Rapid Identification of a Natural Knockout Allele of ARMADILLO REPEAT-CONTAINING KINESIN1 That Causes Root Hair Branching by Mapping-By-Sequencing

In Arabidopsis (Arabidopsis thaliana), branched root hairs are an indicator of defects in root hair tip growth. Among 62 accessions, one accession (Heiligkreuztal2 [HKT2.4]) displayed branched root hairs, suggesting that this accession carries a mutation in a gene of importance for tip growth. We determined 200- to 300-kb mapping intervals using a mapping-by-sequencing approach of F2 pools from crossings of HKT2.4 with three different accessions. The intersection of these mapping intervals was 80 kb in size featuring not more than 36 HKT2.4-specific single nucleotide polymorphisms, only two of which changed the coding potential of genes. Among them, we identified the causative single nucleotide polymorphism changing a splicing site in ARMADILLO REPEAT-CONTAINING KINESIN1. The applied strategies have the potential to complement statistical methods in high-throughput phenotyping studies using different natural accessions to identify causative genes for distinct phenotypes represented by only one or a few accessions.Root hairs are tubular tip outgrowths of single root epidermal cells (trichoblasts). They are an excellent genetic system and serve as a model to study the molecular components regulating tip growth (Carol and Dolan, 2002; Samaj et al., 2004; Lee and Yang, 2008). One of the main regulators of tip growth in root hairs is the small G protein RHO OF PLANTS2 (ROP2; Jones et al., 2002; Payne and Grierson, 2009). ROP2 determines the position of root hairs in incipient epidermal root hair cells and remains localized in the emerging tip during root hair tip growth (Molendijk et al., 2001; Jones et al., 2002). In addition, other factors have been identified to be important for growth and its directionality including phosphoinositides, cytoplasmic [Ca²⁺] gradients and their oscillation, reactive oxygen species, the RAB GTPase homolog A4B, and the cytoskeleton (Foreman et al., 2003; Preuss et al., 2004, 2006; Carol et al., 2005; Thole et al., 2008; Heilmann, 2009).Defects in essential processes for the establishment and maintenance of tip growth lead to deviations in root hair morphology such as branching and waviness (Samaj et al., 2004; Lee and Yang, 2008). Both the microtubules (MTs) and actin are important regulators of tip growth with MTs maintaining one growth point (Bibikova et al., 1999; Miller et al., 1999; Baluska et al., 2000). The latter is evident from the finding that artificially induced [Ca²⁺] gradients can induce additional growth tips when MTs are destroyed by drug treatments (Bibikova et al., 1999).Although the genetic and molecular analysis revealed a well-understood working model for root hair growth, little is known about the natural variation of the underlying processes. Which are the adaptive processes of relevance to specific environmental cues and which have already been selected for in natural accessions? One way to address this question is to link genotype and phenotype by association mapping using various Arabidopsis (Arabidopsis thaliana) accessions. This is greatly facilitated by the 1001 Genomes Project (http://1001genomes.org), providing an increasing number of sequenced accessions. In some cases, phenotypes are only found in one or a few accessions. When the minor allele frequency (AF) is low, the identification of such rare causative alleles with genome-wide association mapping studies is challenging because they cannot be discriminated from false positives (e.g. sequencing errors or synthetic associations; Korte and Farlow, 2013), they are not detectable because of chosen thresholds, or they do not support a statistically significant value (Cantor et al., 2010). Other time-consuming approaches with low mapping resolution, such as quantitative trait loci mapping, need to be followed to identify the causative gene. For this, mapping-by-sequencing, which was originally developed for the identification of mutagen-induced changes in model species (Schneeberger et al., 2009b), can help to rapidly identify causal polymorphisms including nonmodel and nonreference strains (Nordström et al., 2013; Takagi et al., 2013). The resolution of mapping-by-sequencing experiments in Arabidopsis mapping populations is typically between multiple hundreds of kilobase pairs up to a few megabase pairs (James et al., 2013). Although intervals of this size allow the identification of causal mutations in forward genetic screens, they are problematic for the analysis of diverse Arabidopsis accessions because the single nucleotide polymorphism (SNP) density is very high; consequently, hundreds of polymorphisms have to be considered.Here we report on a modification of the mapping-by-sequencing strategy providing a shortcut from distinct, monogenic accession-specific phenotypes to the causative SNP. When studying root hair morphology in 62 accessions for which the genome sequences were released by the 1001 Genomes Project (Cao et al., 2011), we found one accession (Heiligkreuztal2 [HKT2.4]) in which almost all root hairs were branched. To identify the causative gene, we used an approach based on mapping-by-sequencing. Instead of one outcross, we used outcrosses with three different accessions. We selected F2 seedlings exhibiting the distinct, monogenic, recessive root hair branching phenotype for sequencing. Combining the intersection of the three resulting mapping intervals with a selection for accession-specific SNPs revealed two primary candidate genes responsible for the root phenotype. We demonstrate that the causative SNP renders a splicing site in ARMADILLO REPEAT-CONTAINING KINESIN1 (ARK1) inactive and therefore leads to a defective ARK1/MORPHOGENESIS OF ROOT HAIR2 (MRH2) protein that is thought to coordinate actin microfilaments and MTs during tip growth of root hairs (Yang et al., 2007; Yoo and Blancaflor, 2013).     

