bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of supplemented isoenergetic diets varying in cereal fiber and protein content on the bile acid metabolic signature and relation to insulin resistance
Authors: Weickert Martin O. , Hattersley John G. , Kyrou Ioannis , Arafat Ayman M. , Rudovich Natalia , Roden Michael , Nowotny Peter , von Loeffelholz Christian , Matysik Silke , Schmitz Gerd , Pfeiffer Andreas F. H. 
Published: April 2018

Abstract
Bile acids (BA) are potent metabolic regulators influenced by diet. We studied effects of isoenergetic increases in the dietary protein and cereal-fiber contents on circulating BA and insulin resistance (IR) in overweight and obese adults. Randomized controlled nutritional intervention (18 weeks) in 72 non-diabetic participants (overweight/obese: 29/43) with at least one further metabolic risk factor. Participants were group-matched and allocated to four isoenergetic supplemented diets: control; high cereal fiber (HCF); high-protein (HP); or moderately increased cereal fiber and protein (MIX). Whole-body IR and insulin-mediated suppression of hepatic endogenous glucose production were measured using euglycaemic–hyperinsulinemic clamps with [6-62H2] glucose infusion. Circulating BA, metabolic biomarkers, and IR were measured at 0, 6, and 18 weeks. Under isoenergetic conditions, HP-intake worsened IR in obese participants after 6 weeks (M-value: 3.77 ± 0.58 vs. 3.07 ± 0.44 mg/kg/min, p = 0.038), with partial improvement back to baseline levels after 18 weeks (3.25 ± 0.45 mg/kg/min, p = 0.089). No deleterious effects of HP-intake on IR were observed in overweight participants. HCF-diet improved IR in overweight participants after 6 weeks (M-value 4.25 ± 0.35 vs. 4.81 ± 0.31 mg/kg/min, p = 0.016), but did not influence IR in obese participants. Control and MIX diets did not influence IR. HP-induced, but not HCF-induced changes in IR strongly correlated with changes of BA profiles. MIX-diet significantly increased most BA at 18 weeks in obese, but not in overweight participants. BA remained unchanged in controls. Pooled BA concentrations correlated with fasting fibroblast growth factor-19 (FGF-19) plasma levels (r = 0.37; p = 0.003). Higher milk protein intake was the only significant dietary predictor for raised total and primary BA in regression analyses (total BA, p = 0.017; primary BA, p = 0.011). Combined increased intake of dietary protein and cereal fibers markedly increased serum BA concentrations in obese, but not in overweight participants. Possible mechanisms explaining this effect may include compensatory increases of the BA pool in the insulin resistant, obese state; or defective BA transport.
The antioxidant potential of the Mediterranean diet in patients at high cardiovascular risk: an in-depth review of the PREDIMED
Authors: Billingsley Hayley E , Carbone Salvatore 
Published: April 2018

AbstractCardiovascular disease (CVD) is the leading global cause of death. Diet is known to be important in the prevention of CVD. The PREDIMED trial tested a relatively low-fat diet versus a high-fat Mediterranean diet (MedDiet) for the primary prevention of CVD. The resulting reduction of the CV composite outcome resulted in a paradigm shift in CV nutrition. Though many dietary factors likely contributed to this effect, this review focuses on the influence of the MedDiet on endogenous antioxidant systems and the effect of dietary polyphenols. Subgroup analysis of the PREDIMED trial revealed increased endogenous antioxidant and decreased pro-oxidant activity in the MedDiet groups. Moreover, higher polyphenol intake was associated with lower incidence of the primary outcome, overall mortality, blood pressure, inflammatory biomarkers, onset of new-onset type 2 diabetes mellitus (T2DM), and obesity. This suggests that polyphenols likely contributed to the lower incidence of the primary event in the MedDiet groups. In this article, we summarize the potential benefits of polyphenols found in the MedDiet, specifically the PREDIMED cohort. We also discuss the need for further research to confirm and expand the findings of the PREDIMED in a non-Mediterranean population and to determine the exact mechanisms of action of polyphenols.
SNAIL1 action in tumor cells influences macrophage polarization and metastasis in breast cancer through altered GM-CSF secretion
Authors: Brenot Audrey , Knolhoff Brett L. , DeNardo David G. , Longmore Gregory D. 
Published: April 2018

