bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes
Authors: Gwee Pai-Chung , Tay Boon-Hui , Brenner Sydney , Venkatesh Byrappa
Published: February 2009

Background

Vasopressin and oxytocin are mammalian neurohypophysial hormones with distinct functions. Vasopressin is involved mainly in osmoregulation and oxytocin is involved primarily in parturition and lactation. Jawed vertebrates contain at least one homolog each of vasopressin and oxytocin, whereas only a vasopressin-family hormone, vasotocin, has been identified in jawless vertebrates. The genes encoding vasopressin and oxytocin are closely linked tail-to-tail in eutherian mammals whereas their homologs in chicken, Xenopus and coelacanth (vasotocin and mesotocin) are linked tail-to-head. In contrast, their pufferfish homologs, vasotocin and isotocin, are located on the same strand of DNA with isotocin located upstream of vasotocin and separated by five genes. These differences in the arrangement of the two genes in different bony vertebrate lineages raise questions about their origin and ancestral arrangement. To trace the origin of these genes, we have sequenced BAC clones from the neurohypophysial gene loci in a cartilaginous fish, the elephant shark (Callorhinchus milii), and in a jawless vertebrate, the Japanese lamprey (Lethenteron japonicum). We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the amphioxus (Branchiostoma floridae).

Results

The elephant shark neurohypophysial hormone genes encode vasotocin and oxytocin, and are linked tail-to-head like their homologs in coelacanth and non-eutherian tetrapods. Besides the hypothalamus, the two genes are also expressed in the ovary. In addition, the vasotocin gene is expressed in the kidney, rectal gland and intestine. These expression profiles indicate a paracrine role for the two hormones. The lamprey locus contains a single neurohypophysial hormone gene, the vasotocin. The synteny of genes in the lamprey locus is conserved in elephant shark, coelacanth and tetrapods but disrupted in teleost fishes. The amphioxus locus encodes a single neurohypophysial hormone, designated as [Ile4]vasotocin.

Conclusion

The vasopressin- and oxytocin-family of neurohypophysial hormones evolved in a common ancestor of jawed vertebrates through tandem duplication of the ancestral vasotocin gene. The duplicated genes were linked tail-to-head like their homologs in elephant shark, coelacanth and non-eutherian tetrapods. In contrast to the conserved linkage of the neurohypophysial genes in these vertebrates, the neurohypophysial hormone gene locus has experienced extensive rearrangements in the teleost lineage.
The HELLP syndrome: Clinical issues and management. A Review
Authors: Haram Kjell , Svendsen Einar , Abildgaard Ulrich
Published: February 2009

Background

The HELLP syndrome is a serious complication in pregnancy characterized by haemolysis, elevated liver enzymes and low platelet count occurring in 0.5 to 0.9% of all pregnancies and in 10–20% of cases with severe preeclampsia. The present review highlights occurrence, diagnosis, complications, surveillance, corticosteroid treatment, mode of delivery and risk of recurrence.

Methods

Clinical reports and reviews published between 2000 and 2008 were screened using Pub Med and Cochrane databases.

Results and conclusion

About 70% of the cases develop before delivery, the majority between the 27th and 37th gestational weeks; the remainder within 48 hours after delivery. The HELLP syndrome may be complete or incomplete. In the Tennessee Classification System diagnostic criteria for HELLP are haemolysis with increased LDH (> 600 U/L), AST (≥ 70 U/L), and platelets < 100·109/L. The Mississippi Triple-class HELLP System further classifies the disorder by the nadir platelet counts. The syndrome is a progressive condition and serious complications are frequent. Conservative treatment (≥ 48 hours) is controversial but may be considered in selected cases < 34 weeks' gestation. Delivery is indicated if the HELLP syndrome occurs after the 34th gestational week or the foetal and/or maternal conditions deteriorate. Vaginal delivery is preferable. If the cervix is unfavourable, it is reasonable to induce cervical ripening and then labour. In gestational ages between 24 and 34 weeks most authors prefer a single course of corticosteroid therapy for foetal lung maturation, either 2 doses of 12 mg betamethasone 24 hours apart or 6 mg or dexamethasone 12 hours apart before delivery. Standard corticosteroid treatment is, however, of uncertain clinical value in the maternal HELLP syndrome. High-dose treatment and repeated doses should be avoided for fear of long-term adverse effects on the foetal brain. Before 34 weeks' gestation, delivery should be performed if the maternal condition worsens or signs of intrauterine foetal distress occur. Blood pressure should be kept below 155/105 mmHg. Close surveillance of the mother should be continued for at least 48 hours after delivery.
Carboxypeptidase 4 gene variants and early-onset intermediate-to-high risk prostate cancer
Authors: Ross Phillip L , Cheng Iona , Liu Xin , Cicek Mine S , Carroll Peter R , Casey Graham , Witte John S
Published: February 2009

Background

Carboxypeptidase 4 (CPA4) is a zinc-dependent metallocarboxypeptidase on chromosome 7q32 in a region linked to prostate cancer aggressiveness. CPA4 is involved in the histone hyperacetylation pathway and may modulate the function of peptides that affect the growth and regulation of prostate epithelial cells. We examined the association between genetic variation in CPA4 and intermediate-to-high risk prostate cancer.

