Comparison of amino acid sequences of eleven different α-amylases

Summary A comparison was made of the amino acid sequences of 11 different -amylases. The 6 animal -amylases tested were found to be highly homologous (about 80 to 90%, depending on the species compared). Amino acid sequence of Bacillus stearothermophilus -amylase was fairly homologous (about 60%) with that of a thermostable -amylase from Bacillus amyloliquefaciens. Homology was least among the thermolabile amylases from Bacillus subtilis, Aspergillus oryzae, plants and animals. Nevertheless, four highly homologous regions were found in the amino acid sequences of all the enzymes, despite their widely different origins. It was inferred that these four homologous regions were likely to be the active and/or substrate-binding sites.     

Do different surrogate methods detect lateral genetic transfer events of different relative ages?

Non-tree-based ("surrogate") methods have been used to identify instances of lateral genetic transfer in microbial genomes but agreement among predictions of different methods can be poor. It has been proposed that this disagreement arises because different surrogate methods are biased towards the detection of certain types of transfer events. This conjecture is supported by a rigorous phylogenetic analysis of 3776 proteins in Escherichia coli K12 MG1655 to map the ages of transfer events relative to one another.     

Independent duplications of α-amylase in different strains of Aspergillus oryzae

Aspergillus oryzae is a filamentous fungus that has arisen through the ancient domestication of Aspergillus flavus for making traditional oriental foods and beverages. In the many centuries A. oryzae has been used for fermenting the starch in rice to simple sugars, it has undergone selection for increased secretion of starch-degrading enzymes. In particular, all A. oryzae strains investigated thus far have two or more copies of a gene encoding α-amylase, whereas A. flavus has only one. Here we investigate the duplications leading to these copies in three A. oryzae strains. We find evidence of at least three separate duplications of α-amylase, an example of parallel evolution in a micro-organism under artificial selection. At least two of these duplications appear to be associated with activity of transposable elements of the Tc1/mariner class. Both involve a 9.1 kb element that terminates in inverted repeats, encodes a putative transposase and another putative protein of unknown function, and contains an unusual arrangement of four short internal imperfect repeats. Although "unusual Mariners" of this size have previously been identified in A. oryzae, Aspergillus fumigatus and Aspergillus nidulans, this is the first evidence we know of that at least some of them are active in modern times and that their activity can contribute to beneficial genetic changes.     

Is the zooplankton of the tropics different？

The zooplankton, defined a the assemblage of animals and animal-like creatures that lives in the water column of small to big waterbodies, has primarily been studied in the temperate zone, so most "received" concepts about it derive from the temperate, not the tropical belt of this planet. In the present days of biodiversity     

Genetic expression of β-mannosidase activity in different tissues of mice

Beta-Mannosidase activity of liver, kidney, and spleen of two inbred strains of mice and their crosses has been assayed with the synthetic aubstrate p-nitrophenyl-beta-d-mannoside. Activity is low in C57BL/Kl mice and high in DBA/2/Kl mice. Hybrid animals have intermediate levels of beta-mannosidase activity. Segregation of enzyme activities occurs in the F-2 and backcross generations, and there are good correlations between acitities in the three tissuses of F-2 and backcross animals. Some evidence points to a single gene difference in crosses between C57BL and DBA with respect to this mannosidase variation. Curves for enzyme activities at different substrate concentrations and pHs obtained with preparations from DBA and C57BL mice show some differences. These are interpreted as a possible strain variation in a structural gene for this enzyme.     

Plasma concentration of α-tocopherol in different free-ranging birds of prey

In this study, we investigated the α-tocopherol plasma concentrations in healthy free-ranging nestlings of the white-tailed sea eagle (Haliaeetus albicilla) (n = 32), osprey (Pandion haliaetus) (n = 39), northern goshawk (Accipiter gentilis) (n = 25), common buzzard (Buteo buteo) (n = 31), and honey buzzard (Pernis apivorus) (n = 18) as well as of free-ranging adults of the white-tailed sea eagle (n = 10), osprey (n = 31), and northern goshawk (n = 45). α-Tocopherol plasma concentrations were determined by reverse-phase high-performance liquid chromatography. α-Tocopherol plasma concentrations in nestlings of osprey, white-tailed sea eagle, and northern goshawk did not differ significantly amongst the species, but the common buzzard and honey buzzard nestlings had significantly lower α-tocopherol plasma concentrations than nestlings of the other species (both P < 0.001). Adult male ospreys and white-tailed sea eagles had significantly higher α-tocopherol concentrations compared to adult females (both P < 0.005). Adult ospreys and northern goshawks had significantly higher α-tocopherol plasma concentrations compared to their nestlings (both P < 0.001). In adult female northern goshawks, plasma concentrations of α-tocopherol increased significantly before egg laying (P < 0.001). These results demonstrate α-tocopherol plasma concentrations in birds of prey to be species specific and influenced by age and reproductive status.     

