Role of RNA polymerase IV in plant small RNA metabolism.

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

Impact of small indigenous species of fish (SIS) on livelihood of local fishing community in two upazilas of Mymensingh

The fisher folk used to catch small indigenous species of fish (SIS) from rivers, canals, wetlands and floodplains at little or no cost for their livelihood. Surplus fish was sold at the local market to generate some little capital for the households. The livelihood and consumption of SIS in fishing community of two upazilas viz. Trisal and Ishwarganj under Mymensingh district were studied for 3 months in 2004. Most of the fisher folk of the study areas belong to resource-poor section of the society living below the poverty level. Majority of them had no cultivable land. As professional fishers they face many problems during lean fishing period from January to April due to little or non-availability of fish. Majority of the fisher households consumed SIS three to four days a week. The fisher households of Trisal upazila consumed more small fish than those of Ishwargonj upazila. More than 50% respondents consumed <20 g SIS/day and 20% consumed >40 g SIS/day in Trisal upazila. On the other hand, in Ishwargonj upzila, most of the fisher households (66%) were found to consume <20 g SIS/day. SIS was mostly available from July-December in rivers, wetlands (beels), and canals, and income from fishing was reported to be good. The dominant SIS was Puntius spp., Mystus spp., Anabas testudineus, catfishes, mola, and small prawns. Non-indigenous species like tilapia was also dominant in Trisal upzila where aquaculture practices were well established.

Probing small molecule binding to amyloid fibrils.

Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.

A review of experimental trawling from small and medium sized mechanized vessels off Kanikada

The most suitable otter trawl for small boats was found to be a 10.9 to 15m 2-seam trawl with 100cm x 50cm x 35kg horizontally curved otter boards together with long single sweep line. For operation from medium sized trawls, 18.26m 2-seam 18.3m 4-seam and 29.26m long wing trawl were found suitable. An 18.3m 4-seam trawl was netting a considerable quantity of off-bottom fishes. Shrimps predominated in the catches of the 29.26m trawl. Productive grounds for Cynagris species, Psenus species and Decapterus species within 50 to 100m depth ranges off Kakinada were available for profitable exploitation.

On the resources of demersal fishes for bottom trawling in inshore waters off Kakinada by small mechanised boats

An attempt is made to assess the available resources of demersal fishes for bottom trawling off Kakinada, in inshore waters. From the experimental fishing operation during 1964-66, the average catch per hour was 52.79 kg for 9.13 m (30') OAL mechanised boat. The catch composition was dominated by prawns and sciaenids forming 45% of the total catch. The average catch per trawling hour was more during the quarter April - June. An assessment on productive depth range has indicated that catch rate is increasing with increase in the depth of fishing.

Effect of oxidation of dietary fish lipids on the quality of proteins in diet

The paper reports results of a study on the effect of oxidised fish oil in the diet on the quality of dietary fish proteins. With increased oxidation of oil, digestibility and utilization of the protein registered a decrease. Oxidation of fish oil beyond a stage was found to affect the intake of diet itself and rats lost weight rapidly.

Identification and characterization of insect-specific proteins by genome data analysis

Background: Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its

Quality assessment of traditional and solar tunnel dried SIS (Small Indigenous Fish Species) products

Studies were conducted to assessment the quality of traditional and solar tunnel dried SIS products. The moisture content of the solar products ranged from 14.38 to 18.48% with the lowest in batashi and the highest value in tengra. The moisture content of the traditional products was in the range of 23.26 to 26.42%. The range of protein contents on moisture free basis was from 67.57 to 71.90% in solar dried fishes with highest value obtained in dhela and lowest value in batashi. These values were more or less similar to those of traditional dried SIS products which were in the range of 68.02 to 73.54% on dry weight basis. Lipid contents of solar dried SIS varied from 14.10 to 16.26% and on moisture free basis the in the range of 11.73 to 21.98 with highest value found in tengra and lowest in puti. These values were more or less similar to those found for traditional dried products on dry weight basis and ranged from were 12.37 to 22.43%. Maximum reconstitution of solar dried products was obtained at 80°C in all samples and was in the range of 65.26 to 70.51% where the percentage of reconstitution increases with the increase of socking time and reach maximum at the end of up to 60 min. The TVB-N content of solar dried fish is low compared with traditional one ranging from 20.30 to 28.40mg/100g and peroxide value in the range of 12. 54 to 19.20meq./kg oil. The TVB-N of traditionally dried products were in the range of 32.50 to 45.45mg/100g and PO values of the traditionally dried products were in the range of 30.00 to 36.00meq./kg oil. The bacterial load of the solar dried products was in the range of 4.0x10 super(3)/g to 3.6x10 super(5)CFU/g and of the traditionally dried products ranged from 1.45x10 super(5) to 2.52x10 super(6) CFU/g.

