Codon usage bias analysis of genes linked with esophagus cancer

Esophageal cancer involves multiple genetic alternations. A systematic codon usage bias analysis was completed to investigate the bias among the esophageal cancer responsive genes. GC-rich genes were low (average effective number of codon value was 49.28). CAG and GTA are over-represented and under-represented codons, respectively. Correspondence analysis, neutrality plot, and parity rule 2 plot analysis confirmed the dominance over mutation pressure in modulating the codon usage pattern of genes linked with esophageal cancer.     

Bacillus atrophaeus: main characteristics and biotechnological applications – a review

The genus Bacillus includes a great diversity of industrially important strains, including Bacillus atrophaeus (formerly Bacillus subtilis var. niger). This spore-forming bacterium has been established as industrial bacteria in the production of biological indicators for sterilization, in studies of biodefense and astrobiology methods as well as disinfection agents, in treatment evaluation and as potential adjuvants or vehicles for vaccines, among other applications. This review covers an overview of the fundamental aspects of the B. atrophaeus that have been studied to date. Although the emphasis is placed on recent findings, basic information’s such as multicellularity and growth characteristics, spore structure and lifecycle are described. The wide biotechnological application of B. atrophaeus spores, including vegetative cells, is briefly demonstrated, highlighting their use as a biological indicator of sterilization or disinfection.     

Transgenic expression of polygalacturonase-inhibiting proteins in Arabidopsis and wheat increases resistance to the flower pathogen Fusarium graminearum

Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most important diseases of wheat worldwide, resulting in yield losses and mycotoxin contamination. The molecular mechanisms regulating Fusarium penetration and infection are poorly understood. Beside mycotoxin production, cell wall degradation may play a role in the development of FHB. Many fungal pathogens secrete polygalacturonases (PGs) during the early stages of infection, and plants have evolved polygalacturonase-inhibiting proteins (PGIPs) to restrict pectin degradation during fungal infection. To investigate the role of plant PGIPs in restricting the development of FHB symptoms, we first used Arabidopsis thaliana, whose genome encodes two PGIPs (AtPGIP1 and AtPGIP2). Arabidopsis transgenic plants expressing either of these PGIPs under control of the CaMV 35S promoter accumulate inhibitory activity against F.?graminearum PG in their inflorescences, and show increased resistance to FHB. Second, transgenic wheat plants expressing the bean PvPGIP2 in their flowers also had a significant reduction of symptoms when infected with F.?graminearum. Our data suggest that PGs likely play a role in F.?graminearum infection of floral tissues, and that PGIPs incorporated into wheat may be important for increased resistance to FHB.     

Relations between phenotypic changes of spores and biofilm production by Bacillus atrophaeus ATCC 9372 growing in solid-state fermentation

Bacillus spp. spores are usually obtained from strains cultivated in artificial media. However, in natural habitats, spores are predominantly formed from bacteria present in highly surface-associated communities of cells. Solid-state fermentation (SSF) is the culture method that best mimetizes the natural environment of many microorganisms that grow attached to the surface of solid particles. This study aims to confirm that sporulation through SSF of Bacillus atrophaeus occurs by biofilm formation and that this model of fermentation promotes important phenotypic changes in the spores. Sporulation on standard agar and by SSF with sand and sugarcane bagasse as support was followed by a comparative study of the formed spores. Growth characteristics, metabolic and enzymatic profiles confirmed that sporulation through SSF occurs by biofilm formation promoting important phenotypic changes. It was possible to demonstrate that spores coat had different structure and the presence of ridges only on SSF spores' surface. The sporulation conditions did not affect the dry-heat spore resistance. The type of support evaluated also influenced in the phenotypic alterations; however, the used substrates did not cause interference. This work provides novel information about B. atrophaeus response when submitted to different sporulation conditions and proposes a new concept about bacterial biofilm formation by SSF.     

Predicting learning and achievement using GABA and glutamate concentrations in human development

Previous research has highlighted the role of glutamate and gamma-aminobutyric acid (GABA) in learning and plasticity. What is currently unknown is how this knowledge translates to real-life complex cognitive abilities that emerge slowly and how the link between these neurotransmitters and human learning and plasticity is shaped by development. While some have suggested a generic role of glutamate and GABA in learning and plasticity, others have hypothesized that their involvement shapes sensitive periods during development. Here we used a cross-sectional longitudinal design with 255 individuals (spanning primary school to university) to show that glutamate and GABA in the intraparietal sulcus explain unique variance both in current and future mathematical achievement (approximately 1.5 years). Furthermore, our findings reveal a dynamic and dissociable role of GABA and glutamate in predicting learning, which is reversed during development, and therefore provide novel implications for models of learning and plasticity during childhood and adulthood.

