bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of quantitative trait loci for shank length and growth at different development stages in chicken
Authors: Gao Y. , Du Z.‐Q. , Feng C.‐G. , Deng X.‐M. , Li N. , Da Y. , Hu X.‐X. 
Published: November 2009

SummaryShank length affects chicken leg health and longer shanks are a source of leg problems in heavy‐bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F2 chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t, while developmental QTL affected shank growth from time t−1 to time t. Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2–3, 4–5, 5–6, 10–11 and 11–12. A static QTL and a developmental QTL (SQSL1 and DQSL2) were identified at GGA2 (between ADL0190 and ADL0152). SQSL1 explained 2.87–5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.
QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus)
Authors: Miles L. G. , Isberg S. R. , Thomson P. C. , Glenn T. C. , Lance S. L. , Dalzell P. , Moran C. 
Published: November 2009

SummaryThe recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome‐wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex‐specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib‐pair analysis to take advantage of our full‐sib pedigree structure, together with a half‐sib analysis to account for, and take advantage of, the large difference in sex‐specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non‐avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.
A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers
Authors: Cheng L. , Liu L. , Yu X. , Wang D. , Tong J. 
Published: November 2009

SummaryCommon carp (Cyprinus carpio) is an important fish for aquaculture, but genomics of this species is still in its infancy. In this study, a linkage map of common carp based on Amplified Fragment Length Polymorphism (AFLP) and microsatellite (SSR) markers has been generated using gynogenetic haploids. Of 926 markers genotyped, 151 (149 AFLPs, two SSRs) were distorted and eliminated from the linkage analyses. A total of 699 AFLP and 20 microsatellite (SSR) markers were assigned to the map, which comprised 64 linkage groups and covered 5506.9 cM Kosambi, with an average interval distance of 7.66 cM Kosambi. The normality tests on interval map distances showed a non‐normal marker distribution. Visual inspection of the map distance distribution histogram showed a cluster of interval map distances on the left side of the chart, which suggested the occurrence of AFLP marker clusters. On the other hand, the lack of an obvious cluster on the right side showed that there were a few big gaps which need more markers to bridge. The correlation analysis showed a highly significant relatedness between the length of linkage group and the number of markers, indicating that the AFLP markers in this map were randomly distributed among different linkage groups. This study is helpful for research into the common carp genome and for further studies of genetics and marker‐assisted breeding in this species.
A shared 336 kb haplotype associated with the belt pattern in three divergent cattle breeds
Authors: Drögemüller C. , Demmel S. , Engensteiner M. , Rieder S. , Leeb T. 
Published: November 2009

SummaryWe recently mapped the belt mutation in Brown Swiss cattle to a 922 kb interval on BTA3. In this study, we analysed two additional cattle breeds with the belted phenotype: Galloway and Dutch Belted (Lakenvelder). By genotyping microsatellites in solid‐coloured and belted Galloways, we confirmed that the belt mutation in Galloways is strongly associated with the same chromosomal locus as in Brown Swiss cattle. Subsequently, we analysed 36 SNPs in the belt interval in three breeds. We identified a single belt‐associated haplotype for each of the analysed breeds. The three breed‐specific belt haplotypes share alleles in four blocks. Three of these blocks comprise only one single or two consecutive markers, while the largest shared haplotype block encompasses nine consecutive SNPs in a 336 kb interval. The large shared haplotype across divergent breeds suggests a common mutation for the belt phenotype in all three breeds. We identified a potential candidate gene within this interval coding for the developmental transcription factor HES6. We re‐sequenced the complete HES6 coding sequence in belted and solid‐coloured cattle but did not find belt‐associated polymorphisms. In conclusion, our data provide strong evidence in favour of a common founder for the belt phenotype in different cattle breeds and have resulted in an improved fine‐mapping of the causative mutation.
Y‐specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle
Authors: Pérez‐Pardal L. , Royo L. J. , Beja‐Pereira A. , Curik I. , Traoré A. , Fernández I. , Sölkner J. , Alonso J. , Álvarez I. , Bozzi R. , Chen S. , Ponce de León F. A. , Goyache F. 
Published: November 2009

