The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Complex biological systems and cellular networks may underlie most genotype to phenotype relationships. Here, we review basic concepts in network biology, discussing different types of interactome networks and the insights that can come from analyzing them. We elaborate on why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease.

Interactome networks and human disease

[Von Hippel-Lindau disease].

Fragile X syndrome (FXS) is the leading inherited form of intellectual disability and autism spectrum disorder, and patients can present with severe behavioural alterations, including hyperactivity, impulsivity and anxiety, in addition to poor language development and seizures. FXS is a trinucleotide repeat disorder, in which >200 repeats of the CGG motif in FMR1 leads to silencing of the gene and the consequent loss of its product, fragile X mental retardation 1 protein (FMRP). FMRP has a central role in gene expression and regulates the translation of potentially hundreds of mRNAs, many of which are involved in the development and maintenance of neuronal synaptic connections. Indeed, disturbances in neuroplasticity is a key finding in FXS animal models, and an imbalance in inhibitory and excitatory neuronal circuits is believed to underlie many of the clinical manifestations of this disorder. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention, some of which have already moved into clinical trials or clinical practice.

Fragile X syndrome

Moringa oleifera is an interesting plant for its use in bioactive compounds. In this manuscript, we review studies concerning the cultivation and production of moringa along with genetic diversity among different accessions and populations. Different methods of propagation, establishment and cultivation are discussed. Moringa oleifera shows diversity in many characters and extensive morphological variability, which may provide a resource for its improvement. Great genetic variability is present in the natural and cultivated accessions, but no collection of cultivated and wild accessions currently exists. A germplasm bank encompassing the genetic variability present in Moringa is needed to perform breeding programmes and develop elite varieties adapted to local conditions. Alimentary and medicinal uses of moringa are reviewed, alongside the production of biodiesel. Finally, being that the leaves are the most used part of the plant, their contents in terms of bioactive compounds and their pharmacological properties are discussed. Many studies conducted on cell lines and animals seem concordant in their support for these properties. However, there are still too few studies on humans to recommend Moringa leaves as medication in the prevention or treatment of diseases. Therefore, further studies on humans are recommended.

https://blog.baca-villa.com/wp-content/uploads/2015/10/Moringa-Oleifera-Leaves-an-Overview.pdf

Cultivation, Genetic, Ethnopharmacology, Phytochemistry and Pharmacology of Moringa oleifera Leaves: An Overview

The recognition of vitamin C is associated with a history of an unrelenting search for the cause of the ancient haemorrhagic disease scurvy. Isolated in 1928, vitamin C is essential for the development and maintenance of connective tissues. It plays an important role in bone formation, wound healing and the maintenance of healthy gums. Vitamin C plays an important role in a number of metabolic functions including the activation of the B vitamin, folic acid, the conversion of cholesterol to bile acids and the conversion of the amino acid, tryptophan, to the neurotransmitter, serotonin. It is an antioxidant that protects body from free radical damage. It is used as therapeutic agent in many diseases and disorders. Vitamin C protects the immune system, reduces the severity of allergic reactions and helps to fight off infections. However the significance and beneficial effect of vitamin C in respect to human disease such as cancer, atherosclerosis, diabetes, neurodegenerative disease and metal toxicity however remains equivocal. Thus further continuous uninterrupted efforts may open new vistas to understand its significance in disease management.

/pdf/vitamin-c-in-disease-prevention-and-cure-an-overview-aeya39os1l.pdf

Vitamin C in Disease Prevention and Cure: An Overview

The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc., by mutation scanning and DNA chip technology. Further the functional genomics also exploring the expression genetics (hybridization-, PCR- and sequence-based technologies), two-hybrid technology, next generation sequencing with Bioinformatics and computational biology. Advances in microarray “chip” technology as microarrays have allowed the parallel analysis of gene expression patterns of thousands of genes simultaneously. Sequence information collected from the genomes of many individuals is leading to the rapid discovery of single nucleotide polymorphisms or SNPs. Further advances of genetic engineering have also revolutionized immunoassay biotechnology via engineering of antibody-encoding genes and the phage display technology. The Biotechnology plays an important role in the development of diagnostic assays in response to an outbreak or critical disease response need. However, there is also need to pinpoint various obstacles and issues related to the commercialization and widespread dispersal of genetic knowledge derived from the exploitation of the biotechnology industry and the development and marketing of diagnostic services. Implementation of genetic criteria for patient selection and individual assessment of the risks and benefits of treatment emerges as a major challenge to the pharmaceutical industry. Thus this field is revolutionizing current era and further it may open new vistas in the field of disease management.

/pdf/diseases-and-molecular-diagnostics-a-step-closer-to-1oghhe1qr7.pdf

Diseases and Molecular Diagnostics: A Step Closer to Precision Medicine.

The aim of this review was to provide current scenario linking obesity and male fertility. Obesity has been linked to male fertility because of lifestyle changes, internal hormonal environment alterations, and sperm genetic factors. A few studies assessing the impact of obesity on sperm genetic factor have been published, but they did not lead to a strong consensus. Our objective was to explore further the relationship between sperm genetic factor and obesity. There are emerging facts that obesity negatively affects male reproductive potential not only by reducing sperm quality, but in particular it alters the physical and molecular structure of germ cells in the testes and ultimately affects the maturity and function of sperm cells. Inhibition of microRNA in the male pronucleus of fertilized zygotes produces offspring of phenotypes of variable severity depending on miRNAs ratios. Hence, these RNAs have a role in the oocyte development during fertilization and in embryo development, fetal survival, and offspring phenotype. It has been reported that the miRNA profile is altered in spermatozoa of obese males, however, the impact of these changes in fertilization and embryo health remains as yet not known.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/andr.270

Recent scenario of obesity and male fertility.

