Using the noninformative families in family-based association tests: a powerful new testing strategy

For genetic association studies with multiple phenotypes, we propose a new strategy for multiple testing with family-based association tests (FBATs). The strategy increases the power by both using all available family data and reducing the number of hypotheses tested while being robust against population admixture and stratification. By use of conditional power calculations, the approach screens all possible null hypotheses without biasing the nominal significance level, and it identifies the subset of phenotypes that has optimal power when tested for association by either univariate or multivariate FBATs. An application of our strategy to an asthma study shows the practical relevance of the proposed methodology. In simulation studies, we compare our testing strategy with standard methodology for family studies. Furthermore, the proposed principle of using all data without biasing the nominal significance in an analysis prior to the computation of the test statistic has broad and powerful applications in many areas of family-based association studies.     

Loss of <Emphasis Type="Italic">Tc-arrow</Emphasis> and canonical Wnt signaling alters posterior morphology and pair-rule gene expression in the short-germ insect, <Emphasis Type="Italic">Tribolium castaneum</Emphasis>

Wnt signaling has been implicated in posterior patterning in short-germ insects, including the red flour beetle Tribolium castaneum (Bolognesi et al. Curr Biol 18:1624–1629, 2008b; Angelini and Kaufman Dev Biol 283:409–423, 2005; Miyawaki et al. Mech Dev 121:119–130, 2004). Specifically, depletion of Wnt ligands Tc-Wnt1 and Tc-WntD/8 produces Tribolium embryos lacking abdominal segments. Similar phenotypes are produced by depletion of Tc-porcupine (Tc-porc) or Tc-pangolin (Tc-pan), indicating that the signal is transmitted through the canonical Wnt pathway (Bolognesi et al. Curr Biol 18:1624–1629, 2008b). Here we show that RNAi for the receptor Tc-arrow produced similar truncated phenotypes, providing additional evidence supporting canonical signal transduction. Furthermore, since in Tribolium segments are defined sequentially by a pair-rule gene circuit that, when interrupted, produces truncated phenotypes (Choe et al. Proc Natl Acad Sci U S A 103:6560–6564, 2006), we investigated the relationship between loss of Wnt signaling and this pair-rule gene circuit. After depletion of the receptor Tc-arrow, expression of Tc-Wnt1 was noticeably absent from the growth zone, while Tc-WntD/8 was restricted to a single spot of expression in what remained of the posterior growth zone. The primary pair-rule genes Tc-runt (Tc-run) and Tc-even-skipped (Tc-eve) were expressed normally in the anterior segments, but were reduced to a single spot in the remnants of the posterior growth zone. Thus, expression of pair-rule genes and Tc-WntD/8 are similarly affected by depletion of Wnt signal and disruption of the posterior growth zone.     

Power and design considerations for a general class of family-based association tests: quantitative traits

In the present article, we address family-based association tests (FBATs) for quantitative traits. We propose an approach to analytical power and sample-size calculations for general FBATs; this approach can be applied to virtually any scenario (missing parental information, multiple offspring per family, etc.). The power calculations are used to discuss optimal choices of the phenotypes for the FBAT statistic and its power's dependence on ascertainment conditions, on study design, and on the correct specification of the distributional assumptions for the phenotypes. We also compare the general FBAT approach with PDT and QTDT. The practical relevance of our theoretical considerations is illustrated by their application to an asthma study.     

Abscisic acid levels in tomato ovaries are regulated by <Emphasis Type="Italic">LeNCED1</Emphasis> and <Emphasis Type="Italic">SlCYP707A1</Emphasis>