Quality assessment of traditional, rotary and solar tunnel dried small indigenous fish species products

Studies on the quality assessments of three traditional, rotary and solar tunnel dried SIS products were conducted. Organoleptic quality of traditional dried SIS products available in the markets was poor compared to those produced in rotary and solar tunnel dryer. Reconstitution of samples were in the range of 54.26% to 75.24%, 69.37% to 83.73% and 55.08% to 80.24% when soaked at 80°C for traditional, rotary and solar tunnel dried products, respectively. The percentage of reconstitution increased with the increase of soaking time and the uptake of water was maximum after 60 min of soaking. The moisture contents of traditional, rotary and solar tunnel dried products were in the range of 26.02% to 27.33%, 16.23% to 22.84% and 13.71% to 19.30%, respectively. The protein contents were in the range of 60.78% to 72.59%, 62.17% to 76.27% and 61.11% to 76.00%, respectively; lipid contents were in the range of 12.26% to 22.60%, 14.00% to 24.71% and 13.92% to 22.39%, respectively and ash contents in the range of 15.11% to 16.59%, 8.32% to 13.51% and 8.71% to 16.45%, respectively on dry matter basis. The TVB-N content of rotary and solar tunnel dried products was low compared to traditional one ranging from 10.64 to 17.52 mg/100g and 14.34 to 15.68 mg/100g, respectively whereas the TVB-N content of traditional samples was in the range of 15.46 to 20.36 mg/100g. The bacterial load of traditional, rotary and solar tunnel dried products were in the range of 1.43x10 super(8) CFU/g to 2.89 x10 super(80 CFU/g, 1.91x10 super(8) CFU/g to 2.84x10 super(8) CFU/g and 1.95x10 super(8) CFU/g to 2.59x10 super(8) CFU/g, respectively. The results of the study indicated that dried fish products from rotary dryer and solar tunnel dryer were found to be of better quality in nutritional and food quality aspects than those of traditional dried products.

Polyculture of carp with small indigenous fish, bata, Labeo bata (Ham.) at different stocking densities

Small indigenous fish species (SIS) play very important role in the diet of the people of Bangladesh. Until recently, the possibilities of culture them in consideration with the Indian major carp yet to be explored. In view of the above, an experiment on the polyculture of carps with SIS, bata (Labeo bata) was carried out to evaluate their production performance in the on-farm condition during 15 March to 15 September 2003. Three different stocking densities of bata with carp species were given. After six months of rearing, the productions obtained were 2,466±98 kg/ha, 2,395 ±88 kg/ha and 2,074±94 kg/ha from treatments-1, 2 and 3, respectively. The highest production was obtained from treatment-1, when compared with treatments-1 and 2. The contribution of bata in terms of production was 10.31% in treatment-1, while it was 13.36% and 14.38% in treatments-2 and 3, respectively.

The morphology of decorated amyloid fibers is controlled by the conformation and position of the displayed protein.

Self-assembled structures capable of mediating electron transfer are an attractive scientific and technological goal. Therefore, systematic variants of SH3-Cytochrome b(562) fusion proteins were designed to make amyloid fibers displaying heme-b(562) electron transfer complexes. TEM and AFM data show that fiber morphology responds systematically to placement of b(562) within the fusion proteins. UV-vis spectroscopy shows that, for the fusion proteins under test, only half the fiber-borne b(562) binds heme with high affinity. Cofactor binding also improves the AFM imaging properties and changes the fiber morphology through changes in cytochrome conformation. Systematic observations and measurements of fiber geometry suggest that longitudinal registry of subfilaments within the fiber, mediated by the interaction and conformation of the displayed proteins and their interaction with surfaces, gives rise to the observed morphologies, including defects and kinks. Of most interest is the role of small molecule modulation of fiber structure and mechanical stability. A minimum complexity model is proposed to capture and explain the fiber morphology in the light of these results. Understanding the complex interplay between these factors will enable a fiber design that supports longitudinal electron transfer.

