Molecular Analysis of N6-Methyladenine Patterns in \u3cem\u3eTetrahymena thermophila\u3c/em\u3e Nuclear DNA

We have cloned two DNA fragments containing 5\u27-GATC-3\u27 sites at which the adenine is methylated in the macronucleus of the ciliate Tetrahymena thermophila. Using these cloned fragments as molecular probes, we analyzed the maintenance of methylation patterns at two partially and two uniformly methylated sites. Our results suggest that a semiconservative copying model for maintenance of methylation is not sufficient to account for the methylation patterns we found during somatic growth of Tetrahymena. Although we detected hemimethylated molecules in macronuclear DNA, they were present in both replicating and nonreplicating DNA. In addition, we observed that a complex methylation pattern including partially methylated sites was maintained during vegetative growth. This required the activity of a methylase capable of recognizing and modifying sites specified by something other than hemimethylation. We suggest that a eucaryotic maintenance methylase may be capable of discriminating between potential methylation sites to ensure the inheritance of methylation patterns

The inheritance of dynamic and deontic integrity constraints or: Does the boss have more rights?

In [18,23], we presented a language for the specification of static, dynamic and deontic integrity constraints (IC's) for conceptual models (CM's). An important problem not discussed in that paper is how IC's are inherited in a taxonomic network of types. For example, if students are permitted to perform certain actions under certain preconditions, must we repeat these preconditions when specializing this action for the subtype of graduate students, or are they inherited, and if so, how? For static constraints, this problem is relatively trivial, but for dynamic and deontic constraints, it will turn out that it contains numerous pitfalls, caused by the fact that common sense supplies presuppositions about the structure of IC inheritance that are not warranted by logic. In this paper, we unravel some of these presuppositions and show how to avoid the pitfalls. We first formulate a number of general theorems about the inheritance of necessary and/or sufficient conditions and show that for upward inheritance, a closure assumption is needed. We apply this to dynamic and deontic IC's, where conditions arepreconditions of actions, and show that our common sense is sometimes mistaken about the logical implications of what we have specified. We also show the connection of necessary and sufficient preconditions of actions with the specification of weakest preconditions in programming logic. Finally, we argue that information analysts usually assume constraint completion in the specification of (pre)conditions analogous to predicate completion in Prolog and circumscription in non-monotonic logic. The results are illustrated with numerous examples and compared with other approaches in the literature

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors

Background: Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed "Mendelian", an R-package that can be used for heuristic variant filtering. Results: The R-package Mendelian offers fast and convenient filters to analyze putative variants for both recessive and dominant models of inheritance, with variable degrees of penetrance and detectance. Analysis of trios is supported. Filtering against variant databases and annotation of variants is also included. This package is not species specific and supports parallel computation. We validated this package by reanalyzing data from a whole exome sequencing experiment on intellectual disability in humans. In a second example, we identified the mutations responsible for coat color in the dog. This is the first example of whole exome sequencing without prior mapping in the dog. Conclusion: We developed an R-package that enables the identification of disease-causing variants from the long list of variants called in sequencing experiments. The software and a detailed manual are available at https://github.com/BartBroeckx/Mendelian

Adaptability of safflower (Carthamus tinctorius L.) genotypes to some New Zealand environments : a thesis presented in partial fulfilment of the requirements for the degree of Master of Philosophy in Plant Science at Massey University

Seven safflower (Carthamus tinctorius L.) genotypes were grown at three sites (Massey, Aorangi and Flockhouse) in the Manawatu area in years 1978 and 1979. Three additional genotypes from the world germplasm collection were included in the study in 1979. The experimental design was a randomized complete block with three replications. The safflower genotypes were evaluated with respect to several morphological traits, and some important agronomic traits, such as yield, % oil content, % hull content and susceptibility to head rot disease. Data collected on seven safflower genotypes were analysed as a combined experiment with 3 sites and 2 years (Expt. I). The data available on 10 genotypes in 1979 were analysed separately with respect to ten important characters (Expt. II). Of the 23 characters studied in Expt. I, the genotypic variance component (σ2G) was significant only for the following 6 characters: mid stem leaf length, primary head diameter, involucral bract length and length/width, bract spine index and susceptibility to head rot disease. The addition of 3 genotypes in Expt. II had a marked effect on the magnitude σ2G component. Of the environmental components, site x year interaction effect was the most significant for the majority of traits. Most of the characters studied in Expt. I showed significant genotype x environment interactions, and in most instances the second order interaction of genotype x site x year being highly significant. Adaptation analyses were performed following procedures of Finlay and Wilkinson (1963). The genotypes Leed and Dart with adaptation coefficients 1.52 and 1.75 respectively were specifically adapted to favourable environments with respect to yield. Cultivar 0-22 and Rio showed general adaptability to the same trait. For % oil content all genotypes except Rio showed general adaptability. Cultivar Rio was slightly specifically adapted to favourable environments. Two forms of broad sense heritabilities (full and restricted) were estimated. In Expt. I, relatively high restricted heritability estimates were obtained for the following traits: leaf length, primary head diameter, bract length and length/width, spine index and susceptibility to head rot disease. The heritability estimates obtained in Expt. II were higher than Expt. I, due to the additional genetic variability in the population. Of the additional traits studied in Expt. II, lodging and susceptibility to leaf spot disease, showed high heritability estimates. Resistances to two fungal diseases - head rot (Botrytis cinerea Pers.) and leaf spot (Stemphylium/Alternaria species) - were assessed in field conditions. The leaf spot disease was detected only in the second year of this study. The cultivars VFSTP-1 and Partial-hull were highly susceptible to head rot disease. The two genotypes from safflower germplasm collection, PI 262437 and PI 306684 had considerable tolerance to leaf spot disease. The optimum plot allocation study indicated that, disregarding costs, an allocation of 2 years, 4 sites and 2 replications would be more efficient than the present allocation. There was no significant correlation between spininess and bird damage. The % oil content and % hull content were negatively correlated at both phenotypic and genotypic levels. Susceptibility to the two diseases were negatively correlated with yield. The susceptibility to head rot disease also showed a significant negative correlation with the % oil content

Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families.

BackgroundThe causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, parents could use this information to opt for fetal genotyping in subsequent pregnancies, which could inform decisions about elective termination of pregnancy. The use of NGS diagnostic sequencing in families has not been demonstrated to yield benefit in subsequent pregnancies to reduce recurrence. Here we evaluated whether genetic diagnosis in older children in families supports reduction in recurrence of recessive neurogenetic disease.MethodsRetrospective study involving families with a child with a recessive pediatric brain disease (rPBD) that underwent NGS-based molecular diagnosis. Prenatal molecular testing was offered to couples in which a molecular diagnosis was made, to help couples seeking to prevent recurrence. With this information, families made decisions about elective termination. Pregnancies that were carried to term were assessed for the health of child and mother, and compared with historic recurrence risk of recessive disease.ResultsBetween 2010 and 2016, 1172 families presented with a child a likely rPBD, 526 families received a molecular diagnosis, 91 families returned to the clinic with 101 subsequent pregnancies, and 84 opted for fetal genotyping. Sixty tested negative for recurrence for the biallelic mutation in the fetus, and all, except for one spontaneous abortion, carried to term, and were unaffected at follow-up. Of 24 that genotyped positive for the biallelic mutation, 16 were electively terminated, and 8 were carried to term and showed features of disease similar to that of the older affected sibling(s). Among the 101 pregnancies, disease recurrence in living offspring deviated from the expected 25% to the observed 12% ([95% CI 0·04 to 0·20], p = 0·011).ConclusionsMolecular diagnosis in an older child, coupled with prenatal fetal genotyping in subsequent pregnancies and genetic counselling, allows families to make informed decisions to reduce recessive neurogenetic disease recurrence

A framework for lexical representation

In this paper we present a unification-based lexical platform designed for highly inflected languages (like Roman ones). A formalism is proposed for encoding a lemma-based lexical source, well suited for linguistic generalizations. From this source, we automatically generate an allomorph indexed dictionary, adequate for efficient processing. A set of software tools have been implemented around this formalism: access libraries, morphological processors, etc.Comment: 9 page

Development and Validation of Clinical Whole-Exome and Whole-Genome Sequencing for Detection of Germline Variants in Inherited Disease

Context.-With the decrease in the cost of sequencing, the clinical testing paradigm has shifted from single gene to gene panel and now whole-exome and whole-genome sequencing. Clinical laboratories are rapidly implementing next-generation sequencing-based whole-exome and whole-genome sequencing. Because a large number of targets are covered by whole-exome and whole-genome sequencing, it is critical that a laboratory perform appropriate validation studies, develop a quality assurance and quality control program, and participate in proficiency testing. Objective.-To provide recommendations for wholeexome and whole-genome sequencing assay design, validation, and implementation for the detection of germline variants associated in inherited disorders. Data Sources.-An example of trio sequencing, filtration and annotation of variants, and phenotypic consideration to arrive at clinical diagnosis is discussed. Conclusions.-It is critical that clinical laboratories planning to implement whole-exome and whole-genome sequencing design and validate the assay to specifications and ensure adequate performance prior to implementation. Test design specifications, including variant filtering and annotation, phenotypic consideration, guidance on consenting options, and reporting of incidental findings, are provided. These are important steps a laboratory must take to validate and implement whole-exome and whole-genome sequencing in a clinical setting for germline variants in inherited disorders