Algorithm independent properties of RNA secondary structure predictions

Algorithms predicting RNA secondary structures based on different folding criteria – minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) – and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter AUGC alphabet. Computed structures and free energies depend strongly on both the algorithm and the parameter set. Statistical properties, such as mean number of base pairs, mean numbers of stacks, mean loop sizes, etc., are much less sensitive to the choice of parameter set and even of algorithm. Some features of RNA secondary structures, such as structure correlation functions, shape space covering and neutral networks, seem to depend only on the base pairing logic (GC or AUGC alphabet). Received: 16 May 1996 / Accepted: 10 July 1996     

Cryptococcosis as an opportunistic infection in immunodeficiency secondary to paracoccidioidomycosis

We describe the case reports of two patients with immunodeficiency secondary to paracoccidioidomycosis (PCM) and opportunistic Cryptococcus neoformans infections. Secondary immunodeficiency likely occurred as a consequence of the intestinal loss of proteins and lymphocytes associated with malabsorption syndrome due to obstructed lymphatic drainage. Both patients had had severe abdominal involvement during the acute PCM disease. Immunological evaluation showed cellular and humoral immunity impairment. Cryptococcosis manifested as relatively well circumscribed lesions: osteolytic lesions of the skull in one patient, and pulmonary nodules in the other. The latter was treated surgically and with amphotericin B, whereas the other was treated with the combination amphotericin-B and flucytosine. Both patients had a good response to treatment with complete regression of the lesions. They have now 2 and 4 years of follow-up with maintenance therapy and no indication of reactivation of the infection. PCM also did not reactivate. The clinical and immunological characteristics of these patients are discussed and compared to the opportunistic C. neoformans infections of AIDS and transplant patients.     

In vitro Reconstitution of Epicuticular Wax Crystals: Formation of Tubular Aggregates by Long-Chain Secondary Alkanediols

Cuticles of several plant species are covered by tubular wax aggregates that are known to consist mainly of (S)-nonacosan-10-ol. The present work addresses the question whether minor wax components may additionally contribute to these tubules. Thin layer chromatography was used to prepare secondary alkanediol fractions from leaf cuticular waxes of Nelumbo nucifera and Thalictrum flavum, containing nonacosane-3,10-diol, nonacosane-4,10-diol, nonacosane-5,10-diol, nonacosane-7,10-diol, nonacosane-9,10-diol and nonacosane-10,13-diol. From organic solutions all these compounds crystallized in tubular shapes. Possible crystal structures of relevant alkanediol isomers are proposed, in analogy to the lattice geometries of comparable aliphatic compounds. The resulting structural model shows that nonacosan-10-ol and various secondary alkanediols may join in metastable mixed crystals. According to the structural model proposed the admixture of alkanediols to nonacosan-10-ol aggregates should enhance the stability of their tubular habit.     

Statistics of RNA melting kinetics

We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that. assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a landscape of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies. Correspondence to: P. Schuster     

Sequence homology and structure predictions of the creatine kinase isoenzymes

Comparisons of the protein sequences and gene structures of the known creatine kinase isoenzymes and other guanidino kinases revealed high homology and were used to determine the evolutionary relationships of the various guamidino kinases. A CK framework is defined, consisting of the most conserved sequence blocks, and diagnostic boxes are identified which are characteristic for anyone creatine kinase isoenzyme (e.g. for vertebrate B-CK) and which may serve to distinguish this isoenzyme from all others (e.g. from M-CKs and Mi-CKs). Comparison of the guanidino kinases by near-UV and far-UV circular dichroism further indicates pronounced conservation of secondary structure as well as of aromatic amino acids that are involved in catalysis.Abbreviations GuaK guanidino kinase - CK creatine kinase - B-and M-CK brain and muscle cytosolic CK isoenzyme - Mi-CK mitochondrial CK isoenzyme - ArgK arginine kinase - Cr creatine - PCr phosphorylcreatine - PArg phosphorylarginine     

SEXUAL SELECTION IN THE BARN SWALLOW (HIRUNDO RUSTICA). IV. PATTERNS OF FLUCTUATING ASYMMETRY AND SELECTION AGAINST ASYMMETRY

