The effects of testing methods on the flexural fatigue life of human cortical bone

A flexural model of four-point bending fatigue that has been experimentally validated for human cortical bone under load control was used to determine how load and displacement control testing affects the fatigue behavior of human cortical bone in three-point and symmetric four-point bending. Under load control, it was predicted that three-point bending produced no significant differences in fatigue life when compared to four-point bending. However, three-point bending produced less stiffness loss with increasing cycles than four-point bending. In four-point bending, displacement control was predicted to produce about one and a half orders of magnitude greater fatigue life when compared to load control. This prediction agrees with experimental observations of equine cannon bone tested in load and displacement control (Gibson et al., 1998). Displacement controlled three-point bending was found to produce approximately a 25% greater fatigue life when compared to load control. The prediction of longer fatigue life under displacement control may have clinical relevance for the repair of damaged bone. The model can also be adapted to other geometric configurations, including modeling of whole long bones, and with appropriate fatigue data, other cortical bone types.     

A Review of Perceptual Distinctiveness in Landraces Including an Analysis of How Its Roles Have Been Overlooked in Plant Breeding for Low-Input Farming Systems

A Review of Perceptual Distinctiveness in Landraces Including an Analysis of How Its Roles Have Been Overlooked in Plant Breeding for Low-Input Farming Systems. Traits providing perceptual distinctiveness (PD), which allow less commercial farmers in developing countries to recognize and name individual landraces, enable the creation and management of their diversity and the transfer of knowledge of each to other farmers and succeeding generations. Worldwide examples illustrate how PD traits on seeds and vegetative propagules help maintain genetic purity and provide markers at planting time, identifying landraces suitable for planting at particular locations and times and for future household and market needs. PD traits on the yield also enable household members and customers to identify and value landraces for different uses. To fulfill these roles, they are generally highly salient, restricted in number, environment-independent, qualitatively inherited, generally with expression based on one or a few genes, and often culturally significant. Even so, they are seldom mentioned as varietal selection criteria by farmers, who may be unaware of their importance, or in plant breeding programs and in situ conservation of plant genetic resources projects; the need for national variety release committees and policymakers in developing countries to include them is emphasized.     

Bioinformatic and Expression Analyses of Genes Mediating Zinc Homeostasis in Nostoc punctiforme

Zinc homeostasis was investigated in Nostoc punctiforme. Cell tolerance to Zn²⁺ over 14 days showed that ZnCl₂ levels above 22 μM significantly reduced cell viability. After 3 days in 22 μM ZnCl₂, ca. 12% of the Zn²⁺ was in an EDTA-resistant component, suggesting an intracellular localization. Zinquin fluorescence was detected within cells exposed to concentrations up to 37 μM relative to 0 μM treatment. Radiolabeled ⁶⁵Zn showed Zn²⁺ uptake increased over a 3-day period, while efflux occurred more rapidly within a 3-h time period. Four putative genes involved in Zn²⁺ uptake and efflux in N. punctiforme were identified: (i) the predicted Co/Zn/Cd cation transporter, putative CDF; (ii) the predicted divalent heavy-metal cation transporter, putative Zip; (iii) the ATPase component and Fe/Zn uptake regulation protein, putative Fur; and (iv) an ABC-type Mn/Zn transport system, putative zinc ZnuC, ZnuABC system component. Quantitative real-time PCR indicated the responsiveness of all four genes to 22 μM ZnCl₂ within 3 h, followed by a reduction to below basal levels after 24 h by putative ZIP, ZnuC, and Fur and a reduction to below basal level after 72 h by putative CDF efflux gene. These results demonstrate differential regulation of zinc transporters over time, indicating a role for them in zinc homeostasis in N. punctiforme.     

Genomic Consequences of Background Effects on scalloped Mutant Expressivity in the Wing of Drosophila melanogaster

We have evaluated the extent to which SNPs identified by genomewide surveys as showing unusually high levels of population differentiation in humans have experienced recent positive selection, starting from a set of 32 nonsynonymous SNPs in 27 genes highlighted by the HapMap1 project. These SNPs were genotyped again in the HapMap samples and in the Human Genome Diversity Project–Centre d''Etude du Polymorphisme Humain (HGDP–CEPH) panel of 52 populations representing worldwide diversity; extended haplotype homozygosity was investigated around all of them, and full resequence data were examined for 9 genes (5 from public sources and 4 from new data sets). For 7 of the genes, genotyping errors were responsible for an artifactual signal of high population differentiation and for 2, the population differentiation did not exceed our significance threshold. For the 18 genes with confirmed high population differentiation, 3 showed evidence of positive selection as measured by unusually extended haplotypes within a population, and 7 more did in between-population analyses. The 9 genes with resequence data included 7 with high population differentiation, and 5 showed evidence of positive selection on the haplotype carrying the nonsynonymous SNP from skewed allele frequency spectra; in addition, 2 showed evidence of positive selection on unrelated haplotypes. Thus, in humans, high population differentiation is (apart from technical artifacts) an effective way of enriching for recently selected genes, but is not an infallible pointer to recent positive selection supported by other lines of evidence.IN the last 50,000–100,000 years (KY), humans have expanded from being a rare species confined to parts of Africa and the Levant to their current numbers of >6 billion with a worldwide distribution (Jobling et al. 2004). Paleontological and archaeological evidence suggests that key aspects of modern human behavior developed ∼100–50 KYA in Africa (Henshilwood et al. 2002) and behaviorally modern humans then expanded out of Africa ∼60–40 KYA (Mellars 2006). The physical and biological environments encountered outside Africa would have been very different from those inside and included climatic deterioration reaching a glacial maximum ∼20 KYA and subsequent amelioration that permitted the development of agricultural and pastoral lifestyles in multiple independent centers after ∼10 KYA. Neolithic lifestyles would have led to further changes including higher population densities, close contact with animals, and novel foods, in turn leading to new diseases (Jobling et al. 2004). It is likely that genetic adaptations accompanied many of these events.Adaptation, or positive natural selection, leaves an imprint on the pattern of genetic variation found in a population near the site of selection. This pattern can be identified by comparing the DNA variants in multiple individuals from the same and different populations and searching for signals such as unusually extended haplotypes (extended haplotype homozygosity, EHH) (Voight et al. 2006; Sabeti et al. 2007; Tang et al. 2007), high levels of population differentiation (International Hapmap Consortium 2005; Barreiro et al. 2008; Myles et al. 2008), or skewed allele frequency spectra (Carlson et al. 2005). These signals become detectable at different times after the start of selection and are all transient, being gradually eroded by both molecular processes such as mutation, recombination, or further selection and population processes such as migration or demographic fluctuations, with the survival order extended haplotypes < population differentiation < allele frequency spectra (Sabeti et al. 2006). The absolute timescales of survival are not well understood, but extended haplotype tests typically detect selection within the last 10 KY (Sabeti et al. 2006) while unusual allele frequency spectra may detect much older selection. For example, it has been suggested that the signal associated with the FOXP2 gene (Enard et al. 2002) may predate the modern human–Neanderthal split ∼300–400 KYA (Krause et al. 2007), although such an interpretation has been questioned (Coop et al. 2008). However, despite significant uncertainties and limitations, population-genetic analyses are well placed to provide insights into many of the important events within the timescale of recent human evolution.In principle, it should be possible to survey the genome for sites of selection and then interpret this catalog in the light of archaeological, climatic, and other records. Progress toward such a goal has, however, been limited: many factors can confound the detection of selection and only genotype data from previously ascertained SNPs, rather than full resequence data, have thus far been available throughout the whole genome. In practice, the strategy used has therefore been to search the genome for signals that can be detected in available genotype data, such as extended haplotypes or population differentiation, and evaluate the significance of the regions identified by comparing them with empirical distributions of the same statistic, models that incorporate information about the demography, or biological expectations (McVean and Spencer 2006). However, it remains unclear how effective this strategy is: What false positive and false negative rates are associated with its applications? Further evaluation is desirable.The International HapMap Project has carried out the highest-resolution study so far of genetic variation in a set of human populations. In an article published in 2005, genotypes of >1 million SNPs were reported from 270 individuals with ancestry from Africa (Yoruba in Ibadan, Nigeria: YRI), Europe (Utah residents with ancestry from northern and western Europe: CEU), China (Han Chinese in Beijing, China: CHB), and Japan (Japanese in Tokyo, Japan: JPT) (International HapMap Consortium 2005). This article highlighted 32 SNPs from 27 genes that showed particular evolutionary interest because of a combination of two factors: they were nonsynonymous, that is, they changed an amino acid within a protein-coding gene and thus were likely to alter biological function, and they also exhibited a high level of population differentiation equal to or exceeding that of rs2814778, a SNP that is associated with strong biological evidence for population-specific selection. This SNP underlies the FY*0 (Duffy blood group negative) phenotype; FY*0 homozygotes do not express the Duffy blood group antigen on red blood cells and are consequently highly resistant to infection by the malarial parasite, Plasmodium vivax. The *0 allele is nearly fixed in Africa and rare outside, and it is widely believed that this is due to selection for resistance to vivax malaria.However, a number of studies have emphasized that large differences in allele frequency between populations can arise without positive selection: for example, a highly differentiated SNP in the Neuregulin I gene was not accompanied by unusual patterns in adjacent SNPs (Gardner et al. 2007), and large frequency differences can be quite common in empirical data sets, particularly in comparisons between Africa or America and the rest of the world, where population bottlenecks and “allele surfing” may have occurred during the exit from and entrance to these continents, respectively (Hofer et al. 2009). We wished to measure the extent to which the high population differentiation observed at the 27 HapMap genes might have resulted from positive selection and the extent to which it reflected other origins such as demographic factors, chance, or errors. We therefore retyped the same SNPs in the HapMap samples and in a large additional set of human populations and applied alternative tests for selection, either based on long-range haplotypes or based on full resequence data. For the latter, sequence data for 5 of the genes were available from public sources, and four new data sets were generated for this project. We found that, while genotyping errors led to some artifactual high differentiation signals, population differentiation was a useful but by no means infallible guide to recent selection detected by other methods.     

