bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species delimitation, phylogenetic relationships, and two new species in the Cuscuta gracillima complex (Convolvulaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Costea Mihai , Aiston Fiona , Stefanović Saša 
Published: July 2008

Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the nuclear internal transcribed spacer (ITS) regions were used to delimit the species of a recently circumscribed clade of Cuscuta (Convolvulaceae) and to investigate their phylogenetic relationships. This clade comprises the Cuscuta gracillima complex from Mexico, Central and northern South America, a group which is characterized by inflorescences that appear to emerge directly from the host stem. Eight lineages are recognized, with two of them described here as new species: Cuscuta punana Costea & Stefanović, sp. nov. from Ecuador and Cuscuta vandevenderi Costea & Stefanović, sp. nov. from Mexico. Cuscuta colombiana Yunck is redefined to include Cuscuta aristeguietae Yunck., and Cuscuta deltoidea Yunck. is broadened to encompass Cuscuta serruloba Yunck. A taxonomic treatment with an identification key, descriptions, and illustrations is provided; the biogeography and conservation status of the eight species are also discussed.
Morphological, biological, and molecular characteristics of the diatomPseudo-nitzschia delicatissimafrom the Canadian MaritimesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Kaczmarska Irena , Reid Charlotte , Martin Jennifer L. , Moniz Mónica B.J. 
Published: July 2008

Forty-six monoclonal cultures of the diatom Pseudo-nitzschia delicatissima (Cleve) Heiden were isolated from coastal waters of Eastern Canada. Of these, 12 clones were successfully sexualized. The range of their morphological and genetic divergence was used as a reference for clones whose sexual identity remains unknown. All characters that were examined, including valve morphology, the nuclear internal transcribed spacer (ITS) region, and mitochondrial cytochrome c oxidase (cox1) sequences, showed a high degree of similarity within and between mating and nonsexualized clones. Within the 638 bp long aligned fragment in the ITS region, only five variable sites were found and just two were found within the 576 bp fragment of cox1 near the 5′ terminus of the gene. Our own data and those retrieved from GenBank suggest that the northern North Atlantic is populated by a single metapopulation of genetically very similar P. delicatissima, as determined using the ITS sequence of the epitype of the species. The ITS region of our clones was distinct from ITS-types present in isolates that we will refer to as P. delicatissima-like diatoms from the Mediterranean Sea and other low latitude Atlantic sites, thereby providing a means to discriminate between otherwise morphologically indistinguishable (cryptic) species. Such a distribution pattern suggests different physiological and environmental requirements for mating optima. This work furthers our understanding of the relationship between biological, molecular, and morphological species boundaries in diatoms and their ecology, and contributes to evaluation of the utility of ITS and cox1 sequences in DNA barcoding of diatoms.
A survey ofPenicillium brevicompactumandP. bialowiezensefrom indoor environments, with commentary on the taxonomy of theP. brevicompactumgroupThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Scott James A. , Wong Bess , Summerbell Richard C. , Untereiner Wendy A. 
Published: July 2008

We investigated the diversity of the Penicillium brevicompactum Dierckx group in dust from 54 houses in Wallaceburg, Ontario, Canada. Two taxa were predominant, P. brevicompactum and Pencillium bialowiezense Zaleski, accounting for 88.6% and 5.4% of the sample set, respectively. We further characterized multilocus haplotypes of isolates by characterizing three polymorphic genetic loci, β-tubulin (benA), histone 4 (his4A), and the internal transcribed spacer regions of ribosomal DNA (nucITS) amplified by PCR amplification and screened using heteroduplex mobility assay (HMA). Eight unique haplotypes were observed in P. brevicompactum s. str., and two in P. bialowiezense, both with a distribution characteristic of a predominantly clonal reproduction mode. Phylogenetic analysis of the β-tubulin and nucITS loci were carried out for members of the P. brevicompactum group, including ex-type material, that revealed three well-supported lineages corresponding to P. brevicompactum, P. bialowiezense (=Penicillium biourgeianum Zaleski), and Penicillium neocrassum R. Serra & S.W. Peterson. The mycophilic nature of many isolates of P. bialowiezense, and some isolates of P. brevicompactum, suggests that observation of members of the P. brevicompactum group in indoor environments may predict extensive and longterm fungal colonization. We also address some nomenclatural problems in the group and epitypify P. bialowiezense.
Repair Site Integrity after Arthroscopic Transosseous-Equivalent Suture-Bridge Rotator Cuff Repair
Authors: Frank Joshua B. , ElAttrache Neal S. , Dines Joshua S. , Blackburn Allie , Crues John , Tibone James E. 
Published: July 2008

