A Collaborative Model to Implement Flexible, Accessible and Efficient Oncogenetic Services for Hereditary Breast and Ovarian Cancer: The C-MOnGene Study.

Medical genetic services are facing an unprecedented demand for counseling and testing for hereditary breast and ovarian cancer (HBOC) in a context of limited resources. To help resolve this issue, a collaborative oncogenetic model was recently developed and implemented at the CHU de Québec-Université Laval; Quebec; Canada. Here, we present the protocol of the C-MOnGene (Collaborative Model in OncoGenetics) study, funded to examine the context in which the model was implemented and document the lessons that can be learned to optimize the delivery of oncogenetic services. Within three years of implementation, the model allowed researchers to double the annual number of patients seen in genetic counseling. The average number of days between genetic counseling and disclosure of test results significantly decreased. Group counseling sessions improved participants' understanding of breast cancer risk and increased knowledge of breast cancer and genetics and a large majority of them reported to be overwhelmingly satisfied with the process. These quality and performance indicators suggest this oncogenetic model offers a flexible, patient-centered and efficient genetic counseling and testing for HBOC. By identifying the critical facilitating factors and barriers, our study will provide an evidence base for organizations interested in transitioning to an oncogenetic model integrated into oncology care; including teams that are not specialized but are trained in genetics.

Sr-90 soil to plant transfer factor reduction using calcium and polymer soil amendments.

Introducing calcium into soils can inhibit Sr-90 uptake by plants. To test the efficacy of calcium amendments on the inhibition of Sr-90 uptake by edible plants, a number of different calcium applications, including calcium nitrate, calcium thiosulfate and a mixture of both liquid solutions, were used in this study. Pea plants (Pisum sativum 'Sabre') grown in Sr-90 contaminated soil from seeds to maturity were watered with these calcium solutions. Two different polymers, one inert and one nutrient enriched, were incorporated into the contaminated soil where pea seeds were sowed to ascertain a continuous supply of calcium and essential nutrients. Results show that the heterogeneity of Sr-90 distribution in soil translated to disparate Sr-90 contents in plant tissues. However, on average, irrigation with calcium solutions in conjunction with the usage of polymers consistently yielded a reduction in Sr-90 uptake by the plants. The lowest soil-to-plant transfer factor (TF) values were measured in the edible pea part of the plant, followed by the flowers, roots, stems, pea shells and then leaves. TF values for pea shells were between 4.9 and 20.9, and between 0.3 and 2.8 for the peas. Results do not allow the identification of one particular chemical solution that would systematically be the best choice to minimize Sr-90 uptake.

Effects of in vivo exposure to tritium: a multi-biomarker approach using the fathead minnow, Pimephales promelas.

Tritium (3H) is a radioactive isotope of hydrogen. In the environment, the most common form of tritium is tritiated water (HTO). However, tritium can also be incorporated into organic molecules, forming organically bound tritium (OBT). The present study characterized the effects of tritium on the health of the fathead minnow, Pimephales promelas. Fish were exposed to a gradient of HTO (activity concentrations of 12,000, 25,000, and 180,000 Bq/L) and OBT using food spiked with tritiated amino acids (OBT only, with an activity concentration of 27,000 Bq/L). A combined exposure condition where fish were placed in 25,000 Bq/L water and received OBT through feed was also studied. Fish were exposed for 60 days, followed by a 60-day depuration period. A battery of health biomarkers were measured in fish tissues at seven time points throughout the 120 days required to complete the exposure and depuration phases. HTO and OBT were also measured in fish tissues at the same time points. Results showed effects of increasing tritium activity concentrations in water after 60 days of exposure. The internal dose rates of tritium, estimated from the tissue free-water tritium (TFWT) and OBT activity concentrations, reached a maximum of 0.65 µGy/h, which is relatively low considering background levels. No effects were observed on survival, fish condition, and metabolic indices (gonado-, hepato-, and spleno-somatic indexes (GSI, HSI, SSI), RNA/DNA and proteins/DNA ratios). Multivariate analyses showed that several biomarkers (DNA damages, micronucleus frequency, brain acetylcholinesterase, lysosomal membrane integrity, phagocytosis activity, and reactive oxygen species production) were exclusively correlated with fish tritium internal dose rate, showing that tritium induced genotoxicity, as well as neural and immune responses. The results were compared with another study on the same fish species where fish were exposed to tritium and other contaminants in natural environments. Together with the field study, the present work provides useful data to identify biomarkers for tritium exposure and better understand modes of action of tritium on the fathead minnow.

