bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural selection on PHYE by latitude in the Japanese archipelago: insight from locus specific phylogeographic structure in Arcterica nana (Ericaceae)
Authors: IKEDA HAJIME , SETOGUCHI HIROAKI 
Published: June 2010

AbstractPhytochromes play a key role in allowing plants to monitor their surrounding environment and, conversely, adaptation to local environments has driven the evolutionary history of phytochromes. As a result of natural selection, polymorphisms in phytochrome genes would thus be expected to exhibit locus‐specific phylogeographic structure. To evaluate this hypothesis, we conducted a phylogeographic investigation based on four nuclear genes, including two phytochrome genes (PHYB and PHYE) using 155 samples of Arcterica nana from the entire range of the Japanese archipelago. Bayesian clustering revealed geographic differentiation between northern and southern Japan when all four genes were included. However, this geographic differentiation is inconsistent with previously reported genetic structure of genome‐wide polymorphisms based on amplified fragment length polymorphisms, as these did not show geographic differentiation throughout the Japanese archipelago. In contrast, the north–south differentiation was not apparent when PHYE was excluded. This indicates that PHYE alone could be responsible for the north–south differentiation (FCT = 0.15, P < 0.001). Furthermore, a single nonsynonymous polymorphism (C360T) strongly contributed to geographic differentiation (FCT = 0.57, P < 0.001) and its corresponding amino acid replacement (P120L) was significantly under positive selection based on maximum likelihood analysis (P = 0.98). Consequently, the locus‐specific geographic differentiation in PHYE could be caused by natural selection, suggesting the involvement of PHYE in local adaptation between populations of A. nana in northern and southern Japan. This finding is consistent with a previous study on Cardamine nipponica, indicating the importance of PHYE for local adaptation in Japanese alpine plants.
Passing the baton between laps: adhesion and cohesion in Pseudomonas putida biofilms
Authors: Fuqua Clay 
Published: June 2010

SummaryLarge externalized, repeat‐rich proteins are emerging as important factors in the attachment of bacteria to biotic and abiotic surfaces. An intriguing new study of the plant‐associated terrestrial microbe Pseudomonas putida by Manuel Espinosa‐Urgel's group that is reported in this issue of Molecular Microbiology has revealed that LapF, a huge protein (> 6000 aa) associated with the cell surface, is required for microcolony assembly from single attached cells, and in turn, formation of biofilms. Mutants defective in IapF exhibit competitive deficiencies in the rhizosphere. On both biotic and abiotic surfaces, these mutants undergo normal irreversible attachment, but cannot advance beyond this point to form multicellular clusters. The lapF phenotype is nutritionally conditional and is only manifested under a subset of growth regimes. Accordingly, lapF gene expression is controlled by the stress‐responsive sigma factor RpoS and is elevated within growing microcolonies on abiotic surfaces and plant tissues. Earlier work had identified the LapA protein, another enormous cell surface protein (> 8000 aa), as a key requirement for the reversible to irreversible transition during attachment. The current findings support a model in which LapA and LapF act in a relay to drive the stable colonization of surfaces and subsequent assembly of the multicellular structures.
The Actinomyces oris type 2 fimbrial shaft FimA mediates co‐aggregation with oral streptococci, adherence to red blood cells and biofilm development
Authors: Mishra Arunima , Wu Chenggang , Yang Jinghua , Cisar John O. , Das Asis , Ton‐That Hung 
Published: June 2010

SummaryInterbacterial interactions between oral streptococci and actinomyces and their adherence to tooth surface and the associated host cells are key early events that promote development of the complex oral biofilm referred to as dental plaque. These interactions depend largely on a lectin‐like activity associated with the Actinomyces oris type 2 fimbria, a surface structure assembled by sortase (SrtC2)‐dependent polymerization of the shaft and tip fimbrillins, FimA and FimB respectively. To dissect the function of specific fimbrillins in various adherence processes, we have developed a convenient new technology for generating unmarked deletion mutants of A. oris. Here, we show that the fimB mutant, which produced type 2 fimbriae composed only of FimA, like the wild type co‐aggregated strongly with receptor‐bearing streptococci, agglutinated with sialidase‐treated red blood cells, and formed monospecies biofilm. In contrast, the fimA and srtC2 mutants lacked type 2 fimbriae and were non‐adherent in each of these assays. Plasmid‐based expression of the deleted gene in respective mutants restored adherence to wild‐type levels. These findings uncover the importance of the lectin‐like activity of the polymeric FimA shaft rather than the tip. The multivalent adhesive function of FimA makes it an ideal molecule for exploring novel intervention strategies to control plaque biofilm formation.
Genome‐wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation
Authors: GAO LEXUAN , GENG YUPENG , LI BO , CHEN JIAKUAN , YANG JI 
Published: June 2010

