Locating QTLs controlling several adult root traits in an elite Chinese hybrid rice

This study aimed to elucidate the genetics of the adult root system in elite Chinese hybrid rice. Several adult root traits in a recombinant inbred line (RIL) population of Xieyou 9308 and two backcross F₁ (BCF₁) populations derived from the RILs were phenotyped under hydroponic culture at heading stage for quantitative trait locus (QTL) mapping and other statistical analysis. There a total of eight QTLs detected for the root traits. Among of them, a pleiotropic QTL was repeatedly flanked by RM180 and RM5436 on the short arm of chromosome 7 for multiple traits across RILs and its BCF₁ populations, accounting for 6.88% to 25.26% of the phenotypic variances. Only additive/dominant QTLs were detected for the root traits. These results can serve as a foundation for facilitating future cloning and molecular breeding.     

Circadian clock speed increases during aging in the male Syrian hamster: A large-scale study

There are conflicting reports in the literature as to whether or not the circadian period in Syrian hamsters shortens with age, and those studies were conducted with small sample sizes. This report mines data from a large number of experiments resulting in more than 1000 measurements of circadian period in hamsters during aging up to 6 months, and this was correlated with both age and weight. Circadian period was calculated while hamsters were in running wheels in constant darkness. There is a weak correlation between hamster weight and circadian period, and there is significant shortening of circadian period during aging.     

Redox Buffer Capacity in Water-Rock-Microbe Interaction Systems in Subsurface Environments

An incubation experiment was conducted to estimate redox buffer capacity of “water-rock-microbe” interaction systems in sedimentary rocks. The water chemistry, microbial growth and community structure were analyzed during the incubations. The dissolved oxygen (DO) concentrations and oxidation-reduction potential (ORP) values decreased notably in the presence of active microorganisms, whereas abiotic reactions did not lead to reducing conditions during incubation. The change in microbial community structure suggests that nitrate-reducing and sulfate-reducing bacteria played an important role in reduction of water by using lignite-derived organic matter. These results show that the microbial role is extremely important for the redox buffering capacity in sedimentary rock environments.     

Molecular weight distribution and functional group profiles of TEMPO-oxidized lyocell fibers

The effects of TEMPO-mediated oxidation, performed with NaClO, a catalytic amount of NaBr, and 2,2′,6,6′-tetramethylpiperidine-1-oxy radical (TEMPO), were studied on lyocell fibers by means of GPC using multiple detection and group-selective fluorescence labeling according to the CCOA and FDAM methodology. The applied method determines functional group content as a sum parameter, as well as functional group profiles in relation to the molecular weight of the cellulose fibers. Both the CHO and COOH profiles, as well as molecular weight alterations, were analyzed. A significant decrease in the average molecular weight was obtained during the first hour of TEMPO-mediated oxidation, but prolonged oxidation time resulted in no strong additional chain scission. Significant amounts of COOH groups were introduced in the high molecular weight fractions by the oxidation with higher concentrations of NaClO (2.42–9.67 mmol NaClO/g fiber) after modification times of 1 h or longer.     

Computational Design of a Protein-Based Enzyme Inhibitor

While there has been considerable progress in designing protein–protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.     

Low-Molecular-Weight DNA Replication Intermediates in Escherichia coli: Mechanism of Formation and Strand Specificity

Chromosomal DNA replication intermediates, revealed in ligase-deficient conditions in vivo, are of low molecular weight (LMW) independently of the organism, suggesting discontinuous replication of both the leading and the lagging DNA strands. Yet, in vitro experiments with purified enzymes replicating sigma-structured substrates show continuous synthesis of the leading DNA strand in complete absence of ligase, supporting the textbook model of semi-discontinuous DNA replication. The discrepancy between the in vivo and in vitro results is rationalized by proposing that various excision repair events nick continuously synthesized leading strands after synthesis, producing the observed LMW intermediates. Here, we show that, in an Escherichia coli ligase-deficient strain with all known excision repair pathways inactivated, new DNA is still synthesized discontinuously. Furthermore, hybridization to strand-specific targets demonstrates that the LMW replication intermediates come from both the lagging and the leading strands. These results support the model of discontinuous leading strand synthesis in E. coli.     

