Estimating synonymous and nonsynonymous substitution rates

Partitioning the total substitution rate into synnonymous and nonsynonymous components is a key aspect of many analyses in molecular evolution. Numerous methods exist for estimating these rates. However, until recently none of the estimation procedures were based on a sound statistical footing. In this paper, the evolutionary model of Muse and Gaut (1994) is used as the basis for two sets of parameters quantifying silent and replacement substitution rates. The parameters are shown to be equal when the four nucleotides are equally frequent and unequal otherwise. Maximum-likelihood estimation of these parameters is described, and the performance of these estimates is compared to that of existing estimation procedures. It is shown that the estimates of Nei and Gojobori (1986) are not unbiased for either set of parameters, although they provide very good estimates for one set as long as sequence divergence is not too high. However, some disturbing properties are found for the Nei and Gojobori estimates. In particular, it is shown that the expected value of the Nei and Gojobori estimate of silent substitution rate is a function of both the silent and replacement substitution rates. The maximum-likelihood estimates have no such problems.      

Uranyl nitrate induced corpuscular derangement: an early indication of induced acute renal failure.

Erythrocyte structure was studied in rat after uranyl nitrate (UN:5 mg/kg) intoxication. The study of pathogenic progression of UN induced renal failure (ARF) was confined to the early initiation phase (2 hr), late initiation phase (8 hr) and the maintenance phase (24 hr). Erythrocyte structure has been found to be greatly influenced. The UN induced hemolytic syndrome/hypoxia was accompanied by a marked anisocytosis and poikilocytosis during different phases of ARF, which is characteristic of UN poisoning. Subsequent alterations in erythrocyte structure followed by UN administration or during the pathogenic progression of ARF has clinical and diagnostic importance as the alterations were much distinct prior to the clinical manifestation of ARF even at light microscopic level.     

Assessment of direct shoot organogenesis and genetic fidelity in Solanum viarum Dunal—a commercially important medicinal plant

Solanum viarum Dunal is an important medicinal plant with a high quantity of steroidal alkaloids used for the synthesis of contraceptives, corticosteroids, and sex hormones. It is also used by Indian tribal people for the treatment of leprosy, toothache, and diabetes. Therefore, to meet the existing needs for this plant, it is necessary to develop an efficient regeneration system useful for rapid and large-scale clonal propagation with ensured genetic fidelity. An efficient and improved regeneration protocol for prickly and prickleless genotypes of S. viarum has been developed using three explants, leaf, petiole, and internodes, under the influence of two plant growth regulators, thidiazuron (TDZ) and 6-benzyladenine (BA). Effects of genotype, explant type, and concentrations of TDZ and BA were studied. A higher percentage of shoot organogenesis (78.25% ± 2.53) and shoot number per explant (6.79 ± 1.04) were achieved in the leaf segments of prickly genotype cultured on modified Murashige and Skoog (MS) medium supplemented with TDZ (1.50 mg L⁻¹). Furthermore, basal leaf segments showed 100% regeneration from the prickly genotype. A significantly higher content of total phenolics was quantified in prickleless (3.66 μg mg⁻¹) than prickly genotypes (2.73 μg mg⁻¹). The monomorphic banding pattern of random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) analysis confirmed the genetic fidelity of the regenerated plants. Additionally, flow cytometric analysis of regenerants showed no variation in the ploidy levels when compared to the mother (control) plants. These results clearly depicted the efficiency of developed protocol that can be utilized for generating genetically stable population of S. viarum.

     

Bioengineering of the digestive tract: approaching the clinic

The field of regenerative medicine is developing technologies that, in the near future, will offer alternative approaches to either cure diseases affecting the gastrointestinal tract or slow their progression by leveraging the intrinsic ability of our tissues and organs to repair after damage. This article will succinctly illustrate the three technologies that are closer to clinical translation—namely, human intestinal organoids, sphincter bioengineering and decellularization, whereby the cellular compartment of a given segment of the digestive tract is removed to obtain a scaffold consisting of the extracellular matrix. The latter will be used as a template for the regeneration of a functional organ, whereby the newly generated cellular compartment will be obtained from the patient's own cells. Although clinical application of this technology is approaching, product development challenges are being tackled to warrant safety and efficacy.