Incorporating spatial autocorrelation into the general linear model with an application to the yellowfin tuna (Thunnus albacares) longline CPUE data

Catch-per-unit-effort (CPUE) data have often been used to obtain a relative index of the abundance of a fish stock by standardizing nominal CPUE using various statistical methods. The theory underlying most of these methods assumes the independence of the observed CPUEs. This assumption is invalid for a fish population because of their spatial autocorrelation. To overcome this problem, we incorporated spatial autocorrelation into the standard general linear model (GLM). We also incorporated into it a habitat-based model (HBM), to reflect, more effectively, the vertical distributions of tuna. As a case study, we fitted both the standard-GLM and spatial-GLM (with or without HBM) to the yellowfin tuna CPUE data of the Japanese longline fisheries in the Indian Ocean. Four distance models (Gaussian, exponential, linear and spherical) were examined for spatial autocorrelation. We found that the spatial-GLMs always produced the best goodness-of-fit to the data and gave more realistic estimates of the variances of the parameters, and that HBM-based GLMs always produced better goodness-of-fit to the data than those without. Of the four distance models, the Gaussian model performed the best. The point estimates of the relative indices of the abundance of yellowfin tuna differed slightly between standard and spatial GLMs, while their 95% confidence intervals from the spatial-GLMs were larger than those from the standard-GLM. Therefore, spatial-GLMs yield more robust estimates of the relative indices of the abundance of yellowfin tuna, especially when the nominal CPUEs are strongly spatially autocorrelated.     

Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus

ABSTRACT: The complete nucleotide sequence of the mitochondrial genome for the Japanese anchovy Engraulis japonicus (Teleostei: Clupeiformes) was determined. The entire genome was purified by gene amplification using the long polymerase chain reaction (PCR) technique, and products were subsequently used as templates for PCR with 56 fish-versatile primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products demonstrated that the genome (16 675 base pairs [bp]) contained the same 37 mitochondrial genes (two ribosomal RNA, 22 transfer RNA and 13 protein-coding genes) as those found in other vertebrates, with the gene order being identical to that in typical vertebrates. A major non-coding region between the tRNA^Pro and tRNA^Phe genes (1024 bp) was considered to be the control (D-loop) region, as it has several conservative blocks characteristic to this region.     

Asynchronous climate changes in the North Atlantic and Japan during the last termination

Pollen records from the annually laminated sediment sequence in Lake Suigetsu, Japan, suggest a sequence of climate changes during the Last Termination that resembles that of the North Atlantic region but with noticeable differences in timing. An interstadial interval commenced a few centuries earlier [approximately 15,000 years before the present (yr B.P.)] than the North Atlantic GI-1 (B?lling) event. Conversely, the onset of a Younger Dryas (YD)-like cold reversal (12,300 to 11,250 yr B.P.) postdated the North Atlantic GS-1 (YD) event by a few centuries. Climate in the Far East during the Last Termination reflected solar insolation changes as much as Atlantic influences.     

Results of hyperamplification of centrosomes in naturally developing tumors of dogs.

OBJECTIVE: To evaluate results of centrosome hyperamplification in naturally developing tumors of dogs. SAMPLE POPULATION: Tumor specimens from 9 dogs with tumors (rhabdomyosarcoma, osteosarcoma, chondrosarcoma, myxosarcoma, and mammary gland tumor) and 2 canine osteosarcoma cell lines. PROCEDURE: 3 antibodies for centrosome proteins (ie, anti-gamma-tubulin, anti-BRCA1, and anti-pericentrin) were used for immunohistochemical analysis. Double immunostaining for centrosomes was used to confirm the specificity of these antibodies for centrosomes. Mutational analysis of the canine p53 gene was carried out by polymerase chain reaction-single-strand conformation polymorphism analysis, and expression of canine MDM2 protein was evaluated by use of immunohistochemical analysis, using anti-MDM2 antibody. RESULTS: Immunohistochemical analysis of dog osteosarcoma cell lines with apparent aneuploidy revealed frequent hyperamplification of centrosomes in the osteosarcoma cell lines. Similar hyperamplified centrosomes were detected in the tumor tissues from all of the 9 tumors. The frequency of cells with hyperamplified centrosomes (3 to 20/cell) in each tumor tissue ranged from 9.50 to 48.1%, whereas centrosome hyperamplification was not observed in normal lymph nodes from these dogs. In 8 of the 9 tumors, mutation of p53 gene or overexpression of MDM2, or both, was detected. CONCLUSIONS AND CLINICAL RELEVANCE: Various types of naturally developing tumors in dogs often have hyperamplification of centrosomes associated with chromosome instability. Hyperamplification of centrosomes is a novel tumor marker for use in cytologic and histologic examinations of clinical specimens obtained from dogs.     

Analysis of various antigens in golden hamster testis by monoclonal antibodies.

A total of 38 hybridomas producing monoclonal antibodies (mAbs) was established by immunizing BALB/c mice with extracts of the golden hamster testis. Six mAbs stained the acrosome of developing spermatids by immunofluorescence. Two mAbs (1A11 and 4D8) reacted with spermatid components other than acrosome. The mAbs 1C9 and 4D3 recognized a 103 kilodalton (kDa) protein on immunoblots, and were reactive to spermatocytes and early spermatids, but not to late spermatids and spermatozoa. This finding suggests that the protein functions for meiosis or early spermiogenesis. Four mAbs (3G2, 2E5, 2G3, and 3F10) stained all stages of spermatogenic cells. The remaining 24 mAbs showed a positive reaction to the basement membrane of the seminiferous tubule. Two of them, 3D6 and 3E5, recognized approximately 150 kDa major proteins, indicating that the antigen is an extracellular matrix.     

The Arterial Supply of the Male Reproductive System in the Hamster

The major arteries, the testicular, deferential, prostatic, internal pudendal and external pudendal arteries, supply the male genital organs of the hamster. The same arterial patterns are found in three strains, except that the external pudendal artery arises from the external iliac artery or internal iliac artery in the APG strain, but only from the external iliac artery in the CBN and ACN strains. The deferential and prostatic arteries form the arterial loop on the dorsal surface of the ventrolateral lobe of the prostate. This loop may play some importance parts in the functional interaction between the epididymis and the prostate. The caudal epididymal artery arises more frequently from the spermatic cordai portion of the testicular artery than from the cranial epididymal artery, and it never arises directly from the abdominal part of the testicular artery as reported in the rat, mouse and rabbit. The deferential artery may join with the cranial vesicular artery to form the common trunk (umbilical artery), but sometimes these arteries arise directly from the internal iliac artery.