NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

NrichD ( ext-link-type=''uri'' xlink:href=''http://proline.biochem.iisc.ernet.in/NRICHD/'' xlink:type=''simple''>http://proline.biochem.iisc.ernet.in/NRICHD/)< /named-content> is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural `intermediately related sequences' is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been `enriched' with these artificial intermediary sequences. NrichD database currently contains 3 611 010 artificial sequences that have been generated between 27 882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

Evaluation of anti-obesity activities of ethanolic extract of Terminalia paniculata bark on high fat diet-induced obese rats

Background: The prevalence and severity of obesity and associated co-morbidities are rapidly increasing across the world. Natural products-based drug intervention has been proposed as one of the crucial strategies for management of obesity ailments. This study was designed to investigate the anti-obesity activities of ethanolic extract of Terminalia paniculata bark (TPEE) on high fat diet-induced obese rats. Methods: LC-MS/MS analysis was done for ethanolic extract of T. paniculata bark. Male Sprague-Dawley (SD) rats were randomly divided into six groups of six each, normal diet fed (NC), high fat diet-fed (HFD), HFD+ orlistat (standard drug control) administered, and remaining three groups were fed with HFD + TPEE in different doses (100,150 and 200 mg/kg b. wt). For induction of obesity rats were initially fed with HFD for 9 weeks, then, (TPEE) was supplemented along with HFD for 42 days. Changes in body weight, body composition, blood glucose, insulin, tissue and serum lipid profiles, atherogenic index, liver markers, and expression of adipogenesis-related genes such as leptin, adiponectin, FAS, PPARgamma, AMPK-1alpha and SREBP-1c, were studied in experimental rats. Also, histopathological examination of adipose tissue was carried out. Results: Supplementation of TPEE reduced significantly (P < 0.05) body weight, total fat, fat percentage, atherogenic index, blood glucose, insulin, lipid profiles and liver markers in HFD-fed groups, in a dose-dependent manner. The expression of adipogenesis-related genes such as Leptin, FAS, PPARgamma, and SREBP-1c were down regulated while Adiponectin and AMPK-1alpha were up regulated in TPEE + HFD-fed rats. Furthermore, histopathological examination of adipose tissue revealed the alleviating effect of TPEE which is evident by reduced size of adipocytes. Conclusions: Together, the biochemical, histological and molecular studies unambiguously demonstrate the potential anti adipogenic and anti obesity activities of TPEE promoting it as a formidable candidate to develop anti obesity drug.

Validity of Resting Energy Expenditure Predictive Equations before and after an Energy-Restricted Diet Intervention in Obese Women

11 p.

Life History, Diet, Abundance and Distribution, and Length-Frequencies of Selected Invertebrates in Florida Bay, Everglades National Park, Florida

This report presents information on the life history, diet, abundance and distribution, and length-frequency distributions of five invertebrates in Florida Bay, Everglades National Park. Collections were made with an otter trawl in basins on a bi-monthly basis. Non-parametric statistics were used to test spatial and temporal differences in the abundance of invertebrates when numbers were appropriate (i. e., $25). Invertebrate species are presented in four sections. The sections on Life History, and Diet were derived from the literature. The section on Abundance and Distribution consists of data from otter-trawl collections. In addition, comparisons with other studies are included here following our results. The section on Length-frequency Distributions consists of length measurements from all collections, except 1984-1985 when no measurements were taken. Length-frequency distributions were used, when possible, to estimate life stage captured, spawning times, recruitment into Florida Bay for those species which spawn outside the Bay, and growth. Additional material from the literature was added when appropriate. (PDF contains 39 pages)

An annotated bibliography of diet studies of fish of the southeast United States and Gray’s Reef National Marine Sanctuary

One goal of Gray’s Reef National Marine Sanctuary (NMS) is to protect the unique community found within the Sanctuary’s boundaries. An understanding of the ecological interactions, including trophic structure, among these organisms is necessary to realize this goal. Therefore, diet information for 184 fish species was summarized from 113 published studies. Among the fish included are 84 fish species currently known to reside in Gray’s Reef NMS. The locations of these studies ranged from the Atlantic Ocean off the coast of the northeast United States to northern Brazil, the Gulf of Mexico, and the Caribbean. All of the species described in this bibliography occur in the southeast United States and are, therefore, current or potential residents of Gray’s Reef National Marine Sanctuary. Each entry includes the objectives, brief methods, and conclusions of the article. The bibliography is also indexed by species. (PDF contains 64 pages.)

Growth responses and yield of heterotis (Heterotis niloticus) on artificial diet

The growth responses and yield of Heterotis niloticus on artificial diets of varying protein levels were studied in a bid to assess the implication of feeding Heterotis in intensive fish production venture for a rearing period of 84 days. One hundred and twenty juvenile H.niloticus were fed for 12 weeks on 28%, 31%, 34% and 37% dietary crude protein levels. The fish were reared in 4 concrete tanks stocked at the rate of 10 fish per M super(2) 100,00/hectare). Consequently, the weight gain, food conversion ratio, serum protein and albumin-globulin ratio were determined to assess the growth and state of health of the fish. The yield was appraised through economic considerations of cost of production of fish and diets (feed). The varying crude protein levels significantly influenced mean weight gain, percentage weight gain and food conversion ratio however, the 37% crude protein in diet produced the best growth. The serum protein was highest in fish raised on 31% crude protein diet while the highest value was recorded for albumin-globulin ratio on diet containing 34% crude protein. The yield from treatments 1, 2, 3, and 4 were 114.38 of/84 days 571.9kg/g hect);146.79g/84 days 733.95kg/hect), respectively. However, treatment 3 recorded the highest value for profit index

