Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

We derive an analytic expression for site-specific stationary distributions of amino acids from the structurally constrained neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter, measuring the limit of divergent evolutionary changes at a given site, can be predicted from a site-specific topological property, the principal eigenvector of the contact matrix of the native conformation of the protein. These analytic results, obtained without free parameters, are compared with simulations of the SCN model and with the site-specific amino acid distributions obtained from the Protein Data Bank. These results also provide new insights into how the topology of a protein fold influences its designability, i.e., the number of sequences compatible with that fold. The dependence of the effective temperature on the principal eigenvector decreases for longer proteins, as a possible consequence of the fact that selection for thermodynamic stability becomes weaker in this case.     

Thermo-optically Induced Reorganizations in the Main Light Harvesting Antenna of Plants. II. Indications for the Role of LHCII-only Macrodomains in Thylakoids

We have investigated the circular dichroism spectral transients associated with the light-induced reversible reorganizations in chirally organized macrodomains of pea thylakoid membranes and loosely stacked lamellar aggregates of the main chlorophyll a/b light harvesting complexes (LHCII) isolated from the same membranes. These reorganizations have earlier been assigned to originate from a thermo-optic effect. According to the thermo-optic mechanism, fast local thermal transients due to dissipation of the excess excitation energy induce elementary structural changes in the close vicinity of the dissipation [Cseh et al. (2000) Biochemistry 39: 15250–15257]. Here we show that despite the markedly different CD spectra in the dark, the transient (light-minus-dark) CD spectra associated with the structural changes induced by high light in thylakoids and LHCII are virtually indistinguishable. This, together with other close similarities between the two systems, strongly suggests that the gross short-term, thermo-optically induced structural reorganizations in the membranes occur mainly, albeit probably not exclusively, in the LHCII-only domains [Boekema et al. (2000) J Mol Biol 301: 1123–1133]. Hence, LHCII-only domains might play an important role in light adaptation and photoprotection of plants.     

Thermo-optically Induced Reorganizations in the Main Light Harvesting Antenna of Plants. I. Non-Arrhenius Type of Temperature Dependence and Linear Light-intensity Dependencies

Thermo-optically induced structural reorganizations have earlier been identified in isolated LHCII, the main chlorophyll a/b light harvesting complexes of Photosystem II, and in granal thylakoid membranes [Cseh et al. (2000) Biochemistry 39: 15250–15257; Garab et al. (2002) Biochemistry 41: 15121–15129]. According to the thermo-optic mechanism, structural changes can be induced by fast, local thermal transients due to the dissipation of excess excitation energy. In this paper, we analyze the temperature and light-intensity dependencies of thermo-optically induced reversible and irreversible reorganizations in the chiral macrodomains of lamellar aggregates of isolated LHCII and of granal thylakoid membranes. We show that these structural changes exhibit non-Arrhenius type of temperature dependencies, which originate from the ‘combination’ of the ambient temperature and the local thermal transient. The experimental data can satisfactorily be simulated with the aid of a simple mathematical model based on the thermo-optic effect. The model also predicts, in good accordance with experimental data published earlier and presented in this paper, that the reorganizations depend linearly on the intensity of the excess light, a unique property that is probably important in light adaptation and photoprotection of plants.     

Significance of temporal changes when designing a reservoir for conservation of dragonfly diversity

While there has been much focus in biodiversity conservation that transcends place, few studies transcend time. Yet an appreciation of vegetational and hydrological succession is essential for maintaining a habitat that has been created with the aim of conserving a particular group of organisms. This is a study of changes in a dragonfly assemblage over a period of 13 years at a biodiversity-rich, southern hemisphere reservoir. A total of 30 dragonfly species were recorded in this study, compared to 12 species before the reservoir was constructed in 1988, and 26 species in 1993, with 25 species resident in both 1993 and 2001. Two of these are local endemics. One other endemic was lost to succession in 1993 but reappeared in 2001. Three other species never reappeared after succession in 1993, yet six other species appeared after this date. Multivariate analyses identified structural and compositional vegetation, especially marginal forest, percentage vegetation cover, percentage shade, as the most important environmental variables determining dragonfly species composition. Other important environmental variables were grasses of tall, medium and short height categories, submerged vegetation, water flow and amount of open water. Not surprisingly, successional changes in vegetation physiognomy and in water conditions significantly increased Odonata species richness and diversity over the years. More importantly, the study shows that to maintain both high species richness, including endemics, it is essential to maintain a variety of biotopes using selective management of the marginal vegetation without allowing succession to proceed to a point where overgrowth of the bank and silting of the bottom begin to impoverish the fauna.     