Although the hormones, gibberellin and auxin, are known to play a role in the initiation of fruits, no such function has yet been demonstrated for abscisic acid (ABA). However, ABA signaling and ABA responses are high in tomato (Solanum lycopersicum L.) ovaries before pollination and decrease thereafter (Vriezen et al. in New Phytol 177:60–76, 2008). As a first step to understanding the role of ABA in ovary development and fruit set in tomato, we analyzed ABA content and the expression of genes involved in its metabolism in relation to pollination. We show that ABA levels are relatively high in mature ovaries and decrease directly after pollination, while an increase in the ABA metabolite dihydrophaseic acid was measured. An important regulator of ABA biosynthesis in tomato is 9-cis-epoxy-carotenoid dioxygenase (LeNCED1), whose mRNA level in ovaries is reduced after pollination. The increased catabolism is likely caused by strong induction of one of four newly identified putative (+)ABA 8′-hydroxylase genes. This gene was named SlCYP707A1 and is expressed specifically in ovules and placenta. Transgenic plants, overexpressing SlCYP707A1, have reduced ABA levels and exhibit ABA-deficient phenotypes suggesting that this gene encodes a functional ABA 8′-hydroxylase. Gibberellin and auxin application have different effects on the LeNCED1 and SlCYP707A1 gene expression. The crosstalk between auxins, gibberellins and ABA during fruit set is discussed.     

A new species of <Emphasis Type="Italic">Litomosoides</Emphasis> Chandler, 1931 (Nematoda: Filarioidea) from the long-nosed hocicudo <Emphasis Type="Italic">Oxymycterus nasutus</Emphasis> Waterhouse (Rodentia: Cricetidae) in Uruguay

A new species of Litomosoides Chandler, 1931 was collected from the abdominal cavity of Oxymycterus nasutus Waterhouse (Rodentia: Cricetidae) in the grassland of the Departamento Rocha, Uruguay. Litomosoides nasuti n. sp. belongs to the ‘sigmodontis group’, and is characterised by: salient amphids; two ventral and one dorsal labial papillae, but no cephalic papillae; a buccal capsule with a transparent anterior segment and an annular asymmetrical thickening; a muscular oesophagus; a bottle-shaped buccal cavity; the male with symmetrically situated cloacal papillae (one pair ad-cloacal and three pairs post-cloacal); phasmids displaced laterally to the longitudinal axis; and microfilariae without terminal nuclei in the tail tip. It resembles five known species; three of which have been recovered from Oxymycterus spp. in neighbouring countries. However, the new species can be differentiated from L. sigmodontis Chandler, 1931 by the shape and size of the buccal capsule; from L. navonae Notarnicola, 2005 by the muscular oesophagus; from L. legerae Bain, Petit & Berteaux, 1980 by the length of the oesophagus and the cephalic papillae; from L. anguyai Notarnicola, Bain & Navone, 2002 by the absence of lappets in the female tail; and from L. oxymycteri Notarnicola, Bain & Navone, 2000 by absence of pre-cloacal papillae. L. legerae from O. quaestor and L. sigmodontis from Sigmodon hispidus in North America are closely related species, as indicated by Brant & Gardner’s phylogenetic tree based on morphological characters. However, a new analysis is needed to include the recently described Argentinean species for a better understanding of the diversification of this genus.     

Influence of genetic polymorphisms of glutathione S-transferase T1 (<Emphasis Type="Italic">GSTT1</Emphasis>) and M1 (<Emphasis Type="Italic">GSTM1</Emphasis>) on hematological parameters

To find the influence of genetic polymorphisms of glutathione S-transferases M1 (GSTM1) and T1 (GSTT1) on hematological parameters in smoker and non-smoker subjects, the present study was done. This cross-sectional study was conducted on 97 healthy males (24 smokers, 73 non-smokers). The genotypes were determined using a polymerase chain reaction based method. In non-smokers, there was no statistically association between number of active genes and the study parameters. However, in smokers, RBC count was significantly decreased in null genotypes of GSTT1 (t = 3.021, df = 22, P = 0.006) and GSTM1 (t = 2.141, df = 22, P = 0.044). Also, in smokers, RBC count significantly decreased in persons having GSTM1 and GSTT1 null genotypes in comparison with subjects having two active genes (F = 5.554; df = 2, 21; P = 0.012). Because elevated RBC count correlate well with risk of coronary heart disease, it might be concluded that GSTM1 and GSTT1 null genotypes have protective role(s) for developing coronary heart disease.     

