Treasure from garden: Bioactive compounds of buckwheat.

Food Chem. 2020 Jul 24;335:127653

Authors: Huda MN, Lu S, Jahan T, Ding M, Jha R, Zhang K, Zhang W, Georgiev MI, Park SU, Zhou M

Abstract
Buckwheat is a gluten-free crop under the family Polygonaceae abundant with beneficial phytochemicals that provide significant health benefits. It is cultivated and adapted in diverse ecological zones all over the world. Recently its popularity is expanding as a nutrient-rich healthy food with low-calories. The bioactive compounds in buckwheat are flavonoids (i.e., rutin, quercetin, orientin, isoorientin, vitexin, and isovitexin), fatty acids, polysaccharides, proteins, and amino acids, iminosugars, dietary fiber, fagopyrins, resistant starch, vitamins, and minerals. Buckwheat possesses high nutritional value due to these bioactive compounds. Additionally, several essential bioactive factors that have long been gaining interest because these compounds are beneficial for healing and preventing several human diseases. The present review demonstrates an overview of the recent researches regarding buckwheat phytochemicals and particularly focusing on the distinct function of bioactive components with their health benefits.

PMID: 32739818 [PubMed - as supplied by publisher]

Association of taurine with ovarian follicular steroids and postpartum anestrus condition in Murrah buffaloes.

Domest Anim Endocrinol. 2020 Jun 15;74:106511

Authors: Behera A, Sravanthi K, Kumar LK, Vedamurthy GV, Singh D, Onteru SK

Abstract
Taurine is an abundant intracellular beta-amino acid majorly synthesized in the liver and transported through plasma. In mammals, taurine was reported to be involved in various physiological functions, including the enhancement of testosterone levels, the major estradiol precursor. Therefore, we hypothesize that taurine levels are associated with ovarian follicular steroids as well as with a reproductive problem called postpartum anestrus (PPA) in dairy buffaloes. To understand the taurine levels and its possible role in buffalo ovarian follicles, a correlation was established among taurine, estradiol, and testosterone levels in the ovarian follicular fluid. For this purpose, buffalo ovaries were obtained from the slaughterhouse, and follicular fluid samples were collected from small (<4 mm), medium (4-8 mm) and large (>8 mm) follicles. Taurine and steroid levels in the follicular fluid were analyzed by TLC and ELISA, respectively. Taurine and testosterone levels were significantly (P < 0.05) higher in the follicular fluid of small and medium follicles than large follicles, whereas the estradiol levels were significantly (P < 0.001) higher in the large follicles. Thus, taurine showed a positive correlation (r = 0.75) with testosterone and a negative correlation (r = -0.77) with estradiol in buffalo follicular fluid, indicating its possible role in testosterone function during follicular development. Interestingly, significantly (P < 0.001) lower plasma taurine levels in PPA (n = 50) than normal cyclic (n = 50) buffaloes represented its association with PPA. Therefore, our present study recommends the need for future nutrition studies on taurine supplementation to PPA buffaloes.

PMID: 32739763 [PubMed - as supplied by publisher]

Histopathological features of complete pathological response predict recurrence-free survival following neoadjuvant targeted therapy for metastatic melanoma.

Ann Oncol. 2020 Jul 30;:

Authors: Tetzlaff MT, Adhikari C, Lo S, Rawson RV, Amaria RN, Menzies AM, Wilmott JS, Ferguson PM, Ross MI, Spillane AJ, Vu KA, Ma J, Ning J, Haydu L, Saw RPM, Wargo JA, Tawbi HA, Gershenwald JE, Long GV, Davies MA, Scolyer RA

