Distinctive amino acid residue periodicities in terminal sequences of type III and type I secreted proteins from proteobacteria

The Fourier transform (FT) method was applied to specify the distribution of 14 predefined groups of amino acids (64 residues) at both termini of annotated type III and type I secreted proteins from proteobacteria. Type I proteins displayed a higher occurrence of significant periodicities at both C-and N-termini, indicating potent features to discriminate between secretion types, particularly by the use of variables selected from the full periodicity profiles at 19 orders of FT. The Fishers linear discriminant analysis, together with the stepwise selection of variables throughout equal pairs of combinations for all predefined groups of residues, revealed the C-terminal harmonics of aromatic (HFWY) and aliphatic (VLIA) residues as a set of strong predictor variables to classify both types of secreted proteins with an accuracy of 100% for original grouped cases and 96.4% for cross-validated grouped cases. The prediction accuracy of proposed discriminant function was estimated by repeated k-fold cross-validation procedures where the original data set was randomly divided into k subsets, with one of the k-subsets serving as the test set and the remaining data forming the training set. The average error rate computed across all k-trials and repeats did not exceed that of leave-one-out procedure. The proposed set of predictor variables could be used to assess the compatibility between secretion pathways and secretion substrates of proteobacteria by means of discriminant analysis.     

Diel patterns in reproductive events of the blenniid fish <Emphasis Type="Italic">Petroscirtes breviceps</Emphasis> in the temperate waters of southern Japan

Diel patterns in reproductive and feeding activities in the blenniid fish Petroscirtes breviceps, a nest-spawner that provides paternal care, were studied in southern Japan. Spawning primarily occurred in the early morning, and males occasionally mated with several females at the same time. Males may benefit from the simultaneous spawning of multiple females, as individuals are able to allocate the remainder of the daytime period to foraging. This hypothesis was tested using comparative studies of blenniid fishes. This study suggests that time cost associated with reproduction affects the diel pattern in spawning.     

不具有3-碱基周期性的编码序列初探

对120个较短编码序列(＜1 200 bp)的Fourier频谱进行分析表明,3-碱基周期性在短编码序列中并不是绝对存在的.统计分析提示,编码序列有无3-碱基周期性与序列的碱基组成和分布、所编码蛋白质氨基酸的选用和顺序以及同义密码子的使用都有一定的关系.一般地,非周期-3序列中A+U含量高于G+C含量,周期-3序列的情况则相反;非周期-3序列中碱基在密码子三个位点上的分布比周期-3序列中的分布均匀;非周期-3序列密码子和氨基酸的使用偏向没有周期-3序列的大.在利用Fourier分析方法预测DNA序列中的基因和外显子时,应充分考虑到这些现象.     

The influence of site and position in the plant community on the nutrient distribution in,and content of Eichhornia crassipes (Mart.) Solms

The distribution of 26 species of Blastocladiales, Saprolegniales, Lagenidiales and Peronosporales from temperate and sub tropical lakes, situated at different altitude in the same locality, is described. Seasonal periodicity is treated and found to be governed by temperature.     

Occurrence,distribution and seasonal periodicity of some aquatic fungi of Sat-Tal (Nainital), India

The occurrence of 23 species of aquatic fungi belonging to Blastocladiales, Saprolegniales, Lagenidiales and Peronosporales in three lakes and their surrounding cultivated and non-cultivated soils of Sat-Tal area have been studied. The species were found to be different in their habitat and temperature range.     

Diurnal periodicity in Daphnia reproduction

The diurnal periodicity of reproduction in a reservoir population of Daphnia galeata Sars was tested by two methods (egg age distribution analyses and direct observation of hatching). No significant diurnal synchronization of reproduction in the natural cladoceran population was found. A conspicuous shortage of older embryonic stages was parallely revealed by analyses of diurnal changes of egg age distribution. Suggested selective feeding of fish on gravid females of Daphnia brooding embryos with black eye pigmentation is discussed.     

