Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia

Background and Aim. Because genetic and geographic variations in intestinal microbiota are known to exist, the focus of this study was to establish an estimation of microbiota in colorectal cancer (CRC) patients in Saudi Arabia by means of metagenomic studies. Methods. From July 2010 to November 2012, colorectal cancer patients attending our hospital were enrolled for the metagenomic studies. All underwent clinical, endoscopic, and histological assessment. Mucosal microbiota samples were collected from each patient by jet-flushing colonic mucosa with distilled water at unified segments of the colon, followed by aspiration, during colonoscopy. Total purified dsDNA was extracted and quantified prior to metagenomic sequencing using an Illumina platform. Satisfactory DNA samples (n=29) were subjected to metagenomics studies, followed by comprehensive comparative phylogenetic analysis. An equal number of healthy age-matched controls were also examined for colonic mucosal microbiota. Results. Metagenomics data on 29 patients (14 females) in the age range 38–77 years were analyzed. The majority 11 (37%) of our patients were overweight (BMI = 25–30). Rectal bleeding was the presenting symptom in 18/29 (62%), while symptomatic anemia was the presenting symptom in 11/29 (37%). The location of colon cancer was rectal in 14 (48%), while cecal growth was observed in 8 (27%). Hepatic flexure growth was found in 1 (3%), descending colonic growth was found in 2 (6%), and 4 (13%) patients had transverse colon growth. The metagenomics analysis was carried out, and a total of 3.58G reads were sequenced, and about 321.91G data were used in the analysis. This study identified 11 genera specific to colorectal cancer patients when compared to genera in the control group. Bacteroides fragilis and Fusobacterium were found to be significantly prevalent in the carcinoma group when compared to the control group. Conclusion. The current study has given an insight into the microbiota of colorectal cancer patients in Saudi Arabia and has identified various genera significantly present in these patients when compared to those of the control group

Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops

Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species

Calculated and observed ions of peptide masses of Arabian camel <i>HSPB-1</i> protein.

<p>Calculated and observed ions of peptide masses of Arabian camel <i>HSPB-1</i> protein.</p

The secondary structure of Arabian camel <i>HSPB-1</i> protein.

<p>The secondary structure of Arabian camel <i>HSPB-1</i> protein.</p

Agarose gel (1.2%) electrophoresis of PCR products for <i>HSPB-1</i> and <i>β</i>-actin Arabian camel mRNAs, 1500 bp DNA molecular weight marker was used.

<p>Agarose gel (1.2%) electrophoresis of PCR products for <i>HSPB-1</i> and <i>β</i>-actin Arabian camel mRNAs, 1500 bp DNA molecular weight marker was used.</p

Arabian camel <i>HSPB-1</i> mRNA expression levels in SACAS cells at control(37°C) and heat-stressed condition (42°C) for different time points.

<p>The results are expressed relative to that of <i>β</i>-actin as an endogenous control.</p

Molecular cloning, bioinformatics analysis, and expression of small heat shock protein beta-1 from <i>Camelus dromedarius</i>, Arabian camel

<div><p>Small heat shock protein beta-1 (<i>HSPB-1</i>) plays an essential role in the protection of cells against environmental stress.Elucidation of its molecular, structural, and biological characteristics in a naturally wild-type model is essential. Although the sequence information of the <i>HSPB-1</i> gene is available for many mammalian species, the <i>HSPB-1</i> gene of Arabian camel (Arabian camel <i>HSPB-1</i>) has not yet been structurally characterized. We cloned and functionally characterized a full-length of Arabian camel <i>HSPB-1</i> cDNA. It is 791 bp long, with a 5′-untranslated region (UTR) of 34 bp, a 3′-UTR of 151 bp with a poly(A) tail, and an open reading frame (ORF) of 606 bp encoding a protein of 201 amino acids (accession number: MF278354). The tissue-specific expression analysis of Arabian camel <i>HSPB-1</i> mRNA was examined using quantitative real-time PCR (qRT-PCR); which suggested that Arabian camel <i>HSPB-1</i> mRNA was constitutionally expressed in all examined tissues of Arabian camel, with the predominately level in the esophagus tissue. Peptide mass fingerprint-mass spectrometry (PMF-MS) analysis of the purified Arabian camel <i>HSPB-1</i> protein confirmed the identity of this protein. Phylogenetic analysis showed that the <i>HSPB-1</i> protein of Arabian camel is grouped together with those of Bactrian camel and Alpaca. Comparing the modelled 3D structure of Arabian camel <i>HSPB-1</i> protein with the available protein 3D structure of <i>HSPB-1</i> from human confirmed the presence of <i>α</i>-crystallin domain, and high similarities were noted between the two structures by using super secondary structure prediction.</p></div

Glob Plot analysis.

<p>Blue boxes are disordered regions, and green boxes are ordered regions in the Arabian camel <i>HSPB-1</i> protein.</p

Parker hydrophilicity prediction of Arabian camel <i>HSPB-1</i> protein.

<p>The threshold is 1.0. The regions having <i>β</i>-turns in the protein are shown in yellow color, above the threshold value.</p

Nucleotide and amino acid sequences of Arabian camel <i>HSPB-1</i> cDNA (GenBank accession no., MF278354).

<p>The numbers above the nucleotide sequence show the nucleotide positions. The stop codon is represented with an asterisk(*). The putative polyadenylation signal is shown in red.</p