The rabbit alpha-like globin gene cluster is polymorphic both in the sizes of BamHI fragments and in the numbers of duplicated sets of genes

The alpha-like globin gene cluster in rabbits contains embryonic zeta- globin genes, an adult alpha-globin gene, and theta-globin genes of undetermined function. The basic arrangement of genes, deduced from analysis of cloned DNA fragments, is 5'-zeta 0-zeta 1-alpha 1-theta 1- zeta 2-zeta 3-theta 2-3'. However, the pattern of restriction fragments containing zeta- and theta-globin genes varies among individual rabbits. Analysis of BamHI fragments of genomic DNA from 24 New Zealand white rabbits revealed eight different patterns of fragments containing zeta-globin genes. The large BamHI fragments containing genes zeta 0 and zeta 1 are polymorphic in length, whereas a 1.9-kb fragment containing the zeta 2 gene and the 3.5-kb fragment containing the zeta 3 gene do not vary in size. In contrast to this constancy in the size of the restriction fragments, the copy number of the zeta 2 and zeta 3 genes does vary among different rabbits. No length polymorphism was detected in the BamHI fragments containing the theta-globin genes, but again the copy number varies for restriction fragments containing the theta 2 gene. The alpha 1- and theta 1-globin genes are located in a nonpolymorphic 7.2-kb BamHI fragment. The combined data from hybridization with both zeta and theta probes shows that the BamHI cleavage pattern does not vary within the region 5'-alpha 1-theta 1- zeta 2-zeta 3-theta 2-3', but the pattern genomic blot-hybridization patterns for the progeny of parental rabbits with different zeta-globin gene patterns shows that the polymorphic patterns are inherited in a Mendelian fashion. Two different haplotypes have been mapped based on the genomic blot-hybridization data. The variation in the alpha-like globin gene cluster in the rabbit population results both from differences in the copy number of the duplication block containing the zeta-zeta-theta gene set and from the presence or absence of polymorphic BamHI sites.      

Trimethyloxonium modification of single batrachotoxin-activated sodium channels in planar bilayers. Changes in unit conductance and in block by saxitoxin and calcium

Single batrachotoxin-activated sodium channels from rat brain were modified by trimethyloxonium (TMO) after incorporation in planar lipid bilayers. TMO modification eliminated saxitoxin (STX) sensitivity, reduced the single channel conductance by 37%, and reduced calcium block of inward sodium currents. These effects always occurred concomitantly, in an all-or-none fashion. Calcium and STX protected sodium channels from TMO modification with potencies similar to their affinities for block. Calcium inhibited STX binding to rat brain membrane vesicles and relieved toxin block of channels in bilayers, apparently by competing with STX for the toxin binding site. These results suggest that toxins, permeant cations, and blocking cations can interact with a common site on the sodium channel near the extracellular surface. It is likely that permeant cations transiently bind to this superficial site, as the first of several steps in passing inward through the channel.     

Association between pygmy right whales (Caperea marginata) and areas of high marine productivity off Australia and New Zealand

Abstract

Opportunistic sightings and strandings of Caperea marginata (n=196) from the vicinity of Australia and New Zealand (1884 to early 2007) were used to relate geographic and temporal patterns to oceanographic and broad-scale climatic variability. Records were not uniformly distributed along the coast and more (69%) were from Australia than New Zealand. Seven coastal whale ‘hotspots’ were identified which accounted for 61% of records with locality data. Half of the hotspot records were from southeast (37) and northwest (20) Tasmania—others each had 9–15 events. Upwelling and/or high zooplankton abundance has been documented near all whale hotspots. Records of C. marginata occurred in all months, with 75% in spring and summer. Inter-annual variability showed broad agreement between increased whale records (usually in spring/summer) and strongly positive ‘Niño 3.4’ during 1980–1995 but not thereafter. Coastal upwelling and productivity increase during climatic phenomena such as El Niño and are likely to be quickly beneficial to plankton-feeding whales such as C. marginata.     

