In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles

Background  

In silico candidate gene prioritisation (CGP) aids the discovery of gene functions by ranking genes according to an objective relevance score. While several CGP methods have been described for identifying human disease genes, corresponding methods for prokaryotic gene function discovery are lacking. Here we present two prokaryotic CGP methods, based on phylogenetic profiles, to assist with this task.     

Age dependency of the meiotic process in an F<Subscript>1</Subscript> interspecific hybrid of <Emphasis Type="Italic">Solanum lnnaeum</Emphasis> L. × <Emphasis Type="Italic">Solanum incanum</Emphasis>

A study of the meiotic process in first- and second-year plants of an F₁ interspecific hybrid of Solanum linnaeum L. × Solanum incanum L. has been carried out. Fruits with seeds were obtained during the second year of vegetation. The numbers of univalents and tetravalents, as well as the percentage of basic impairments, decreased as the age of plants increased. The process of meiosis in the parental forms was normal. A conclusion was made regarding the connection between the regularity of meiosis in the F₁ heterozygotes of Solanum lynnaeum L. × Solanum incanum L., on the one hand, and the hybrid nature of the genotype and age and the influence of environmental factors, on the other hand.     

Meiosis passing age dependence in Solanum linnaeum L. x solanum incanum L. F1 interspecific hybrid

Meiosis passing in the first- and second-year-plants of F1 interspecific hybrid Solanum linnaeum L. x Solanum incanum L. has been carried out. Fruit with seeds were formed during a second year of vegetation. The quantities of uni- and tetravalents and main disorders frequency lowered with plant age. Meiosis in parental forms was normal. The conclusion was drawn about F1 Solanum linnaeum L. x Solanum incanum L. meiosis regularity connection with heterozygous genotype, influence of environmental factors and plant age.     

Process of meiosis in interspecific hybrid F1 Lycopersicon esculentum Mill. x Lycopersicon chilense Dun

The investigation concerns meiosis behaviour in embryo-culture-obtained Lycopersicon esculentum Mill. (mutant seedline Mo 638) x L. chilense Dun. F1 hybrid and its parental forms. It was determined that chiasma frequency decreased while univalent and meiotic disorder frequencies increased in F1 plants in comparison with parents forms. Univalent number and the percent of main disorders lowered with bud tier increasing. The conclusion was made about meiosis regularity connection with the influence of environment factors and heterozygous genotype of F1 plants Lycopersicon esculentum x L. chilense.     

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

Background

DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (Taq^αI and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system.

Results

With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region.

Conclusions

With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.     

Oncogenic comparison of human papillomavirus type 58 E7 variants

Human papillomavirus 58 (HPV58) ranks the second or third in East Asian cervical cancers. Current studies on HPV58 are scarce and focus on the prototype. Previously, we identified the three most common circulating HPV58 E7 strains contained amino acid alterations: G41R/G63D (51%), T20I/G63S (22%) and T74A/D76E (14%) respectively. Among them, the T20I/G63S variant (V1) had a stronger epidemiological association with cervical cancer. We therefore suggested that V1 possessed stronger oncogenicity than the other two variants. Here, we performed phenotypic assays to characterize and compare their oncogenicities with HPV58 E7 prototype. Our results showed that overexpression of V1 conferred a higher colony‐forming ability to primary murine epithelial cells than prototype (P < 0.05) and other variants, implicating its higher immortalising potential. Further experiments showed that both V1 and prototype enhanced the anchorage‐independent growth of NIH/3T3 cells (P < 0.001), implicating their stronger transforming power than the two other variants. Moreover, they possessed an increased ability to degrade pRb (P < 0.001), which is a major effector pathway of E7‐driven oncogenesis. Our work represents the first study to compare the oncogenicities of HPV58 E7 prototype and variants. These findings deepened our understanding of HPV58 and might inform clinical screening and follow‐up strategy.     

Chromatin structure and the state of human organism

The state of chromatin in human buccal epithelium cell nuclei upon the influence of sport trainings was investigated. Chromatin state was evaluated in interphase buccal cell nuclei after orcein staining. The heterochromatin granule quantity (HGQ) was estimated in 30 nuclei per sample, and for every donor the mean HGQ value per 30 cells was determined. Donors of masculine sex, aged from 18 to 48 years performed training walks and samples of buccal epithelium were collected. Sportive charges induced the process of chromatin condensation in cell nuclei. After the period of repose (24-48 h) the HGQ decreased to control level therefore the process of chromatin decondensation was observed. The state of chromatin changes in connection with circadian rhythm. Chromatin became more condensed at nighttime and less condensed in the morning. Hormones such as adrenaline, noradrenaline, and hydrocortisone in vitro induced the increase of HGQ.     

Course of meiosis in F1 interspecific hybrids of Lycopersicon esculentum Mill. × Licopersicon chilense Dun.

A study was conducted into the course of meiosis in F₁ interspecific hybrids of Lycopersicum esculentum Mill (mutant line Mo 638) × Lycopersicum chinense Dul. and its parental forms. An F₁ interspecific hybrid was obtained through the embryo culture technique. A decrease in the chiasma frequency and an increase in the frequency of univalents and meiotic abnormalities compared to their parental forms were detected in hybrid plants. The number of univalents and the percentage of main impairments decreased, as the height of bud tier locations increased. A conclusion was made regarding the connection between the regularity of meiosis in the examined F₁ interspecific hybrids of Lycopersicon esculentum × Lycopersicon chilense, on the one hand, and the hybrid nature of genotypes and the influence of environmental factors, on the other hand.     

Chiasma frequencies in the meiocytes from the anther diametrical zones in species from the genus <Emphasis Type="Italic">Capsicum</Emphasis> L.

A study of the chiasma frequencies in the meiocytes from three anther diametrical zones (free end, middle, and base) in plants from species of the genus Capsicum was carried out. It was found that the maximum values of the total chiasma frequencies were observed in the meiocytes from the anther free end compared to its middle zone and base. It was concluded that the peculiarities of the distribution of crossover events lengthwise along the anther were the result of its anatomic structure.     

Structural basis for the specificity of PPM1H phosphatase for Rab GTPases

LRRK2 serine/threonine kinase is associated with inherited Parkinson’s disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal‐dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110‐residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3‐D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab‐specific interaction domain within a conserved phosphatase fold.