The impact of trauma exposure on explicit and implicit memory.

Objectives: The present study aimed to determine whether explicit and implicit memory systems are modulated by the type of content (neutral, emotional trauma-related and generally-emotional) in sexual abuse victims who did not develop PTSD, compared to non-exposed controls.Design: A mixed-factorial design with Content (neutral, trauma-related, generally-emotional) as a within-subject variable and Group (victims, controls) as a between-subject variable was used in two experiments.Methods: In both experiments, participants were required to learn three stories presented orally: a neutral, an emotional trauma-related (sexual abuse) and a generally-emotional story. In Experiment 1, participants' memory was tested with two explicit tasks (free recall and Remember/Know/Guess) and one implicit task (word-fragment completion task). In Experiment 2, a modified version of the word-fragment completion task was presented, followed by an awareness questionnaire to ensure the implicit character of the test.Results: Victims showed lower performances with neutral contents, relative to controls, in explicit and implicit tasks. However, this difference was not observed with trauma-related contents suggesting this information is preferentially processed by trauma-exposed participants (with increased attentional resources).Conclusions: Our results show that trauma exposure may itself be associated with implicit and explicit memory alterations, even for individuals who did not develop PTSD.

Straightforward extraction and selective bioconversion of high purity chitin from Bombyx eri larva: Toward an integrated insect biorefinery.

Chitins of different purity grades (45%, 89.7% and 93.3%) were efficiently extracted from Bombyx eri larva and fully physico-chemically characterized. Compared to commercially available and extracted α-chitin from shrimp shell, the collected data showed that insect chitins had similar characteristics in terms of crystallographic structures (α-chitin), thermal stability and degree of acetylation (>87%). The major differences lay in the crystallinity indexes (66% vs 75% for shrimp chitin) and in the morphological structures. Furthermore, low ash contents were determined for the insect chitins (1.90% vs 21.73% for shrimp chitin), making this chitin extraction and purification easier, which is highly valuable for an industrial application. Indeed, after only one step (deproteinization), the obtained chitin from Bombyx eri showed higher purity grade than the one extracted from shrimp shells under the same conditions. Insect chitins were then subjected to room temperature ionic liquid (RTIL) pretreatment prior to enzymatic degradation and presented a higher enzymatic digestibility compared to commercial one whatever their purity grade and would be thus a more relevant source for the selective production of N-acetyl-D-glucosamine (899.2 mg/g of chitin-2 stepsvs 760 mg/g of chitin com). Moreover, for the first time, the fermentescibility of chitin hydrolysates was demonstrated with Scheffersomyces stipitis used as ethanologenic microorganism.

Wheat Bran Pretreatment by Room Temperature Ionic Liquid-Water Mixture: Optimization of Process Conditions by PLS-Surface Response Design.