Effects of pure microcystin-LR on the transcription of immune related genes and heat shock proteins in larval stage of zebrafish (Danio rerio)

Microcystins (MCs) are cyanobacterial toxins in water blooms that have received increasing attention as a public biohazard for human and animal health. Previous studies were mainly focused on the toxic effects on adult fish, rather than juvenile or larvae, and the response of fish immune system were usually neglected. This paper presents the first data of the effects of microcystin-LR (MC-LR) on transcription of several genes essential for early lymphoid development (Rag1, Rag2, Ikaros, GATA1, Lck and TCR alpha) and heat shock proteins (HSP90, HSP70, HSP60, HSP27) in zebrafish larvae. Relative changes of mRNA transcription were analyzed by real time PCR. The transcription of Rag1, Rag2, Ikaros, GATA1, Lck and TCR alpha were up-regulated when following exposure to 800 mu g/L MC-LR, which may indicate that specific lymphocytes differentiation and TCR/lg arrangement are induced to counteract the toxic effects of MC-LR. It was also interesting to note the dramatically increased transcription of HSP90. HSP70, HSP60 and HSP27, which may indicate their important roles as molecular chaperones under oxidative stress. (C) 2009 Elsevier B.V. All rights reserved.

Impacts of a small dam on riverine zooplankton

In order to explore the temporal impacts of a small dam on riverine zooplankton, monthly samples were conducted from November 2005 to June 2006 in a reach of Xiangxi River, China, which is affected by a small hydropower plant. A total of 56 taxa of zooplankton were recorded during the study and rotifers were the most abundant group, accounting for 97% of total taxa, while the others were copepod nauplii and copepod adults. This study indicated that: (1) the small dam in the Xiangxi River study area created distinct physical and ecological conditions relative to free-flowing lotic reaches despite the constrained channel and small size of the dam; (2) the existence of the plant's small dam had a significant effect on the zooplankton community. In long periods of drought or dry seasons the effect of the dam on potamoplankton was more pronounced (e.g., November, February, March, and May). But the downfall or the connectivity of channel appeared to decrease the effect of small hydropower plants on riverine zooplankton (e.g., April). The present observation underscores the need for additional studies that provide more basic data on riverine zooplankton communities and quantify ecological responses to dam construction over longer time spans.

Short and long peptidoglycan recognition proteins (PGRPs) in zebrafish, with findings of multiple PGRP homologs in teleost fish

Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect and mammals. Using a database mining approach and RT-PCR, multiple peptidoglycan recognition protein (PGRP) like genes have been discovered in fish including zebrafish Danio rerio, Japanese pufferfish TakiFugu rubripes and spotted green pufferfish Tetraodon nigroviridis. They share the common features of those PGRPs in arthropod and mammals, by containing a conserved PGRP domain. Based on the predicted structures, the identified zebrafish PGRP homologs resemble short and long PGRP members in arthropod and mammals. The identified PGRP genes in T. nigroviridis and TakiFugu rubripes resemble the long PGRPs, and the short PGRP genes have not been found in T. nigroviridis and TakiFugu rubripes databases. Computer modelling of these molecules revealed the presence of three alpha-helices and five or six beta-strands in all fish PGRPs reported in the present study. The long PGRP in teleost fish have multiple alternatively spliced forms, and some of the identified spliced variants, e.g., tnPGRP-L3 and tnPGRP-L4 (in: Tetraodon nigroviridis), exhibited no characters present in the PGRP homologs domain. The coding regions of zfPGRP6 (zf: zebrafish), zfPGRP2-A, zfPGRP2-B and zfPGRP-L contain five exons and four introns; however, the other PGRP-like genes including zfPGRPSC1a, zfPGRPSC2, tnPGRP-L1-, tnPGRP-L2 and frPGRP-L (fr: Takifugu rubripes) contain four exons and three introns. In zebrafish, long and short PGRP genes identified are located in different chromosomes, and an unknown locus containing another long PGRP-like gene has also been found in zebrafish, demonstrating that multiple PGRP loci may be present in fish. In zebrafish, the constitutive expressions of zfPGRP-L, zfPGRP-6 and zfPGRP-SC during ontogeny from unfertilized eggs to larvae, in different organs of adult, and the inductive expression following stimulation by Flavobacterium columnare, were detected by real-time PCR, but the levels and patterns varied for different PGRP genes, implying that different short and long PGRPs may play different roles in innate immune response. (c) 2007 Elsevier Ltd. All rights reserved.