Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

Background

It has been reported in the quantitative trait locus (QTL) literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases.Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach.We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster.

Results

Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis.

Conclusion

We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

     

Isolation and analysis of natural compounds from silkworm pupae and effect of its extracts on alcohol detoxification

Silkworm pupae have much potential and many applications as a natural medicine to promote human health. However, their chemical components have not been fully characterized or understood. HPLC analysis was conducted to determine the content ratio (%) of individual amino acids in total protein of the pupae. It showed that glutamic acid (18.3%), histidine (14.6%) and alanine (10.2%) are the most common amino acids in silkworm pupae. Fatty acid composition of silkworm pupae oil was revealed by high‐pressure liquid chromatography and gas chromatography – mass spectroscopy analyses. They contain a high ratio of essential fatty acids, [α‐linolenic acid (ω‐3 fatty acid]+ linoleic acid) (49.0%), and also contain non‐essential fatty acids, oleic acid (19.9%), palmitoleic acid (2.5%), palmitic acid (19.7%), stearic acid (8.6%), and eicosapentaenoic acid (EPA) (0.3%). In addition, they also contain antioxidants, quercetin diglucoside and nutritionally important riboflavin (vitamin B2). This study suggests that silkworm pupae are a nutritionally valuable food product and are applicable as cosmetic components with essential amino acids, essential fatty acids, antioxidants and vitamins. The animal experiment showed that alcohol dehydrogenase (ADH) activity was significantly higher in the liver of mice orally administered with 0.5 mg/mL of silkworm extract and alcohol than with commercial Dawn808? and alcohol, indicating that silkworm pupae extracts have alcohol detoxification activity.     

News from the Biological Stain Commission No. 5

In this fifth issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory Affairs, the BSC's International Affairs Committee provides more information from the meeting of the International Standards Organization ISO/TC 212 Committee that took place on June 2–4, 2008 at Vancouver, Canada. In addition, we give an update on the current situation regarding the supplies of hematoxylin.     

High and low temperature tolerances and their relationships to distribution of agaves

Abstract. The potential influence of tissue tolerances to extreme temperatures on distributional limits was investigated for 15 taxa (14 species) of leaf-succulent agaves from the south-western United States and northern Mexico. As a group, the agaves exhibited a moderate low temperature tolerance of – 11°C (based on a 50% inhibition in the number of mesophyll cells taking up a stain, neutral red). However, nearly all of the species were able to tolerate extremely high tissue temperatures of over 60°C. Nocturnal acid accumulation by these crassulacean acid metabolism plants was about 6°C more sensitive to temperature extremes than was cellular membrane integrity.
High and low temperature acclimation in response to changing day/night air temperatures was observed in all 15 taxa, with high temperature acclimation averaging two-fold greater than low temperature acclimation (3.8°C versus 2.0°C per 10°C change in ambient temperature). Species occupying the coldest habitats exhibited the greatest low temperature tolerances and acclimation; several such species, such as Agave utahensis and A. schottii , had small rosette sizes which resulted in higher minimum leaf temperatures. Species from the hottest habitats had among the greatest high temperature tolerances and acclimation; the two species from open desert scrub habitats, A. deserti and A. lecheguilla , had the lowest leaf shortwave absorptances observed, which would result in lower maximum leaf temperatures. Thus morphology and tissue tolerances to stressful temperatures reflect the temperature extremes of a plant's native habitat, although low temperature tolerance appears to limit the distribution of agaves more than high temperature tolerance.     

Root Respiration for Agave deserti: Influence of Temperature, Water Status and Root Age on Daily Patterns

Root respiration, measured as CO₂ efflux, was studied for asucculent perennial from the Sonoran Desert, Agave deserti,with a new technique using individual, attached roots. The dailypatterns of root respiration closely followed the daily patternsof root temperature for both established roots and rain roots,with higher rates during the day when root temperature averaged27?C and lower rates at night when root temperature averaged17?C. When root temperature was raised from 5?C to 40?C, rootrespiration increased about 7-fold; from 45 ?C to 55 ?C, rootrespiration decreased about 2-fold, except for old establishedroots. Root respiration per unit dry weight for both root typesdecreased with age, the initial decrease being greater for rainroots than for established roots. Root respiration rates forrain roots were reduced to zero at a soil water potential (_soil)of –0.9 MPa and did not recover upon rewatering. Upondrying, root respiration rates for established roots were maintainedat about 12% of maximum, even when _soil fell to –1.6 MPa,and fully recovered 1.5 d after rewatering the soil. Such responsesof rain and established roots must be taken into account whenassessing the carbon costs for the root system. Key words: Agave deserti, CO₂ exchange, root respiration, temperature, soil water potential     

Spatial pattern analysis of entomopathogenic and other free‐living nematodes at landscape scales

Spatial patterns of entomopathogenic and other free‐living nematode populations were analyzed at the landscape scale. Free‐living bacterial feeder populations can be classified into trophic groups based on their functional and life history characteristics. Differences in life history traits were hypothesized to result in different spatial structures of populations. Spatial autocorrelations (Moran's I index) and exponential variogram models were calculated and estimated for each trophic group, including entomopathogenic nematodes, and comparisons were made among them. Spatial autocorrelation results showed that the spatial structure of entomopathogenic nematode populations is similar to that of relatively r‐selected free‐living bacterial feeders, which share several life history traits with entomopathogenic nematodes.     

Newly developed polymorphic microsatellite markers in Job's tears (Coix lacryma‐jobi L.)

A microsatellite‐enriched library of Job's tears (Coix lacryma‐jobi L. var. Ma‐yuen Stapf) was constructed using a modified biotin–streptavidin capture method. After screening, 17 polymorphic microsatellites were used for diversity analysis among 30 Job's tears accessions. The number of alleles ranged from one to five alleles per locus with an average of 2.8 alleles. Expected heterozygosity (H_E) and polymorphism information content (PIC) ranged from 0 to 0.676 and from 0 to 0.666, respectively. The newly developed microsatellite markers are expected to be very valuable tools for evaluation of genetic diversity among large germplasm collection of Job's tears present in our Korean Gene Bank.     

Immature Stages of Tomapoderus(T.) ruficollis Fabricius (Coleoptera: Attelabidae) from Korea

Eggs, larvae and pupae of Tomapoderus (T.) ruficollis Fabricius are described and illustrated. The species is found on host plants, Zelkova serrata Makino and Ulmus davidiana var. japonica Nakai. and is a well‐known forest pest. Taxonomic notes and cradle structure of this species are provided.     

Cloning and Characterization of the cDNA Encoding the Masquerade-like Serine Proteinase Homologue Gene of the Silkworm, Bombyx mori

ABSTRACT From Bombyx mori larvae, RT-PCR and cDNA library screening isolated masquerade-like serine proteinase homologue cDNA gene, proposed to be related to insect immunity and its characteristics were examined. The isolated gene is composed of 1.3 kb of nucleotide and 420 amino acid residues were encoded. According to the results of database search, the isolated gene showed high sequence homology with Holotrichia and Tenebrio's 45 kDa protein, Drosophila CG5390 gene. Moreover, it is composed of regulatory domain and catalytic domain, which is characteristic of serine proteinase that can be found in the insect immune reaction and embryonic development processes. Enzyme activation site by proteolytic cleavage and the sequence of three amino acids participate in the catalytic triad of enzyme and 14 cystein residues used in disulfide bridges are well conserved with the compared genes. The mRNA expression was increased following E. coli injection and constitutive expression was also observed before injection by Northern blot analysis.