[Linear lesions: A key dermatological feature of X-linked ectodermal dysplasia in a young girl]. / Lésions linéaires : un signe dermatologique clé de la dysplasie ectodermique liée à l'X chez la fille.

INTRODUCTION: X-linked hypo/anhidrotic ectodermal dysplasia (AED) is the most common form of AED. It is manifested in boys by involvement of the adnexa, teeth and sweat glands. In girls, signs are usually minor and may include linear lesions that are poorly known since they are reported infrequently or overlooked. Herein we report 3 cases. PATIENTS AND METHODS: There were two female patients who had been followed for several years, as well as the mother of one of the patients. Both of the younger patients had early diagnosis of DEA in childhood based on severe dental abnormalities, i.e. hypodontia and conical teeth, a typical facies, and cutaneous xerosis. The mother had milder signs and the diagnosis was made at the time of her daughter's diagnosis. All 3 had hypopigmented linear skin lesions (arms, buttocks or back), associated with a decrease in hair in one of them. Genetic analysis showed the R156H missense mutation at exon 3 of the EDA gene in all 3 patients. CONCLUSION: These hypopigmentation linear lesions, sometimes with hair loss, are well known to pediatric clinicians and dermatologists concerning early diagnosis of AED in girls, especially where the other signs are mild. Early diagnosis enables appropriate therapeutic management and genetic counseling regarding future pregnancy.

Genome-Wide Association Study of Arabidopsis thaliana Identifies Determinants of Natural Variation in Seed Oil Composition.

The renewable source of highly reduced carbon provided by plant triacylglycerols (TAGs) fills an ever increasing demand for food, biodiesel, and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in seed oil composition in nature provides targets for bioengineering fatty acid proportions optimized for various industrial and nutrition goals. Here, we characterized the seed oil composition of 391 world-wide, wild accessions of Arabidopsis thaliana, and performed a genome-wide association study (GWAS) of the 9 major fatty acids in the seed oil and 4 composite measures of the fatty acids. Four to 19 regions of interest were associated with the seed oil composition traits. Thirty-four of the genes in these regions are involved in lipid metabolism or transport, with 14 specific to fatty acid synthesis or breakdown. Eight of the genes encode transcription factors. We have identified genes significantly associated with variation in fatty acid proportions that can be used as a resource across the Brassicaceae. Two-thirds of the regions identified contain candidate genes that have never been implicated in lipid metabolism and represent potential new targets for bioengineering.

Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants.

Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions.

DACTAL: divide-and-conquer trees (almost) without alignments.

MOTIVATION: While phylogenetic analyses of datasets containing 1000-5000 sequences are challenging for existing methods, the estimation of substantially larger phylogenies poses a problem of much greater complexity and scale. METHODS: We present DACTAL, a method for phylogeny estimation that produces trees from unaligned sequence datasets without ever needing to estimate an alignment on the entire dataset. DACTAL combines iteration with a novel divide-and-conquer approach, so that each iteration begins with a tree produced in the prior iteration, decomposes the taxon set into overlapping subsets, estimates trees on each subset, and then combines the smaller trees into a tree on the full taxon set using a new supertree method. We prove that DACTAL is guaranteed to produce the true tree under certain conditions. We compare DACTAL to SATé and maximum likelihood trees on estimated alignments using simulated and real datasets with 1000-27 643 taxa. RESULTS: Our studies show that on average DACTAL yields more accurate trees than the two-phase methods we studied on very large datasets that are difficult to align, and has approximately the same accuracy on the easier datasets. The comparison to SATé shows that both have the same accuracy, but that DACTAL achieves this accuracy in a fraction of the time. Furthermore, DACTAL can analyze larger datasets than SATé, including a dataset with almost 28 000 sequences. AVAILABILITY: DACTAL source code and results of dataset analyses are available at www.cs.utexas.edu/users/phylo/software/dactal.

SuperFine: fast and accurate supertree estimation.

Many research groups are estimating trees containing anywhere from a few thousands to hundreds of thousands of species, toward the eventual goal of the estimation of a Tree of Life, containing perhaps as many as several million leaves. These phylogenetic estimations present enormous computational challenges, and current computational methods are likely to fail to run even on data sets in the low end of this range. One approach to estimate a large species tree is to use phylogenetic estimation methods (such as maximum likelihood) on a supermatrix produced by concatenating multiple sequence alignments for a collection of markers; however, the most accurate of these phylogenetic estimation methods are extremely computationally intensive for data sets with more than a few thousand sequences. Supertree methods, which assemble phylogenetic trees from a collection of trees on subsets of the taxa, are important tools for phylogeny estimation where phylogenetic analyses based upon maximum likelihood (ML) are infeasible. In this paper, we introduce SuperFine, a meta-method that utilizes a novel two-step procedure in order to improve the accuracy and scalability of supertree methods. Our study, using both simulated and empirical data, shows that SuperFine-boosted supertree methods produce more accurate trees than standard supertree methods, and run quickly on very large data sets with thousands of sequences. Furthermore, SuperFine-boosted matrix representation with parsimony (MRP, the most well-known supertree method) approaches the accuracy of ML methods on supermatrix data sets under realistic conditions.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.

