Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids

We analyzed the proteome of undifferentiated plastids from a tobacco BY-2 cell culture by shotgun proteomics following multidimensional protein fractionation. The fractionation strategy initiated with the serial extraction of proteins from membranes which allowed us to distinguish soluble, peripheral, and integral membrane proteins. The majority of the identified proteins have a function in the cellular metabolism and most of them are active in amino acid synthesis pathways. A significant number of the identified proteins was not identified in chloroplast proteome analyses before. This suggests BY-2 plastid specific functions that differ from the major activities of chloroplasts. We have used the BY-2 plastid proteins reported here to assess the metabolic activities of undifferentiated heterotrophic plastids and compared the functional profile with that of differentiated heterotrophic amyloplasts. Comparative shotgun proteome analyses as reported here provide information about prevalent metabolic activities of different plastid types.     

Genomic organization of Tropomodulins 2 and 4 and unusual intergenic and intraexonic splicing of YL-1 and Tropomodulin 4

Background

Single nucleotide polymorphisms (SNPs) are the foundation of powerful complex trait and pharmacogenomic analyses. The availability of large SNP databases, however, has emphasized a need for inexpensive SNP genotyping methods of commensurate simpliCity, robustness, and scalability. We describe a solution-based, microtiter plate method for SNP genotyping of human genomic DNA. The method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification of the signal using fluorescent primers. Only the probe with a 3' base complementary to the SNP is circularized by ligation.

Results

SNP scoring by ligation was optimized to a 100,000 fold discrimination against probe mismatched to the SNP. The assay was used to genotype 10 SNPs from a set of 192 genomic DNA samples in a high-throughput format. Assay directly from genomic DNA eliminates the need to preamplify the target as done for many other genotyping methods. The sensitivity of the assay was demonstrated by genotyping from 1 ng of genomic DNA. We demonstrate that the assay can detect a single molecule of the circularized probe.

Conclusions

Compatibility with homogeneous formats and the ability to assay small amounts of genomic DNA meets the exacting requirements of automated, high-throughput SNP scoring.     

Annual gametogenic cycle of the freshwater pearl mussel,Lamellidens marginalis (Lamarck, 1819) collected from a perennial lentic habitat of Bangladesh

ABSTRACT

We investigated the annual gametogenic phenology of the freshwater pearl mussel, Lamellidens marginalis (Lamarck, 1819), collected from a lentic habitat at Mymensingh, Bangladesh, using biometry and histology through monthly sampling from August 2015 to July 2016. After biometric measurements, thin slices of dorso-ventral sections were cut from the middle of the mussels for histology to determine sex and level of gonadal maturation. The condition index (CI) ranged from 0.64 (March) to 0.99 (January) over the study period. The CI peaked three times (January, April and July) indicating that the mussels were ripe during these months and subsequent decreases in CI indicated spawning, which was consistent with histology. Both males and females exhibited similar patterns in terms of gonadal development, maturation and spawning activity. It was confirmed that natural populations of L. marginalis spawn throughout the year with remarkable temporal variations, except during December when the surface water temperature reaches annual minima (16.5°C). Highest spawning activity of L. marginalis was noted during February–March, May and July–November. The data obtained in the present study could be useful for the conservation managers of this commercial species by allowing harvesting of better quality mussels to be timed without interrupting major spawning activity.     

Induction of chromosomal aberrations and sister chromatid exchanges by chlormadinone acetate in human lymphocytes: a possible role of reactive oxygen species

Genotoxicity study of a synthetic progestin chlormadinone acetate (CMA) was carried out in human lymphocytes using chromosomal aberrations (CAs) and sister chromatid exchanges (SCEs) as parameter. Effect of CMA was studied at 10, 20, 30 and 40 microM. CMA was genotoxic at 30 and 40 microM. With a view to study the possible mechanism of genotoxicity of CMA, superoxide dismutase (SOD) and catalase (CAT) were used separately and in combination along with the CMA (40 microM) at different doses. SOD treatment increased CAs and SCEs at both the doses. CAT treatment decreased the frequencies of CAs and SCEs in both, separately and in combination with SOD, suggesting a possible role of reactive oxygen species for the genotoxic damage.     

RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding

RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.     

Comparative toxic potential of market formulation of two organophosphate pesticides in transgenic Drosophila melanogaster (hsp70-lacZ)

This study investigated the working hypothesis that two widely used organophosphate pesticides; Nuvan and Dimecron, exert toxic effects in Drosophila. Transgenic D. melanogaster (hsp70-lacZ) was used as a model for assaying stress gene expression and AchE activity as an endpoint for toxicity and also to evaluate whether stress gene expression is sufficient to protect against toxic insult of the chemicals and to prevent tissue damage. The study was extended to investigate the effect of the pesticides on the life cycle and reproduction of the organism. The study showed that Nuvan affected emergence of the exposed flies more drastically than Dimecron and the effect was lethal at the highest tested concentration (0.075 ppm). While Nuvan at 0.0075 and 0.015 ppm concentrations affected reproduction of the flies significantly, the effect of Dimecron was significant only at 0.015 and 0.075 ppm. Nuvan-exposed third-instar larvae exhibited a 1.2-fold to 1.5-fold greater hsp70 expression compared to Dimecron at concentrations ranging from 0.0075 to 0.075 ppm following 12 and 18 h exposure. While maximum expression of hsp70 was observed in Nuvan-exposed third-instar larval tissues following 18 h exposure at 0.075 ppm, Dimecron at the same dietary concentration induced a maximum expression of hsp70 following 24 h exposure. Further, concomitant with a significant induction of hsp70, significant inhibition of AchE was observed following chemical exposure and temperature shock. Concurrent with a significant decline in hsp70 expression in Nuvan-exposed larvae after 48 h at 0.075 ppm, tissue damage was evident. Dimecron-exposed larvae exhibited a plateau in hsp70 induction even after 48 h exposure and moderate tissue damage was observed in these larvae. The present study suggests that Nuvan is more cytotoxic than Dimecron in transgenic Drosophila melanogaster.     

Progress in Wheat Resistance to Spot Blotch in Bangladesh

Spot blotch, caused by Cochliobolus sativus, is considered one of the most destructive diseases of wheat (Triticum aestivum) in the warm areas of South Asia. Over the past 20 years, wheat breeding efforts in the region have improved spot blotch resistance in susceptible commercial cultivars. This study assessed resistance and spot blotch‐induced yield losses in newly released wheat cultivars developed in Bangladesh since the release of the landmark wheat variety ‘Kanchan’. Replicated field studies were conducted during the 2003 and 2004 wheat seasons at two sites: a farmer's field and a research station in a warm region of Bangladesh where spot blotch has been a serious problem. Spot blotch affected 60% of the crop and caused yield losses of from 2% to 22%. Disease severity and disease‐induced grain yield reductions were less in wheat genotypes developed since 1983, with a corresponding trend towards higher yield in newly developed varieties. The level of resistance to spot blotch in the new cultivars and advanced breeding lines represents considerable progress in breeding for resistance over the past two decades.