Color discrimination in halobacteria: spectroscopic characterization of a second sensory receptor covering the blue-green region of the spectrum

Halobacterium halobium is attracted by green and red light and repelled by blue-green and shorter wavelength light. a photochromic, rhodopsin-like protein in the cell membrane, sensory rhodopsin sR587, has been identified as the receptor for the long-wavelength and near-UV stimuli. Discrepancies between the action spectrum for the repellent effect of blue light and the absorption spectrum of sR587 and its photocycle intermediate S373 strongly suggest the existence of an additional photoreceptor for the blue region of the spectrum. Transient light-induced absorbance changes in intact cells and cell membranes show, in addition to sR587, the presence of a second photoactive pigment with maximal absorption near 480 nm. It undergoes a cyclic photoreaction with a half-time of 150 msec. One intermediate state with maximal absorption near 360 nm has been resolved. The spectral properties of the new pigment are consistent with a function as the postulated photoreceptor for the repellent effect of blue light. The phototactic reactions and both pigments are absent when retinal synthesis is blocked; both can be restored by the addition of retinal. These results confirm and extend similar observations by Takahashi et al. [Takahashi, T., Tomioka, H., Kamo, N. & Kobatake, Y. (1985) FEMS Microbiol. Lett. 28, 161-164]. The archaeobacterium H. halobium thus uses two different mechanisms for color discrimination; it uses two rhodopsin-like receptors with different spectral sensitivities and also the photochromicity of at least one of these receptors to distinguish between three regions covering the visible and near-UV spectrum.

High-calcium intake abolishes hyperoxaluria and reduces urinary crystallization during a 20-fold normal oxalate load in humans

BACKGROUND

The aim of the study was to test whether increasing dietary calcium intake lowers intestinal oxalate absorption and thereby prevents hyperoxaluria and urinary crystallization during a 20-fold normal oxalate load in healthy subjects.

METHODS

Fourteen healthy male volunteers (age 23-44 years, BMI 21.5-27.7 kg/m2) collected 24-h urines while on free-choice diet as well as on two standardized diets. The latter contained 2545 kcal, 2500 ml of mineral water, 102 g of protein, 13.6 g of sodium chloride and 2220 mg of oxalate (approximately 20-fold content of an average diet). Subjects were studied twice while on the standardized diet, once while eating a normal amount of calcium (1211 mg/day, oxalate-rich diet), and once while eating 3858 mg of calcium/day (calcium and oxalate-rich diet).

RESULTS

Compared with the free-choice diet (322+/-36 micromol/d), UOx x V increased to 780+/-72 micromol/d on the oxalate-rich diet (P=0.001) and fell again to 326+/-31 micromol/d on calcium and oxalate-rich diet (P=0.001 vs oxalate-rich diet). Urinary glycolate (a metabolic precursor of Ox) always remained below the upper limit of the normal range and did not change between different diets, indicating that changes in UOX x V reflect respective variations in intestinal absorption of Ox. Uca x V was 4.60+/-0.45 mmol/d on the free-choice diet and 3.20+/-0.32 mmol/d on the oxalate-rich diet (P=0.011 vs free-choice diet); it increased to 7.28+/-0.74 mmol/d on the calcium- and oxalate-rich diet (P=0.001 vs free-choice and oxalate-rich diets). As indicated by the AP (CaOx) index (Tiselius), urinary supersaturation did not vary significantly between the three diets. In freshly voided morning urines (studied in 8/14 subjects) on the oxalate-rich diet, CaOx crystals or crystal aggregates of up to 80 microm diameter were found in 5/8 urines, whereas this never occurred on the free-choice diet and only t once on the calcium- and oxalate-rich diet.

CONCLUSION

. Increasing calcium intake while eating Ox-rich food prevents dietary hyperoxaluria and reduces CaOx crystallization in healthy subjects. This further illustrates that dietary counseling to idiopathic calcium-stone formers should ensure sufficient calcium intake, especially during oxalate-rich meals.