Fusion of bolaamphiphile micelles: a method to prepare stable supported biomimetic membranes.

Supported biomimetic membranes (SBMs) on solid substrates have been commonly prepared from vesicle-forming double-tail lipids, such as zwitterionic phospholipids, using the method of vesicle fusion. Here we report on the preparation of SBMs on silica surfaces via a similar process of "micelle fusion" from a cationic single-tail bolaamphiphile GLH-20 that forms spherical and elongated thread-like micelles in solution. We demonstrate that, in contrast to zwitterionic phospholipids, GLH-20 self-assembles into a stable contiguous SBM at both low and high ionic strengths. The cationic charge of GLH-20 promotes the formation of a stable SBM through enhanced double-layer interactions with the negatively charged silica surface. It is also shown that spinach aquaporin PM-28 was successfully incorporated within bolaamphiphile SBM in a manner similar to SBMs prepared by vesicle/proteoliposome fusion; thereby the inherent curvature of the micelle surface does not inhibit protein reconstitution. The results suggest that SBMs based on charged bolaamphiphiles might be an attractive platform for applications such as water purification and biosensors, where the stability and low defect rate of SBMs in diverse conditions are crucial for achieving desired performance.

Localization of Friedreich ataxia phenotype with selective vitamin E deficiency to chromosome 8q by homozygosity mapping.

Friedreich ataxia and ataxia with selective vitamin E deficiency (AVED) share very similar clinical phenotypes. We have mapped the AVED locus to proximal 8q with only three large consanguinous Tunisian families, representing to our knowledge the first use of homozygosity mapping for primary linkage analysis. Subsequently, three additional families showed linkage with the same markers. A maximum lod score of 17.9 was obtained at theta = 0 for the haplotype D8S260-D8S510, consisting of the two closest markers. With only 6 families, the AVED locus is therefore mapped precisely as illustrated by the lod-1 confidence interval of 2.4 cM on either side of D8S260-D8S510. Isolation of a yeast artificial chromosome contig > 800 kilobases (kb) showed that D8S260 and D8S510 are less than 400 kb apart.

CFTR expression is regulated during both the cycle of the seminiferous epithelium and the oestrous cycle of rodents.

Severely reduced fertility is a common finding in cystic fibrosis (CF). We used in situ hybridization to examine the cell-specific expression of CFTR in the reproductive organs of rodents. In males CFTR mRNA is found in the round spermatids (spermatogenic stages V-X) and in the principal cells that line the initial segment of the epididymis. In both the testis and the epididymis, CFTR expression is developmentally regulated suggesting that the defect in the genital tract of male CF patients is of developmental origin. CFTR expression in the luminal and glandular epithelium of the uterus is regulated during the oestrous cycle and is maximal at pro-oestrus. Our results provide a biological rationale for the reduced fertility of CF patients, and suggest a possible cause for the comparatively poorer prognosis for women with CF.

Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice.

Targeted mutagenesis in mice, a powerful tool for the analysis of gene function and human disease, makes extensive use of 129 mouse substrains. Although all are named 129, we document that outcrossing of these substrains, both deliberate and accidental, has lead to extensive genetic variability among substrains and embryonic stem cells derived from them. This clearer understanding of 129 substrain variability allows consideration of its negative impact on targeting technology, including: homologous recombination frequencies, preparation of inbred animals, and availability of appropriate controls. Based on these considerations we suggest a number of recommendations for future experimental design.

Quantitative trait loci involved in regulating seed oil composition in Arabidopsis thaliana and their evolutionary implications.

