Comparative analysis of Neph gene expression in mouse and chicken development

Neph proteins are evolutionarily conserved members of the immunoglobulin superfamily of adhesion proteins and regulate morphogenesis and patterning of different tissues. They share a common protein structure consisting of extracellular immunoglobulin-like domains, a transmembrane region, and a carboxyl terminal cytoplasmic tail required for signaling. Neph orthologs have been widely characterized in invertebrates where they mediate such diverse processes as neural development, synaptogenesis, or myoblast fusion. Vertebrate Neph proteins have been described first at the glomerular filtration barrier of the kidney. Recently, there has been accumulating evidence suggesting a function of Neph proteins also outside the kidney. Here we demonstrate that Neph1, Neph2, and Neph3 are expressed differentially in various tissues during ontogenesis in mouse and chicken. Neph1 and Neph2 were found to be amply expressed in the central nervous system while Neph3 expression remained localized to the cerebellum anlage and the spinal cord. Outside the nervous system, Neph mRNAs were also differentially expressed in branchial arches, somites, heart, lung bud, and apical ectodermal ridge. Our findings support the concept that vertebrate Neph proteins, similarly to their Drosophila and C. elegans orthologs, provide guidance cues for cell recognition and tissue patterning in various organs which may open interesting perspectives for future research on Neph1-3 controlled morphogenesis.     

Immunofluorescent visualisation of focal adhesion kinase in human skeletal muscle and its associated microvasculature

Within animal skeletal muscle, focal adhesion kinase (FAK) has been associated with load-dependent molecular and metabolic adaptation including the regulation of insulin sensitivity. This study aimed to generate the first visual images of the localisation of FAK within human skeletal muscle fibres and its associated microvasculature using widefield and confocal immunofluorescence microscopy. Percutaneous muscle biopsies, taken from five lean, active males, were frozen and 5-μm cryosections were incubated with FAK antibodies for visualisation in muscle fibres and the microvasculature. Anti-myosin heavy chain type I was used for fibre-type differentiation. Muscle sections were also incubated with anti-dihydropyridine receptor (DHPR) to investigate co-localisation of FAK with the t-tubules. FITC-conjugated Ulex europaeus Agglutinin I stained the endothelium of the capillaries, whilst anti-smooth muscle actin stained the vascular smooth muscle of arterioles. Fibre-type differences in the intensity of FAK immunofluorescence were determined with image analysis software. In transversely and longitudinally orientated fibres, FAK was localised at the sarcolemmal regions. In longitudinally orientated fibres, FAK staining also showed uniform striations across the fibre and co-staining with DHPR suggests FAK associates with the t-tubules. There was no fibre-type difference in sarcoplasmic FAK content. Within the capillary endothelium and arteriolar smooth muscle, FAK was distributed heterogeneously as clusters. This is the first study to visualise FAK in human skeletal muscle microvasculature and within the (sub)sarcolemmal and t-tubule regions using immunofluorescence microscopy. This technique will be an important tool for investigating the role of FAK in the intracellular signalling of human skeletal muscle and the endothelium of its associated microvasculature.     

A homologue of the human STRIPAK complex controls sexual development in fungi

Sexual development in fungi is a complex process involving the generation of new cell types and tissues - an essential step for all eukaryotic life. The characterization of sterile mutants in the ascomycete Sordaria macrospora has led to a number of proteins involved in sexual development, but a link between these proteins is still missing. Using a combined tandem-affinity purification/mass spectrometry approach, we showed in vivo association of developmental protein PRO22 with PRO11, homologue of mammalian striatin, and SmPP2AA, scaffolding subunit of protein phosphatase 2A. Further experiments extended the protein network to the putative kinase activator SmMOB3, known to be involved in sexual development. Extensive yeast two-hybrid studies allowed us to pinpoint functional domains involved in protein-protein interaction. We show for the first time that a number of already known factors together with new components associate in vivo to form a highly conserved multi-subunit complex. Strikingly, a similar complex has been described in humans, but the function of this so-called striatin interacting phosphatase and kinase (STRIPAK) complex is largely unknown. In S. macrospora, truncation of PRO11 and PRO22 leads to distinct defects in sexual development and cell fusion, indicating a role for the fungal STRIPAK complex in both processes.     

