Estimation of time of divergence from phylogenetic studies.

Recent studies with comparative data on base sequences of homologous DNA's or amino acid sequences of homologous proteins indicate that simultaneous estimation of phylogenetic structure and time of divergence is often cumbersome and time consuming. On the other hand, when the topology of an evolutionary tree is known, it is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment. The method is illustrated with amino acid sequence data on various globin molecules and cytochrome c. The evolutionary significance of some of the estimates is also discussed.     

Effects of plant extract Centella asiatica (Linn.) on cold restraint stress ulcer in rats.

Extract of C. asiatica (Linn.) inhibited significantly gastric ulceration induced by cold and restraint stress (CRS) in Charles-Foster rats, Antiulcer activity of plant extract was compared with famotidine (H2-antagonist) and sodium valproate (anti-epileptic). Plant extract, formotidine and sodium valproate showed a dose dependent reduction of gastric ulceration. Plant extract increased brain GABA level which was also dose dependent. Pretreatment with bicuculline methiodide (specific GABAA-antagonist) at the dose level of 0.5 mg/kg im, reversed the antiulcerogenic activity of both plant extract and sodium valproate. Bicuculline as such did not induce gastric ulceration in normal rat.     

Collagenolytic activity of a soil actinomycete

A soil actinomycete hydrolyzed collagen extracted from bovine Achilles tendon, calf skin, carp swim-bladder and rat tail tendon. Glucose, mannose, aspartic acid and asparagine increased its collagenolytic activity which was optimum at 28 °C and at pH 7.2 – 7.5. Metallic ions, NaEDTA, cysteine, 4-chloromercuribenzoate, glutathione and sodium azide were inhibitory.     

Statistical Studies on Protein Polymorphism in Natural Populations II. Gene Differentiation between Populations

With the aim of testing the validity of the mutation-drift hypothesis, we examined the pattern of genetic differentiation between populations by using data from Drosophila, fishes, reptiles, and mammals. The observed relationship between genetic identity and correlation of heterozygosities of different populations or species was generally in good agreement with the theoretical expectations from the mutation-drift theory, when the variation in mutation rate among loci was taken into account. In some species of Drosophila, however, the correlation was unduly high. The relationship between the mean and variance of genetic distance was also in good agreement with the theoretical prediction in almost all organisms. We noted that both the distribution of heterozygosity within species and the pattern of genetic differentiation between species can be explained by the same set of genetic parameters in each group of organisms. Alternative hypotheses for explaining these observations are discussed.     

Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies

MOTIVATION: In a typical gene expression profiling study, our prime objective is to identify the genes that are differentially expressed between the samples from two different tissue types. Commonly, standard analysis of variance (ANOVA)/regression is implemented to identify the relative effects of these genes over the two types of samples from their respective arrays of expression levels. But, this technique becomes fundamentally flawed when there are unaccounted sources of variability in these arrays (latent variables attributable to different biological, environmental or other factors relevant in the context). These factors distort the true picture of differential gene expression between the two tissue types and introduce spurious signals of expression heterogeneity. As a result, many genes which are actually differentially expressed are not detected, whereas many others are falsely identified as positives. Moreover, these distortions can be different for different genes. Thus, it is also not possible to get rid of these variations by simple array normalizations. This both-way error can lead to a serious loss in sensitivity and specificity, thereby causing a severe inefficiency in the underlying multiple testing problem. In this work, we attempt to identify the hidden effects of the underlying latent factors in a gene expression profiling study by partial least squares (PLS) and apply ANCOVA technique with the PLS-identified signatures of these hidden effects as covariates, in order to identify the genes that are truly differentially expressed between the two concerned tissue types. RESULTS: We compare the performance of our method SVA-PLS with standard ANOVA and a relatively recent technique of surrogate variable analysis (SVA), on a wide variety of simulation settings (incorporating different effects of the hidden variable, under situations with varying signal intensities and gene groupings). In all settings, our method yields the highest sensitivity while maintaining relatively reasonable values for the specificity, false discovery rate and false non-discovery rate. Application of our method to gene expression profiling for acute megakaryoblastic leukemia shows that our method detects an additional six genes, that are missed by both the standard ANOVA method as well as SVA, but may be relevant to this disease, as can be seen from mining the existing literature.     

Molecular and biochemical characterization of mungbean yellow mosaic India virus resistance in leguminous host <Emphasis Type="Italic">Vigna mungo</Emphasis>

Mungbean yellow mosaic India virus (MYMIV)—the causal agent of the yellow mosaic disease is responsible for severe damage of crops that are of great economic importance. In the current study, we explored the process of MYMIV infection and its natural resistance by analysing the expression of early and late viral genes at different time points in the leaves of resistant and susceptible Vigna mungo plants. Accordingly, we have periodically evaluated several biochemical parameters commonly associated with oxidative status of resistant and susceptible V. mungo plants during MYMIV infection. Our study revealed that accumulation levels of the early as well as late expressed genes of MYMIV were low and high in the resistant and susceptible plants, respectively; whereas membrane stability index (MSI) exhibited an opposite response. Moreover, a decrease in the malondialdehyde levels along with an increase in the activities/levels of different antioxidant enzymes, total phenol and H₂O₂ was noted during the early stages of infection in the resistant plants. Such observations argue in favour of strong defensive capability of the resistant plants in restricting the accumulation of viral RNA and generation of harmful free radicals within the studied tissue. Collectively, it appears that obstruction of viral invasion in plant cell wall, restriction in viral DNA replication, and early onset of antioxidant defense responses altogether might be responsible for MYMIV natural resistance. Such information is helpful in understanding the pathogenesis of MYMIV infection and its resistance in V. mungo and other economically important crops.     

Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations

The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 53 red pandas from two populations in southwestern China. Seventeen polymorphic sites were found, together with a total of 25 haplotypes, indicating a high level of genetic diversity in the red panda. However, no obvious genetic divergence was detected between the Sichuan and Yunnan populations. The consensus phylogenetic tree of the 25 haplotypes was starlike. The pairwise mismatch distribution fitted into a pattern of populations undergoing expansion. Furthermore, Fu's F(S) test of neutrality was significant for the total population (F(S) = -7.573), which also suggests a recent population expansion. Interestingly, the effective population size in the Sichuan population was both larger and more stable than that in the Yunnan population, implying a southward expansion from Sichuan to Yunnan.