AbstractThe EMT inducer SNAIL1 regulates breast cancer metastasis and its expression in human primary breast tumor predicts for poor outcomes. During tumor progression SNAIL1 has multiple effects in tumor cells that can impact metastasis. An inflammatory tumor microenvironment also impacts metastasis and recently SNAIL1 has been implicated as modulating the secretion of cytokines that can influence the tumor immune infiltrate. Using a spontaneous genetic model of breast cancer metastasis and syngeneic orthotopic transplant experiments we show that the action of SNAIL1 in primary breast tumor cells is required for breast tumor growth and metastasis. It does so, in part, by regulating production of GM-CSF, IL1α, IL-6, and TNFα by breast cancer cells. The SNAIL1-dependent tumor cell secretome modulates the primary tumor-associated macrophage (TAM) polarization. GM-CSF alone modulates TAM polarization and impacts breast cancer metastasis in vivo. This study highlights another role for breast tumor SNAIL1 in cancer progression to metastasis—modulation of the immune microenvironment of primary breast tumors.
Increased mtDNA copy number promotes cancer progression by enhancing mitochondrial oxidative phosphorylation in microsatellite-stable colorectal cancer
Authors: Sun Xiacheng , Zhan Lei , Chen Yibing , Wang Gang , He Linjie , Wang Qian , Zhou Feng , Yang Fang , Wu Jin , Wu Yousheng , Xing Jinliang , He Xianli , Huang Qichao 
Published: April 2018

AbstractColorectal cancer is one of the leading causes of cancer death worldwide. According to global genomic status, colorectal cancer can be classified into two main types: microsatellite-stable and microsatellite-instable tumors. Moreover, the two subtypes also exhibit different responses to chemotherapeutic agents through distinctive molecular mechanisms. Recently, mitochondrial DNA depletion has been shown to induce apoptotic resistance in microsatellite-instable colorectal cancer. However, the effects of altered mitochondrial DNA copy number on the progression of microsatellite-stable colorectal cancer, which accounts for the majority of colorectal cancer, remain unclear. In this study, we systematically investigated the functional role of altered mitochondrial DNA copy number in the survival and metastasis of microsatellite-stable colorectal cancer cells. Moreover, the underlying molecular mechanisms were also explored. Our results demonstrated that increased mitochondrial DNA copy number by forced mitochondrial transcription factor A expression significantly facilitated cell proliferation and inhibited apoptosis of microsatellite-stable colorectal cancer cells both in vitro and in vivo. Moreover, we demonstrated that increased mitochondrial DNA copy number enhanced the metastasis of microsatellite-stable colorectal cancer cells. Mechanistically, the survival advantage conferred by increased mitochondrial DNA copy number was caused in large part by elevated mitochondrial oxidative phosphorylation. Furthermore, treatment with oligomycin significantly suppressed the survival and metastasis of microsatellite-stable colorectal cancer cells with increased mitochondrial DNA copy number. Our study provides evidence supporting a possible tumor-promoting role for mitochondrial DNA and uncovers the underlying mechanism, which suggests a potential novel therapeutic target for microsatellite-stable colorectal cancer.
Multiple mechanisms drive phage infection efficiency in nearly identical hosts
Authors: Howard-Varona Cristina , Hargreaves Katherine R , Solonenko Natalie E , Markillie Lye Meng , White Richard Allen , Brewer Heather M , Ansong Charles , Orr Galya , Adkins Joshua N , Sullivan Matthew B 
Published: April 2018

Abstract
Phage–host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature’s own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18’s transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18’s transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage–host interaction dynamics that occur in nature.
Syntrophic pathways for microbial mercury methylation
Authors: Yu Ri-Qing , Reinfelder John R , Hines Mark E , Barkay Tamar 
Published: April 2018