Long-term effects of the rhapontic rhubarb extract ERr 731® on estrogen-regulated targets in the uterus and on the bone in ovariectomized rats

The efficacy of ERr 731(?), a commercially available extract isolated from Rheum rhaponticum, in terms of menopausal complaints like hot flushes, depression, anxiety and vaginal dryness has been proven in a two-year clinical study. Further a recent preclinical study excluded unwanted side effects on the endometrium by showing a lack of stimulation of proliferation marker genes by ERr 731(?) or its constituents in the 3-day uterotrophic assay. The present study aimed at further substantiating the safety of ERr 731(?) in terms of endometrial hyperplasia and at the same time test for potential estrogenic effects in the bone. Therefore, ovariectomized (ovx) rats were treated in a dietary long-term administration for 90 days. Hence, the modulation of proliferation in the uterus was investigated by examining the effects on the mRNA expression of proliferation marker genes (Mki67, Pcna), on the estrogen-responsive gene C3 and on the estrogen receptors ERα and ERβ. We additionally performed densitometry analysis of the proximal tibia metaphysis using peripheral computed tomography (pQCT) and quantified bone homeostasis markers in the serum to examine potential effects on the bone. In this study design, neither an uterotrophic response nor a modulation of proliferation marker genes on mRNA level has been observed as response to the long-term application of the rhapontic extract. Furthermore, no impact of the two administered ERr 731(?) doses on the E2 deprivation-induced bone loss has been evident at the end of the study. In conclusion, the observations from previous trials regarding the endometrial safety of ERr 731(?) have been supported by our experimental findings that exclude a stimulatory activity on proliferation in the uterus in a long-term administration in the young adult rat but no effect on the bone mineral density could be observed.     

Molecular characterization of three 3-ketosteroid-Δ(1)-dehydrogenase isoenzymes of Rhodococcus ruber strain Chol-4

Rhodococcus ruber strain Chol-4 isolated from a sewage sludge sample is able to grow on minimal medium supplemented with steroids, showing a broad catabolic capacity. This paper reports the characterization of three different 3-ketosteroid-Δ(1)-dehydrogenases (KstDs) in the genome of R. ruber strain Chol-4. The genome of this strain does not contain any homologues of a 3-keto-5α-steroid-Δ(4)-dehydrogenase (Kst4d or TesI) that appears in the genomes of Rhodococcus erythropolis SQ1 or Comamonas testosteroni. Growth experiments with kstD2 mutants, either a kstD2 single mutant, kstD2 double mutants in combination with kstD1 or kstD3, or the triple kstD1,2,3 mutant, proved that KstD2 is involved in the transformation of 4-androstene-3,17-dione (AD) to 1,4-androstadiene-3,17-dione (ADD) and in the conversion of 9α-hydroxy-4-androstene-3,17-dione (9OHAD) to 9α-hydroxy-1,4-androstadiene-3,17-dione (9OHADD). kstD2,3 and kstD1,2,3 R. ruber mutants (both lacking KstD2 and KstD3) did not grow in minimal medium with cholesterol as the only carbon source, thus demonstrating the involvement of KstD2 and KstD3 in cholesterol degradation. In contrast, mutation of kstD1 does not alter the bacterial growth on the steroids tested in this study and therefore, the role of this protein still remains unclear. The absence of a functional KstD2 in R. ruber mutants provoked in all cases an accumulation of 9OHAD, as a branch product probably formed by the action of a 3-ketosteroid-9α-hydroxylase (KshAB) on the AD molecule. Therefore, KstD2 is a key enzyme in the AD catabolism pathway of R. ruber strain Chol-4 while KstD3 is involved in cholesterol catabolism.     

Novel 2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl)acetic acids: discovery and hit-to-lead evolution of a selective CRTh2 receptor antagonist chemotype

Hit-to-lead evolution of 2-(2-((2-(4-chlorophenoxy)ethyl)thio)-1H-benzo[d]imidazol-1-yl)acetic acid (1), discovered in a high-throughput screening campaign as a novel chemotype of CRTh2 receptor antagonist, is presented. SAR development as well as in vitro and in vivo DMPK properties of selected representatives of substituted 2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl)acetic acids are discussed.     

Construction and functionalization of fused pyridine ring leading to novel compounds as potential antitubercular agents

A series of fused and functionalized pyridine derivatives were designed, synthesized and tested for their potential antitubercular properties. All these novel compounds were prepared by using multistep methods involving the construction of pyridine ring as a key synthetic step. Some of these compounds were found to be interesting when tested for their antitubercular properties in vitro and one of them appeared as an attractive and potential antitubercular agent.     

Linking landscape history and dispersal traits in grassland plant communities

Dispersal limitation and long-term persistence are known to delay plant species’ responses to habitat fragmentation, but it is still unclear to what extent landscape history may explain the distribution of dispersal traits in present-day plant communities. We used quantitative data on long-distance seed dispersal potential by wind and grazing cattle (epi- and endozoochory), and on persistence (adult plant longevity and seed bank persistence) to quantify the linkages between dispersal and persistence traits in grassland plant communities and current and past landscape configurations. The long-distance dispersal potential of present-day communities was positively associated with the amounts of grassland in the historical (1835, 1938) landscape, and with a long continuity of grazing management—but was not associated with the properties of the current landscape. The study emphasises the role of history as a determinant of the dispersal potential of present-day grassland plant communities. The importance of long-distance dispersal processes has declined in the increasingly fragmented modern landscape, and long-term persistent species are expected to play a more dominant role in grassland communities in the future. However, even within highly fragmented landscapes, long-distance dispersed species may persist locally—delaying the repayment of the extinction debt.     