Room Temperature Ionic Liquids (RTILs) pretreatment are well-recognized to improve the enzymatic production of platform molecules such as sugar monomers from lignocellulosic biomass (LCB). The conditions for implementing this key step requires henceforth optimization to reach a satisfactory compromise between energy saving, required RTIL amount and hydrolysis yields. Wheat bran (WB) and destarched wheat bran (DWB), which constitute relevant sugar-rich feedstocks were selected for this present study. Pretreatments of these two distinct biomasses with various 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc])-water mixtures prior to hydrolysis catalyzed by hemicellulolytic cocktail (Cellic CTec2) were finely investigated. The main operating conditions such as pretreatment temperature (25-150°C), time (40-180 min), WB and DWB loading (2-5% w/v) and concentration of [C2mim][OAc] in water [10-100% (v/v)] were screened through glucose and xylose yields and then optimized through a Partial Least Square (PLS)-Second Order Design. In an innovative way, the PLS results showed that the four factors and their interactions could be well-fitted by a second-order model (p < 0.05). The quadratic PLS models were used to predict optimal pretreatment conditions. Thus, maximum glucose (83%) and xylose (95%) yields were obtained from enzymatic hydrolysis of WB pretreated at 150°C for 40 min with 10% of [C2mim][OAc] in water and 5% of WB loading. For DWB, maximum glucose (100%) and xylose (57%) yields were achieved for pretreatment temperatures of 150°C and 25°C, respectively. The required duration was still 40 min, with 20% of [C2mim][OAc] in water and a 5% DWB loading. Then, Multiple Response Optimization (MRO) performed by Nelder-Mead Simplex Method displayed sugar yields similar to those obtained by individual PLS optimization. This complete statistical study confirmed that the established models were appropriate to predict the sugar yields achieved after different pretreatment conditions from WB and DWB biomasses. Finally, Scanning Electron microscopy (SEM) studies allowed us to establish clearer link between structural changes induced by pretreatment and the best enzymatic performances obtained.

Effects of 90Sr on Tree Swallow Nestlings Near Groundwater Contaminant Plumes.

Discharge of groundwater contaminant plumes has created elevated concentrations of Sr in some aquatic sediments at Chalk River Laboratories. Tree swallows (Tachycenita bicolor) feed and supply their nestlings almost exclusively with airborne insects that developed as larvae in aquatic sediments. To monitor the uptake and test for potential detriment due to Sr in a terrestrial animal, we measured the gross beta concentrations in the bone of 12-d-old tree swallow nestlings in areas having sediments with elevated levels of gross beta (Sr and Y) and in several control areas where sediment gross beta was primarily due to naturally occurring K. Nesting behavior and reproductive success of the tree swallows were similar regardless of the gross beta concentrations in sediments near their nest boxes. Radiation can damage DNA and cause micronuclei to form in cells, so we examined the frequency of micronuclei in erythrocytes of nestlings. The formation of micronuclei in the erythrocytes of the nestlings was also similar wherever nestlings were analyzed. The results revealed no significant increases even near sediments with the highest gross beta levels. At Perch Lake, where Chalk River Laboratories has a large area of Sr-contaminated sediments, the bones of 12-d-old nestlings contained gross beta concentrations as high as 29 Bq g. This would produce a skeletal dose rate of 9 µGy h, which is one-fourth of the threshold dose rate of 40 µGy h, above which detriment could occur. Failing to find any indication of detriment in the field study, we irradiated wild eggs in the lab and returned them to their nest for natural incubation, hatching, and feeding by the parents. There was an increase in formation of micronuclei following a dose of 3.2 Gy, and the other results were consistent with existing literature.

Biofilm-Constructing Variants of Paraburkholderia phytofirmans PsJN Outcompete the Wild-Type Form in Free-Living and Static Conditions but Not In Planta.

Members of the genus Burkholderia colonize diverse ecological niches. Among the plant-associated strains, Paraburkholderia phytofirmans PsJN is an endophyte with a broad host range. In a spatially structured environment (unshaken broth cultures), biofilm-constructing specialists of P. phytofirmans PsJN colonizing the air-liquid interface arose at high frequency. In addition to forming a robust biofilm in vitro and in planta on Arabidopsis roots, those mucoid phenotypic variants display a reduced swimming ability and modulate the expression of several microbe-associated molecular patterns (MAMPs), including exopolysaccharides (EPS), flagellin, and GroEL. Interestingly, the variants induce low PR1 and PDF1.2 expression compared to that of the parental strain, suggesting a possible evasion of plant host immunity. We further demonstrated that switching from the planktonic to the sessile form did not involve quorum-sensing genes but arose from spontaneous mutations in two genes belonging to an iron-sulfur cluster: hscA (encoding a cochaperone protein) and iscS (encoding a cysteine desulfurase). A mutational approach validated the implication of these two genes in the appearance of variants. We showed for the first time that in a heterogeneous environment, P. phytofirmans strain PsJN is able to rapidly diversify and coexpress a variant that outcompete the wild-type form in free-living and static conditions but not in plantaIMPORTANCEParaburkholderia phytofirmans strain PsJN is a well-studied plant-associated bacterium known to induce resistance against biotic and abiotic stresses. In this work, we described the spontaneous appearance of mucoid variants in PsJN from static cultures. We showed that the conversion from the wild-type (WT) form to variants (V) correlates with an overproduction of EPS, an enhanced ability to form biofilm in vitro and in planta, and a reduced swimming motility. Our results revealed also that these phenotypes are in part associated with spontaneous mutations in an iron-sulfur cluster. Overall, the data provided here allow a better understanding of the adaptive mechanisms likely developed by P. phytofirmans PsJN in a heterogeneous environment.

