Community Structure of Fishes and Habitat Complexity on a Tropical Rocky Shore

The relationship between the variables of reef fish community structure (fish richness, fish diversity and total number of fishes) and those of habitat complexity (total surface area, substratum diversity, topographic complexity, number of holes, percent cover of turf algae, zoanthids, millepores, massive corals, bare rock, encrusting calcareous algae, urchins, other sessile organisms and Sargassum) were examined on three different rocky shores (FA, FB and FT) at Arraial do Cabo, a tropical region located on Brazilian southeastern coast (23° S, 42° W). Fish abundance and vertical distribution were assessed by a visual census technique using strip transects. Percentage cover of benthic organisms and other substratum types were calculated by replicated transects using a chain laid down on the substratum. Topographic complexity was determined by the chain link method and number of holes were estimated by direct counts on replicated transects. More than 91 fishes belonging to 37 families were seen in all study sites during one year of visual census effort. FA and FB sites had similar fish community structure and habitat complexity characteristics, while FT showed different habitat characteristics and higher fish diversity and richness, plus total number of fishes. Vertical distribution of fishes along the rocky shores studied seemed to be predictable and was determined by factors such as feeding habits and behavior, availability of refuges and social interactions. The habitat variables that best explained the higher diversity and number of fishes observed in FT site were total surface area of rocky shores and the abundance of benthic sessile invertebrates; these conditions were typical of rocky shores more exposed to wave surge.     

Pre‐/post‐otic rhombomeric interactions control the emergence of a fetal‐like respiratory rhythm in the mouse embryo

How regional patterning of the neural tube in vertebrate embryos may influence the emergence and the function of neural networks remains elusive. We have begun to address this issue in the embryonic mouse hindbrain by studying rhythmogenic properties of different neural tube segments. We have isolated pre‐ and post‐otic hindbrain segments and spinal segments of the mouse neural tube, when they form at embryonic day (E) 9, and grafted them into the same positions in stage‐matched chick hosts. Three days after grafting, in vitro recordings of the activity in the cranial nerves exiting the grafts indicate that a high frequency (HF) rhythm (order: 10 bursts/min) is generated in post‐otic segments while more anterior pre‐otic and more posterior spinal territories generate a low frequency (LF) rhythm (order: 1 burst/min). Comparison with homo‐specific grafting of corresponding chick segments points to conservation in mouse and chick of the link between the patterning of activities and the axial origin of the hindbrain segment. This HF rhythm is reminiscent of the respiratory rhythm known to appear at E15 in mice. We also report on pre‐/post‐otic interactions. The pre‐otic rhombomere 5 prevents the emergence of the HF rhythm at E12. Although the nature of the interaction with r5 remains obscure, we propose that ontogeny of fetal‐like respiratory circuits relies on: (i) a selective developmental program enforcing HF rhythm generation, already set at E9 in post‐otic segments, and (ii) trans‐segmental interactions with pre‐otic territories that may control the time when this rhythm appears. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006     

Calculation of relative binding free energy difference of DHFR inhibitors by a finite difference thermodynamic integration (FDTI) approach.

We have implemented a Finite Difference Thermodynamic Integration (FDTI) approach to estimate the binding free energy relative to methotrexate (MTX) of three unreported inhibitors of DHFR. The validity of the calculation methodology was first proved by evaluating the relative binding free energy difference for two well-known anticancer agents aminopterin and methotrexate. The usefulness of the method in drug design has been demonstrated by the fact that inhibitor 5, designed by us was found to bind more tightly than MTX, by as much 7.5 kcal/mole and is a worthy candidate for further pharmacological investigations.     

Theoretical study of the NMR chemical shift of Xe in supercritical condition

In this work we investigate the level of theory necessary for reproducing the non-linear variation of the ¹²⁹Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the ¹²⁹Xe chemical shift depends under supercritical conditions on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xe _n clusters (n =?2 ? 8 depending on the density). The analysis of the relativistic effects is made at the level of 4-component Hartree-Fock calculations (4c-HF) and electron correlation effects are considered using second order Møller-Plesset perturbation theory (MP2). To simplify the calculations of the relativistic and electron correlation effects we adopted an additive scheme, where the calculations on the Xe _n clusters are carried out at the non-relativistic Hartree-Fock (HF) level, while electron correlation and relativistic corrections are added for all the pairs of Xe atoms in the clusters. Using this approach we obtain very good agreement with the experimental data, showing that the chemical shift of ¹²⁹Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects.     