SummaryFive cattle Y‐specific microsatellites, totalling six loci, were selected from a set of 44 markers and genotyped on 608 Bos taurus males belonging to 45 cattle populations from Europe and Africa. A total of 38 haplotypes were identified. Haplogroups (Y1 and Y2) previously defined using single nucleotide polymorphisms did not share haplotypes. Nine of the 27 Y2‐haplotypes were only present in African cattle. Network and correspondence analyses showed that this African‐specific subfamily clustered separately from the main Y2‐subfamily and the Y1 haplotypes. Within‐breed genetic variability was generally low, with most breeds (78%) showing haplotypes belonging to a single haplogroup. amova analysis showed that partitioning of genetic variation among breeds can be mainly explained by their geographical and haplogroup assignment. Between‐breed genetic variability summarized via Principal Component Analysis allowed the identification of three principal components explaining 94.2% of the available information. Projection of principal components on geographical maps illustrated that cattle populations located in mainland Europe, the three European Peninsulas and Mediterranean Africa presented similar genetic variation, whereas those breeds from Atlantic Europe and British Islands (mainly carrying Y1 haplotypes) and those from Sub‐Saharan Africa (belonging to Y2‐haplogroup) showed genetic variation of a different origin. Our study confirmed the existence of two large Y‐chromosome lineages (Y1 and Y2) in taurine cattle. However, Y‐specific microsatellites increased analytical resolution and allowed at least two different Y2‐haplotypic subfamilies to be distinguished, one of them restricted to the African continent.
Autoantibody-mediated regulation of B cell responses by functional anti-CD22 autoantibodies in patients with systemic sclerosis
Authors: Odaka M , Hasegawa M , Hamaguchi Y , Ishiura N , Kumada S , Matsushita T , Komura K , Sato S , Takehara K , Fujimoto M 
Published: November 2009

Summary
Studies have demonstrated that B cells play important roles in systemic sclerosis (SSc), especially through the CD19/CD22 autoimmune loop. CD22 is a B cell-specific inhibitory receptor that dampens B cell antigen receptor (BCR) signalling via tyrosine phosphorylation-dependent mechanism. In this study, we examined the presence and functional property of circulating autoantibodies reacting with CD22 in systemic sclerosis. Serum samples from 10 tight skin (TSK/+) mice and 50 SSc patients were assessed for anti-CD22 autoantibodies by enzyme-linked immunosorbent assays using recombinant mouse or human CD22. The association between anti-CD22 antibodies and clinical features was also investigated in SSc patients. Furthermore, the influence of SSc serum including anti-CD22 autoantibodies for CD22 tyrosine phosphorylation was examined by Western blotting using phosphotyrosine-specific antibodies reacting with four major tyrosine motifs of CD22 cytoplasmic domain. Anti-CD22 autoantibodies were positive in 80% of TSK/+ mice and in 22% of SSc patients. Patients positive for anti-CD22 antibodies showed significantly higher modified Rodnan skin thickness score compared with patients negative for anti-CD22 antibodies. Furthermore, anti-CD22 antibodies from patients' sera were capable of reducing phosphorylation of all four CD22 tyrosine motifs, while sera negative for anti-CD22 antibodies did not affect CD22 phosphorylation. Thus, a subset of SSc patients possessed autoantibodies reacting with a major inhibitory B cell response regulator, CD22. Because these antibodies can interfere CD22-mediated suppression onto B cell activation in vitro, SSc B cells produce functional autoantibodies that can enhance their own activation. This unique regulation may contribute to the autoimmune aspect of SSc.
Effects of land use on aquatic macrophyte diversity and water quality of ponds
Authors: AKASAKA MUNEMITSU , TAKAMURA NORIKO , MITSUHASHI HIROMUNE , KADONO YASURO 
Published: November 2009

Summary1. Aquatic macrophyte diversity and water quality of 55 ponds in western Japan were related to land use and morphometric variables to identify the environmental factors that sustain biodiversity and the spatial extent at which these factors operate.2. The relevant spatial extent for floating‐leaved macrophyte richness (500 m from pond edge) was larger than that for submerged macrophyte occurrence (10, 75 and 100 m), whereas emergent macrophyte richness was best explained at much larger extents (1000 m). Total macrophyte richness was explained at the extent of 500, 750 and 1000 m. The extents relevant for explaining the physicochemical condition of pond water (100 and 250 m) were similar to those for submerged and floating‐leaved macrophytes, suggesting that these two growth forms are more sensitive to water quality compared to emergent macrophytes.3. Diversity of all three growth forms and that of total macrophytes collectively were inversely related to turbidity and nutrient concentration; among the three growth forms, submerged macrophytes were most affected by water quality.4. Negative relationships were found between the proportion of urban area and the diversity of the three growth forms and that of total macrophytes and water quality. Species richness of emergent, floating‐leaved and total macrophytes decreased with depth and increased with surface area up to about 5000 m2, above which it declined.5. Urbanisation and enlargement of ponds were the two main factors that decreased aquatic macrophyte diversity in irrigation ponds. To alleviate the adverse effects of urban areas on aquatic macrophyte diversity, our results suggest that management efforts should focus on the creation of buffer zones within the relevant spatial extent from the pond edge.
Fish species richness in spring‐fed ponds: effects of habitat size versus isolation in temporally variable environments
Authors: UCHIDA YUKI , INOUE MIKIO 
Published: November 2009