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a d_N/d_S-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.Receptor-like kinases (RLKs) constitute one of the largest gene families in plants and expanded massively in land plants (Embryophyta; Lehti-Shiu et al., 2009, 2012). For plant RLK gene families, the functions of most members are often not known (especially in recently expanded families), but some described functions include innate immunity (Albert et al., 2010), pathogen response (Dodds and Rathjen, 2010), abiotic stress (Yang et al., 2010), development (De Smet et al., 2009), and sometimes multiple functions (Lehti-Shiu et al., 2012). The RLKs usually consist of three domains: an N-terminal extracellular domain, a transmembrane domain, and a C-terminal kinase domain (KD). In plants, the KD usually has a Ser/Thr specificity (Shiu and Bleecker, 2001), but Tyr-specific RLKs were also described (e.g. BRASSINOSTEROID INSENSITIVE1; Oh et al., 2009). Interestingly, it was estimated that approximately 20% of RLKs contain a catalytically inactive KD (e.g. STRUBBELIG and CORYNE; Chevalier et al., 2005; Castells and Casacuberta, 2007; Gish and Clark, 2011). In Arabidopsis (Arabidopsis thaliana), 44 RLK subgroups (SGs) were defined by inferring the phylogenetic relationships between the KDs (Shiu and Bleecker, 2001). Interestingly, different SGs show different duplication/retention rates (Lehti-Shiu et al., 2009). Specifically, RLKs involved in stress responses show a high number of tandemly duplicated genes whereas those involved in development do not (Shiu et al., 2004), which suggests that some RLK genes are important for the responses of land plants to a changing environment (Lehti-Shiu et al., 2012). There seem to be relatively few RLK pseudogenes compared with other large gene families, and copy retention was argued to be driven by both drift and selection (Zou et al., 2009; Lehti-Shiu et al., 2012). As most SGs are relatively old and RLK subfamilies expanded independently in several plant lineages, duplicate retention cannot be explained by drift alone, and natural selection is expected to be an important driving factor in RLK gene family retention (Lehti-Shiu et al., 2009).Leucine-rich repeat-receptor-like kinases (LRR-RLKs), which contain up to 30 leucine-rich repeat (LRRs) in their extracellular domain, constitute the largest RLK family (Shiu and Bleecker, 2001). Based on the KD, 15 LRR-RLK SGs have been established in Arabidopsis (Shiu et al., 2004; Lehti-Shiu et al., 2009). So far, two major functions have been attributed to them: defense against pathogens and development (Tang et al., 2010b). LRR-RLKs involved in defense are predominantly found in lineage-specific expanded (LSE) gene clusters, whereas LRR-RLKs involved in development are mostly found in nonexpanded groups (Tang et al., 2010b). It was also discovered that the LRR domains are significantly less conserved than the remaining domains of the LRR-RLK genes (Tang et al., 2010b). In addition, a study of four plant genomes (Arabidopsis, grape [Vitis vinifera], poplar [Populus trichocarpa], and rice [Oryza sativa]) showed that LRR-RLK genes from LSE gene clusters show significantly more indications of positive selection or relaxed constraint than LRR-RLKs from nonexpanded groups (Tang et al., 2010b).The genomes of flowering plants (angiosperms) have been shown to be highly dynamic compared with most other groups of land plants (Leitch and Leitch, 2012). This dynamic is mostly caused by the frequent multiplication of genetic material, followed by a complex pattern of differential losses (i.e. the fragmentation process) and chromosomal rearrangements (Langham et al., 2004; Leitch and Leitch, 2012). Most angiosperm genomes sequenced so far show evidence for at least one whole-genome multiplication event during their evolution (Jaillon et al., 2007; D’Hont et al., 2012; Tomato Genome Consortium, 2012). At a smaller scale, tandem and segmental duplications are also very common in angiosperms (Arabidopsis Genome Initiative, 2000; International Rice Genome Sequencing Project, 2005; Rizzon et al., 2006). Although the most common fate of duplicated genes is to be progressively lost, in some cases they can be retained in the genome, and adaptive as well as nonadaptive scenarios have been discussed to play a role in this preservation process (for review, see Moore and Purugganan, 2005; Hahn, 2009; Innan, 2009; Innan and Kondrashov, 2010). Whole-genome sequences also revealed that the same gene may undergo several rounds of duplication and retention. These LSE genes were shown to evolve under positive selection more frequently than single-copy genes in angiosperms (Fischer et al., 2014). That study analyzed general trends over whole genomes. Here, we ask if, and to what extent, this trend is observable at LRR-RLK genes. As this gene family is very dynamic and large, and in accordance with the results of Tang et al. (2010b), we expect the effect of positive selection to be even more pronounced than in the whole-genome average.We analyzed 33 Embryophyta genomes to investigate the evolutionary history of the LRR-RLK gene family in a phylogenetic framework. Twenty LRR-RLK SGs were identified, and from this data set, we deciphered the evolutionary dynamics of this family within angiosperms. The expansion/reduction rates were contrasted between SGs and species as well as in ancestral branches of the angiosperm phylogeny. We then focused on genes whose number increased dramatically in an SG- and/or species-specific manner (i.e. LSE genes). Those genes are likely to be involved in species-specific cellular processes or adaptive interactions and were used as a template to infer the potential occurrence of positive selection. This led to the identification of sites at which positive selection likely acted. We discuss our results in the light of angiosperm genome evolution and current knowledge of LRR-RLK functions. Positive selection footprints identified in LSE genes highlight the importance of combining evolutionary analysis and functional knowledge to guide further investigations.     

Successful immunotherapy with matrix metalloproteinase-derived peptides in adjuvant arthritis depends on the timing of peptide administration

We have recently found that matrix metalloproteinases (MMPs) are targets for T-cell and B-cell reactivity in experimental arthritis. In the present article, we investigate whether modulation of MMP-specific T-cell responses could influence the course of adjuvant arthritis (AA). Lewis rats were treated nasally with MMP peptides prior to or after AA induction. Administration of the MMP-10 or the MMP-16 peptide prior to AA induction reduced the arthritic symptoms. In contrast, administration of the MMP-10 peptide after AA induction aggravated the arthritic symptoms. The present study shows the possible usefulness of MMP peptides for immunotherapy. However, a clear understanding of proper timing of peptide administration is crucial for the development of such therapies.     