Abstract
Exposure to dietary sources of methylmercury (MeHg) is the focus of public health concerns with environmental mercury (Hg) contamination. MeHg is formed in anoxic environments by anaerobic microorganisms. This process has been studied mostly with single-species culture incubations, although the relevance of such studies to Hg(II)-methylation in situ is limited because microbial activities in the environment are critically modulated by interactions among microbial functional groups. Here we describe experiments in which Hg(II)-methylation was examined within the context of various microbial syntrophies. We show enhanced Hg(II)-methylation under conditions that established syntrophy by interspecies hydrogen and acetate transfer. Relative to activity of monocultures, interactions of Hg(II) methylating sulfate-reducing bacteria with a methanogen stimulated potential Hg(II)-methylation rates 2-fold to 9-fold, and with Syntrophobacter sp. 1.7-fold to 1.8-fold; those of a Hg(II) methylating Syntrophobacter sp. with a methanogen increased Hg(II)-methylation 2-fold. Under sulfate-depleted conditions, higher Hg(II)-methylation rates in the syntrophic incubations corresponded to higher free energy yields (ΔG°′) than in the monocultures. Based on energetic considerations, we therefore propose that syntrophic microbial interactions are likely a major source of MeHg in sulfate- and iron-limited anoxic environments while in sulfate-replete environments, MeHg formation via sulfate reduction dominates.
Thermophilic endospores associated with migrated thermogenic hydrocarbons in deep Gulf of Mexico marine sediments
Authors: Chakraborty Anirban , Ellefson Emily , Li Carmen , Gittins Daniel , Brooks James M , Bernard Bernie B , Hubert Casey R J 
Published: April 2018

Abstract
Dormant endospores of thermophilic bacteria (thermospores) can be detected in cold marine sediments following high-temperature incubation. Thermospores in the cold seabed may be explained by a dispersal history originating in deep biosphere oil reservoir habitats where upward migration of petroleum fluids at hydrocarbon seeps transports viable cells into the overlying ocean. We assessed this deep-to-shallow dispersal hypothesis through geochemical and microbiological analyses of 111 marine sediments from the deep water Eastern Gulf of Mexico. GC-MS and fluorescence confirmed the unambiguous presence of thermogenic hydrocarbons in 71 of these locations, indicating seepage from deeply sourced petroleum in the subsurface. Heating each sediment to 50 °C followed by 16S rRNA gene sequencing revealed several thermospores with a cosmopolitan distribution throughout the study area, as well as thermospores that were more geographically restricted. Among the thermospores having a more limited distribution, 12 OTUs from eight different lineages were repeatedly detected in sediments containing thermogenic hydrocarbons. A subset of these were significantly correlated with hydrocarbons (p &lt; 0.05) and most closely related to Clostridiales previously detected in oil reservoirs from around the world. This provides evidence of bacteria in the ocean being dispersed out of oil reservoirs, and suggests that specific thermospores may be used as model organisms for studying warm-to-cold transmigration in the deep sea.
Low-frequency and rare variants may contribute to elucidate the genetics of major depressive disorder
Authors: Yu Chenglong , Arcos-Burgos Mauricio , Baune Bernhard T. , Arolt Volker , Dannlowski Udo , Wong Ma-Li , Licinio Julio 
Published: April 2018

AbstractMajor depressive disorder (MDD) is a common but serious psychiatric disorder with significant levels of morbidity and mortality. Recent genome-wide association studies (GWAS) on common variants increase our understanding of MDD; however, the underlying genetic basis remains largely unknown. Many studies have been proposed to explore the genetics of complex diseases from a viewpoint of the “missing heritability” by considering low-frequency and rare variants, copy-number variations, and other types of genetic variants. Here we developed a novel computational and statistical strategy to investigate the “missing heritability” of MDD. We applied Hamming distance on common, low-frequency, and rare single-nucleotide polymorphism (SNP) sets to measure genetic distance between two individuals, and then built the multi-dimensional scaling (MDS) pictures. Whole-exome genotyping data from a Los Angeles Mexican-American cohort (203 MDD and 196 controls) and a European-ancestry cohort (473 MDD and 497 controls) were examined using our proposed methodology. MDS plots showed very significant separations between MDD cases and healthy controls for low-frequency SNP set (Pvalue < 2.2e−16) and rare SNP set (Pvalue = 7.681e−12). Our results suggested that low-frequency and rare variants may play more significant roles in the genetics of MDD.
A multiple myeloma-specific capture sequencing platform discovers novel translocations and frequent, risk-associated point mutations in IGLL5
Authors: White Brian S. , Lanc Irena , O’Neal Julie , Gupta Harshath , Fulton Robert S. , Schmidt Heather , Fronick Catrina , Belter Edward A. , Fiala Mark , King Justin , Ahmann Greg J. , DeRome Mary , Mardis Elaine R. , Vij Ravi , DiPersio John F. , Levy Joan , Auclair Daniel , Tomasson Michael H. 
Published: April 2018

AbstractMultiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide variants (SNVs). To enable integrative studies across these diverse mutation types, we developed a capture-based sequencing platform to detect their occurrence in 465 genes altered in MM and used it to sequence 95 primary tumor-normal pairs to a mean depth of 104×. We detected cases of hyperdiploidy (23%), deletions of 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), and 17p (4%), and amplification of 1q (19%). We also detectedIGHandMYCtranslocations near expected frequencies and non-silent SNVs inNRAS(24%),KRAS(21%),FAM46C(17%),TP53(9%),DIS3(9%), andBRAF(3%). We discovered frequent mutations inIGLL5(18%) that were mutually exclusive ofRASmutations and associated with increased risk of disease progression (p = 0.03), suggesting thatIGLL5may be a stratifying biomarker. We identified novelIGLL5/IGHtranslocations in two samples. We subjected 15 of the pairs to ultra-deep sequencing (1259×) and found that although depth correlated with number of mutations detected (p = 0.001), depth past ~300× added little. The platform provides cost-effective genomic analysis for research and may be useful in individualizing treatment decisions in clinical settings.
Mechanically induced Ca2+ oscillations in osteocytes release extracellular vesicles and enhance bone formation
Authors: Morrell Andrea E. , Brown Genevieve N. , Robinson Samuel T. , Sattler Rachel L. , Baik Andrew D. , Zhen Gehua , Cao Xu , Bonewald Lynda F. , Jin Weiyang , Kam Lance C. , Guo X. Edward 
Published: April 2018

AbstractThe vast osteocytic network is believed to orchestrate bone metabolic activity in response to mechanical stimuli through production of sclerostin, RANKL, and osteoprotegerin (OPG). However, the mechanisms of osteocyte mechanotransduction remain poorly understood. We’ve previously shown that osteocyte mechanosensitivity is encoded through unique intracellular calcium (Ca2+) dynamics. Here, by simultaneously monitoring Ca2+ and actin dynamics in single cells exposed to fluid shear flow, we detected actin network contractions immediately upon onset of flow-induced Ca2+ transients, which were facilitated by smooth muscle myosin and further confirmed in native osteocytes ex vivo. Actomyosin contractions have been linked to the secretion of extracellular vesicles (EVs), and our studies demonstrate that mechanical stimulation upregulates EV production in osteocytes through immunostaining for the secretory vesicle marker Lysosomal-associated membrane protein 1 (LAMP1) and quantifying EV release in conditioned medium, both of which are blunted when Ca2+ signaling was inhibited by neomycin. Axial tibia compression was used to induce anabolic bone formation responses in mice, revealing upregulated LAMP1 and expected downregulation of sclerostin in vivo. This load-related increase in LAMP1 expression was inhibited in neomycin-injected mice compared to vehicle. Micro-computed tomography revealed significant load-related increases in both trabecular bone volume fraction and cortical thickness after two weeks of loading, which were blunted by neomycin treatment. In summary, we found mechanical stimulation of osteocytes activates Ca2+-dependent contractions and enhances the production and release of EVs containing bone regulatory proteins. Further, blocking Ca2+ signaling significantly attenuates adaptation to mechanical loading in vivo, suggesting a critical role for Ca2+-mediated signaling in bone adaptation.
Deregulation of ATG9A by impaired AR signaling induces autophagy in prostate stromal fibroblasts and promotes BPH progression
Authors: Jiang Chen-Yi , Yang Bo-Yu , Zhao Sheng , Shao Si-Hui , Bei Xiao-Yu , Shi Fei , Sun Qian , Deng Zheng , Wang Xiao-Hai , Han Bang-Min , Zhao Fu-Jun , Xia Shu-Jie , Ruan Yuan 
Published: April 2018

