Pedigreed crosses to estimate recessive virulence allele frequencies in natural populations of gall midges

Monitoring changes in rare, recessive allele frequencies in natural populations can be accomplished using pedigreed individuals sampled from these populations. A pedigree keeps track of and limits the mating of sampled individuals, to preserve information about the genotype of the sampled individual in the phenotypes of its descendents. To estimate allele frequencies in a natural population using pedigreed crosses, four relations must be specified: (1) a method to determine whether the pedigreed line carries the desired allele; (2) a method to estimate the phenotypic frequency of the trait among the pedigreed lines and a credibility limit for the estimate; (3) the genetic relation between the phenotype frequency among the lines and the allele frequency in the natural population; and (4) a method to estimate the probability that the first method did not detect the trait, assuming that the allele was present in the sampled individual. Knowledge about the segregation patterns of the allele enables specification of (3) and (4). Bayesian statistics were used to estimate the phenotypic frequency of the trait among the pedigreed lines. The method determining whether the pedigreed line carries the desired allele will vary with the species and trait of concern. We focused on monitoring of vGm1, a recessive autosomal allele, and vGm2, a recessive sex‐linked allele, which provide virulence against certain rice resistance genes in rice gall midge, Orseolia oryzae (Wood‐Mason) (Diptera: Cecidomyiidae). We show how three pedigrees can be used to estimate these allele frequencies. An F₁ field screen challenges the F₁ offspring of sampled individuals on the rice differentials. A P₁ test‐cross mates the sampled individual with a homozygous lab colony for the allele of interest, and evaluates their offspring on the rice differentials. A conditional F₁ test‐cross takes the offspring from pedigrees that were negative in an F₁ field screen, and test‐crosses these offspring with the homozygous laboratory colony. We also indicate how to test for independent assortment when a double (or multiple) homozygote laboratory colony is used in a test‐cross, how to test for differences among samples, and how to pool data to produce a single estimate based on a larger number of pedigreed lines. These methods may encourage the development of a variety of pedigreed monitoring strategies that could improve and prolong the use of scarce plant resistance alleles in rice and other plants.     

Review: “Doctor,will that x-ray harm my unborn child?”

Abstract: Exposure to ionizing radiation can be a source of anxiety for many pregnant women and their health care providers. An awareness of the radiation doses delivered by different techniques and the acceptable exposure thresholds can help both patients and practitioners. We describe exposure to radiodiagnostic procedures during pregnancy and suggest an approach to assess the potential risk.Case 1: A 29-year-old patient underwent an upper gastrointestinal series as part of the diagnosis of prolonged heartburn. She comes to see you 1 week later and is very upset because her period is 1 week late and she was about 4 weeks pregnant at the time of the procedure. The patient asks you to schedule the termination of her pregnancy on the advice of several family members.Case 2: A 40-year-old woman arrives at the emergency department with acute pleuritic chest pain and shortness of breath. The patient is 15 weeks'' pregnant. To rule out a pulmonary embolus, should you perform a ventilation-perfusion scan or computed tomography (CT) angiography?Case 3: A 37-year-old woman who is 20-weeks pregnant reports persistent pain in her right upper thigh that is exacerbated after jogging. The pain is localized and has no radicular properties. A physical examination shows localized tenderness on the right hip joint without any abnormal neurological findings. You suspect hip bursitis but want to order a radiograph to rule out osteoarthritis with degenerative changes. The patient is nervous about the possible effects of the radiation on her baby; how would you counsel her?Many women are exposed to radiation from diagnostic imaging procedures before they know they are pregnant or because it is necessary during a known pregnancy. These patients often question the potential effects of the radiation on the developing fetus, and they may perceive radiation as being very harmful.^1–4 A realistic and informed approach to counselling these patients can minimize the anxiety felt by both patients and health care providers.Humans are exposed to both background and man-made sources of radiation. For the purpose of this review, “radiation” refers to ionizing radiation (e.g., x-rays, γ-rays, radionuclides) and not to other forms of radiation (e.g., long-wavelength electromagnetic waves such as radar, microwaves, diathermy and FM radio waves).Ionizing radiation in the form of x-rays and γ-rays are short-wavelength electromagnetic rays. Low-energy photons in x-rays and high-energy photons in γ-rays can alter the normal structure of a living cell both directly and indirectly. The direct mechanism involves disruption of the atom''s structure to produce an ionized compound and a free electron. The indirect mechanism involves radiolysis of water and generation of free radicals.⁵Ionizing radiation can cause two types of effects.⁵ First, loss of tissue function (deterministic effect) can occur. This type of injury has tissue-specific thresholds and may involve various repair and compensatory mechanisms. If the radiation dose is fractionated, there is greater repair and proliferation, hence there is greater tolerance of the tissue to the radiation. Second, damage can occur from a single random modification in a cell component (e.g., DNA) (stochastic effect). There is no dose threshold for stochastic effects.Since invention of the x-ray in 1895, ionizing radiation has been harnessed for diagnostic and therapeutic purposes. With the atomic bombings in World War II, the world became aware of the serious potential carcinogenic, teratogenic and mutagenic effects of ionizing radiation. Despite the increase in concern about the health effects of ionizing radiation, the medical use of x-rays has continued to grow. In 1980, the number of radiographs performed in the United States was 225 million, including about 80 million fertile men and women.⁵ In 2006, the estimated total number of radiographs in the US was about 330 million.⁶ The fetus is exposed to unavoidable (background) radiation from cosmic rays, terrestrial radiation from ground and building and naturally occurring radioisotopes that are inhaled or ingested. The total fetal dose from background radiation sources is 0.1 rad or less during the entire pregnancy.⁵     