Fatty acid composition is an important determinant of seed oil quality. Overall, 72 QTL for 12 fatty acid traits that control seed oil composition were identified in four recombinant inbred line (RIL) populations (Ler-0 × Sha, Ler-0 × Col-4, Ler-2 × Cvi, Ler-0 × No-0) of Arabidopsis thaliana. The identified QTL explained 3.2-79.8% of the phenotypic variance; 33 of the 59 QTL identified in the Ler-0 × Sha and the Ler-0 × Col RIL populations co-located with several a priori candidate genes for seed oil composition. QTL for fatty acids 18:1, 18:2, 22:1, and fatty acids synthesized in plastids was identified in both Ler-0 × Sha and Ler-0 × Col-4 RIL populations, and QTL for 16:0 was identified in the Ler-0 × Sha and Ler-0 × No-0 RIL populations providing strong support for the importance of these QTL in determining seed oil composition. We identified melting point QTL in three RIL populations, and fatty acid QTL collocated with two of them, suggesting that the loci could be under selection for altering the melting point of seed oils to enhance adaptation and could be useful for breeding purposes. Nuclear-cytoplasmic interactions and epistasis were rare. Analysis of the genetic correlations between these loci and other fatty acids indicated that these correlations would tend to strongly enhance selection for desirable fatty acids.

Characteristics of laparoscopic and open hernia repair simulation models: a systematic review.

PURPOSE: Barriers to education in open and laparoscopic hernia repair technique include a steep learning curve and reduced theatre time for junior surgical trainees. This is particularly evident during the current COVID-19 pandemic. Simulation models may provide further opportunities for training in hernia repair outside of the traditional surgical apprenticeship model. METHODS: A systematic review was carried out following PRISMA guidelines to identify and evaluate simulation models in hernia repair. Of the 866 records screened, 27 were included in the analysis. These were assessed for face, content and construct validity, as well as their attempt to measure educational impact. RESULTS: Simulation models were identified comprising of animal tissues, synthetic materials and virtual reality (VR) technology. Models were designed for instruction in repair of inguinal, umbilical, incisional and diaphragmatic hernias. Twenty-one laparoscopic hernia repair models were described. Many models demonstrated validity across several domains, and three showed transferability of skills from simulation to the operating room. Of the six open hernia repair simulation models, none were found to have demonstrated an educational impact in addition to assessing validity. CONCLUSION: Few models individually were able to demonstrate validity and educational impact. Several novel assessment tools have been developed for assessment of progress when performing simulated and real laparoscopic inguinal hernia repair. More study is required, particularly for open hernia repair, including randomized controlled trials with large sample sizes to assess the transferability of skills.

Sarcoma in neurofibromatosis 2: case report and review of the literature.

Neurofibromatosis type 2 (NF2) is associated with the development of several types of benign nervous system tumours, while malignancies are rare. We report a 22-year-old man who presented with retroperitoneal and spinal high-grade sarcomas with epithelial features. Samples showed a mixed epithelioid and spindled cell content with little associated matrix and inconclusive immunochemistry. Genetic analysis of a schwannoma and matched blood samples demonstrated a constitutional de novo substitution at the splice donor site of intron 8 of the NF2 gene and aa acquired large deletion of the entire NF2 gene as a second hit, with some loss of SMARCB1. The sarcoma also showed evidence of loss of SMARCB1 and NF2 with loss of INI1 staining. Unfortunately the mass was unresectable and the patient died 6 months after diagnosis. This malignancy was most consistent with SMARCB1-deficient epithelioid malignant peripheral nerve sheath tumour, although a significant differential was proximal-type epithelial sarcoma. Each differential has previously been reported only once with NF2. This demonstrates an extremely rare potential complication of the condition.

Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids.

Angiosperm systematics has progressed to the point where it is now expected that multiple, independent markers be used in phylogenetic studies. Universal primers for amplifying informative regions of the chloroplast genome are readily available, but in the faster-evolving nuclear genome it is challenging to discover priming sites that are conserved across distantly related taxa. With goals including the identification of informative markers in rosids, and perhaps other angiosperms, we screened 141 nuclear primer combinations for phylogenetic utility in two distinct groups of rosids at different taxonomic levels-Psiguria (Cucurbitaceae) and Geraniaceae. We discovered three phylogenetically informative regions in Psiguria and two in Geraniaceae, but none that were useful in both groups. Extending beyond rosids, we combined our findings with those of another recent effort testing these primer pairs in Asteraceae, Brassicaceae, and Orchidaceae. From this comparison, we identified 32 primer combinations that amplified regions in representative species of at least two of the five distantly related angiosperm families, giving some prior indication about phylogenetic usefulness of these markers in other flowering plants. This reduced set of primer pairs for amplifying low-copy nuclear markers along with a recommended experimental strategy provide a framework for identifying phylogenetically informative regions in angiosperms.

Transport properties of highly ordered heterogeneous ion-exchange membranes.

