Generalized linear models with random effects; salamander mating revisited.

In recent years much effort has been devoted to extending regression methodology to non-Gaussian data, where responses are not independent. These methods for dependent responses are suitable for data from longitudinal studies or nested designs. However, use of these methods for crossed designs seems to have serious limitations due to the intensive computations involved because of the intractable nature of the joint distribution. In this paper, we cast the problem in a Bayesian framework and use a Monte Carlo method, the Gibbs sampler, to avoid current computational limitations. The flexibility of this approach is illustrated by analyzing the interesting salamander mating data reported by McCullagh and Nelder (1989, Generalized Linear Models, 2nd edition, London: Chapman and Hall).     

HIV-1 Vpr Modulates Macrophage Metabolic Pathways: A SILAC-Based Quantitative Analysis

Human immunodeficiency virus type 1 encoded viral protein Vpr is essential for infection of macrophages by HIV-1. Furthermore, these macrophages are resistant to cell death and are viral reservoir. However, the impact of Vpr on the macrophage proteome is yet to be comprehended. The goal of the present study was to use a stable-isotope labeling by amino acids in cell culture (SILAC) coupled with mass spectrometry-based proteomics approach to characterize the Vpr response in macrophages. Cultured human monocytic cells, U937, were differentiated into macrophages and transduced with adenovirus construct harboring the Vpr gene. More than 600 proteins were quantified in SILAC coupled with LC-MS/MS approach, among which 136 were significantly altered upon Vpr overexpression in macrophages. Quantified proteins were selected and clustered by biological functions, pathway and network analysis using Ingenuity computational pathway analysis. The proteomic data illustrating increase in abundance of enzymes in the glycolytic pathway (pentose phosphate and pyruvate metabolism) was further validated by western blot analysis. In addition, the proteomic data demonstrate down regulation of some key mitochondrial enzymes such as glutamate dehydrogenase 2 (GLUD2), adenylate kinase 2 (AK2) and transketolase (TKT). Based on these observations we postulate that HIV-1 hijacks the macrophage glucose metabolism pathway via the Vpr-hypoxia inducible factor 1 alpha (HIF-1 alpha) axis to induce expression of hexokinase (HK), glucose-6-phosphate dehyrogenase (G6PD) and pyruvate kinase muscle type 2 (PKM2) that facilitates viral replication and biogenesis, and long-term survival of macrophages. Furthermore, dysregulation of mitochondrial glutamate metabolism in macrophages can contribute to neurodegeneration via neuroexcitotoxic mechanisms in the context of NeuroAIDS.     

Ultrastructure of the pineal gland of the tropical bat Rousettus leschenaulti

The ultrastructure of the pineal organ was studied in the tropical megachiropteran Rousettus leschenaulti. The pineal lies deep beneath the hemispheres adjacent to the third ventricle and is traversed by the habenular commissure anteriorly. Its parenchyma consists of a uniform population of light and occasional dark pinealocytes which appear to differ only in the degree of cytoplasmic staining. Pinealocytes are characterized by well developed Golgi bodies associated with numerous small vesicles, many mitochondria and polyribosomes, and frequent subsurface cisternae. Lipid droplets and elements of smooth endoplasmic reticulum are scant. Cisternae of granular endoplasmic reticulum are occasionally dilated. A distinct feature is the abundance of clear vesicles in the pinealocyte pericapillary terminals, which also frequently contain granular vesicles and a very large vacuole. The pineal is further characterized by the presence of a small number of glial cells and myelinated nerve fibers. A broad perivascular space investing numerous capillaries contains glial-cell and pinealocyte processes, collagen fibrils and abundant unmyelinated nerve fibers. Tortuous extensions of the perivascular space enter the pineal parenchyma where they come in close proximity to branched intercellular channels or canaliculi characterized by specialized junctions and microvilli. Differences between the pineal of the non-hibernating megachiropteran Rousettus and that of the hibernating microchiropteran bats, and structural similarities to the pineal of tropical rodents are discussed.     

Salt Tolerance ofEchinochloa crusgalli

Salt tolerance ofEchinochloa crusgalli was studied using gravel culture with root medium electrical conductivity between 3 to 25 dS m^-1. Salinity depressed germination and shoot yield. A 50 % reduction in shoot yield occurred at 15.9 dS m^-1. The plant was able to maintain its tissue water content and K concentration in the tissue water while Na, Ca and Cl increased and Mg decreased with increasing root zone salinity.     

The effect of age on the response of the detrusor to intracellular mechanical stimulus: DNA replication and the cell actin matrix.

Benign prostatic hypertrophy and posterior urethral valves present at both extremes of the age spectrum. Both disease processes can obstruct the urinary stream and ultimately have pathophysiological effects on detrusor structure and function. The mechanisms regulating the structural reorganization of the detrusor to a mechanical outflow obstruction are not known. In an attempt to identify maturational differences in myocyte ultrastructure and consequent effects these might have in modifying the response of the detrusor to mechanical stimulus, we studied differences in dynamic nuclear-cytoskeletal interactions in detrusor tissue in an animal model. Using a drug which specifically severs actin, cytochalasin D (CD), as an intracellular mechanical stimulus, we measured changes in nuclear area and the rate of DNA synthesis in detrusor myocytes from young (2-3 week) and old (8-12 mon) guinea pigs. We found that there were age specific differences to intracellular mechanical stimuli in detrusor muscle. Nuclei of myocytes from young animals showed elastic recoil on severing the cell actin matrix and the tissue from young animals increased replicative DNA synthesis with an intracellular stimulus. In contrast, nuclear shape changes in myocytes from old animals suggested less elasticity, and there was no increase in DNA synthesis with disruption of the cell actin matrix. Anti-alpha-smooth muscle actin antibody and rhodamine phalloidin staining of actin in cytochalasin D treated primary explants of detrusor myocytes showed dose dependent disruption of the actin component of the cytoskeleton. These results suggest that there are fundamental modifications in detrusor myocyte ultrastructure with age. These maturational changes might result in differences in the pathophysiological and structural reorganization of the detrusor in response to outflow obstruction in infancy and adulthood. Furthermore, they suggest that 1) a tensile equilibrium exists between the myocyte nucleus and cytoskeleton; 2) there appears to be a decrease in myocyte nuclear elasticity with ageing; 3) release of nuclear template restrictions increases activity of DNA polymerase alpha in young, but not old, detrusor myocytes; and 4) mechanico-chemical signal transduction in detrusor myocytes may be mediated via the cytoskeleton. In addition, based on previous reports of actin within the nucleus, the results suggest that 1) nuclear actin may have a homeostatic structural role, maintaining the tensile equilibrium between nucleus and cytoskeleton, and 2) integrity of nuclear actin may function to maintain the spatial template restriction on DNA polymerase alpha activity.     

Plant protoplasts and genetic engineering II

Book Review

Plant protoplasts and genetic engineering IIY.P.S. Bajaj (Ed.), (Biotechnology in Agriculture and Forestry, Vol. 9). Berlin: Springer-Verlag, 1989. 510 pages. DM398.00. ISBN 3-540-50789-2     

Ecology of deepwater rice-fields in Bangladesh 4. Nitrogen fixation by blue-green algal communities

1. Aquatic macrophytes formed dense beds in fallow areas during the four and a half months of the flood season in all but one deepwater rice-growing location in Bangladesh; these included several types of life-form, but the fine-leaved species, Myriophyllum sp., Najas indica, Utricularia stellaris were often especially abundant. The same species grew inside deepwater rice fields, but at much lower densities. A similar contrast occurred for the algae, although deepwater rice often developed dense masses of epiphytes on aquatic roots, stems and leaf sheaths, when plants were growing in isolated, well-illuminated situations.
2. Two widespread algae, Aulosira fertilissima and Scytonema mirabile, were equally successful on soil in the period prior to the arrival of floodwaters and floating on the surface of the water during the flood season. Other species common during the flood season differed from those common on soil.
3. Most blue-green algae inside deepwater rice fields were heterocystous; the only species not so, but forming distinct colonies, was Aphanothece stagnina. However only non-heterocystous forms were found at one location in south Bangladesh (Phaltita) and a change from heterocystous to non-heterocystous forms was noted at the main research site (near Sonargaon) during late September in at least one year. The water column at the former was almost entirely anoxic, while the change at the latter occurred at a time when the water sometimes became anoxic during the night. It is suggested that differences in ability to tolerate anoxic periods may be a key factor in determining the success of the algal and vascular plant species in the different micro-habitats within these DWR-growing areas.
4. Although diatoms were quantitatively only a minor component of the algal biomass, they became more frequent later in the season when the water became microaerobic or anoxic for part of the day. Navicula confervacea was overall the most abundant species at the two main research locations.

     

Growth and ionic relations of six triticale cultivars as affected by salinity

Growth and ionic relations were studied in six triticale cultivars of different geographical origins grown in a greenhouse in nutrient solution with or without the addition of 100 mM NaCl. In 21 d old plants of all the six cultivars growth was little affected in the salt treatment, whereas in the subsequent three harvests during vegetative phase (after 31, 38 and 45 d), growth reduction effects of salinity were progressively pronounced. Generally, shoots of all the six cultivars accumulated relatively more K+ as compared to Na+ or Cl-. Differential accumulation of K+, Na+ and Cl- by various cultivars was coupled with variable rates of Na+ and Cl- transport from root to shoot which were — to some extent- related to cultivar differences in growth in saline root media. Chloride content of shoots of the six cultivars was negatively correlated with the relative growth reduction due to salinity at the four harvests.     

Nutritional status and age at secondary sterility in rural Bangladesh

In a prospective study of 2324 women in Matlab, Bangladesh, the occurrence of primary and 2ndary sterility by age groups was examined. The results were related to the nutritional status of the women, as assessed by measurements of height, weight, arm circumference and ponderal index. Approximately 98% of the women who were in the age group 15-19 were found to be fertile. This proportion decreases gradually up to the age group 30-34 years and thereafter declines sharply, reaching only 31% in the age group 45-49. The height data suggest no significant difference in the age pattern of sterility among the 3 groups of women, although there is a slight tendency that women who were less tall reached menopause earlier than the other 2 groups. Variations in weight are more conspicuous than in height. There is the suggestion that thinner women may experience an earlier menopause. Women having an arm circumference less than 21 cm, between 21-22 cm, and 23 cm and above, and currently aged 17 years, have an expected fertile life estimated at 25.0, 25.8, and 26.6 years respectively. The median ages at sterility were 42.8, 44.0, and 44.3 years respectively with a difference of about 1 year between the 1st 2 groups. This suggests that sterility occurs earlier among the thinner women. Since detailed investigation of nutritional status was not possible, it was assessed by anthropometry. There was strong evidence that nutritional status is an important factor in the estimated age at sterility, with thinner women experiencing an earlier menopause. Although it is impossible to measure the onset of sterility, one can obtain a minimum estimate of it from the age-specific distribution of the proportion of women who have not produced a child for 5 years of being at risk.