can be long, and may be the result of a lack of disease awareness and screening programs. Since acromegaly is an uncommon disease, finding ways to increase recognition and diagnosis that would permit early detection in a logical and cost-effective manner could be a challenge.

Methods
We conducted a retrospective literature review for information relating to the screening and diagnosis of acromegaly using PubMed. The aim was to assess whether an acromegaly-screening program in Latin America (and elsewhere) would be both of use and be feasible.

Findings and conclusions
An earlier diagnosis allows earlier initiation of treatment, such as surgery and/or drugs, which leads to more successful disease management (biochemical control) and better outcomes. Since the delay in diagnosis can be long, we believe that clear opportunities exist for earlier (and increased) detection of acromegaly. This can be achieved by increasing disease awareness for earlier recognition of symptoms and by using targeted screening (rather than mass screening) programs.
Does broodstock nutritional history affect the response of progeny to different first-feeding diets? A whole-body transcriptomic study of rainbow trout alevins
Authors: Lazzarotto Viviana , Corraze Geneviève , Larroquet Laurence , Mazurais David , Médale Françoise 
Published: April 2016

AbstractThe whole-body transcriptome of trout alevins was characterised to investigate the effects of long-term feeding of rainbow trout broodstock females a diet free of fishmeal and fish oil on the metabolic capacities of progeny. Effects were studied before first feeding and after 3 weeks of feeding diets containing different proportions of marine and plant ingredients. Feeding alevins plant-based diets resulted in lower fish body weight, irrespective of maternal nutritional history. No differences in whole-body lipids were found between treatments, and the tissue fatty acid profile strongly reflected that of the respective broodstock or first-feeding diets. We showed that the maternal diet history did not significantly affect expressions of any genes before the first feeding. Interestingly, we found an effect of maternal nutritional history on gene expression in alevins after 3 weeks of feeding. The major differences in the transcriptome of alevins from plant-based diet-fed females compared with those from commercial-fed females were as follows: (i) down-regulation of genes involved in muscle growth/contraction and (ii) up-regulation of genes involved in carbohydrate and energy metabolism related to the delay in growth/development observed with plant-based diets. Our findings also showed an effect of the first-feeding diets, irrespective of maternal nutritional history. Specifically, the introduction of plant ingredients resulted in the up-regulation of genes involved in amino acid/protein and cholesterol metabolism and in differences in the expressions of genes related to carbohydrate metabolism. Information gained through this study opens up avenues for further reduction of marine ingredients in trout diets, including the whole rearing cycle.
The danger of “new norms” and the continuing relevance of IHL in the post-9/11 era
Authors: Lellio Anna Di , Castano Emanuele 
Published: April 2016

AbstractIn the post-9/11 era, the label “asymmetric wars” has often been used to question the relevance of certain aspects of international humanitarian law (IHL); to push for redefining the combatant/civilian distinction; and to try to reverse accepted norms such as the bans on torture and assassination. In this piece, we focused on legal and policy discussions in the United States and Israel because they better illustrate the dynamics of State-led “norm entrepreneurship”, or the attempt to propose opposing or modified norms as a revision of IHL. We argue that although these developments are to be taken seriously, they have not weakened the normative power of IHL or made it passé. On the contrary, they have made it more relevant than ever. IHL is not just a complex (and increasingly sophisticated) branch of law detached from reality. Rather, it is the embodiment of widely shared principles of morality and ethics, and stands as a normative “guardian” against processes of moral disengagement that make torture and the acceptance of civilian deaths more palatable.
Diverse human extracellular RNAs are widely detected in human plasma
Authors: Freedman Jane E. , Gerstein Mark , Mick Eric , Rozowsky Joel , Levy Daniel , Kitchen Robert , Das Saumya , Shah Ravi , Danielson Kirsty , Beaulieu Lea , Navarro Fabio C. P. , Wang Yaoyu , Galeev Timur R. , Holman Alex , Kwong Raymond Y. , Murthy Venkatesh , Tanriverdi Selim E. , Koupenova Milka , Mikhalev Ekaterina , Tanriverdi Kahraman 
Published: April 2016

