Application of the Tweedie distribution to zero-catch data in CPUE analysis

We focus on the zero-catch problem of CPUE (catch per unit effort) standardization. Because the traditional CPUE model with a log-normal error structure cannot be applied in this case, three methods have often been utilized as follows:

(1) Ad hoc method adds a small constant value to all response variables.

(2) Catch model with a Poisson or negative-binomial (NB) error structure.

(3) Delta-type two-step method such as the delta-normal model (after estimating the ratio of zero-catch using a logit or probit model, a model such as CPUE log-normal or Catch-Poisson is applied to CPUE without zero-data).

However, there are some statistical problems with each of these methods.In this paper, we carried out the CPUE standardization mainly using the Tweedie distribution model based on the actual by-catch data (silky shark, Carcharhimus falciformis, in the North Pacific Ocean caught by Japanese training vessels) including many observations with zero-catch (>2/3rd) and tuna fishery data as a target (yellowfin tuna, Thunnus albacares, in the Indian Ocean caught by Japanese commercial vessels) where the ratio of zero-catch is not so high (<1/3rd). The Tweedie model is an extension of compound Poisson model derived from the stochastic process where the weight of the counted objects (i.e., number of fish) has a gamma distribution and has an advantage of handling the zero-catch data in a unified way.We also compared four candidate models, the Catch-NB model, ad hoc method, Delta-lognormal model (delta-type two-step method) and Tweedie distribution, through CPUE analyses of actual fishery data in terms of the statistical performance. Square error and Pearson's correlation coefficient were calculated based on the observed CPUE and the corresponding predicted CPUE using the n-fold cross-validation.As a result, the differences in the trend of CPUE between years and model performance between the ad hoc method and Tweedie model were found to be not so large in the example of yellowfin tuna (target species). However, the statistical performance of Tweedie distribution is rather better than Delta-lognormal model, the Catch-NB distribution and ad hoc method in the example of silky shark (by-catch species). Standardized CPUE year trend of ad hoc method was found to be quite different from that of the Tweedie distribution and other two models. Model performance of the Tweedie distribution is good judging from the 5-fold cross-validation using the fishery data if including many zero-catch data such as by-catch species.     

Identification of putative defense-related genes in Japanese pear against <Emphasis Type="Italic">Alternaria alternata</Emphasis> infection using suppression subtractive hybridization and expression analysis

The Japanese pear pathotype of Alternaria alternata, a toxin-dependent necrotrophic pathogen, causes black spot of Japanese pear by producing the host-specific AK-toxin. Pre-inoculation with nonpathogenic A. alternata or pretreatment with an elicitor prepared from A. alternata reduced disease symptoms caused by the pathogen. Salicylic acid- and jasmonic acid-dependent signaling pathways are not involved in the induced resistance to infection by the pathogen. The expression of multiple defense-related genes in Japanese pear leaves inoculated with nonpathogenic A. alternata was examined using suppression subtractive hybridization. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank database as accessions DC993229–DC993535.     

The incidence of disseminated intravascular coagulation in dogs with malignant tumor

The incidence of DIC in 208 dogs with a malignant tumor was evaluated. The incidence of DIC was 9.6% in dogs with a malignant tumor which was a solid tumor in all. In 164 dogs with a malignant solid tumor, the incidence of DIC was 12.2%. The incidence of DIC in dogs with hemangiosarcoma, mammary gland carcinoma and adenocarcinoma of the lung was significantly higher than that in dogs with other malignant tumors. These results suggested that special care in looking for DIC should be taken in dogs with a malignant solid tumor.     