Duckweed (Lemna paucicostata Heglem ex Engle) in the diet of tilapia (Sarotherodon galilaeus)

The growth of Sarotherodon galilaeus fingerlings fed with test diet of 33% crude protein and containing 10% duckweed was compared with standard KLRI/40/6 feed of 40% crude protein. From an initial mean weight of 1.18gm and 1.17gm, the fingerlings in the test diet and control respectively grew to a final mean weight of 2.17gm and 1.98gm after seven weeks. With mean growth rate of 2.02% and 1.65% of their body weight per day respectively for the test diet and the control, it was obvious that the test diet was better and had a higher food conversion than the control. The duckweed must have therefore, supplied some essential amino acids to the test diet thereby making it a higher quality feed

Possible inclusion of fish waste (scales and fins) in the diet of fishes in aquaculture

The scales and fins of some freshwater fish species (Sarotherodon galilaeus, Oreochromis niloticus, Tilapia zillii, Barbus callipterus, Hemichromis fasciatus) from Kainji Lake, Nigeria were analyzed for their organic and inorganic matter. The aim of such study is to determine the usefulness of these waste parts of the fish in fish feed preparation. In all instances, the inorganic matter was found to be quite high in the fish exoskeleton, and calcium formed the highest element in the scales and the fins. These waste materials are therefore, considered as possible replacement for mineral sources in fish feed and probably the feed for other livestock

Comparison of extruded and non-extruded soy meals in the diet of genetically improved mudfish Heterobranchus longifilis juveniles

Raw soybeans were subjected to three different processing methods viz Parboiling, Toasting and Extrusion with an Intra Pro Extruder. The processed soybean meals were thereafter incorporated at equal levels into the diets of genetically improved mudfish Heterobranchus longifilis juveniles. The fish were fed the experimental diets in triplicate at 5% of their body weight for eight weeks. The growth performance and food utilization indices, namely Mean Weight Gain (MWG), Food Conversion Ratio (FCR), Specific Growth Rate (SGR%) and Protein Efficient Ratio (PER), were monitored bi-weekly. The results show that fish fed the control fishmeal diets were highest in growth performance, which was significantly different (P>0.05) from others. Among the fish fed the test diets, those fed toasted soybean had higher MWG, SGR, FCR and PER than juveniles fed the parboiled soybean diet. The juveniles fed the extruded soybean diet recorded the least growth performance. The implication of these results in diet formulation is discussed

Selectivity of three aquatic weeds as diet for Nile tilapia (Oreochromis niloticus)

A total of sixty juvenile Oreochromis niloticus (Nile tilapia) were fed three species of aquatic weed, namely Azolla filiculoides (water fern), Elodea sp. and Pistia stratiotes (water lettuce) to determine which of the weeds will be selectively consumed, and preferred of all. A control group of twenty Nile tilapia was fed compounded feed. The selectivity of the weeds was observed based on their utilization as food source, and Azolla filiculoides was found to be highly utilized, followed by Elodea sp. and the roots of Pistia stratiotes. The growth response of the fish to the diets was found to be highest for fish fed compounded feed followed by Azolla filiculoides and Elodea sp., while Pistia stratiotes produced a negative growth trend. It is therefore postulated that Azolla filiculoides and Pista sp. are good feedstuffs for O. niloticus especially when used together with other feedstuffs

Studies on the nutritional value of cassava (Manihot utillisima) peels as energy source in the diet of Oreochromis niloticus fry fed in indoor glass aquaria

This study, though, has as its core objective cost reduction in aquaculture nutrition was equally designed to investigate the value of the peels of cassava (Manihot utillisima) as energy source in the diet of Oreochromis niloticus fry. Three levels of cassava peels diet and a control (100% yellow maize in the carbohydrate mixture) was prepared and tested on O. niloticus fry for ten (10) weeks. The fry with mean weight of 0.32g were grouped fifteen (15) in each of the glass aquaria measuring 60x30x30cm with a maximum capacity of 52 litres of water. The fry were fed twice daily at 10% biomass. Weekly, the fry were weighed to determine the weight increment or otherwise and the quality of feed adjusted accordingly. Water quality parameters like temperature, pH and dissolved oxygen (D.0) were monitored and found to be at desirable level. DT 3 (97 % cassava peels and 3% yellow maize) in the carbohydrate mixture gave the best growth performance. The fry fed, this diet gained mean weight of 1.18g for the period of the experiment. However, the poorest performance in terms of growth was from fry fed the control diet (100%yellow maize in the carbohydrate mixture) fry fed this diet gained mean weight of 0.80 for the duration of the experiment. Analysis of the various growth indices like SGR, PER, FCR and NPU shows that DT3 was the overall best diet with an SGR value of2.40 and FCR of 43.83. However, DT 1 (70% cassava peels and 30% yellow maize) gave the poorest SGR of 1.61 and FCR of 67.58. The difference in weight gain among the fry fed the three levels of cassava peels diet and the control was not statically significant (P>0.05)

Effect of fish meal in formulated diet on the growth of Heterotis niloticus in semi-intensive pond culture system

The aim of the investigation is to know the percentage of fish meal required to support the best growth of Heterotis niloticus in a semi intensive pond culture system. To achieve this, feed was formulated with equal percentages of blood meal, and corn meal and varying levels of fish meal. The experiment was in four treatments. Results showed that the mean weight gained was directly proportional to the quantity of fish meal made available to the fish fence 31.58g, 33.79g, 45.15g and 51.24g were recorded for treatments I, II, III and IV respectively. Result from this study when compared with previous works, shows that size of the water body to a greater extent affects the growth. The availability of fish meal in the feed made it more acceptable to the fish and hence a commensurate conversion in to flesh. The analysis of variance showed that there is significant difference in the growth performance in the treatments