Phylogenetic spread of sequence data affects fitness of SOD1 consensus enzymes: Insights from sequence statistics and structural analyses

Non‐natural protein sequences with native‐like structures and functions can be constructed successfully using consensus design. This design strategy is relatively well understood in repeat proteins with simple binding function, however detailed studies are lacking in globular enzymes. The SOD1 family is a good model for such studies due to the availability of large amount of sequence and structure data motivated by involvement of human SOD1 in the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). We constructed two consensus SOD1 enzymes from multiple sequence alignments from all organisms and eukaryotic organisms. A significant difference in their catalytic activities shows that the phylogenetic spread of the sequences used affects the fitness of the construct obtained. A mutation in an electrostatic loop and overall design incompatibilities between bacterial and eukaryotic sequences were implicated in this disparity. Based on this analysis, a bioinformatics approach was used to classify mutations thought to cause familial ALS providing a unique high level view of the physical basis of disease‐causing aggregation of human SOD1.     

Reproductive phenology of two Mimusops species in relation to climate,tree diameter and canopy position in Benin (West Africa)

Assessing species phenology provides useful understanding about their autecology, to contribute to management strategies. We monitored reproductive phenology of Mimusops andongensis and Mimusops kummel, and its relationship with climate, tree diameter and canopy position. We sampled trees in six diameter classes and noted their canopy position. For both species flowering began in the dry season through to the rainy season, but peaked in the dry season, whilst fruiting occurred in the rainy season and peaked during the most humid period. Flowering was positively correlated with temperature. Conversely, fruiting was negatively correlated with temperature and positively with rainfall, only in the Guineo‐Sudanian zone. For M. andongensis, flowering and fruiting prevalences were positively linked to stem diameter, while only flowering was significantly related to canopy position. For M. kummel, the relationship with stem diameter was significant for flowering prevalence only and in the Guineo‐Sudanian zone. Results suggest that phylogenetic membership is an important factor restricting Mimusops species phenology. Flowering and fruiting of both species are influenced by climate, and consequently climate change might shift their phenological patterns. Long‐term investigations, considering flowering and fruiting abortion, will help to better understand the species phenology and perhaps predict demographic dynamics.     

Stabilization of G-quadruplex structure on vascular endothelial growth factor gene promoter depends on CpG methylation site and cation type

Background

DNA methylation at the 5-position of cytosine is an epigenetic modification of CpG dinucleotides. In addition to CpG methylation, the G-quadruplex (G4) structure has been reported as a regulator of gene expression. The identification of G4 forming sequences in CpG islands suggests an involvement of CpG-methylated G4 structures in biological processes; however, few reports have addressed the effects of CpG methylation on G4 structure.

The periodically forced Droop model for phytoplankton growth in a chemostat

 It is proved that the periodically forced Droop model for phytoplankton growth in a chemostat has precisely two dynamic regimes depending on a threshold condition involving the dilution rate. If the dilution rate is such that the sub-threshold condition holds, the phytoplankton population is washed out of the chemostat. If the super-threshold condition holds, then there is a unique periodic solution, having the same period as the forcing, characterized by the presence of the phytoplankton population, to which all solutions approach asymptotically. Furthermore, this result holds for a general class of models with monotone growth rate and monotone uptake rate, the latter possibly depending on the cell quota. Received 10 October 1995; received in revised form 26 March 1996     

Purification, characterization and stability of barley grain peroxidase BP 1, a new type of plant peroxidase

The major peroxidase of barley grain (BP 1) has enzymatic and spectroscopic properties that are very differeant from those of other known plant peroxidases (EC 1.11.1.7) and can therefore contribute to the understanding of the many physiological functions ascribed to these enzymes. To study the structure-function relationships of this unique model peroxidase, large-scale and Jaboratory-scale purifications have been developed. The two batches of pure BP 1 obtained were identical in their enzymatic and spectral properties, and confirmed that BP 1 is different from the prototypical horseradish peroxidase isoenzyme C (HRP C). However, when measuring the specific activity of BP 1 at pH 4.0 in the presence of 1 m M C_aCl₂, the enzyme was as competent as HRP C at neutral pH towards a variety of substrates (m M mg⁻¹ min⁻¹): coniferyl alcohol (930±48), caffeic acid (795±53), ABTS (2,2'-azino-di-[3-ethyl-benzothiazoline-(6)-sulfonic acid]) (840±47), ferulic acid (415±20), p -coumaric acid (325±12), and guaiacol (58±3). The absorption spectrum of BP 1 is blue-shifted compared to that of HRP C with a Soret maximum of 399–402 nm, depending on pH. The prosthetic group was shown to be iron-protoporphyrin IX, which is characteristic of plant peroxidases. BP 1 is stable from pH 3 to 11, indicating that its unusual spectral characteristics do not result from enzyme instability. The thermostability is also normal with a melting temperature of 75°C at pH 6.6, and 67°C at pH 4.0 and 8.3. It is clear that the unusual properties of BP 1 are genuine, and reflect a novel regulation of plant peroxidase function.     