Methods

We studied 1012 men (506 cases and 506 controls) from Cleveland, Ohio. All cases had Gleason ≥ 7, clinical stage ≥ T2c, or PSA ≥ 10 ng/mL at diagnosis. Six CPA4 single-nucleotide polymorphisms were genotyped, and evaluated for their relation to prostate cancer. We also evaluated whether CPA4 variants influence risk of disease among men diagnosed at an earlier age (< 66 years).

Results

The nonsynonymous coding SNP (rs2171492, Cys303Gly) in CPA4 was associated with an increased risk of aggressive prostate cancer among younger patients (< 66 years). Specifically, men carrying the TT genotype had an approximately two-fold increased risk for being diagnosed with intermediate-to-high risk disease (Odds Ratio = 1.83, p = 0.04). In the overall population (all ages) none of the CPA4 SNPs demonstrated a statistically significant association with prostate cancer.

Conclusion

Coding variation in CPA4 may confer increased risk of intermediate-to-high risk prostate cancer among younger patients. Further work is needed to identify the functional aspects of this variation and understand its biological effects on prostate cancer. Such work may translate into more precise screening of higher risk individuals as well as guiding clinicians and patients toward earlier and more definitive treatment modalities in patients genetically identified as higher risk.
A multi-Fc-species system for recombinant antibody production
Authors: Moutel Sandrine , El Marjou Ahmed , Vielemeyer Ole , Nizak Clément , Benaroch Philippe , Dübel Stefan , Perez Franck
Published: February 2009

Background

Genomic, transcriptomic and proteomic projects often suffer from a lack of functional validation creating a strong demand for specific and versatile antibodies. Antibody phage display represents an attractive approach to select rapidly in vitro the equivalent of monoclonal antibodies, like single chain Fv antibodies, in an inexpensive and animal free way. However, so far, recombinant antibodies have not managed to impose themselves as efficient alternatives to natural antibodies.

Results

We developed a series of vectors that allow one to easily fuse single chain Fv antibodies to Fc domains of immunoglobulins, improving their sensitivity and facilitating their use. This series enables the fusion of single chain Fv antibodies with human, mouse or rabbit Fc so that a given antibody is no longer restricted to a particular species. This opens up unlimited multiplexing possibilities and gives additional value to recombinant antibodies. We also show that this multi-Fc species production system can be applied to natural monoclonal antibodies cloned as single chain Fv antibodies and we converted the widely used 9E10 mouse anti-Myc-tag antibody into a human and a rabbit antibody.

Conclusion

Altogether, this new expression system, that brings constant quality, sensitivity and unique versatility, will be important to broaden the use of recombinant and natural monoclonal antibodies both for laboratory and diagnosis use.
Opioid substitution treatment with sublingual buprenorphine in Manipur and Nagaland in Northeast India: what has been established needs to be continued and expanded
Authors: Kumar M Suresh , Natale Richard D , Langkham B , Sharma Charan , Kabi Rachel , Mortimore Gordon
Published: February 2009

Manipur and Nagaland in northeast India report an antenatal HIV prevalence of > 1% and the current HIV prevalence among injecting drug users is 24% and 4.5% respectively. Through support from DFID's Challenge Fund, Emmanuel Hospital Association (EHA) established thirteen drop-in-centres across the two states to deliver opioid substitution treatment with sublingual buprenorphine for 1200 injecting drug users. Within a short span of time the treatment has been found to be attractive to the clients and currently 1248 injecting opioid users are receiving opioid substitution treatment. The project is acceptable to the drug users, the families, the communities, religious as well as the militant groups. The treatment centres operate all days of the week, have trained staff members, utilize standardized protocols and ensure a strict supervised delivery system to prevent illicit diversion of buprenorphine. The drug users receiving the substitution treatment are referred to HIV voluntary counselling and testing. As this treatment has the potential to change HIV related risk behaviours, what has been established in the two states needs to be continued and expanded with the support from the Government of India.
Human prostate supports more efficient replication of HIV-1 R5 than X4 strains ex vivo
Authors: Le Tortorec Anna , Satie Anne-Pascale , Denis Hélène , Rioux-Leclercq Nathalie , Havard Laurence , Ruffault Annick , Jégou Bernard , Dejucq-Rainsford Nathalie
Published: February 2009

Background

In order to determine whether human prostate can be productively infected by HIV-1 strains with different tropism, and thus represent a potential source of HIV in semen, an organotypic culture of prostate from men undergoing prostatic adenomectomy for benign prostate hypertrophy (BPH) was developed. The presence of potential HIV target cells in prostate tissues was investigated using immunohistochemistry. The infection of prostate explants following exposures with HIV-1 R5, R5X4 and X4 strains was analyzed through the measure of RT activity in culture supernatants, the quantification of HIV DNA in the explants and the detection of HIV RNA+ cells in situ.