Efficient p-value estimation in massively parallel testing problems

We present a new method to efficiently estimate very large numbers of p-values using empirically constructed null distributions of a test statistic. The need to evaluate a very large number of p-values is increasingly common with modern genomic data, and when interaction effects are of interest, the number of tests can easily run into billions. When the asymptotic distribution is not easily available, permutations are typically used to obtain p-values but these can be computationally infeasible in large problems. Our method constructs a prediction model to obtain a first approximation to the p-values and uses Bayesian methods to choose a fraction of these to be refined by permutations. We apply and evaluate our method on the study of association between 2-way interactions of genetic markers and colorectal cancer using the data from the first phase of a large, genome-wide case-control study. The results show enormous computational savings as compared to evaluating a full set of permutations, with little decrease in accuracy.     

Identification of flanking SSR markers for a major rice gall midge resistance gene <Emphasis Type="Italic">Gm1</Emphasis> and their validation

Host-plant resistance is the preferred strategy for management of Asian rice gall midge (Orseolia oryzae), a serious pest in many rice-growing countries. The deployment of molecular markers linked to gall midge resistance genes in breeding programmes can accelerate the development of resistant cultivars. In the present study, we have tagged and mapped a dominant gall midge resistance gene, Gm1, from the Oryza sativa cv. W1263 on chromosome 9, using SSR markers. A progeny-tested F₂ mapping population derived from the cross W1263/TN1 was used for analysis. To map the gene locus, initially a subset of the F₂ mapping population consisting of 20 homozygous resistant and susceptible lines each was screened with 63 parental polymorphic SSR markers. The SSR markers RM316, RM444 and RM219, located on chromosome 9, are linked to Gm1 at genetic distances of 8.0, 4.9 and 5.9 cM, respectively, and flank the gene locus. Further, gene/marker order was also determined. The utility of the co-segregating SSR markers was tested in a backcross population derived from the cross Swarna/W1263//Swarna, and allelic profiles of these markers were analysed in a set of donor rice genotypes possessing Gm1 and in a few gall midge-susceptible, elite rice varieties.     

Influence of ginger rhizome (Zingiber officinale Rosc) on survival, glutathione and lipid peroxidation in mice after whole-body exposure to gamma radiation

The radioprotective effect of the hydroalcoholic extract of ginger rhizome, Zingiber officinale (ZOE), was studied. Mice were given 10 mg/kg ZOE intraperitoneally once daily for five consecutive days before exposure to 6-12 Gy of gamma radiation and were monitored daily up to 30 days postirradiation for the development of symptoms of radiation sickness and mortality. Pretreatment of mice with ZOE reduced the severity of radiation sickness and the mortality at all doses. The ZOE treatment protected mice from GI syndrome as well as bone marrow syndrome. The dose reduction factor for ZOE was found to be 1.15. The optimum protective dose of 10 mg/kg ZOE was 1/50 of the LD50 (500 mg/kg). Irradiation of the animals resulted in a dose-dependent elevation in the lipid peroxidation and depletion of GSH on day 31 postirradiation; both effects were lessened by pretreatment with ZOE. ZOE also had a dose-dependent antimicrobial activity against Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli and Candida albicans.     

Natural ozone scavenger prevents asthma in sensitized rats

The assumption that ozone is not only a strong oxidant, but also an important inflammatory mediator, is heavily supported by the ample literature on the pulmonary toxicity and biological effects of environmental ozone and by the recent discovery that antibodies, human neutrophils, and inflammatory lesions catalyze the formation of ozone in vivo. We hypothesized that the pulmonary inflammation in asthma involves a vicious circle of ozone production and recruitment of white blood cells, which produce more ozone. Accordingly, we predicted that electron-rich olefins, which are known ozone scavengers, could be used for prophylactic treatment of asthma. In particular, volatile, unsaturated monoterpenes, could saturate the pulmonary membranes and thereby equip the airways with local chemical protection against either exogenous or endogenous ozone. Here we present experimental evidence using a sensitized rat model to support this hypothesis. Examination of the pulmonary function of sensitized rats that inhaled either limonene (unsaturated, ozone scavenger) or eucalyptol (saturated, inert to ozone) showed that limonene inhalation significantly prevents bronchial obstruction while eucalyptol inhalation does not cause any effect. The anti-inflammatory effect of limonene was also evident from pathological parameters, such as diminished peribronchiolar and perivascular inflammatory infiltrates.     

