Guillermo Thode

Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafishDanio reio

Abstractthe chromosome complement ofDanio rerio was investigated by Giemsa staining and C-banding, Ag-NORs and replication banding. The diploid number of this species is 2n=50 and the arm number (NF)=100. Constitutive heterochromatin was located at the centromeric position of all chromosome pairs. Nucleolus organizer regions appeared in the terminal position of the long arms of chromosomes 1, 2 and 8. Replication banding pattern allowed the identification of each chromosome pair.

Gene annotation from scientific literature using mappings between keyword systems

MOTIVATION The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene. RESULTS To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%). AVAILABILITY The algorithm can be publicly accessed and used for the annotation of sequences through a web server at http://www.bork.embl.de/kat

Chromosome relationships in the genus Blennius (Blenniidae Perciformes) C-banding patterns suggest two karyoevolutional pathways

The karyotypes of the Mediterranean blenniid species: Blennius gattorugine, B. ponticus incognitus, B. pavo, B. sanguinolentus, B. galerita, B. trigloides and B. pholis were analyzed by means of conventional, silver staining and C-banding techniques. All have shown 2n=48, except B. pholis with 2n=46, while the NF varies from 54 to 72. Only two NORs, in terminal position on the short arms of the carrier pair, were detected in all species. These regions have proved to be structurally polymorphic in four species. Two markedly different C-banding patterns lead us to separate the species into two different karyoevolutionary categories, whose taxonomic and specialization implications are discussed.

Multiple Chromosome Polymorphism in Gobius paganellus (Teleostei, Perciformes)

Chromosome preparations from 46 specimens of G. paganellus were studied, revealing seven different karyomorphs: D2 (2n=46, NF=46), D1 (2n=47, NF=47), B (2n=48, NF=48), F1 (2n=47, NF=48), F2 (2n=46, NF=48), D1F1 (2n=46, NF=47), I1 (2n=48, NF=49). It is proposed that the mechanisms involved are deletions, fusions and inversions. The meiotic results suggest that the same chromosome pair was engaged in both the fusion and the deletion rearrangements. Intra-individual polymorphism was found in only one specimen. This and the range of karyomorphs suggest that this variation is regularly inherited.

Early replication bands in two scorpion fishes, Scorpaena porcus and S. notata (order Scorpaneiformes)

The use of the BrdU-FPG methodology in the scorpion fish (Scorpaena porcus) has allowed us to estimate the mean cell cycle duration in kidney cells in vivo as being approximately 32.5 h. On the basis of this datum, replication protocols from 30 to 10 h of BrdU incorporation were employed revealing a precise order in the replication of the chromosomes. Treatments of 18–20 h proved to be the most useful in getting optimum replication bands and were used to elaborate the RBG-banding pattern karyotypes of S. porcus and S. notata. Their comparison confirms the high karyotypic distance between these morphologically similar species.

A complex chromosomal polymorphism in Gobius fallax (Gobiidae, Perciformes)

Chromosome analysis of 53 specimens from a population of Gobius fallax has revealed inter- and intra-individual variation in the diploid number (2n=38–43) arising mainly through Robertsonian translocations. The presence of a small biarmed chromosome in a few cells from 3 males as well as the numerous multivalent configurations in meiotic plates and the apparent association between the NOR-chromosomes and other acrocentrics suggest that this polymorphism has an inherited as well as a somatic origin and that some translocations may involve more than two acrocentric pairs simultaneously.

A new Robertsonian fusion in the multiple chromosome polymorphism of a mediterranean population of Gobius paganellus (Gobiidae, Perciformes)

Karyotypic analysis of 67 individuals of a Mediterranean population of G. paganellus has revealed three new karyomorphs: D2F′1, (2n = 45, NF = 46), F2F′1, (2n = 45, NF = 48), D1F1F′1, (2n = 45, NF = 47), in addition to the seven previously reported by Thode et al. (1985). The C-banding pattern and the meiotic configurations clearly show that the mechanism involved is a new centromeric fusion. The high level of intra-individual variability for this rearrangement suggests a possible origin within this population. The involvements of this fusion in the polymorphism of G. paganellus are discussed mainly in comparison with another centromeric fusion.

DNA Content and Chromosome Complement of Chromis Chromis (Pommacentridae, Perciformes)

SUMMARYSomatic and germinal chromosomes of Chromis chromis were analysed and the diploid number was determined to be 48, the same as its F. N. The haploid amount of DNA was estimated by Feulgen cytophotometry at 1, 2 pg. The karyotype and DNA content are discussed as a contribution to the understanding the evolution of this species inside the family. The study helps to establish the location of this family on the evolutionary scale within the teleosts.

Semirna: Searching for Plant miRNAs Using Target Sequences

Many plant genomes are already known, and new ones are being sequenced every year. The next step for researchers is to identify all of the functional elements in these genomes, including the important class of functional elements known as microRNAs (miRNAs), which are involved in posttranscriptional regulatory pathways. However, computational tools for predicting new plant miRNAs are limited, and there is a particular need for tools that can be used easily by laboratory researchers. We present semirna, a new tool for predicting miRNAs in plant genomes, available as a Web server. This tool takes a putative target sequence such as a messenger RNA (mRNA) as input, and allows users to search for miRNAs that target this sequence. It can also be used to determine whether small RNA sequences from massive sequencing analysis represent true miRNAs and to search for miRNAs in new genomes using homology. Semirna has shown a high level of accuracy using various test sets, and gives users the ability to search for miRNAs with several different adjustable parameters. Semirna, a user-friendly and intuitive Web server for predicting miRNA sequences, can be reached at http://www.bioinfocabd.upo.es/semirna/ . It is useful for researchers searching for miRNAs involved in particular pathways, as well as those searching for miRNAs in newly sequenced genomes.

Phylogenetic interpretation of chromosomal and nuclear-DNA-content data in the genus Blennius (Blenniidae: Perciformes)

The haploid DNA content and karyotypes of eight species of Blennius are studied. Six species had 2n=48, two had 2n=46.The karyotypes of these species have been compared with those of related species of the genus and it was suggested that pericentric inversions played an important role in the evolution of their karyotypes. No sex chromosomes were morphologically identifiable in these gonochorist species. The data are discussed in connection with possible lines of evolution within the genus.