AbstractThe activation of androgen receptor (AR) signaling plays an essential role in both prostate stromal cells and epithelial cells during the development of benign prostatic hyperplasia (BPH). Here we demonstrated that androgen ablation after 5α-reductase inhibitor (5-ARI) treatment induced autophagy in prostate stromal fibroblasts inhibiting cell apoptosis. In addition, we found that ATG9A expression was increased after androgen ablation, which facilitated autophagic flux development. Knockdown of ATG9A not only inhibited autophagy notably in prostate stromal fibroblasts, but also reduced the volumes of prostate stromal fibroblast and epithelial cell recombinant grafts in nude mice. In conclusion, our findings suggested that ATG9A upregulation after long-term 5-ARI treatment constitutes a possible mechanism of BPH progression. Thus, combined treatment with 5-ARI and autophagy inhibitory agents would reduce the risk of BPH progression.
Astrocytic metabolic switch is a novel etiology for Cocaine and HIV-1 Tat-mediated neurotoxicity
Authors: Natarajaseenivasan Kalimuthusamy , Cotto Bianca , Shanmughapriya Santhanam , Lombardi Alyssa A. , Datta Prasun K. , Madesh Muniswamy , Elrod John W. , Khalili Kamel , Langford Dianne 
Published: April 2018

AbstractCalcium (Ca2+) dynamics and oxidative signaling control mitochondrial bioenergetics in the central nervous system, where astrocytes are a major energy source for neurons. Cocaine use exacerbates HIV-associated neurocognitive disorders, but little is known about disruptions in astrocyte metabolism in this context. Our data show that the HIV protein Tat and cocaine induce a metabolic switch from glucose to fatty acid oxidation in astrocytes, thereby limiting lactate transport to neurons. Mechanistic analyses revealed increased Mitochondrial Ca2+ Uniporter (MCU)-mediated Ca2+ uptake in astrocytes exposed to Tat and cocaine due to oxidation of MCU. Since our data suggest that mitochondrial oxidation is dependent in part on MCU-mediated Ca2+ uptake, we targeted MCU to restore glycolysis in astrocytes to normalize extracellular lactate levels. Knocking down MCU in astrocytes prior to Tat and cocaine exposure prevented metabolic switching and protected neurons. These findings identify a novel molecular mechanism underlying neuropathogenesis in HIV and cocaine use.
Alarmin HMGB1 induces systemic and brain inflammatory exacerbation in post-stroke infection rat model
Authors: Kim Il-Doo , Lee Hahnbie , Kim Seung-Woo , Lee Hye-Kyung , Choi Juli , Han Pyung-Lim , Lee Ja-Kyeong 
Published: April 2018

AbstractPost-stroke infection (PSI) is known to worsen functional outcomes of stroke patients and accounts to one-third of stroke-related deaths in hospital. In our previous reports, we demonstrated that massive release of high-mobility group box protein 1 (HMGB1), an endogenous danger signal molecule, is promoted by N-methyl-d-aspartic acid-induced acute damage in the postischemic brain, exacerbating neuronal damage by triggering delayed inflammatory processes. Moreover, augmentation of proinflammatory function of lipopolysaccharides (LPS) by HMGB1 via direct interaction has been reported. The aim of this study was to investigate the role of HMGB1 in aggravating inflammation in the PSI by exacerbating the function of LPS. PSI animal model was produced by administrating a low-dose LPS at 24 h post-middle cerebral artery occlusion (MCAO). Profound aggravations of inflammation, deterioration of behavioral outcomes, and infarct expansion were observed in LPS-injected MCAO animals, in which serum HMGB1 surge, especially disulfide type, occurred immediately after LPS administration and aggravated brain and systemic inflammations probably by acting in synergy with LPS. Importantly, blockage of HMGB1 function by delayed administrations of therapeutic peptides known to inhibit HMGB1 (HMGB1 A box, HPep1) or by treatment with LPS after preincubation with HMGB1 A box significantly ameliorated damages observed in the rat PSI model, demonstrating that HMGB1 plays a crucial role. Furthermore, administration of Rhodobacter sphaeroides LPS, a selective toll-like receptor 4 antagonist not only failed to exert these effects but blocked the effects of LPS, indicating its TLR4 dependence. Together, these results indicated that alarmin HMGB1 mediates potentiation of LPS function, exacerbating TLR4-dependent systemic and brain inflammation in a rat PSI model and there is a positive-feedback loop between augmentation of LPS function by HMGB1 and subsequent HMGB1 release/serum. Therefore, HMGB1 might be a valuable therapeutic target for preventing post-stroke infection.