Results

The overall prostate characteristics were retained for 21/2 weeks in culture. Numerous potential HIV-1 target cells were detected in the prostate stroma. Whilst HIV-1 R5SF162 strain consistently productively infected prostatic T lymphocytes and macrophages, the prototypic X4IIIB strain and a primary R5X4 strain showed less efficient replication in this organ.

Conclusion

The BPH prostate is a site of HIV-1 R5 replication that could contribute virus to semen. A limited spreading of HIV-1 X4 and R5X4 in this organ could participate to the preferential sexual transmission of HIV-1 R5 strains.
Perceptions of short-term medical volunteer work: a qualitative study in Guatemala
Authors: Green Tyler , Green Heidi , Scandlyn Jean , Kestler Andrew
Published: February 2009

Background

Each year medical providers from wealthy countries participate in short-term medical volunteer work in resource-poor countries. Various authors have raised concern that such work has the potential to be harmful to recipient communities; however, the social science and medical literature contains little research into the perceptions of short-term medical volunteer work from the perspective of members of recipient communities. This exploratory study examines the perception of short-term medical volunteer work in Guatemala among groups of actors affected by or participating in these programs.

Methods

The researchers conducted in-depth, semi-structured interviews with 72 individuals, including Guatemalan healthcare providers and health authorities, foreign medical providers, non-medical personnel working on health projects, and Guatemalan parents of children treated by a short-term volunteer group. Detailed notes and summaries of these interviews were uploaded, coded and annotated using Atlas.ti (Scientific Software Development GmbH, Berlin) to identify recurrent themes from the interviews.

Results

Informants commonly identified a need for increased access to medical services in Guatemala, and many believed that short-term medical volunteers are in a position to offer improved access to medical care in the communities where they serve. Informants most frequently cited appropriate patient selection and attention to payment systems as the best means to avoid creating dependence on foreign aid. The most frequent suggestion to improve short-term medical volunteer work was coordination with and respect for local Guatemalan healthcare providers and their communities, as insufficient understanding of the country's existing healthcare resources and needs may result in perceived harm to the recipient community.

Conclusion

The perceived impact of short-term medical volunteer projects in Guatemala is highly variable and dependent upon the individual project. In this exploratory study, project characteristics were identified that are consistently perceived to be either positive or negative. These findings have direct implications for anyone involved in the planning and execution of short-term medical volunteer projects, including local and foreign medical team members, project planners and coordinators, and health authorities. Most importantly, this preliminary study suggests avenues for future study and evaluation of the impact of short-term medical volunteer programs on local health care services.
Biocompatibility of Poly-ε-caprolactone-hydroxyapatite composite on mouse bone marrow-derived osteoblasts and endothelial cells
Authors: Yu Haiying , Wooley Paul H , Yang Shang-You
Published: February 2009

Background

Tissue-engineered bone may be developed by seeding the cells capable of both osteogenesis and vascularization on biocompatible composite scaffolds. The current study investigated the performance of mice bone marrow-derived osteogenic cells and endothelial cells as seeded on hydroxyapatite (HA) and poly-ε-caprolactone (PCL) composite scaffolds.

Methods

Mononuclear cells were induced to osteoblasts and endothelial cells respectively, which were defined by the expression of osteocalcin, alkaline phosphatase (ALP), and deposits of calcium-containing crystal for osteoblasts, or by the expression of vascular endothelial growth factor receptor-2 (VEGFR-2) and von Willebrand factor (vWF), and the formation of a capillary network in Matrigel™ for endothelial cells. Both types of cell were seeded respectively on PCL-HA scaffolds at HA to PCL weight ratio of 1:1, 1:4, or 0:1 and were evaluated using scanning electron microscopy, ALP activity (of osteoblasts) and nitric oxide production (of endothelial cells) plus the assessment of cell viability.

Results

The results indicated that HA led to a positive stimulation of osteoblasts viability and ALP activity, while HA showed less influence on endothelial cells viability. An elevated nitric oxide production of endothelial cells was observed in HA-containing group.

Conclusion

Supplement of HA into PCL improved biocompatible for bone marrow-derived osteoblasts and endothelial cells. The PCL-HA composite integrating with two types of cells may provide a useful system for tissue-engineered bone grafts with vascularization.
Detergent resistant membrane-associated IDE in brain tissue and cultured cells: Relevance to Aβ and insulin degradation
Authors: Bulloj Ayelén , Leal María C , Surace Ezequiel I , Zhang Xue , Xu Huaxi , Ledesma Maria D , Castaño Eduardo M , Morelli Laura
Published: February 2009

Background

Insulin degrading enzyme (IDE) is implicated in the regulation of amyloid β (Aβ) steady-state levels in the brain, and its deficient expression and/or activity may be a risk factor in sporadic Alzheimer's disease (AD). Although IDE sub-cellular localization has been well studied, the compartments relevant to Aβ degradation remain to be determined.

