Potential functions and applications of diverse microbial exopolysaccharides in marine environments.

Exopolysaccharides (EPSs) from microorganisms are essential harmless natural biopolymers used in applications including medications, nutraceuticals and functional foods, cosmetics, and insecticides. Several microbes can synthesize and excrete EPSs with chemical properties and structures that make them suitable for several important applications. Microbes secrete EPSs outside their cell walls, as slime or as a "jelly" into the extracellular medium. These EPS-producing microbes are ubiquitous and can be isolated from aquatic and terrestrial environments, such as freshwater, marine water, wastewater, and soils. They have also been isolated from extreme niches like hot springs, cold waters, halophilic environments, and salt marshes. Recently, microbial EPSs have attracted interest for their applications such as environmental bio-flocculants because they are degradable and nontoxic. However, further efforts are required for the cost-effective and industrial-scale commercial production of microbial EPSs. This review focuses on the exopolysaccharides obtained from several extremophilic microorganisms, their synthesis, and manufacturing optimization for better cost and productivity. We also explored their role and applications in interactions between several organisms.

Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii.

Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. We discovered a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the corresponding nucleotide content of these C. reinhardtii organelle genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. We reveal specific biases and patterns in rNMP distributions in the algal mitochondrial, chloroplast, and nuclear DNA. Moreover, we identified the C. reinhardtii orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.

Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine.

Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporation remain poorly characterized. Here, by using ribose-seq and Ribose-Map techniques, we built and analyzed high-throughput sequencing libraries of rNMPs derived from mitochondrial and nuclear DNA of budding and fission yeast. We reveal both common and unique features of rNMP sites among yeast species and strains, and between wild type and different ribonuclease H-mutant genotypes. We demonstrate that the rNMPs are not randomly incorporated in DNA. We highlight signatures and patterns of rNMPs, including sites within trinucleotide-repeat tracts. Our results uncover that the deoxyribonucleotide immediately upstream of the rNMPs has a strong influence on rNMP distribution, suggesting a mechanism of rNMP accommodation by DNA polymerases as a driving force of rNMP incorporation. Consistently, we find deoxyadenosine upstream from the most abundant genomic rCMPs and rGMPs. This study establishes a framework to better understand mechanisms of rNMP incorporation in DNA.

Capture of Ribonucleotides in Yeast Genomic DNA Using Ribose-Seq.

Experiments conducted in yeast cells have recently shown abundant presence of ribonucleotides (rNMPs) embedded both in nuclear and mitochondrial DNA. Indeed, rNMPs are the most frequent, nonstandard nucleotides found in cellular DNA. rNMPs have a highly reactive 2'-hydroxyl group in the ribose sugar that gives rise to genome instability by altering the structure, function, and properties of DNA. In order to profile rNMPs embedded in yeast genomic DNA, as well as any other genomic DNA of interest, we developed "ribose-seq." Ribose-seq utilizes Arabidopsis thaliana tRNA ligase (AtRNL), which enables ligation of 2'-phosphate termini of DNA molecules terminating with an rNMP to the 5'-phosphate end of the same DNA molecules. Thus, a unique feature of ribose-seq is its capacity to specifically and directly capture the rNMPs present in DNA. Here we describe how ribose-seq is applied to yeast Saccharomyces cerevisiae DNA to capture rNMPs that are incorporated in the yeast genome and build libraries of rNMP incorporation for high-throughput sequencing. We also provide the advancements over our original ribose-seq protocol at the end of Subheading 1, and the specific details are provided in the methods part of this chapter.

The effect of hyperbaric oxygen therapy on improving bony stability in LeFort I maxillary advancement.

OBJECTIVE: The present study was designed to investigate the effect of hyperbaric oxygen therapy (HBO2T) on improving bony stability in LeFort I maxillofacial surgery. METHODS: Sixteen cases (n = 16) with severe skeletal anteroposterior discrepancies and who had ceased growing were used as subjects. The samples were categorized into two groups: Group A comprised one-piece LeFort I procedures with HBO2T administered seven days after surgery (n = 8), and Group B comprised the same surgical procedure without HBO2T (n = 8). Lateral cephalometric radiographs were taken for each subject to record the occurrence of bony relapse: prior to surgery (T1); seven days after surgery (T2); and a third (T3) taken 12 months after surgery. Each patient underwent preoperative and postoperative full-fixed orthodontic treatment. The first group was administered HBO2T for 60 minutes, at 2.5 ATA (atmospheres absolute) for five consecutive days after the T2 stage, and the second group served as a control, as they had not received HBO2T. For both groups the mean values of T1 stages were calculated and compared to those of T2 and T3 stages in the same group. RESULTS: Comparison between the two groups regarding the percentage of change in measurements at T2 and at T3 showed that there were significant differences between groups in all measurements at T3. In the HBO2T group, there was no statistical significant difference in all parameters between the mean values of T2 and T3, indicating minor or no relapse. Meanwhile in the group without HBO2T, there was a highly significant statistical difference in the mean values between T2 and T3 in all studied parameters, indicating significant relapse. CONCLUSIONS: It is suggested that administration of hyperbaric oxygen therapy may aid in the postoperative stability of orthognathic LeFort I surgical corrections of patients with severe dentofacial deformities.