PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

Rapid identification of mutations in GJC2 in primary lymphoedema using whole exome sequencing combined with linkage analysis with delineation of the phenotype.

Background: Primary lymphoedema describes a chronic, frequently progressive, failure of lymphatic drainage. This disorder is frequently genetic in origin, and a multigenerational family in which eight individuals developed postnatal lymphoedema of all four limbs was ascertained from the joint Lymphoedema/Genetic clinic at St George's Hospital. Methods: Linkage analysis was used to determine a locus, and exome sequencing was employed to look for causative variants. Results: Linkage analysis revealed cosegregation of a 16.1 Mb haplotype on chromosome 1q42 that contained 173 known or predicted genes. Whole exome sequencing in a single affected individual was undertaken, and the search for the causative variant was focused to within the linkage interval. This approach revealed two novel non-synonymous single nucleotide substitutions within the chromosome 1 locus, in NVL and GJC2. NVL and GJC2 were sequenced in an additional cohort of individuals with a similar phenotype and non-synonymous variants were found in GJC2 in four additional families. Conclusion: This report demonstrates the power of exome sequencing efficiently applied to a traditional positional cloning pipeline in disease gene discovery, and suggests that the phenotype produced by GJC2 mutations is predominantly one of 4 limb lymphoedema

Amyloodinium ocellatum infestation in the broodstock of silver pompano Trachinotus blochii (Lacepede, 1801) and its therapeutic control

A case of amyloodiniosis caused by infestation of the dinoflagellate Amyloodinium ocellatum in the silver pompano (Trachinotus blochii) maintained for broodstock development is reported. Grossly, erosion of the operculum and excessive secretion of mucus on gills was observed. Microscopic examination of gill filaments showed the presence of trophonts. Histopathologically, gills showed erosion and necrosis of the primary and secondary lamellae. The causative organism A. ocellatum was identified based on the clinical signs as well as gross and microscopic examinations. Among many treatment methods tested, dip treatment with chloroquine phosphate (500 mg per 100 l of water) or with low saline water mixed with Oodinol 1000 were found useful in healthy maintenance of silver pompano broodstock

Survival and growth of juvenile silver pompano Trachinotus blochii (Lacepède, 1801) at different salinities in tropical conditions

The objectives of the present study were to evaluate the tolerance of juvenile silver pompano to different salinity conditions in order to determine the minimum salinity required for survival and also to study the effect of different salinities on survival and growth. Wild caught juveniles of the silver pompano Trachinotus blochii (average initial length: 4.38±0.44 cm, average initial weight: 1.6±0.09 g) were used in the experiments. The experiments were conducted in triplicate with 15 fish per tank. Control groups were maintained at 34±1 ppt. Juvenile silver pompano reared at ambient salinity (34±1ppt) were transferred directly to lower salinities (25, 15, 10, 5, 4, 3 and 1 ppt) and monitored for survival. Results indicated that the minimum salinity required for the survival of juvenile T. blochii is 4 ppt and 100% mortality was observed within 7-8 h in 1 ppt salinity. In another experiment, three salinity reduction protocols were followed and the three treatment groups were exposed to 25, 15 and 5 ppt salinity for a period of 56 days and the growth and survival were monitored. Survival and growth in terms of weight was not significantly different in the treatments from the control group except in the case of 5 ppt, which showed comparatively lower survival and specific growth rate (SGR). The results indicate that the culture of juvenile pompano might be feasible in salinities up to 15 ppt in tropical conditions

Long-term Sustainable Investment for Retirement

We consider whether sustainable investment can deliver performance comparable to conventional investment in investors’ long-term retirement plans. On the capital markets, sustainable investment can be achieved through various instruments and strategies, one of them being investment in mutual funds that subscribe to ESG (environmental, social, and governance) principles. First, we compare the investment performance of ESG funds with matched conventional funds over the period 1994–2020, in Europe and the U.S. We find no significant evidence of differing performance (at 5% level) despite using a number of investment performance metrics. Second, we perform a historical backtest to model a UK personal retirement plan from 2000 till 2020, taking full account of investment management fees and transaction costs. We find that investing in an index-tracker fund overlaid with ESG screening delivers a pension which is 10.4% larger than is achieved if the index-tracker fund is used without screening. This is also 20.2% larger than is achieved by investing in a collection of actively managed funds with a sustainable purpose. We conclude that an ESG-screened long-term passive investment approach for retirement plans is likely to be successful in satisfying the twin objectives of a secure retirement income and of sustainability

