Navigating within thiamine diphosphate-dependent decarboxylases: Sequences,structures, functional positions,and binding sites

Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of C C bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.     

Effect of different K+ concentrations on cryptococcus neoformans phenoloxidase activity

Melanin synthesis in Cryptococcus neoformans, catalyzed by phenoloxidase activity, is one of the oldest virulence factors known. However, until now, the relationship between melanin production in C. neoformans and its virulence has been poorly understood. Among different chemical compounds only Fe³⁺ and Cu²⁺ cations enhance the phenoloxidase activity in C. neoformans. A few reports in the literature describe the influence of different cations on C. neoformans phenoloxidase activity, excluding iron [1–3]. In this study, 13 C. neoformans strains isolated from AIDS patients and 7 from bird droppings (B.D.), were examined in order to clarify the effect of different K⁺ concentrations on phenoloxidase activity. A new solid and liquid caffeic acid minimal synthetic medium (MSM-CAF) containing only caffeic acid and ferric citrate with different potassium concentrations was used to evaluate C. neoformans phenoloxidase activity. In the MSM-CAF solid medium the degree of brown pigmentation on the agar plates was read on days 1, 2 and 3 of incubation, and the pigmentation of the C. neoformans strains was classed into 5 categories. The brown pigment of the liquid MSM-CAF test tubes were checked after 24 hours of incubation by measuring the optical density (O.D.) at 480 nm. Three C. neoformans AIDS and B.D. strains, randomlychosen, were tested for phenoloxidase activity, according to the modified protocols of Polachecket al., Torres-Guerrero et al. and Rhodes [2–4]. According to the results obtained, it has been observed that K⁺ does not activate the phenoloxidase activity in the C. neoformans AIDS and B.D. strains. In particular, with an increase in potassium concentrations in the MSM-CAF solid and liquid medium, there was a corresponding inhibition of the phenoloxidase activity on both the C. neoformans AIDS and B.D. strains.This revised version was published online in October 2005 with corrections to the Cover Date.     

Construction and expression of an adenosine deaminase::lacZ fusion gene

A eukaryotic expression vector was constructed in which the coding nucleotide sequences (ADA) of human adenosine deaminase (ADA) were fused in frame with the coding sequences of the bacterial gene lacZ encoding beta-galactosidase (beta Gal). This ADA::lacZ fusion gene was anticipated to encode a hybrid protein that has retained the biological functions of both proteins. Transfection of mammalian cells with the fusion gene resulted in the synthesis of both ADA and beta Gal. Cells expressing the gene could therefore be detected with the histochemical staining procedure that relies on the conversion of the indicator, XGal, by beta Gal. In addition, the transfected cells could be sorted on a fluorescence-activated cell sorter with the use of a vital staining procedure described for the selection of beta Gal-producing cells. Cell lines that harbored the fusion gene were tested for ADA overexpression by exposing them to the cytotoxic adenosine analog 9-beta-D-xylofuranosyl adenine (Xyl-A), in the presence of the ADA inhibitor deoxycoformycin (dCF). Resistance to Xyl-A/dCF was observed in the lines carrying ADA::lacZ and moreover, the fraction of cells that survived a stringent selection for ADA overexpression also exhibited significantly increased levels of beta Gal, which confirmed the direct linkage between ADA and lacZ expression. The use of this and other fusion genes might be useful in the development of gene-therapy protocols where they could help to meet the demand for versatile methods to detect and select cells with newly introduced genes.     

Chromosomal evidence of hemiclonal and all-paternal offspring production in Bacillus rossius-grandii benazzii (Insecta Phasmatodea)

The stick insects Bacillus rossius-grandii benazzii and B. rossius-grandii grandii naturally reproduce by hybridogenesis and androgenesis. The hybrid karyotype of the former (2n=35, XX female; 34, X0 male) clearly sums up a B. rossius haploset (r) with n=18 and a B. grandii benazzii one (gb) with n=17. The two sets keep the parental features for C-heterochromatin amount (much larger in the gb complement) and satellites/NORs (nuclear organizer regions) (more numerous and variably located in the r set); hybridogenetically produced males always show severely impaired gametogenesis and are therefore sterile, whereas hybridogenetic females are fertile. Reproductive, karyological and cytogenetical properties of the hybridogenetic system have been exploited to obtain the chromosomal evidence of whole haploset exchanges. In progenies obtained by crossing B. rossiusgrandii benazzii females to B. rossius males with either standard or repatterned (with Robertsonian fusions) karyotypes, there has always been complete agreement between electrophoretically genotyped and karyologically analyzed hybridogenetic offspring: the unassorted maternal r haploset (r ^m) is transmitted and the gb ^m haploset replaced by that of the fathering male (r ^p), thus evidencing the hemiclonal reproduction and the new r ^m-r ^p chromosomal constitution. New karyotype traits of the offspring relate to chromosome number (2n=36, female; 35, male), C-heterochromatin pattern (the heterochromatin-rich gb haploset completely disappears) and satellite/NOR features (corresponding to r ^m plus r ^p locations). The same crosses also produce genetically and chromosomally all-paternal descendants (androgenetics), of both sexes and fully fertile, with an r ^p r ^p structure. These androgenetic progeny show segregation for alleles and chromosomes at which fathering males are heterozygous: it was therefore possible to demonstrate that androgenetics can derive from syngamy of two sperm nuclei, of the several present in the polyspermic hybridogenetic egg. The production of androgenetics from field fertilized females of B. rossius-grandii benazzii, B. rossius-grandii grandii and parthenogenetic Bacillus whitei (=B. rossius/grandii grandii) suggests the occurrence of unsuspected relationships between hybrids and their parental species, so that the hybrids cannot be simply considered as sexual parasites. Furthermore, there is a suggestion of evolution of parthenogenetic clonal species from selection of initially hybridogenetic strains. The ability to produce uniparental progeny naturally from the spermatic genome may open a new field of investigation on genomic imprinting.     