AbstractThere is growing appreciation for the importance of non-protein-coding genes in development and disease. Although much is known about microRNAs, limitations in bioinformatic analyses of RNA sequencing have precluded broad assessment of other forms of small-RNAs in humans. By analysing sequencing data from plasma-derived RNA from 40 individuals, here we identified over a thousand human extracellular RNAs including microRNAs, piwi-interacting RNA (piRNA), and small nucleolar RNAs. Using a targeted quantitative PCR with reverse transcription approach in an additional 2,763 individuals, we characterized almost 500 of the most abundant extracellular transcripts including microRNAs, piRNAs and small nucleolar RNAs. The presence in plasma of many non-microRNA small-RNAs was confirmed in an independent cohort. We present comprehensive data to demonstrate the broad and consistent detection of diverse classes of circulating non-cellular small-RNAs from a large population.
Encapsulation of zinc-rifampicin complex into transferrin-conjugated silver quantum-dots improves its antimycobacterial activity and stability and facilitates drug delivery into macrophages
Authors: Pati Rashmirekha , Sahu Rojalin , Panda Jagannath , Sonawane Avinash 
Published: April 2016

AbstractIn order to improve the chemotherapy of tuberculosis, there is an urgent need to enhance the efficacy of existing agents and also to develop more efficient drug delivery systems. Here, we synthesized a novel anti-TB drug complex consisting of zinc and rifampicin (Zn-RIF) and encapsulated it into transferrin-conjugated silver quantum-dots (Zn-RIF-Tf-QD) to improve delivery in macrophages. Successful synthesis of Zn-RIF and Zn-RIF-Tf-QD was confirmed by UV/Vis-spectroscopy, TEM, FTIR, photoluminescence, XRD, XPS and NMR. The sizes of silver QDs and transferrin-conjugated QDs were found to be in the range of 5–20 nm. Activity assays showed that Zn-RIF-Tf-QD exhibited 10-fold higher antibacterial activity against Mycobacterium smegmatis and Mycobacterium bovis-BCG as compared to Zn-RIF, RIF and Zn. Immunofluorescence studies showed that Zn-RIF-Tf-QD-conjugates were actively endocytosed by macrophages and dendritic cells, but not by lung epithelial cells. Treatment with Zn-RIF-Tf-QD efficiently killed mycobacteria residing inside macrophages without exhibiting cytotoxicity and genotoxicity. Moreover, the conjugates remained stable for upto 48 h, were taken up into the late endosomal compartment of macrophages and released the drug in a sustainable manner. Our data demonstrate that Zn-RIF-Tf-QDs have a great potential as anti-TB drugs. In addition, transferrin-conjugated QDs may constitute an effective drug delivery system for tuberculosis therapy.
Unique behavior of Trypanosoma cruzi mevalonate kinase: A conserved glycosomal enzyme involved in host cell invasion and signaling
Authors: Ferreira Éden Ramalho , Horjales Eduardo , Bonfim-Melo Alexis , Cortez Cristian , da Silva Claudio Vieira , De Groote Michel , Sobreira Tiago José Paschoal , Cruz Mário Costa , Lima Fabio Mitsuo , Cordero Esteban Mauricio , Yoshida Nobuko , da Silveira José Franco , Mortara Renato Arruda , Bahia Diana 
Published: April 2016

AbstractMevalonate kinase (MVK) is an essential enzyme acting in early steps of sterol isoprenoids biosynthesis, such as cholesterol in humans or ergosterol in trypanosomatids. MVK is conserved from bacteria to mammals and localizes to glycosomes in trypanosomatids. During the course of T. cruzi MVK characterization, we found that, in addition to glycosomes, this enzyme may be secreted and modulate cell invasion. To evaluate the role of TcMVK in parasite-host cell interactions, TcMVK recombinant protein was produced and anti-TcMVK antibodies were raised in mice. TcMVK protein was detected in the supernatant of cultures of metacyclic trypomastigotes (MTs) and extracellular amastigotes (EAs) by Western blot analysis, confirming its secretion into extracellular medium. Recombinant TcMVK bound in a non-saturable dose-dependent manner to HeLa cells and positively modulated internalization of T. cruzi EAs but inhibited invasion by MTs. In HeLa cells, TcMVK induced phosphorylation of MAPK pathway components and proteins related to actin cytoskeleton modifications. We hypothesized that TcMVK is a bifunctional enzyme that in addition to playing a classical role in isoprenoid synthesis in glycosomes, it is secreted and may modulate host cell signaling required for T. cruzi invasion.
A web-based resource for designing therapeutics against Ebola Virus
Authors: Dhanda Sandeep Kumar , Chaudhary Kumardeep , Gupta Sudheer , Brahmachari Samir Kumar , Raghava Gajendra P. S. 
Published: April 2016

AbstractIn this study, we describe a web-based resource, developed for assisting the scientific community in designing an effective therapeutics against the Ebola virus. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses. It was observed that three species can potentially be targeted by a single siRNA (19mer) and 75 siRNAs can potentially target at least two species. A web server, EbolaVCR, has been developed that incorporates all the above information and useful computational tools (http://crdd.osdd.net/oscadd/ebola/).
Unconventional magnetisation texture in graphene/cobalt hybrids
Authors: Vu A. D. , Coraux J. , Chen G. , N’Diaye A. T. , Schmid A. K. , Rougemaille N. 
Published: April 2016

AbstractMagnetic domain structure and spin-dependent reflectivity measurements on cobalt thin films intercalated at the graphene/Ir(111) interface are investigated using spin-polarised low-energy electron microscopy. We find that graphene-covered cobalt films have surprising magnetic properties. Vectorial imaging of magnetic domains reveals an unusually gradual thickness-dependent spin reorientation transition, in which magnetisation rotates from out-of-the-film plane to the in-plane direction by less than 10° per cobalt monolayer. During this transition, cobalt films have a meandering spin texture, characterised by a complex, three-dimensional, wavy magnetisation pattern. In addition, spectroscopy measurements suggest that the electronic band structure of the unoccupied states is essentially spin-independent already a few electron-Volts above the vacuum level. These properties strikingly differ from those of pristine cobalt films and could open new prospects in surface magnetism.
Assessment of Fat distribution and Bone quality with Trabecular Bone Score (TBS) in Healthy Chinese Men
Authors: Lv Shan , Zhang Aisen , Di Wenjuan , Sheng Yunlu , Cheng Peng , Qi Hanmei , Liu Juan , Yu Jing , Ding Guoxian , Cai Jinmei , Lai Bin 
Published: April 2016

AbstractWhether fat is beneficial or detrimental to bones is still controversial, which may be due to inequivalence of the fat mass. Our objective is to define the effect of body fat and its distribution on bone quality in healthy Chinese men. A total of 228 men, aged from 38 to 89 years, were recruited. BMD, trabecular bone score (TBS), and body fat distribution were measured by dual-energy X-ray absorptiometry. Subcutaneous and visceral fat were assessed by MRI. In the Pearson correlation analysis, lumbar spine BMD exhibited positive associations with total and all regional fat depots, regardless of the fat distribution. However, the correlation disappeared with adjusted covariables of age, BMI, HDL-C, and HbA1c%. TBS was negatively correlated with fat mass. In multiple linear regression models, android fat (and not gynoid, trunk, or limbs fat) showed significant inverse association with TBS (β = −0.611, P < 0.001). Furthermore, visceral fat was described as a pathogenic fat harmful to TBS, even after adjusting for age and BMI (β = −0.280, P = 0.017). Our findings suggested that body fat mass, especially android fat and visceral fat, may have negative effects on bone microstructure; whereas body fat mass contributes to BMD through mechanical loading.
The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics
Authors: Beng Kingsly Chuo , Tomlinson Kyle W. , Shen Xian Hui , Surget-Groba Yann , Hughes Alice C. , Corlett Richard T. , Slik J. W. Ferry 
Published: April 2016

AbstractMetabarcoding potentially offers a rapid and cheap method of monitoring biodiversity, but real-world applications are few. We investigated its utility in studying patterns of litter arthropod diversity and composition in the tropics. We collected litter arthropods from 35 matched forest-plantation sites across Xishuangbanna, southwestern China. A new primer combination and the MiSeq platform were used to amplify and sequence a wide variety of litter arthropods using simulated and real-world communities. Quality filtered reads were clustered into 3,624 MOTUs at ≥97% similarity and the taxonomy of each MOTU was predicted. We compared diversity and compositional differences between forests and plantations (rubber and tea) for all MOTUs and for eight arthropod groups. We obtained ~100% detection rate after in silico sequencing six mock communities with known arthropod composition. Ordination showed that rubber, tea and forest communities formed distinct clusters. α-diversity declined significantly between forests and adjacent plantations for more arthropod groups in rubber than tea, and diversity of order Orthoptera increased significantly in tea. Turnover was higher in forests than plantations, but patterns differed among groups. Metabarcoding is useful for quantifying diversity patterns of arthropods under different land-uses and the MiSeq platform is effective for arthropod metabarcoding in the tropics.
Expression of GhNAC2 from G. herbaceum, improves root growth and imparts tolerance to drought in transgenic cotton and Arabidopsis
Authors: Gunapati Samatha , Naresh Ram , Ranjan Sanjay , Nigam Deepti , Hans Aradhana , Verma Praveen C. , Gadre Rekha , Pathre Uday V. , Sane Aniruddha P. , Sane Vidhu A. 
Published: April 2016

