Effect of follicular wave stage on potential fertility predictors and their repeatability coefficient in prepubertal Bos indicus (Nellore) and Bos taurus (Caracu) heifers.

In an attempt to develop accessible methods for the precocious individual selection based on phenotypic attributes related to reproductive superiority, this study evaluated the effects of follicular wave stages (emergence and dominance) and the repeatability coefficients of potential fertility predictors (vulvar morphometry, uterine biometry, echogenicity and echotexture, ovarian biometry, and antral follicle count - AFC) in two breeds of purebred prepubertal heifers. Nellore (n = 30) and Caracu (n = 28) heifers were submitted to a sequence of 11 evaluations conducted every 48 h (D0 - random day of the antral follicular wave until D20) to study potential fertility indicators under natural conditions. The data obtained were compared according to breed and follicular wave stage. Statistical analysis included the fixed effects of breed, evaluation day, and their statistical interaction and was performed using MIXED, GENMOD, GLM, and CORR procedures of the SAS program. Breed was found to influence rima height, ovarian area, and AFC, which were greater in Nellore heifers (P < 0.02). The follicular wave stage also influenced most of the potential predictors, highlighting AFC which was higher in the presence of a dominant follicle in both breeds (P < 0.0001). The repeatability coefficients for vulvar width (0.76 and 0.66), ovarian area (0.70 and 0.62), and AFC (0.76 and 0.74) were considered to be high in Nellore and Caracu heifers, respectively. Only ovarian biometry was able to predict AFC (Pearson correlation coefficient ≥ 0.66; P < 0.0001) in prepubertal heifers. The results indicate that most of the phenotypic reproductive parameters analyzed can be characterized throughout prepuberty using a single measure since they are intrinsic attributes of the individual.

Norine: A powerful resource for novel nonribosomal peptide discovery.

Since its first release in 2008, Norine remains the unique resource completely devoted to nonribosomal peptides (NRPs). They are very attractive microbial secondary metabolites, displaying a remarkable diversity of structure and functions. Norine (http://bioinfo.lifl.fr/NRP) includes a database now containing more than 1160 annotated peptides and user-friendly interfaces enabling the querying of the database, through the annotations or the structure of the peptides. Dedicated tools are associated for structural comparison of the compounds and prediction of their biological activities. In this paper, we start by describing the knowledgebase and the dedicated tools. We then present some user cases to show how useful Norine is for the discovery of novel nonribosomal peptides.

HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, "retroviral signatures" of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution.

Previous analyses of retroviral nucleotide sequences, suggest a so-called "scrambled duplicative stepwise molecular evolution" (many sectors with successive duplications/deletions of short and longer motifs) that could have stemmed from one or several starter tandemly repeated short sequence(s). In the present report, we tested this hypothesis by focusing on the long terminal repeats (LTRs) (and flanking sequences) of 24 human and 3 simian immunodeficiency viruses. By using a calculation strategy applicable to short sequences, we found consensus overrepresented motifs (often containing CTG or CAG) that were congruent with the previously defined "retroviral signature." We also show many local repetition patterns that are significant when compared with simply shuffled sequences. First- and second-order Markov chain analyses demonstrate that a major portion of the overrepresented oligonucleotides can be predicted from the dinucleotide compositions of the sequences, but by no means can biological mechanisms be deduced from these results: some of the listed local repetitions remain significant against dinucleotide-conserving shuffled sequences; together with previous results, this suggests that interspersed and/or local mononucleotide and oligonucleotide repetitions could have biased the dinucleotide compositions of the sequences. We searched for suggestive evolutionary patterns by scrutinizing a reliable multiple alignment of the 27 sequences. A manually constructed alignment based on homology blocks was in good agreement with the polypeptide alignment in the coding sectors and has been exhaustively assessed by using a multiplied alphabet obtained by the promising mathematical strategy called the N-block presentation (taking into account the environment of each nucleotide in a sequence). Sector by sector, we hypothesize many successive duplication/deletion scenarios that fit our previous evolutionary hypotheses. This suggests an important duplication/deletion role for the reverse transcriptase, particularly in inducing stuttering cryptic simplicity patterns.