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Current Genomics

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https://www.readbyqxmd.com/read/30532651/model-microbial-consortia-as-tools-for-understanding-complex-microbial-communities
#1
REVIEW
Shin Haruta, Kyosuke Yamamoto
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532650/metabolic-modeling-of-microbial-community-interactions-for-health-environmental-and-biotechnological-applications
#2
REVIEW
Kok Siong Ang, Meiyappan Lakshmanan, Na-Rae Lee, Dong-Yup Lee
In nature, microbes do not exist in isolation but co-exist in a variety of ecological and biological environments and on various host organisms. Due to their close proximity, these microbes interact among themselves, and also with the hosts in both positive and negative manners. Moreover, these interactions may modulate dynamically upon external stimulus as well as internal community changes. This demands systematic techniques such as mathematical modeling to understand the intrinsic community behavior. Here, we reviewed various approaches for metabolic modeling of microbial communities...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532649/diverse-distribution-of-resistomes-in-the-human-and-environmental-microbiomes
#3
REVIEW
Mi Young Lim, Youna Cho, Mina Rho
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532648/design-principles-of-microbial-communities-from-understanding-to-engineering
#4
EDITORIAL
Hyun-Seob Song
No abstract text is available yet for this article.
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532647/epigenetic-changes-associated-with-early-life-experiences-saliva-a-biospecimen-for-dna-methylation-signatures
#5
Elaine L Bearer, Brianna S Mulligan
Background: Adverse Childhood Experiences (ACEs), which include traumatic injury, are associated with poor health outcomes in later life, yet the biological mechanisms mediating this association are unknown. Neurocircuitry, immune system and hormone regulation differ from normal in adults reporting ACEs. These systems could be affected by epigenetic changes, including methylation of cytosine (5mC) in genomic DNA, activated by ACEs. Since 5mC levels influence gene expression and can be long-lasting, altered 5mC status at specific sites or throughout the genome is hypothesized to influence mental and physical outcomes after ACE(s)...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532646/intergenerational-transmission-of-dna-methylation-signatures-associated-with-early-life-stress
#6
REVIEW
Ludwig Stenz, Daniel S Schechter, Sandra Rusconi Serpa, Ariane Paoloni-Giacobino
Early life stress in humans (i.e. maltreatment, violence exposure, loss of a loved one) and in rodents (i.e. disrupted attachment or nesting, electric shock, restraint, predator odor) occurs during critical steps of neural circuit formation. ELS in humans is associated with increased risk for developmental psychopathology, including anxious and depressive phenotypes. The biological mechanisms underlying these potentially persistent maladaptive changes involve long-term epigenetic modifications, which have been suggested to be potentially transmissible to subsequent generations...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532645/how-stress-gets-under-the-skin-early-life-adversity-and-glucocorticoid-receptor-epigenetic-regulation
#7
REVIEW
Patrick Z Liu, Robin Nusslock
Early life adversity is associated with both persistent disruptions in the hypothalamic-pituitary-adrenal (HPA) axis and psychiatric symptoms. Glucocorticoid receptors (GRs), which are encoded by the NR3C1 gene, bind to cortisol and other glucocorticoids to create a negative feedback loop within the HPA axis to regulate the body's neuroendocrine response to stress. Excess methylation of a promoter sequence within NR3C1 that attenuates GR expression, however, has been associated with both early life adversity and psychopathology...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532644/epigenetic-programming-effects-of-early-life-stress-a-dual-activation-hypothesis
#8
REVIEW
Vanessa Lux
Epigenetic processes during early brain development can function as 'developmental switches' that contribute to the stability of long-term effects of early environmental influences by programming central feedback mechanisms of the HPA axis and other neural networks. In this thematic review, we summarize accumulated evidence for a dual-activation of stress-related and sensory networks underlying the epigenetic programming effects of early life stress. We discuss findings indicating epigenetic programming of stress-related genes with impact on HPA axis function, the interaction of epigenetic mechanisms with neural activity in stress-related neural networks, epigenetic effects of glucocorticoid exposure, and the impact of stress on sensory development...