The rat Ruby (<Emphasis Type="Italic">R</Emphasis>) locus is <Emphasis Type="Italic">Rab38</Emphasis>: identical mutations in Fawn-hooded and Tester-Moriyama rats derived from an ancestral Long Evans rat sub-strain

Hermansky-Pudlak syndrome (HPS) is a group of rare, recessive disorders in which oculocutaneous albinism, progressive pulmonary fibrosis, bleeding diathesis, and other abnormalities result from defective biogenesis of multiple cytoplasmic organelles. Seven different HPS genes are known in humans; in mouse, at least 16 loci are associated with HPS-like mutant phenotypes. In the rat, only two HPS models are known, Fawn-hooded (FH) and Tester Moriyama (TM), non-complementing strains in which HPS-like hypopigmentation and platelet storage pool deficiency result from a mutation of the Ruby (red eyed dilution; R) locus on Chromosome (Chr) 1. We have identified the R locus as the Rab38 gene, establishing that rat R is homologous to mouse chocolate (cht). Further, we show that FH and TM rats have identical Rab38 Met1Ile mutations, occurring on an identical Chr 1 marker allele haplotype, indicating that these two strains derive from a common ancestor. This ancestor appears to have been a sub-strain of the outbred Long Evans (LE) strain, and several modern LE sub-strains carry the Rab38 Met1Ile R mutation on the same Chr 1 marker haplotype. These findings have significant implications for the many past and ongoing studies that involve the FH and LE-derivative rat strains. Hermansky-Pudlak syndrome (HPS; MIM 203300) is a group of autosomal recessive diseases in which oculocutaneous albinism (OCA), progressive and fatal pulmonary fibrosis, and bleeding diathesis due to platelet storage pool deficiency result from defects in the biogenesis of specific cytoplasmic organelles and granules: melanosomes, lysosomes, and platelet dense granules (reviewed in Spritz 1999, 2000; Spritz et al. 2003). In humans, seven different HPS genes are known (Oh et al. 1996; DellAngelica et al. 1999; Anikster et al. 2001; Suzuki et al. 2002; Li et al. 2003; Zhang et al. 2003). In the mouse, at least 16 loci associated with HPS-like mutant phenotypes are known, seven of which are homologous to the human HPS loci (Swank et al. 1998; Bennett and Lamoreux 2003). The nucleotide sequence data reported in this paper have been submitted to GenBank and have been assigned the accession number AY425759. (Naoki Oiso) Present address: Department of Dermatology, Saiseikai Tondabayashi Hospital, Tondabayashi, Osaka 584-0082, Japan.     

Antarctic associations: the parasitic relationship between the gastropod <Emphasis Type="Italic">Bathycrinicola tumidula</Emphasis> (Thiele, 1912) (Ptenoglossa: Eulimidae) and the comatulid <Emphasis Type="Italic">Notocrinus virilis</Emphasis> Mortensen, 1917 (Crinoidea: Notocrinidae) in the Ross Sea

The first case of parasitic association between an eulimid mollusc (Gastropoda, Ptenoglossa) and a comatulid (Echinodermata: Crinoidea) is reported for Antarctica. The mollusc involved in the association is Eulima tumidula Thiele, 1912, which has now been ascribed to the genus Bathycrinicola Bouchet & Warén, 1986, never recognized before in Antarctica. This genus is present only in the NE Atlantic Ocean and the Mediterranean Sea, and encompass species which are specific parasites of the sessile stalked crinoids of the family Bathycrinidae. However, in Antarctica, Bathycrinicola tumidula (Thiele, 1912) exploits the endemic vagile comatulid Notocrinus virilis Mortensen, 1917, and attains the largest known dimensions (∼1 cm) for a Bathycrinicola species. The absence of suitable Bathycrinidae host in modern Antarctic benthic assemblages, as well as the long paleontological history of the genus Notocrinus in Antarctica, suggest a possible ‘host-switch’ phenomenon. This event could reasonably have occurred when many species underwent considerable bathymetric shifts, during the dramatic climatic changes that affected Antarctica.     

Redescription and designation of a neotype for <Emphasis Type="Italic">Aphthalmichthys kuro</Emphasis> Kuroda 1947, and its placement in <Emphasis Type="Italic">Callechelys</Emphasis> (Anguilliformes: Ophichthidae)

Aphthalmichthys kuro, described by Kuroda (1947) based on a specimen from Suruga Bay, Japan, is referred to Callechelys (family Ophichthidae, subfamily Ophichthinae). It differs from its congeners in its vertebral number (142–146), tail length (2.0–2.1 in TL), and coloration (brownish black). The holotype is lost; we herein designate a neotype and redescribe and illustrate the species based on 5 specimens from Japan and 2 from Taiwan.     

