The frequency distribution of nucleotide variation in Drosophila simulans.

Patterns of codon bias in Drosophila suggest that silent mutations can be classified into two types: unpreferred (slightly deleterious) and preferred (slightly beneficial). Results of previous analyses of polymorphism and divergence in Drosophila simulans were interpreted as supporting a mutation-selection-drift model in which slightly deleterious, silent mutants make significantly greater contributions to polymorphism than to divergence. Frequencies of unpreferred polymorphisms were inferred to be lower than frequencies of other silent polymorphisms. Here, I analyzed additional D. simulans data to reevaluate the support for these ideas. I found that D. simulans has fixed more unpreferred than preferred mutations, suggesting that this lineage has not been at mutation-selection-drift equilibrium at silent sites. Frequencies of polarized unpreferred polymorphisms are not skewed toward rare alleles. However, frequencies of unpolarized unpreferred codons are lower in high-bias genes than in low-bias genes. This supports the idea that unpreferred codons are borderline deleterious mutations. Purifying selection on silent sites appears to be stronger at twofold-degenerate codons than at fourfold-degenerate codons. Finally, I found that X-linked polymorphisms occur at a higher average frequency than polymorphisms on chromosome arm 3R, even though an average X-linked site is significantly less likely to be polymorphic than an average site on 3R. This result supports a previous analysis of D. simulans indicating different population genetics of X-linked versus autosomal mutations.     

k-长DNA子序列频数分布研究

在详细阐述了生成DNA序列分形图像的Hao方法后,提出一种能够直观显示k-长DNA子序列频数分布差异性的三维频数分布图生成方法。把3D频数分布图转化为1D对数频谱图,突出显示了频数分布的局部特征,提出k-长DNA子序列频数区划分准则,并详细研究了甚高频数区的n阶零间隔现象,指出n阶零间隔分布就是基因组进化过程所留痕迹的假设,并给出对数频谱图特征的生物学解释。实验发现许多DNA序列频数概率分布近似服从非中心F分布,对于分布呈多峰现象的基因组序列,可采用多个非中心F分布的叠加来拟合。在比较非中心F分布与Gamma分布后,提出一种结合二者在拟合方面具有互补优势的新分布,实验证明这种新分布能够更好地吻合实际DNA序列的频数分布。最后研究了两种特异出现频数(最高出现频数与出现频数为1的k-长子序列个数)与k值的关系,发现不同物种的这两种关系具有良好的一致性。     

CG sites and their nucleotide environment in the human gamma-delta-beta-globin gene cluster: distribution, frequency and possible frame for differential methylation

Available restriction endonucleases including CG dinucleotides in their target sequences (most of them being unable to cut the DNA when the cytosine of the CG sequence is methylated) have been used to map cloned DNA covering the human gamma-delta-beta globin gene cluster. Since the human DNA fragments were cloned in Escherichia coli, only the internal cytosine in the sequence CCAT GG could be methylated. Thus, any recognized "CG enzyme" site can be detected since they are unmethylated. Results show that frequencies of "CG enzyme" sites regularly decrease from the gamma-globin region to the beta-globin region, the latter being very poor in "CG enzyme"' sites. The array of enzymes used here detects 4 times more CG sites than the classical MspI/HpaII system. Examination of previously sequenced parts of the gamma-delta-beta globin gene cluster shows that CG dinucleotides correspond to an average frequency of 1 out of 104 nucleotides in the gamma-globin region and 1 out of 138 nucleotides in the beta-globin region. In the gamma-globin region, 1 CG out of 4 or 5 may be detected by the enzymes used; the detected frequency is less than 1 out of 10 CG in the beta-region. Analysis of nucleotide environment around CG dinucleotides shows occurrence of local differences, the main sequences being CGG in the 5' side flanking the gamma genes and ACG in the corresponding area of the beta gene. The results presented introduce some new considerations about analysis of cytosine methylation which has been previously proposed as playing a role in the control of the activity of gamma, delta and beta genes respectively.     

The nucleotide sequence and protein-coding capability of the transposable element IS5

The nucleotide sequence of IS5, a bacterial insertion sequence, has been determined. It is 1195 bp long and contains an inverted terminal repetition of 16 bp with one mismatch. One open reading frame, spanning nearly the entire length of the element, could encode a polypeptide of 338 amino acids. Upon insertion into a DNA segment, IS5 causes a duplication of 4 bp. Based on seven examples, this site of insertion appears to be nonrandom, and the consensus target site sequence is C . T/A . A . G/A (or C/T . T . A/T . G on the opposite strand). The nucleotide sequences of IS5 insertions into the B and cim genes of bacteriophage Mu have allowed tentative identification of the protein-coding frames of B and cim.     