Correlated responses for DNA damage, phagocytosis activity and lysosomal function revealed in a comparison between field and laboratory studies: Fathead minnow exposed to tritium.

Tritium entering the aquatic environment can confer a whole body internal radiological dose to aquatic organisms. Multiple stressors inherent in natural environments, however, confound estimates for observable radiation specific responses. To disentangle differences between field and laboratory outcomes to tritium exposures, a multivariate analysis comparing biomarkers for radiation exposure at the cellular level with changes in biological processes within tissues is described for fathead minnows (Pimephales promelas). Over tritium activity concentrations up to 180,000 Bq/L, DNA damage in the field were lower than DNA damage in the laboratory. This finding does not support an increase in morbidity of biota in field exposures. Energy deposited by tritium decay produces oxidised free radicals, yet the biological responses in brain, muscle and liver to oxidative stress differed between the studies and were not related to the tritium. For both studies, DNA damage in gonad and blood increased with increased tritium as did the fluorescence associated with lysosomal function in spleen. The studies differed in spleen phagocytosis activity were, in the laboratory but not the field, activity increased with increased tritium-and was correlatd with lysosomal function (Spearman coefficient of 0.98 (p = 0.001). The higher phagocytosis activity in the field reflects exposures to unmeasured factors that were not present within the laboratory. In the laboratory, DNA damage and lysosomal function were correlated: Spearman coefficients of 0.9 (Comet, p = 0.03) and 0.9 (micronuclei, p = 0.08). In the field, DNA damage by the Comet assay, but not by micronucleus frequency, correlated with lysosomal function: Spearman coefficients of 0.91 (Comet, p < 0.001) and 0.47 (micronuclei, p = 0.21). These observations highlight a need for better physiologic understanding of linkages between radiation-induced damage within cells and responses at higher levels of biological organization.

The establishment of a new culture of Hyalella azteca that would permit toxicity tests to be conducted on low-ionic strength waters.

The objective of the present study was to establish a culture of Hyalella azteca that could be used for laboratory toxicity testing in low-ionic strength waters with electrical conductivities of <200 µS/cm. A wild strain of H. azteca was collected from Twin Lake, a small seepage lake with an electrical conductivity of 81 ± 27 µS/cm located on the property of Chalk River Laboratories in Chalk River, Canada. To determine the minimum aqueous ion requirements for an optimal culturing medium for the Twin Lake strain, Twin Lake was monitored for water quality and ionic content over 4 yr. Water quality parameters were averaged and used to formulate a medium containing NaHCO3 , CaCl2 , MgSO4 , KCl, NaBr, NaF, and LiCl, with an electrical conductivity of 89 ± 3 µS/cm. By evaluating survival and reproduction, it was concluded that this artificial medium promoted survival and supported reproduction (10 ± 4 neonates/female/wk) of the Twin Lake amphipod. The Twin Lake strain of H. azteca can, therefore, be maintained in laboratory settings, and this allows for toxicity testing to be conducted on low-ionic strength waters. Environ Toxicol Chem 2019;38:585-590. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

Kluyveromyces marxianus, an Attractive Yeast for Ethanolic Fermentation in the Presence of Imidazolium Ionic Liquids.