Improving deep learning method for biomedical named entity recognition by using entity definition information

Background

For differential abundance analysis, zero-inflated generalized linear models, typically zero-inflated NB models, have been increasingly used to model microbiome and other sequencing count data. A common assumption in estimating the false discovery rate is that the p values are uniformly distributed under the null hypothesis, which demands that the postulated model fit the count data adequately. Mis-specification of the distribution of the count data may lead to excess false discoveries. Therefore, model checking is critical to control the FDR at a nominal level in differential abundance analysis. Increasing studies show that the method of randomized quantile residual (RQR) performs well in diagnosing count regression models. However, the performance of RQR in diagnosing zero-inflated GLMMs for sequencing count data has not been extensively investigated in the literature.

Results

We conduct large-scale simulation studies to investigate the performance of the RQRs for zero-inflated GLMMs. The simulation studies show that the type I error rates of the GOF tests with RQRs are very close to the nominal level; in addition, the scatter-plots and Q–Q plots of RQRs are useful in discerning the good and bad models. We also apply the RQRs to diagnose six GLMMs to a real microbiome dataset. The results show that the OTU counts at the genus level of this dataset (after a truncation treatment) can be modelled well by zero-inflated and zero-modified NB models.

Conclusion

RQR is an excellent tool for diagnosing GLMMs for zero-inflated count data, particularly the sequencing count data arising in microbiome studies. In the supplementary materials, we provided two generic R functions, called rqr.glmmtmb and rqr.hurdle.glmmtmb, for calculating the RQRs given fitting outputs of the R package glmmTMB.

     

Species of <Emphasis Type="Italic">Teratorhabditis</Emphasis> (Osche, 1952) Dougherty, 1953 (Nematoda:Rhabditida) from sewage and manure samples in India including a discussion on relationships within the genus

Three species of the genus Teratorhabditis (Osche, 1952) Dougherty, 1953 collected from sewage and manure samples of North India are described. The species T. andrassyi Tahseen & Jairajpuri (1988) synonymised by Sudhaus (1991) has been reinstated and is characterized by oviparous females having bluntly rounded lips with labial sensilla not raised beyond labial contour; lip margins and axils heavily cuticularised; three lines in lateral field; considerably wide and tubular stoma having swollen metastegostomal walls with prismatic inner lining bearing five teeth on each plate; basal bulb with usually single haustrulum; tail conoid with a terminal spike; eggs with ridged shells and males with 40–45% distally-fused spicules and a smooth, non-indented bursa having slender papillae in 2/4 + p + 3 configuration. Other populations identified as T. synpapillata and T. palmarum Gerber and Giblin-Davis (1990) are reported for the first time from India. An identification key to species is provided. Relationships within the genus are discussed. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users Handling editor: K. Martens     

Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays

Background  

The Audic-Claverie method [1] has been and still continues to be a popular approach for detection of differentially expressed genes in the SAGE framework. The method is based on the assumption that under the null hypothesis tag counts of the same gene in two libraries come from the same but unknown Poisson distribution. The problem is that each SAGE library represents only a single measurement. We ask: Given that the tag count samples from SAGE libraries are extremely limited, how useful actually is the Audic-Claverie methodology? We rigorously analyze the A-C statistic that forms a backbone of the methodology and represents our knowledge of the underlying tag generating process based on one observation.     

The Role of Organic Acids in the Domestication of <Emphasis Type="Italic">Oxalis tuberosa</Emphasis>: A New Model for Studying Domestication Resulting in Opposing Crop Phenotypes<Superscript>1</Superscript>

