Nucleotide sequence of the cybB gene encoding cytochrome b561 in Escherichia coli K12

Summary The complete nucleotide sequence of the Escherichia coli cybB gene for diheme cytochrome b ₅₆₁ and its flanking region was determined. The cybB gene comprises 525 nucleotides and encodes a 175 amino acid polypeptide with a molecular weight of 20160. From its deduced amino acid sequence, cytochrome b ₅₆₁ is predicted to be very hydrophobic (polarity 33.7%) and to have three membrane spanning regions. Histidines, canonical ligand residues for protohemes, are localized in these regions, and the heme pockets are thought to be in the cytoplasmic membrane. No significant homology of the primary structure of cytochrome b ₅₆₁ with those of other bacterial b-type cytochromes was observed.     

A simple method for calculation of free metal ion concentrations in the presence of a chelating agent and multiple metal ions by successive approximation

Calculation of free metal ion concentrations in the presence of a chelating agent (ligand) and multiple metal ions is complicated. In this paper we describe a simple method for calculation of free ion concentrations from given total ion concentrations. The outline of this method is as follows: i) Using an arbitrarily chosen provisional value of free ligand concentration (p-Lf), calculate a total ligand concentration (Lt). ii) Divide the p-Lf by the ratio, the calculated Lt (c-Lt)/the specified Lt (s-Lt). Take the resulting value as the next p-Lf and repeat the calculation until c-Lt is close enough to s-Lt. At this point, p-Lf is supposed to be set to a good approximation of true free ligand concentration. iii) Finally, calculate free metal concentrations from the above approximation.     

Respiration-Dependent Proton and Sodium Pumps in a Psychrophilic Bacterium, Vibrio sp. Strain ABE-1

Respiration-dependent proton and sodium flows in a psychrophilicbacterium, Vibrio sp. strain ABE-1, were examined. At alkalinepH, this bacterium grew without being affected by a proton conductor,carbonylcyanide m-chlorophenylhydrazone (CCCP). O₂-pulse intoanaerobic cell suspensions prepared with Na^$-free buffers inducedtransient alkalization in the presence of CCCP and acidificationat pH 8.5 and 6.5, respectively. However, using cells preparedwith Na^$-containing buffer, the transient pH changes of thecell suspension could be simultanously detected at both pHs.Several inhibitory experiments suggested that the acidificationand alkalization should be attributed to a respiration-dependentprimary H^$ pump and Na^$ pump, respectively, and that the latterwas similar to that first reported in a marine bacterium, Vibrioalginolyticus. This Na^$ pump may have supported the CCCP-resistantgrowth at alkaline pH. The H^$ and Na^$ pumps operated very actively at low temperatures,such as 5?C, and should markedly help sustain bacterial growthat low temperatures. (Received May 30, 1987; Accepted November 13, 1987)     

Responses in muscle sympathetic activity to acute hypoxia in humans

Responses in muscle sympathetic activity (MSA) to acute hypoxia were studied in 13 healthy male subjects under hypobaric hypoxic conditions at a simulated altitude of 4,000, 5,000, and 6,000 m. Efferent postganglionic MSA was recorded directly with a tungsten microelectrode inserted percutaneously into the tibial nerve. Heart rate (HR) and respiratory rate (RR) were counted respectively from the R wave of an electrocardiogram and from the respiratory tracing recorded by the strain-gauge method. The average values of the MSA burst rate and total activity of MSA (burst rate x mean burst amplitude) at 4,000, 5,000, and 6,000 m were 36.4 +/- 2.6, 39.1 +/- 3.1, and 40.2 +/- 4.2 (SE) bursts/min and 616 +/- 138, 794 +/- 190, and 764 +/- 227 arbitrary units, respectively. These values were significantly higher than the values of 27.1 +/- 2.9 bursts/min and 446 +/- 28 at sea level. HR increased significantly at altitudes, but RR did not show significant change. Under severe hypoxic conditions beyond 5,000 m, there were large interindividual differences in the MSA responsiveness to hypoxia. The results indicate that MSA is activated under hypoxia by stimulating the chemoreceptors. However, the central controlling mechanisms that would be affected by hypoxia may also influence the MSA responsiveness under severe hypoxia.     

Cloning, Nucleotide Sequences and Differential Expression of the nifH and nifH-Like (frxC) Genes from the Filamentous Nitrogen-Fixing Cyanobacterium Plectonema boryanum

The frxC gene, found in liverwort chloroplast DNA, encodes aprotein of unknown function. The deduced amino acid sequenceof the protein shows significant homology to that of ni-trogenaseFe-protein encoded by the nifH gene. We have cloned the frxCand nifH genes from the nitrogen-fixing cyanobacterium Plectonemaboryanum, using frxC- and nifH-specific probes, and have determinedtheir nucleotide sequences. The amino acid sequence deducedfrom the frxC gene of P. boryanum exhibits 83% homology to thatof the protein encoded by the/rxCgene from liverwort, whereasit exhibits only 34% homology to that encoded by the nifH genefrom the same organism, namely, P. boryanum. Northern blot analysisshowed that the frxC gene was transcribed more actively undernitrogenase-repressed conditions than under nitrogenase-inducedconditions, suggesting that the FrxC protein has a functiondistinct from nitrogen fixation. These results, together withthe phylogenetic relationship between the nifH and frxC genes,indicate that the frxC and nifH genes are derived from a commonancestral gene but have evolved independently to encode proteinswith different functions. (Received April 27, 1991; Accepted August 12, 1991)     