General Description of Partly Meromictic Hypertrophic Lake Verevi,its Ecological Status,Changes during the Past Eight Decades,and Restoration Problems

The present study describes generally the ecosystem of Lake Verevi while more detailed approaches are presented in the same issue. The main task of the article is to estimate long-term changes and find the best method for the restoration of good ecological status. Lake Verevi (surface 12.6 ha, mean depth 3.6 m, maximum depth 11 m, drainage area 1.1 km², water exchange 0.63-times per year) is a hypertrophic hard-water lake located in town Elva (6400 inhabitants). Long-term complex limnological investigations have taken place since 1929. The lake has been contaminated by irregular discharge of urban wastewaters from oxidation ponds since 1978, flood from streets, and infiltrated waters from the surrounding farms. The so-called spring meromixis occurred due to extremely warm springs in recent years. The index value of buffer capacity of Lake Verevi calculated from natural conditions is on the medium level. Water properties were analysed according to the requirements of the EU Water Framework Directive. According to the classification, water quality as a long-term average of surface layers is moderate-good, but the water quality of bottom layers is bad. Values in deeper layers usually exceed 20–30 times the calculated reference values by Vighi and Chiaudani’s model. Naturally, at the beginning of the 20th century the limnological type of the lake was moderately eutrophic. During the 1980s and 1990s the ecosystem was out of balance by abiotic characteristics as well as by plankton indicators. Rapid fluctuations of species composition and abundance can be found in recent years. Seasonal variations are considerable and species composition differs remarkably also in the water column. The dominating macrophyte species vary from year to year. Since the annual amount of precipitation from the atmosphere onto the lake surface is several times higher, the impact of swimmers could be considered irrelevant. Some restoration methods were discussed. The first step, stopping external pollution, was completed by damming the inlet. Drainage (siphoning) of the hypolimnetic water is discussed. Secondary pollution occurs because Fe:P values are below the threshold. The authors propose to use phosphorus precipitation and hypolimnetic aeration instead of siphoning.     

On the functional role of Arg172 in substrate binding and allosteric transition in Escherichia coli glucosamine-6-phosphate deaminase

Glucosamine-6-phosphate deaminase from Escherichia coli (EC 3.5.99.6) is an allosteric enzyme, activated by N-acetylglucosamine 6-phosphate, which converts glucosamine-6-phosphate into fructose 6-phosphate and ammonia. X-ray crystallographic structural models have showed that Arg172 and Lys208, together with the segment 41-44 of the main chain backbone, are involved in binding the substrate phospho group when the enzyme is in the R activated state. A set of mutants of the enzyme involving the targeted residues were constructed to analyze the role of Arg172 and Lys208 in deaminase allosteric function. The mutant enzymes were characterized by kinetic, chemical, and spectrometric methods, revealing conspicuous changes in their allosteric properties. The study of these mutants indicated that Arg172 which is located in the highly flexible motif 158-187 forming the active site lid has a specific role in binding the substrate to the enzyme in the T state. The possible role of this interaction in the conformational coupling of the active and the allosteric sites is discussed.     