Summary1. Species richness in a habitat patch is determined by immigration (regional) and extinction (local) processes, and understanding their relative importance is crucial for conservation of biodiversity. In this study, we applied the Island Biogeography concept to spring ponds connected to a river in southwestern Japan to examine how immigration and extinction processes interact to determine fish species richness in temporally variable environments.2. Fish censuses were conducted 15 times in 13 study ponds at 1–4 month intervals from August 1998 through October 2000. Effects of habitat size (pond area), isolation (distance from the river) and temporal environmental variability (water level fluctuation) on (i) species richness, (ii) immigration and extinction rates and (iii) population size and persistence of each fish species were assessed.3. The results revealed predominant effects of distance on species richness, immigration/extinction rates and population size and persistence. Species richness decreased with increasing distance but was not related to either pond area or water level fluctuation. A negative effect of distance on immigration rate was detected, while neither pond area nor water level fluctuation had significant effects on extinction rate. Further, population size and persistence of four species increased with decreasing distance, suggesting that, in ponds close to the river, immigrants from the river reduce the probability of extinction (i.e. provide a rescue effect), contributing to the maintenance of high species richness.4. Overall results emphasise the importance of immigration processes, rather than extinction, in shaping patterns of species richness in our system. The predominant importance of immigration was probably because of (i) high temporal variability that negates habitat‐size effects and (ii) continuous immigration that easily compensates for local extinctions. Our results suggest that consideration of regional factors (e.g. connectivity, locations of source populations and barriers to colonisation) is crucial for conservation and restoration of local habitats.
Expression of cyclin D1 and retinoblastoma protein in Paget’s disease of the vulva and breast: an immunohistochemical study of 108 cases
Authors: Ellis Patricia E , MacLean Allan B , Crow Julie C , Wong Te Fong L F , Rolfe Kerstin J , Perrett Christopher W 
Published: November 2009

Aims:  Loss of retinoblastoma protein expression and overexpression of cyclin D1 have been implicated in the development and progression of some cancers. Paget’s disease of the vulva (PDV) and Paget’s disease of the breast (PDB) are uncommon conditions and the pathogenesis of these diseases is still unclear. The aim was to examine the expression of the retinoblastoma and cyclin D1 proteins in PDV and PDB and to correlate any differences between PDV and PDB, and in the presence or absence of an underlying carcinoma.Methods and results:  Seventy‐two archival cases of PDV including 10 with invasive disease and 36 cases of PDB were evaluated immunohistochemically for the expression of cyclin D1 and retinoblastoma protein. Forty‐four percent (32/72) of cases of PDV showed loss of expression of the retinoblastoma protein, compared with 67% (24/36) of PDB cases. Fifty‐nine percent (41/69) of PDV overexpressed cyclin D1. In PDB, 8% (3/34) overexpressed cyclin D1. There were no significant differences in the expression of retinoblastoma and cyclin D1 in PDV cases with or without underlying invasive disease. There were significant differences between the expression of retinoblastoma (P = 0.03) and cyclin D1 (P < 0.001) in PDV compared with PDB.Conclusions:  The differences in the expression of cyclin D1 and retinoblastoma may indicate the differences in the pathogenesis of PDV and PDB.
Ketamine cystitis as a mimic of carcinoma in situ
Authors: Oxley Jon D , Cottrell Angela M , Adams Susan , Gillatt David 
Published: November 2009

