Relative Amino Acid Composition Signatures of Organisms and Environments

Background

Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment.

Methodologies/Principal Findings

To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny.

Conclusions

Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.     

Carvedilol Decrease IL-1β and TNF-α, Inhibits MMP-2, MMP-9, COX-2, and RANKL Expression,and Up-Regulates OPG in a Rat Model of Periodontitis

Periodontal diseases are initiated primarily by Gram-negative, tooth-associated microbial biofilms that elicit a host response that causes osseous and soft tissue destruction. Carvedilol is a β-blocker used as a multifunctional neurohormonal antagonist that has been shown to act not only as an anti-oxidant but also as an anti-inflammatory drug. This study evaluated whether Carvedilol exerted a protective role against ligature-induced periodontitis in a rat model and defined how Carvedilol affected metalloproteinases and RANKL/RANK/OPG expression in the context of bone remodeling. Rats were randomly divided into 5 groups (n = 10/group): (1) non-ligated (NL), (2) ligature-only (LO), and (3) ligature plus Carvedilol (1, 5 or 10 mg/kg daily for 10 days). Periodontal tissue was analyzed for histopathlogy and using immunohistochemical analysis characterized the expression profiles of MMP-2, MMP-9, COX-2, and RANKL/RANK/OPG and determined the presence of IL-1β, IL-10 and TNF-α, myeloperoxidase (MPO), malonaldehyde (MDA) and, glutathione (GSH). MPO activity in the group with periodontal disease was significantly increased compared to the control group (p<0.05). Rats treated with 10 mg/kg Carvedilol presented with significantly reduced MPO and MDA concentrations (p<0.05) in addition to presenting with reduced levels of the pro-inflammatory cytokines IL-1 β and TNF-α (p<0.05). IL-10 levels in Carvedilol-treated rats remained unaltered. Immunohistochemical analysis demonstrated reduced expression of MMP-2, MMP-9, RANK, RANKL, COX-2, and OPG in rats treated with 10 mg/kg Carvedilol. This study demonstrated that Carvedilol affected bone formation/destruction and anti-inflammatory activity in a rat model of periodontitis.     

High FUT3 expression is a marker of lower overall survival of breast cancer patients

Glycoconjugate Journal - The complex enzyme network responsible for glycan synthesis suffers significant changes during the first steps of tumor development, leading to the early formation of...     

Comparative larval ontogeny of two fish species (Characiformes and Siluriformes) endemic to the São Francisco River in Brazil

The aim of the present study was to perform comparative histological analyses of the ontogenetic development of two fish species endemic to the São Francisco River in Brazil: Prochilodus argenteus and Lophiosilurus alexandri. Histological analyses were performed every 24 h from the moment of hatching until 14 days post-hatching (dph) for the observation of larval development and until 39 dph for the observation of gonadal development. Whole larvae were fixed in Bouin's solution and the histological slides were stained with haematoxylin–eosin. Lophiosilurus alexandri larvae had a larger body size compared with P. argenteus larvae since hatching. Lophiosilurus alexandri larvae had mouth opening and pigmentation of the eyes upon hatching, whereas these events were observed at 1 dph in P. argenteus larvae. The visualisation and the inflation of the swim bladder occurred at 1 and 3 dph, respectively, in the P. argenteus, whereas these events occurred at 2 and 8 dph, respectively, in L. alexandri. Yolk granules were absorbed at 4 dph in P. argenteus and the 10 dph in L. alexandri. At 7 dph, the digestive tube was more differentiated in L. alexandri than P. argenteus and at 14 dph, the digestive system of both species had features of their eating habits: broad stomach and short intestine in L. alexandri, typical of carnivorous habits; stomach with a mechanical function and long intestine in P. argenteus, typical of detritivorous habits. The epithelial lining tissue, formed by a single layer of cells in the newly hatched larvae (0 dph), differentiated throughout the study, exhibiting scales in P. argenteus and numerous club cells in the middle epithelial region of L. alexandri at 39 dph. Undifferentiated gonads with somatic cells and primordial germ cells were observed at 39 dph, with caudal-cranial migration since 1 dph in both species. The anatomic changes during the ontogeny of P. argenteus and L. alexandri larvae are directly associated with the evolutionary history of each species, which explains their feeding habits, behaviour and distribution in the environment: Prochilodus argenteus is detritivorous and actively swims in the water column, whereas L. alexandri is carnivorous and inhabits bottom regions. At 39 dph neither species exhibited sexual differentiation.     

Babassu palm (Attalea speciosa Mart.) super-dominance shapes its surroundings via multiple biotic,soil chemical,and physical interactions and accumulates soil carbon: a case study in eastern Amazonia

Plant and Soil - Aggressive ruderal plant species pose an increasing problem in anthropically degraded lands. They both affect and are affected by other vegetation and by soil fertility in their...     

Selenium improves photosynthesis and induces ultrastructural changes but does not alleviate cadmium-stress damages in tomato plants

Protoplasma - The application of Se to plants growing under Cd contamination may become an alternative strategy to minimize Cd damage. However, there is no specific information available regarding...     

Role of Zinc in Zinc-α2-Glycoprotein Metabolism in Obesity: a Review of Literature

Biological Trace Element Research - Excessive adipose tissue promotes the manifestation of endocrine disorders such as reduction of the secretion of zinc-α2-glycoprotein (ZAG), an adipokine...     

Water deficit modulates growth,morphology, and the essential oil profile in Lippia alba L. (Verbenaceae) grown in vitro

Lippia alba (Miller) N.E. Brown is an aromatic plant species of great economic importance due to the medicinal properties of its essential oils, which provide stress relief, respiratory and gastrointestinal disease control, and anti-inflammatory and natural sedative effects. The plant is also effective in biological control against various pathogens and in food preservation. Water deficit is the most critical abiotic factor limiting plant growth and morpho-physiological development, as well as production of secondary metabolism compounds. The objective of this work was to evaluate the effect of water deficit on growth, photosynthesis, essential oil profile, and the expression of genes related to the biosynthesis of these compounds in L. alba grown in vitro. Nodal segments were cultured on medium supplemented with 0, 1, 2, and 3% (w/v) polyethylene glycol for 45 days. Water stress had a negative effect on primary metabolism indicators, such as growth, leaf area, and photosynthetic rate; but a positive effect on amino acid and total protein content. Similarly, secondary metabolism exhibited an increase in linalool but a reduction in germacrene levels under water deficit. These findings provide a deeper understanding of how water deficit affects primary and secondary metabolism in L. alba, showing the potential of this medicinal species to adapt to soils with low water availability, while still being able to grow and synthesize essential oils.

     

Molecular Identification of Candida Species in the Oral Microbiota of Individuals with Down Syndrome: A Case–Control Study

Mycopathologia - Candida species are common in the human oral microbiota and may cause oral candidiasis (OC) when the microbiota equilibrium is disturbed. Immunosuppressed individuals are...