中国东部石炭纪以来双气囊花粉富集规律与古气候演变

中国东部双气囊花粉首次出现于早石炭世末期,迄今已有近3亿年的历史。晚石炭世以来,包括松科、罗汉松科、古老松柏粉类、具缝双囊粉类、原始无肋双囊粉类及具肋双囊粉类在内的双气囊花粉,在地质发展历史上不仅仅展现为随时间的新老交替过程,而且呈现出明显周期性富集现象。3亿年来,双气囊花粉至少存在三个层次的周期性盛衰过程。一级周期时限约45-50Ma,双气囊花粉往往在其早期阶段富集出现,晚期阶段明显衰退。中国东部重要的双气囊花粉富集期包括：晚石炭世晚期一早二叠世早期、晚二叠世末期一早三叠世早期、晚三叠世末期一早侏罗世早中期、晚侏罗世晚期一早白垩世早期、早白垩世末期一晚白垩世早期、晚白垩世末期古近纪早期、新近纪中期至更新世。双气囊花粉盛衰过程的二级周期时限约15-17Ma,该级周期叠加在一级周期之上,并使其复杂化。一般情况下,在任意一个一级周期之内,前两个二级周期之早、中期阶段,双气囊花粉可达到较高的富集程度,而第三个二级周期内,双气囊花粉往往不甚发育,这是由一级周期本身的性质所决定的。双气囊花粉类盛衰过程还存在着超级周期性,这种超级周期由两个一级周期组成,时限约为100Ma。地史上,此级别周期有4期,其地质时限如下：石炭纪一中二叠世末期、晚二叠世早期一晚侏罗世初期、晚侏罗世早期晚白垩世晚期(马斯特里赫特早期)、晚白垩世末期至今。在同一超级周期之内,两个一级周期转折处双气囊花粉仍占据较突出地位,为弱转折所在。不同超级周期之间,一级周期转折处双气囊花粉含量急剧衰减,且喜热耐干孢粉类型富集出现,特化类型分布普遍,为强转折所在。双气囊花粉类盛衰过程还明显地与古气候演化、全球构造变动、海平面升降、缺氧沉积发育、以及盆地演化过程之间存在着明显的相关性。这些规律表明,全球自然背景演化过程有着统一的机制,而双气囊花粉类盛衰历史为发现这些自然背景演化过程基本规律,以及探索其演化机制提供了重要线索。     

Endogenous and exogenous factors affecting periodicities of female calling and male sex pheromone response in Grapholitha molesta (Busck)

In Grapholitha molesta periodicities of both female calling and male response to sex pheromone by wing fanning while walking were determined in part by circadian rhythms. The lights-on photoperiodic cue was at least partly responsible for setting the phase of the female calling rhythm. Absolute temperature levels and not necessarily a decrease in temperature modified the timing of calling; there were both high and low thresholds of temperature and, at particular photoperiod times, a temperature range optimal for calling. When the previous performance of calling was prevented by subthreshold temperatures, calling during the next period commenced earlier if temperatures were favourable. Thus, the previous performance of calling may establish a refractory period, or temperature decrease may act as a cue resetting the phase of the calling rhythm. The ability to use both an endogenous clock and exogenous temperature cues to synchronize sexual activity appears adaptive for a temperate zone insect whose multiple generations are exposed to both long periods of favourable climatic conditions in summer and harsh, unpredictable conditions in spring or fall.     

HABITAT DIFFERENCES IN THE TIMING OF REPRODUCTION OF THE INVASIVE ALGA SARGASSUM MUTICUM (PHAEOPHYTA,SARGASSACEAE) OVER TIDAL AND LUNAR CYCLES1

Sargassum muticum (Yendo) Fensholt is an invasive species that is firmly established on intertidal and subtidal rocky shores of Europe and the Pacific coast of North America. Local success and spread of S. muticum is thought to rely on its reproductive potential that seems dependent on exogenous factors like tidal and lunar cycles. This study is the first to compare the reproductive patterns (periodicity of egg expulsion and embryo settlement) of this invader in two different habitats: the middle and low intertidal. The combination of monthly, daily, and tidal samples at triplicate sites within each habitat showed a semilunar periodicity of egg expulsion and embryo settlement coincident with increasing tidal amplitude just before full and new moons. In both habitats, duration of each egg expulsion event was ～1 week, and embryo settlement occurred during the first daily low tide and with the incoming high tide during spring tides. However, both expulsion and settlement started 1–2 d earlier, expulsion saturation was faster, and settlement was higher in the mid‐ compared to the low intertidal. Our results suggest that the exact timing of gamete expulsion and embryo release of S. muticum responds to local factors, including tidal cues, which result in differences between mid‐ and low‐intertidal habitats.     