Background Successful healing after arthroscopic rotator cuff repair remains a challenge. Earlier studies have shown a relatively high rate of failure. New surgical techniques may improve healing potential. The purpose of this study was to provide an objective evaluation of repair site integrity after arthroscopic transosseous-equivalent suture-bridge rotator cuff repair. Hypothesis Rotator cuff tears repaired using the transosseous-equivalent suture-bridge technique will show a higher intact rate on postoperative magnetic resonance imaging (MRI) evaluation. Study Design Case series; Level of evidence, 4. Methods The first 25 patients who underwent arthroscopic rotator cuff repair using the transosseous-equivalent suture-bridge technique underwent MRI evaluation of the postoperative shoulder. Minimum follow-up was 1 year. Demographic, clinical, and surgical factors, including tear size, were evaluated. Results Postoperative MRI demonstrated intact surgical repair sites in 22 of 25 patients (88%). Tears limited to the supraspinatus tendon were intact in 16 of 18 patients (89%). Tears of the supraspinatus involving part or all of the infraspinatus showed an 86% intact rate (6 of 7 patients). Of these tears, 3 were considered massive (complete 2-tendon or greater). These demonstrated an intact cuff on MRI. Conclusions The transosseous-equivalent suture-bridge technique demonstrates a high healing rate on imaging studies at 1 year. Of the first 25 patients repaired with the technique, 88% had an intact rotator cuff repair on MRI evaluation. This indicates excellent cuff healing, as judged by the intact repair sites, compared with most standard arthroscopic rotator cuff repair series. In this early report of the technique, a persistent tear could not be correlated with age or initial tear size; however, this may be due to the relatively small sample size.
Transplantation of De Novo Scaffold-Free Cartilage Implants into Sheep Knee Chondral Defects
Authors: Jubel Axel , Andermahr Jonas , Schiffer Gereon , Fischer Jürgen , Rehm Klaus E. , Stoddart Martin J. , Häuselmann Hans J. 
Published: July 2008

Background New cell-based treatments for articular cartilage repair are needed. As the optimal scaffold for cartilage repair has yet to be developed, scaffold-free cartilage implants may remove the complications caused by suboptimal scaffolds. Hypothesis The implantation of a scaffold-free, autologous de novo cartilage implant into standardized full-thickness cartilage defects of femoral condyles in sheep leads to a qualitatively better regenerative tissue than does periosteal flap alone or no treatment. Study Design Controlled laboratory study. Methods Chondral defects 4 mm in diameter (1 per sheep) were created in the center of 1 medial femoral condyle of 48 sheep. Twelve defects were allowed to heal spontaneously, 16 defects were covered with periosteal flaps alone, and 20 defects were filled with autologous de novo cartilage graft and overlaid with a periosteal flap. Differences were assessed macroscopically using the International Cartilage Repair Society score and microscopically using the International Cartilage Repair Society histological score and Mankin score at 26 and 52 weeks. Results The results of the International Cartilage Repair Society Cartilage repair assessment showed that the transplant group was better than was the untreated control at both time periods but not significantly different than was the periosteal flap group. Implanted groups demonstrated a marked improvement in grade of defect filling, cartilage stability, cell distribution, and matrix assessments in each method of assessment. In the transplant group, 2 defects were filled with hyaline cartilage, 5 with mixed hyaline and fibrocartilage, and 2 with fibrocartilage alone. Conclusion Chondral defects treated with de novo cartilage transplantation show qualitatively better microscopic and macroscopic regeneration than do those treated with periosteal flaps alone. Clinical Relevance Results of the current study show that third-generation autologous chondrocyte transplantation is a promising development in the field of biologic cartilage regeneration. Future studies should compare this technique with the original Brittberg technique.
Repair of the Ruptured Distal Biceps Tendon
Authors: Chavan Prithviraj R. , Duquin Thomas R. , Bisson Leslie J. 
Published: July 2008