First evidence of cell division in circulating haemocytes from the Manila clam Tapes philippinarum

In the present study, we report on haemocyte distribution, determined by a Coulter Counter, in the clam Tapes philippinarum. In addition, cytoskeleton components of haemocytes were examined using specific probes for F-actin and alpha-tubulin. The mean number of circulating haemocytes was 5 (x10(6))cells/ml haemolymph. Two main haemocyte populations were found in the haemolymph: small cells, 2-3microm in diameter and 10-100fl in volume; and large cells, 6-10microm in diameter and 150-400fl in volume. Analysis of the haemocyte cytoskeleton revealed bundles of actin filaments oriented according to the cell major axis, and microtubules radiating from the microtubule-organizing centre in proximity of the nucleus. Interestingly, mitotic spindles were also found radiating from the microtubule-organizing centres, located at the spindle poles (centrosomes) of undifferentiated cells. On the basis of both our previous findings regarding circulating stem cells (Cima, F., Matozzo, V., Marin, M.G., Ballarin, L., 2000. Haemocytes of the clam Tapes philippinarum (Adams & Reeve, 1850): morphofunctional characterisation. Fish Shellfish Immunol 10, 677-693) and new information from the present study, we suggest that haemoblasts are able to divide in the haemolymph of T. philippinarum. To our knowledge, this is the first report of mitotic spindles in circulating haemocytes from a bivalve species.     

Functional mechanisms shaping lateral geniculate responses to artificial and natural stimuli

Functional models of the early visual system should predict responses not only to simple artificial stimuli but also to sequences of complex natural scenes. An ideal testbed for such models is the lateral geniculate nucleus (LGN). Mechanisms shaping LGN responses include the linear receptive field and two fast adaptation processes, sensitive to luminance and contrast. We propose a compact functional model for these mechanisms that operates on sequences of arbitrary images. With the same parameters that fit the firing rate responses to simple stimuli, it predicts the bulk of the firing rate responses to complex stimuli, including natural scenes. Further improvements could result by adding a spiking mechanism, possibly one capable of bursts, but not by adding mechanisms of slow adaptation. We conclude that up to the LGN the responses to natural scenes can be largely explained through insights gained with simple artificial stimuli.     

Non-dipper treated hypertensive patients do not have increased cardiac structural alterations

Background

Non-dipping pattern in hypertensive patients has been shown to be associated with an excess of target organ damage and with an adverse outcome. The aim of our study was to assess whether a reduced nocturnal fall in blood pressure (BP), established on the basis of a single 24-h BP monitoring, in treated essential hypertensives is related to more prominent cardiac alterations.

Methods

We enrrolled 229 treated hypertensive patients attending the out-patient clinic of our hypertension centre; each patient was subjected to the following procedures : 1) clinic BP measurement; 2) blood and urine sampling for routine blood chemistry and urine examination; 3) standard 12-lead electrocardiogram; 4) echocardiography; 5) ambulatory BP monitoring (ABPM). For the purpose of this study ABPM was carried-out in three subgroups with different clinic BP profile : 1) patients with satisfactory BP control (BP < 140/90 mmHg; group I, n = 58); 2) patients with uncontrolled clinic BP (clinic BP values ≥ 140 and/or 90 mmHg) but lower self-measured BP (< 20 mmHg for systolic BP and/or 10 mmHg for diastolic BP; group II, n = 72); 3) patients with refractory hypertension, selected according to WHO/ISH guidelines definition (group III, n = 99). Left ventricular hypertrophy (LVH) was defined by two gender-specific criteria (LV mass index ≥125/m² in men and 110 g/m² in women, ≥51/gm^2.7 in men and 47/g/m^2.7 in women).

Results

Of the 229 study participants 119 (51.9%) showed a fall in SBP/DBP < 10% during the night (non-dippers). The prevalence of non-dippers was significantly lower in group I (44.8%) and II (41.6%) than in group III (63.9%, p < 0.01 III vs II and I). The prevalence of LVH varied from 10.3 to 24.1% in group I, 31.9 to 43.1% in group II and from 60.6 to 67.7% in group III (p < 0.01, III vs II and I). No differences in cardiac structure, analysed as continuous variable as well as prevalence of LVH, were found in relationship to dipping or non-dipping status in the three groups.

Conclusions

In treated essential hypertensives with or without BP control the extent of nocturnal BP decrease is not associated with an increase in LV mass or LVH prevalence; therefore, the non-dipping profile, diagnosed on the basis of a single ABPM, does not identify hypertensive patients with greater cardiac damage.     

Autosomal recessive familial exudative vitreoretinopathy is associated with mutations in LRP5

Familial exudative vitreoretinopathy (FEVR) is a hereditary eye disorder that affects both the retina and vitreous body. Autosomal recessive FEVR was diagnosed in multiple individuals from three consanguineous families of European descent. A candidate-locus-directed genome scan shows linkage to the region on chromosome 11q flanked by markers D11S905 and D11S1314. The maximum LOD score of 3.6 at theta =0 is obtained with marker D11S987. Haplotype analysis confirms that the critical region is the 22-cM (311-Mb) interval flanked by markers D11S905 and D11S1314. This region contains LRP5 but not FZD4; mutations in both of these genes cause autosomal dominant FEVR. Sequencing of LRP5 shows, in all three families, homozygous mutations R570Q, R752G, and E1367K. This suggests that mutations in this gene can cause autosomal recessive as well as autosomal dominant FEVR.