bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific expression of lacZ and cre recombinase in fetal thymic epithelial cells by multiplex gene targeting at the Foxn1 locus
Authors: Gordon Julie , Xiao Shiyun , Hughes Bernard , Su Dong-ming , Navarre Samuel P , Condie Brian G , Manley Nancy R 
Published: June 2007

Abstract

Background
Thymic epithelial cells (TECs) promote thymocyte maturation and are required for the early stages of thymocyte development and for positive selection. However, investigation of the mechanisms by which TECs perform these functions has been inhibited by the lack of genetic tools. Since the Foxn1 gene is expressed in all presumptive TECs from the early stages of thymus organogenesis and broadly in the adult thymus, it is an ideal locus for driving gene expression in differentiating and mature TECs.

Results
We generated two knock-in alleles of Foxn1 by inserting IRES-Cre or IRES-lacZ cassettes into the 3' UTR of the Foxn1 locus. We simultaneously electroporated the two targeting vectors to generate the two independent alleles in the same experiment, demonstrating the feasibility of multiplex gene targeting at this locus. Our analysis shows that the knockin alleles drive expression of Cre or lacZ in all TECs in the fetal thymus. Furthermore, the knockin alleles express Cre or lacZ in a Foxn1-like pattern without disrupting Foxn1 function as determined by phenotype analysis of Foxn1 knockin/Foxn1 null compound heterozygotes.

Conclusion
These data show that multiplex gene targeting into the 3' UTR of the Foxn1 locus is an efficient method to express any gene of interest in TECs from the earliest stage of thymus organogenesis. The resulting alleles will make possible new molecular and genetic studies of TEC differentiation and function. We also discuss evidence indicating that gene targeting into the 3' UTR is a technique that may be broadly applicable for the generation of genetically neutral driver strains.
Troponin T isoform expression is modulated during Atlantic Halibut metamorphosis
Authors: Campinho Marco A , Silva Nádia , Nowell Mari A , Llewellyn Lynda , Sweeney Glen E , Power Deborah M 
Published: June 2007

AbstractBackgroundFlatfish metamorphosis is a thyroid hormone (TH) driven process which leads to a dramatic change from a symmetrical larva to an asymmetrical juvenile. The effect of THs on muscle and in particular muscle sarcomer protein genes is largely unexplored in fish. The change inTroponin T(TnT), a pivotal protein in the assembly of skeletal muscles sarcomeres and a modulator of calcium driven muscle contraction, during flatfish metamophosis is studied.ResultsIn the present study five cDNAs for halibutTnTgenes were cloned; three were splice variants arising from a singlefast TnT(fTnT) gene; a fourth encoded a novel teleost specific fTnT-like cDNA (AfTnT) expressed exclusively in slow muscle and the fifth encoded the teleost specificsTnT2. THs modified the expression of halibutfTnTisoforms which changed from predominantly basic to acidic isoforms during natural and T4 induced metamorphosis. In contrast, expression of red muscle specific genes,AfTnTandsTnT2, did not change during natural metamorphosis or after T4 treatment. Prior to and after metamorphosis no change in the dorso-ventral symmetry or temporal-spatial expression pattern ofTnTgenes and muscle fibre organization occurred in halibut musculature.ConclusionMuscle organisation in halibut remains symmetrical even after metamorphosis suggesting TH driven changes are associated with molecular adaptations. We hypothesize that species specific differences inTnTgene expression in teleosts underlies different larval muscle developmental programs which better adapts them to the specific ecological constraints.
Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis
Authors: Abernathy Jason W , Xu Peng , Li Ping , Xu De-Hai , Kucuktas Huseyin , Klesius Phillip , Arias Covadonga , Liu Zhanjiang 
Published: June 2007

Abstract

Background
The ciliate protozoan Ichthyophthirius multifiliis (Ich) is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of this parasite has been lacking. To study gene expression involved in Ich pathogenesis and virulence, our goal was to generate expressed sequence tags (ESTs) for the development of a powerful microarray platform for the analysis of global gene expression in this species. Here, we initiated a project to sequence and analyze over 10,000 ESTs.

Results
We sequenced 10,368 EST clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate). Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons. These unique sequences represent over two million base pairs (~10% of Plasmodium falciparum genome, a phylogenetically related protozoan). BLASTX searches produced 2,518 significant (E-value < 10-5) hits and further Gene Ontology (GO) analysis annotated 1,008 of these genes. The ESTs were analyzed comparatively against the genomes of the related protozoa Tetrahymena thermophila and P. falciparum, allowing putative identification of additional genes. All the EST sequences were deposited by dbEST in GenBank (GenBank: EG957858–EG966289). Gene discovery and annotations are presented and discussed.