Results

Our results of live immunofluorescence, immuno gold electron-microscopy and gradient fractionation concurred to the demonstration that endogenous IDE from brain tissues and cell cultures is, in addition to its other localizations, a detergent-resistant membrane (DRM)-associated metallopeptidase. Our pulse chase experiments were in accordance with the existence of two pools of IDE: the cytosolic one with a longer half-life and the membrane-IDE with a faster turn-over. DRMs-associated IDE co-localized with Aβ and its distribution (DRMs vs. non-DRMs) and activity was sensitive to manipulation of lipid composition in vitro and in vivo. When IDE was mis-located from DRMs by treating cells with methyl-β-cyclodextrin (MβCD), endogenous Aβ accumulated in the extracellular space and exogenous Aβ proteolysis was impaired. We detected a reduced amount of IDE in DRMs of membranes isolated from mice brain with endogenous reduced levels of cholesterol (Chol) due to targeted deletion of one seladin-1 allele. We confirmed that a moderate shift of IDE from DRMs induced a substantial decrement on IDE-mediated insulin and Aβ degradation in vitro.

Conclusion

Our results support the notion that optimal substrate degradation by IDE may require its association with organized-DRMs. Alternatively, DRMs but not other plasma membrane regions, may act as platforms where Aβ accumulates, due to its hydrophobic properties, reaching local concentration close to its Km for IDE facilitating its clearance. Structural integrity of DRMs may also be required to tightly retain insulin receptor and IDE for insulin proteolysis. The concept that mis-location of Aβ degrading proteases away from DRMs may impair the physiological turn-over of Aβ in vivo deserves further investigation in light of therapeutic strategies based on enhancing Aβ proteolysis in which DRM protease-targeting may need to be taken into account.
Protein-protein interaction as a predictor of subcellular location
Authors: Shin Chang Jin , Wong Simon , Davis Melissa J , Ragan Mark A
Published: February 2009

Background

Many biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As protein-protein interactions (PPIs) and subcellular location (SCL) are discoveredviaseparate empirical approaches, PPI and SCL annotations are independent and might complement each other in helping us to understand the role of individual proteins in cellular networks. We expect reliable PPI annotations to show that proteins interactingin vivoare co-located in the same cellular compartment. Our goal here is to evaluate the potential of using PPI annotation in determining SCL of proteins in human, mouse, fly and yeast, and to identify and quantify the factors that contribute to this complementarity.

Results

Using publicly available data, we evaluate the hypothesis that interacting proteins must be co-located within the same subcellular compartment. Based on a large, manually curated PPI dataset, we demonstrate that a substantial proportion of interacting proteins are in fact co-located. We develop an approach to predict the SCL of a protein based on the SCL of its interaction partners, given sufficient confidence in the interaction itself. The frequency of false positive PPIs can be reduced by use of six lines of supporting evidence, three based on type of recorded evidence (empirical approach, multiplicity of databases, and multiplicity of literature citations) and three based on type of biological evidence (inferred biological process, domain-domain interactions, and orthology relationships), with biological evidence more-effective than recorded evidence. Our approach performs better than four existing prediction methods in identifying the SCL of membrane proteins, and as well as or better for soluble proteins.

Conclusion

Understanding cellular systems requires knowledge of the SCL of interacting proteins. We show how PPI data can be used more effectively to yield reliable SCL predictions for both soluble and membrane proteins. Scope exists for further improvement in our understanding of cellular function through consideration of the biological context of molecular interactions.
C. elegans CARMIL negatively regulates UNC-73/Trio function during neuronal development
Authors: Vanderzalm Pamela J. , Pandey Amita , Hurwitz Michael E. , Bloom Laird , Horvitz H. Robert , Garriga Gian
Published: February 2009

Whereas many molecules that promote cell and axonal growth cone migrations have been identified, few are known to inhibit these processes. In genetic screens designed to identify molecules that negatively regulate such migrations, we identified CRML-1, the C. elegans homolog of CARMIL. Although mammalian CARMIL acts to promote the migration of glioblastoma cells,we found that CRML-1 acts as a negative regulator of neuronal cell and axon growth cone migrations. Genetic evidence indicates that CRML-1 regulates these migrations by inhibiting the Rac GEF activity of UNC-73, a homolog of the Rac and Rho GEF Trio. The antagonistic effects of CRML-1 and UNC-73 can control the direction of growth cone migration by regulating the levels of the SAX-3(a Robo homolog) guidance receptor. Consistent with the hypothesis that CRML-1 negatively regulates UNC-73 activity, these two proteins form a complex in vivo. Based on these observations, we propose a role for CRML-1 as a novel regulator of cell and axon migrations that acts through inhibition of Rac signaling.
Krüppel-like factor 2 cooperates with the ETS family protein ERG to activateFlk1expression during vascular development
Authors: Meadows Stryder M. , Salanga Matthew C. , Krieg Paul A.
Published: February 2009