Background Reinsertion of the acutely ruptured distal biceps is the preferred method of treatment for most patients and is designed to restore flexion and supination strength. It is not clear which, if any, method of fixation is superior or whether a 2-incision or single-incision approach is associated with fewer complications or better outcomes. Hypotheses (1) There is no difference in biomechanical performance between currently used fixation methods, (2) there is no difference in incidence of complications between the 2-incision and single-incision approach, and (3) there is no difference in clinical outcomes between the 2-incision and single-incision approach. Study Design Systematic review; Level of evidence, 4. Methods The authors performed a systematic review of the literature studying treatment of the ruptured distal biceps tendon to determine optimal fixation method as well as surgical approach with lowest incidence of complications and highest proportion of satisfactory results. Results The review identified 8 articles that had relevant biomechanical data, 23 with relevant complication data, and 19 with relevant clinical results data. EndoButton fixation performed best in comparative biomechanical studies. There was no difference in overall incidence of complications between 2-incision approaches (16%) and single-incision approaches (18%), but there were significantly more instances of significant loss of forearm rotation with the 2-incision approach. There were significantly more unsatisfactory clinical results in the 2-incision repair group (31 % vs 6%; odds ratio, 7.6; 95% confidence interval, 3.2-17.7), with the majority of unsatisfactory results in the 2-incision group due to loss of forearm rotation or rotational strength. Conclusion EndoButton fixation has the highest load and stiffness of currently available fixation methods. Two-incision repairs have a significantly greater proportion of unsatisfactory results than do single-incision repairs.
Molecular analysis of t(15;17) genomic breakpoints in secondary acute promyelocytic leukemia arising after treatment of multiple sclerosis
Authors: Hasan Syed Khizer , Mays Ashley N. , Ottone Tiziana , Ledda Antonio , La Nasa Giorgio , Cattaneo Chiara , Borlenghi Erika , Melillo Lorella , Montefusco Enrico , Cervera José , Stephen Christopher , Satchi Gnanam , Lennard Anne , Libura Marta , Byl Jo Ann W. , Osheroff Neil , Amadori Sergio , Felix Carolyn A. , Voso Maria Teresa , Sperr Wolfgang R. , Esteve Jordi , Sanz Miguel A. , Grimwade David , Lo-Coco Francesco 
Published: July 2008

AbstractTherapy-related acute promyelocytic leukemia (t-APL) with t(15;17) translocation is a well-recognized complication of cancer treatment with agents targeting topoisomerase II. However, cases are emerging after mitoxantrone therapy for multiple sclerosis (MS). Analysis of 12 cases of mitoxantrone-related t-APL in MS patients revealed an altered distribution of chromosome 15 breakpoints versus de novo APL, biased toward disruption within PML intron 6 (11 of 12, 92% vs 622 of 1022, 61%: P = .035). Despite this intron spanning approximately 1 kb, breakpoints in 5 mitoxantrone-treated patients fell within an 8-bp region (1482-9) corresponding to the “hotspot” previously reported in t-APL, complicating mitoxantrone-containing breast cancer therapy. Another shared breakpoint was identified within the approximately 17-kb RARA intron 2 involving 2 t-APL cases arising after mitoxantrone treatment for MS and breast cancer, respectively. Analysis of PML and RARA genomic breakpoints in functional assays in 4 cases, including the shared RARA intron 2 breakpoint at 14 446-49, confirmed each to be preferential sites of topoisomerase IIα-mediated DNA cleavage in the presence of mitoxantrone. This study further supports the presence of preferential sites of DNA damage induced by mitoxantrone in PML and RARA genes that may underlie the propensity to develop this subtype of leukemia after exposure to this agent.
Generation of enhanced stability factor VIII variants by replacement of charged residues at the A2 domain interface
Authors: Wakabayashi Hironao , Varfaj Fatbardha , DeAngelis Jennifer , Fay Philip J. 
Published: July 2008

