Consistent probabilistic outputs for protein function prediction

In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one another; for example, the predictor may assign a specific GO term to a given protein ('purine nucleotide binding') but not assign the parent term ('nucleotide binding'). Such predictions are difficult to interpret. In this work, we focus on methods for calibrating and combining independent predictions to obtain a set of probabilistic predictions that are consistent with the topology of the ontology. We call this procedure 'reconciliation'. We begin with a baseline method for predicting GO terms from a collection of data types using an ensemble of discriminative classifiers. We apply the method to a previously described benchmark data set, and we demonstrate that the resulting predictions are frequently inconsistent with the topology of the GO. We then consider 11 distinct reconciliation methods: three heuristic methods; four variants of a Bayesian network; an extension of logistic regression to the structured case; and three novel projection methods - isotonic regression and two variants of a Kullback-Leibler projection method. We evaluate each method in three different modes - per term, per protein and joint - corresponding to three types of prediction tasks. Although the principal goal of reconciliation is interpretability, it is important to assess whether interpretability comes at a cost in terms of precision and recall. Indeed, we find that many apparently reasonable reconciliation methods yield reconciled probabilities with significantly lower precision than the original, unreconciled estimates. On the other hand, we find that isotonic regression usually performs better than the underlying, unreconciled method, and almost never performs worse; isotonic regression appears to be able to use the constraints from the GO network to its advantage. An exception to this rule is the high precision regime for joint evaluation, where Kullback-Leibler projection yields the best performance.     

Age-based demography and reproductive biology of three <Emphasis Type="Italic">Epinephelus</Emphasis> groupers, <Emphasis Type="Italic">E. polyphekadion,E. tauvina,</Emphasis> and <Emphasis Type="Italic">E. howlandi</Emphasis> (Serranidae), inhabiting coral reefs in Okinawa

The demography and reproductive biology of three Epinephelus groupers (Serranidae), namely E. polyphekadion, E. tauvina, and E. howlandi in the Yaeyama Islands, Okinawa, were examined based on age assessment using otoliths and gonadal histology. The maximum ages for these three species were 26 year, 23 year, and 17 year. The von Bertalanffy growth functions were also determined for each species. The size and age at 50% female maturity were estimated to be 358 mm in total length (TL) and 6.0 year for E. polyphekadion, 371 mm TL and 6.7 year for E. tauvina, and 327 mm TL and 4.1 year for E. howlandi, respectively. Significant differences between the sexes in size and age frequencies were found in all three species, with males being larger and older than females, or transitional individuals. These results strongly indicated that the population of these three grouper species showed monandric protogynous hermaphroditism. The sex ratios of E. polyphekadion and E. tauvina were biased in favor of females, but that of E. howlandi was equivalent between sexes. The relative sizes of ripe testes indicated that the intensity of sperm competition varied among species suggesting different mating system of each species. Reproductive seasonality was similar among species, with active vitellogenesis coinciding with the annual rise in water temperature. The active spawning period was determined to be between April and May for E polyphekadion, in May for E. howlandi, and from March to June for E. tauvina.     

Evaluating the effect of silver nanoparticles on testes of adult albino rats (histological,immunohistochemical and biochemical study)

Silver nanoparticles (AgNPs) are widely used in medicine, however, they have toxic impacts on different organs. AgNPs distribution to the testes was reported, so, we aimed to study the effect of intraperitoneal injection of AgNPs, at different concentrations and different time durations, on adult rat testes. Sixty healthy adult male Wistar albino rats were divided into three groups; control group (Group I) and two experimental groups (Groups II & III), each of which were subdivided into two subgroups. Rats in group II were exposed for 7 days to low and high doses of AgNPs, respectively. Rats in group III were exposed for 28 days to low and high doses of AgNPs, respectively. Testicular sections were stained with H&E, Toluidine blue, Immunohistochemical staining for Ki-67 and CD68 and Electron microscope examination were performed. Serum testosterone level and Quantitative Real-Time PCR for spermatogenesis genes were measured. Group IIa & IIb showed thickened capsule studded with nanoparticles, congested blood vessels, disorganized seminiferous tubules (Sts) and detached germinal epithelium. Group IIIa & IIIb showed marked reduction in the germinal epithelium, and shrunken Sts with the absence of sperms in most of them, which was more evident with higher doses of AgNPs. Significant decrease in cell proliferation and increase in interstitial tissue macrophages were more detected in groups II & III than in the control group. Decreased serum testosterone and decreased expression levels of spermatogenesis genes in groups IIa, IIb & IIIa, IIIb than in the control group were observed. In conclusion: intraperitoneal injection of AgNPs adversely affected the structure of adult rat testes. The tissue damage was more manifested with increased dose and duration of exposure.     

Impacts of enhanced UVB radiation on photosynthetic characteristics of the marine diatom <Emphasis Type="Italic">Phaeodactylum tricornutum</Emphasis> (Bacillariophyceae,Heterokontophyta)

Solar ultraviolet B (UVB) irradiance at the Earth’s surface is increasing due to anthropogenic influences. To evaluate the effects of enhanced UVB radiation on photosynthetic characteristics of the marine diatom Phaeodactylum tricornutum, the species was exposed to four levels of UVB radiation, 0, 0.25, 0.75, and 1.50 KJ m^?2 day^?1 for 7 days. Effects of UVB stress on net photosynthetic rate, net respiration rate, variable chlorophyll (Chl) fluorescence parameters, Chl a and carotenoid contents, and UV-absorbing compounds (UVACs) were investigated. Results showed that there were no significant differences in terms of net respiration rate or maximal photochemical efficiency of photosystem II (F_v/F_m) between the treatments in the short or long term. However, enhanced UVB radiation at an intensity of 0.16 W m^?2 had a negative effect on the net photosynthetic rate, electron transport rate, and on the pathway of excess energy dissipation over the short term (1 to 5 days). Carotenoid and UVACs content increased under UVB radiation. Photosynthetic parameters were unaffected by UVB radiation on the seventh day indicating that P. tricornutum can adapt to UVB radiation in the long term. Results of the present study indicate that there is a dynamic balance between damage and adaptation in microalgae that enables them to adapt to UVB-induced photosystem alterations during both short-term and long-term exposure.     

Comparative analysis of Histone modifications and DNA methylation at <Emphasis Type="Italic">OsBZ8</Emphasis> locus under salinity stress in IR64 and Nonabokra rice varieties

Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties. Expression analysis indicates that the OsBZ8 gene is highly induced in Nonabokra plants even in the absence of salt stress, whereas in IR64, the expression significantly increases only during salt stress. Sequence analysis and nucleosomal arrangement within the region ?2000 to +1000 of OsBZ8 gene show no difference between the two rice varieties. However, there was a considerable difference in histone modifications and DNA methylation at the locus between these varieties. In Nonabokra, the upstream region was hyperacetylated at H3K9 and H3K27, and this acetylation did not change during salt stress. However, in IR64, histone acetylation was observed only during salt stress. Moreover, the upstream region of OsBZ8 gene has highly dynamic nucleosome arrangement in Nonabokra, compared to IR64. Furthermore, loss of DNA methylation was observed at OsBZ8 locus in Nonabokra control plants along with low H3K27me3 and high H3K4me3. Control IR64 plants show high DNA methylation and enriched H3K27me3. Collectively these results indicate a significant difference in chromatin modifications between the rice varieties that regulates differential expression of OsBZ8 gene during salt stress.     

Medium chain fatty acids in intrauterine growth restricted and small for gestational age pregnancies

Introduction

Low birth weight is associated with an increased risk of heart disease, high blood pressure and diabetes in adult life. Fetal growth is determined by nutrient availability, which is related to placenta nutrient transport. Medium chain fatty acids (MCFAs) are a particular class of nutrients, known to be a readily available energy source. Until now no data are reported on these MCFAs in low birth weight fetus.