Catabolism of 4-Hydroxyacids and 4-Hydroxynonenal via 4-Hydroxy-4-phosphoacyl-CoAs

4-Hydroxyacids are products of ubiquitously occurring lipid peroxidation (C₉, C₆) or drugs of abuse (C₄, C₅). We investigated the catabolism of these compounds using a combination of metabolomics and mass isotopomer analysis. Livers were perfused with various concentrations of unlabeled and labeled saturated 4-hydroxyacids (C₄ to C₁₁) or 4-hydroxynonenal. All the compounds tested form a new class of acyl-CoA esters, 4-hydroxy-4-phosphoacyl-CoAs, characterized by liquid chromatography-tandem mass spectrometry, accurate mass spectrometry, and ³¹P-NMR. All 4-hydroxyacids with five or more carbons are metabolized by two new pathways. The first and major pathway, which involves 4-hydroxy-4-phosphoacyl-CoAs, leads in six steps to the isomerization of 4-hydroxyacyl-CoA to 3-hydroxyacyl-CoAs. The latter are intermediates of physiological β-oxidation. The second and minor pathway involves a sequence of β-oxidation, α-oxidation, and β-oxidation steps. In mice deficient in succinic semialdehyde dehydrogenase, high plasma concentrations of 4-hydroxybutyrate result in high concentrations of 4-hydroxy-4-phospho-butyryl-CoA in brain and liver. The high concentration of 4-hydroxy-4-phospho-butyryl-CoA may be related to the cerebral dysfunction of subjects ingesting 4-hydroxybutyrate and to the mental retardation of patients with 4-hydroxybutyric aciduria. Our data illustrate the potential of the combination of metabolomics and mass isotopomer analysis for pathway discovery.     

A new monogenean genus from an ephippid fish off Peninsular Malaysia

Sundatrema langkawiense n. g., n. sp. (Monogenea: Ancyrocephalidae) is described from the gills of the orbfish Ephippus orbis (Bloch) (Ephippidae) off the Island of Langkawi, Malaysia, in the Andaman Sea. This new genus has the ancyrocephalid characteristics of four anchors, 14 marginal hooks and two bars, but differs from other four-anchored monogenean genera, and notably from Parancylodiscoides Caballero & Bravo Hollis, 1961 (found on the ephippids Chaetodipterus spp. off Central and South America), by having a unique combination of features. These include a muscular genital sucker and a vas deferens and vagina on the same (sinistral) side of the body. It is similar to Parancylodiscoides in having four haptoral reservoirs opening at the anchoral apertures, four anchors, similar connecting bars and small marginal hooks. The new species is characterised by the above generic features and by possessing a small, short copulatory organ lacking an accessory piece. Diplectanum longiphallus MacCallum, 1915 (previously attributed to Ancyrocephalus Creplin, 1839, Tetrancistrum Goto & Kikuchi, 1917 and Pseudohaliotrema Yamaguti, 1953) is transferred to Parancylodiscoides as P. longiphallus (MacCallum, 1915) n. comb.     