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30532643/a-genomic-and-epigenomic-approach-for-studying-neuropsychiatric-disorders-associated-to-early-life-stress-part-ii
#9
EDITORIAL
Xena Giada Pappalardo, Sebastiano Cavallaro
No abstract text is available yet for this article.
December 2018: Current Genomics
https://www.readbyqxmd.com/read/30386174/a-network-biology-approach-for-assessing-the-role-of-pathologic-adipose-tissues-in-insulin-resistance-using-meta-analysis-of-microarray-datasets
#10
Aditya Saxena, Kumar Sachin
Background: The role of adipose tissue in Insulin resistance (IR) and Type 2 Diabetes (T2D) has well been received in the biomedical community; being a precursor of T2D, identification of the molecular basis of IR is therefore, vital to elucidate T2D- pathogenesis and meta-analysis of previously conducted microarray studies provides an inexpensive approach to achieve this end. Methods: In this study, we have carried out a statistical meta-analysis of 157 microarray datasets from five independent studies and identified a meta-signature of 1,511 genes; their functional meaning was elucidated by integrated pathways-analysis...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386173/interplay-between-micrornas-and-targeted-genes-in-cellular-homeostasis-of-adult-zebrafish-danio-rerio
#11
Ludivine Renaud, Willian A da Silveira, William B Glen, Edward S Hazard, Gary Hardiman
Background: Cellular homeostasis is regulated by the intricate interplay between a plethora of signaling pathways and "energetic sensors" in organs. In order to maintain energy balance, induction or repression of metabolic pathways must be regulated and act in concert with the energetic demands of the cell at a given point in time. A new class of small noncoding RNAs, the microRNAs (miRNAs), has added yet further complexity to the control of metabolic homeostasis. Objective: Understanding the damages induced by toxins in the liver and the intestine as well as the interplay between the miRNome and transcriptome first requires baseline characterization in these tissues in healthy animals under cellular homeostasis...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386172/parallel-algorithms-for-inferring-gene-regulatory-networks-a-review
#12
REVIEW
Omid Abbaszadeh, Ali Reza Khanteymoori, Ali Azarpeyvand
System biology problems such as whole-genome network construction from large-scale gene expression data are sophisticated and time-consuming. Therefore, using sequential algorithms are not feasible to obtain a solution in an acceptable amount of time. Today, by using massively parallel computing, it is possible to infer large-scale gene regulatory networks. Recently, establishing gene regulatory networks from large-scale datasets have drawn the noticeable attention of researchers in the field of parallel computing and system biology...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386171/early-life-stress-and-epigenetics-in-late-onset-alzheimer-s-dementia-a-systematic-review
#13
REVIEW
Erwin Lemche
Involvement of life stress in Late-Onset Alzheimer's Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have successfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper-phosphorylation and amyloidogenic processing...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386170/preterm-birth-and-the-risk-of-neurodevelopmental-disorders-is-there-a-role-for-epigenetic-dysregulation
#14
REVIEW
Eamon Fitzgerald, James P Boardman, Amanda J Drake
Preterm Birth (PTB) accounts for approximately 11% of all births worldwide each year and is a profound physiological stressor in early life. The burden of neuropsychiatric and developmental impairment is high, with severity and prevalence correlated with gestational age at delivery. PTB is a major risk factor for the development of cerebral palsy, lower educational attainment and deficits in cognitive functioning, and individuals born preterm have higher rates of schizophrenia, autistic spectrum disorder and attention deficit/hyperactivity disorder...
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30386169/editorial-a-genomic-and-epigenomic-approach-for-studying-neuropsychiatric-disorders-associated-to-early-life-stress-part-i
#15
EDITORIAL
Xena Giada Pappalardo, Sebastiano Cavallaro
No abstract text is available yet for this article.