Imidazolium ionic liquids (ILs) are promising solvents for lignocellulosic biomass (LCB) pretreatment and allow the achievement of higher ethanolic yields after enzymatic hydrolysis and ethanolic fermentation. However, residual ILs entrapped in pretreated biomass are often toxic for fermentative microorganisms, but interaction mechanisms between ILs and cells are still unknown. Here we studied the effects of 1-ethyl-3-methylimidazolium acetate [Emim][OAc] and 1-ethyl-3-methylimidazolium methylphosphonate [Emim][MeO(H)PO2] on Kluyveromyces marxianus, a thermotolerant ethanologenic yeast. Morphological impacts induced by ILs on K. marxianus were characterized by Scanning Electron Microscopy analysis and showed wrinkled, softened, and holed shapes. In Yeast-Malt-Dextrose (YMD) medium, K. marxianus tolerated IL additions up to 2% for [Emim][OAc] and 6% for [Emim][MeO(H)PO2]. Below these thresholds, some IL concentrations enhanced ethanolic yields up to +34% by switching the metabolic status from respiratory to fermentative. Finally, K. marxianus fermentation was applied on several substrates pretreated with [Emim][OAc] or [Emim][MeO(H)PO2] and enzymatically hydrolyzed: a model long fiber cellulose and two industrial LCBs, softwood (spruce) and hardwood (oak) sawdusts. The maximum ethanolic yields obtained were 1.8 to 3.9 times higher when substrates were pretreated with imidazolium ILs. Therefore K. marxianus is an interesting fermentative yeast in a second-generation bioethanol process implying IL pretreatment.

Impact of two ionic liquids, 1-ethyl-3-methylimidazolium acetate and 1-ethyl-3-methylimidazolium methylphosphonate, on Saccharomyces cerevisiae: metabolic, physiologic, and morphological investigations.

BACKGROUND: Ionic liquids (ILs) are considered as suitable candidates for lignocellulosic biomass pretreatment prior enzymatic saccharification and, obviously, for second-generation bioethanol production. However, several reports showed toxic or inhibitory effects of residual ILs on microorganisms, plants, and animal cells which could affect a subsequent enzymatic saccharification and fermentation process. RESULTS: In this context, the impact of two hydrophilic imidazolium-based ILs already used in lignocellulosic biomass pretreatment was investigated: 1-ethyl-3-methylimidazolium acetate [Emim][OAc] and 1-ethyl-3-methylimidazolium methylphosphonate [Emim][MeO(H)PO2]. Their effects were assessed on the model yeast for ethanolic fermentation, Saccharomyces cerevisiae, grown in a culture medium containing glucose as carbon source and various IL concentrations. Classical fermentation parameters were followed: growth, glucose consumption and ethanol production, and two original factors: the respiratory status with the oxygen transfer rate (OTR) and carbon dioxide transfer rate (CTR) of yeasts which were monitored online by respiratory activity monitoring systems (RAMOS). In addition, yeast morphology was characterized by environmental scanning electron microscope (ESEM). The addition of ILs to the growth medium inhibited the OTR and switched the metabolism from respiration (conversion of glucose into biomass) to fermentation (conversion of glucose to ethanol). This behavior could be observed at low IL concentrations (≤5% IL) while above there is no significant growth or ethanol production. The presence of IL in the growth medium also induced changes of yeast morphology, which exhibited wrinkled, softened, and holed shapes. Both ILs showed the same effects, but [Emim][MeO(H)PO2] was more biocompatible than [Emim][OAc] and could be better tolerated by S. cerevisiae. CONCLUSIONS: These two imidazolium-derived ILs were appropriate candidates for useful pretreatment of lignocellulosic biomass in the context of second-generation bioethanol production. This fundamental study provides additional information about the toxic effects of ILs. Indeed, the investigations highlighted the better tolerance by S. cerevisiae of [Emim][MeO(H)PO2] than [Emim][OAc].

Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia.

