Relic thermosensitive gene expression in a turtle with genotypic sex determination

The evolution of sex determination remains one of the most fascinating enigmas in biology. Transitions between genotypic sex determination (GSD) and temperature‐dependent sex determination (TSD) have occurred multiple times during vertebrate evolution, however, the molecular basis and consequences of these transitions in closely related taxa remain unresolved. Here I address a critical question: Do species with GSD derived from ancestors possessing TSD retain any ancestral thermal sensitivity in the developmental pathways underlying gonadal differentiation? Results from an expression study of a gene involved in early gonadogenesis in GSD (Apalone mutica) and TSD (Chrysemys picta) turtles, support the hypothesis that Wt1 in A. mutica displays such a relic thermal sensitivity. This retention is likely enabled by Sf1, a gene immediately downstream from Wt1 whose expression is independent of temperature in this species. My results constitute the first empirical evidence of a GSD vertebrate exhibiting thermal sensitivity in the expression of a gene regulating gonadogenesis. This novel finding reveals an undocumented source of raw material for future evolutionary change that may exist in other GSD taxa, and one that enhances the evolutionary potential of the gene networks underlying sexual differentiation and contributes to the astonishing ability of sex‐determining mechanisms.     

The bacteriophage lambda DNA packaging enzyme: identification of four structural domains of the gpNu1 subunit using limited proteolysis.

Lambda DNA terminase, the enzyme that cleaves virion-length chromosomes from multigenomic concatemers and packages them into the bacteriophage head, is composed of two subunits, gpNu1 and gpA. Direct determination of the structure of gpNu1, the smaller subunit, has not been possible because of its insolubility in aqueous solutions. Therefore, to identify smaller and potentially water-soluble domains of gpNu1, we analyzed the nature of the products obtained by limited digestion of the protein with several proteases. The gpNu1 subunit was obtained from E. coli cells transfected with the plasmid pH6-Nu1 that overproduces the protein. Incubation of gpNu1 solubized in 2.5 M guanidinium chloride with chymotrypsin resulted in the formation of at least eight discrete protein bands, while treatment with endoproteinase glu-C and bromelain yielded three and one major bands, respectively. The peptides generated by digestion with the various proteases were separated by two-dimensional gel electrophoresis and transferred to Immobilon membranes. Amino acid sequencing of the peptides allowed for the precise assignment of their N-terminal amino acid, while their estimated molecular weights permitted the identification of their C-terminal ends. The results reveal that in the presence of 2.5 M guanidinium chloride, gpNu1 is partially folded in at least four distinct structural domains that correspond to functional domains as determined by previously reported genetic experiments. This information is key to design new plasmids to overproduce these domains for further structural analysis.     

Towards pan-genome read alignment to improve variation calling

Background

Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation.

Results

We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation – a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC.

Conclusions

Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.

     

Pinus pollen season trend in South Spain

In Andalusia (southern Spain), Pinus species are found in mountainous areas and nature reserves, though some species are also grown as ornamentals in cities. Annual airborne pollen trends are regarded as an indicator of variations in climate prompted by overall climate change. Airborne pollen concentration also provides a useful tool for analyzing alterations in the distribution of vegetation in response to environmental factors and to changes in land use. The present study analyzed the Pinus pollen season over 22 years (1993–2014) in 4 Andalusian cities (Córdoba, Granada, Jaén, and Málaga), and examined correlations between airborne pollen concentrations and meteorological parameters (temperature and rainfall). Pinus pollen season lasted from March to June, starting first in Málaga and later in eastern Andalusia. Differences between the pollen curves for each city were attributable to differing proportions of pine species in each province. Temperatures during the months prior to flowering tended to fall, prompting delayed onset of the pollen season in most cities. No significant results were observed for rainfall patterns in most cities. Total pollen concentrations increased at most sites, suggesting that the recorded decline in pine-nut output was not influenced by flowering rates, but to the impact of a local pest.     

Immunogenicity and safety assessment of the Cuban recombinant hepatitis B vaccine in healthy adults.

Manufactures of biotechnological/biological products (including vaccines) frequently make changes to manufacturing processes of products both during development and after approval. In our case, a non-inferiority bridging study was carried out to demonstrate that changes in the production plant facilities of Cuban recombinant hepatitis B vaccine, Heberbiovac HB, did not affect the safety and immunogenicity of the vaccine. This controlled, randomized, doubled-blinded trial included 501 volunteers, aged between 20 and 64, who were given three doses of vaccine (20 microg HBsAg/mL) at month 0, 1, and 2. Four lots were evaluated (three corresponding to the new production facilities and a control one produced in the older facilities). One month after the third dose, were observed protective levels of anti-HBsAg in 97% of the subjects that concluded the study with a geometric mean antibody titer (GMT) of 931.18 IU/L. Normal values of body mass index (BMI), the younger ages, and being a female, were significantly related to a good antibody response. The vaccine was well tolerated. Pain at the injection site was the most commonly reported symptom. We conclude that Heberbiovac HB vaccine maintains its characteristics after the modifications carried out in the production plant facilities and both, lot obtained in previous facilities and in the new ones, are comparable in terms of safety and immunogenicity.     

Safety Evaluation of Transgenic Tilapia with Accelerated Growth

Recent advances in modern marine biotechnology have permitted the generation of new strains of economically important fish species through the transfer of growth hormone genes. These transgenic fish strains show improved growth performance and therefore constitute a better alternative for aquaculture programs. Recently, we have obtained a transgenic tilapia line with accelerated growth. However, before introducing this line into Cuban aquaculture, environmental and food safety assessment was required by national authorities. Experiments were performed to evaluate the behavior of transgenic tilapia in comparison to wild tilapia as a way to assess the environmental impact of introducing transgenic tilapia into Cuban aquaculture. Studies were also conducted to evaluate, according to the principle of substantial equivalence, the safety of consuming transgenic tilapia as food. Behavior studies showed that transgenic tilapia had a lower feeding motivation and dominance status than controls. Food safety assessment indicated that tilapia growth hormone has no biological activity when administered to nonhuman primates. Furthermore, no effects were detected in human healthy volunteers after the consumption of transgenic tilapia. These results showed, at least under the conditions found in Cuba, no environmental implications for the introduction of this transgenic tilapia line and the safety in the consumption of tiGH-transgenic tilapia as an alternative feeding source for humans. These results support the culture and consumption of these transgenic tilapia. Received: March 9, 1998; accepted June 25, 1998.