The VEGF receptor, FLK1, is essential for differentiation of the endothelial lineage and for embryonic vascular development. Using comparative genomics, we have identified conserved ETS and Krüppel-like factor (KLF)binding sites within the Flk1 enhancer. In transgenic studies,mutation of either site results in dramatic reduction of Flk1reporter expression. Overexpression of KLF2 or the ETS transcription factor ERG is sufficient to induce ectopic Flk1 expression in the Xenopus embryo. Inhibition of KLF2 function in the Xenopusembryo results in a dramatic reduction in Flk1 transcript levels. Furthermore, we show that KLF2 and ERG associate in a physical complex and that the two proteins synergistically activate transcription of Flk1. Since the ETS and KLF protein families have independently been recognized as important regulators of endothelial gene expression, cooperation between the two families has broad implications for gene regulation during development,normal physiology and vascular disease.
Crossveinless and the TGFβ pathway regulate fiber number in theDrosophilaadult jump muscle
Authors: Jaramillo MaryAnn S. , Lovato Candice V. , Baca Erica M. , Cripps Richard M.
Published: February 2009

Skeletal muscles are readily characterized by their location within the body and by the number and composition of their constituent muscle fibers. Here, we characterize a mutation that causes a severe reduction in the number of fibers comprising the tergal depressor of the trochanter muscle (TDT, or jump muscle), which functions in the escape response of the Drosophila adult. The wild-type TDT comprises over 20 large muscle fibers and four small fibers. In crossveinless (cv) mutants,the number of large fibers is reduced by 50%, and the number of small fibers is also occasionally reduced. This reduction in fiber number arises from a reduction in the number of founder cells contributing to the TDT at the early pupal stage. Given the role of cv in TGFβ signaling, we determined whether this pathway directly impacts TDT development. Indeed,gain- and loss-of-function manipulations in the TGFβ pathway resulted in dramatic increases and decreases, respectively, in TDT fiber number. By identifying the origins of the TDT muscle, from founder cells specified in the mesothoracic leg imaginal disc, we also demonstrate that the TGFβ pathway directly impacts the specification of founder cells for the jump muscle. Our studies define a new role for the TGFβ pathway in the control of specific skeletal muscle characteristics.
Visualizing anti-tumor immune responses in vivo
Authors: Perentes Jean Y. , Duda Dan G. , Jain Rakesh K.
Published: February 2009

Real-time imaging of stromal and immune cells in tumors is an emerging field that will greatly help us to understand the role of these non-malignant tumor components in tumor progression and therapy
Nine human factors contributing to the user acceptance of telemedicine applications: a cognitive-emotional approach
Authors: Buck Susanne
Published: February 2009

Much attention is paid to the technical aspects of telemedicine in the development of new applications, but the enthusiasm about what is technically possible very often leads to the user acceptance of such products being neglected. The number of successful and sustainable telemedicine applications would be much higher if developers concentrated more on matters related to the cognitive-emotional situation of the users involved in telemedicine. The users include the care and cure providers, as well as the care and cure receivers. Based on an informal literature search and discussions with telemedicine implementation staff, nine factors have been identified which are essential for the user acceptance of telemedicine applications. All of them are connected more to the cognitive-emotional than to the cognitive-rational side of information processing. This suggests that in the future the cognitive-emotional side will need more attention. This in turn implies that the nine points mentioned above have to find their way into requirements engineering, development processes and product life cycles.
Mortality risk for diabetes patients in a care coordination, home-telehealth programme
Authors: Chumbler Neale R , Chuang Ho-Chih , Wu Samuel S , Wang Xinping , Kobb Rita , Haggstrom David , Jia Huanguang
Published: February 2009

We assessed a home monitoring/care coordination programme for veterans with diabetes. Patients enrolled in the programme ( n = 387) were followed for four years and compared with a retrospective control group ( n = 387). Each patient in the intervention group used a messaging device in the home that was connected by a conventional telephone line. Care coordinators monitored the answers from the devices daily so that early interventions could be made. There were significantly more deaths in the control group ( n = 102, 26%) compared with the intervention group ( n = 75, 19%). There was longer survival for the intervention group versus the control group (mean survival time 1348 vs 1278 days; P = 0.015). A multivariate analyses indicated that the telemonitoring programme was associated with reduced 4-year all-cause mortality (hazard ratio = 0.7, 95% CI 0.5–0.9, P = 0.013). The results suggest that daily management of patients with diabetes through home monitoring by a registered nurse reduces mortality.
Feasibility of using videoconferencing to provide diabetes education: a pilot study
Authors: Timmerberg Brady D , Wurst Jennie , Patterson James , Spaulding Ryan J , Belz Norbert E
Published: February 2009

We conducted a pilot study of the effectiveness of individual counselling sessions provided by a dietician through telemedicine for patients with diabetes. All participants received a single group education session via videoconference. Those who were randomized to the intervention also received two additional follow-up sessions, four and eight weeks later. Glycosylated haemoglobin and total cholesterol were measured at the start and again 16 weeks later. The patients completed diabetes quality-of-life and telemedicine patient satisfaction surveys. Thirty-two participants consented to participate. Complete data were collected on 13 intervention and 13 control patients. There was a 1% fall in HbA1c in the intervention group from pre- to post-assessment, although this was not significant. The control group showed a significantly larger fall in HbA1c levels than the intervention group ( P = 0.043). Total cholesterol decreased in both groups, although not significantly. All control and intervention group participants indicated that they would participate in videoconferencing nutritional counselling again. The results suggest that providing nutritional therapy via videoconferencing may be useful in assisting patients to manage their conditions.
Differential 3′ splice site recognition of SMN1 and SMN2 transcripts by U2AF and U2 snRNP
Authors: Martins de Araújo Mafalda , Bonnal Sophie , Hastings Michelle L. , Krainer Adrian R. , Valcárcel Juan
Published: February 2009