Identification of nitrogen sources and transformations within karst springs using isotope tracers of nitrogen

Isotope analyses of nitrate and algae were used to gain better understanding of sources of nitrate to Florida’s karst springs and processes affecting nitrate in the Floridan aquifer at multiple scales. In wet years, δ¹⁵N and δ¹⁸O of nitrate ranged from +3 to +9‰ in headwater springs in north Florida, indicating nitrification of soil ammonium as the dominant source. With below normal rainfall, the δ¹⁵N and δ¹⁸O of nitrate were higher in almost all springs (reaching +20.2 and +15.3‰, respectively) and were negatively correlated with dissolved oxygen. In springs with values of δ¹⁵N-NO₃ and δ¹⁸O-NO₃ greater than +10‰, nitrate concentrations declined 40–50% in dry years and variations in the δ¹⁵N and δ¹⁸O of nitrate were consistent with the effects of denitrification. Modeling of the aquifer as a closed system yielded in situ fractionation caused by denitrification of 9 and 18‰ for Δ¹⁸O and Δ¹⁵N, respectively. We observed no strong evidence for local sources of nitrate along spring runs; concentrations declined downstream (0.42–3.3?μmol-NO₃ L^?1 per km) and the isotopic dynamics of algae and nitrate indicated a closed system. Correlation between the δ¹⁵N composition of nitrate and algae was observed at regional and spring-run scales, but the relationship was complicated by varying isotopic fractionation factors associated with nitrate uptake (Δ ranged from 2 to 13‰). Our study demonstrates that nitrate inputs to Florida’s springs are derived predominantly from non-point sources and that denitrification is detectable in aquifer waters with relatively long residence time (i.e., matrix flow).     

A proteomic approach to paclitaxel chemoresistance in ovarian cancer cell lines

Ovarian cancer is the leading cause of gynaecological cancer mortality. Paclitaxel is used in the first line treatment of ovarian cancer, but acquired resistance represents the most important clinical problem and a major obstacle to a successful therapy. Several mechanisms have been implicated in paclitaxel resistance, however this process has not yet been fully explained. To better understand molecular resistance mechanisms, a comparative proteomic approach was undertaken on the human epithelial ovarian cancer cell lines A2780 (paclitaxel sensitive), A2780TC1 and OVCAR3 (acquired and inherently resistant). Proteins associated with chemoresistance process were identified by DIGE coupled with mass spectrometry (MALDI-TOF and LC-MS/MS). Out of the 172 differentially expressed proteins in pairwise comparisons among the three cell lines, 151 were identified and grouped into ten main functional classes. Most of the proteins were related to the category of stress response (24%), metabolism (22%), protein biosynthesis (15%) and cell cycle and apoptosis (11%), suggesting that alterations of those processes might be involved in paclitaxel resistance mechanisms. This is the first direct proteomic comparison of paclitaxel sensitive and resistant ovarian cancer cells and may be useful for further studies of resistance mechanisms and screening of resistance biomarkers for the development of tailored therapeutic strategies.     