BACKGROUND: Congenital multiple intestinal atresia (MIA) is a severe, fatal neonatal disorder, involving the occurrence of obstructions in the small and large intestines ultimately leading to organ failure. Surgical interventions are palliative but do not provide long-term survival. Severe immunodeficiency may be associated with the phenotype. A genetic basis for MIA is likely. We had previously ascertained a cohort of patients of French-Canadian origin, most of whom were deceased as infants or in utero. The goal of the study was to identify the molecular basis for the disease in the patients of this cohort. METHODS: We performed whole exome sequencing on samples from five patients of four families. Validation of mutations and familial segregation was performed using standard Sanger sequencing in these and three additional families with deceased cases. Exon skipping was assessed by reverse transcription-PCR and Sanger sequencing. RESULTS: Five patients from four different families were each homozygous for a four base intronic deletion in the gene TTC7A, immediately adjacent to a consensus GT splice donor site. The deletion was demonstrated to have deleterious effects on splicing causing the skipping of the attendant upstream coding exon, thereby leading to a predicted severe protein truncation. Parents were heterozygous carriers of the deletion in these families and in two additional families segregating affected cases. In a seventh family, an affected case was compound heterozygous for the same 4bp deletion and a second missense mutation p.L823P, also predicted as pathogenic. No other sequenced genes possessed deleterious variants explanatory for all patients in the cohort. Neither mutation was seen in a large set of control chromosomes. CONCLUSIONS: Based on our genetic results, TTC7A is the likely causal gene for MIA.

Synthesis, surface tension properties and antibacterial activities of amphiphilic D-galactopyranose derivatives.

Several amphiphilic d-galactopyranose derivatives were synthesized in which the glycosidic moiety was separated from the hydrophobic alkyl chain (along 8 or 12 carbon atoms) by a spacer arm (butyl, butynyl or benzyl) in order to increase their surfactant properties and to obtain new antibacterial compounds. The surface tensions of the products were analyzed by Critical Micelle Concentration (CMC) and γCMC measurements and the antimicrobial activities were assayed against 10 bacterial species by Minimum Inhibitory Concentration (MIC) determination in liquid broth. The introduction of an aliphatic spacer arm increased the amphiphilic properties of the compounds and the CMC values were 40-500 times lower than their analogs without spacer arm. In the same manner, the spacer arms significantly increased the antibacterial power of the compounds. The products 4d and 4e exhibiting a C12 alkyl chain and an aliphatic spacer arm (butyl and butynyl) were the best surfactants (CMC = 0.023 and 0.032 mmol/L, respectively) and presented also the best antibacterial activities (MIC = 15.62 and 3.91 µg/mL for Micrococcus luteus, respectively). But the antibacterial activity of the newly synthesized products seemed to depend more on the cell wall composition of the bacteria than only on the amphiphilic character of the compounds.

Enzymatic hydrolysis of ionic liquid-pretreated celluloses: contribution of CP-MAS 13C NMR and SEM.

The supramolecular structure of four model celluloses was altered prior to their enzymatic saccharification using two ionic liquid pretreatments: one with the commonly used 1-ethyl-3-methylimidazolium acetate ([Emim](+)[CH(3)COO](-)) and the other with the newly developed 1-ethyl-3-methylimidazolium methylphosphonate ([Emim](+)[MeO(H)PO(2)](-)). The estimation of crystallinity index (CrI) by solid state (13)C nuclear magnetic resonance for each untreated/pretreated celluloses was compared with the performances of their enzymatic hydrolysis. For α-cellulose, both pretreatments led to a significant decrease in CrI from 25% to 5% but had no effect on glucose yields. In contrast, The [Emim](+)[MeO(H)PO(2)](-) pretreatment on the long fibers of cellulose had no significant effect on the CrI although a conversion yield in glucose of 88% is obtained versus 32% without pretreatment. However, scanning electron microscopy analysis suggested a loss of fiber organization induced by both ionic liquid pretreatments leading to a larger accessibility by cellulases to the cellulose surface.

Osmoregulated trehalose-derived oligosaccharides in Sinorhizobium meliloti.