Larviculture and seed production of the silver pompano, Trachinotus blochii (Lacepede, 1801) for the first time in India

Larviculture and seed production protocols for the silver pompano Trachinotus blochii, which is one of the promising finfish species for brackishwater and marine aquaculture was developed based on six trials for the first time in India. The newly hatched larvae were stocked at a density of 20 larvae l-1 in 2 t FRP tanks with 1.5 t of seawater. Green water technique was employed during larviculture upto the weaning period. Enriched S-type rotifers were fed at a density of 10-12 nos. ml-1 until 3 day post hatch (dph) and the enriched L-type rotifers were given at a density of 6-8 nos. ml-1 from 7 dph and thereafter with enriched Artemia at a density of 3-5 nos. ml-1. Weaning started from 15 dph and by 20-25 dph metamorphosis was completed. The survival on completion of metamorphosis ranged from 10-15% and the specific growth rate in terms of length (mm) was 8% per day. The larval morphology and growth pattern are also described

Climate change affecting oil palm agronomy, and oil palm cultivation increasing climate change, require amelioration

Palm oil is used in various valued commodities and is a large global industry worth over US$ 50 billion annually. Oil palms (OP) are grown commercially in Indonesia and Malaysia and other countries within Latin America and Africa. The large-scale land-use change has high ecological, economic, and social impacts. Tropical countries in particular are affected negatively by climate change (CC) which also has a detrimental impact on OP agronomy, whereas the cultivation of OP increases CC. Amelioration of both is required. The reduced ability to grow OP will reduce CC, which may allow more cultivation tending to increase CC, in a decreasing cycle. OP could be increasingly grown in more suitable regions occurring under CC. Enhancing the soil fauna may compensate for the effect of CC on OP agriculture to some extent. The effect of OP cultivation on CC may be reduced by employing reduced emissions from deforestation and forest degradation plans, for example, by avoiding illegal fire land clearing. Other ameliorating methods are reported herein. More research is required involving good management practices that can offset the increases in CC by OP plantations. Overall, OP-growing countries should support the Paris convention on reducing CC as the most feasible scheme for reducing CC.Portuguese Foundation for Science and Technology (FCT), Grant/Award Number: UID/ BIO/04469/2013, COMPETE 2020 (POCI01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004); European Regional Development Fund through Norte2020—Programa Operacional Regional do Norteinfo:eu-repo/semantics/publishedVersio

Broodstock development through regulation of photoperiod and controlled breeding of silver pompano, Trachinotus blochii (Lacepede, 1801) in India

The silver pompano, Trachinotus blochii is recognised as a promising species for mariculture. In India, broodstock development, controlled breeding and seed production of silver pompano was achieved for the first time at Mandapam Regional Centre of Central Marine Fisheries Research Institute. Sub-adult fishes collected from the wild were grown in circular sea cages of 6 m diameter and 3.5 m depth. Twelve fishes were selected from a sea cage and acclimatized to laboratory conditions. Among these, four fishes (1 female and 3 males) were pre-conditioned to sexual maturity in a 10 t FRP tank with photoperiod control facility (2000 lux; 14 L: 10 D). In about 2 months, the gonads reached right stage for spawning. The brooders were administered human chorionic gonadotropin (hCG) intramuscularly, at a dosage of 350 IU kg body weight-1. A total of 5 experiments were conducted and successful spawnings were obtained resulting in the production of fertilized eggs. The time taken for spawning ranged from 30-36 h. The total number of eggs spawned ranged from 0.08 to 0.184 million. The fertilization percentage varied from 75 to 95. Freshly spawned eggs measured above 900 μ. The success obtained in all the consecutive five experiments indicated that predictable spawnings of pompano could be achieved by employing the techniques developed