The patterns of variation in fluctuating asymmetry were studied in four morphological characters of the barn swallow Hirundo rustica. The level of absolute and relative asymmetry was larger in the secondary sexual character “outer tail length” than in three nonsexual morphological traits (wing, central tail, and tarsus length). The extent of individual asymmetry in outer tail length was negatively correlated with tail-ornament size, whereas the relationship between asymmetry of all other morphological characters and their size was flat or U-shaped. Asymmetry in outer tail length was unrelated to asymmetry in other morphological characters, whereas asymmetries in the length of wing, central tail, and tarsus were positively correlated. Male bam swallows exhibited larger asymmetry in outer tail length than females. Asymmetry of most morphological traits exhibited intermediate repeatabilities between years, with the exception of male and female outer tail length, which were highly repeatable. Tail asymmetry of offspring weakly, though significantly, resembled that of their parents. Asymmetry in wing and outer tail length was also significantly related to several fitness components. Male barn swallows that acquired a mate were less asymmetric in wing and outer tail length than unmated males. Females with more asymmetrical tails laid eggs significantly later. Annual reproductive success was unrelated to fluctuating asymmetry. Male barn swallows that survived were less asymmetric in wing and outer tail length than nonsurvivors, whereas female survivors were less asymmetric in outer tail length than nonsurvivors. These results suggest that levels of fluctuating asymmetry in barn swallows are associated with differences in fitness.     

Kinetics of leucrose formation from sucrose by dextransucrase

Leucrose formation from sucrose and fructose by dextransucrase is of practical interest. It has been investigated at different experimental conditions, including the influence of temperature on reaction rate and selectivity. Under appropriate conditions high product yield can be obtained. Furthermore, a model is presented that allows interpretation of the experimental data.     

Leaf chemistry and food selection by common langurs (Presbytis entellus) in Rajaji National Park,Uttar Pradesh,India

Food selection in folivorous primates has been hypothesized to be correlated with leaf chemistry. To test this hypothesis, we conducted a 5-month study on Presbytis entellusin a moist deciduous forest in the Rajaji National Park,Uttar Pradesh, India. The study period covered two seasons, winter and spring. We used the percentage time spent feeding on each food item as an index of food selection, which we estimated from group scan data collected from one study group for 6 days each month. We estimated the selection ratio for each item as the ratio of time spent feeding to availability. We estimated food availability from vegetation sampling and phenological data in the home range of the study group. We estimated crude protein (CP), acid detergent fiber (ADF) and tannins in mature and young leaves of 12 major food species in the laboratory. Food selection is positively correlated with CP in winter and negatively correlated with ADF in both seasons. It also is correlated with CPJADF ratio, but to a lesser extent than the best predictor in winter and spring. Selection ratio is not correlated with CP and ADF in both seasons. It is probable that the inclusion of other factors, such as micronutrients,condensed tannins, and digestibility, might give a better prediction of food selection.     

The biosynthesis of rosmarinic acid in suspension cultures of Coleus blumei

Suspension cultures of Coleus blumei accumulate very high amounts of rosmarinic acid, an ester of caffeic acid and 3,4-dihydroxyphenyllactate, in medium with elevated sucrose concentrations. Since the synthesis of this high level of rosmarinic acid occurs in only five days of the culture period, the activities of the enzymes involved in the biosynthesis are very high. Therefore all the enzymes necessary for the formation of rosmarinic acid from the precursors phenylalanine and tyrosine could be isolated from cell cultures of Coleus blumei: phenylalanine ammonia-lyase, cinnamic acid 4-hydroxylase, hydroxycinnamoyl:CoA ligase, tyrosine aminotransferase, hydroxyphenylpyruvate reductase, rosmarinic acid synthase and two microsomal 3- and 3-hydroxylases. The main characteristics of these enzymes of the proposed biosynthetic pathway of rosmarinic acid will be described.Abbreviations DHPL 3,4-dihydroxyphenyllactate - DHPP 3,4-dihydroxyphenylpyruvate - pHPL 4-hydroxyphenyllactate - pHPP 4-hydroxyphenylpyruvate - RA rosmarinic acid