Spinal Muscular atrophy is a prevalent genetic disease caused by mutation of the SMN1 gene, which encodes the SMN protein involved in assembly of small nuclear ribonucleoprotein (snRNP) complexes. A paralog of the gene, SMN2, cannot provide adequate levels of functional SMN because exon 7 is skipped in a significant fraction of the mature transcripts. A C to T transition located at position 6 of exon 7 is critical for the difference in exon skipping between SMN1 and SMN2. Here we report that this nucleotide difference results in increased ultraviolet light-mediated crosslinking of the splicing factor U2AF65 with the 3′ splice site of SMN1 intron 6 in HeLa nuclear extract. U2 snRNP association, analyzed by native gel electrophoresis, is also more efficient on SMN1 than on SMN2, particularly under conditions of competition, suggesting more effective use of limiting factors. Two trans-acting factors implicated in SMN regulation, SF2/ASF and hnRNP A1, promote and repress, respectively, U2 snRNP recruitment to both RNAs. Interestingly, depending on the transcript and the regulatory factor, the effects on U2 binding not always correlate with changes in U2AF65 crosslinking. Furthermore, blocking recognition of a Tra2-β1-dependent splicing enhancer located in exon 7 inhibits U2 snRNP recruitment without affecting U2AF65 crosslinking. Collectively, the results suggest that both U2AF binding and other steps of U2 snRNP recruitment can be control points in SMN splicing regulation.
Novel application of Phi29 DNA polymerase: RNA detection and analysis in vitro and in situ by target RNA-primed RCA
Authors: Lagunavicius Arunas , Merkiene Egle , Kiveryte Zivile , Savaneviciute Agne , Zimbaite-Ruskuliene Vilma , Radzvilavicius Tomas , Janulaitis Arvydas
Published: February 2009

We present a novel Phi29 DNA polymerase application in RCA-based target RNA detection and analysis. The 3′→5′ RNase activity of Phi29 DNA polymerase converts target RNA into a primer and the polymerase uses this newly generated primer for RCA initiation. Therefore, using target RNA-primed RCA, padlock probes may be targeted to inner RNA sequences and their peculiarities can be analyzed directly. We demonstrate that the exoribonucleolytic activity of Phi29 DNA polymerase can be successfully applied in vitro and in situ. These findings expand the potential for detection and analysis of RNA sequences distanced from 3′-end.
A method for detecting and preventing negative RNA interference in preparation of lentiviral vectors for siRNA delivery
Authors: Zhou Demin , Zhang Jing , Wang Cuiying , Bliesath Joshua R. , He Qiuchen , Yu Dehua , Li-He Zhang , Wong-Staal Flossie
Published: February 2009

The lentiviral vector is a useful tool for delivery of hairpin siRNA (shRNA) into mammalian cells. However, the efficiency of this system for carrying double-stranded siRNA (dsRNA) has not been explored. In this study we cloned the two forms of siRNA-coding sequence, a palindromic DNA with a spacer loop for shRNA and a double-stranded DNA with opposing Pol III promoters for dsRNA, into lentiviral DNA vectors, and compared their viral vector production yields. Our results indicate that sharply lower titer vector was obtained for dsRNA while much higher titer vector was produced for shRNA, posing a fundamental concern whether siRNA-carrying viral RNA itself is an inherent target of RNAi. Further experimental analyses using packaging cells that either allow or do not allow siRNA transcription indicate that the shRNA-carrying viral RNA is resistant to RNAi but the viral RNA carrier for dsRNA is not, offering a linker of RNAi bias–target secondary structure that causes shRNA vector to evade RNAi degradation. More importantly, the poor yield of dsRNA vector production was restored when a novel packaging cell line was used that blocks the antisense strand from dsRNA duplexes. This method has important implications for the RNAi field, especially for those who are using lentiviral dsRNA and dsRNA libraries for various biological discovery and therapeutic interventions.
Generating Aptamers for Recognition of Virus-Infected Cells
Authors: Tang Zhiwen , Parekh Parag , Turner Pete , Moyer Richard W , Tan Weihong
Published: February 2009

Background: The development of molecular probes capable of recognizing virus-infected cells is essential to meet the serious clinical, therapeutic, and national-security challenges confronting virology today. We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells.

Methods: To create aptamer probes capable of recognizing virus-infected cells, we used cell-SELEX (systematic evolution of ligands via exponential enrichment), which uses intact infected live cells as targets for aptamer selection. In this study, vaccinia virus–infected and –uninfected lung cancer A549 cells were chosen to develop our model probes.