Background:�Prostatecancerisoneofthemostcommoncancersafflictingmentoday.�Prostatebiopsy,�an� invasiveprocedureisgenerallyusedfordiagnosesbutattemptsarebeingmadetofindaccurateandprecisenon- invasivebiomarkers.�Diagnosticaccuracyofprostatespecificantigen�(PSA)�hasbeenwelldocumented.��Serum� interleukin-18�(IL-18)�andinterleukin-10�(IL-10)�haveshowntheirdiagnosticabilityinothercancersbutnot� investigatedwellinprostatecancer.�Thisstudy,�thusdeterminesthediagnosticandprognosticsignificanceof� PSA,�IL-18�andIL-10�prospectivelyinpatientswithcarcinomaprostate.��Methods:�Atotalof�149�patients,�aged� 40-84�yrswereinvestigatedduringApril�2007�toJuly�2010�andrecruitedforthisstudyafterInstitutionalethical� approval.�Ofthetotalof�149�patients,�71�hadbiopsyprovenprostatecancers�(TNMstage:�T2=17,�T3=26�and� T4=28)�and�78�clinicalbenignprostatehyperplasia�(BPH).�Peripheralbloodsamplesofallpatientsand�71�age� matchedcontrolsubjectswereobtainedatbaselineandestimationofPSA,�IL-18�andIL-10�wasdonebyenzyme� linkedimmunosorbentassay�(ELISA).�Carcinomaprostatepatientswerefollowedforthreeyears.�Datawere� analyzedwithANOVA,�ROCcurveanalysisandsurvivalanalysis.��Results:�ThebaselinelevelsofPSA,�IL-18� andIL-10�inallgroupsofcarcinomaprostatewerefoundtobesignificantly� (p<0.01)�higherthanbothControl� andBPH.��ThelevelsofIL-18�andIL-10�alsofoundtobeelevatedsignificantlyinstageT3�(p<0.05)�andT4� (p<0.01)�ascomparedtostageT2.�ThelevelsespeciallyofIL-18�isfoundtobewellassociatedwithprogression� ofthediseaseofvariousgroups�(r=0.84,�p<0.01).�Incontrast,�IL-10�showedsignificantdirectassociationwith� progressionofcarcinoma�(r=0.84,�p<0.01)�whileinverserelationwithsurvivalduration�(r=-0.48,�p<0.01)�and� survivalrate�(χ2=8.98,�p=0.0027;�Hazardratio=0.37,�95%�CI=0.18-0.69).�Conclusions:�Studyconcludedthat� serumIL-18�haspotentialtobeabetterdiagnosticmarkerwithhigherspecificityandsensitivityandIL-10�may� bevaluableasaprognosticmarkerthanPSAincarcinomaprostate.

Diagnostic and Prognostic Significance of Prostate Specific Antigen and Serum Interleukin 18 and 10 in Patients with Locally Advanced Prostate Cancer: A Prospective Study

Human genome draft has shown presence of less than 25,000–28,000 genes in the human genome from such huge genomic contents, so a shift has occurred in the focus of research from mRNAs to noncoding RNAs. MicroRNAs (miRNAs), non-coding short RNA molecules are known hot area of research since past two decades, which regulate gene expression by binding to target mRNAs, resulting in translational repression and gene silencing. Approximately 3000 miRNA molecules have been explored in the mammalian genome, from which over 2000 belong to the human genome. Many major cellular functions such as development, differentiation, growth, and metabolism are known to be regulated by miRNAs. Propinquity to distinct genes in the genome and their locations in introns of coding genes, non-coding genes and exons have been explored to have a major influence on the level of gene expressions in eukaryotic cells. The biogenesis of miRNAs, includes various steps and precise cellular machinery facilitating transcription of miRNAs as small inverted repeats of a double-stranded RNA (dsRNA) stem loop, encompassing 70 bp long and exist in both introns and intergenic clusters in the genome. RNA polymerase II is accountable for the synthesis of the introns and exons of both protein-coding and non-coding transcripts from where miRNAs are generated. Initially, inside the nucleus of the cell, miRNAs are transcribed as primary pri-miRNA transcripts and then are trimmed to form the precursor pre-miRNA stem loop structure before moving into the cytoplasm. Further, inside the nucleus they are processed by the Dicer RNAase III endonuclease and thus mature miRNA of 21–23 nucleotides are produced. The first miRNA lin-4, was discovered in Caenorhabditis elegans in 1993 and then second C. elegans miRNA, let-7 but the identification approach was not same. However, the field of miRNA research has since grown with over 17,000 miRNAs discovered to date in 142 species, including humans. The key word ‘‘miRNA’’ currently hits more than 25,000 publications from PubMed, and the first miRNA-targeted drug has now entered a phase II clinical trial (http://www.ClinicalTrials.gov), demonstrating early promise. As miRNAs are evolutionary conserved from ancestry, and now established as regulatory bio-molecules in various biological pathways, so currently these molecules are being explored in various human diseases [1].

/pdf/micrornas-and-diseases-promising-biomarkers-for-diagnosis-pnkqv41q3a.pdf

Shailendra Dwivedi

Papers

Vitamin C in Disease Prevention and Cure: An Overview

Diseases and Molecular Diagnostics: A Step Closer to Precision Medicine.

Recent scenario of obesity and male fertility.

Diagnostic and Prognostic Significance of Prostate Specific Antigen and Serum Interleukin 18 and 10 in Patients with Locally Advanced Prostate Cancer: A Prospective Study

MicroRNAs and Diseases: Promising Biomarkers for Diagnosis and Therapeutics.