ABSTRACT Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome‐wide methylation profiling using methylation‐sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome‐wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors.
A founder mutation in BBS2 is responsible for Bardet‐Biedl syndrome in the Hutterite population: utility of SNP arrays in genetically heterogeneous disorders
Authors: Innes AM , Boycott KM , Puffenberger EG , Redl D , MacDonald IM , Chudley AE , Beaulieu C , Perrier R , Gillan T , Wade A , Parboosingh JS 
Published: June 2010

Innes AM, Boycott KM, Puffenberger EG, Redl D, MacDonald IM, Chudley AE, Beaulieu C, Perrier R, Gillan T, Wade A, Parboosingh JS. A founder mutation in BBS2 is responsible for Bardet‐Biedl syndrome in the Hutterite population: utility of SNP arrays in genetically heterogeneous disorders.Bardet‐Biedl syndrome (BBS) is a multisystem genetically heterogeneous disorder, the clinical features of which are largely the consequence of ciliary dysfunction. BBS is typically inherited in an autosomal recessive fashion, and mutations in at least 14 genes have been identified. Here, we report the identification of a founder mutation in the BBS2 gene as the cause for the increased incidence of this developmental disorder in the Hutterite population. To ascertain the Hutterite BBS locus, we performed a genome‐wide single nucleotide polymorphism (SNP) analysis on a single patient and his three unaffected siblings from a Hutterite family. The analysis identified two large SNP blocks that were homozygous in the patient but not in his unaffected siblings, one of these regions contained the BBS2 gene. Sequence analysis and subsequent RNA studies identified and confirmed a novel splice site mutation, c.472‐2A>G, in BBS2. This mutation was also found in homozygous form in three subsequently studied Hutterite BBS patients from two different leuts, confirming that this is a founder mutation in the Hutterite population. Further studies are required to determine the frequency of this mutation and its role, if any, in the expression of other ciliopathies in this population.
Successful treatment of recurrent focal segmental glomerulosclerosis combined with calcineurin inhibitor nephrotoxicity four yr after kidney transplantation
Authors: Mitome Jun , Yamamoto Hiroyasu , Maruyama Yukio , Kobayashi Akimitsu , Yaginuma Tatsuhiro , Matsuo Nanae , Tanno Yudo , Hayakawa Hiroshi , Miyazaki Youichi , Yokoyama Keitaro , Utsunomiya Yasunori , Yamaguchi Yutaka , Hosoya Tatsuo 
Published: June 2010

Mitome J, Yamamoto H, Maruyama Y, Kobayashi A, Yaginuma T, Matsuo N, Tanno Y, Hayakawa H, Miyazaki Y, Yokoyama K, Utsunomiya Y, Yamaguchi Y, Hosoya T. Successful treatment of recurrent focal segmental glomerulosclerosis combined with calcineurin inhibitor nephrotoxicity four yr after kidney transplantation. Clin Transplant 2010: 24 (Suppl. 22): 48–53. © 2010 John Wiley & Sons A/S.Abstract:  A 31‐yr‐old Japanese man with end‐stage kidney disease caused by primary focal segmental glomerulosclerosis (FSGS) underwent living related kidney transplantation at the age of 26 yr. The allograft functioned well immediately after surgery, and we did not observe histological findings of rejection and recurrent FSGS in protocol biopsies at two months and one yr after transplantation. Four years after transplantation, the urine protein excretion reached 11 g/d, and the serum creatinine increased over 2.5 mg/dL. We diagnosed nephrotic syndrome due to recurrent FSGS with graft dysfunction and confirmed FSGS lesions with severe endothelial injury with an allograft biopsy, associated with calcineurin inhibitor (CNI) nephrotoxicity. Thereafter, we performed plasmapheresis and steroid therapy with subsequent low‐density lipoprotein adsorption, combined with the reduction of tacrolimus. The nephrotic syndrome improved dramatically with the multiple therapeutic approaches. Primary FSGS recurs frequently in patients immediately after kidney transplantation. Post‐transplant FSGS has various causes, such as recurrent primary disease, obesity, hyperfiltration, donor‐related nephrosclerosis, and CNI‐induced arteriolopathy. In the case of nephrotic syndrome after kidney transplantation, we should consider not only recurrent FSGS, but also CNI‐induced nephrotoxicity to determine the optimal treatment.
Induction of tolerance in clinical kidney transplantation
Authors: Kawai Tatsuo , Benedict Cosimi A. 
Published: June 2010