Experimental and clinical studies on plasma leptin in obese dogs

Leptin is a protein synthesized and secreted primarily by adipocytes, and the circulating leptin concentration is elevated in obese humans and rodents. Recently, we have established a sandwich enzyme-linked immunosorbent assay for canine leptin. In the present study, plasma leptin concentrations were measured in experimentally developed obese beagles and in clinically obese dogs. When 5 male beagles were given a high-energy diet for 3 months, all of them became obese and the plasma leptin concentration significantly increased from 2.4+/-1.2 to 4.9+/-0.9 ng/ml, positively correlating with body fat content estimated by the deuterium oxide dilution method (r=0.87). The leptin concentrations of plasma samples collected from 59 dogs in veterinary practices were compared with their body condition scores (BCS). The plasma leptin concentrations of obese dogs were 9.7+/-0.7 and 12.3+/-1.5 ng/ml at BCS=4 and BCS=5, respectively, which were significantly higher than those of optimal (BCS=3) dogs (2.7+/-0.3 ng/ml). There was no significant effect of sex and breed. A weak positive correlation (r=0.37) was found between the plasma leptin concentration and age, probably due to the lesser content of visceral fat in puppies younger than 1 year old. These results indicate that plasma leptin is a good index of adiposity in dogs regardless of breed, age and sex, and may be useful for quantitative assessment of obesity in small animal practice.     

Phytotoxin produced by the netted scab pathogen, <Emphasis Type="Italic">Streptomyces turgidiscabies</Emphasis> strain 65, isolated in Sweden

Streptomyces spp. are a highly diverse group of bacteria most of which are soil-inhabiting saprophytes. A few are plant pathogens that produce a family of phytotoxins called thaxtomins and cause significant economic losses, e.g., by reducing the marketability of potato tubers (Solanum tuberosum). In northern Europe, S. scabies, S. turgidiscabies and S. europaeiscabiei are the most common plant pathogenic species. In this study, a Streptomyces strain isolated from a netted scab lesion on a tuber of potato cv. Bintje in northern Sweden was identified as S. turgidiscabies but was found to differ in the genomic region carrying genes required for thaxtomin biosynthesis. Our results showed that the strain did not produce thaxtomin but rather phytotoxin fridamycin E, which is an anthraquinone novel to plant pathogenic Streptomyces spp. Fridamycin E was shown to reduce or inhibit sprouting of potato microtubers in vitro. While fridamycin E is known to have antibiotic activity against Gram-positive bacteria, the inhibitory activity of fridamycin E on plant growth is a novel finding.     

Detection and quantification of protein residues in food grade amino acids and nucleic acids using a dot-blot fluorescent staining method

Food allergies represent an important health problem in industrialized countries, such that detection and quantitative analysis of the protein considered to be the main allergen is crucial. A dot-blot fluorescent staining method for the detection and quantitative analysis of protein residues in food grade amino acids and nucleic acids is presented. This method combines fluorescence staining with dot-blotting onto PVDF membrane. Several standard proteins, such as bovine serum albumin (66 kDa), lysozyme (14 kDa), ubiquitin (8.6 kDa), bovine insulin (5.7 kDa), and oxidized insulin B chain (3.5 kDa), were detectable at 0.1 ppm using SYPRO Ruby blot stain. Twenty-five different amino acids and two different nucleic acids of food grade were analyzed using this method combined with an internal standard addition method using BSA as an internal standard. All amino acids and nucleic acids were dissolved in 3.6% aqueous HCl and dot-blotted onto PVDF membrane before a large amount of amino acids and nucleic acid were removed. Protein residues and the internal standard protein immobilized on the membrane were stained using SYPRO ruby blot stain. The internal standard in all samples was detectable at 0.1 ppm. Samples were dissolved at 120 or 70 mg/mL, according to their solubility under acidic conditions. The detection limit of protein residues per weight was 0.8-1.4 ppm in amino acids and nucleic acids; residual protein was not detected in any sample.     

In vitro but not in planta encapsidation of Rice gall dwarf virus core particles by the outer capsid P8 protein of Rice dwarf virus expressed in transgenic rice plants

Transencapsidation of the Rice gall dwarf virus (RGDV) inner core by the Rice dwarf virus (RDV) outer capsid P8 protein was examined in vitro and in planta. When RGDV core particles were incubated with an extract from RDV P8-transgenic rice leaf tissue, RDV P8 encapsidated the RGDV core particles to form double-shelled virus-like particles in vitro. In contrast, when RDV P8-transgenic rice plants were inoculated with RGDV, progeny RGDV particles contained RGDV P8 but RDV P8 was not detectable in the virions. No significant differences were found in acquisition by the vector insects and subsequent transmission rates between RGDV infecting nontransgenic rice plants and those infecting RDV P8-transgenic rice plants. These results indicate that mechanisms of and/or requirements for interactions between P8 and the inner core particles of phytoreoviruses differ between in vitro and in planta.