Gene Expression Prediction and Hierarchical Clustering Analysis of Plant <Emphasis Type="Italic">CCD</Emphasis> genes

Plant carotenoid cleavage dioxygenase (CCD) catalyses the formation of industrially important apocarotenoids. Here, we applied codon-based classification for 72 CCD genes from 35 plant species using hierarchical clustering analysis. The codon adaptation index (CAI) and relative codon bias (RCB) were utilized to estimate the level of gene expression. The codon-based cluster tree result shows neatly clustered subclass of CCD genes except BoCCD1 gene of Bixa orellana. Correlation analysis of CAI values with RCB indicates an overall low-level expression of CCD across different species. Similarly, the closeness in the codon cluster with same CAI values was not reflected in 3-D structural report of selected CCD genes. These finding not only enhances our insights into the classification of CCD gene across the species but also identifies the critical factors responsible for this variation, which could aid in prediction of gene expression and function for newly reported CCD genes.     

Cost of mating in male Menochilus sexmaculatus (Fabricius) (Coleoptera: Coccinellidae)

Mating and reproduction not only provide benefits but can also incur substantial costs. An increasing number of recent studies have indicated that mate searching, mating, and ejaculate production requires large amount of energy which can result in high cost to males. Here, we examine the effect of number of matings of males and mating duration on mating and reproductive success in Menochilus sexmaculatus (Coleoptera: Coccinellidae) by subjecting them to 3 consecutive matings of 30, 60, 90 min, and complete mating (a) with no interval and (b) with interval of 24 hr between the matings. The results reveal a reduction in reproductive performance for both the setup and reduction is more when mating is consecutive without gap. This shows that between subsequent matings males require time to recuperate the sperm/ejaculate. As a male engages in a greater number of matings, the time it takes to begin mating when paired with a female increases and the overall duration of mating decreases. However, frequent mating attempts made by males result in reduction in their body weight. Thus, in this ladybird beetle mating and related physiological process consume lots of energy and the body weight of males tend to decrease which further modifies their reproductive performance. The study helps us to identify the cost of mating from male's perspective and indicates that males need to rejuvenate between the matings.     

Molecular Insights into Rab7‐Mediated Endosomal Recruitment of Core Retromer: Deciphering the Role of Vps26 and Vps35

Retromer, a peripheral membrane protein complex, plays an instrumental role in host of cellular processes by its ability to recycle receptors from endosomes to the trans‐Golgi network. It consists of two distinct sub‐complexes, a membrane recognizing, sorting nexins (SNX) complex and a cargo recognition, vacuolar protein sorting (Vps) complex. Small GTPase, Rab7 is known to recruit retromer on endosomal membrane via interactions with the Vps sub‐complex. The molecular mechanism underlying the recruitment process including the role of individual Vps proteins is yet to be deciphered. In this study, we developed a FRET‐based assay in HeLa cells that demonstrated the interaction of Rab7 with Vps35 and Vps26 in vivo. Furthermore, we showed that Rab7 recruits retromer to late endosomes via direct interactions with N‐terminal conserved regions in Vps35. However, the single point mutation, which disrupts the interaction between Vps35 and Vps26, perturbed the Rab7‐mediated recruitment of retromer in HeLa cells. Using biophysical measurements, we demonstrate that the association of Vps26 with Vps35 resulted in high affinity binding between the Vps sub‐complex and the activated Rab7 suggesting for a possible allosteric role of Vps26. Thus, this study provides molecular insights into the essential role of Vps26 and Vps35 in Rab7‐mediated recruitment of the core retromer complex.      

Peptide Similarity Search Based and Virtual Screening Based Strategies to Identify Small Molecules to Inhibit CarD–RNAP Interaction in M. tuberculosis

International Journal of Peptide Research and Therapeutics - Inhibition of protein–protein interaction is considered as an innovative approach in the drug development field. In the present...     