Floating mats: their occurrence and influence on shoreline distribution of emergent vegetation

1. A study was conducted on the northern shore of Lake Victoria (Uganda) to determine the factors controlling the occurrence of floating root mats and the influence of the floating mats on the distribution of emergent vegetation. 2. Environmental conditions within 78 bays in the study area were characterised using bay size, wave exposure, water depth, littoral slope, sediment characteristics and water level fluctuations. Emergent plants that form floating root mats occur along the shores of these bays. The way in which commonly occurring shoreline vegetation was distributed across a wave‐exposure gradient was compared with their distribution across a water level fluctuation gradient. 3. Results suggested that wind–wave action and water level fluctuations are important factors determining the occurrence of floating mats. Mat‐forming plants occur in the most sheltered locations along the shore and in waterbodies with modest water level fluctuations. 4. The ability to form mats facilitated the lakeward expansion of emergent plants. Plants forming floating root mats had a larger depth range than non‐mat forming plants. 5. The initiation mechanisms for the floating mats of emergent vegetation in Lake Victoria appear to be: (i) invasion of mats of free‐floating plants by emergent vegetation; and (ii) detachment of emergent plants from the lake bed following flooding. 6. The formation of floating mats comes with a cost and benefit to emergent plants. The cost is increased vulnerability to damage by water level fluctuations or wind–wave action, leading to reduced horizontal distribution. The benefit is that deep flooding is avoided, thus increasing vertical distribution. The net effect may be to lead to dominance of mat‐forming plants in low‐energy environments and non‐mat‐forming plants in high‐energy environments.     

Atlantic oakwoods in Great Britain: Factors influencing their definition,distribution and occurrence

Summary

Atlantic oakwoods are the oceanic oak-dominated woodlands that fringe the western coast of Britain and Ireland and, due to their high humidity and rich and luxuriant lower plant assemblages, have been regarded as ‘temperate rainforest’. However, unlike the similarly iconic Caledonian pinewoods, Atlantic oakwoods have no formal designation or associated woodland classification type, which gives some uncertainty to the extent of the oakwoods habitat on its fringes. This paper examines the various elements central to the concept of an ‘Atlantic oakwood’ and discuses their occurrence in Great Britain.     

The phenology of molting,breeding and their overlap in central Amazonian birds

The energetically challenging periods of molting and breeding are usually temporally separated in temperate birds, but can occur simultaneously in tropical birds, a condition known as molt–breeding overlap. Here, we document great variation in the timing and duration of molting and breeding, and in the extent of molt–breeding overlap, among 87 species of understory passerines in central Amazonia. We analyzed molt and breeding from 26 871 birds captured over a 30‐yr period near Manaus, Brazil. Although most species typically bred during the late dry season (about October through January), many thamnophilids apparently bred year‐round, whereas a few other species from a variety of families bred mainly during the wet season (about January through May). Of all breeding birds with an active brood patch, 12.7% were simultaneously molting. Molt–breeding overlap was more frequently observed among suboscines (13.3%), especially thamnophilids (23.0%), than oscines (6.4%). Some families had <5% molt–breeding overlap frequency, including Tyrannidae (4.4%), Tityridae (0.0%), Pipridae (1.5%), Turdidae (0.0%), and Thraupidae (0.0%), indicating that not all tropical species exhibit molt–breeding overlap. Among 31 well‐sampled species (n ≥15 brood patches), variation in molt–breeding overlap frequency was positively correlated with each species’ average duration of flight feather replacement (range 98–301 d). We also measured feather growth rates of individual birds in nine species; in five of these, slower‐growing feathers increased with an individual's probability of having molt–breeding overlap. Among furnariids, molt–breeding overlap occurred either at the beginning or end of the molt cycle, suggesting that physiological mechanisms typically separate molting from breeding. Thamnophilids showed a much different pattern; molt–breeding overlap occurred at any stage of feather replacement, apparently not regulated to be independent of breeding. These results reveal substantial life‐history variation among Amazonian birds. Future work to resolve the physiological regulation of molting and breeding in tropical birds will greatly contribute to understanding these patterns and their relevance to avian diversity.     

The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap.

The nucleotide sequence of the genes encoding methyltransferase TaqI (M.TaqI) and restriction endonuclease TaqI (R.TaqI) with the recognition sequence, TCGA, were analyzed in clones isolated from independent libraries. The genes, originally reported as 363 and 236 codons long [Slatko et al., Nucleic Acids Res. 15 (1987) 9781-9796] were redetermined as 421 and 263 codons long, respectively. The C terminus of the taqIM gene overlaps the N terminus of the taqIR gene by 13 codons, as observed with the isoschizomeric TthHB8I restriction-modification system [Barany et al., Gene 112 (1992) 13-20]. Removal of the overlapping codons did not interfere with in vivo M.TaqI activity. We postulate the overlap plays a role in regulating taqIR expression.     

On finding poorly translated codons based on their usage frequency

Long stretches of “rare” codons are known to severely inhibit the efficiency of translation. Understanding the distribution of such rare codons is of critical importance in improving the efficiency of heterologous gene expression systems. Accurate estimates of codon usage take the abundance of each protein into consideration. In this paper, we analyze the correlation between approximate measures of codon usage and the availability of tRNA at various growth rates in E coli. We show that the computationally derived estimates of tRNA isoacceptor concentration enable the finding of poorly translated codons.     

