Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis

Background

A new subgroup of HIV-1, designated Group P, was recently detected in two unrelated patients of Cameroonian origin. HIV-1 Group P phylogenetically clusters with SIVgor suggesting that it is the result of a cross-species transmission from gorillas. Until today, HIV-1 Group P has only been detected in two patients, and its degree of adaptation to the human host is largely unknown. Previous data have shown that pandemic HIV-1 Group M, but not non-pandemic Group O or rare Group N viruses, efficiently antagonize the human orthologue of the restriction factor tetherin (BST-2, HM1.24, CD317) suggesting that primate lentiviruses may have to gain anti-tetherin activity for efficient spread in the human population. Thus far, three SIV/HIV gene products (vpu, nef and env) are known to have the potential to counteract primate tetherin proteins, often in a species-specific manner. Here, we examined how long Group P may have been circulating in humans and determined its capability to antagonize human tetherin as an indicator of adaptation to humans.

Results

Our data suggest that HIV-1 Group P entered the human population between 1845 and 1989. Vpu, Env and Nef proteins from both Group P viruses failed to counteract human or gorilla tetherin to promote efficient release of HIV-1 virions, although both Group P Nef proteins moderately downmodulated gorilla tetherin from the cell surface. Notably, Vpu, Env and Nef alleles from the two HIV-1 P strains were all able to reduce CD4 cell surface expression.

Conclusions

Our analyses of the two reported HIV-1 Group P viruses suggest that zoonosis occurred in the last 170 years and further support that pandemic HIV-1 Group M strains are better adapted to humans than non-pandemic or rare Group O, N and P viruses. The inability to antagonize human tetherin may potentially explain the limited spread of HIV-1 Group P in the human population.     

Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex

Two regions of the genome, a 1-kbp portion of the zeste locus and a 1.1- kbp portion of the yolk protein 2 locus, were sequenced in six individuals from each of four species: Drosophila melanogaster, D. simulans, D. mauritiana, and D. sechellia. The species and strains were the same as those of a previous study of a 1.9-kbp region of the period locus. No evidence was found for recent balancing or directional selection or for the accumulation of selected differences between species. Yolk protein 2 has a high level of amino acid replacement variation and a low level of synonymous variation, while zeste has the opposite pattern. This contrast is consistent with information on gene function and patterns of codon bias. Polymorphism levels are consistent with a ranking of effective population sizes, from low to high, in the following order: D. sechellia, D. melanogaster, D.mauritiana, and D. simulans. The apparent species relationships are very similar to those suggested by the period locus study. In particular, D. simulans appears to be a large population that is still segregating variation that arose before the separation of D. mauritiana and D. sechellia. It is estimated that the separation of ancestral D. melanogaster from the other species occurred 2.5-3.4 Mya. The separations of D. sechellia and D. mauritiana from ancestral D. simulans appear to have occurred 0.58- 0.86 Mya, with D. mauritiana having diverged from ancestral D. simulans 0.1 Myr more recently than D. sechellia.      

Palynological variation in Balsaminoid Ericales. II. Balsaminaceae, Tetrameristaceae, Pellicieraceae and general conclusions

BACKGROUND AND AIMS: The objective of this study is to examine the palynological diversity of Balsaminaceae (two genera/+/-1000 species), Tetrameristaceae (two genera/two species) and Pellicieraceae (one genus/one species). The diversity found will be used to infer the systematic value of pollen features within the balsaminoid clade. METHODS: Pollen morphology and ultrastructure of 29 species, representing all families of the balsaminoid clade except Marcgraviaceae, are investigated by means of light microscopy, scanning electron microscopy and transmission electron microscopy. KEY RESULTS: Balsaminaceae pollen is small to medium sized with three to four apertures, which can be either colpate or porate, and a sexine sculpturing varying from coarsely reticulate to almost microreticulate. Tetrameristaceae pollen is small sized, 3-colporate, with a heterobrochate reticulate sculpturing and granules present in the lumina. Pellicieraceae pollen is large sized, 3-colporate with long ectocolpi and a perforate sexine sculpturing with large verrucae. Furthermore, Pelliciera is characterized by the occurrence of aggregated orbicules, while orbicules are completely absent in both Balsaminaceae and Tetrameristaceae. Balsaminaceae pollen differs from the other balsaminoid families due to the occurrence of colpate or porate grains with an oblate to peroblate shape, a very thin foot layer and a lamellated endexine. CONCLUSIONS: From a pollen morphological point of view, Balsaminaceae are completely different from the other balsaminoid families. Therefore, no pollen morphological synapomorphies could be defined for the balsaminoid clade. However, various pollen features were observed that could indicate a possible relationship between Tetrameristaceae, Pellicieraceae and Marcgraviaceae. Despite the palynological similarities in the latter three families, it remains unclear to what extent they are related to each other.     