In Silico Analysis of Usher Encoding Genes in Klebsiella pneumoniae and Characterization of Their Role in Adhesion and Colonization

Chaperone/usher (CU) assembly pathway is used by a wide range of Enterobacteriaceae to assemble adhesive surface structures called pili or fimbriae that play a role in bacteria-host cell interactions. In silico analysis revealed that the genome of Klebsiella pneumoniae LM21 harbors eight chromosomal CU loci belonging to γκп and ϭ clusters. Of these, only two correspond to previously described operons, namely type 1 and type 3-encoding operons. Isogenic usher deletion mutants of K. pneumoniae LM21 were constructed for each locus and their role in adhesion to animal (Intestine 407) and plant (Arabidopsis thaliana) cells, biofilm formation and murine intestinal colonization was investigated. Type 3 pili usher deleted mutant was impaired in all assays, whereas type 1 pili usher deleted mutant only showed attenuation in adhesion to plant cells and in intestinal colonization. The LM21ΔkpjC mutant was impaired in its capacity to adhere to Arabidopsis cells and to colonize the murine intestine, either alone or in co-inoculation experiments. Deletion of LM21kpgC induced a significant decrease in biofilm formation, in adhesion to animal cells and in colonization of the mice intestine. The LM21∆kpaC and LM21∆kpeC mutants were only attenuated in biofilm formation and the adhesion abilities to Arabidopsis cells, respectively. No clear in vitro or in vivo effect was observed for LM21∆kpbC and LM21∆kpdC mutants. The multiplicity of CU loci in K. pneumoniae genome and their specific adhesion pattern probably reflect the ability of the bacteria to adhere to different substrates in its diverse ecological niches.     

Design of the Endobronchial Valve for Emphysema Palliation Trial (VENT): a non-surgical method of lung volume reduction

Background

Lung volume reduction surgery is effective at improving lung function, quality of life, and mortality in carefully selected individuals with advanced emphysema. Recently, less invasive bronchoscopic approaches have been designed to utilize these principles while avoiding the associated perioperative risks. The Endobronchial Valve for Emphysema PalliatioN Trial (VENT) posits that occlusion of a single pulmonary lobe through bronchoscopically placed Zephyr^® endobronchial valves will effect significant improvements in lung function and exercise tolerance with an acceptable risk profile in advanced emphysema.

Methods

The trial design posted on Clinical trials.gov, on August 10, 2005 proposed an enrollment of 270 subjects. Inclusion criteria included: diagnosis of emphysema with forced expiratory volume in one second (FEV₁) < 45% of predicted, hyperinflation (total lung capacity measured by body plethysmography > 100%; residual volume > 150% predicted), and heterogeneous emphysema defined using a quantitative chest computed tomography algorithm. Following standardized pulmonary rehabilitation, patients were randomized 2:1 to receive unilateral lobar placement of endobronchial valves plus optimal medical management or optimal medical management alone. The co-primary endpoint was the mean percent change in FEV₁ and six minute walk distance at 180 days. Secondary end-points included mean percent change in St. George's Respiratory Questionnaire score and the mean absolute changes in the maximal work load measured by cycle ergometry, dyspnea (mMRC) score, and total oxygen use per day. Per patient response rates in clinically significant improvement/maintenance of FEV₁ and six minute walk distance and technical success rates of valve placement were recorded. Apriori response predictors based on quantitative CT and lung physiology were defined.

Conclusion

If endobronchial valves improve FEV₁ and health status with an acceptable safety profile in advanced emphysema, they would offer a novel intervention for this progressive and debilitating disease.

Trial Registration

ClinicalTrials.gov: NCT00129584     

Portable light transmission measuring system for preserved corneas

Background  

The authors have developed a small portable device for the objective measurement of the transparency of corneas stored in preservative medium, for use by eye banks in evaluation prior to transplantation.     

Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage

Background  

Tenascins are a family of glycoproteins found primarily in the extracellular matrix of embryos where they help to regulate cell proliferation, adhesion and migration. In order to learn more about their origins and relationships to each other, as well as to clarify the nomenclature used to describe them, the tenascin genes of the urochordate Ciona intestinalis, the pufferfish Tetraodon nigroviridis and Takifugu rubripes and the frog Xenopus tropicalis were identified and their gene organization and predicted protein products compared with the previously characterized tenascins of amniotes.     

A novel surface protein of Trichomonas vaginalis is regulated independently by low iron and contact with vaginal epithelial cells

Background  

Trichomonosis caused by Trichomonas vaginalis is the number one, non-viral sexually transmitted disease (STD) that affects more than 250 million people worldwide. Immunoglobulin A (IgA) has been implicated in resistance to mucosal infections by pathogens. No reports are available of IgA-reactive proteins and the role, if any, of this class of antibody in the control of this STD. The availability of an IgA monoclonal antibody (mAb) immunoreactive to trichomonads by whole cell (WC)-ELISA prompted us to characterize the IgA-reactive protein of T. vaginalis.