Are the different hypotheses on the emergence of life as different as they seem?

This paper calls attention to a philosophical presupposition, coined here the continuity thesis which underlies and unites the different, often conflicting, hypotheses in the origin of life field. This presupposition, a necessary condition for any scientific investigation of the origin of life problem, has two components. First, it contends that there is no unbridgeable gap between inorganic matter and life. Second, it regards the emergence of life as a highly probable process. Examining several current origin-of-life theories. I indicate the implicit or explicit role played by the continuity thesis in each of them. In addition, I identify the rivals of the thesis within the scientific community — the almost miracle camp. Though adopting the anti-vitalistic aspect of the continuity thesis, this camp regards the emergence of life as involving highly improbable events. Since it seems that the chemistry of the prebiotic stages and of molecular self-organization processes rules out the possibility that life is the result of a happy accident, I claim that the almost miracle view implies in fact, a creationist position.     

Effect of TNFα on activities of different promoters of human apolipoprotein A-I gene

Human apolipoprotein A-I (ApoA-I) is a major structural and functional protein component of high-density lipoproteins. The expression of the apolipoprotein A-I gene (apoA-I) in hepatocytes is repressed by pro-inflammatory cytokines such as IL-1β and TNFα. Recently, two novel additional (alternative) promoters for human apoA-I gene have been identified. Nothing is known about the role of alternative promoters in TNFα-mediated downregulation of apoA-I gene. In this article we report for the first time about the different effects of TNFα on two alternative promoters of human apoA-I gene. Stimulation of HepG2 cells by TNFα leads to activation of the distal alternative apoA-I promoter and downregulation of the proximal alternative and the canonical apoA-I promoters. This effect is mediated by weakening of the promoter competition within human apoA-I 5′-regulatory region (apoA-I promoter switching) in the cells treated by TNFα. The MEK1/2-ERK1/2 cascade and nuclear receptors PPARα and LXRs are important for TNFα-mediated apoA-I promoter switching.     

Have main types of primary aldosteronism different phenotype?

Primary aldosteronism (PA) is the most common cause of endocrine hypertension with a high frequency of cardiovascular complications. We found in our previous study higher occurrence of metabolic disturbances in patients with idiopathic hyperaldosteronism (IHA) compared to subjects with aldosterone-producing adenoma (APA). The aim of our present study is to evaluate potential differences in the frequency of end-organ damage (arterial stiffness and microalbuminuria) between two main types of PA. The diagnosis of the particular form of PA was based on adrenal venous sampling and/or histopathological examination. We analyzed clinical and laboratory data from 72 patients with PA (36 with IHA, 36 with APA). The arterial stiffness was expressed as the carotid-femoral pulse wave velocity (PWV) and the renal damage as urinary albumin excretion levels (UAE). Patients with IHA had significantly (p<0.03) higher prevalence of metabolic syndrome (17 % in APA, 35 % in IHA), higher triglycerides (1.37+/-0.71 mmol/l in APA, 1.85+/-0.87 mmol/l in IHA), lower HDL cholesterol (1.25+/-0.28 mmol/l in APA, 1.06+/-0.25 mmol/l in IHA), higher PWV (7.91+/-1.61 m/s in APA, 8.99+/-1.77 m/s in IHA) and higher UAE (12.93+/-2.21 mg/l in APA, 28.09+/-6.66 mg/l in IHA). It seems that patients with IHA may have a slightly different phenotype compared to APA.     

Molecular detection of Epstein–Barr virus in different types of lymphoma

Molecular Biology Reports - Epstein-Barr virus (EBV) is a member of the γ herpesvirus subfamily. It is widely spread, potentially oncogenic and has been studied in different human cancers such...     

