Household consumption pattern and buying behavior for fish in an area Mymensingh, Bangladesh

The study was conducted on 238 households in Bangladesh Agricultural University campus and its adjoining areas in Mymensingh. The household were divided into four groups based on their per capita income. Monthly expenditure on fish, income elasticity of demand and marginal propensity to consume were calculated. 'Weighted average' method was used to study the level of preference for fish by sex and age groups and frequency of its purchase. The per capita monthly expenditure on fish of overall households was found to be Tk. 178.83. The consumption increased considerably between and among the income groups rising from Tk. 63.95 in the lowest income group to Tk. 249.11 in the highest income group. Based on income elasticity the proportion of income spent on fish was found to be greater than the proportion of increase in income for lower middle and upper middle income groups. However, percent expenditure decreased from 8.15 in lowest to 5.49 in the highest income group. Female members between 20 and 40yrs had the highest preference for fish in general followed by male members of above 40 yrs. Children (0 to 8 yrs), on the other band, had the least preference for fish, Sing and Magur (Catfishes) were the most preferred fish species for each age and sex group. Rui, a carp, was the single most purchased fish while the introduced exotic fishes were the least bought. Freshness was found to be the most important factor followed by the appearance and taste perception that positively affected the fish purchase

Applications of microsatellite markers to genetic management of carps in aquaculture

Carp aquaculture in South Asia suffers severely from a lack of genetic management, which has eroded the genetic quality of both captive and wild populations. Use of molecular markers, especially microsatellites, has revolutionized genetic management of hatchery stocks through its ability to detect kinship between individuals and hence in controlling level of inbreeding and loss of genetic diversity. In the present PhD work, microsatellite markers were applied to breeding programmes for silver carp (Hypophthalmichthys molitrix) and common carp (Cyprinus carpio) to study different genetic management aspects and new markers were generated from rohu (Labeo rohita). A set of newly isolated microsatellite markers from silver carp were characterized and two pentaplex PCR reactions were optimized to enable rapid genotyping of large number of individuals at 10 microsatellite loci. The utility of these markers in parentage, sibship and relatedness analysis were assessed by applying them to groups of fish with known relationship. These markers were used for parentage analysis in a breeding programme designed to estimate heritability of harvest weight and length in silver carp. Full- and half-sib families were created in three sets of partly factorial mating and all the families from each set were reared in communal ponds from very early life stages. With ten microsatellites 96.3% of the offspring could be assigned to a single family. Heritability estimates were found to be 0.65 ± 0.13 for weight and 0.50 ± 0.13 for length. High estimates of h2 suggested that this population should respond rapidly to selection for increased harvest size. Microsatellite markers were also applied to monitor the early stages of a mass selection programme in common carp (Cyprinus carpio). The selection was initiated from a base population synthesized from six different stocks. The selected individuals were divided to create two separate lines. The aims of this study were to monitor whether the stocks were represented in the intended proportions in the F1 selected populations, to investigate the relative contribution of families and its impact on effective population size and to identify any loss of molecular genetic variation. Five highly polymorphic microsatellites were used for parentage analysis of the selected fish to track stock and family contribution. Overall, large perturbations were observed in the relative contributions of two major stocks. Family contribution was also highly variable, causing the Ne to drop to below half the census size. A loss of 6.9%-12.2% of microsatellite alleles was observed but loss of heterozygosity was not very prominent. The replicate lines showed significant differences in allelic distribution after the first generation of selection, but not in genotypic distribution. Finally, 52 microsatellite markers were isolated from a partial genomic library of rohu using a selective hybridization protocol. Characterization of these markers resulted in 36 polymorphic loci, which will be useful in future work on conservation and management of both wild and captive rohu populations

Novel Computationally Intelligent Machine Learning Algorithms for Data Mining and Knowledge Discovery

This thesis addresses three major issues in data mining regarding feature subset selection in large dimensionality domains, plausible reconstruction of incomplete data in cross-sectional applications, and forecasting univariate time series. For the automated selection of an optimal subset of features in real time, we present an improved hybrid algorithm: SAGA. SAGA combines the ability to avoid being trapped in local minima of Simulated Annealing with the very high convergence rate of the crossover operator of Genetic Algorithms, the strong local search ability of greedy algorithms and the high computational efficiency of generalized regression neural networks (GRNN). For imputing missing values and forecasting univariate time series, we propose a homogeneous neural network ensemble. The proposed ensemble consists of a committee of Generalized Regression Neural Networks (GRNNs) trained on different subsets of features generated by SAGA and the predictions of base classifiers are combined by a fusion rule. This approach makes it possible to discover all important interrelations between the values of the target variable and the input features. The proposed ensemble scheme has two innovative features which make it stand out amongst ensemble learning algorithms: (1) the ensemble makeup is optimized automatically by SAGA; and (2) GRNN is used for both base classifiers and the top level combiner classifier. Because of GRNN, the proposed ensemble is a dynamic weighting scheme. This is in contrast to the existing ensemble approaches which belong to the simple voting and static weighting strategy. The basic idea of the dynamic weighting procedure is to give a higher reliability weight to those scenarios that are similar to the new ones. The simulation results demonstrate the validity of the proposed ensemble model

