To determine the origins of DNA sequences isolated from the rumen microbial ecosystem using a self-organizing map (SOM). DNA sequences other than 16S small subunit ribosomal RNA (SSU rRNA) gene ...sequences that were detected from the rumen were analysed by the SOM method reported by Abe et al. 2000, Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 365, 27-34. Because query sequences positioned by SOM were scattered on the master drawing of SOM, it was suggested that many DNA sequences isolated from the rumen were collected from a broad range of micro-organisms. Although the results obtained by SOM were similar to those obtained by the neighbour-joining (NJ) method, SOM was able to presume the phylotypes of the query sequences without information about the 16S SSU rRNA gene sequences and homology searches, and to reveal existence of novel micro-organisms deduced to be cellulolytic bacteria, archaea and methanotrophic bacterium. As the SOM method defined phylotypes of unreported rumen micro-organisms, it is presumed that these phylotypes would be involved in rumen fermentation in cooperation with known rumen micro-organisms. Moreover, it is demonstrated that SOM is a useful tool for affiliating DNA sequences, which have no matches in databases. Through SOM analysis, a better means of identifying rumen micro-organisms and estimating their roles in rumen function was provided.
We investigated the hierarchical genetic structure of SSR (simple sequence repeats) and cpDNA (chloroplast DNA) polymorphisms among and within populations of Primula sieboldii, a heterostylous clonal ...herb. Seven out of eight populations at the study site, located in a mountainous region of Nagano Prefecture, had each developed alongside a different stream, and the other occurred on a flat area 70 m from the nearest stream. The magnitude of genetic differentiation among streamside populations in maternally inherited cpDNA (Φ = 0.341) was much higher than that in biparentally inherited SSRs (Φ = 0.011). This result suggests that seed dispersal among streams was restricted, and pollen was the primary agent of gene flow among streamside populations. In contrast, genetic differentiation among subpopulations within streams were low at both markers (Φ = 0.053 for cpDNA, Φ = 0.025 for SSR). This low differentiation among subpopulations in cpDNA compared with that among streamside populations suggest that seed dispersal occur along the stream probably during flooding. This hypothesis was supported by the fact that in cpDNA haplotypes, no clear genetic structure was detected within the streamside population, while a significant genetic structure was found within 20 m in the nonstreamside population. Furthermore, within the streamside populations, two pairs of ramets with identical multilocus genotypes for eight SSR loci were distantly (> 50 m) distributed along the same streamside, suggesting dispersal of clonal propagule. Our study showed that the heterogeneity of the landscape can influence gene flow and hence spatial genetic structure.
Summary
We evaluated the effects of vardenafil on testicular androgen‐binding protein secretion (ABP). Bilaterally obstructed azoospermic (OA)‐men (n = 19) (group A) underwent unilateral testicular ...biopsy. A group of nonobstructed azoospermic (NOA)‐men (n = 68) (group B) underwent bilateral testicular biopsy. ABP secretion in vitro by testicular tissue was assessed in each participant of every group. In addition, intracytoplasmic sperm injection (ICSI) cycles were performed in several couples of group A or group B using frozen/thawed spermatozoa from the biopsy material. Ten OA‐men (group A1), 14 NOA‐men (group B1), and nine different NOA‐men (group B2) had been positive for spermatozoa in the biopsy but pregnancies were not achieved in the respective female partners. Men of groups A1, B1 and B2 were treated with vardenafil, vardenafil and l‐carnitine respectively. Then, the men of groups A1, B1 and B2 underwent a second testicular (unilateral) biopsy. Within the group A1 and within the group B1, ABP secretion rate was significantly larger after vardenafil treatment than prior to vardenafil treatment. In addition, fertilisation rates in ICSI cycles within groups A1 or B1 were not affected by vardenafil administration. Vardenafil administration in NOA‐men increased ABP secretion and did not affect detrimentally the presence of testicular foci of advanced spermatogenesis.
1. The effects of leaf display and biomass partitioning on light capture efficiency were examined in a non-branching understorey palm, Licuala arbuscula, by using a three-dimensional geometric ...simulation model. This species has several fan-shaped laminae, attached on long petioles at a mostly constant deflection angle (Dp). The petiole of the youngest leaf was almost vertical, and slanted downwards as it aged. 2. The combination of large Dpand small Zmax(zenith angle of the oldest leaf's petiole) maximized light capture for a plant with few leaves; this combination kept the lamina facing in the approximate direction of the zenith with high light intensity. For a plant with many leaves, the combination of large Zmaxand small Dpincreased light capture because it reduced self-shading. 3. For a given total leaf biomass, the plant increased its total leaf area by producing many small leaves. This occurred because the leaf area per unit biomass decreased with increasing biomass per individual leaf. This effect was most pronounced in larger plants. However, an increasing number of leaves intensified self-shading among leaves. Allocation of biomass to the petioles reduced self-shading, but decreased leaf area. 4. There was an optimal allocation of biomass to petioles and an optimal number of leaves that maximized the crown's light capture. Greater investment in petioles as the number of leaves increased was the favoured strategy for larger plants. 5. In most cases, the leaf geometry and biomass partitioning in the plants were close to the optima predicted by a simulation model developed in this study. There were noticeable differences in a few cases, but the reduction in the crown's light capture due to these differences was small.
