Genomic analysis of Drosophila melanogaster telomeres: full-length copies of HeT-A and TART elements at telomeres

The repetitive nature of heterochromatin hampers its analysis in general genome-sequencing projects. Specific studies are needed to extend the sequence into telomeric and centromeric heterochromatin. Drosophila telomeres lack the telomerase-generated repeats that are characteristic of other eukaryotic chromosomes. Instead, they consist of tandem arrays of HeT-A and TART elements. Herein, we present the genomic organization of the telomeres in the isogenic strain (y; cn bw sp) that was used for the Drosophila melanogaster sequencing project. The data indicate that the canonical features of telomere organization are widely conserved in evolution. In addition, we have identified full-length elements, likely competent elements, for HeT-A and TART.     

The Genomic HyperBrowser: inferential genomics at the sequence level

The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no.     

Genomic distribution of the retrovirus-like element ZAM in Drosophila

The mobile element ZAM, recently identified in Drosophila melanogaster, is similar in structure and coding potential to vertebrate retroviruses. In this paper, we analyze the insertional and structural polymorphism of this element and show that members of this family appear to have a long evolutionary history in the genome of Drosophila. It is present in all the species of the D. melanogaster subgroup and in more distantly related species like D. takahashii, D. ananassae, or D. virilis but in a lower copy number or with a lower homology. Two categories of strains have been previously identified in D. melanogaster: strains with a high copy number of ZAM and strains with a low copy number. Here, we show that ZAM is at least in a low copy number in each tested strain of the species analyzed. The study of ZAM's genomic distribution by FISH mapping analysis to salivary gland polytene chromosomes or on mitotic chromosomes indicates that most of the insertion sites of ZAM elements are associated with the constitutive heterochromatin regardless of the ZAM copy number. In addition, our results suggest that multiple ZAM elements are present at the insertion sites visualized by in situ experiments. This revised version was published online in August 2006 with corrections to the Cover Date.     

The origin of nematode sperm: Progenesis at the cellular level

Analysis of the development and structure of aberrant sperm of nematodes and other metazoans with internal insemination showed that these spermatozoa have several unusual, but shared features: (1) the absence of a flagellum and an axoneme, an unusual arrangement of centrioles; (2) an amoeboid shape and amoeboid motility due to cytoskeleton components; (3) the poor condensation of nuclear chromatin, which may be diffuse, thread-like, and discrete; (4) the absence of a nuclear envelope; (5) multiple unmodified mitochondria; (6) the absence of an acrosome; (7) unique membranous components derived from the Golgi complex; and (8) the large size of spermatozoa due to prominent cytoplasm filled with a great number of components. These shared features of aberrant spermatozoa may be explained by the conservation of a number of features that are characteristic of the primitive undifferentiated cell (the predecessor of all specialized gametes). The primitive cell features of numerous versions of aberrant sperm reflect the arrest of cytoplasm specialization of male gametes at an early stage of development. This pattern of gamete evolution is quite consistent with the conception of progenesis (retention of juvenile characters by precocious, sexually mature morphologically juvenile stage). Thus, the origin of the aberrant sperm of nematodes and many other metazoans may be interpreted as progenesis at the cellular level.     

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis.     

Genomic structure of human polyoma virus JC: nucleotide sequence of the region containing replication origin and small-T-antigen gene

The nucleotide sequence of the region of human polyoma virus JC DNA between 0.5 and 0.7 map units from a unique EcoRI cleavage site was determined and compared with those of the corresponding regions of another human polyoma virus, BK, and simian virus 40 DNAs. Within this region consisting of 945 base pairs, we located the origin of DNA replication near 0.7 map units, the entire coding region for small T antigen, and the splice junctions for large-T-antigen mRNA. The deduced amino acid sequences for small T antigen and the part of large T antigen markedly resembled those of polyoma virus BK and simian virus 40. The results strongly suggest that polyoma virus JC has the same organization of early genome as polyoma virus BK and simian virus 40 on the physical map, with the EcoRI site as a reference point.     

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale,Merino and Creole sheep

The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip^®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F_ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F_ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F_ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.     

Genomic signatures of local adaptation in the Drosophila immune response

As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.     

Analysis of the nucleotide sequence and electrostatic potential distribution in the <Emphasis Type=Italic>Escherichia coli</Emphasis> genome

Analysis of the oligonucleotide composition of the complete E. coli genome and its σ⁷⁰-specific promoters shows that promoter DNA mainly contains AT-rich hexanucleotides that have functionally important physical properties (propensity to form ‘low-melting’ regions and helix bends). Comparative analysis of the electrostatic characteristics reveals that hexanucleotides corresponding to more electronegative surroundings are mostly found in promoter DNA.     

Predation and refugia: implications for Chaoborus abundance and species composition

1. Previous studies have suggested that the occurrence of larval Chaoborus in lakes may be affected by fish predation, pH, elevation, temperature, nutrient level, water transparency and interspecific competition, but so far, a detailed statistical evaluation of these findings has not been performed. 2. The aim of this study was to apply regression and ordination techniques to a large data set of 56 lakes in order to test which variables related to lake morphology, water chemistry, and fish predation determine (1) the abundance of individual Chaoborus species and (2) their species composition. 3. Individual Chaoborus species were influenced by very different sets of environmental factors. Nutrient levels positively affected the largest species, Chaoborus americanus, which was restricted to fishless lakes. Abundance of the smallest and most transparent species, C. punctipennis, seemed to be controlled more by the larger Chaoborus species than by fish. Larger chaoborids required low water clarity in order to co‐exist with fish, probably to increase refuge availability. Generally, small lakes (for C. flavicans/C. trivittatus) and shallow lakes (for C. punctipennis) supported higher abundances of Chaoborus.     

The nucleotide sequence of the araC regulatory gene in Salmonella typhimurium LT2

The nucleotide sequence of the araC regulatory gene of Salmonella typhimurium LT2 has been determined. This sequence and the predicted araC translational product are compared to their counterparts in Escherichia coli. The two genes code for similar products although the S. typhimurium protein is eleven amino acids shorter than the E. coli protein. The predicted amino acid sequences are 92% conserved and the DNA sequences are 82% conserved for the common regions of the two genes.     

Land-use diversity index: a new means of detecting diversity at landscape level

Preservation of ecological diversity is a guiding principle of landscape management and planning. Although diversity is often quantified with measurable indices, common approaches used to measure diversity, for example the Shannon–Weaver index, are not adequate for many landscape studies, because they are affected by scale and sampling efforts. A robust index for measurement of landscape diversity should be able to quantify distinctive components of a landscape mosaic. This paper provides a new diversity index for landscape studies that improves the measurement of diversity at landscape level. The key features of the method are inclusion of an implication of physical moment and quantification of diversity by placing greater weight on the structure and composition of a patch. We have named the new index the land-use diversity index, or LUDI, and have concluded that the LUDI is the preferred measure of diversity at landscape level.