Model "ordered" heterogeneous ion exchange membranes are made with ion exchange particles heaving ion exchange capacity in the range 3 to 2.5 meq/gr (dry basis) and diameters ranging from 37 to 7 microm and 2 component room-temperature vulcanizing silicon rubber as a polymeric matrix, by applying an electric field normal to the membrane surface during preparation. These membranes were shown to have an improved ionic conductivity compared with "nonordered" membranes based on the same ion exchange content (for instance, at 10% resin content "nonordered" membranes show <10(-5) mS/cm while "ordered" membranes have conductivity of 1 mS/cm). The transport properties of ordered membranes were compared with those of nonordered membranes, through the current-voltage characteristics. Limiting currents measured for the ordered membranes were significantly higher than those of the nonordered membranes with the same resin concentration. In addition, higher limiting currents were observed in ordered membranes as the resin particles became smaller. Energy dispersion spectrometry analyses revealed that the concentration of cation exchange groups on the membrane surface was higher for ordered membrane as compared to that of nonordered membranes. This implies that the local current density for the conducting domains at the surface of the nonordered membranes is higher, leading to higher concentration polarization and, eventually, to lower average limiting current densities. The effect of ordering the particles on the membrane conductivity and transport properties was studied, and the advantages of the ordered membranes are discussed.

Synthesis of novel cationic bolaamphiphiles from vernonia oil and their aggregated structures.

The present study describes the synthesis of a novel class of vesicle-forming bolaamphiphiles with choline ester head groups. These bolaamphiphiles were derived from vernonia oil, whose main constituent is vernolic acid, a fatty acid with a unique combination of epoxy, carboxy and unsaturated double bonds. A series of bolaamphiphiles containing amido or ester groups within the hydrophobic domain were synthesized from N,N'-alkylenebis (vernolamides) and alpha,omega-alkylene divernolate ester in a two-stage synthesis comprising opening of the epoxy ring with chloroacetic acid, followed by quaternization with N,N-dimethylaminoethyl acetate to form choline ester head groups. The products were characterized by FT-IR, (1)H and (13)C NMR, and ESI-MS. Vesicles prepared from these bolaamphiphiles have the potential to serve as a targeted drug delivery systems with selective decapsulation in the presence of the enzyme acetylcholine esterase, resulting in site-specific release of the drug.

Understanding the relationship between cell death and tissue shrinkage via a stochastic agent-based model.

Cell death, a process which can occur both naturally and in response to insult, is both a complex and diverse phenomenon. Under some circumstances, dying cells actively contract and cause their neighbors to rearrange and maintain tissue integrity. Under other circumstances, dying cells leave behind gaps, which results in tissue separation. A better understanding of how the cellular scale features of cell death manifest on the population scale has implications ranging from morphogenesis to tumor response to treatment. However, the mechanistic relationship between cell death and population scale shrinkage is not well understood, and computational methods for studying these relationships are not well established. Here we propose a mechanically robust agent-based cell model designed to capture the implications of cell death on the population scale. In our agent-based model, algorithmic rules applied on the cellular level emerge on the population scale where their effects are quantified. To better quantify model uncertainty and parameter interactions, we implement a recently developed technique for conducting a variance-based sensitivity analysis on the stochastic model. From this analysis and subsequent investigation, we find that cellular scale shrinkage has the largest influence of all model parameters tested, and that by adjusting cellular scale shrinkage population shrinkage varies widely even across simulations which contain the same fraction of dying cells. We anticipate that the methods and results presented here are a starting point for significant future investigation toward quantifying the implications of different mechanisms of cell death on population and tissue scale behavior.

Histone H1 expressed in Saccharomyces cerevisiae binds to chromatin and affects survival, growth, transcription, and plasmid stability but does not change nucleosomal spacing.

Histone H1 is proposed to serve a structural role in nucleosomes and chromatin fibers, to affect the spacing of nucleosomes, and to act as a general repressor of transcription. To test these hypotheses, a gene coding for a sea urchin histone H1 was expressed from the inducible GAL1 promoter in Saccharomyces cerevisiae by use of a YEp vector for high expression levels (strain YCL7) and a centromere vector for low expression levels (strain YCL1). The H1 protein was identified by its inducibility in galactose, its apparent molecular weight, and its solubility in 5% perchloric acid. When YCL7 was shifted from glucose to galactose for more than 40 h to achieve maximal levels of H1, H1 could be copurified in approximately stoichiometric amounts with core histones of Nonidet P-40-washed nuclei and with soluble chromatin fractionated on sucrose gradients. While S. cerevisiae tolerated the expression of low levels of H1 in YCL1 without an obvious phenotype, the expression of high levels of H1 correlated with greatly reduced survival, inhibition of growth, and increased plasmid loss but no obvious change in the nucleosomal repeat length. After an initial induction, RNA levels for GAL1 and H1 were drastically reduced, suggesting that H1 acts by the repression of galactose-induced genes. Similar effects, but to a lower extent, were observed when the C-terminal tail of H1 was expressed.