Investigating the predictability of essential genes across distantly related organisms using an integrative approach

Rapid and accurate identification of new essential genes in under-studied microorganisms will significantly improve our understanding of how a cell works and the ability to re-engineer microorganisms. However, predicting essential genes across distantly related organisms remains a challenge. Here, we present a machine learning-based integrative approach that reliably transfers essential gene annotations between distantly related bacteria. We focused on four bacterial species that have well-characterized essential genes, and tested the transferability between three pairs among them. For each pair, we trained our classifier to learn traits associated with essential genes in one organism, and applied it to make predictions in the other. The predictions were then evaluated by examining the agreements with the known essential genes in the target organism. Ten-fold cross-validation in the same organism yielded AUC scores between 0.86 and 0.93. Cross-organism predictions yielded AUC scores between 0.69 and 0.89. The transferability is likely affected by growth conditions, quality of the training data set and the evolutionary distance. We are thus the first to report that gene essentiality can be reliably predicted using features trained and tested in a distantly related organism. Our approach proves more robust and portable than existing approaches, significantly extending our ability to predict essential genes beyond orthologs.     

Stability of telomeric G-quadruplexes

In most eukaryotes, telomeric DNA consists of repeats of a short motif that includes consecutive guanines and may hence fold into G-quadruplexes. Budding yeasts have telomeres composed of longer repeats and show variation in the degree of repeat homogeneity. Although telomeric sequences from several organisms have been shown to fold into G-quadruplexes in vitro, surprisingly, no study has been dedicated to the comparison of G-quadruplex folding and stability of known telomeric sequences. Furthermore, to our knowledge, folding of yeast telomeric sequences into intramolecular G-quadruplexes has never been investigated. Using biophysical and biochemical methods, we studied sequences mimicking about four repetitions of telomeric motifs from a variety of organisms, including yeasts, with the aim of comparing the G-quadruplex folding potential of telomeric sequences among eukaryotes. G-quadruplex folding did not appear to be a conserved feature among yeast telomeric sequences. By contrast, all known telomeric sequences from eukaryotes other than yeasts folded into G-quadruplexes. Nevertheless, while G(3)T(1-4)A repeats (found in a variety of organisms) and G(4)T(2,4) repeats (found in ciliates) folded into stable G-quadruplexes, G-quadruplexes formed by repetitions of G(2)T(2)A and G(2)CT(2)A motifs (found in many insects and in nematodes, respectively) appeared to be in equilibrium with non-G-quadruplex structures (likely hairpin-duplexes).     

Dung beetle assemblages on tropical land‐bridge islands: small island effect and vulnerable species

Aim Using dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae) in a tropical land‐bridge island system, we test for the small island effect (SIE) in the species–area relationship and evaluate its effects on species richness and community composition. We also examine the determinants of species richness across island size and investigate the traits of dung beetle species in relation to their local extinction vulnerability following forest fragmentation. Location Lake Kenyir, a hydroelectric reservoir in north‐eastern Peninsular Malaysia. Methods We sampled dung beetles using human dung baited pitfall traps on 24 land‐bridge islands and three mainland sites. We used regression tree analyses to test for the SIE, as well as species traits related to local rarity, as an indication of extinction vulnerability. We employed generalized linear models (GLMs) to examine determinants for species richness at different scales and compared the results with those from conventional linear and breakpoint regressions. Community analyses included non‐metric multidimensional scaling, partial Mantel tests, nestedness analysis and abundance spectra. Results Regression tree analysis revealed an area threshold at 35.8 ha indicating an SIE. Tree basal area was the most important predictor of species richness on small islands (<35.8 ha). Results from GLMs supported these findings, with isolation and edge index also being important for small islands. The SIE also manifested in patterns of dung beetle community composition where communities on small islands (<35.8 ha) departed from those on the mainland and larger islands, and were highly variable with no significant nestedness, probably as a result of unexpected species occurrences on several small islands. The communities exhibited a low degree of spatial autocorrelation, suggesting that dispersal limitation plays a part in structuring dung beetle assemblages. Species with lower baseline density and an inability to forage on the forest edge were found to be rarer among sites and hence more prone to local extinction. Main conclusions We highlight the stochastic nature of dung beetle community composition on small islands and argue that this results in reduced ecosystem functionality. A better understanding of the minimum fragment size required for retaining functional ecological communities will be important for effective conservation management and the maintenance of tropical forest ecosystem stability.     

Regulation of MMP-2 expression and activity by β-1,3-<Emphasis Type="Italic">N</Emphasis>-acetylglucosaminyltransferase-8 in AGS gastric cancer cells

β-1,3-N-acetylglucosaminyltransferase-8(β3Gn-T8) catalyzes the transfer of GlcNAc to the non-reducing terminus of the Galβ1-4GlcNAc of tetraantennary N-glycan in vitro. It has been reported to be involved in malignant tumors, but a comprehensive understanding of how the glycolsyltransferase correlates with the invasive potential of human gastric cancer is not currently available. Therefore, we investigated the ability and possible mechanism involved with β3Gn-T8 in modulating matrix metalloproteinase-2 (MMP-2) and tissue inhibitor of metalloproteinase-2 (TIMP-2) in AGS gastric cancer cells. Here, we found out that siRNA-mediated suppression of the β3Gn-T8 could directly reduce the MMP-2 expression and activity as observed in RT-PCR, western blot and gelatin zymography analysis. Meanwhile, TIMP-2 expression had been increased. Cell invasion assay using matrigel matrix-coated transwell inserts showed that the invasive property was greatly suppressed in β3Gn-T8 siRNA transfected cells. Furthermore, cells overexpressing β3Gn-T8 gene (when transfected with pEGFP-C1 plasmid) also expressed MMP-2 gene, but TIMP-2 expression had been inhibited. The invasive ability of these cells was also enhanced. Protein–protein interaction analysis using STRING database showed that β3Gn-T8 and MMP-2 may have related signal pathway. In summary, our results reveal a new mechanism by which β3Gn-T8 can regulate MMP-2 and TIMP-2. We suggest that β3Gn-T8 can be used as a novel therapeutic target for human gastric treatment.     

Analysis of the genetic variation of vascular endothelial growth factor gene in three Chinese indigenous cattle breeds

PCR–SSCP and DNA sequencing methods were employed to screen the genetic variation of vascular endothelial growth factor (VEGF) gene in 675 individuals belonging to three Chinese indigenous cattle breeds including Qinchuan (QC), Jiaxian Red (JX) and Nanyang (NY) breed. Three new single nucleotide polymorphisms (SNPs) (g.6765T > C ss130456744, g.6860A > G ss130456745, g.6893T > C ss130456746) were found. One SNP (g.6765T > C) was detected in intron II of VEGF gene in all three breeds and the other two SNPs (g.6860A > G, g.6893T > C) were in exon III of VEGF gene only in NY breed. Among them, two synonymous mutations of exon III were identified: CCA (Pro) > CCG (Pro) at position 65th amino acid (aa) and TGT (Cys) > TGC (Cys) at position 76th aa of VEGF(190aa) in NY breed. Our study revealed that NY breed exhibited the most abundant genetic diversity in VEGF gene within the three cattle breeds. Furthermore, JX cattle breed was more similar to QC breed than to NY breed. Our genetic data in the present study supported the hypothesis that the distribution pattern of Chinese indigenous cattle breeds was closely related to the geographical and climatic background again.     

Intermittent hypobaric hypoxia improves postischemic recovery of myocardial contractile function via redox signaling during early reperfusion

Intermittent hypobaric hypoxia (IHH) protects hearts against ischemia-reperfusion (I/R) injury, but the underlying mechanisms are far from clear. ROS are paradoxically regarded as a major cause of myocardial I/R injury and a trigger of cardioprotection. In the present study, we investigated whether the ROS generated during early reperfusion contribute to IHH-induced cardioprotection. Using isolated perfused rat hearts, we found that IHH significantly improved the postischemic recovery of left ventricular (LV) contractile function with a concurrent reduction of lactate dehydrogenase release and myocardial infarct size (20.5 ± 5.3% in IHH vs. 42.1 ± 3.8% in the normoxic control, P < 0.01) after I/R. Meanwhile, IHH enhanced the production of protein carbonyls and malondialdehyde, respective products of protein oxidation and lipid peroxidation, in the reperfused myocardium and ROS generation in reperfused cardiomyocytes. Such effects were blocked by the mitochondrial ATP-sensitive K(+) channel inhibitor 5-hydroxydecanoate. Moreover, the IHH-improved postischemic LV performance, enhanced phosphorylation of PKB (Akt), PKC-ε, and glycogen synthase kinase-3β, as well as translocation of PKC-ε were not affected by applying H(2)O(2) (20 μmol/l) during early reperfusion but were abolished by the ROS scavengers N-(2-mercaptopropionyl)glycine (MPG) and manganese (III) tetrakis (1-methyl-4-pyridyl)porphyrin. Furthermore, IHH-reduced lactate dehydrogenase release and infarct size were reversed by MPG. Consistently, inhibition of Akt with wortmannin and PKC-ε with εV1-2 abrogated the IHH-improved postischemic LV performance. These findings suggest that IHH-induced cardioprotection depends on elevated ROS production during early reperfusion.     

NAD<Superscript>+</Superscript> Treatment Induces Delayed Autophagy in Neuro2a Cells Partially by Increasing Oxidative Stress

NAD⁺ plays important roles in various biological processes. In this study, we reported that treatment of NAD⁺ induces delayed autophagy in Neuro2a cells. Moreover, the effects of NAD⁺ on the autophagy in the cells appear to be, at least partially, mediated by oxidative stress. However, nicotinamide, a degradation product of NAD⁺, does not affect the autophagy. Our experiments have further indicated that the NAD⁺-induced autophagy contributes to the NAD⁺-induced decrease in the survival of these cells. In summary, our study has provided the first evidence that NAD⁺ treatment induces autophagy in cancer cells such as Neuro2a cells, which contributes to the NAD⁺-induced decrease in cancer cell survival.