Abstract
BACKGROUND: Recent clinical trials demonstrated safety and efficacy of neoadjuvant dabrafenib and trametinib (DT) among patients with surgically resectable clinical stage III BRAFV600E/K mutant melanoma. Although patients achieving a complete pathological response (pCR) exhibited superior recurrence-free survival (RFS) versus those who did not, 30% of pCR patients relapsed. We sought to identify whether histopathological features of the pathological response further delineated risk of relapse.
METHODS: Surgical resection specimens from DT-treated patients in two phase 2 clinical trials were reviewed. Histopathological features, including relative amounts of viable tumour, necrosis, melanosis, and fibrosis (hyalinized or immature/proliferative) were assessed for associations with patient outcomes.
RESULTS: Fifty-nine patients underwent surgical resection following neoadjuvant DT. Patients achieving pCR (49%) had longer RFS compared with patients who did not (p=0.005). Patients whose treated tumour showed any hyalinized fibrosis had longer RFS versus those without (p=0.014), whereas necrosis (p=0.012) and/or immature/proliferative fibrosis (p=0.026) correlated with shorter RFS. Multivariable analyses showed absence of pCR or presence of immature fibrosis independently predicted shorter RFS. Among pCR patients, mature/hyalinized-type fibrosis correlated with improved RFS (p=0.035).
CONCLUSIONS: The extent and composition of the pathological response following neoadjuvant DT in BRAFV600E/K mutant melanoma correlates with RFS, including pCR patients. These findings support the need for detailed histological analysis of specimens collected after neoadjuvant therapy.

PMID: 32739408 [PubMed - as supplied by publisher]

RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data.

BMC Bioinformatics. 2020 Aug 01;21(1):340

Authors: Li F, Xing X, Xiao Z, Xu G, Yang X

Abstract
BACKGROUND: Ribosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools designed for dissection of the translatome from different aspects. However, as the studies of translation advance quickly, the current toolbox still falls in short, and more specialized tools are in urgent need for deeper and more efficient mining of the important and new features of the translation landscapes.
RESULTS: Here, we present RiboMiner, a bioinformatics toolset for mining of multi-dimensional features of the translatome with ribosome profiling data. RiboMiner performs extensive quality assessment of the data and integrates a spectrum of tools for various metagene analyses of the ribosome footprints and for detailed analyses of multiple features related to translation regulation. Visualizations of all the results are available. Many of these analyses have not been provided by previous methods. RiboMiner is highly flexible, as the pipeline could be easily adapted and customized for different scopes and targets of the studies.
CONCLUSIONS: Applications of RiboMiner on two published datasets did not only reproduced the main results reported before, but also generated novel insights into the translation regulation processes. Therefore, being complementary to the current tools, RiboMiner could be a valuable resource for dissections of the translation landscapes and the translation regulations by mining the ribosome profiling data more comprehensively and with higher resolution. RiboMiner is freely available at https://github.com/xryanglab/RiboMiner and https://pypi.org/project/RiboMiner .

PMID: 32738892 [PubMed - as supplied by publisher]

Extreme environmental conditions reduce coral reef fish biodiversity and productivity.

Nat Commun. 2020 Jul 31;11(1):3832

Authors: Brandl SJ, Johansen JL, Casey JM, Tornabene L, Morais RA, Burt JA

Abstract
Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world's hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth's hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss.

PMID: 32737315 [PubMed - as supplied by publisher]

Signatures of co-deregulated genes and their transcriptional regulators in colorectal cancer.