November 2018: Current Genomics
https://www.readbyqxmd.com/read/30258280/neuroarray-a-custom-cgh-microarray-to-decipher-copy-number-variants-in-alzheimer-s-disease
#16
Denis Cuccaro, Maria Guarnaccia, Rosario Iemmolo, Velia D'Agata, Sebastiano Cavallaro
Background: Copy Number Variants (CNVs) represent a prevailing type of structural variation (deletions or duplications) in the human genome. In the last few years, several studies have demonstrated that CNVs represent significant mutations in Alzheimer's Disease (AD) hereditability. Currently, innovative high-throughput platforms and bioinformatics algorithms are spreading to screening CNVs involved in different neurological diseases. In particular, the use of custom arrays, based on libraries of probes that can detect significant genomic regions, have greatly improved the resolution of targeted regions and the identification of chromosomal aberrations...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258279/an-effective-pipeline-based-on-relative-coverage-for-the-genome-assembly-of-phytoplasmas-and-other-fastidious-prokaryotes
#17
Cesare Polano, Giuseppe Firrao
Background: For the plant pathogenic phytoplasmas, as well as for several fastidious prokaryotes, axenic cultivation is extremely difficult or not possible yet; therefore, even with second generation sequencing methods, obtaining the sequence of their genomes is challenging due to host sequence contamination. Objective: With the Phytoassembly pipeline here presented, we aim to provide a method to obtain high quality genome drafts for the phytoplasmas and other uncultivable plant pathogens, by exploiting the coverage differential in the ILLUMINA sequences from the pathogen and the host, and using the sequencing of a healthy, isogenic plant as a filter...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258278/artificial-neural-network-as-a-classifier-for-the-identification-of-hepatocellular-carcinoma-through-prognosticgene-signatures
#18
Satya Eswari Jujjavarapu, Saurabh Deshmukh
Background: Artificial Neural Networks (ANNs) can be used to classify tumor of Hepatocellular carcinoma based on their gene expression signatures. The neural network is trained with gene expression profiles of genes that were predictive of recurrence in liver cancer, the ANNs became capable of correctly classifying all samples and distinguishing the genes most suitable for the organization. The ability of the trained ANN models in recognizing the Cancer Genes was tested as we analyzed additional samples that were not used beforehand for the training procedure, and got the correctly classified result in the validation set...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258277/regulation-of-age-related-decline-by-transcription-factors-and-their-crosstalk-with-the-epigenome
#19
REVIEW
Xin Zhou, Ilke Sen, Xin-Xuan Lin, Christian G Riedel
Aging is a complex phenomenon, where damage accumulation, increasing deregulation of biological pathways, and loss of cellular homeostasis lead to the decline of organismal functions over time. Interestingly, aging is not entirely a stochastic process and progressing at a constant rate, but it is subject to extensive regulation, in the hands of an elaborate and highly interconnected signaling network. This network can integrate a variety of aging-regulatory stimuli, i.e. fertility, nutrient availability, or diverse stresses, and relay them via signaling cascades into gene regulatory events - mostly of genes that confer stress resistance and thus help protect from damage accumulation and homeostasis loss...
September 2018: Current Genomics
https://www.readbyqxmd.com/read/30258276/genetic-alterations-of-periampullary-and-pancreatic-ductal-adenocarcinoma-an-overview
#20
REVIEW
Nilabja Sikdar, Gourab Saha, Ashmita Dutta, Shibajyoti Ghosh, Shailesh V Shrikhande, Sudeep Banerjee
Pancreatic Ductal AdenoCarcinoma (PDAC) is one of the most lethal malignancies of all solid cancers. Precancerous lesions for PDAC include PanIN, IPMNs and MCNs. PDAC has a poor prognosis with a 5-year survival of approximately 6%. Whereas Periampulary AdenoCarcinoma (PAC) having four anatomic subtypes, pancreatic, Common Bile Duct (CBD), ampullary and duodenum shows relative better prognosis. The highest incidence of PDAC has been reported with black with respect to white population. Similarly, incidence rate of PAC also differs with different ethnic populations...
September 2018: Current Genomics
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