Plasma Total Nitric Oxide and Endothelial Constitutive Nitric Oxide Synthase (ecNOS) Gene Polymorphism: A Study in a South Indian Population

In an analysis of the possible association of endothelial constitutive nitric oxide synthase (ecNOS) gene polymorphism and plasma nitric oxide levels in patients with acute coronary syndrome, we investigated 106 patients with the syndrome and 100 healthy controls. Genotype was determined using the polymerase chain reaction; plasma nitric oxide levels were found using ELISA. The genotype frequencies for the a/b polymorphism in the control group were 77% for bb, 19% for ab, and 4% for aa. In the patients, genotype frequencies were 55% bb, 34% ab, and 11% aa. The allele frequencies were 28% a and 72% b among the patients and 13% a and 87% b among control subjects. Our findings showed a significant association of the ecNOS gene polymorphism with acute coronary syndrome in the South Indian population.     

Glucose and lipid metabolism alterations in liver and adipose tissue pre-dispose p47phox knockout mice to systemic insulin resistance

Oxidative stress due to enhanced production or reduced scavenging of reactive oxygen species (ROS) has been associated with diet (dyslipidemia) induced obesity and insulin resistance (IR). The present study was undertaken to assess the role of p47^phox in IR using wild type (WT) and p47^phox?/? mice, fed with different diets (HFD, LFD or Chow). Augmented body weight, glucose intolerance and reduced insulin sensitivity were observed in p47^phox?/? mice fed with 45% HFD and 10% LFD. Further, body fat and circulating lipids were increased significantly with 5 weeks LFD feeding in p47^phox?/? mice, while parameters of energy homeostasis were reduced as compared with WT mice. LFD fed knockout (KO) mice showed an enhanced hepatic glycogenolysis, and reduced insulin signalling in liver and adipose tissue, while skeletal muscle tissue remained unaffected. A significant increase in hepatic lipids, adiposity, as well as expression of genes regulating lipid synthesis, breakdown and efflux were observed in LFD fed p47^phox?/? mice after 5 weeks. On the other hand, mice lacking p47^phox demonstrated altered glucose tolerance and tissue insulin sensitivity after 5 weeks chow feeding, while changes in body weight, respiratory exchange ratio (RER) and heat production are non-significant. Our data demonstrate that lack of p47^phox is sufficient to induce IR through altered glucose and lipid utilization by the liver and adipose tissue.     

SPARC regulates extracellular matrix organization through its modulation of integrin-linked kinase activity

SPARC, a 32-kDa matricellular glycoprotein, mediates interactions between cells and their extracellular matrix, and targeted deletion of Sparc results in compromised extracellular matrix in mice. Fibronectin matrix provides provisional tissue scaffolding during development and wound healing and is essential for the stabilization of mature extracellular matrix. Herein, we report that SPARC expression does not significantly affect fibronectin-induced cell spreading but enhances fibronectin-induced stress fiber formation and cell-mediated partial unfolding of fibronectin molecules, an essential process in fibronectin matrix assembly. By phage display, we identify integrin-linked kinase as a potential binding partner of SPARC and verify the interaction by co-immunoprecipitation and colocalization in vitro. Cells lacking SPARC exhibit diminished fibronectin-induced integrin-linked kinase activation and integrin-linked kinase-dependent cell-contractile signaling. Furthermore, induced expression of SPARC in SPARC-null fibroblasts restores fibronectin-induced integrin-linked kinase activation, downstream signaling, and fibronectin unfolding. These data further confirm the function of SPARC in extracellular matrix organization and identify a novel mechanism by which SPARC regulates extracellular matrix assembly.     