Conclusion
This set of ESTs represents a significant proportion of the Ich transcriptome, and provides a material basis for the development of microarrays useful for gene expression studies concerning Ich development, pathogenesis, and virulence.
Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
Authors: Li Ping , Peatman Eric , Wang Shaolin , Feng Jinian , He Chongbo , Baoprasertkul Puttharat , Xu Peng , Kucuktas Huseyin , Nandi Samiran , Somridhivej Benjaporn , Serapion Jerry , Simmons Micah , Turan Cemal , Liu Lei , Muir William , Dunham Rex , Brady Yolanda , Grizzle John , Liu Zhanjiang 
Published: June 2007

Abstract

Background
EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish.

Results
A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing.

Conclusion
The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.
Detection and mapping of homologous and homoeologous segments in homoeologous groups of allotetraploid cotton by BAC-FISH
Authors: Wang Kai , Guo Wangzhen , Zhang Tianzhen 
Published: June 2007

Abstract

Background
Cotton, as an allopolyploid species, contains homoeologous A and D subgenomes. The study of the homoeologous (duplicated) segments or chromosomes can facilitate insight into the evolutionary process of polyploidy and the development of genomic resources. Fluorescence in situ hybridization (FISH) using bacterial artificial chromosome (BAC) clones as probes has commonly been used to provide a reliable cytological technique for chromosome identification. In polyploids, it also presents a useful approach for identification and localization of duplicated segments. Here, two types of BACs that contained the duplicated segments were isolated and analyzed in tetraploid cotton by FISH.

Results
Homologous and homoeologous BACs were isolated by way of SSR marker-based selection and then used to develop BAC-FISH probes. Duplicated segments in homoeologous chromosomes were detected by FISH. The FISH and related linkage map results followed known reinforced the relationships of homoeologous chromosomes in allotetraploid cotton, and presented a useful approach for isolation of homoeologous loci or segments and for mapping of monomorphic loci. It is very important to find that the large duplicated segments (homologous BACs) do exist between homoeologous chromosomes, so the shot-gun approach for genome sequencing was unavailable for tetraploid cotton. However, without doubt, it will contain more information and promote the research for duplicated segments as well as the genome evolution in cotton.

Conclusion
These findings and the analysis method by BAC-FISH demonstrated the powerful nature and wide use for the genome and genome evolutionary researches in cotton and other polyploidy species.
Brucella suis urease encoded by ure 1 but not ure 2 is necessary for intestinal infection of BALB/c mice
Authors: Bandara Aloka B , Contreras Andrea , Contreras-Rodriguez Araceli , Martins Ana M , Dobrean Victor , Poff-Reichow Sherry , Rajasekaran Parthiban , Sriranganathan Nammalwar , Schurig Gerhardt G , Boyle Stephen M 
Published: June 2007

Abstract

Background
In prokaryotes, the ureases are multi-subunit, nickel-containing enzymes that catalyze the hydrolysis of urea to carbon dioxide and ammonia. The Brucella genomes contain two urease operons designated as ure 1 and ure 2. We investigated the role of the two Brucella suis urease operons on the infection, intracellular persistence, growth, and resistance to low-pH killing.

Results
The deduced amino acid sequence of urease-α subunits of operons-1 and -2 exhibited substantial identity with the structural ureases of alpha- and beta-proteobacteria, Gram-positive and Gram-negative bacteria, fungi, and higher plants. Four ure deficient strains were generated by deleting one or more of the genes encoding urease subunits of B. suis strain 1330 by allelic exchange: strain 1330Δure 1K (generated by deleting ureD and ureA in ure 1 operon), strain 1330Δure 2K (ureB and ureC in ure 2 operon), strain 1330Δure 2C (ureA, ureB, and ureC in ure 2 operon), and strain 1330Δure 1KΔure 2C (ureD and ureA in ure 1 operon and ureA, ureB, and ureC in ure 2 operon). When grown in urease test broth, strains 1330, 1330Δure 2K and 1330Δure 2C displayed maximal urease enzyme activity within 24 hours, whereas, strains 1330Δure 1K and 1330Δure 1KΔure 2C exhibited zero urease activity even 96 h after inoculation. Strains 1330Δure 1K and 1330Δure 1KΔure 2C exhibited slower growth rates in tryptic soy broth relative to the wild type strain 1330. When the BALB/c mice were infected intraperitoneally with the strains, six weeks after inoculation, the splenic recovery of the ure deficient strains did not differ from the wild type. In contrast, when the mice were inoculated by gavage, one week after inoculation, strain 1330Δure 1KΔure 2C was cleared from livers and spleens while the wild type strain 1330 was still present. All B. suis strains were killed when they were incubated in-vitro at pH 2.0. When the strains were incubated at pH 2.0 supplemented with 10 mM urea, strain 1330Δure 1K was completely killed, strain 1330Δure 2C was partially killed, but strains 1330 and 1330Δure 2K were not killed.