Kawai T, Benedict Cosimi A. Induction of tolerance in clinical kidney transplantation. Clin Transplant 2010: 24 (Suppl. 22): 2–5. © 2010 John Wiley & Sons A/S.Abstract:  Induction of donor‐specific tolerance has been an ultimate goal in organ transplantation. Although numerous regimens for the induction of allograft tolerance have been developed in rodents, their application to primates has been limited. The approaches that have been successfully applied in primates can be divided into (i) use of total lymphoid irradiation, (ii) costimulatory blockade, (iii) profound depletion of recipient T cells, (iv) infusion of regulatory cells and (v) donor bone marrow (DBM) infusion/transplantation. Among these approaches, successful allograft tolerance has been achieved in clinical kidney transplantation using DBM transplantation.
Histopathology of xenografts in pig to non‐human primate discordant xenotransplantation
Authors: Shimizu Akira , Yamada Kazuhiko 
Published: June 2010

Shimizu A, Yamada K. Histopathology of xenografts in pig to non‐human primate discordant xenotransplantation. Clin Transplant 2010: 24 (Suppl. 22): 11–15. © 2010 John Wiley & Sons A/S.Abstract:  Xenotransplantation could provide a solution to the critical shortage of organs for transplantation in humans. Swine have been proposed as a suitable donor species. Swine organs, however, when transplanted to primates, are rapidly rejected by hyperacute rejection (HAR) and acute humoral xenograft rejection (AHXR). Both HAR and AHXR are triggered by xenoreactive natural antibodies directed against a specific epitope (galactose α1‐3 galactose: Gal) on porcine vascular endothelium. In attempt to prevent HAR and AHXR, α1,3‐galactosyltransferase gene knockout (GalT‐KO) pigs have been produced. GalT‐KO pig organs do not express the Gal epitope (antigen), and it therefore can eliminate the anti‐Gal antibody – Gal antigen immunoreaction in xenotransplantation. We reported our initial study of kidney transplantation from GalT‐KO miniature swine to baboons with either immunosuppression protocol or with a tolerance inducing protocol. Here, we discussed the pathology of xenografts in GalT‐KO pig to non‐human primate kidney transplantation.
Plasma cell‐rich acute rejection after renal transplantation in a patient with pyoderma gangrenosum: a case report
Authors: Horie Katsunori , Fujita Takashi , Tsuyuki Mikito , Nishio Fumitoshi , Watanabe Tatsuaki , Kanou Yasuko , Kuzuya Akihiko , Sato Motoyoshi , Kinukawa Tsuneo 
Published: June 2010

Horie K, Fujita T, Tsuyuki M, Nishio F, Watanabe T, Kanou Y, Kuzuya A, Sato M, Kinukawa T. Plasma cell‐rich acute rejection after renal transplantation in a patient with pyoderma gangrenosum: a case report. Clin Transplant 2010: 24 (Suppl. 22): 39–43. © 2010 John Wiley & Sons A/S.Abstract:  A 40‐yr‐old female received a living‐related renal transplantation on January 29, 2008. She had type I diabetes mellitus and pyoderma gangrenosum (PG). Induction immunosuppressive therapy consisted of tacrolimus, mycophenolate mofetil, basiliximab, and prednisolone. Intravenous methylprednisolone pulse therapy was administered to prevent ulceration at the surgical site. The postoperative outcome was almost uneventful, and renal graft function was well preserved for 11 months. Her graft function deteriorated on December 24, 2008 and thus an episode biopsy was performed. The histopathological findings were consistent with plasma cell‐rich acute rejection (PCAR). During hospitalization, it was noted that the patient was non‐compliant. We then performed steroid pulse therapy, and her graft function and histological findings improved. This is the first report of PCAR in a patient with PG who received a renal allograft. It was thought that PCAR was triggered because of her non‐compliance. Thus, we should recognize the importance of enhancing compliance in transplant recipients.
Progressive interstitial fibrosis of kidney allograft early after transplantation from a non‐heart beating donor: possible role of persistent ischemic injury
Authors: Masutani Kohsuke , Kitada Hidehisa , Yamada Shunsuke , Tsuchimoto Akihiro , Noguchi Hideko , Tsuruya Kazuhiko , Katafuchi Ritsuko , Tanaka Masao , Iida Mitsuo 
Published: June 2010

Masutani K, Kitada H, Yamada S, Tsuchimoto A, Noguchi H, Tsuruya K, Katafuchi R, Tanaka M, Iida M. Progressive interstitial fibrosis of kidney allograft early after transplantation from a non‐heart beating donor: Possible role of persistent ischemic injury. Clin Transplant 2010: 24 (Suppl. 22): 70–74. © 2010 John Wiley & Sons A/S.Abstract:  The donor was 63‐yr‐old woman with subarachnoid hemorrhage. As she developed severe hypotension for more than four h before cardiac arrest, we biopsied the grafts and decided to transplant those kidneys. Recipient 1 was a 23‐yr‐old man on 13‐yr dialysis program. After 19 d of delayed graft function (DGF), we discontinued hemodialysis (HD). However, the decrease in serum creatinine (sCr) was poor. The minimum sCr was 4.3 mg/dL on post‐operative day (POD) 40, and increased to 6.5 mg/dL. The contralateral graft was transplanted to a 61‐yr‐old man (recipient 2) with 18‐yr HD. After 15 d of DGF period, sCr decreased gradually and has been stable at 1.9 mg/dL. In recipient 1, graft biopsies performed on POD 15, 69, and 110, revealed progressive interstitial fibrosis and tubular atrophy (IF/TA) without evidences of acute rejection, tacrolimus associated injury, reflux nephropathy, or viral nephropathy. The second biopsy on POD 69 showed typical findings of acute tubular necrosis. We compared the clinical courses of the two recipients because certain features of recipient 1, such as age, duration of HD, total ischemic time, and body size were advantageous, whereas graft function was poorer than that in recipient 2. Recipient 1 developed severe anemia following the dissociation of graft function from recipient 2. In this case, posttransplant anemia and lower blood pressure might promote IF/TA through persistent ischemic tubular damage, and positive CMV antigenemia and its treatment could promote anemia. Especially in the kidney allograft from a marginal donor, we should consider various factors to obtain a better graft outcome.
A case report of recurrence of mixed cryoglobulinemic glomerulonephritis in a renal transplant recipient
Authors: Takeda Asami , Ootsuka Yasuhiro , Suzuki Taisei , Yamauchi Yukako , Tsujita Makoto , Kawaguchi Takehiko , Horike Keiji , Oikawa Tadashi , Goto Norihiko , Nagasaka Takaharu , Watarai Yoshihiko , Uchida Kazuharu , Morozumi Kunio 
Published: June 2010

Takeda A, Ootsuka Y, Suzuki T, Yamauchi Y, Tsujita M, Kawaguchi T, Horike K, Oikawa T, Goto N, Nagasaka T, Watarai Y, Uchida K, Morozumi K. A case report of recurrence of mixed cryoglobulinemic glomerulonephritis in a renal transplant recipient. Clin Transplant 2010: 24 (Suppl. 22): 44–47. © 2010 John Wiley & Sons A/S.Abstract:  Recurrence of glomerulonephritis (GN) is one of the major risk factors of long‐surviving renal graft dysfunction. Cryoglobulinemic glomerulonephritis of hepatitis‐C virus (HCV)‐negative patient is a rare cause of end‐stage renal disease. There is little case report of recurrent cryoglobulinemic glomerulonephritis in negative HCV recipients after renal transplantation. We represent a renal allograft recipient of an interesting recurrent cryoglobulinemic glomerulonephritis. The patient was diagnosed with mixed cryoglobulinemic glomerulonephritis by kidney biopsy at the age of 32 . He had no HCV, HBV nor liver dysfunction. He received immunosuppressive therapy, however, was introduced to hemodialysis treatment after 13 yr. He received a cadaveric renal transplantation at the age of 50, and immunosuppressive treatment was started with ciclosporin, prednisolone and mycophenolate mofetil (MMF). Four yr after transplantation, he developed fever and purpura of lower limbs. His serum creatinine level did not increase, however, proteinuria, hematuria, hypocomplementemia, positive rheumatoid factor and mixed cryoglobulinemia were noted. Detailed analysis failed to reveal the composition of mixed cryoglobulinemia. The renal allograft biopsy showed membranoproliferative‐type GN with monocyte and polynuclear leukocyte accumulation of capillary loops and small cellular crescent. Immunofluorescent study showed C3, IgG and IgM deposition of mesangial and capillary pattern. Regardless of steroid pulse therapy, hypocomplementemia and positive rheumatoid factor did not improve. Ten yr after transplantation, he was affected by cellulitis and sepsis. Afterward, rising of serum creatinine and nephrotic range proteinuria developed. The allograft biopsy revealed advanced cryoglobulinemic glomerulonephritis with characteristic vascular lesions. Electron microscopy showed organized subendothelial deposits compatible with cryoglobulinemic glomerulonephritis and proteinaceous thrombus in arteriole.
Pseudogene rescue: an adaptive mechanism of codon reassignment
Authors: JOHNSON L. J. 
Published: June 2010