The widespread occurrence and tissue distribution of the imidazolopyrazine luciferins

Bioluminescence has been reported to occur in 17 phyla and at least 700 genera. However, the luciferin chemistry of the majority of luminous organisms has yet to be determined. The most common chemistry which is known to occur in deep sea bioluminescence is imidazolopyrazine bioluminescence. The main aim of this study was to examine the phyletic and tissue distribution of imidazolopyrazine luciferins. This will facilitate analysis of imidazolopyrazine bioluminescence at the cellular and molecular levels and, in particular, how and when its chemistry is controlled and expressed in vivo. Assays for both known imidazolopyrazines were established and a range of fresh organisms and tissue were analysed, i.e. fish, cephalopods, copepods, ostracods, amphipods and euphausiids. The main findings were that the number of genera in which coelenterazine has been detected has been increased from 52 to about 90. Also, for the first time, the other known imidazolopyrazine luciferin,Vargula-type luciferin, was quantified in the ostracod Cypridina dentata, but was not detected in any of its potential predators. Neither imidazolopyrazine luciferin was found in several luminous stomiiform fish assayed. Coelenterazine was measured in the livers and photophores of a number of cephalopods and it is apparent that coelenterazine is responsible for both modes of luminescence. © 1997 John Wiley & Sons, Ltd.     

Life at the edge: Roe deer occurrence at the opposite ends of their geographical distribution,Norway and Portugal

In the face of climate change and habitat fragmentation there is an increasingly urgent need to learn more about factors that influence species distribution patterns and levels of environmental tolerance. Particular insights can be obtained by looking at the edges of a species range, especially from species with wide distributions. The European roe deer was chosen as a model species due to its widespread distribution. By using pellet group counts, we studied summer and winter habitat use of this herbivore at two of the extreme edges of its distribution – southwest of Portugal, and northeast of Norway – in relation to a range of fine-scale environmental factors including forest structure, vegetation characteristics and human disturbance. Our first prediction that roe deer would respond differently to human activity in both counties was supported. While in Norway roe deer are always close to houses, in Portugal they are either far (in summer) or indifferent (winter). However, everywhere and in every season, roe deer are far from roads. Our second prediction that roe deer better tolerate anthropogenic disturbances in the area where the importance of limiting factors is higher (Norway) was validated. However, our third prediction that anthropogenic disturbance would be less tolerated by roe deer outside the limiting seasons in each country was not supported. Our results suggest that roe deer perceive human activities differently in the two countries and that roe deer better tolerate anthropogenic disturbances in Norway.     

Classification of nucleotide sequences over their frequency dictionaries reveals a relation between the structure of sequences and taxonomy of their bearers

Classification of 16S RNA sequences over their frequency dictionaries, both real ones, and transformed ones was studied. Two entities were considered to be close each other from the point of view of their structure, if their frequency dictionaries were close, in Eucledian metric. A transformation procedure of a frequency dictionary has been implemented that reveals the peculiarities of information structure of a nucleotide sequence. A comparative study of two classification developed over the real frequency dictionary vs. that one developed over the transformed frequency dictionary was carried out. The strong correlation is revealed between the classification and the taxonomy of 16S RNA bearer. For the classes isolated, the information valuable words were identified. These words are the main factors of a difference between the classes. The frequency dictionaries containing the words of the length 3 exhibit the best correlation between a class and a genus. A genus, as a rule, is included into the same class, and the exclusion are sporadic. A development of hierarchy classification over the transformed frequency dictionaries separated one or two taxonomy groups, as each stage of classification. The unexpectedly frequent, or contrary, unexpectedly rare occurred of words (of the length 3) in entities under consideration make the structure difference between the classes of the nucleotide sequences.     

Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.

The 2694 ORFs originally annotated as potential genes in the genome of Aeropyrum pernix can be categorized into three clusters (A, B, C), according to their nucleotide composition at three codon positions. Coding potential was found to be responsible for the phenomenon of three clusters in a 9-dimensional space derived from the nucleotide composition of ORFs: ORFs assigned to cluster A are coding ones, while those assigned to clusters B and C are non-coding ORFs. A "codingness" index called the AZ score is defined based on a clustering method used to recognize protein-coding genes in the A. pernix genome. The criterion for a coding or non-coding ORF is based on the AZ score. ORFs with AZ > 0 or AZ < 0 are coding or non-coding, respectively. Consequently, 620 out of 632 ORFs with putative functions based on the original annotation are contained in cluster A, which have positive AZ scores. In addition, all 29 ORFs encoding putative or conserved proteins newly added in RefSeq annotation also have positive AZ scores. Accordingly, the number of re-recognized protein-coding genes in the A. pernix genome is 1610, which is significantly less than 2694 in the original annotation and also much less than 1841 in the RefSeq annotation curated by NCBI staff. Annotation information of re-recognized genes and their AZ scores are available at: http://tubic.tju.edu.cn/Aper/.