Natural selection at the MJD locus: phenotypic diversity, survival and fertility among Machado-Joseph Disease patients from the Azores.

Machado-Joseph Disease (MJD) is an autosomal dominant neurodegenerative disorder of adult onset, associated with the expansion of a (CAG)n tract in the coding region of the causative gene, localized on 14q32.1. Machado-Joseph Disease shows non-Mendelian features typical of other triplet repeat disorders, including clinical heterogeneity, variable age at onset and anticipation. Three phenotypes have been proposed (clinical types 1, 2 and 3). Type 1 is associated with early age at onset and a high repeat number of the CAG sequence, and Types 2 and 3 have later onset and lower numbers of CAG repeats. This paper investigates whether there is selection against the MJD gene, acting through differential survival. nuptiality and fertility associated with clinical type and age at onset. The study sample comprised 40 MJD patients from the Azores (Portugal) having fully documented reproductive histories and known dates of death. The proportion of married patients of each clinical type increased from 0.22 among Type 1 patients, to 0.40 in Type 2 and 0.95 in Type 3. Age at onset and length of survival were also associated with marital status, with the married cases having later mean age at onset and longer mean survival time. In the whole sample, clinical type was associated with fertility, with significantly fewer children born to Type 1 patients. Among married patients clinical type was not associated with age at marriage, reproductive span or number of children. No reduction of fertility was detected among married patients in whom the onset of MJD was below the age of 50. The authors' interpretation of these results is that the high-repeat CAG haplotypes associated with early age at onset and clinical Type 1 are selected against through reduced survival and fertility. The fertility component of selection is mediated by nuptiality rather than marital fertility.     

Leishmanial antigens in the diagnosis of active lesions and ancient scars of American tegumentary leishmaniasis patients.

Cutaneous biopsies (n = 94) obtained from 88 patients with American tegumentary leishmaniasis were studied by conventional and immunohistochemical techniques. Specimens were distributed as active lesions of cutaneous leishmaniasis (n = 53) (Group I), cicatricial lesions of cutaneous leishmaniasis (n = 35) (Group II) and suggestive scars of healed mucosal leishmaniasis patients (n = 6) (Group III). In addition, active cutaneous lesions of other etiology (n = 24) (Group C1) and cutaneous scars not related to leishmaniasis (n = 10) (Group C2) were also included in the protocol. Amastigotes in Group I biopsies were detected by routine histopathological exam (30.2%), imprint (28.2%), culture (43.4%), immunofluorescence (41.4%) and immunoperoxidase (58.5%) techniques; and by the five methods together (79.3%). In Group II, 5.7% of cultures were positive. Leishmanial antigen was also seen in the cytoplasm of macrophages and giant cells (cellular pattern), vessel walls (vascular pattern) and dermal nerves (neural pattern). Positive reaction was detected in 49 (92.5%), 20 (57%) and 4 (67%) biopsies of Groups I, II and III, respectively. Antigen persistency in cicatricial tissue may be related to immunoprotection or, on the contrary, to the development of late lesions. We suggest that the cellular, vascular and neural patterns could be applied in the immunodiagnosis of active and cicatricial lesions in which leishmaniasis is suspected.     

Conformation of N-terminal HIV-1 Tat (fragment 1-9) peptide by NMR and MD simulations.

The N-terminal portion of HIV-1 Tat covering residues 1-9 is a competitive inhibitor of dipeptidyl peptidase IV (DP IV). We have used 1H NMR techniques, coupled with molecular dynamics methods, to determine the conformation of this peptide in the three diverse media: DMSO-d6, water (pH 2.7) and 40% HFA solution. The results indicate that in both DMSO-d6 and HFA the peptide has a tendency to acquire a type I beta-turn around the segment Asp5-Pro6-Asn7-IIe8. The N-terminal end is seen to be as a random coil. In water, the structure is best described as a left-handed polyproline type II (PPII) helix for the mid segment region Asp2 to Pro6. The structures obtained in this study have been compared with an earlier report on Tat (1-9).