AbstractFactor VIII consists of a heavy chain (A1A2B domains) and light chain (A3C1C2 domains), whereas the contiguous A1A2 domains are separate subunits in the cofactor, factor VIIIa. The intrinsic instability of the cofactor results from weak affinity interactions of the A2 subunit within factor VIIIa. The charged residues Glu272, Asp519, Glu665, and Glu1984 appear buried at the interface of the A2 domain with either the A1 or A3 domain, and thus may impact protein stability. To determine the effects of these residues on procofactor/cofactor stability, these residues were individually replaced with either Ala or Val, and stable BHK cell lines expressing the B-domainless proteins were prepared. Specific activity and thrombin generation parameters for 7 of the 8 variants were more than 80% the wild-type value. Factor VIII activity at 52°C to 60°C and the decay of factor VIIIa activity after thrombin activation were monitored. Six of the 7 variants showing wild-type-like activity demonstrated enhanced stability, with the Glu1984Val variant showing a 2-fold increase in thermostability and an approximately 4- to 8-fold increase in stability of factor VIIIa. These results indicate that replacement of buried charged residues is an effective alternative to covalent modification in increasing factor VIII (VIIIa) stability.
Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
Authors: Botton Alessandro , Galla Giulio , Conesa Ana , Bachem Christian , Ramina Angelo , Barcaccia Gianni 
Published: July 2008

Abstract

Background
After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology.

Results
Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species.

Conclusion
Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.
Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer
Authors: Heinonen Henna , Nieminen Anni , Saarela Matti , Kallioniemi Anne , Klefström Juha , Hautaniemi Sampsa , Monni Outi 
Published: July 2008

Abstract

Background
The 70 kDa ribosomal protein S6 kinase (RPS6KB1), located at 17q23, is amplified and overexpressed in 10–30% of primary breast cancers and breast cancer cell lines. p70S6K is a serine/threonine kinase regulated by PI3K/mTOR pathway, which plays a crucial role in control of cell cycle, growth and survival. Our aim was to determine p70S6K and PI3K/mTOR/p70S6K pathway dependent gene expression profiles by microarrays using five breast cancer cell lines with predefined gene copy number and gene expression alterations. The p70S6K dependent profiles were determined by siRNA silencing of RPS6KB1 in two breast cancer cell lines overexpressing p70S6K. These profiles were further correlated with gene expression alterations caused by inhibition of PI3K/mTOR pathway with PI3K inhibitor Ly294002 or mTOR inhibitor rapamycin.

Results
Altogether, the silencing of p70S6K altered the expression of 109 and 173 genes in two breast cancer cell lines and 67 genes were altered in both cell lines in addition to RPS6KB1. Furthermore, 17 genes including VTCN1 and CDKN2B showed overlap with genes differentially expressed after PI3K or mTOR inhibition. The gene expression signatures responsive to both PI3K/mTOR pathway and p70S6K inhibitions revealed previously unidentified genes suggesting novel downstream targets for PI3K/mTOR/p70S6K pathway.

Conclusion
Since p70S6K overexpression is associated with aggressive disease and poor prognosis of breast cancer patients, the potential downstream targets of p70S6K and the whole PI3K/mTOR/p70S6K pathway identified in our study may have diagnostic value.
Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase
Authors: Santini Sébastien , Monchois Vincent , Mouz Nicolas , Sigoillot Cécile , Rousselle Tristan , Claverie Jean-Michel , Abergel Chantal 
Published: July 2008

Abstract

Background
In search of new antifungal targets of potential interest for pharmaceutical companies, we initiated a comparative genomics study to identify the most promising protein-coding genes in fungal genomes. One criterion was the protein sequence conservation between reference pathogenic genomes. A second criterion was that the corresponding gene in Saccharomyces cerevisiae should be essential. Since thiamine pyrophosphate is an essential product involved in a variety of metabolic pathways, proteins responsible for its production satisfied these two criteria.

Results
We report the enzymatic characterization and the crystallographic structure of the Candida albicans Thiamine pyrophosphokinase. The protein was co-crystallized with thiamine or thiamine-PNP.

Conclusion
The presence of an inorganic phosphate in the crystallographic structure opposite the known AMP binding site relative to the thiamine moiety suggests that a second AMP molecule could be accommodated in the C. albicans structure. Together with the crystallographic structures of the enzyme/substrate complexes this suggests the existence of a secondary, less specific, nucleotide binding site in the Candida albicans thiamine pyrophosphokinase which could transiently serve during the release or the binding of ATP. The structures also highlight a conserved Glutamine residue (Q138) which could interact with the ATP α-phosphate and act as gatekeeper. Finally, the TPK/Thiamine-PNP complex is consistent with a one step mechanism of pyrophosphorylation.