AbstractAlterations to the genetic code – codon reassignments – have occurred many times in life’s history, despite the fact that genomes are coadapted to their genetic codes and therefore alterations are likely to be maladaptive. A potential mechanism for adaptive codon reassignment, which could trigger either a temporary period of codon ambiguity or a permanent genetic code change, is the reactivation of a pseudogene by a nonsense suppressor mutant transfer RNA. I examine the population genetics of each stage of this process and find that pseudogene rescue is plausible and also readily explains some features of extant variability in genetic codes.
Bimodal pollination system of the bromeliad Aechmea nudicaulis involving hummingbirds and bees
Authors: Schmid S. , Schmid V. S. , Zillikens A. , Harter‐Marques B. , Steiner J. 
Published: June 2010

AbstractIn order to compare the effectiveness of birds and insects as pollinators, we studied the floral biology of the bromeliad Aechmea nudicaulis (L.) Grisebach in the biome of the Atlantic rain forest, southern Brazil. On Santa Catarina Island, flowering extends from mid‐September to the end of December, with diurnal anthesis. The reproductive system is obligatory xenogamy, thus pollinator‐dependent. Flowers secrete 31.84 μl of nectar per day, with a mean sugar concentration of 23.2%. Highest nectar volume and sugar concentration occur at the beginning of anthesis. Most floral traits are characteristic for ornithophily, and nectar production appears to be adapted to the energy demand of hummingbirds. Continued secretion of the sucrose‐dominated nectar attracts and binds visitors to inflorescences, strengthening trapline foraging behaviour. Experiments assessing seed set after single flower visits were performed with the most frequent visitors, revealing the hummingbird Thalurania glaucopis as the most effective pollen vector. In addition, bees are also functional pollinators, as substantiated by their high visitation frequency. We conclude that this pollination system is bimodal. Thus, there is redundancy in the pollination service provided by birds and bees, granting a high probability of successful reproduction in Ae. nudicaulis.
Effect of abandonment and plant classification on carbohydrate reserves of meadow plants
Authors: Janeček Š. , Lanta V. , Klimešová J. , Doležal J. 
Published: June 2010

AbstractWe studied the effect of cessation of management on carbohydrate reserves of plants in meadows with different environmental characteristics and plant composition. We recorded storage carbohydrates and seasonal changes for 40 plant species. We asked whether there are differences in responses of carbohydrate reserves in forbs versus graminoids and in plants storing starch versus plants storing osmotically active carbohydrates. We analysed belowground organs before the meadows were mown and at the end of the vegetation season in mown versus recently abandoned plots. Whereas starch and fructans were widely distributed, raffinose family oligosaccharides were the main carbohydrate reserves of the Lamiaceae and Plantago lanceolata. Properties of carbohydrate reserves differed between forbs and graminoids but no difference was found between plants storing starch versus osmotically active carbohydrates. Graminoids had lower carbohydrate concentrations than forbs. We observed a positive effect of mowing on carbohydrate concentrations of graminoids in the dry, calcium‐rich meadow and higher seasonal fluctuations of these values in the acid, wet meadow, suggesting that local factors and/or the species pool affect carbohydrate reserves. Despite local conditions, graminoids represent a distinct functional group in meadows from the point of view of their storage economy. We suggest that as well as growth, storage processes should also be considered for understanding the functioning of meadow plant communities.