Three-dimensional primate molar enamel thickness

Molar enamel thickness has played an important role in the taxonomic, phylogenetic, and dietary assessments of fossil primate teeth for nearly 90 years. Despite the frequency with which enamel thickness is discussed in paleoanthropological discourse, methods used to attain information about enamel thickness are destructive and record information from only a single plane of section. Such semidestructive planar methods limit sample sizes and ignore dimensional data that may be culled from the entire length of a tooth. In light of recently developed techniques to investigate enamel thickness in 3D and the frequent use of enamel thickness in dietary and phylogenetic interpretations of living and fossil primates, the study presented here aims to produce and make available to other researchers a database of 3D enamel thickness measurements of primate molars (n=182 molars). The 3D enamel thickness measurements reported here generally agree with 2D studies. Hominoids show a broad range of relative enamel thicknesses, and cercopithecoids have relatively thicker enamel than ceboids, which in turn have relatively thicker enamel than strepsirrhine primates, on average. Past studies performed using 2D sections appear to have accurately diagnosed the 3D relative enamel thickness condition in great apes and humans: Gorilla has the relatively thinnest enamel, Pan has relatively thinner enamel than Pongo, and Homo has the relatively thickest enamel. Although the data set presented here has some taxonomic gaps, it may serve as a useful reference for researchers investigating enamel thickness in fossil taxa and studies of primate gnathic biology.     

A detailed study of leaf micromorphology and anatomy of New World Vitis L. subgenus Vitis within a phylogenetic and ecological framework reveals evolutionary convergence

We investigated leaf anatomy and micromorphology in the New World Vitis using light and scanning electron microscopy to understand the correlation of these traits to molecular phylogenetic relationships and environmental affinity. We observed traits known to differ among species of Vitis with importance in traditional taxonomy of Vitis: trichome type, stomata morphology, mesophyll organization, and midrib vascularization. We found that traits associated with water conductance and photosynthesis comprised the highest loadings of axis one of a principal components analysis (PCA) while traits related to gas exchange (i.e., the stomatal apparatus) had high loadings on axis two. Using the PCA, we identified seven clusters of species, which showed little correlation to recently reported molecular phylogenetic relationships. Moreover, analyses using Bayes Traits and Bayesian Binary Method revealed little to no phylogenetic signal in trait evolution. PCA axes one and two separated species occurring in dry southwestern North American habitats from those in mesic places. For example, a cluster of V. monticola and V. arizonica occurred adjacent to a cluster of V. californica and V. girdiana in ordination space, and the latter three species share key leaf anatomical traits. Nevertheless, among these, only V. arizonica and V. girdiana are closely related according to molecular phylogeny. Thus, the leaf micromorphological/anatomical traits of Vitis observed in this study are highly correlated with environment, but not phylogenetic relationships. We expect that trait similarities among distantly related species may result from evolutionary convergences, especially within xeric habitats of western North America.     

Contributions toward understanding the biodiversity of Passiflora in North America: Updates and a new combination from the Baja California Peninsula,Mexico and vicinity

The Baja California Peninsula and surrounding landmasses harbor an abundant flora in an otherwise harsh and arid environment. Of the many plant groups native to this peninsular and insular region, passionflowers (Passiflora, Passifloraceae) are represented by several conspicuous taxa that all belong to a single lineage, section Dysosmia. Basic questions remain regarding this group, particularly the taxonomic status among the Passiflora arida complex. Therefore, we investigated the claims of endemism, habitat characteristics, and taxon boundaries with in section Dysosmia in the Baja California region using extensive sampling of herbarium specimens and iNaturalist observations. We confirmed that only one of the native Passiflora taxa (P. fruticosa) was endemic to the Baja California Peninsula, with an additional taxon (P. palmeri) considered near‐endemic. Environmental data revealed significant distinctions between the habitats of many of the native taxa as well as within the P. arida complex, especially with respect to precipitation and temperature tolerances. Geometric morphometric analyses of leaf shape were largely not successful at separating taxa, indicating leaf shape may not be a good indicator of taxon identity in this particular group. Based on ecological differences and discrete macro‐ and micromorphological features, a varietal name is here synonymized and a new combination is proposed: Passiflora pentaschista.     