Nano-fibers produced by viral infection of amoeba visualized by atomic force microscopy

In the course of an atomic force microscopy investigation of mimivirus, we observed that disrupted virions released masses of fibers that were several hundreds of nanometers in length and that could not be explained as nucleic acid or polysaccharide. The fibers exhibited a strong 7 nm periodicity along their lengths. They existed singly, and also as ribbons, cables, and in multi stranded coils. In the aggregate structures, the periodic bands of the individual fibers aligned laterally to produce ribbons and other superstructures having a corresponding pattern of 7 nm periodic transverse bands. We have not observed such fibers in studies of other virus and cellular systems. The fibers are mechanically flexible and resistant to breakage. Occasionally fibers were associated with toroidal protein complexes, assumed to be processive enzyme complexes, apparently in the act of modifying the fibers.     

Using Triplet Periodicity of Nucleotide Sequences for Finding Potential Reading Frame Shifts in Genes

We introduce a novel approach for the detection of possible mutations leading to a reading frame (RF) shift in a gene. Deletions and insertions of DNA coding regions are considerable events for genes because an RF shift results in modifications of the extensive region of amino acid sequence coded by a gene. The suggested method is based on the phenomenon of triplet periodicity (TP) in coding regions of genes and its relative resistance to substitutions in DNA sequence. We attempted to extend 326 933 regions of continuous TP found in genes from the KEGG databank by considering possible insertions and deletions. We revealed totally 824 genes where such extension was possible and statistically significant. Then we generated amino acid sequences according to active (KEGG''s) and hypothetically ancient RFs in order to find confirmation of a shift at a protein level. Consequently, 64 sequences have protein similarities only for ancient RF, 176 only for active RF, 3 for both and 581 have no protein similarity at all. We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed.     

Studies on the local dispersal of the New Zealand flatworm, a predator of earthworms, in Edinburgh between 1993 and 1999

The flatworm Artioposthia triangulata was found, from studies using weighted down plastic sheeting, to move predominantly through the soil rather than over it and to use earthworm burrows. Under compost‐filled plastic sacks the flatworm was most active at night although its numbers were similar to those during the day. The transfer of specimens into an area covered with weighted plastic sheeting had no lasting effect on their numbers. The flatworm was regularly removed over 6 years from under paving stones, sheets of newspaper and cardboard placed on the ground in a garden. The rise and fall of the numbers of the flatworm under this debris suggest a predator‐prey periodicity between the flatworm and earthworms of 3 years.     

Identification of latent periodicity in amino acid sequences of protein families

For detection of the latent periodicity of the protein families responsible for various biological functions, methods of information decomposition, cyclic profile alignment, and the method of noise decomposition have been used. The latent periodicity, being specific to a particular family, is recognized in 94 of 110 analyzed protein families. Family specific periodicity was found for more than 70% of amino acid sequences in each of these families. Based on such sequences the characteristic profile of the latent periodicity has been deduced for each family. Possible relationship between the recognized latent periodicity, evolution of proteins, and their structural organization is discussed.     

Seasonal Fluctuation in Species Composition of Aquatic Hyphomycetous Flora in a Temperate Freshwater Stream of Central Himalaya,India

The frequency of occurrence and seasonal periodicity of aquatic hyphomycetes in a temperate freshwater stream of Central Himalaya were studied. The number of aquatic hyphomycetes species was found to vary inversely with temperature (r= −0.499; not significant), which explained 25 % of the variability. There were two maxima, one in spring and the other in autumn. On the basis of their occurrence, the species observed have been categorised into three groups. Constant species were Campylospora chaetocladia, Flagellospora penicilloides, Lemonniera aquatica and Tetracladium marchalianum.     

Seasonal periodicity of aquatic fungi in tanks at Kurukshetra,India

The occurrence, distribution and seasonal periodicity of 49 species of aquatic fungi belonging to the orders Chytridiales, Lagenidiales, Blastocladiales, Saprolegniales and Peronosporales from two tanks of Kurukshetra, India, is described. Seasonal periodicity was found to be governed by temperature.     

人类基因组核苷酸多态性位点核小体定位分析

研究人类基因组核苷酸多态性位点周围核小体的定位,对于分析核苷酸的变异机制有重要意义.分析了人类基因组单核苷酸多态性(SNP)位点、简单插入位点、插入删除位点和删除位点的分布规律,以及这些位点周围的核小体定位特征.结果表明:转录起始位点下游的核苷酸多态性位点分布呈现约211 bp的周期特征,单核苷多态位点另有一个146 bp的周期;约211 bp的周期与转录起始位点下游核小体的分布周期204 bp非常接近,146 bp的周期恰是核小体核心DNA的长度.这些结果说明核小体与多态性位点的分布关系密切.进一步研究证实,单核苷酸多态性位点多分布于核心DNA上,且多位于核心DNA的两端,这使得单核苷酸多态性位点具有146 bp周期,而插入、插入删除、删除多态性位点多分布于核小体排开区域,间隔约为204 bp.转录起始位点下游核小体等间隔的规则分布使得多态性位点的分布也具有周期性.研究表明,相对于核小体,不同类型变异发生的位置不同,核小体定位在基因组多态性位点的形成过程中具有重要作用.     