New records of rare derogenids (Digenea: Hemiuroidea) from Mediterranean sparids,including the description of a new species of <Emphasis Type="Italic">Magnibursatus</Emphasis> Naidenova, 1969 and redescription of <Emphasis Type="Italic">Derogenes adriaticus</Emphasis> Nikolaeva, 1966

Records of derogenid digeneans in the Mediterranean and Black Sea region are scarce and tend to be restricted to a small number of host-groups, but especially to sparid fishes. This work reports on the presence of derogenine and halipegine derogenids from two sparids, Diplodus annularis (L.) and D. sargus (L.), from off the Mediterranean coast of Spain. Five derogenid forms were recovered. Derogenes adriaticus Nikolaeva, 1966 is redescribed from Diplodus annularis, and Derogenes sp. is described from the same host but differentiated from the former species. Magnibursatus barretti n. sp. is described from Diplodus sargus and distinguished from other species of the genus especially by its smaller body size and smaller eggs. M. bartolii Kostadinova, Power, Fernández, Balbuena, Raga & Gibson, 2003 is redescribed from D. sargus, a new host for this species. A single specimen from D. sargus, somewhat similar to M. minutus Kostadinova, Power, Fernández, Balbuena, Raga & Gibson, 2003, is also described, as it exhibits some morphometric differences from the latter species.     

How can we improve antibody-based cancer therapy?

Monoclonal antibodies (mAbs) as a class of novel oncology therapeutics are demonstrating clinical efficacy as measured by tumor response (shrinkage in tumor size), and prolongations in progression-free survival (PFS) and overall survival (OS). However, clinical benefits are often limited to when antibodies are used in combination with chemotherapy or radiation modalities, with tumor responses only seen in a fraction of patients, and improvements in PFS and OS are incremental.¹ The potential of mAbs and mAb constructs has yet to be fully exploited for maximal clinical benefit. New approaches to further improve the effectiveness of these mAb therapies include (1) selection of patients who may derive the most benefit based on the molecular characteristics of their tumors; (2) improvements in biodistribution to maximize delivery of mAbs to susceptible tumor cells; and (3) optimization of antibody immune effector mechanisms such as antibody-dependent cellular cytotoxicity (ADCC).Key words: monoclonal antibodies, solid tumors, cancer, pharmacogenomics, biodistribution, bioengineeringMonoclonal antibodies (mAbs) as a class of novel oncology therapeutics are demonstrating clinical efficacy as measured by tumor response (shrinkage in tumor size), and prolongations in progression-free survival (PFS) and overall survival (OS). However, clinical benefits are often limited to when antibodies are used in combination with chemotherapy or radiation modalities, with tumor responses only seen in a fraction of patients, and improvements in PFS and OS are incremental.¹ The potential of mAbs and mAb constructs has yet to be fully exploited for maximal clinical benefit. New approaches to further improve the effectiveness of these mAb therapies include (1) selection of patients who may derive the most benefit based on the molecular characteristics of their tumors; (2) improvements in biodistribution to maximize delivery of mAbs to susceptible tumor cells; and (3) optimization of antibody immune effector mechanisms such as antibody-dependent cellular cytotoxicity (ADCC) (Fig. 1).Open in a separate windowFigure 1Efficacy of monoclonal antibodies may be improved by selecting responding patient subpopulations, improving biodistribution and delivery of antibody to the tumor and maximizing antibody-mediated immune responses through application of protein and glyco-engineering.     

Mapping SNP-anchored genes using high-resolution melting analysis in almond

Peach and almond have been considered as model species for the family Rosaceae and other woody plants. Consequently, mapping and characterisation of genes in these species has important implications. High-resolution melting (HRM) analysis is a recent development in the detection of SNPs and other markers, and proved to be an efficient and cost-effective approach. In this study, we aimed to map genes corresponding to known proteins in other species using the HRM approach. Prunus unigenes were searched and compared with known proteins in the public databases. We developed single-nucleotide polymorphism (SNP) markers, polymorphic in a mapping population produced from a cross between the cloned cultivars Nonpareil and Lauranne. A total of 12 SNP-anchored putative genes were genotyped in the population using HRM, and mapped to an existing linkage map. These genes were mapped on six linkage groups, and the predicted proteins were compared to putative orthologs in other species. Amongst those genes, four were abiotic stress-responsive genes, which can provide a starting point for construction of an abiotic resistance map. Two allergy and detoxification related genes, respectively, were also mapped and analysed. Most of the investigated genes had high similarities to sequences from closely related species such as apricot, apple and other eudicots, and these are putatively orthologous. In addition, it was shown that HRM can be an effective means of genotyping populations for the purpose of constructing a linkage map. Our work provides basic genomic information for the 12 genes, which can be used for further genetic and functional studies.