Molecular cloning and characterization of the macaque sperm associated antigen 9 (SPAG9): an orthologue of human SPAG9 gene

The present study was conducted to isolate macaque proteomic homologue of human SPAG9 (EMBL nomenclature human sperm associated antigen 9: hSPAG9; Shankar et al., 1998: Biochem Biophys Res Commun 243:561-565) in order to find out whether the macaque can provide a suitable model for examining its immunocontraception effects. Macaque SPAG9 was cloned and sequenced from the macaque testis cDNA library. The macaque cDNA contained open reading frame encoding 712 amino acids. A 84.9% and 94% homology between macaque and human SPAG9 was found at protein and DNA levels. Northern analysis and RNA in situ hybridization experiments revealed testis- and stage-specific expressions of macaque SPAG9 mRNA, mainly confined to round spermatid suggesting haploid germ cell expression. Anti-human SPAG9 antibodies recognized native SPAG9 in macaque sperm extract in Western blotting and the acrosomal compartment region of macaque sperm in indirect immunofluorescence. Flow cytometry analysis further revealed surface localization of macaque SPAG9 in live macaque sperm. The amino acid sequence data for nonhuman primate SPAG9 suggest that antibodies generated by vaccinating macaque with hSPAG9 will recognize nonhuman primate SPAG9, supporting the testing of SPAG9 contraceptive vaccine based on hSPAG9 in the nonhuman primate model.     

In vitro regeneration of plantlets from shoot callus of mature trees ofDalbergia latifolia

A successful procedure was established for in vitro mass multiplication of Indian rosewood (Dalbergia latifolia Roxb.). In vitro regeneration of plantlets was achieved from callus of shoot tips and shoot segments of over 50-year-old elite trees on Murashige & Skoog's medium containing naphthaleneacetic acid (NAA) and benzylaminopurine (BAP). For rooting, regenerated shoots from the calli were excised and first treated with White's liquid medium or half-strength Murashige & Skoog's medium, supplemented with indole-3-acetic acid, indole-3-butyric acid and naphthaleneacetic acid for 48 h to 72 h. Following this treatment, plantlets were transferred to hormone-free half-strength MS medium. Rooted plantlets were then transferred to pots and grown in the greenhouse.Abbreviations BAP 6-benzylamino pruine - CH casein hydrolysate - CM coconut milk - 2, 4-D dichlorophenoxyacetic acid - GA gibberellic acid - IAA indole-3-acetic acid - IBA indole-3-butyric acid - NAA naphthaleneacetic acid - PVP-10 polyvinyl pyrrolidone - YE yeast extract     

Clonal propagation of Cinnamomum zeylanicum Breyn. by tissue culture

Multiple shoot formation was induced directly from seeds of Cinnamomum zeylanicum Breyn. and also from seedling explants on Murashige and Skoog's medium containing different concentrations and combinations of auxins and cytokinins. Individual shoots were excised and induced to root on White's liquid medium. These plantlets were then transferred to pots in the green house and were eventually grown successfully under field conditions. Explants from the nodal region of these in vitro rooted plants were also subcultured to fresh medium. They produced a new crop of multiple shoots which could again be rooted by the same procedure.Abbreviations BAP 6-Benzylamino purine - 2,4-D 2,4-Dichlorophenoxy acetic acid - IAA Indole-3-acetic acid - IBA Indole-3-butyric acid - IPA Indole-3-propionic acid - KN Kinetin - NAA -Naphthalene acetic acid     

Versatile cassettes designed for the copper inducible expression of proteins in yeast

A series of yeast expression vectors and cassettes utilizing the CUP1 gene of Saccharomyces cerevisiae have been constructed. The cassettes contain multiple cloning sites for gene fusions and were created by inserting a 27-bp polylinker at the +14 position of the CUP1 gene. The cassettes are portable as restriction fragments and enable copper-regulated expression of foreign proteins in S. cerevisiae. In copper sensitive yeast, multiple copies of the CUP1 cassettes confer copper resistance due to the production of the copper metallothionein. Genes cloned into the CUP1 cassettes, however, usually prevent translation of the metallothionein leading to a loss of resistance. This could be useful for one-step cloning into yeast.