The Role of Organic Acids in the Domestication of Oxalis tuberosa: A New Model for Studying Domestication Resulting in Opposing Crop Phenotypes. Though few crops display directly opposing domesticated phenotypes, these crops may be the key to understanding domestication processes that address conflicting selective pressures in the agricultural ecosystem. Two relatively well-known examples are cassava (Manihot esculenta Crantz), which has high-cyanide and low-cyanide varieties, and potato (Solanum section Petota). Among the potatoes are several species, including the common potato (Solanum tuberosum L.), that have low levels of glycoalkaloids and there are other species of “bitter potato” with elevated levels of glycoalkaloids. We propose that Oxalis tuberosa Molina, “oca,” may represent a third example of such a crop system, with opposing high organic acid and low organic acid cultivars. Each cultivar set has different cultural food preparation practices (“use-categories”), similar to the “use-categories” that have been described for potatoes in the Andes (Brush et al. Economic Botany 35;70–88, 1981; Zimmerer Journal of Biogeography 18;165–178, 1991). Our initial analyses suggest that organic acids in tubers may be an important biochemical difference between use-categories, based on both oxalic acid and pH data. Here, we review our understanding of organic acids in oca tubers, while highlighting areas that merit further investigation.     

Fine mapping of <Emphasis Type="Italic">qSTV11</Emphasis><Superscript><Emphasis Type="Italic">TQ</Emphasis></Superscript>, a major gene conferring resistance to rice stripe disease

The indica rice cultivar, Teqing, shows a high level of resistance to rice stripe virus (RSV). It is believed that this resistance is controlled by the gene, qSTV11 ^TQ . For positional cloning of the resistance gene, a set of chromosome single segment substitution lines (CSSSLs) was constructed, all of which had the genetic background of the susceptible japonica cultivar, Lemont, with different single substituted segments of Teqing on chromosome 11. By identifying the resistance of the CSSSLs-2006 in a field within a heavily diseased area, the resistance gene qSTV11 ^TQ was mapped between the markers Indel7 and RM229. Furthermore, in that region, six new markers were developed and 52 subregion CSSSLs (CSSSLs-2007) were constructed. The natural infection experiment was conducted again at different sites, with two replicates used in each site in order to identify the resistance phenotypes of the CSSSLs-2007 and resistant/susceptible controls in 2007. Through the results of 2007, qSTV11 ^TQ was localized in a region defined by the markers, CAPs1 and Indel4. In order to further confirm the position of qSTV11 ^TQ , another set of subregion CSSSLs (CSSSLs-2009) was constructed. Finally, qSTV11 ^TQ was localized to a 55.7 kb region containing nine annotated genes according to the genome sequence of japonica Nipponbare. The relationship between qSTV11 ^TQ and Stvb-i (Hayano-Saito et al. in Theor Appl Genet 101:59–63, 2000) and the reliability of the markers used on both sides of qSTV11 ^TQ for marker-assisted breeding of resistance to rice stripe disease are discussed.     

Immunology (1955–1975): The Natural Selection Theory, the Two Signal Hypothesis and Positive Repertoire Selection

Observations suggesting the existence of natural antibody prior to exposure of an organism to the corresponding antigen, led to the natural selection theory of antibody formation of Jerne in 1955, and to the two signal hypothesis of Forsdyke in 1968. Aspects of these were not only first discoveries but also foundational discoveries in that they influenced contemporaries in a manner that, from our present vantage point, appears to have been constructive. Jerne’s later hypothesis (1971, European Journal of Immunology 1: 1–9), that antibody-like receptors on lymphocytes were selected over evolutionary time for reactivity with the major histocompatibility complex (MHC) antigens of the species, was a first, but it was incorrect, and was foundational only to the extent that it emphasized the need to explain the Simonsen phenomenon. Although easily construed as derivative of Jerne (1971), the affinity/avidity model of Forsdyke (1975, Journal of Theoretical Biology 52: 187–198), which predicted that cell-surface components, including MHC antigens, would restrict antigen-reactivity by somatically shaping lymphocyte repertoires, was actually an extension of the two signal hypothesis. While presenting a mechanism for the positive selection of lymphocyte repertoires, and explaining the Simonsen phenomenon, the affinity/avidity model was not foundational in that it had to be independently rediscovered. For science to advance optimally we must seek to close temporal gaps so that first discoveries are also foundational. Listening to young scientists may be part of the solution.     