Bone inflammation and altered gene expression with type I diabetes early onset

Type I diabetes is associated with bone loss and marrow adiposity. To identify early events involved in the etiology of diabetic bone loss, diabetes was induced in mice by multiple low dose streptozotocin injections. Serum markers of bone metabolism and inflammation as well as tibial gene expression were examined between 1 and 17 days post‐injection (dpi). At 3 dpi, when blood glucose levels were significantly elevated, body, fat pad and muscle mass were decreased. Serum markers of bone resorption and formation significantly decreased at 5 dpi in diabetic mice and remained suppressed throughout the time course. An osteoclast gene, TRAP5 mRNA, was suppressed at early and late time points. Suppression of osteogenic genes (runx2 and osteocalcin) and induction of adipogenic genes (PPARγ2 and aP2) were evident as early as 5 dpi. These changes were associated with an elevation of serum cytokines, but more importantly we observed an increase in the expression of cytokines in bone, supporting the idea that bone, itself, exhibits an inflammatory response during diabetes induction. This inflammation could in turn contribute to diabetic bone pathology. IFN‐γ (one of the key cytokines elevated in bone and known to be involved in bone regulation) deficiency did not prevent diabetic bone pathology. Taken together, our findings indicate that bone becomes inflamed with the onset of T1‐diabetes and during this time bone phenotype markers become altered. However, inhibition of one cytokine, IFN‐γ was not sufficient to prevent the rapid bone phenotype changes. J. Cell. Physiol. 218: 575–583, 2009. © 2008 Wiley‐Liss, Inc.     

CaV1.3 as pacemaker channels in adrenal chromaffin cells: specific role on exo- and endocytosis?

Voltage-gated L-type calcium channels (LTCCs) are expressed in adrenal chromaffin cells. Besides shaping the action potential (AP), LTCCs are involved in the excitation-secretion coupling controlling catecholamine release and in Ca (2+) -dependent vesicle retrieval. Of the two LTCCs expressed in chromaffin cells (CaV1.2 and CaV1.3), CaV1.3 possesses the prerequisites for pacemaking spontaneously firing cells: low-threshold, steep voltage-dependence of activation and slow inactivation. By using CaV1 .3 (-/-) KO mice and the AP-clamp it has been possible to resolve the time course of CaV1.3 pacemaker currents, which is similar to that regulating substantia nigra dopaminergic neurons. In mouse chromaffin cells CaV1.3 is coupled to fast-inactivating BK channels within membrane nanodomains and controls AP repolarization. The ability to carry subthreshold Ca (2+) currents and activate BK channels confers to CaV1.3 the unique feature of driving Ca (2+) loading during long interspike intervals and, possibly, to control the Ca (2+) -dependent exocytosis and endocytosis processes that regulate catecholamine secretion and vesicle recycling.     

The Impact of Sexual Abuse in Patients Undergoing Colonoscopy

Background

Sexual abuse has been linked to strong effects on gastrointestinal health. Colonoscopy can provoke intense emotional reactions in patients with a sexual abuse history and may lead to avoidance of endoscopic procedures.

Objective

To determine whether care around colonoscopy needs adjustment for patients with sexual abuse experience, thereby exploring targets for the improvement of care around colonoscopic procedures.

Methods

Questionnaires were mailed to patients (n = 1419) from two centers within 11 months after colonoscopy. Differences in experience of the colonoscopy between patients with and without a sexual abuse history were assessed and patients'' views regarding physicians'' inquiry about sexual abuse and care around endoscopic procedures were obtained.

Results

A total of 768 questionnaires were analyzed. The prevalence of sexual abuse was 3.9% in male and 9.5% in female patients. Patients born in a non-western country reported more sexual abuse (14.9%) than those born in a western country (6.3%; p = 0.008). Discomfort during colonoscopy was indicated on a scale from 0 to 10, mean distress score of patients with sexual abuse was 4.8(±3.47) compared to 3.5(±3.11) in patients without a sexual abuse history (p = 0.007). Abdominal pain was a predictor for higher distress during colonoscopy (β = −0.019 (SE = 0.008); p = 0.02, as well as the number of complaints indicated as reason for colonoscopy (β = 0.738 (SE = 0.276); p = 0.008). Of patients with sexual abuse experience, 53.8% believed gastroenterologists should ask about it, 43.4% said deeper sedation during colonoscopy would diminish the distress.

Conclusions

Sexual abuse is prevalent in patients presenting for colonoscopy. Patients with a sexual abuse history experience more distress during the procedure and indicate that extra attention around and during colonoscopy may diminish this distress.     