The interaction of α-chymotrypsin with isosteric substrates of different charge type

1. The synthesis of three substrates of alpha-chymotrypsin of closely similar steric requirements but different charge type is reported. 2. The interaction of these compounds [SS-dimethyl-(l-3-carboxymethyl-3-acetamido)propyl sulphonium iodide, l-2-acetamido-5-methylhexanoic acid methyl ester and N-acetyl-l-glutamic acid alpha-methyl ester] with alpha-chymotrypsin has been studied. 3. For the charged substrates, values of k(0) are two orders of magnitude smaller than, and values of K(m) two orders of magnitude larger than, the corresponding values for the uncharged isostere. 4. The results are interpreted in terms of the known specificity of the enzyme, and the relationship between binding and kinetic specificities is discussed.     

Angular transformation – another effect of different sample sizes

Angular transformation has been widely used to analyze proportions or percentages in ecology. A new type of artifact can arise by applying angular transformation to proportions or percentages. Proportions with the same mean or expected value, but with different sample sizes (denominator of proportions), have different means or expected values after this transformation. Overdispersion causes a larger deviation of the expected value after the transformation. Angular transformation should be avoided unless the sample size (denominator of proportions) is the same for all the proportions analyzed.     

Modulation of the presynaptic inhibition of spinal α-motoneurons during mechanical stimulation of different types

Using the method of assessing the presynaptic inhibition of heteronymous Ia afferents and α motoneurons of the m. soleus during a homonymous vibration effect on the tendo calcaneus in ten subjects, changes in the inhibition of spinal α motoneurons during 15 min of the aftereffect of mechanical stimulation of different types were studied. Intense mechanical stimuli and weak tactile, vibratory stimuli applied in combination intensify inhibitory processes in the afferent fibers of group Ia, their effects differing in the value of the increase in the presynaptic inhibition of spinal α motoneurons.     

The formation of amyloid-like fibrils of α-chymotrypsin in different aqueous organic solvents

The formation of amyloid-like fibrils of α-chymotrypsin was studied in aqueous ethanol, methanol, tertbutanol, dimethylformamide and acetonitrile. Thioflavin T (ThT), Congo red (CR) and 1-anilino-8-naphthalenesulfonic acid (ANS) binding, turbidity, intrinsic fluorescence and far-UV circular dichroism measurements were employed to characterize the amyloid fibril formation. The greatest extent of fibril formation after incubation for 24 h at pH 7.0 and at 24 °C was in ethanol at 55%, in methanol and dimethylformamide (DMF) at 60-70% and in tert-butanol at 60-80%. The ANS binding and intrinsic fluorescence results showed that the hydrophobic residues are more solvent-exposed in the aggregated form of α-chymotrypsin. The ThT, CR binding and far-UV CD measurements indicated that the formation of the cross-β structure of α-chymotrypsin depends on the polarity of the organic solvent. To determine the role of surface charges in the aggregation, chemically modified forms of α-chymotrypsin were prepared. The citraconylated and succinylated enzymes exhibited a higher and the enzyme forms modified with aliphatic aldehydes a lower propensity for aggregation. These results suggest the important role of surface charges in the aggregation of α-chymotrypsin.     

Comparison of rhizobitoxine-induced inhibition of β-cystathionase from different bradyrhizobia and soybean genotypes

The enzyme -cystathionase catalyzes the conversion of cystathionine to homocysteine in both plants and bacteria. Preparations of this enzyme taken from both Salmonella and spinach (Spinacia oleracea L.) have been shown to be irreversibly inhibited by low concentrations of rhizobitoxine (RT), a chlorosis-inducing phytotoxin produced by some strains of soybean bradyrhizobia. The sensitivities of -cystathionase from bradyrhizobia and soybean are not well characterized. Therefore, we purified -cystathionase from selected bradyrhizobia and soybean genotypes that have been shown to exhibit differences in RT production and apparent RT sensitivities, respectively. Enzyme purified from E. coli strain DH52 was used for comparison. The enzymes differed in their physiological properties and RT sensitivities. Overall, the -cystathionase enzymes purified from bradyrhizobia were more sensitive to RT than were those from the soybean cultivars. Kinetic studies showed that the nature of the RT-induced inhibition also differed between the two sources. The enzymes from bradyrhizobia exhibited inhibition that was [RT]-dependent, whereas the enzymes from soybean showed a time-dependent inhibition. These contrasting characteristics may in part reflect differences in active site accessibility, amino acid components, and associated RT diffusion rates. However, in all cases the inhibition caused by RT showed a typical substrate-competitive inhibition pattern.Abbreviations RT rhizobitoxine - PLP pyridoxal phosphate - DTT dithioerythritol - PMSF phenylmethylsulfonyl fluoride - HTP hydroxyapatite Published as Paper No. 1571 in the Journal Series of the Delaware Agricultural Experiment Station.     