Design of glycolysis

The design of the glycolytic pathway resulting from the continuous refinement of evolution is discussed with regard to three aspects. 1. Functional and structural properties of individual enzymes. The catalytic constants of the glycolytic enzymes are remarkably optimized; the turnover numbers are within one order of magnitude. The same is true for the molarities of catalytic centres in the cytosol, as is noted for yeast. Functional properties of the enzymes are reflected in their tertiary and quaternary structures. 2. Regulatory mechanisms of single enzymes. A classification of the various types of enzymic control mechanisms operating in the glycolytic pathway is given. In addition to the usual Michaelis-Menten saturation kinetics and the various types of inhibition there is control by positive and negative effectors based on oligomeric structures (fast acting, fine control) as well as regulation by chemical interconversion structures (fast acting, fine control) as well as regulation by chemical based on enzymes cascades (slow acting, very effective). 3. Functional and regulatory mechanisms of the whole glycolytic reaction pathway. A prominent feature is the high enzyme:substrate ratio, which guarantees fast response times. However, a quantitative treatment of the overall kinetics is limited by an incomplete knowledge of the enzymes' dynamic and chemical compartmentation as well as some of their control properties. From an analysis of the oscillatory state, certain control points in the glycolytic chain can be located that coincide with major branching points to other metabolic pathways. These points are controlled by fast-acting cooperative enzymes that operate in a flip-flop mechanism together with the respective antagonistic enzymes, preventing futile cycles. The gating enzymes leading to the glycogen store and the citric acid cycle are of the slow-acting but very effective interconvertible type. The combination of all the complex and intricate features of design yields a glycolytic network that enables the cell to respond to its various metabolic needs quickly, effectively and economically.

The structure of the core of the spiral wave in the belousov-zhabotinskii reaction

The quantitative structure of the core of the spiral-shaped traveling wave of chemical activity appearing in a thin excitable layer of the Belousov-Zhabotinskii reaction, in which the oxidation and decarboxylation of malonic acid by bromate ions is catalyzed by ferroin, was analyzed experimentally. Light absorption by ferroin as the reduced reaction catalyst and indicator was measured by means of a video-and computer-based two-dimensional spectrophotometer with 10-micrometer spatial, 2-second temporal, and 256-digital units intensity resolution. The spiral core is a singular site (diameter, 30 micrometers or less) at which intensity modulations due to ferroin-ferriin distributions are at least ten times smaller than in the surrounding area of spiral propagation. Archimedian spirals were fitted to isoconcentration lines.

Targeted disruption of the arylsulfatase B gene results in mice resembling the phenotype of mucopolysaccharidosis VI

Mucopolysaccharidosis VI (MPS VI) is a lysosomal storage disease with autosomal recessive inheritance caused by a deficiency of the enzyme arylsulfatase B (ASB), which is involved in degradation of dermatan sulfate and chondroitin 4-sulfate. A MPS VI mouse model was generated by targeted disruption of the ASB gene. Homozygous mutant animals exhibit ASB enzyme deficiency and elevated urinary secretion of dermatan sulfate. They develop progressive symptoms resembling those of MPS VI in humans. Around 4 weeks of age facial dysmorphia becomes overt, long bones are shortened, and pelvic and costal abnormalities are observed. Major alterations in bone formation with perturbed cartilaginous tissues in newborns and widened, perturbed, and persisting growth plates in adult animals are seen. All major parenchymal organs show storage of glycosaminoglycans preferentially in interstitial cells and macrophages. Affected mice are fertile and mortality is not elevated up to 15 months of age. This mouse model will be a valuable tool for studying pathogenesis of MPS VI and may help to evaluate therapeutical approaches for lysosomal storage diseases.

Phototaxis of Spiral Waves

The drift of spiral waves toward regions of higher light intensity was observed experimentally in the ruthenium-catalyzed Belousov-Zhabotinsky reaction. A light gradient can thus be used to manipulate optical information in new computational systems based on photochemical media. The drift of a gradient that is rotationally invariant in space is three to four times as fast as that of a translationally invariant gradient. Simulations based on the use of a cellular automaton, which is made isotropic by a semirandom distribution of cells, are in agreement with the experimental results.

Chaotic dynamics in yeast glycolysis under periodic substrate input flux

The numerical analysis for a glycolytic model containing the enzymes phosphofructokinase and pyruvate kinase reveals different types of entrainment, as well as chaotic response under sinusoidal substrate input. Entrainment with response periods 1, 2, 3, 5 and 7-times the input flux period and aperiodic behaviour is verified by measurements of NADH fluorescence in extracts of Saccharomyces cerevisiae in the theoretically predicted range. The stroboscopic transfer function obtained from the aperiodic signal admits period 3, implying chaos according to the Li-Yorke theorem.

Behavioral assessment of aging in male Fischer 344 and brown Norway rat strains and their F1 hybrid

Male Fischer-344 (F344) and Brown Norway (BN) rats 7-, 13-, and 24-month-old and their F344 x BN hybrid (F1) 7-, 13-, 24- and 31-month-old were tested in a behavioral battery (15-min and 24-h locomotor activity, inclined screen, rod suspension, rotorod, shock-motivated learning in a straight runway and 14-unit T maze). Necropsy was performed 3 days later and the results rated for pathology (i.e., severity of lesions observed). Age-related performance declines were observed in all behavioral tests except 15-min locomotor activity. Strain effects were observed in 15-min (BN more active than F344 and F1) and 24-h locomotor activity test (F344 more active than BN and F1 strains); rotorod performance (F344 fell more than BN and F1); and in all measures [errors (E), runtime (RT)], shock frequency (SF), and duration (SD)] in the 14-unit T maze (F344 worse than BN, BN worse than F1). T maze performance of 31-month-old F1 rats was deficient in RT, SD, and SF but E performance was equivalent to that of 7-month-old F1 rats. In a second experiment, only 7- and 31-month-old F1 rats were tested in the 14-unit T maze and the results obtained in Experiment 1 were replicated. Gross necropsy revealed age and strain effects in the number of lesions observed and the mean ratings of pathology. The 24-month-old F344 rats exhibited the greatest number of lesions and had the highest ratings (generally observed as chronic nephrosis and enlarged spleens characteristic of mononuclear cell leukemia). BN rats exhibited a high incidence of hydronephrosis at all age levels. While experiencing less obvious pathology, F1 rats experienced a significant number of lesions in the 31-month-old group. Pathology ratings correlated with behavioral performance but only for a few tests (e.g., SD and RT in 14 unit T maze in 24-month-old F344). Thus, behavioral performance declined with age and the battery of tests differentiated between the strains tested (in general, F344 worse than BN; BN worse than F1). The correlation of pathology ratings at gross necropsy with behavior did not appear to be systematic, suggesting that morbidity was not responsible for the age-related performance declines. However, more extensive evaluation of the relationship of age-related changes in health status to behavior with larger samples of rats is suggested.

Low bone mass in idiopathic renal stone formers: magnitude and significance

To assess bone mineral density (BMD) in idiopathic calcium nephrolithiasis, dual-energy x-ray absorptiometry was performed at lumbar spine, upper femur (femoral neck, Ward's triangle, and total area), distal tibial diaphysis, and distal tibial epiphysis in 110 male idiopathic calcium stone formers (ICSF); 49 with and 61 without hypercalciuria on free-choice diet). Results were compared with those obtained in 234 healthy male controls, using (1) noncorrected BMD, (2) BMD corrected for age, height, and BMI, and (3) a skeletal score based on a tercile distribution of BMD values at following four sites: lumbar spine, Ward's triangle, tibial diaphysis, and tibial epiphysis. After correction, BMD--and therefore also skeletal score--tended to be lower in the stone formers than in controls at five of the six measurement sites, that is, lumbar spine, upper femur, Ward's triangle, tibial diaphysis, and tibial epiphysis, limit of significance being reached for the last two sites without difference between hypercalciuric (HCSF) and normocalciuric stone formers (NCSF). Estimated current daily calcium intake was significantly lower in patients (616 +/- 499 mg/24 h, mean +/- SEM) than in controls (773 +/- 532, p = 0.02). Of 17 patients who in the past had received a low-calcium diet for at least 1 year, 10 had a low skeletal score (4-6) whereas only 1 had a high score (10-12; p = 0.037). Of the 12 stone formers in the study with skeletal score 4 (i.e., the lowest), 8 had experienced in the past one or more fractures of any kind versus only 19 of the remaining 77 patients with skeletal score 5-12 (p = 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)

Mitochondrial adenosine triphosphatase from yeast, Saccharomyces cerevisiae. Purification, subunit structure and kinetics

1. A procedure for the purification of ATPase extracted by chloroform from baker's yeast (Saccharomyces cerevisiae) is reported. The yield based on submitochondrial particles was 55% and the purification was 100-fold. The isolated complex was homogenous as assessed by gel filtration, ion-exchange chromatography, sedimentation in sucrose gradient and in the analytical ultracentrifuge. The molecular weight determined by gel filtration was 400000 +/- 20000. Ultracentrifugation yielded s020,w = 12.50 +/- 0.13 S and the laser light scattering study gave a diffusion coeficient of D20w - 2.92 X 10(-7) cm2 s-1. The amino acid composition as well as absorption, fluorescence, and circular dichroism spectra, from which the helicity of 39% was evaluated, are given. 2. On polyacrylamide gel electrophoresis in the presence of sodium dodecylsulfate, six components with molecular weights of 58500(alpha), 55000 (beta), 42000, 34000 (gamma), 10000(delta), and 8600 (epsilon) were observed with a stoichiometry of 3:3:1:1:1:1. The amino acid composition is given for alpha + beta and gamma as well as delta and epsilon components. 3. The maximum specific activity of the enzyme was 200 U/mg under the optimum conditions. The enzyme was inactivated by incubation at 0 degrees C and strongly inhibited by the antibiotic Dio-9 but not by oligomycin and N, N'-dicyclohexyl-carbodiimide. The effects of kinetic parameters and anions on the enzyme are reported. Two active sites for Mg-ATP with Km values of 0.045mM and 0.37mM and a single activie site for Mg-ITP with Km = 0.179mM were found. A study of the temperature dependence of the maximum activity revealed a straight line in the Arrhenius plots with an activation energy of 11.0 kcal/mol (= 46 kH/mol).

Biochemical and photochemical properties of the photophobic receptors from Halobacterium halobium and Natronobacterium pharaonis

The phototaxis of Halobacterium halobium is initiated by two photoreceptors, the sensory rhodopsins sR-I and sR-II. An sR-II-like pigment has also been described in Natronobacterium pharaonis. In this work it was shown that N. pharaonis cells are repelled by light with a wavelength of 500 nm. A further comparison of membrane preparations from H. halobium (mutant D1) containing only sR-II and from N. pharaonis [strain SP1(28)] with a chromophoric protein (psR-II) resembling sR-II revealed substantial similarities. The biochemical and photochemical properties of the pigments are quite similar, with psR-II being more stable to external conditions such as pH and ionic strength of the buffer. Both pigments are bleached by low concentrations of hydroxylamine and can be reconstituted by the addition of all-trans-retinal. The absorption spectrum of psR-II is quite similar to sR-II including the shoulder on the short-wavelength side. After light excitation sR-II and psR-II undergo photocycles with at least three intermediates. The earliest intermediate has an absorption maximum above 520 nm and decays to a species which has a characteristic absorption (approximately 380 nm) of a deprotonated Schiff base. The final step is the regeneration of the original ground state via a red-shifted intermediate absorbing around 540 nm. From this cumulative evidence it can be concluded that, not only sR-II, but also the pigment from N. pharaonis is a photophobic photoreceptor.

Inhibition of calcium oxalate monohydrate crystal aggregation by urine proteins

Normal urine inhibits both the growth and the aggregation of calcium oxalate monohydrate (COM) crystals but the molecules that inhibit aggregation are not well defined. We have developed a spectrophotometric assay method to measure the aggregation of COM crystals in vitro under conditions that avoid simultaneous crystal growth. At pH 7.2 and 90 mM NaCl, Tamm-Horsfall glycoprotein (THP) and nephrocalcin (NC), a major urinary inhibitor of COM crystal growth, inhibit COM crystal aggregation at concentrations as low as 2 X 10(-9) and 1 X 10(-8) M, respectively. When increasing NaCl to 270 mM or lowering pH to 5.7, inhibition by both glycoproteins, but more markedly by THP, is decreased. Urinary NC from calcium oxalate renal stone formers (SF NC) and NC isolated from calcium oxalate renal stones (stone NC) both inhibit COM crystal aggregation 10-fold less than NC from normal urine. Citrate is ineffective even at millimolar concentrations. Thus THP and NC are two major inhibitors of COM crystal aggregation in normal urine; SF NC and stone NC are defective aggregation inhibitors.

