Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA,alpha-tubulin and HSP90 genes: Implications for the evolutionary history of the double karyomastigont of diplomonads

Background  

Fornicata is a relatively recently established group of protists that includes the diplokaryotic diplomonads (which have two similar nuclei per cell), and the monokaryotic enteromonads, retortamonads and Carpediemonas, with the more typical one nucleus per cell. The monophyly of the group was confirmed by molecular phylogenetic studies, but neither the internal phylogeny nor its position on the eukaryotic tree has been clearly resolved.     

Statins but not fibrates improve the atherogenic to anti-atherogenic lipoprotein particle ratio: a randomized crossover study

Background  

Prior studies suggested low density lipoprotein particle (LDLP) size is a predictor of atherosclerosis. Knowledge of effects of lipid lowering drugs on lipoprotein subclasses is useful. We treated subjects with hyperlipidemia sequentially with statins and fibrates, the 2 main classes of lipid lowering therapy and studied changes in NMR lipoprotein subclasses.     

New insights in Salicornia L. and allied genera (Chenopodiaceae) inferred from nrDNA sequence data

A phylogenetic analysis was performed based on ITS DNA sequences of fourteen samples from different sources of six species of Salicornia, the three allied genera Arthrocnemum, Sarcocornia and Halocnemum of the same tribe Salicornieae, and other genera of the subfamily Salicornioideae used in previous studies. Bassia hirsuta, Camphorosma monspeliaca (subfamily Chenopodioideae) and four species of Suaeda (subf. Suaedoideae) were chosen as outgroups. Results show that the annual genus Salicornia is a sister group to the perennial genera Sarcocornia, Arthrocnemum and Halocnemum. Moreover, the phylogenetic analysis based on ITS results distinguished two groups of Salicornia species which fitted with ploidy level: one group consisted of diploid species, and the second of tetraploid ones. Sarcocornia and Arthrocnemum are shown to be closely related, even though the species investigated here exhibited an evident distance between their ITS sequences. On the basis of our results, these two genera should be united. Bienertia (already separated as Bienertieae) was confirmed as probable outgroup to the subf. Salicornioideae, while Kalidium (subf. Salicornioideae, tribe Halopeplideae) was an outgroup to the rest of the Salicornioideae (tribe Salicornieae). The group Allenrolfea plus Halocnemum was the most basal of the tribe Salicornieae amongst those investigated in this study. The two samples of Halocnemum strobilaceum used in this work displayed numerous changes (transitions and transversions) in their respective sequences, probably related to their morphological and chorological differentiation. On the basis of our analysis, the most probable basal chromosome number for Salicornieae appears to be 2n = 18. The same number would also be the base number for the annual genus Salicornia and the perennial Arthrocnemum ( + Sarcocornia), with polyploidy arising independently in the two groups.     

Substructure of the glomerular slit diaphragm in freeze-fractured normal rat kidney

In the renal glomerulus, the narrow slits between adjacent epithelial podocytes are bridged by a diaphragm (2, 8, 11). In rat and mouse kidneys fixed by perfusion with tannic acid and glutaraldehyde (TAG), it has recently been discovered that this diaphragm has a highly ordered, isoporous substructure (9). It consists of a regular array of alternating cross bridges extending from the podocyte plasma membranes to a centrally running filament. This zipperlike pattern results in two rows of rectangular pores, approximately 40 X 140 A in cross section, dimensions consistent with the proposed role of the diaphragm as an important filtration barrier to plasma proteins (6). In the present study, we found in freeze-cleaved and in freeze-etched normal rat glomeruli that the surface of the slit diaphragm has an appearance conforming to the pattern found in sectioned material.     

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

Background  

MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions.     

Genome-Wide Analysis of the Expansin Gene Superfamily Reveals Grapevine-Specific Structural and Functional Characteristics

Background

Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP) comprises four distinct families: expansin A (EXPA), expansin B (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB). There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera) genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far.

Methodology/Principal Findings

We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon–intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa), compared to those from Arabidopsis thaliana and rice (Oryza sativa). We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering.

Conclusion

Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the functional characterization of grapevine gene families by combining phylogenetic analysis with global gene expression profiling.