Animal genomics and infectious disease resistance in poultry

Avian pathogens are responsible for major costs to society, both in terms of huge economic losses to the poultry industry and their implications for human health. The health and welfare of millions of birds is under continued threat from many infectious diseases, some of which are increasing in virulence and thus becoming harder to control, such as Marek's disease virus and avian influenza viruses. The current era in animal genomics has seen huge developments in both technologies and resources, which means that researchers have never been in a better position to investigate the genetics of disease resistance and determine the underlying genes/mutations which make birds susceptible or resistant to infection. Avian genomics has reached a point where the biological mechanisms of infectious diseases can be investigated and understood in poultry and other avian species. Knowledge of genes conferring disease resistance can be used in selective breeding programmes or to develop vaccines which help to control the effects of these pathogens, which have such a major impact on birds and humans alike

A comparative study on the embryonic development of gynogen, triploid, haploid and normal diploid embryos of stinging catfish, Heteropneustes fossilis

UV irradiation and cold shock were applied on the eggs of stinging catfish, Heteropneustes fossilis, to produce haploid,. gynogen and triploid embryos. A comparative account of the various features· of embryonic development in chromosomally manipulated groups viz. haploid, gynogen and triploid and non-manipulated normal diploid group of H fossilis has been discussed. A slow development and delayed hatching were observed in gynogen and triploid embryos compared to those in normal diploid (control) groups. Mass mortality was observed in all chromosomally manipulated groups particularly during the gastrulation stage. The hatchlings of the gynogen, triploid and normal diploid were similar in overall appearance

The Involvement of Caspases in the Process of Nuclear Removal During Lens Fiber Cell Differentiation

The terminal differentiation of lens fiber cells involves elimination of their organelles, which must occur while still maintaining their functionality throughout a lifetime. Removal of non-nuclear organelles is accomplished through induction of autophagy following the spatiotemporal suppression of the PI3K/Akt signaling axis. However, blocking this pathway is not alone sufficient to induce removal of fiber cell nuclei. While the final steps in fiber cell nuclear elimination are highlighted by the appearance of TUNEL-positive nuclei, which are associated with activation of the lens-specific DNaseIIβ, there are many steps in the process that precede the appearance of double stranded DNA breaks. We showed that this carefully regulated process, including the early changes in nuclear morphology resulting in nuclear condensation, cleavage of lamin B, and labeling by pH2AX, is reminiscent of the apoptotic process associated with caspase activation. Multiple caspases are known to be expressed and activated during lens cell differentiation. In this study, we investigated the link between two caspase downstream targets associated with apoptosis, ICAD, whose cleavage by caspase-3 leads to activation of CAD, a DNase that can create both single- and double-stranded DNA cleavages, and lamin B, a primary component of the nuclear lamina. We discovered that the specific inhibition of caspase-3 activation prevents both lamin B and DNA cleavage. Inhibiting caspase-3 did not prevent nuclear condensation or removal of the nuclear membrane. In contrast, a pan-caspase inhibitor effectively suppressed condensation of fiber cell nuclei during differentiation. These studies provide evidence that caspases play an important role in the process of removing fiber cell nuclei during lens differentiation

Examining pi3K-Signaling-Dependent Regulation of Lens Organelle Free Zone Formation via Immunolocalization and Immunoblotting in Chick Embryos

The elimination of lens organelles during development, required for mature lens function, is an autophagy-dependent mechanism induced through suppression of PI3K signaling. Here, we present a protocol for investigating the signaling pathways responsible for induction of the formation of this lens organelle free zone. We describe steps for preparation of lens organ culture and use of signaling pathway inhibitors. We then detail procedures for analyzing their impact using both confocal microscopy imaging of immunolabeled lens cryosections and immunoblot approaches. For complete details on the use and execution of this protocol, please refer to Gheyas et al. (2022)

Detection and prediction of insider threats to cyber security: a systematic literature review and meta-analysis

Cyber security is vital to the success of today’s digital economy. The major security threats are coming from within, as opposed to outside forces. Insider threat detection and prediction are important mitigation techniques. This study addresses the following research questions: 1) what are the research trends in insider threat detection and prediction nowadays? 2) What are the challenges associated with insider threat detection and prediction? 3) What are the best-to-date insider threat detection and prediction algorithms? We conduct a systematic review of 37 articles published in peer-reviewed journals, conference proceedings and edited books for the period of 1950–2015 to address the first two questions. Our survey suggests that game theoretic approach (GTA) is a popular source of insider threat data; the insiders’ online activities are the most widely used features in insider threat detection and prediction; most of the papers use single point estimates of threat likelihood; and graph algorithms are the most widely used tools for detecting and predicting insider threats. The key challenges facing the insider threat detection and prediction system include unbounded patterns, uneven time lags between activities, data nonstationarity, individuality, collusion attacks, high false alarm rates, class imbalance problem, undetected insider attacks, uncertainty, and the large number of free parameters in the model. To identify the best-to-date insider threat detection and prediction algorithms, our meta-analysis study excludes theoretical papers proposing conceptual algorithms from the 37 selected papers resulting in the selection of 13 papers. We rank the insider threat detection and prediction algorithms presented in the 13 selected papers based on the theoretical merits and the transparency of information. To determine the significance of rank sums, we perform “the Friedman two-way analysis of variance by ranks” test and “multiple comparisons between groups or conditions” tests

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance

Whole genome sequences of 234 indigenous African chickens from Ethiopia

Indigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes