Construction of Partially Balanced Incomplete Block Designs with Nested Rows and Columns

A number of methods of construction of partially balanced incomplete block designs with nested rows and columns are developed and new balanced incomplete block designs with nested rows and columns are obtained as a by-product.     

Microbial metabolism of chlorosalicylates: effect of prolonged subcultivation on constructed strains

The hybrid strain Pseudomonas sp. WR4016 was subcultivated with increasing concentrations of 5-chlorosalicylate (510 mM) as sole carbon source over a period of 9 months. At intervals of approximately 3 months derivative strains WR4017, WR4018 and WR4019 were isolated which exhibited higher growth rates and increased substrate tolerance. Comparative analysis of the turnover rates of the key enzymes in chlorosalicylate degradation showed that the adaptation process did not result from structural modifications of these proteins. Instead, balanced over-production of the salicylate hydroxylase and catechol 1,2-dioxygenase prevented the accumulation of toxic chlorocatechols and accounted for the reduction of the doubling times with 4- or 5-chlorosalicylate. A comparative analysis of a genetically engineered chlorosalicylate degrader PL300-1 showed similar regulatory patterns as the most advanced isolate WR4019 from the adaptation series.     

Requirement of trypsin inhibitor for measurement of 3-hydroxy-3-methylglutaryl coenzyme A reductase in intestinal mucosa of rat

A method was developed for the determination of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in the microsomal fraction of crypt cells and villi of rat intestinal mucosa. Addition of trypsin inhibitor to homogenizing and incubation media at a proper concentration appeared inevitable for measurement of the activity of the villi fraction. The reductase in crypt cells was also slightly enhanced by the addition of the inhibitor. Using this technique, the enzyme activity in villi was found to be as active as the crypt cell fraction. Since other types of protease inhibitors were not necessarily effective, it was suggested that specific enzyme(s) inactivates the mucosal reductase in the course of measurement.     

Differences between genetic and physical centromere distances in the case of two genes for male sterility in barley

Summary Linkage studies with thirty translocations (one of the two chromosomes involved being number 4) in relation to msg24 (chromosome 4) and thirteen translocations (one of the two chromosomes involved being number 6) in relation to msg6 (chromosome 6) show without exception close linkage for all combinations tested. The results indicate that both genes are located genetically in or close to the centromere regions of their chromosomes.Cytological analysis of two BTT stocks (balanced tertiary trisomics) ascertained the respective chromosome arms (both msg24 and msg6 on the short arms) and revealed marked differences between genetic and physical centromere distances. The reason is obviously the high content of centromeric heterochromatin occupying both the chromosome arms involved.     

Regulation of the utilization of 4-hydroxybenzoate and vanillate in batch and continuous cultures of Pseudomonas acidovorans

In Pseudomonas acidovorans, the pathways of 4-hydroxybenzoate and vanillate metabolism converge on the early intermediate, protocatechuate, which undergoes meta-cleavage. The methoxyl group of vanillate is almost completely oxidized, as shown by an experiment with (¹⁴C-methoxyl) vanillate. In batch cultures, 4-hydroxybenzoate and vanillate are simultaneously oxidized. Simultaneous oxidation was explained above all by the fact that both substrates mutually repress the ability of the cells to utilize the partner substrate.If P. acidovorans is growing in a turbidostat on one of the two substrates and is suddenly exposed to an equimolar mixture of both substrates, the respiration rates for the two substrates reciprocate, the for the substrate utilized first passing through a transient minimum, that for the added substrate passing through a transient maximum. Finally, a balance appears to be established, the for 4-hydroxybenzoate being slightly above that for vanillate. Transient phenomena also occur if a chemostat culture with both substrates is suddenly operated as a turbidostat culture or if cells not adapted to either substrate are suddenly exposed to a mixture of both substrates in the turbidostat.If a chemostat culture of P. acidovorans, growing at the expense of an equimolar mixture of 4-hydroxybenzoate and vanillate, is operated under conditions of increasing oxygen deficiency, the utilization ratio of the two substrates increases in favour of 4-hydroxybenzoate. However, if the culture is operated under conditions of increasing nitrogen deficiency, the utilization ratio increases in favour of vanillate.Abbreviations 4HB 4-hydroxybenzoate - VA vanillate - OD optical density     

Plasmodium falciparum: physiological interactions with the human sickle cell.