Molecular characterization of PVAS3: An asparagine synthetase gene from common bean prevailing in developing organs

In common bean, asparagine synthetase (AS; EC 6.3.5.4) is encoded by three members of a multigene family called PVAS1, PVAS2 and PVAS3. Two of these genes, PVAS1 and PVAS2, have been extensively studied, but little is known about PVAS3, remaining unclear whether PVAS3 function is redundant to the other AS or if it plays a specific role in Phaseolus vulgaris metabolism. In this work, we used a molecular approach to characterize PVAS3 expression and to gain some knowledge about its physiological function. We showed that, in contrast to PVAS1 and PVAS2, PVAS3 was expressed in all organs analyzed. Interestingly, PVAS3 was the AS gene most highly expressed in nodules, leaves and pods at the earliest stages of development, and its expression decreased as these organs developed. Expression of PVAS3 parallels the accumulation of AS protein and the asparagine content during the earliest stages of nodule, leaf and pod development, suggesting an important role for PVAS3 in the synthesis of asparagine in that period. Furthermore, PVAS3 was not repressed by light, as most class-II AS genes. Surprisingly, fertilization of nodulated plants with nitrate or ammonium, conditions that induce PVAS1 and PVAS2 and the shift from ureides to amide synthesis, repressed the expression of PVAS3 in nodules and roots. The possible implications of this regulation are discussed.     

Hydrogen sulfide donor sodium hydrosulfide-improved heat tolerance in maize and involvement of proline

Hydrogen sulfide (H₂S) has long been considered as a phytotoxin, but nowadays as a cell signal molecule involved in growth, development, and the acquisition of stress tolerance in higher plants. In the present study, hydrogen sulfide donor, sodium hydrosulfide (NaHS), pretreatment markedly improved germination percentage of seeds and survival percentage of seedlings of maize under heat stress, and alleviated an increase in electrolyte leakage of roots, a decrease in tissue vitality and an accumulation of malondialdehyde (MDA) in coleoptiles of maize seedlings. In addition, pretreatment of NaHS could improve the activity of Δ¹-pyrroline-5-carboxylate synthetase (P5CS) and lower proline dehydrogenase (ProDH) activity, which in turn induced accumulation of endogenous proline in maize seedlings. Also, application of proline could enhance endogenous proline content, followed by mitigated accumulation of MDA and increased survival percentage of maize seedlings under heat stress. These results suggest that sodium hydrosulfide pretreatment could improve heat tolerance of maize and the acquisition of this heat tolerance may be involved in proline.     

Overwintering strategy of endoparasitoids in Chilo suppressalis: a perspective from the cold hardiness of a host

Although parasitoids ultimately kill their host, koinobiont parasitoids must protect not only themselves but also their hosts against extreme environments. In this study, the parasitism rate of Chilo suppressalis Walker (Lepidoptera: Pyralidae) was investigated, and the average body weights, supercooling points, and concentrations of glycerol (acting as a cryoprotectant) in the hemolymph were compared between parasitized and non‐parasitized larvae. Five species of koinobiont endoparasitoids parasitized the overwintering C. suppressalis larvae and the total parasitism rate was 47.6% (n = 1 537). Average body weight of parasitized larvae was significantly lower than that of non‐parasitized larvae, and the parasitism rate of the lighter group (20–30 mg) was highest. The supercooling point of parasitized C. suppressalis larvae (?15.7 ± 0.3 °C) was significantly lower than that of the non‐parasitized larvae (?14.3 ± 0.2 °C). In addition, supercooling points were not correlated with body weights between parasitized and non‐parasitized larvae, indicating that cold hardiness of parasitized larvae was enhanced by endoparasitoids. Furthermore, the concentration of glycerol in the hemolymph was significantly higher in parasitized larvae (205.0 ± 7.1 μmol ml^?1) than in non‐parasitized larvae (169.8 ± 14.4 μmol ml^?1), which suggests that the mechanism that decreases the supercooling point of parasitized larvae was associated with glycerol. All these results indicated that the cold hardiness of parasitized C. suppressalis larvae was enhanced by their endoparasitoids, which benefitted overwintering endoparasitoids.