Solution structure and function of a conserved protein SP14.3 encoded by an essential Streptococcus pneumoniae gene

Streptococcus pneumoniae is a major human pathogen that causes high mortality and morbidity rates and has developed resistance to many antibiotics. The genome of S. pneumoniae has recently been completely sequenced revealing many genes encoding hypothetical proteins of unknown function. We have found that the gene encoding one such conserved protein, SP14.3, is essential for growth of S. pneumonia. Since it is essential, SP14.3 represents a potential target for drug discovery. Here, we describe the three-dimensional solution structure of SP14.3 as determined by NMR spectroscopy. The structure consists of two domains each with an alpha/beta-fold. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. The N-terminal domain of the protein contains a highly negatively charged surface and resembles the fold of the N-terminal domain of Thermus thermophilus ribosomal protein S3. The C-terminal domain has a protein fold similar to human small nuclear ribonucleoprotein Sm D3 and Haloarcula marismortui ribosomal protein L21E. The two domains of the protein tumble in solution overall as a whole with an overall molecular rotational correlation time (tau(m)) of 12.9 ns at 25 degrees C. The relative orientation of the two domains is not defined by the nuclear Overhauser effect data. Indeed, residual dipolar couplings and the structure calculations indicate that the relative orientation of the two domains is not rigidly oriented with respect to one another in solution.     

Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein

The severe acute respiratory syndrome (SARS) virus belongs to the Coronaviridea family of viruses. Its virion encodes several proteins including a replicase and four structural proteins. Here we describe the three-dimensional structure of the N-terminal domain of the SARS coronavirus (CoV) nucleocapsid protein. The protein consists of a five-stranded beta sheet with a folding topology distinct from other RNA-binding proteins. Single-stranded RNAs bind to the protein surface at the junction between a flexible, positively charged beta hairpin and the core structure. NMR-based screening was used to identify low molecular weight compounds that bind to this site.     

Structural biology of the Bcl-2 family of proteins

The proteins of the Bcl-2 family are important regulators of programmed cell death. Structural studies of Bcl-2 family members have provided many important insights into their molecular mechanism of action and how members of this family interact with one another. To date, structural studies have been performed on six Bcl-2 family members encompassing both anti- (Bcl-x(L), Bcl-2, KSHV-Bcl-2, Bcl-w) and pro-apoptotic (Bax, Bid) members. They all show a remarkably similar fold despite an overall divergence in amino acid sequence and function (pro-apoptotic versus anti-apoptotic). The three-dimensional structures of Bcl-2 family members consist of two central, predominantly hydrophobic alpha-helices surrounded by six or seven amphipathic alpha-helices of varying lengths. A long, unstructured loop is present between the first two alpha-helices. The structures of the Bcl-2 proteins show a striking similarity to the overall fold of the pore-forming domains of bacterial toxins. This finding led to experiments which demonstrated that Bcl-x(L), Bcl-2, and Bax all form pores in artificial membranes. A prominent hydrophobic groove is present on the surface of the anti-apoptotic proteins. This groove is the binding site for peptides that mimic the BH3 region of various pro-apoptotic proteins such as Bak and Bad. Structures of Bcl-x(L) in complex with these BH3 peptides showed that they bind as an amphipathic alpha-helix and make extensive hydrophobic contacts with the protein. These data have not only helped to elucidate the interactions important for hetero-dimerization of Bcl-2 family members but have also been used to guide the discovery of small molecules that block Bcl-x(L) and Bcl-2 function. In the recently determined structure of the anti-apoptotic Bcl-w protein, the protein was also found to have a hydrophobic groove on its surface capable of binding BH3-containing proteins and peptides. However, in the native protein an additional carboxy-terminal alpha-helix interacts with the hydrophobic groove. This is reminiscent of how the carboxy-terminal alpha-helix of the pro-apoptotic protein Bax binds into its hydrophobic groove. This interaction may play a regulatory role and for Bax may explain why it is found predominately in the cytoplasm prior to activation. The hydrophobic groove of the pro-apoptotic protein, Bid protein, is neither as long nor as deep as that found in Bcl-x(L), Bcl-2, or Bax. In addition, Bid contains an extra alpha-helix, which is located between alpha1 and alpha2 with respect to Bcl-x(L), Bcl-2, and Bax. Although there are still many unanswered questions regarding the exact mechanism by which the Bcl-2 family of proteins modulates apoptosis, structural studies of these proteins have deepened our understanding of apoptosis on the molecular level.     