A Trade-Off between Reproduction and Feather Growth in the Barn Swallow (Hirundo rustica)

Physiological trade-offs mediated by limiting energy, resources or time constrain the simultaneous expression of major functions and can lead to the evolution of temporal separation between demanding activities. In birds, plumage renewal is a demanding activity, which accomplishes fundamental functions, such as allowing thermal insulation, aerodynamics and socio-sexual signaling. Feather renewal is a very expensive and disabling process, and molt is often partitioned from breeding and migration. However, trade-offs between feather renewal and breeding have been only sparsely studied. In barn swallows (Hirundo rustica) breeding in Italy and undergoing molt during wintering in sub-Saharan Africa, we studied this trade-off by removing a tail feather from a large sample of individuals and analyzing growth bar width, reflecting feather growth rate, and length of the growing replacement feather in relation to the stage in the breeding cycle at removal and clutch size. Growth bar width of females and length of the growing replacement feather of both sexes were smaller when the original feather had been removed after clutch initiation. Importantly, in females both growth bar width and replacement feather length were negatively predicted by clutch size, and more strongly so for large clutches and when feather removal occurred immediately after clutch completion. Hence, we found strong, coherent evidence for a trade-off between reproduction, and laying effort in particular, and the ability to generate new feathers. These results support the hypothesis that the derived condition of molting during wintering in long-distance migrants is maintained by the costs of overlapping breeding and molt.     

Raised Soluble P-Selectin Moderately Accelerates Atherosclerotic Plaque Progression

Soluble P-selectin (sP-selectin), a biomarker of inflammatory related pathologies including cardiovascular and peripheral vascular diseases, also has pro-atherosclerotic effects including the ability to increase leukocyte recruitment and modulate thrombotic responses in vivo. The current study explores its role in progressing atherosclerotic plaque disease. Apoe ^−/− mice placed on a high fat diet (HFD) were given daily injections of recombinant dimeric murine P-selectin (22.5 µg/kg/day) for 8 or 16 weeks. Saline or sE-selectin injections were used as negative controls. In order to assess the role of sP-selectin on atherothrombosis an experimental plaque remodelling murine model, with sm22α-hDTR Apoe^−/− mice on a HFD in conjunction with delivery of diphtheria toxin to induce targeted vascular smooth muscle apoptosis, was used. These mice were similarly given daily injections of sP-selectin for 8 or 16 weeks. While plaque mass and aortic lipid content did not change with sP-selectin treatment in Apoe^−/− or SM22α-hDTR Apoe^−/− mice on HFD, increased plasma MCP-1 and a higher plaque CD45 content in Apoe ^−/− HFD mice was observed. As well, a significant shift towards a more unstable plaque phenotype in the SM22α-hDTR Apoe^−/− HFD mice, with increased macrophage accumulation and lower collagen content, leading to a lower plaque stability index, was observed. These results demonstrate that chronically raised sP-selectin favours progression of an unstable atherosclerotic plaque phenotype.     

Rust mite resistance in apple assessed by quantitative trait loci analysis

The aim of this study was to assess the genetic basis of rust mite (Aculus schlechtendali) resistance in apple (Malus × domestica). A. schlechtendali infestation of apple trees has increased as a consequence of reduced side effects of modern fungicides on rust mites. An analysis of quantitative trait loci (QTLs) was carried out using linkage map data available for F₁ progeny plants of the cultivars ‘Fiesta’ × ‘Discovery’. Apple trees representing 160 different genotypes were surveyed for rust mite infestation, each at three different sites in two consecutive years. The distribution of rust mites on the individual apple genotypes was aggregated and significantly affected by apple genotype and site. We identified two QTLs for A. schlechtendali resistance on linkage group 7 of ‘Fiesta’. The AFLP marker E35M42-0146 (20.2 cM) and the RAPD marker AE10-400 (45.8 cM) were closest positioned to the QTLs and explained between 11.0% and 16.6% of the phenotypic variability. Additionally, putative QTLs on the ‘Discovery’ chromosomes 4, 5 and 8 were detected. The SSR marker Hi03a10 identified to be associated to one of the QTLs (AFLP marker E35M42-0146) was traced back in the ‘Fiesta’ pedigree to the apple cultivar ‘Wagener’. This marker may facilitate the breeding of resistant apple cultivars by marker assisted selection. Furthermore, the genetic background of rust mite resistance in existing cultivars can be evaluated by testing them for the identified SSR marker. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.