A novel apoptotic pathway as defined by lectin cellular initiation

In this study of lectin-induced apoptosis we found that wheat germ agglutinin (WGA) initiated an accelerated type of programmed cell death developing after only 30 min of incubation with tumor cells. To analyze possible mechanisms, studies were focused using the WGA lectin whose carbohydrate specificity is well defined. We found that WGA could induce apoptosis by binding to either N-acetylneuraminic acid or N-acetylglucosamine (GlcNAc) on the cell surface of normal and malignant cells. We also showed that it is unlikely that WGA triggers apoptosis by binding to the carbohydrate portion of Fas. CrmA gene transfection did not inhibit WGA-mediated apoptosis of Jurkat cells. In addition, Jurkat-R cells selected for resistance to Fas signaled apoptosis manifested high sensitivity to WGA as did Fas-negative BL6 melanoma cells. WGA-induced apoptosis is also caspase-3-independent and was found to be triggered via a mitochondrial pathway. WGA induced a loss of transmembrane potential, disruption of the inner mitochondria membrane, and release of cytochrome c and caspase-9 activation after 30 min of cell interaction. Interestingly, Bcl-2 gene transfection did not affect sensitivity of Jurkat cells to WGA. The Jurkat-R subline that has been shown to be Bax and Bak deficient and resistant to various apoptotic signals was highly sensitive to WGA-induced apoptosis. In summary, WGA triggers a unique pattern of apoptosis that is extremely fast, Fas- and caspase-3-independent, and is mediated via a mitochondrial pathway. However, its mitochondrial component is unrestrained by the loss of Bax and Bak or the upregulation of Bcl-2 expression.     

Remote sensing and geographic information systems in the spatial temporal dynamics modeling of infectious diseases

Similar to species immigration or exotic species invasion,infectious disease transmis-sion is strengthened due to the globalization of human activities. Using schistosomiasis as an exam-ple,we propose a conceptual model simulating the spatio-temporal dynamics of infectious diseases. We base the model on the knowledge of the interrelationship among the source,media,and the hosts of the disease. With the endemics data of schistosomiasis in Xichang,China,we demonstrate that the conceptual model is feasible; we introduce how remote sensing and geographic information systems techniques can be used in support of spatio-temporal modeling; we compare the different effects caused to the entire population when selecting different groups of people for schistosomiasis control. Our work illustrates the importance of such a modeling tool in supporting spatial decisions. Our mod-eling method can be directly applied to such infectious diseases as the plague,lyme disease,and hemorrhagic fever with renal syndrome. The application of remote sensing and geographic informa-tion systems can shed light on the modeling of other infectious disease and invasive species studies.     

Alterations in DNA methylation and genome structure in two rice mutant lines induced by high pressure

Pressure is expected to be an important parameter to affect characteristics of matters and control rate and equilibrium of chemical reactions. As a fundamental thermodynamic variable, it also has effects on bio-macromolecules and a lot of physiological an…     

Dietary patterns and changes in body weight in women

Objective: Our objective was to examine the association between adherence to dietary patterns and weight change in women. Research Methods and Procedures: Women (51,670, 26 to 46 years old) in the Nurses’ Health Study II were followed from 1991 to 1999. Dietary intake and body weight were ascertained in 1991, 1995, and 1999. A Western pattern, characterized by high intakes of red and processed meats, refined grains, sweets and desserts, and potatoes, and a prudent pattern, characterized by high intakes of fruits, vegetables, whole grains, fish, poultry, and salad dressing, were identified with principal component analysis, and associations between patterns and change in body weight were estimated. Results: Women who increased their Western pattern score had greater weight gain (multivariate adjusted means, 4.55 kg for 1991 to 1995 and 2.86 kg for 1995 to 1999) than women who decreased their Western pattern score (2.70 and 1.37 kg for the two time periods), adjusting for baseline lifestyle and dietary confounders and changes in confounders over time (p < 0.001 for both time periods). Furthermore, among women who increased their prudent pattern score, weight gain was smaller (multivariate‐adjusted means, 1.93 kg for 1991 to 1995 and 0.66 kg for 1995 to 1999) than among women who decreased their prudent pattern score (4.83 and 3.35 kg for the two time periods) (p < 0.001). The largest weight gain between 1991 and 1995 and between 1995 and 1999 was observed among women who decreased their prudent pattern score while increasing their Western pattern score (multivariate adjusted means, 6.80 and 4.99 kg), whereas it was smallest for the opposite change in patterns (0.87 and ?0.64 kg) (p < 0.001). Discussion: Adoption of a Western dietary pattern is associated with larger weight gain in women, whereas a prudent dietary pattern may facilitate weight maintenance.