Transitions between oscillatory modes in a glycolytic model system

A glycolytic model system consisting of the enzymes phosphofructokinase (EC 2.7.1.11) and pyruvate kinase (EC 2.7.1.40) is analyzed when subject to periodic substrate addition. The calculations are performed by using detailed rate laws that have been derived for the enzymes of Escherichia coli. Due to linear relationships between the metabolite concentrations, the numerical solutions can be displayed inside a trapezium, so that the concentrations of four different metabolites are indicated along the trapezium edges. The analysis reveals a rich variety of time patterns, corresponding to different periodic, quasiperiodic, and chaotic attractors. These patterns undergo complex hysteresis loops when bifurcation parameters are slowly changed-for example, by modulating the input amplitude. By using this technique up to four attractors coexisting in phase space are found. The time patterns corresponding to coexisting attractors can be switched into one another by triggering the system with short substrate pulses. Furthermore, conditions exist at which the triggering is autonomous-i.e., self-sustained (intermittent) switchings occur. The time between these switchings can be set externally by the value of the input amplitude. For conditions in which the periods of the oscillations are in the order of minutes, the self-sustained switching-which modulates these oscillations-can be in the order of hours.

Spatial patterns from oscillating microtubules

Microtubules are fibers of the cytoskeleton involved in the generation of cell shape and motility. They can be highly dynamic and are capable of temporal oscillations in their state of assembly. Solutions of tubulin (the subunit protein of microtubules) and guanosine triphosphate (GTP, the cofactor required for microtubule assembly and oscillations) can generate various dissipative structures. They include traveling waves of microtubule assembly and disassembly as well as polygonal networks. The results imply that cytoskeletal proteins can form dynamic spatial structures by themselves, even in the absence of cellular organizing centers. Thus the microtubule system could serve as a simple model for studying pattern formation by biomolecules in vitro.

Preventive treatment of nephrolithiasis with alkali citrate—a critical review

Using the keywords "urolithiasis and citrate treatment", "nephrolithaisis and citrate treatment", "kidney stones and citrate treatment", a Medline search revealed 635 articles published between 1 January 1966 and 1 December 2004. For the present analysis, only studies meeting all of the following criteria were included: (1) publications in English or German, (2) studies on preventive alkali citrate treatment in patients with calcium oxalate, uric acid and infection stone disease, (3) clinical studies including at least ten subjects, and (4) treatment phases of at least 1 week duration. A total of 43 studies met the inclusion criteria and were further subclassified according to intermediate or ultimate endpoints as well as to study design. With stone recurrence as the ultimate endpoint, 21 uncontrolled studies in almost 1,000 patients demonstrated a reduction in stone forming rate by 47-100%. In four randomized controlled trials including 227 patients, 53.5% on alkali citrate vs 35% on placebo remained stone-free after at least 1 year of treatment (P<0.0005). Similar values (66% vs 27.5% for alkali citrate vs placebo, P<0.0005) were obtained in 104 patients from two randomized trials with dissolution/clearance of residual stones as endpoint. Unfortunately, up to 48% of alkali citrate treated patients left the studies prematurely, primarily due to adverse effects such as eructation, bloating, gaseousness or frank diarrhea.

Metabolic evaluation of patients with recurrent idiopathic calcium nephrolithiasis

BACKGROUND

Metabolic evaluation in recurrent idiopathic calcium renal stone-formers (RCSF) was analysed with respect to the following questions: (1) do three 24-h urines provide more diagnostic accuracy in the metabolic evaluation of RCSF than 1 or 2 urines?; (2) does time after stone event influence the diagnostic yield?; (3) is urine composition at weekends different from that at mid-week?; (4) what are the prevalences of the most important risk factors (RF) of idiopathic calcium nephrolithiasis, i.e. low volume (LV), hypercalciuria (HC), hyperoxaluria (HO), hyperuricosuria (HU), hypocitraturia (Hypo-Cit), and hypomagnesiuria (Hypo-Mg)?; and (5) do male RCSF differ from females with respect to urinary RFs?

METHODS

Seventy-five RCSF (59 men, 16 women) collected three 24-h urines (U1-3) while on free-choice diet. To account for possible variations in lifestyle and diet, U1 and U3 had to be collected midweek and U2 at a weekend.