NPJ Syst Biol Appl. 2020 Jul 31;6(1):23

Authors: Mastrogamvraki N, Zaravinos A

Abstract
The deregulated genes in colorectal cancer (CRC) vary significantly across different studies. Thus, a systems biology approach is needed to identify the co-deregulated genes (co-DEGs), explore their molecular networks, and spot the major hub proteins within these networks. We reanalyzed 19 GEO gene expression profiles to identify and annotate CRC versus normal signatures, single-gene perturbation, and single-drug perturbation signatures. We identified the co-DEGs across different studies, their upstream regulating kinases and transcription factors (TFs). Connectivity Map was used to identify likely repurposing drugs against CRC within each group. The functional changes of the co-upregulated genes in the first category were mainly associated with negative regulation of transforming growth factor β production and glomerular epithelial cell differentiation; whereas the co-downregulated genes were enriched in cotranslational protein targeting to the membrane. We identified 17 hub proteins across the co-upregulated genes and 18 hub proteins across the co-downregulated genes, composed of well-known TFs (MYC, TCF3, PML) and kinases (CSNK2A1, CDK1/4, MAPK14), and validated most of them using GEPIA2 and HPA, but also through two signature gene lists composed of the co-up and co-downregulated genes. We further identified a list of repurposing drugs that can potentially target the co-DEGs in CRC, including camptothecin, neostigmine bromide, emetine, remoxipride, cephaeline, thioridazine, and omeprazole. Similar analyses were performed in the co-DEG signatures in single-gene or drug perturbation experiments in CRC. MYC, PML, CDKs, CSNK2A1, and MAPKs were common hub proteins among all studies. Overall, we identified the critical genes in CRC and we propose repurposing drugs that could be used against them.

PMID: 32737302 [PubMed - as supplied by publisher]

Mitochondrial spongiotic brain disease: astrocytic stress and harmful rapamycin and ketosis effect.

Life Sci Alliance. 2020 Sep;3(9):

Authors: Ignatenko O, Nikkanen J, Kononov A, Zamboni N, Ince-Dunn G, Suomalainen A

Abstract
Mitochondrial DNA (mtDNA) depletion syndrome (MDS) is a group of severe, tissue-specific diseases of childhood with unknown pathogenesis. Brain-specific MDS manifests as devastating spongiotic encephalopathy with no curative therapy. Here, we report cell type-specific stress responses and effects of rapamycin treatment and ketogenic diet (KD) in mice with spongiotic encephalopathy mimicking human MDS, as these interventions were reported to improve some mitochondrial disease signs or symptoms. These mice with astrocyte-specific knockout of Twnk gene encoding replicative mtDNA helicase Twinkle (TwKOastro) show wide-spread cell-autonomous astrocyte activation and mitochondrial integrated stress response (ISRmt) induction with major metabolic remodeling of the brain. Mice with neuronal-specific TwKO show no ISRmt Both KD and rapamycin lead to rapid deterioration and weight loss of TwKOastro and premature trial termination. Although rapamycin had no robust effects on TwKOastro brain pathology, KD exacerbated spongiosis, gliosis, and ISRmt Our evidence emphasizes that mitochondrial disease treatments and stress responses are tissue- and disease specific. Furthermore, rapamycin and KD are deleterious in MDS-linked spongiotic encephalopathy, pointing to a crucial role of diet and metabolism for mitochondrial disease progression.

PMID: 32737078 [PubMed - as supplied by publisher]

O-GlcNAcylation of Mef2c regulates myoblast differentiation.

Biochem Biophys Res Commun. 2020 Aug 27;529(3):692-698

Authors: Kim HB, Seo HG, Son S, Choi H, Kim BG, Kweon TH, Kim S, Pai J, Shin I, Yang WH, Cho JW

Abstract
Unlike other types of glycosylation, O-GlcNAcylation is a single glycosylation which occurs exclusively in the nucleus and cytosol. O-GlcNAcylation underlie metabolic diseases, including diabetes and obesity. Furthermore, O-GlcNAcylation affects different oncogenic processes such as osteoblast differentiation, adipogenesis and hematopoiesis. Emerging evidence suggests that skeletal muscle differentiation is also regulated by O-GlcNAcylation, but the detailed molecular mechanism has not been fully elucidated. In this study, we showed that hyper-O-GlcNAcylation reduced the expression of myogenin, a transcription factor critical for terminal muscle development, in C2C12 myoblasts differentiation by O-GlcNAcylation on Thr9 of myocyte-specific enhancer factor 2c. Furthermore, we showed that O-GlcNAcylation on Mef2c inhibited its DNA binding affinity to myogenin promoter. Taken together, we demonstrated that hyper-O-GlcNAcylation attenuates skeletal muscle differentiation by increased O-GlcNAcylation on Mef2c, which downregulates its DNA binding affinity.

PMID: 32736694 [PubMed - as supplied by publisher]

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