Palynological variation in balsaminoid ericales. I. Marcgraviaceae

BACKGROUND AND AIMS: Marcgraviaceae are a rather small family of seven genera and approx. 130 neotropical species. This study aims to present a detailed palynological survey of the family in order to comment on the intrafamily relationships and possible correlations with pollinators. METHODS: In total, 119 specimens representing 67 species and all genera are observed using light microscopy and scanning electron microscopy. Furthermore, eight species from five genera are studied with transmission electron microscopy. KEY RESULTS: Our results show that pollen grains of Marcgraviaceae are small (20-35 microm), have three equatorial apertures, granules on the colpus membrane, oblate spheroidal to prolate spheroidal shapes, mainly psilate to perforate ornamentations, and lalongate colpus-shaped thinnings at the inner layer of the exine, and show the presence of orbicules. Based on our fragmentary knowledge of the pollination biology of the family, there are no clear correlations between pollinators and pollen features. CONCLUSIONS: The genus Marcgravia has a high percentage of reticulate sexine patterns and a relatively thin nexine. Sarcopera can be defined by the presence of an oblate spheroidal to even suboblate shape, while Ruyschia and Souroubea typically show prolate spheroidal to subprolate pollen grains. The presence of a thick foot layer in the pollen wall is characteristic of the genera Norantea, Sarcopera and Schwartzia. Pollen features that are taxonomically useful within the family are the shape, sexine sculpturing, and ultrastructure of the pollen wall.     

TNT and nitroaromatic compounds are chemoattractants for Burkholderia cepacia R34 and Burkholderia sp. strain DNT

Nitroaromatic compounds are toxic and potential carcinogens. In this study, a drop assay was used to detect chemotaxis toward nitroaromatic compounds for wild-type Burkholderia cepacia R34, wild-type Burkholderia sp. strain DNT, and a 2,4-dinitrotoluene (2,4-DNT) dioxygenase mutant strain (S5). The three strains are chemotactic toward 2,4,6-trinitrotoluene (TNT), 2,3-DNT, 2,4-DNT, 2,5-DNT, 2-nitrotoluene (NT), 4NT, and 4-methyl-5-nitrocatechol (4M5NC), but not toward 2,6-DNT. Of these, only 2,4-DNT is a carbon and energy source for B. cepacia R34 and Burkholderia sp. strain DNT, and 4M5NC is an intermediate in the 2,4-DNT degradation pathway. It was determined that the 2,4-DNT dioxygenase genes are not required for the chemotaxis for these nitroaromatic compounds because the DNT DDO mutant S5 has a chemotactic response toward 2,4-DNT although 2,4-DNT is not metabolized by S5; hence, 2,4-DNT itself is the chemoattractant. This is the first report of chemotaxis toward TNT, 2,3-DNT, 2,4-DNT, 2,5-DNT, 2NT, 4NT, and 4M5NC.     

Spikelet structure and development in Cyperoideae (Cyperaceae): a monopodial general model based on ontogenetic evidence

Background and Aims

In Cyperoideae, one of the two subfamilies in Cyperaceae, unresolved homology questions about spikelets remained. This was particularly the case in taxa with distichously organized spikelets and in Cariceae, a tribe with complex compound inflorescences comprising male (co)florescences and deciduous female single-flowered lateral spikelets. Using ontogenetic techniques, a wide range of taxa were investigated, including some controversial ones, in order to find morphological arguments to understand the nature of the spikelet in Cyperoideae. This paper presents a review of both new ontogenetic data and current knowledge, discussing a cyperoid, general, monopodial spikelet model.

Methods

Scanning electron microscopy and light microscopy were used to examine spikelets of 106 species from 33 cyperoid genera.

Results

Ontogenetic data presented allow a consistent cyperoid spikelet model to be defined. Scanning and light microscopic images in controversial taxa such as Schoenus nigricans, Cariceae and Cypereae are interpreted accordingly.

Conclusions

Spikelets in all species studied consist of an indeterminate rachilla, and one to many spirally to distichously arranged glumes, each subtending a flower or empty. Lateral spikelets are subtended by a bract and have a spikelet prophyll. In distichously organized spikelets, combined concaulescence of the flowers and epicaulescence (a newly defined metatopic displacement) of the glumes has caused interpretational controversy in the past. In Cariceae, the male (co)florescences are terminal spikelets. Female single-flowered spikelets are positioned proximally on the rachis. To explain both this and the secondary spikelets in some Cypereae, the existence of an ontogenetic switch determining the development of a primordium into flower, or lateral axis is postulated.     

The accuracy of several multiple sequence alignment programs for proteins

Background  

There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs.     

Compression or tension? The stress distribution in the proximal femur

Background  

Questions regarding the distribution of stress in the proximal human femur have never been adequately resolved. Traditionally, by considering the femur in isolation, it has been believed that the effect of body weight on the projecting neck and head places the superior aspect of the neck in tension. A minority view has proposed that this region is in compression because of muscular forces pulling the femur into the pelvis. Little has been done to study stress distributions in the proximal femur. We hypothesise that under physiological loading the majority of the proximal femur is in compression and that the internal trabecular structure functions as an arch, transferring compressive stresses to the femoral shaft.