Conclusion
These findings suggest that the ure 1 operon is necessary for optimal growth in culture, urease activity, resistance against low-pH killing, and in vivo persistence of B. suis when inoculated by gavage. The ure 2 operon apparently enhances the resistance to low-pH killing in-vitro.
Restricted cell elongation in Arabidopsishypocotyls is associated with a reduced average pectin esterification level
Authors: Derbyshire Paul , McCann Maureen C , Roberts Keith 
Published: June 2007

AbstractBackgroundCell elongation is mainly limited by the extensibility of the cell wall. Dicotyledonous primary (growing) cell walls contain cellulose, xyloglucan, pectin and proteins, but little is known about how each polymer class contributes to the cell wall mechanical properties that control extensibility.ResultsWe present evidence that the degree of pectin methyl-esterification (DE%) limits cell growth, and that a minimum level of about 60% DE is required for normal cell elongation inArabidopsishypocotyls. When the average DE% falls below this level, as in two gibberellic acid (GA) mutantsga1-3andgai, and plants expressing pectin methyl-esterase (PME1) fromAspergillus aculeatus, then hypocotyl elongation is reduced.ConclusionLow average levels of pectin DE% are associated with reduced cell elongation, implicating PMEs, the enzymes that regulate DE%, in the cell elongation process and in responses to GA. At high average DE% other components of the cell wall limit GA-induced growth.
Transcriptional activation and localization of expression of Brassica juncea putative metal transport protein BjMTP1
Authors: Muthukumar Balasubramaniam , Yakubov Bakhtiyor , Salt David E 
Published: June 2007

Abstract

Background
Metal hyperaccumulators, including various Thlaspi species, constitutively express the putative metal transporter MTP1 to high levels in shoots. Here we present data on the transcriptional regulation and localization of expression of the homologous gene BjMTP1 in Brassica juncea. Though B. juncea lacks the ability to hyperaccumulate metals, its relatively high biomass, rapid growth and relatedness to true metal hyperaccumulating plants makes it a promising starting point for the development of plants for phytoremediation. Our goal in this study is to determine the transcriptional regulation of MTP1 in order to start to better understanding the physiological role of MTP1 in B. juncea.

Results
Steady-state mRNA levels of BjMTP1 were found to be enhanced 8.8, 5.9, and 1.6-fold in five-day-old B. juncea seedlings after exposure to Ni2+, Cd2+ or Zn2+, respectively. This was also reflected in enhanced GUS activity in B. juncea seedlings transformed with BjMTP1 promoter::GUSPlus after exposure to these metals over a similar range of toxicities from mild to severe. However, no increase in GUS activity was observed after exposure of seedlings to cold or heat stress, NaCl or hydrogen peroxide. GUS expression in Ni2+ treated seedlings was localized in roots, particularly in the root-shoot transition zone. In four- week- old transgenic plants BjMTP1 promoter activity also primarily increased in roots in response to Ni2+ or Cd2+ in plants transformed with either GUS or mRFP1 as reporter genes, and expression was localized to the secondary xylem parenchyma. In leaves, BjMTP1 promoter activity in response to Ni2+ or Cd2+ spiked after 24 h then decreased. In shoots GUS expression was prominently present in the vasculature of leaves, and floral parts.

Conclusion
Our studies establish that a 983 bp DNA fragment upstream of the BjMTP1 translational start site is sufficient for the specific activation by Ni2+ and Cd2+ of BjMTP1 expression primarily in roots. Activation of expression by both metals in roots is primarily localized to the xylem parenchyma cells. This study is the first to identify specific Ni2+ and Cd2+ transcriptional regulation and tissue localization of BjMTP1.
Integration in primary community care networks (PCCNs): examination of governance, clinical, marketing, financial, and information infrastructures in a national demonstration project in Taiwan
Authors: Lin Blossom Yen-Ju 
Published: June 2007

Abstract
Background
Taiwan's primary community care network (PCCN) demonstration project, funded by the Bureau of National Health Insurance on March 2003, was established to discourage hospital shopping behavior of people and drive the traditional fragmented health care providers into cooperate care models. Between 2003 and 2005, 268 PCCNs were established. This study profiled the individual members in the PCCNs to study the nature and extent to which their network infrastructures have been integrated among the members (clinics and hospitals) within individual PCCNs.