Comparative mapping of the oat <Emphasis Type="Italic">Dw6/dw6</Emphasis> dwarfing locus using NILs and association with vacuolar proton ATPase subunit H

Seven pairs of oat near-isogenic lines (NILs) (Kibite in Crop Sci 41:277–278, 2001) contrasting for the Dw6 dwarfing gene were used to test for correlation between tall/dwarf phenotype and polymorphic genotype using restriction fragment length polymorphism (RFLP) and other molecular markers selected from the Kanota × Ogle (K×O) (Wight et al. in Genome 46:28–47, 2003) and Terra × Marion (De Koeyer et al. in Theor Appl Genet 108:1285–1298, 2004) recombination maps. This strategy located the Dw6/dw6 locus to a small chromosomal region on K×O linkage group (LG) KO33, near or at a putative RFLP locus aco245z. Aco245z and other tightly linked flanking markers have potential for use in marker-assisted selection (MAS), and PCR-based markers were developed from several of these. RFLP genotyping of the Dw6 NILs indicated that 13 of the 14 individual lines were homogeneously maternal or paternal for a large genomic region near Dw6/dw6, an unexpected result for NILs. The cDNA clone aco245 codes for a vacuolar proton ATPase subunit H, a potential candidate gene for Dw6. Vacuolar proton ATPase enzymes have a central role in plant growth and development and a mutation in subunit C is responsible for the det3 dwarfing mutation in Arabidopsis thaliana (Schumacher et al. in Genes Dev 13:3259–3270, 1999). Aco245 affords the potential of designing highly precise diagnostic markers for MAS for Dw6. The Dw6 NILs have potential utility to investigate the role of vacuolar proton ATPases in growth and development in plants.     

Influence of cell distribution and diabetes status on the association between mitochondrial DNA copy number and aging phenotypes in the InCHIANTI study

Mitochondrial DNA copy number (mtDNA‐CN) estimated in whole blood is a novel marker of mitochondrial mass and function that can be used in large population‐based studies. Analyses that attempt to relate mtDNA‐CN to specific aging phenotypes may be confounded by differences in the distribution of blood cell types across samples. Also, low or high mtDNA‐CN may have a different meaning given the presence of diseases associated with mitochondrial damage. We evaluated the impact of blood cell type distribution and diabetes status on the association between mtDNA‐CN and aging phenotypes, namely chronologic age, interleukin‐6, hemoglobin, and all‐cause mortality, among 672 participants of the InCHIANTI study. After accounting for white blood cell count, platelet count, and white blood cell proportions in multivariate models, associations of mtDNA‐CN with age and interleukin‐6 were no longer statistically significant. Evaluation of a statistical interaction by diabetes status suggested heterogeneity of effects in the analysis of mortality (P < 0.01). The magnitude and direction of associations between mtDNA‐CN estimated from blood samples and aging phenotypes are influenced by the sample cell type distribution and disease status. Therefore, accounting for these factors may aid understanding of the relevance of mitochondrial DNA copy number to health and aging.     

Correcting Misperceptions about the History of <Emphasis Type="Italic">Castanea</Emphasis> Stands in <Emphasis Type="Italic">Satoyama</Emphasis> in Japan

Correcting Misperceptions about the History of Castanea Stands in Satoyama in Japan. Mistaken ideas about the naturalness of past and present landscapes are widespread in diverse cultures and in the scientific literature, and many of these ideas are only now being seriously challenged by current research (e.g., Erickson 2006; Fairhead and Leach 1996; Hall 1998; Ramankutty and Foley 1999; Willis et al. 2004). For example, the chestnut, Castanea crenata, has long been an important tree in Japanese culture, which has been cultivated, among other things, for its much loved edible nut and its valuable timber. Today, the widely-held view in Japan, which also appears in the scholarly and popular literature, is that in the past Castanea stands covered a large area throughout Japan, and these stands only disappeared because of economic development, especially in association with railway construction. Otaru, Hokkaido, is one of the places where people believe Castanea stands covered a large area and were deforested only recently. Local people in Otaru believe that the stand in Temiya Park has existed since the Jomon Period. For a more accurate historical perspective on Japanese forestation, we have performed pollen analysis to clarify the timing of the introduction of the Castanea tree into Otaru region and to reveal the history of this specific Castanea stand in Temiya Park. The results indicate that Castanea was first found in Otaru region 7100 B.P., but that it was not cultivated extensively until recently. Based on our study, and on data from this area dating to the late 19th century, we concluded instead that the Castanea stand we studied in Temiya Park, Otaru, was established after the mid-20th century. We believe the results of this study are applicable to Castanea stands in other parts of Japan as well.