Results: A panel of aptamers has been evolved by means of the infected cell–SELEX procedure. The results demonstrate that the aptamers bind selectively to vaccinia virus–infected A549 cells with apparent equilibrium dissociation constants in the nanomolar range. In addition, these aptamers can specifically recognize a variety of target infected cell lines. The aptamers’ target is most likely a viral protein located on the cell surface.

Conclusions: The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell–SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells.
The Bioethical Vacuum: National Policies on Human Embryonic Stem Cell Research in India and China
Authors: Sleeboom-Faulkner Margaret , Patra Prasanna Kumar
Published: February 2009

Developing countries have sought to profit from the

Secondly, we discuss government policies on the institutional aspects of hESR that have made China relatively attractive to foreign investors compared to India. In the concluding part, we discuss various dimensions of bioethics with regards to hESR, and how governing bodies mobilise cultural resources as economic capital.
The Role of Ethics and Morality in EU Law
Authors: Herrmann Janne Rothmar , Rowlandson Malene
Published: February 2009

The aim of this article is to reflect on the role of ethics and morality in EU law. Two specific biolegal fields of study constitute the primary object in this regard; funding of research into human embryonic stem cells (hESCs) and the patentability hereof. The reason why the choice has fallen upon these aspects in particular is that they are both pivotal to the pursuit and realisation of the therapeutic and commercial prospects ascribed to hESC research. Whilst the said prospects are enormous the Member States' different outlook upon the permissibility of engaging in such activities is, however, equally immense because of their different cultural background and religious inheritance. Due to the various approaches towards the ethical issues raised in this regard the European Community is therefore faced with a great challenge. It is in the light of this challenge that the reflections on the role of ethics and morality in EU law are to be seen.
More Altruism, Please
Authors: Scott Niall
Published: February 2009

This paper addresses the need for more attention to be paid to altruism as a fundamentally underpinning any bioethical enquiry. I argue along with Bernard Williams that altruism is necessary to morality, and if this is the case, it is necessary for bioethics. In following a Kantian line on altruism, I take issue with the consequentialist component of Beau-champ and Childress treatment of beneficence, and argue that altruism paired with solidarity is a better match. However, even here it is my contention that altruism is required to give solidarity normative force.
Anisotropic Stiffness Measurements in a Stress-Path Triaxial Cell
Authors: Kuwano R , Connolly TM , Jardine RJ
Published: February 2009

Anisotropy plays a significant role in many geotechnical problems. This paper describes how the anisotropic stiffness properties of soils may be assessed through stress path triaxial tests. Local strain instrumentation has been optimised to identify the linear elastic region of sand without sacrificing the ability to study behavior at strains up to 15%; the system described performs equally well with sands, silts and clays. A novel technique has been developed in which multi-directional shear wave velocity measurements are combined with static tests to provide a complete description of the soil's cross-anisotropic elastic properties through a simple manipulation of classical elastic theory. Results obtained in tests on a dense sand are presented to demonstrate the system capabilities, show how the theoretical approach may be applied in practice, and draw attention to some interesting features of the soil's elastic anisotropy.
Sample Preparation Technique for Artificially Cemented Soils
Authors: Ismail MA , Joer HA , Randolph MF
Published: February 2009

Design of offshore foundations in cemented calcareous sediments requires a full understanding of the strength and deformation properties of the cemented soils. However, obtaining natural undisturbed samples from offshore sites is very expensive, and so there is a need to prepare reconstituted soils in the laboratory to replicate the natural material. Traditionally, cementing of the soils has been modelled by mixing Portland cement or gypsum powder with the uncemented soil in appropriate proportions to obtain a given strength.

This note describes a new sample preparation technique to provide high quality lightly-cemented samples of consistent density. Although the technique is suitable for many different forms of cementing agents, it is used here in conjunction with the Calcite Insitu Precipitation System (CIPS), where cementation is effected by flushing a special solution through the soil, leading to precipitation of calcite on the soil grains. This leads to a form of cementation that simulates the natural material much more closely than using conventional particulate cementing agents. The sample preparation technique is described, and example results are presented for a range of soils. Comparisons are given between the stress-strain response of CIPS-cemented and Portland-cemented soil, with the former exhibiting more brittle behavior after failure, and a greater tendency for volumetric collapse.
Liquefaction and Instability of a Granular Fill Material
Authors: Leong WK , Chu J , Teh CI
Published: February 2009

The granular fills used for land reclamation in Singapore are usually dredged from the sea and contain a relatively high percent of shells. The engineering behavior of this type of granular fill may be different from that of clean sand. A series of laboratory studies were carried out to investigate the liquefaction and instability behavior of the granular fill under static loading conditions. Both static liquefaction and instability were observed to occur for loose granular fill. The instability occurred in the form of run-away deformation at a stress state below failure. The conditions for the occurrence of instability were established. The differences between liquefaction and instability were discussed.
Swelling Behavior of a Desiccated Clay
Authors: Rao KSS , Rao SM , Gangadhara S
Published: February 2009