RESULTS

When considering all three urines together (U1 + U2 + U3), the number of RF abnormalities/patient was 2.8 +/- 0.1, higher than numbers of any combination of two urines or of any single urine (P = 0.0001 for all comparisons). The number of RF abnormalities also rose with time after stone event, from 0.8 +/- 0.1 (range 0-4) in U1 to 1.1 +/- 0.1 (range 0-4) in U3 (P = 0.011 vs U1). Whereas all other RF did not change between collections, urine volume was lower in U2 (1793 +/- 90 ml) than in U1 (2071 +/- 97 ml, P = 0.0001 vs U2) and U3 (1946 +/- 97 ml, P = 0.046 vs U2). At least 1 abnormality was found in 85.3% of all RCSF, and multiple abnormalities occurred in 47%. The most frequent RF was HC (39%), followed by HO and LV (32% each), Hypo-Cit (29%), HU (23%) and Hypo-Mg (19%). Males more often had Hypo-Cit (P < 0.001) and Hypo-Mg (P < 0.01) than females, whereas HO was more frequent in female RCSF (P < 0.025 vs males).

CONCLUSIONS

Diagnostic accuracy of metabolic evaluation in RCSF increases both with the number of urines collected and the time passing after a stone event. Urines collected at weekends differ from those of the week only by their lower volumes. Abnormalities of RF for calcium nephrolithiasis can be detected in 85.3% of RCSF, and HC is the most common RF both in male and female RCSF.

Metachromatic leukodystrophy: molecular genetics and an animal model

Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by the deficiency of arylsulphatase A (ASA; EC 3.1.6.8). Deficiency of this enzyme causes intralysosomal storage of the sphingolipid cerebroside sulphate. This lipid is abundant in myelin and it may thus not be surprising that storage mainly affects oligodendrocytes. Patients suffer from a progressive demyelination causing various neurological symptoms. The disease is fatal and treatment is not available. The human ASA gene has been cloned and more than 40 mutations have been analysed that cause metachromatic leukodystrophy. Few of these alleles are frequent among patients, whereas most mutant alleles have only been found in single families. Since MLD has only been described in humans and no naturally occurring animal model has been described, ASA-deficient mice have been generated by homologous recombination. The ASA knockout mice are unable to degrade sulphatide and store the lipid intralysosomally. The pattern of lipid storage in neuronal and non-neuronal tissues resembles that described for patients. In the nervous system, lipid storage is found in oligodendrocytes, astrocytes and some neurons. Animals display an astrogliosis and a decreased average axonal diameter. Purkinje cells and Bergmann glia of the cerebellum are morphologically aberrant. Demyelination is seen in the acoustic ganglion and occurs between the ages of 6 and 12 months. The animals are deaf at this age and display various neuromotor abnormalities. However, compared to humans the mice have a surprisingly mild phenotype, since they have a normal life span and do not develop widespread demyelination. ASA-deficient mice have been transplanted with bone marrow, which was transduced with a retroviral vector expressing arylsulphatase A. The majority of transplanted animals display sustained expression of arylsulphatase A from the retroviral construct up to 5 months after transplantation. However, preliminary data suggest that this therapeutic approach does not reduce storage material.

Critical size and curvature of wave formation in an excitable chemical medium

The critical radius for the outward propagation of waves in an excitable solution of the Belousov-Zhabotinskii reaction was experimentally analyzed and found to be approximately 20 mum, being in a range predicted by theory. Thus, the wave initiation depends on the critical radius in an all-or-none fashion. For waves having high positive curvature of wave fronts, a linear relationship between the curvature and their normal velocity was established, allowing computation of a diffusion coefficient of 1.9 x 10(-5) cm(2)/s for the autocatalytic species, which agrees well with results previously obtained for negatively curved wave fronts. The analysis of the dispersion of wave velocity yielded the decrease of wave velocity for small initiation periods as predicted theoretically.

Two-dimensional spectrophotometry and pseudo-color representation of chemical reaction patterns

The formation of spatio-temporal patterns in layers of chemical and biochemical media is observed and quantified by a two-dimensional spectrophotometer based on a computerized video equipment with high spatial, temporal, and intensity resolution. Images are shown, to some extent, in pseudo-colors. The use of pseudo-colors and three-dimensional perspective representations enhances the perception of the information contained in an image and the inherent order of the spatial structures.