AbstractNAC proteins are plant-specific transcription factors that play essential roles in regulating development and responses to abiotic and biotic stresses. We show that over-expression of the cotton GhNAC2 under the CaMV35S promoter increases root growth in both Arabidopsis and cotton under unstressed conditions. Transgenic Arabidopsis plants also show improved root growth in presence of mannitol and NaCl while transgenic cotton expressing GhNAC2 show reduced leaf abscission and wilting upon water stress compared to control plants. Transgenic Arabidopsis plants also have larger leaves, higher seed number and size under well watered conditions, reduced transpiration and higher relative leaf water content. Micro-array analysis of transgenic plants over-expressing GhNAC2 reveals activation of the ABA/JA pathways and a suppression of the ethylene pathway at several levels to reduce expression of ERF6/ERF1/WRKY33/ MPK3/MKK9/ACS6 and their targets. This probably suppresses the ethylene-mediated inhibition of organ expansion, leading to larger leaves, better root growth and higher yields under unstressed conditions. Suppression of the ethylene pathway and activation of the ABA/JA pathways also primes the plant for improved stress tolerance by reduction in transpiration, greater stomatal control and suppression of growth retarding factors.
Alteration of the serum microbiome composition in cirrhotic patients with ascites
Authors: Santiago Alba , Pozuelo Marta , Poca Maria , Gely Cristina , Nieto Juan Camilo , Torras Xavier , Román Eva , Campos David , Sarrabayrouse Guillaume , Vidal Silvia , Alvarado-Tapias Edilmar , Guarner Francisco , Soriano German , Manichanh Chaysavanh , Guarner Carlos 
Published: April 2016

AbstractThe progression of cirrhosis is associated with alterations in the composition of the gut microbiome. To assess microbial translocation, we compared the serum microbial composition of patients with and without ascites and characterized the ascitic fluid microbiome using 16S rDNA high-throughput sequencing data. A complex and specific microbial community was detected in the serum and ascitic fluid of patients with cirrhosis but barely detectable in the serum of healthy controls. The serum microbiome of patients with ascites presented higher levels of lipopolysaccharide binding protein, a marker of microbial translocation, associated with higher diversity and relative abundance of Clostridiales and an unknown genus belonging to the Cyanobacteria phylum compared to patients without ascites. The composition of the fecal microbiome was also more altered in patients with than without ascites, confirming previous studies on fecal microbiome. We propose that alteration of the serum and fecal microbiome composition be considered indicators of cirrhosis progression.
Hypomethylation of ERVs in the sperm of mice haploinsufficient for the histone methyltransferase Setdb1 correlates with a paternal effect on phenotype
Authors: Daxinger Lucia , Oey Harald , Isbel Luke , Whitelaw Nadia C. , Youngson Neil A. , Spurling Alex , Vonk Kelly K. D. , Whitelaw Emma 
Published: April 2016

AbstractThe number of reports of paternal epigenetic influences on the phenotype of offspring in rodents is increasing but the molecular events involved remain unclear. Here, we show that haploinsufficiency for the histone 3 lysine 9 methyltransferase Setdb1 in the sire can influence the coat colour phenotype of wild type offspring. This effect occurs when the allele that directly drives coat colour is inherited from the dam, inferring that the effect involves an “in trans” step. The implication of this finding is that epigenetic state of the sperm can alter the expression of genes inherited on the maternally derived chromosomes. Whole genome bisulphite sequencing revealed that Setdb1 mutant mice show DNA hypomethylation at specific classes of transposable elements in the sperm. Our results identify Setdb1 as a paternal effect gene in the mouse and suggest that epigenetic inheritance may be more likely in individuals with altered levels of epigenetic modifiers.
Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China
Authors: Wang Ting , Wang Zhen , Xia Fan , Su Yingjuan 
Published: April 2016

AbstractCephalotaxus oliveriis an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution ofC. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22C. oliverinatural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition,C. oliveripossessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations ofC. oliverifrom south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies.