Unsupervised statistical clustering of environmental shotgun sequences

Background  

The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. While previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed.     

Strong light elevates thermotolerance of photosynthetic apparatus and the content of membranes and polar lipids in wheat leaves

The influence of excess irradiance on resistance of wheat (Triticum aestivum L.) photosynthetic apparatus to heating in darkness and in the light was investigated and compared with changes in leaf cell ultra-structure and composition of cell lipids and fatty acids. The leaves of 14- to 16-day-old plants grown at low irradiance (about 20 W/m²) were exposed for 1 h to irradiance of 370 or 600 W/m² PAR. Using infrared gas analysis, we found that the preexposure of leaves to excess irradiation elevated resistance of apparent photosynthesis to 10-min heat treatment at 40–45°C. The rate of Hill reaction (reduction of 2,6-dichlorophenolindophenol by isolated chloroplasts) was higher for leaves heated at high irradiance than for leaves heated in darkness. During illumination of leaves with strong light, mesophyll cells became more abundant in mitochondria and peroxysomes, as well as in cisternae of endoplasmic reticulum and Golgi complex. The chloroplast thylakoids and grana became more extensive and numerous. At the same time, the leaf content of main classes of membrane glycerolipids increased in parallel with the increase in the phospholipid/glycolipid and lipid/chlorophyll ratios. The unsaturation index of fatty acids of membrane lipids increased because of the elevated content of linolenic acid. Thus, excessive light (not fully utilized in photosynthesis) induced in wheat leaves a series of nonspecific adaptive changes that were similar to those occurring under the action of other environmental factors, such as heat shock, cooling, salinity, and osmotic stresses.     

Heat shock increases thermotolerance of photosynthetic electron transport and the content of chloroplast membranes and lipids in wheat leaves

Preliminary heating of 15-16-day-old wheat (Triticum aestivum L.) plants for 3 h at 37–38°C (heat shock, HS) increased the tolerance of photosynthetic electron transport (determined as the reduction of 2,6-dichlorophenol indophenol by isolated chloroplasts) toward heating of leaves at 42–48°C in high light (100 klx). At the same time, HS did not affect the activity of the xanthophyll cycle reactions in the 30–48°C temperature range. HS exposure induced an increase in the thylakoid length, the number of grana, and the average number of thylakoids per granum. The volume of the thylakoid system increased 1.4-fold. Such indices as the total content of chlorophylls (a + b), the chlorophyll a/b ratio, as well as the contents of individual carotenoids, chloroplast membrane proteins, and the soluble leaf proteins remained unchanged. The de novo photosynthetic membrane formation was accompanied by the 1.5-fold increase in major chloroplast lipids. It was concluded that, in mature wheat chloroplasts, HS induced the formation of thylakoids characterized by a changed molecular structure and by increased lipid/protein and lipid/chlorophyll ratios.     

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

We describe strand-specific, base-resolution detection of 5-hydroxymethylcytosine (5-hmC) in genomic DNA with single-molecule sensitivity, combining a bioorthogonal, selective chemical labeling method of 5-hmC with single-molecule, real-time (SMRT) DNA sequencing. The chemical labeling not only allows affinity enrichment of 5-hmC-containing DNA fragments but also enhances the kinetic signal of 5-hmC during SMRT sequencing. We applied the approach to sequence 5-hmC in a genomic DNA sample with high confidence.     

Heat-Induced Increase in the Tolerance of the Wheat Photosynthetic Apparatus to Combined Action of High Temperature and Visible Light: CO2 Fixation,Photosynthetic Pigments,and Chloroplast Ultrastructure

Heating of the leaves of 15-day-old wheat (Triticum aestivum L.) plants at 42°C in the light (370 W/m² PAR) suppressed their ability to fix CO₂ twice stronger than heating in darkness. Heat hardening (3 h at 38–39°C) improved the tolerance of photosynthesis to combined action of high light and temperature but did not affect the tolerance to photoinhibition at 30°C. Hardening did not induce changes in the levels of photosynthetic pigments and their ratios. De-epoxidation of violaxanthin turned out to be more tolerant to photoinhibition at 42°C than CO₂ fixation. Protective effect of hardening was not related to the accumulation of zeaxanthin and activation of the xanthophyll cycle. Hardening protected the most sensitive population of chloroplasts against heat-induced photodamage and simultaneously increased the number and length of thylakoids. An increase in the volume of the thylakoid system was also induced by heating at 42°C and exposure to high light at 30°C. The formation of additional thylakoids and grana of shade type was not associated with improved tolerance of photosynthesis to heat and light stresses.     

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

DNA methylation is the most common form of DNA modification in prokaryotic and eukaryotic genomes. We have applied the method of single-molecule, real-time (SMRT®) DNA sequencing that is capable of direct detection of modified bases at single-nucleotide resolution to characterize the specificity of several bacterial DNA methyltransferases (MTases). In addition to previously described SMRT sequencing of N6-methyladenine and 5-methylcytosine, we show that N4-methylcytosine also has a specific kinetic signature and is therefore identifiable using this approach. We demonstrate for all three prokaryotic methylation types that SMRT sequencing confirms the identity and position of the methylated base in cases where the MTase specificity was previously established by other methods. We then applied the method to determine the sequence context and methylated base identity for three MTases with unknown specificities. In addition, we also find evidence of unanticipated MTase promiscuity with some enzymes apparently also modifying sequences that are related, but not identical, to the cognate site.     

Protective and injuring action of visible light on photosynthetic apparatus in wheat plants during hyperthermia treatment

Illumination of wheat (Triticum aestivum L.) leaves during heat treatment produced either additional injury or protection of photosynthetic apparatus depending on irradiance and the heating dose. Furthermore, illumination of leaves during hyperthermia exerted differential impacts on thermal tolerances of photosynthesis and photosystem II-driven electron transport assessed from the reduction of 2,6-dichlorophenolindophenol (DCPIP). Measurements with infrared gas analyzer showed that mild heating of leaves in darkness (10 min at 38–40°C) had stronger inhibitory effect on CO₂ uptake than heating of leaves exposed to low and moderate complex irradiances (3–30 klx), as well as excessive irradiance (75–100 klx). When the leaves were heated at higher temperatures (42–44°C), the low and moderate irradiances had a protective action, while high-intensity light aggravated the inhibition of photosynthesis. Illumination of leaves with weak light during heat treatment mitigated the impairment of chloroplast ultrastructure, whereas irradiation with high-intensity light (100 klx) destroyed the sensitive population of chloroplasts. The heat-stimulated photoinhibition was stronger for leaf photosynthesis than for DCPIP reduction in chloroplasts isolated from heat-treated leaves. No correlation was observed between the extent of violaxanthin deepoxidation, zeaxanthin accumulation, and the protective effect of light on photosynthetic apparatus during heat treatments.