[Genetic changes and biological potential of proliferative nodule in congenital pigmented nevus]

Objective: To study the genetic changes and biological potential of proliferative nodule in congenital melanocytic nevus. Methods: Whole-exome sequencing was carried out using the technique of next-generation sequencing (NGS) in order to detect the genomic alterations of two cases of proliferative nodules (PN) in congenital melanocytic nevi (CMN). Twelve cases of CMN and ten cases of malignant melanoma were used as benign and malignant controls, respectively. Mutated genes that possessed statistically significant difference between benign and malignant controls were listed, according to what benign and malignant statuses were classified and clustered. The heatmaps of clustering analyses were depicted using heatmap package. Fluorescence in situ hybridization (FISH) was also used to validate the above results. Results: Eighty-six common somatic gene mutations were detected in two samples of PN. Compared with CMN, PN had 52 more mutated genes. Furthermore, 22 of these 52 mutated genes were also detected in malignant melanoma samples. Two cases of PN fell between benign CMN and malignant melanoma in germline mutation clustering. Both cases of PN were positive in the FISH tests. Conclusions: The genetic changes of PN partially overlap with those of CMN and malignant melanoma. Therefore, although most of the PN manifest as a benign lesion clinically, it may have certain malignant potential at the genetic level, and warrant long-term monitoring and follow-up.

Pathway and Gene Discovery from Natural Hosts and Organisms

Information in public sequence databases on the genomes and metagenomes of microbes and plants has grown rapidly. In conjunction with technological developments in computational identification of biosynthetic gene clusters, molecular biology, synthetic biology, and analytical tools, this has revealed genes for enzymes with optimal and targeted function, as well as a rich pool of uncharacterized metabolic pathways. This chapter discusses different approaches to discovery of genes and metabolic pathways in microbes and plants in nature, such as genomic mining, transcriptome analysis, and metabolite profiling.

Production of a Human Recombinant Polyclonal Fab Antivenom against Iranian Viper Echis carinatus

Venomous snakebite is a life-threatening injury in many tropical and subtropical areas including Iran. The gold standard treatment option for human envenomation is the use of antivenoms. Despite the unique effects of horse-derived antivenoms on the treatment of snakebite, they are not fully perfect and need improvements. In this study, human recombinant Fab fragment antivenom was produced in Rosetta-g bacterium using a gene library constructed in the previous study. The prepared Fab was purified in several steps, desalted, and lipopolysaccharide-depleted using ammonium sulfate solution and dialysis against phosphate buffer and Triton X-114 solution, respectively. Subsequently, the product was initially confirmed by the sodium dodecyl sulfate polyacrylamide gel electrophoresis and enzyme-linked immunosorbent assay (ELISA), respectively. Finally, the neutralization potency of the product was investigated in laboratory Syrian Mice. The obtained results showed corresponding reduced bands to Fab fragment with the molecular weight of about 28 kDa at a concentration of 3.1 mg/ml. There was a significant difference between the groups in terms of ELISA test (P<0.05). The neutralization potency of the product against the venom of Echis carinatus (E. carinatus) was about 7 LD50/ml (54.6 µg/ml) when tested on mice. Based on the results, the Fab fragment antivenom had the ability to neutralize the in vivo biological activity of the venom of Iranian E. carinatus. However, further studies are recommended to reach a suitable concentration of antivenom fragment.

Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites

Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic‐ring‐hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil‐impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished. Based on a deduced ARHD peptide sequences consensus phylogeny, we examined trends and divergences in the sequence phylogenetic clustering from the different sites. The taxonomic affiliation of the OPF revealed that Pseudomonas, Streptomyces, Variovorax, Bordetella and Rhodococcus were the five most abundant genera, considering all sites. The functional diversity analysis showed the enzymatic prevalence of benzene 1,2‐dioxygenase, 3‐phenylpropionate dioxygenase and naphthalene 1,2‐dioxygenase, in addition to 10.98% of undefined category ARHDs. The ARHD gene correlation analysis among different sites was essentially important to gain insights on spatial distribution patterns, genetic congruence and ecological coherence of the bacterial groups found. This work revealed the genetic potential from the mangrove sediment for AH biodegradation and a considerable evolutionary proximity among the dioxygenase OPFs found in Antarctica and South America sites, in addition to high level of endemism in each continental region.

High quality RNA isolation from ployphenol-, polysaccharide- and protein-rich tissues of lentil (Lens culinaris)

Current RNA isolation methods have limitations in their ability to yield good quality and quantity of RNA from plants that have high content of phenols, polysaccharides and storage proteins. Existing methods also do not eliminate accompanying chromosomal DNA in RNA preparation that causes false positives in gene expression studies. Standard isolation technique was modified for rapid and quick extraction of RNA, and lentil tissue most appropriate to extract good quality RNA was determined. The concentration of the phenol blocker polyvinylpyrrolidone in the extraction buffer was determined, DNase I was added to eliminate chromosomal DNA and the timing of this step was optimized. RNA up to 568 μg of RNA from 1 g of tissue was isolated from four different tissues of lentil in less than half the time typically required by reported methods. The method avoids the use of toxic phenol–chloroform, hazardous guanidinium thiocyanate (GTC) and laborious CsCl ultracentrifugation. Absorbance A260/A280 ratio of 1.9 and A260/A230 ratio of 2.7 reveal RNA to be of high purity. Modified method yielded RNA that was free from contaminants and suitable for RT-PCR and cDNA library construction.