This study examines the impact of varying the compaction (dry) density and water content on the swelling behavior of desiccated clay soil. Specimens in the shrunken state that have a history of four cycles of wetting and drying are referred to as desiccated specimens in this study. Experimental results showed that the volumetric swell potentials of the desiccated soil specimens were independent of their compaction water contents, but were strongly influenced by their initial void ratios. Comparatively, the vertical swell potentials of the desiccated specimens were independent of their initial water contents and initial void ratios. The results of this study indicated the existence of an optimum void ratio for the examined compacted specimens. Specimens compacted to this void ratio exhibit similar volumetric swell potentials in the as-compacted state and after cycles of wetting and drying.
Direct Shear Interface Test for Shaft Capacity of Piles in Sand
Authors: Reddy ES , Chapman DN , Sastry VVRN
Published: February 2009

For precise estimation of shaft capacity of a pile, it is essential to determine accurately the soil-pile interface friction angle (δ). The apparatus available to measure the value of δ, the miniature pile test apparatus and the soil-pile-slip test apparatus are only available for research purposes. This paper presents the details of an investigation carried out using the conventional direct shear test apparatus to measure the value of δ for soil-pile interface. The direct shear interface tests were conducted using four types of surfaces and two types of sands. The values of δ obtained from these tests are compared with the internal friction angle (φ) of the sand and with the results obtained from soil-pile-slip tests. The interface test results are also used to estimate the shaft capacity of a few model piles embedded in sand.
Apparatus and Procedures for Assessing Inorganic Diffusion Coefficients for Geosynthetic Clay Liners
Authors: Rowe RK , Lake CB , Petrov RJ
Published: February 2009

The apparatus and procedure for performing tests to obtain inorganic diffusion coefficients for Geosynthetic Clay Liners (GCLs) are described, and the processes (diffusion, anion exclusion and osmosis) that can affect the interpretation of these tests are discussed. Results from several inorganic diffusion tests on GCL and bentonite specimens show that the diffusion coefficients deduced for sodium (Na+) and chloride (Cl−) are directly related to the final bentonite void ratio. It is shown that diffusion through GCLs (or thin bentonite layers) can be modeled using a bulk porous media diffusion coefficient (Dp) consisting of the total porosity, nt, and a deduced diffusion coefficient, Dt, (Dp = ntDt) without the need to establish the true effective diffusion coefficient () without the need to establish the true effective diffusion coefficient (De) and effective porosity (ne). However, for a longer bentonite plug sample it is shown that the true effective diffusion coefficient (De) and effective porosity (ne) must be established to predict the contaminant transport through the sample.
The Physicochemical Interaction Between PHPA Polymer Slurry and Cement Mortar
Authors: Ata A , O'Neill M
Published: February 2009

The aim of the present study was to improve understanding of the interaction of drilled shaft concrete, polymer slurry (used to stabilize boreholes during construction of the drilled shaft), and the foundation soil. Interface shear tests were performed in the laboratory to investigate the shear resistance between soil and a cement mortar interface after exposing the interface to a high-molecular-weight polymer slurry. Two types of soils were investigated: (a) stiff silty clay and (b) medium-dense sand. Results showed that for curing periods of 7 days the interface shear resistance was 28% to 46% higher when the interface was exposed to the polymer slurry relative to the interface shear strength of the standard unexposed samples. The ability of the polymer slurry to penetrate and stretch through the pores of silty clay and dense sand soils was demonstrated by investigating the exposed soil masses using scanning electron microscopy (SEM). Exposing the outside surface of cement mortar specimens to the polymer slurry for a period of 14 days caused pitting (roughening) of the mortar surface, which explains the increased interface shear resistance between the soil and the cement mortar after exposure to polymer slurry. The laboratory behavior was verified with full-scale field tests.
Assessment of Localized Deformations in Sand Using X-Ray Computed Tomography
Authors: Alshibli KA , Sture S , Costes NC , Frank ML , Lankton MR , Batiste SN , Swanson RA
Published: February 2009

The internal fabric and localized deformation patterns of triaxial sand specimens were investigated using computed tomography (CT). Three displacement-controlled, conventional, drained axisymmetric (triaxial) experiments were conducted on dry Ottawa sand specimens at very low effective confining stresses (0.05, 0.52, and 1.30 kPa) in a microgravity environment aboard the Space Shuttle during the NASA STS-79 mission. CT scanning was performed on these flight specimens, as well as on an uncompressed specimen and a specimen tested in a terrestrial laboratory at 1.30 kPa effective confining stress. CT demonstrated high accuracy in detecting specimen inhomogeneity and localization patterns. Formation of deformation patters is dependent on the effective confining stress and gravity. Multiple symmetrical radial shear bands were observed in the specimens tested in a microgravity environment. In the axial direction, two major conical surfaces were developed. Nonsymmetrical spatial deformation was observed in the 1-G specimen. Analysis tools were developed to quantify the spatial density change. Void ratio variation within and outside the shear bands is calculated and discussed.