Molecular Characterization of the D Surface Protein Gene Subfamily in Paramecium tetraurelia

ABSTRACT. When Paramecium tetraurelia expresses the D serotype, detectable by serum tests, high molecular mRNA could be isolated, which corresponds to the molecular mass of the D surface protein. Using this D specific mRNA as a probe for screenings in different genomic libraries a subfamily of five very similar genes was found, named α-51D, _γ1-51D, _γ2-51D, δ-51D and ε-51D. Each of them is about 8-kb long, they show regions of identity to each other, and there is no evidence that any are defective genes or pseudogenes. Up to now serotype D is the only known serotype showing this phenomenon. Another novel feature is that two of the D isogenes are closely linked. The sequence for the entire coding region of the α-51D gene has been determined, as well as the upstream and downstream noncoding regions. Its deduced amino acid sequence shows the same characteristic cysteine periodicity displayed by all other immobilization antigen (i-ag) genes from Paramecium. However, in contrast to most other such genes, tandem repeats are missing from the 7599-bp long coding region of the α-51D gene. When the sequences of the type 51D genes are compared to each other, the similarity is very high and extends to coding as well as to noncoding regions. Similarity within noncoding regions is usually only observed for allelic i-ag genes. We conclude that the type D genes constitute a family of isogenes that are nonallelic. They contain slightly different consensus sequences with possible functions as regulatory regions.     

Localization and characterization of curved DNA in the human erythropoietin receptor gene by experimental and theoretical approaches.

We report here the locations of curved DNA in the human erythropoietin receptor gene. A total of 13 DNA bend sites were mapped by circular permutation assays, appearing at an average interval of 651.2+/-214.6 (S.D.) in the 8-kb region. The bend centers in these 13 bend sites were confirmed by oligonucleotide-based assays where most of these centers had bend angles higher than that shown by (AAACCGGGCC) x (A)20 and lower than that shown by (AAACCGGGCC)2 x (A)10. DNA curvature mapping by TRIF software, which is based on the distribution of dinucleotides, primarily AA and TT, provided a highly accurate prediction for the locations of the bend sites. They showed approximately 20 degrees to 40 degrees of bend angles demonstrated by the oligonucleotide assays and by computer analysis.     

Enamel incremental periodicity in the pig-tailed macaque: A polychrome fluorescent labeling study of dental hard tissues

Bromage and Dean originally outlined a nondestructive method for the study of enamel formation and concluded that early hominids resembled the extant apes more closely than they did modern humans in their rates of growth and maturation. The method used assumed that an enamel circadian rhythmicity was referable to a longer near-weekly period represented by perikymata (periodic surface growth features). This assumption became a matter of debate and discussion. In this study, developing teeth in Macaca nemestrina were labeled with polychrome fluorescent dyes. Examination of the distribution of these dyes in two sectioned teeth provides experimental confirmation of enamel circadian periodicity.     

Diel variation in diet composition of a riverine fish community

Although diel food habit studies have been undertaken on a number of individual species, few studies have examined diel variation in the diets of fish communities. We examined the diel diet variation and feeding periodicity of a fish community in the Juniata River, Pennsylvania. Nine species, totalling 1,098 fish, were collected at 4-h intervals over a 24-h period in October 1989, in numbers sufficient to describe their diel variation in diet composition. Diel variation in diet composition was evident in all species, as no single prey taxon was dominant in the diet of any species during any 4-h interval. Ephemeropterans were the most important prey taxa for four species of centrarchids, whereas chironomids were the main prey of banded killifish, mimic shiners, and spotfin shiners. Algae was the major component in the diet of spottail shiners, whereas bluntnose minnows contained mostly detritus. Feeding activities of rock bass, redbreast sunfish, and pumpkinseed occurred at low levels throughout the day; peak feeding occurred from 2000 to 0400 hours. Food consumption of smallmouth bass increased throughout the day with peak consumption occurring at 2000 hours. Non-centrarchids fed little during daylight hours and showed peak activity at 2000–2400 h. Construction of a 24-hour diet from six 4-h interval estimates and feeding periodicity data provided a comprehensive representation of the diel feeding ecology of all species collected.