The malaria parasite, Plasmodium falciparum, enhances the rate and extent of sickling of infected hemoglobin S heterozygous human erythrocytes. Upon sickling of the host cell, the parasite is killed. Parasite-free lysates of highly infected cells were analyzed to determine the mechanism by which sickling is enhanced. The intraerythrocytic pH of the infected cell was estimated to be 0.4 units below that of the uninfected cell, a difference which could result in a 20-fold increase in the extent of sickling under physiological conditions. Sickle-cell hemoglobin (HbS) heterozygous (AS) erythrocytes had decreased intracellular potassium after 24 hr of culture under conditions which cause sickling and parasite death. When infected AS cells were cultured in high-potassium medium under these conditions the parasites were protected. The medium did not prevent sickling but did maintain normal intracellular potassium levels. It is suggested that sequestration of trophozoite-infected AS cells in the venules leads to the sickling of the host cell, loss of erythrocytic potassium, and parasite death. The resulting attenuation of parasite multiplication would favor the survival of the HbS heterozygote and maintain the HbS gene at high frequencies in areas endemic for falciparum malaria.     

Negative regulation of the hepatic fibrogenic response by suppressor of cytokine signaling 1

Suppressor of cytokine signaling 1 (SOCS1) is an indispensable regulator of IFNγ signaling and has been implicated in the regulation of liver fibrosis. However, it is not known whether SOCS1 mediates its anti-fibrotic functions in the liver directly, or via modulating IFNγ, which has been implicated in attenuating hepatic fibrosis. Additionally, it is possible that SOCS1 controls liver fibrosis by regulating hepatic stellate cells (HSC), a key player in fibrogenic response. While the activation pathways of HSCs have been well characterized, the regulatory mechanisms are not yet clear. The goals of this study were to dissociate IFNγ-dependent and SOCS1-mediated regulation of hepatic fibrogenic response, and to elucidate the regulatory functions of SOCS1 in HSC activation. Liver fibrosis was induced in Socs1^−/−Ifng^−/− mice with dimethylnitrosamine or carbon tetrachloride. Ifng^−/− and C57BL/6 mice served as controls. Following fibrogenic treatments, Socs1^−/−Ifng^−/− mice showed elevated serum ALT levels and increased liver fibrosis compared to Ifng^−/− mice. The latter group showed higher ALT levels and fibrosis than C57BL/6 controls. The livers of SOCS1-deficient mice showed bridging fibrosis, which was associated with increased accumulation of myofibroblasts and abundant collagen deposition. SOCS1-deficient livers showed increased expression of genes coding for smooth muscle actin, collagen, and enzymes involved in remodeling the extracellular matrix, namely matrix metalloproteinases and tissue inhibitor of metalloproteinases. Primary HSCs from SOCS1-deficient mice showed increased proliferation in response to growth factors such as HGF, EGF and PDGF, and the fibrotic livers of SOCS1-deficient mice showed increased expression of the Pdgfb gene. Taken together, these data indicate that SOCS1 controls liver fibrosis independently of IFNγ and that part of this regulation may occur via regulating HSC proliferation and limiting growth factor availability.     

Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing

Disease associated chromosomal rearrangements often have break points located within disease causing genes or in their vicinity. The purpose of this study is to characterize a balanced reciprocal translocation in a girl with intellectual disability and seizures by positional cloning and whole genome sequencing. The translocation was identification by G- banding and confirmed by WCP FISH. Fine mapping using BAC clones and whole genome sequencing using Oxford nanopore long read sequencing technology for a 1.46 X coverage of the genome was done. The positional cloning showed split signals with BAC RP11-943 J20. Long read sequencing analysis of chimeric reads carrying parts of chromosomes X and 20 helped to identify the breakpoints to be in intron 2 of ARHGEF9 gene on Xp11.1 and on 20p13 between RASSF2 and SLC23A2 genes. This is the first report of translocation which successfully delineated to single base resolution using Nanopore sequencing. The genotype-phenotype correlation is discussed.     

De novo balanced translocation (2;10)(q24;q22) associated with mental retardation

We report a case of a reciprocal translocation between the long arms of the 2 and 10 chromosomes observed in a 14-year-old male with mild mental impairment, compulsive and obsessive behavior. The apparently balanced translocation was characterized by fluorescence in situ hybridization and the karyotype was 46, XY, t(2;10)(q24;q22). The way by balanced chromosomal translocations can lead to a disease phenotype are reviewed and discussed.