Analysis of bacterial populations in a grassland soil according to rates of development on solid media

Abstract The process of colony formation by bacteria from grassland soil sampled in April, July and September was simulated by a colony-forming curve (CFC). The CFC was a super-imposition of several component curves (cCFC) given theoretically by the first order reaction (FOR) model [3,6]. The pattern of FOR model curves was not influenced by the time of sampling and four cCFCs were always recognized during an incubation period of 160 h. It was considered that the CFC describes an inherent property of the bacterial population of the field. Bacterial isolates were obtained from colonies produced in each of four cCFCs on agar plates. Isolates corresponding to one cCFC were classified as one group. The bacterial isolates were characterized by morphological and physiological tests and subsequently clustered. Few oligotrophic bacteria were obtained among bacteria which produced visible colonies within 63 h of incubation time. On the other hand, approx. 50% of bacteria which produced v colonies after 63 h were oligotrophic bacteria. The time required for the appearance of the first colony, t _r of the FOR model, was very similar in the isolates belonging to one group. A close linear relationship was observed between t _r value and doubling time of isolates.     

Morphology,physics, chemistry and biology of Lake Rara in West Nepal

A survey of oligotrophic Lake Rara, the biggest lake in Nepal, was carried out from 1982 till 1984. Mean depth is 100 m, and maximum depth is 167 m. The surface area covers 9.8 km², and the lake contains 0.98 km³ volume of water. Transparency was about 16 m, photoquantum yield decreased exponentially with depth below 5 m, and the extinction coefficient was 8.3 × 10⁻². The concentration of Chl.-a was in the range of 0.06–0.46 mg m⁻³, and total nitrogen was 18–30 μg 1⁻¹. The whole water column was well oxygenated. Primary productivity was extremely low. It has more than 30 inflowing brooks and one outlet. The water quality of the brooks changes drastically with their location. The pH, electrical conductivity, and EDTA hardness in the waters from a landslide area were high. In the waters from a rich pine forest they were extremely low. The zooplankton consisted of two species of protozoa, five species of rotifers, two species of Cladocera, and two species of Copepoda. The zooplankton density range was 6200–16200 individuals m⁻³. The minimum was on November 11th, 1983 and the maximum on August 19th, 1983.     

Structural elucidation of a hydrophobic box in bovine alpha-lactalbumin by NMR: nuclear Overhauser effects

The proton nuclear Overhauser effects of bovine alpha-lactalbumin were studied at 200 MHz by irradiation of an upfield ring current shifted methylene at -2.45 ppm (assigned to Ile-95) and two aromatic protons, Tyr-103 (8.36 ppm) and Trp-60 (5.85 ppm). The experimental results were consistent with a putative three-dimensional alpha-lactalbumin model [Warne, P. K., Momany, F. A., Rumball, S. V., Tuttle, R. W., & Scheraga, H. A. (1974) Biochemistry 13, 768-782], which predicted the close proximity of Ile-95, Tyr-103, Trp-60, and Trp-104. Several of the assignments correlated with those previously made from chemically induced dynamic nuclear polarization experiments [Berliner, L. J., & Kaptein, R. (1981) Biochemistry 20, 799-807]. Subtle differences in the structure of this hydrophobic box region in alpha-lactalbumin were found between the Ca(II) and apo forms of the protein. The existence of this "hydrophobic box" in alpha-lactalbumin was strikingly similar to that in lysozyme, as verified in solution.     

IgE heavy chain constant region genes in atopic dermatitis and senile erythroderma patients

By Southern hybridization using a genomic DNA fragment carrying a human IgE heavy chain constant region gene (C ) as a probe, we analyzed the organization of human C genes and their flanking regions in 23 atopic dermatitis and 6 senile erythroderma patients with elevated serum IgE levels, and 6 atopic dermatitis patients with normal IgE levels. On Barn HI, Hind III, and Eco RI digestions, we detected three hybridizable fragments containing three human C genes, C 1, C 2, and C 3, respectively, in all leukocyte DNAs. These fragments were almost identical in size among patients and healthy donors. Pst I digestion generated a genetic polymorphism. We, however, could find no correlation between this polymorphism and the disorders. It was concluded that among the patients and healthy donors, there was no marked difference in the organization of the functional C gene and its flanking region containing a class switch region. Our conclusion cannot rule out the presence of genetic abnormalities of this region in some atopic dermatitis patients which are not resolvable by our method. In the course of this study, we found a novel C -like gene in placenta DNA which differs from the three C genes commonly present in normal human DNA.