两个水稻骨干恢复系重要农艺性状的遗传基础研究

水稻骨干恢复系是指在杂交稻育种中广泛应用的一类恢复系。探明骨干恢复系的遗传基础,发掘其重要农艺性状基因/QTL,对分子标记辅助选择水稻恢复系育种具有重要应用价值。本研究以生产上广泛应用的三系骨干恢复系成恢727和两系骨干恢复系9311为亲本,培育了具有250个系的重组自交系群体。分别在2015年三亚和2016年合肥两个环境下进行了9个重要农艺性状表型和SSR分子标记基因型鉴定,用SAS9.2分析表型数据,用QTL Ici Mapping v4.1进行QTL定位分析。在三亚和合肥两个环境下共检测到39个QTL,三亚检测到16个,分布于第1、2、4、7、8、10、11和12染色体上;合肥检测24个,分布于第1、2、3、7、8、9、10和12染色体上。其中qPH1-1在三亚和合肥两个环境下都能检测到,加性效应分别为-1.75和-2.46。在检测到的39个QTL中,有24个QTL的增效等位基因来自恢复系成恢727,15个QTL的增效等位基因来自9311。共计有26个QTL曾被前人定位,13个属于尚未见文献报道的新QTL。另外,在RM279~RM521、RM336~RM3534、RM25~RM547、RM553~RM160、RM222~RM271区段内检测到5个多效性QTL位点。其中RM25~RM547位点与已经克隆的基因Ghd8位置相近。RM553~RM160位点是一个新的多效性位点,分别控制每穗实粒数、单株产量和结实率,而且效应和表型变异贡献率都较大。其余3个位点在前人的研究中分别有所报道,但其多效性则是在本研究中首次发现。在本研究新发掘到的QTL中,控制穗数的QTL qPN12-1,控制穗长的QTL qPL1-2和qPL10-1,控制总粒数的QTL qSNP2-1和qSNP10-1,控制结实率的QTL qSF3-1,控制千粒重QTL qTGW7-1和控制产量的QTL qGY1-1效应均比较大,解释的表型遗传变异比例也较高。本研究的结果将会为相关性状QTL的精细定位、克隆和育种应用奠定基础。     

Translation of Henrich Klebahn's 'Damaging agents of the klippfish - a contribution to the knowledge of the salt-loving organisms'

Background

Henrich Klebahn was a German linguist, mycologist and phytopathologist, who was known as Dr. Dr. h. c. Henrich Klebahn, Hauptcustos a. D., Honorarprofessor an der Hanischen Universität. He was born February 20, 1859 in Bremen, and died October 5, 1942 in Hamburg. He taught linguistics from 1885-1899, studied Natural Science at the Universities of Jena and Berlin (1881) and received his PhD from the University of Jena. In 1899, he was appointed scientific assistant at the Hamburg botanical garden, where he worked until 1905. From 1905 to 1930, he was at the agricultural institute of Bromberg. In 1921, he was named honorary professor and lecturer in cryptogams and soil biology at the Institut für Allgemeine Botanik where he taught until 1934. He is well known for his work on gas vesicles and halophiles, among other topics. This re-print of 'Die Schädlinge des Klippfisches. Ein Beitrag zur Kenntnis der salzliebenden Organismen. Von H. Klebahn. Mit zwei Tafeln und vier Abbildungen im Text.' was originally published in 1919 in the Jahrbuch der Hamb. Wissensch. Anstaltes. XXXVI. Beiheft pages 11-69, by Latcke & Waltt, E. H. Buchdrucker. The translators have tried to remain faithful to the contents and to the original sense of the article by minimizing modifications.

Results

The original paper reported the conclusions of a 3 year long study of the microbes causing damage to the fish industry as well as a summation of work on the subject up until 1919. The findings were that the causative agents were fungi and other microbes, the chief of which was a red, Gram-negative rod-shaped bacillus, Bacillus halobius ruber, that formed pale reddish colonies and was found to oscillate, but after extensive testing, was found not possess flagella. The initial appearance of "a shiny corpuscle" at the ends of cells was determined not to be spores; rather that it was the "result of the coherence of the light beams due to a total reflection of the light in the optically denser little rods". The cells were osmotically sensitive to the addition of water. In addition, a Gram-negative, red Sarcina morrhuae that appeared pinker in color, was less salt-sensitive than the red bacillus, in fact surviving the transfer to water. These were "round individual cells or groups of only two or four cells, usually; however, there are eight or more round cells that are arranged like cube corners to great cube-like or irregular packages lying together, just in the same manner as with the familiar Sarcina ventriculi." This organism was also identified from the walls of a fish storage room. Finally, a third, red microorganism was isolated: a Gram-negative micrococcus, Micrococcus (Diplococcus) morrhuae, which was "spherically rounded" and barely sensitive to water: "If one distributes a sample of a colony in water, the cells partly separate, to a great degree; however, they stay together in groups of two or four cells."

Conclusions

This article provides evidence for identification of halophilic microbes as the major cause of fish spoilage, and is one of the earliest publications in the field of halophile microbiology.