Climatic and biogeographical associations of southern African dung beetles (Coleoptera: Scarabaeidae s. str.)

Climatic and biogeographical associations of southern African dung beetles (Scarabaeinae, Coprinae) were analysed from a collection amassed between 1971 and 1986. Endemism to Africa south of 15°S was much greater in southwesterly climates (winter rainfall, bimodal spring/autumn rainfall, arid late summer rainfall) than to the north‐east in the moist, mid‐summer rainfall region. Major biogeographical groups centred to the south‐west comprised predominantly southern African endemics, Western/Eastern Cape coast, Karoo, Karoo/Namib, northern Namibia and the south‐western Kalahari. Biogeographical groups centred on the south‐eastern highlands and the subtropical east coast (mid‐summer rainfall) also comprised predominantly southern African endemics. All other major groups centred to the north‐east in the mid‐summer rainfall region comprised predominantly species with widespread tropical biogeographical affiliations, pan‐southern Africa but centred in the east, pan‐mid‐summer rainfall region, eastern mid‐summer rainfall region, tropical east Zimbabwe/central Moçambique, subtropical/tropical game reserves (non‐ruminant dung specialists). There were cross‐climatic differences in taxonomic composition of the fauna. Within the winter rainfall region, percentage species composition of Scarabaeinae was greater whereas that of the coprine tribe, Onthophagini, was lower than within the other three climatic regions. Percentage species richness of most other tribes of Coprinae differed little between most climates but that of Scarabaeinae declined from west to east (Canthonini, Scarabaeini), east to west (Sisyphini) or to either side of the late summer rainfall region (Gymnopleurini).     

Quantitative analysis of CryIA(b) expression in Bt maize plants,tissues, and silage and stability of expression over successive generations

The range and stability of expression of the transgenic CryIA(b) protein was examined in Ciba Seeds Bt maize plants derived from Event 176. Specifically, CryIA(b) levels were determined for: (1) various plant tissues and developmental stages in three maize lines from 1993 field tests; (2) pollen and leaves from plants representing four backcross generations of two genotypes; (3) leaves of 6 precommercial hybrids; and (4) silage from one Bt maize hybrid. Significant levels were found only in pollen and leaves. Genetic background did not greatly impact the level seen in either tissue. CryIA(b) expression in maize plants derived from transformation Event 176 was stable over at least four successive generations. On a per acre basis, the highest amount of CryIA(b) protein (estimated to be 2-4 g CryIA(b) protein/acre) was found to occur at anthesis, consistent with the stage at which maximum plant vegetative biomass is reached. CryIA(b) was not detected in silage prepared from CryIA(b)-expression plants. The maize-expressed CryIA(b) protein was found to have the expected size and to be immunoreactive with antibodies prepared against crystals from Bacillus thuringiensis subsp. kurstaki.     

非线性接触率和种群动力学对SI传染病模型的影响

本文研究了具有一般非线性接触率和易感类中具有Logistic增长的SI传染病模型的正不变集、平衡位置以及平衡位置的稳定性．     

浙江省商品粮基地县粮食生产力的评价与分析

利用系统聚类法和稳定性测度的Finlay和Wilkinson模型分析了浙江21个商品粮基地县的粮食生产力水平及其稳定性．结果表明：21个县（市）的粮食生产力水平可以分成4类,而绍兴与海盐为生产力最高的一类,同时绍兴县的生产力稳定性高于平均稳定性．生产力的年度稳定性之间存在显著差异,其中1984年与1985年的生产力稳定性分别显著与极显著地高于平均稳定性,而1988年的稳定性却显著地低于平均稳定性;然而,生产力的地区稳定性之间却无显著差异．本文还依据分析结果就维持生产力稳定性问题提出了建议.     

Degradative covalent reactions important to protein stability

Commonly observed chemical modifications that occur in proteins during their in vitro purification, storage, and handling are discussed. Covalent modifications described include deamidation and isoaspartate formation, cleavage of peptide bonds at aspartic acid residues, cystine destruction and thioldisulfide interchange, oxidation of cysteine and methionine residues, and the glycation and carbamylation of amino groups.