Methods
The thorough questionnaire items, covering the network working infrastructures – governance, clinical, marketing, financial, and information integration in PCCNs, were developed with validity and reliability confirmed. One thousand five hundred and fifty-seven clinics that had belonged to PCCNs for more than one year, based on the 2003–2005 Taiwan Primary Community Care Network List, were surveyed by mail. Nine hundred and twenty-eight clinic members responded to the surveys giving a 59.6 % response rate.

Results
Overall, the PCCNs' members had higher involvement in the governance infrastructure, which was usually viewed as the most important for establishment of core values in PCCNs' organization design and management at the early integration stage. In addition, it found that there existed a higher extent of integration of clinical, marketing, and information infrastructures among the hospital-clinic member relationship than those among clinic members within individual PCCNs. The financial infrastructure was shown the least integrated relative to other functional infrastructures at the early stage of PCCN formation.

Conclusion
There was still room for better integrated partnerships, as evidenced by the great variety of relationships and differences in extent of integration in this study. In addition to provide how the network members have done for their initial work at the early stage of network forming in this study, the detailed surveyed items, the concepts proposed by the managerial and theoretical professionals, could be a guide for those health care providers who have willingness to turn their business into multi-organizations.
Power for tests of interaction: effect of raising the Type I error rate
Authors: Marshall Stephen W 
Published: June 2007

Abstract
Background
Power for assessing interactions during data analysis is often poor in epidemiologic studies. This is because epidemiologic studies are frequently powered primarily to assess main effects only. In light of this, some investigators raise the Type I error rate, thereby increasing power, when testing interactions. However, this is a poor analysis strategy if the study is chronically under-powered (e.g. in a small study) or already adequately powered (e.g. in a very large study). To demonstrate this point, this study quantified the gain in power for testing interactions when the Type I error rate is raised, for a variety of study sizes and types of interaction.

Methods
Power was computed for the Wald test for interaction, the likelihood ratio test for interaction, and the Breslow-Day test for heterogeneity of the odds ratio. Ten types of interaction, ranging from sub-additive through to super-multiplicative, were investigated in the simple scenario of two binary risk factors. Case-control studies of various sizes were investigated (75 cases & 150 controls, 300 cases & 600 controls, and 1200 cases & 2400 controls).

Results
The strategy of raising the Type I error rate from 5% to 20% resulted in a useful power gain (a gain of at least 10%, resulting in power of at least 70%) in only 7 of the 27 interaction type/study size scenarios studied (26%). In the other 20 scenarios, power was either already adequate (n = 8; 30%), or else so low that it was still weak (below 70%) even after raising the Type I error rate to 20% (n = 12; 44%).

Conclusion
Relaxing the Type I error rate did not usefully improve the power for tests of interaction in many of the scenarios studied. In many studies, the small power gains obtained by raising the Type I error will be more than offset by the disadvantage of increased "false positives". I recommend investigators should not routinely raise the Type I error rate when assessing tests of interaction.
Solitary fibrous tumor of the thigh with epithelioid features: a case report
Authors: Martorell Miguel , Pérez-Vallés Ana , Gozalbo Francisco , Garcia-Garcia Jose Angel , Gutierrez Jair , Gaona John 
Published: June 2007

Abstract

Background
Extrapleural Solitary Fibrous tumors (SFTs) have been increasingly reported. The retroperitoneum, deep soft tissues of proximal extremities, abdominal cavity, trunk, head and neck are the most common extraserosal locations reported. Microscopically they show a wide range of morphological features, and so the differential diagnosis is extensive. Immunohistochemically, they commonly express CD34, vimentin, bcl-2 and CD99. Epithelial membrane antigen (EMA) and smooth muscle actin (SMA) may occasionally be expressed. Epithelioid morphology in extrapleural SFT has only very occasionally been described (five cases reported), some of them with biphasic pattern and others with malignant characteristics.

Case presentation
A SFT of the thigh with epithelioid areas in a 63 year old woman is reported. Microscopically the tumor showed areas hypo and hipercellular. At the periphery of the hipercellular areas there were nodules composed of epithelioid cells. Immunohistochemically both the spindle and epithelioid cells were positive for CD34, vimentin, bcl-2 and CD99. Epithelial, neural and muscular markers were negative. Molecular study was done and ruled out a synovial sarcoma.

Conclusion
Ten cases of SFT of the thigh have been reported but to our knowledge this is the first case with epithelioid morphology affecting the extremities. Identification of this pattern of SFT is of importance, to avoid misdiagnosis with other more aggressive conditions in soft tissue.