Aims:  To describe the histopathological features of a series of patients with ketamine‐related cystitis.Methods and results:  Seventeen patients with ketamine‐related cystitis, who had undergone biopsy, were identified and reviewed. Twelve showed ulceration with significant urothelial atypia. In 10 of these, immunohistochemistry was performed; 9/10 had high p53 immunoreactivity and 7/10 had moderate to high levels of Ki67 reactivity, but all were negative for cytokeratin 20.Conclusions:  Ketamine can lead to reactive urothelial changes that can mimic carcinoma in situ, but the long‐term cancer risk remains unknown.
Activation of ERK, AKT and JNK signalling pathways in human schwannomas in situ
Authors: Hilton David A , Ristic Natalia , Hanemann Clemens O 
Published: November 2009

Aims:  Schwannomas are common tumours that may be multiple in neurofibromatosis type 2, when they may be difficult to treat without significant morbidity using surgery and radiosurgery. Previous in vitro work has suggested that merlin loss is associated with activation of the JNK/JUN, PI3K/AKT and MEK/ERK pathways and that these pathways may be susceptible to pharmacological inhibition. The aim was to investigate the expression of proteins involved in these pathways in human schwannomas in situ.Methods and results:  Immunohistochemistry using antibodies to AKT, pAKT, MEK, pMEK, ERK, pERK, JUN and pJUN was applied to 16 schwannomas (sporadic and NF2), and the results were compared with those seen in traumatic neuromas. Increased expression of pMEK, pERK and pJUN was seen in the schwannomas samples and of pAKT in schwannomas and controls.Conclusions:  These findings provide further direct evidence for activation of the JNK/JUN, PI3K/AKT and MEK/ERK signalling pathways in schwannomas and support the development of therapeutic agents directed against these pathways for the treatment of this group of tumours.
Soy, phyto‐oestrogens and male reproductive function: a review
Authors: Cederroth Christopher R. , Auger Jacques , Zimmermann Céline , Eustache Florence , Nef Serge 
Published: November 2009

SummaryThere is growing interest in the possible health threat posed by the effects of endocrine disruptors on reproduction. Soy and soy‐derived products contain isoflavones that mimic the actions of oestrogens and may exert adverse effects on male fertility. The purpose of this review was to examine the evidence regarding the potential detrimental effects of soy and phyto‐oestrogens on male reproductive function and fertility in humans and animals. Overall, there are some indications that phyto‐oestrogens, alone or in combination with other endocrine disruptors, may alter reproductive hormones, spermatogenesis, sperm capacitation and fertility. However, these results must be interpreted with care, as a result of the paucity of human studies and as numerous reports did not reveal any adverse effects on male reproductive physiology. Further investigation is needed before a firm conclusion can be drawn. In the meantime, caution would suggest that perinatal phyto‐oestrogen exposure, such as that found in infants feeding on soy‐based formula, should be avoided.
Differences in mouse models of diabetes mellitus in studies of male reproduction
Authors: O’Neill J. , Czerwiec A. , Agbaje I. , Glenn J. , Stitt A. , McClure N. , Mallidis C. 
Published: November 2009

SummaryDiabetes Mellitus (DM) has been found to have subtle yet profound effects on the metabolic status of the testis, the expression of numerous spermatogenic genes and is associated with increased numbers of sperm with nuclear DNA damage. The precise mechanism causing these detrimental effects remains unknown. The presence of increased levels of the most prominent member (carboxymethyllysine – CML) of the advanced glycation end product adducts and their receptor (RAGE) in the reproductive tract of DM men has provided a new avenue for research. As there are suspicions that the antibiotic (streptozotocin – STZ) employed to induce DM is also capable of causing oxidative stress and DNA damage, we compared CML and RAGE levels in the reproductive tract and sperm nDNA status of STZ mice with the levels in the Ins2Akita mouse to determine which more closely mimics the situation described in the human diabetic. CML was observed in the testes, epididymes and sperm of all animals. Sperm from DM mice showed particularly strong CML immunolocalization in the acrosomal cap, the equatorial region and whenever present, cytoplasmic droplets. Although increased, the level of CML on the sperm of the STZ and Ins2Akita DM mice did not reach statistical significance. RAGE was present on the developing acrosome and epididymal sperm of all animals and in discrete regions of the epididymes of the DM models. Only the epididymal sperm of the Ins2Akita mice were found to have significantly increased (p < 0.0001) nDNA damage. The Ins2Akita mouse therefore appears to more accurately reflect the conditions found in the human and, as such, is a more representative model for the study of diabetes and glycation’s influence on male fertility.