Phytophage–entomophage interactions at different stages of mass reproduction of forest insects

A model that implies highly inertial regulation of phytophage numbers by entomophages has been applied for the analysis of phytophage–entomophage interactions during different phases of the gradation cycle of phyllophagous insects. The data on population dynamics and the degree of parasite infestation in pupae of the pine looper Bupalus piniarius L. and fir looper Ectropis (=Boarmia) bistortata Gz are used to verify the model. The results of field studies apparently are in good agreement with the model of highly inertial regulation in the “phytophage–entomophage” system. The model that is proposed explains the decisive roles of different factors (entomophages, predators, or diseases) in the population dynamics of phytophages under different conditions.     

Analysis of different cell death processes of prepubertal rat oocytes in vitro

The processes of cell death were studied in vitro in populations of oocytes isolated from prepubertal rats. In order to identify apoptosis, the externalized phosphatidylserine was recognized with Annexin-V coupled to FITC and the fragmentation of DNA was demonstrated by means of electrophoresis. Oocytes were tested for autophagy by means of the incorporation of monodansylcadaverine and monitoring Lc3-I/Lc3-II by western blot. The expression of mRNA marker genes of autophagy and of apoptosis was studied by means of RT–PCR in pure populations of oocytes. Some oocytes expressed at least one of the following markers: caspase-3, lamp1 and Lc3. Some oocytes were positive to Annexin-V or to monodansylcadaverine. However, most of them were simultaneously positive to both markers. The relative frequency of oocytes simultaneously positive to markers of apoptosis and autophagy did not change in the different ages studied. The transformation of Lc3-I in Lc3-II was present in all populations of oocytes studied. The mRNAs for caspase-3, lamp1 and Lc3 were present in all populations of oocytes analyzed. Our results demonstrate that oocytes of rats from new born to prepubertal age are eliminated by means of three different cell death processes: apoptosis, autophagy and a mixed event in which both routes to cell death participate in the same cell.     

What is the clinical relevance of different lung compartments?

The lung consists of at least seven compartments with relevance to immune reactions. Compartment 1 - the bronchoalveolar lavage (BAL), which represents the cells of the bronchoalveolar space: From a diagnostic point of view the bronchoalveolar space is the most important because it is easily accessible in laboratory animals, as well as in patients, using BAL. Although this technique has been used for several decades it is still unclear to what extent the BAL represents changes in other lung compartments. Compartment 2 - bronchus-associated lymphoid tissue (BALT): In the healthy, BALT can be found only in childhood. The role of BALT in the development of the mucosal immunity of the pulmonary surfaces has not yet been resolved. However, it might be an important tool for inhalative vaccination strategies. Compartment 3 - conducting airway mucosa: A third compartment is the bronchial epithelium and the submucosa, which both contain a distinct pool of leukocytes (e.g. intraepithelial lymphocytes, IEL). This again is also accessible via bronchoscopy. Compartment 4 - draining lymph nodes/Compartment 5 - lung parenchyma: Transbronchial biopsies are more difficult to perform but provide access to two additional compartments - lymph nodes with the draining lymphatics and lung parenchyma, which roughly means "interstitial" lung tissue. Compartment 6 - the intravascular leukocyte pool: The intravascular compartment lies between the systemic circulation and inflamed lung compartments. Compartment 7 - periarterial space: Finally, there is a unique, lung-specific space around the pulmonary arteries which contains blood and lymph capillaries. There are indications that this "periarterial space" may be involved in the pulmonary host defense. All these compartments are connected but the functional network is not yet fully understood. A better knowledge of the complex interactions could improve diagnosis and therapy, or enable preventive approaches of local immunization.