Over-expression of the human MDM2 p53 binding domain by fusion to a p53 transactivation peptide

MDM2 binds to the tumor suppressor protein p53 and regulates the level of p53 in cells. Although it is possible to prepare a small amount of the region of MDM2 that binds to p53, the expression level of this fragment of MDM2 is relatively low, limiting the studies involving this protein. Here, we describe a construct for the optimized bacterial expression and purification of the MDM2 p53 binding domain. We found that the expression level of the soluble MDM2 p53 binding domain in bacteria was increased dramatically by fusing it to its interaction partner, the p53 transactivation peptide. Attachment of the p53 transactivation peptide (residues 17-29) to the N-terminus of MDM2 resulted in a more than 200-fold increase of soluble protein expression of the p53 binding domain in bacteria. To obtain the final MDM2 p53 binding domain (residues 5-109) we inserted a tobacco etch virus protease recognition site between the P53 peptide and the MDM2 p53 binding domain. To weaken the protein/peptide interaction and facilitate the separation of the protein from the complex, we introduced a point mutation of one of the key interaction residues (F19A or W23A) in the p53 peptide. The advantages of our new construct are high yield and easy purification of the MDM2 protein.     

Solution structure of the BHRF1 protein from Epstein-Barr virus, a homolog of human Bcl-2

The three-dimensional structure of BHRF1, the Bcl-2 homolog from Epstein-Barr virus (EBV), has been determined by NMR spectroscopy. Although the overall structure is similar to other Bcl-2 family members, there are important structural differences. Unlike some of the other Bcl-2 family members, BHRF1 does not contain the prominent hydrophobic groove that mediates binding to pro-apoptotic family members. In addition, in contrast to the anti-apoptotic Bcl-2 proteins, BHRF1 does not bind tightly to peptides derived from the pro-apoptotic proteins Bak, Bax, Bik, and Bad. The lack of an exposed, pre-formed binding groove in BHRF1 and the lack of significant binding to peptides derived from pro-apoptotic family members that bind to other anti-apoptotic family members, suggest that the mechanism of the BHRF1 anti-apoptotic activity does not parallel that of cellular Bcl-x(L) or Bcl-2.     

Lactones 12. Enzymatic lactonization of gamma,delta-epoxy esters by the apple fruit and Jerusalem artichoke bulb

The enzymatic lactonization of three acyclic gamma, delta-epoxy esters (ethyl 3,7-dimethyl-4,5-epoxyoctanoate, ethyl 3,7,7-trimethyl-4,5-epoxyoctanoate, and ethyl 3,3,7-trimethyl-4,5-epoxyoctanoate) by apple fruit (Malus silvestris) and Jerusalem artichoke bulb (Helianthus tuberosus L.) was investigated. The substrates were transformed into a mixture of isomeric delta-hydroxy-gamma-lactones and gamma-hydroxy-delta-lactones. The gamma-lactones (yields ranging from 45-70%) predominated over delta-lactones (yields ranging from 8-40%). The composition of the product mixture depended on the structure of substrate as well as the biocatalyst. The enzymatic system in these biocatalysts also exhibited diastereoselectivity and enantioselectivity.     

Home-based versus hospital-based cardiac rehabilitation after myocardial infarction or revascularisation: design and rationale of the Birmingham Rehabilitation Uptake Maximisation Study (BRUM): a randomised controlled trial [ISRCTN72884263]

Background

Cardiac rehabilitation following myocardial infarction reduces subsequent mortality, but uptake and adherence to rehabilitation programmes remains poor, particularly among women, the elderly and ethnic minority groups. Evidence of the effectiveness of home-based cardiac rehabilitation remains limited. This trial evaluates the effectiveness and cost-effectiveness of home-based compared to hospital-based cardiac rehabilitation.

Methods/design

A pragmatic randomised controlled trial of home-based compared with hospital-based cardiac rehabilitation in four hospitals serving a multi-ethnic inner city population in the United Kingdom was designed. The home programme is nurse-facilitated, manual-based using the Heart Manual. The hospital programmes offer comprehensive cardiac rehabilitation in an out-patient setting.

Patients

We will randomise 650 adult, English or Punjabi-speaking patients of low-medium risk following myocardial infarction, coronary angioplasty or coronary artery bypass graft who have been referred for cardiac rehabilitation.

Main outcome measures

Serum cholesterol, smoking cessation, blood pressure, Hospital Anxiety and Depression Score, distance walked on Shuttle walk-test measured at 6, 12 and 24 months. Adherence to the programmes will be estimated using patient self-reports of activity. In-depth interviews with non-attendees and non-adherers will ascertain patient views and the acceptability of the programmes and provide insights about non-attendance and aims to generate a theory of attendance at cardiac rehabilitation. The economic analysis will measure National Health Service costs using resource inputs. Patient costs will be established from the qualitative research, in particular how they affect adherence.

Discussion

More data are needed on the role of home-based versus hospital-based cardiac rehabilitation for patients following myocardial infarction and revascularisation, which would be provided by the Birmingham Rehabilitation Uptake Maximisation Study (BRUM) study and has implications for the clinical management of these patients. A novel feature of this study is the inclusion of non-English Punjabi speakers.