A longitudinal study of human subjects from primary school to university reveals that concentrations of GABA and glutamate in the parietal cortex predict mathematical learning and achievement. During development, the relationships between these neurotransmitters and learning are dynamic, reversing between childhood and young adulthood.     

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

Much effort and interest have focused on assessing the importance of natural selection, particularly positive natural selection, in shaping the human genome. Although scans for positive selection have identified candidate loci that may be associated with positive selection in humans, such scans do not indicate whether adaptation is frequent in general in humans. Studies based on the reasoning of the MacDonald–Kreitman test, which, in principle, can be used to evaluate the extent of positive selection, suggested that adaptation is detectable in the human genome but that it is less common than in Drosophila or Escherichia coli. Both positive and purifying natural selection at functional sites should affect levels and patterns of polymorphism at linked nonfunctional sites. Here, we search for these effects by analyzing patterns of neutral polymorphism in humans in relation to the rates of recombination, functional density, and functional divergence with chimpanzees. We find that the levels of neutral polymorphism are lower in the regions of lower recombination and in the regions of higher functional density or divergence. These correlations persist after controlling for the variation in GC content, density of simple repeats, selective constraint, mutation rate, and depth of sequencing coverage. We argue that these results are most plausibly explained by the effects of natural selection at functional sites—either recurrent selective sweeps or background selection—on the levels of linked neutral polymorphism. Natural selection at both coding and regulatory sites appears to affect linked neutral polymorphism, reducing neutral polymorphism by 6% genome-wide and by 11% in the gene-rich half of the human genome. These findings suggest that the effects of natural selection at linked sites cannot be ignored in the study of neutral human polymorphism.     

NOR regions of polychaete worms of the genus Ophryotrocha studied by chromosome banding techniques and FISH

This article reports the results of cytogenetic analyses carried out on 10 species of polychaete worms belonging to the genus Ophryotrocha (Dorvilleidae). Nucleolar organizer regions (NORs) were characterized by Ag staining, C-banding, CMA3 staining, and ribosomal fluorescent in situ hybridization (rDNA FISH). Extensive intraspecific variation in NOR number and distribution were observed in O. costlowi, O. sp. macrovifera, O. notoglandulata, O.l. labronica, O. l. pacifica (2n = 6), O. p. puerilis, O. diadema (2n = 8), O. hartmanni, O. gracilis (2n = 10). In O. sp. robusta (2n = 10), Ag-NORs were always located on a single chromosome pair. CMA3 staining suggests a possible trend toward a GC-rich rDNA compartmentalization. In O.l. labronica, O. p. puerilis, O. diadema, and O. sp. robusta rDNA FISH shows that Ag and FISH signals coincide. Results from C-banding seem to indicate that the increased genome size (GS) observed in O. sp. macrovifera (0.8 pg) and O. hartmanni (1.16 pg) compared to the base GS value of the genus (0.4 pg) cannot be attributed to variation in the heterochromatin content.     

EVOLUTION OF BIPARENTAL CARE IN THE HERMAPHRODITIC POLYCHAETE WORM OPHRYOTROCHA DIADEMA

Ophryotrocha diadema is a simultaneously hermaphroditic polychaete worm with a brief adolescent protandrous phase. In the mating system of this worm, pairs are formed preferentially between simultaneous hermaphrodites. Both partners of a pair regularly alternate sex roles, reciprocate egg exchange, and care for developing embryos. It was experimentally shown that neglected eggs have a 31% probability of dying, but eggs cared for by both parents, by a single parent, or even by an unrelated individual have a 95% probability of developing. In pairs experimentally prevented from caring for eggs, intruders succeeded in substituting one of the partners significantly more frequently than in pairs allowed to care for eggs. Thus, the main adaptive value of biparental care would be to guarantee a partner for egg reciprocation. Protandrous males are inefficient brooders, and biparental care becomes fully established only when individuals are able to reciprocate egg exchange, i.e., they have reached the simultaneously hermaphroditic stage.