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Protein lipid modification of cysteine residues, referred to as S-palmitoylation or S-acylation, is an important secondary and reversible modification that regulates membrane association, trafficking, and function of target proteins. This enzymatic reaction is mediated by protein S-acyl transferases (PATs). Here, the phylogeny, genomic organization, protein topology, expression, and localization pattern of the 24 PAT family members from Arabidopsis (Arabidopsis thaliana) is described. Most PATs are expressed at ubiquitous levels and tissues throughout the development, while few genes are expressed especially during flower development preferentially in pollen and stamen. The proteins display large sequence and structural variations but exhibit a common protein topology that is preserved in PATs from various organisms. Arabidopsis PAT proteins display a complex targeting pattern and were detected at the endoplasmic reticulum, Golgi, endosomal compartments, and the vacuolar membrane. However, most proteins were targeted to the plasma membrane. This large concentration of plant PAT activity to the plasma membrane suggests that the plant cellular S-acylation machinery is functionally different compared with that of yeast (Saccharomyces cerevisiae) and mammalians.Cellular functions are regulated by various protein modifications. These modifications can occur in a controlled, reversible, and transient manner in response to different signals (Huber and Hardin, 2004; Stulemeijer and Joosten, 2008). Protein phosphorylation is the most prominent modification and is regulated by the balanced activities of protein kinases and protein phosphatases (Hardie, 1999; Luan, 2003). However, other modifications, like ubiquitination and sumoylation (Miura and Hasegawa, 2010) or nitrosylation (Lamattina et al., 2003), also regulate protein functions.A less well characterized reversible lipid modification is the thioesterification of Cys residues, which is known as S-palmitoylation or more generally referred to as S-acylation (Hemsley and Grierson, 2008; Sorek et al., 2009). S-acyl modifications mainly affect membrane attachment and trafficking of proteins. They are required for the dynamic association of proteins with membrane subdomains (Sorek et al., 2007, 2010) and for the cycling between different cellular membranes (Rocks et al., 2005). In addition, S-acylation can influence the stability of proteins (Valdez-Taubas and Pelham, 2005; Abrami et al., 2006), modulates the functions of proteins (Gubitosi-Klug et al., 2005), or mediates the interaction between different proteins (Charrin et al., 2002; Flannery et al., 2010).S-acyl modification of proteins is brought about by palmitoyltransferases, correctly referred to as protein S-acyltransferases (PATs; Mitchell et al., 2006). Originally, these enzymes were identified in yeast (Saccharomyces cerevisiae; Lobo et al., 2002; Roth et al., 2002). Sequence analyses of the yeast PAT enzymes revealed that they share a common structure mainly composed of four predicted transmembrane domains (TMDs) and a stretch of Asp-His-His-Cys (DHHC) within a Cys-rich domain (CRD; Pfam accession, PF01529; InterPro entry, IPR001594). Mutational analyses revealed that the Cys residue of the DHHC stretch is necessary for autoacylation and for the modification of target proteins. Therefore, this domain appears to represent the active site of these enzymes (Lobo et al., 2002; Roth et al., 2002). Detailed analyses of the lipid modifications of Rho-of-plants6 (ROP6; Sorek et al., 2007) and of the Calcineurin-B like (CBL) proteins 1 and 2 (Batistič et al., 2008, 2012) revealed that plant PATs either transfer palmitate or stearate to these substrates.In plants, so far only one PAT was characterized in detail. A screen of Arabidopsis (Arabidopsis thaliana) mutants resulted in the identification of TIP GROWTH DEFECTIVE1 (TIP1), which is affected in root hair formation and growth (Schiefelbein et al., 1993; Ryan et al., 1998). Mapping of the mutant allele revealed that TIP1 encodes a DHHC-CRD-containing protein, and it was shown that this protein is indeed S-acylated (Hemsley et al., 2005, 2008). Moreover, TIP1 contains N-terminal ankyrin repeats, related to the yeast PAT Akr1, and is able to complement the PAT function in the akr1Δ yeast strain, corroborating that TIP1 has a PAT enzyme function (Hemsley et al., 2005). Although our knowledge about the plant S-acylome and S-acylation machinery is still limited (Hemsley, 2009), previous studies on the S-acylation of plant proteins revealed that these modifications could occur at different cellular membranes like the endoplasmic reticulum (ER; Adjobo-Hermans et al., 2006; Batistič et al., 2008), the Golgi (Zeng et al., 2007), or directly at the plasma membrane (PM; Sorek et al., 2007). Furthermore, recent studies on the lipid modification of the tonoplast-associated CBL2 protein from Arabidopsis implicated that S-acylation can also occur at the vacuolar membrane (Batistič et al., 2012). These findings suggested that the PAT enzymes that modify these targets reside at different membranes within the plant cell.In this report, the complement of the Arabidopsis PAT gene loci was examined to perform a comprehensive analysis of this gene and protein family. These analyses revealed that at least 24 PAT gene loci are encoded in the Arabidopsis genome. All Arabidopsis PATs are expressed. Expression occurs mainly at steady levels throughout development and in most tissues examined. However, some PATs are preferentially expressed at certain developmental stages or cell types especially during flowering and in pollen, respectively. Phylogenetic analysis revealed that the proteins are highly divergent. Nevertheless, most PAT proteins harbor a similar structural topology and preserved sequence motifs that are representative of this class of enzymes. Functional analyses on several proteins by yeast complementation analyses indicate that Arabidopsis PATs represent active enzymes, even if their sequence deviates from the regular standard sequence composition previously reported for functional PATs. Moreover, the protein localizations of all 24 Arabidopsis PATs were examined. This revealed a complex targeting pattern of PATs showing that S-acylation can occur at different cellular membranes within the cell. Remarkably, the plant PATs analyzed are mainly targeted to the PM, indicating that the plant S-acylation machinery has a different organization and function compared with the mammalian and yeast PAT machinery.     

Genomic and morphological evidence converge to resolve the enigma of Strepsiptera

The phylogeny of insects, one of the most spectacular radiations of life on earth, has received considerable attention. However, the evolutionary roots of one intriguing group of insects, the twisted-wing parasites (Strepsiptera), remain unclear despite centuries of study and debate. Strepsiptera exhibit exceptional larval developmental features, consistent with a predicted step from direct (hemimetabolous) larval development to complete metamorphosis that could have set the stage for the spectacular radiation of metamorphic (holometabolous) insects. Here we report the sequencing of a Strepsiptera genome and show that the analysis of sequence-based genomic data (comprising more than 18 million nucleotides from nearly 4,500 genes obtained from a total of 13 insect genomes), along with genomic metacharacters, clarifies the phylogenetic origin of Strepsiptera and sheds light on the evolution of holometabolous insect development. Our results provide overwhelming support for Strepsiptera as the closest living relatives of beetles (Coleoptera). They demonstrate that the larval developmental features of Strepsiptera, reminiscent of those of hemimetabolous insects, are the result of convergence. Our analyses solve the long-standing enigma of the evolutionary roots of Strepsiptera and reveal that the holometabolous mode of insect development is more malleable than previously thought.