Sinorhizobium meliloti is a soil bacterium accumulating glutamate, N-acetylglutaminyl glutamine amide and trehalose in hyperosmolarity. Besides these compatible solutes, we highlighted several compounds in S. meliloti Rm1021 wild-type strain. The purification and the structural characterization based on liquid chromatography evaporative light scattering detector, electrospray ionization high resolution mass spectrometry and nuclear magnetic resonance techniques showed they were four linear oligosaccharides composed of 3, 4, 5 and 6 glucose units all linked by alpha-(1-->2) linkages except a terminal alpha-(1<-->1) linkage. These oligosaccharides were cytoplasmic and were observed in several wild-type strains suggesting they were common features in S. meliloti strains grown in hyperosmolarity.

Founder SH3TC2 mutations are responsible for a CMT4C French-Canadians cluster.

Charcot-Marie-Tooth polyneuropathies (CMT) are clinically and genetically heterogeneous. We describe a French-Canadian cluster of 17 recessive CMT cases belonging to 10 families with variable early-onset CMT and scoliosis. The patients demonstrate great intra- and inter-familial variability. Linkage analysis confirmed that all families are linked to CMT4C locus on chromosome 5q32 (multipoint LOD score of 9.06). Haplotype analysis suggests that two SH3TC2 mutations are present in this cohort. The majority of carrier chromosomes, 26 of 34 (76%), carry the c.2860C-->T mutation. Despite extensive sequencing, the other mutation is not yet uncovered. This study demonstrates that the clinical variability observed in CMT4C is due to other factors than the nature of the mutation and that further work is needed to better define the SH3TC2 gene to ensure the identification of all CMT4C mutations.

Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce.

BACKGROUND: To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (Picea glauca [Moench] Voss) and black spruce (Picea mariana [Mill.] B.S.P.). RESULTS: Each array included 768 SNPs, identified by resequencing genomic DNA from parents of each mapping population. For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations. For each of these successful SNPs, on average, valid genotyping scores were obtained for over 99% of progeny. SNP data were integrated to pre-existing ALFP, ESTP, and SSR markers to construct two individual linkage maps and a composite map for white spruce and black spruce genomes. The white spruce composite map contained 821 markers including 348 gene loci. Also, 835 markers including 328 gene loci were positioned on the black spruce composite map. In total, 215 anchor markers (mostly gene markers) were shared between the two species. Considering lineage divergence at least 10 Myr ago between the two spruces, interspecific comparison of homoeologous linkage groups revealed remarkable synteny and marker colinearity. CONCLUSION: The design of customized highly multiplexed Illumina SNP arrays appears as an efficient procedure to enhance the mapping of expressed genes and make linkage maps more informative and powerful in such species with poorly known genomes. This genotyping approach will open new avenues for co-localizing candidate genes and QTLs, partial genome sequencing, and comparative mapping across conifers.

Mutations in senataxin responsible for Quebec cluster of ataxia with neuropathy.

Senataxin recently was identified as the mutated gene in ataxia-oculomotor apraxia 2, which is characterized by ataxia, oculomotor apraxia, and increased alpha-fetoprotein levels. In this study, we evaluated 24 ataxic patients from 10 French-Canadian families. All cases have a homogeneous phenotype consisting of a progressive ataxia appearing between 2 and 20 (mean age, 14.8) years of age with associated dysarthria, saccadic ocular pursuit, distal amyotrophy, sensory and motor neuropathy, and increased alpha-fetoprotein levels but absence of oculomotor apraxia. Linkage disequilibrium was observed with markers in the ataxia-oculomotor apraxia 2 locus on chromosome 9q34. We have identified four mutations in senataxin in the French-Canadian population including two novel missense mutations: the 5927T-->G mutation changes the leucine encoded by codon 1976 to an arginine in the helicase domain (L1976R), and the 193G-->A mutation changes a glutamic acid encoded by codon 65 into a lysine in the N-terminal domain of the protein (E65K). The common L1976R mutation is shared by 17 of 20 (85%) carrier chromosomes. The study of this large French-Canadian cohort better defines the phenotype of this ataxia and presents two novel mutations in senataxin including the more common founder mutation in the French-Canadian population.