Aim

This is a prospective study conducted in a tertiary center of prenatal diagnosis to investigate the maternal and fetal MCFAs levels in appropriate for gestational age (AGA), intrauterine growth restricted (IUGR), and small for gestational age (SGA) pregnancies.

Method

The plasmatic levels of MCFAs in AGA, IUGR and SGA mother–infant pairs were quantified by gas chromatography–mass spectrometry. The analytical method had a linearity range of 0.1–50 mg/L and a limit of quantification of 0.03 mg/L. Reduced fetal growth was defined as an estimated fetal weight below the 3rd–10th percentile for gestational age, with (IUGR) or without (SGA) fetal Doppler abnormalities.

Result

Maternal and fetal MCFAs plasma levels were significantly different among SGA, IUGR and AGA groups. Additionally, the observed MCFAs fetal to maternal ratio is >1 for IUGR group, whilst for SGA and AGA the fetal to maternal ratio is less than one.

Conclusion

Changes in MCFAs levels in fetal and maternal plasma are not related to placental functionality or nutrients availability, suggesting the presence of a de novo biosynthesis.

     

Different acclimatization mechanisms of two grass pea cultivars to osmotic stress in in vitro culture

Grass pea (Lathyrus sativus L.) is a legume crop known from its tolerance to various abiotic stresses, especially drought. In this study, we investigated: (1) the response of grass pea seedlings to osmotic stress generated in vitro by polyethylene glycol (PEG); (2) potential drought acclimatization mechanisms of two polish grass pea cultivars. Grass pea seeds of two cultivars were sown on media containing different PEG concentrations (0, 5.5, 11.0 mM) and cultivated for 14 days in controlled conditions. Plants’ dry matter increased under osmotic stress (regardless of PEG concentration). In turn, the highest dose of PEG caused a reduction in seedling growth in both cultivars. Furthermore, PEG caused the peroxidase activity increase in whole seedlings and catalase (CAT) activity in roots. However, differences between cultivars were noted in: CAT activity in shoots; while phenols and anthocyanin content as well as electrolyte leakage in shoots and roots. In turn, in both tested genotypes, accumulation of proline increased in shoots under osmotic stress. Obtained results indicate that the examined plants, although belonging to the same species, differ in acclimatization processes leading to elevated tolerance to osmotic stress.     

Attenuation of Axonal Degeneration by Calcium Channel Inhibitors Improves Retinal Ganglion Cell Survival and Regeneration After Optic Nerve Crush

Axonal degeneration is one of the initial steps in many traumatic and neurodegenerative central nervous system (CNS) disorders and thus a promising therapeutic target. A focal axonal lesion is followed by acute axonal degeneration (AAD) of both adjacent axon parts, before proximal and distal parts follow different degenerative fates at later time points. Blocking calcium influx by calcium channel inhibitors was previously shown to attenuate AAD after optic nerve crush (ONC). However, it remains unclear whether the attenuation of AAD also promotes consecutive axonal regeneration. Here, we used a rat ONC model to study the effects of calcium channel inhibitors on axonal degeneration, retinal ganglion cell (RGC) survival, and axonal regeneration, as well as the molecular mechanisms involved. Application of calcium channel inhibitors attenuated AAD after ONC and preserved axonal integrity as visualized by live imaging of optic nerve axons. Consecutively, this resulted in improved survival of RGCs and improved axonal regeneration at 28 days after ONC. We show further that calcium channel inhibition attenuated lesion-induced calpain activation in the proximity of the crush and inhibited the activation of the c-Jun N-terminal kinase pathway. Pro-survival signaling via Akt in the retina was also increased. Our data thus show that attenuation of AAD improves consecutive neuronal survival and axonal regeneration and that calcium channel inhibitors could be valuable tools for therapeutic interventions in traumatic and degenerative CNS disorders.