Summary
Cryptorchidism, a common anomaly of the male genitalia, affects 2–4% of male infants. The post‐fertilization effects of unilateral cryptorchidism model in the rat and the effects of ...antioxidant treatment were investigated. Six‐week‐old male Wistar rats were randomly separated into four groups. Unilateral cryptorchidism was induced in the right testis of three groups. One group was treated with saline intraperitoneally (i.p.) (Crypto), one group was treated with taurine (500 mg/kg, i.p.; Tau), and another group was treated with sivelestat (15 mg/kg i.p.; Siv). The control group was treated with saline i.p. The treatment was daily for 8 weeks. Five days before sacrifice, mating studies were performed. Body, testicular, and epididymal weights were recorded. Malondialdehyde (MDA) levels in the seminal vesicular fluid (SVF) were measured. Testicular levels of MDA and 8‐hydroxy‐2′‐deoxyguanosine (8‐OHdG) were determined bilaterally. TUNEL assay was used to examine DNA fragmentation bilaterally. Histological examination and the Johnsen score were used to evaluate morphological testicular alterations. The Crypto group demonstrated significantly lower right testicular and epididymal weights, significantly increased SVF‐MDA levels, testicular MDA and 8‐OHdG levels, and the apoptotic score bilaterally compared to the controls. Furthermore, histological evaluation revealed significantly reduced spermatogenesis and mild injury to the cryptorchid testes compared to the control. Treatment with both taurine and sivelestat significantly reduced SVF‐MDA levels, testicular MDA, 8‐OHdG, and apoptosis bilaterally compared to the Crypto group. Antioxidant treatment was unable to ameliorate spermatogenesis. Newborns delivered by females that mated with Crypto‐males had significantly lower body weight compared with the respective animals from the control, Tau and Siv groups. The present study demonstrated that unilateral cryptorchidism‐induced testicular damage can significantly affect the contralateral testis as well having further deleterious post‐fertilization effect on the development of newborns. Treatment with antioxidants can partially improve the testicular damage bilaterally with beneficial effects for the newborns.
Summary
The aim of the study was to investigate the hypothesis that Y chromosome microdeletions are directly implicated in testicular maldescent. Genomic DNA was extracted from the peripheral blood ...of 292 subjects. This population consisted of (i) 180 children with all phenotypes of isolated (non‐syndromic) testicular maldescent from 174 index families, (ii) affected adult relatives available (n = 12) and (iii) 100 unrelated children with normal external genitalia (controls). The sequence‐tagged site primer set and the conditions of conventional polymerase chain reaction amplification were based on the current laboratory guidelines for molecular diagnosis of Y chromosome microdeletions recommended by the European Academy of Andrology and the European Molecular Genetics Quality Network. Two multiplex reactions were designed to screen the regions of azoospermic factors a, b and c. Each multiplex reaction included adequate internal and external amplification controls. Amplification products were submitted to electrophoresis on 2% agarose gel impregnated with ethidium bromide dye solution for 80 volt‐h and visualised under ultraviolet light. No microdeletions were detected in any subject. These results indicate that Y chromosome microdeletions are not directly implicated in the pathogenesis of testicular maldescent. Other factors should be investigated to potentially explain the genetic predisposition that seems to exist in at least a subgroup of these patients.
To detect sensor histidine protein kinases (HPKs) similar to accessory gene regulator C (AgrC) from the rumen microbial ecosystem. Genes related to sensor HPKs were amplified by PCR using two pairs ...of agrC-specfic primers from DNA extracted from bovine rumen contents. The PCR products were cloned, sequenced and phylogenetically analysed. It appeared that two sequences were HPKs. Although amino acid sequences deduced from the nucleotide sequences obtained in this study showed high similarities with sensor HPKs responding to citrate or C₄-dicarboxylates, they did not show high similarities with AgrC. This study revealed the presence in the rumen of sensor HPKs responding to citrate or C₄-dicarboxylates, which could stimulate rumen fermentation. Therefore, it has been shown that citrate or C₄-dicarboxylate metabolism is partially regulated by a two-component regulatory system in some rumen bacteria.
Summary
The aim of this family‐based study was to investigate the potential association/genetic linkage of the (TAAAA)n polymorphism of sex hormone‐binding globulin gene proximal promoter with ...testicular maldescent (TMD). Genomic DNA was extracted from the peripheral blood of 487 subjects (174 index families): (i) 180 children with all phenotypes of TMD, (ii) 307 parents (156 mothers and 151 fathers). Conventional polymerase chain reaction amplification products were electrophoresed on 10% nondenaturating polyacrylamide gel and visualised by silver staining. After excluding ambiguous parental–child trios and most cases of index families with missing parental genotypes, 429 individuals were left for analysis: 138 completely typed nuclear families (five included a second affected child) and five child–parent couples (one parent missing). Eight fathers presented history of TMD, that is, a total of 156 cases with TMD were analysed. Alleles were analysed with the affected family‐based control method and logistic regression‐based extension of the transmission disequilibrium test for multiallelic loci. (ΤΑΑΑΑ)n polymorphism analysis revealed six alleles based on repeat numbers (n = 5–10). No association/genetic linkage between the (TAAAA)n polymorphism and TMD was detected. Other factors should be investigated to potentially explain the genetic predisposition that seems to exist in at least a subgroup of these patients.
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