Role of the GNOM gene in Arabidopsis apical-basal patterning--From mutant phenotype to cellular mechanism of protein action.

How the apical-basal axis of polarity is established in embryogenesis is still a mystery in plant development. This axis appeared specifically compromised by mutations in the Arabidopsis GNOM gene. Surprisingly, GNOM encodes an ARF guanine-nucleotide exchange factor (ARF-GEF) that regulates the formation of vesicles in membrane trafficking. In-depth functional analysis of GNOM and its closest relative, GNOM-LIKE 1 (GNL1), has provided a mechanistic explanation for the development-specific role of a seemingly mundane trafficking regulator. The current model proposes that GNOM is specifically involved in the endosomal recycling of the auxin-efflux carrier PIN1 to the basal plasma membrane in provascular cells, which in turn is required for the accumulation of the plant hormone auxin at the future root pole through polar auxin transport. Thus, the analysis of GNOM highlights the importance of cell-biological processes for a mechanistic understanding of development.

A colorectal cancer classification system that associates cellular phenotype and responses to therapy.

Colorectal cancer (CRC) is a major cause of cancer mortality. Whereas some patients respond well to therapy, others do not, and thus more precise, individualized treatment strategies are needed. To that end, we analyzed gene expression profiles from 1,290 CRC tumors using consensus-based unsupervised clustering. The resultant clusters were then associated with therapeutic response data to the epidermal growth factor receptor-targeted drug cetuximab in 80 patients. The results of these studies define six clinically relevant CRC subtypes. Each subtype shares similarities to distinct cell types within the normal colon crypt and shows differing degrees of 'stemness' and Wnt signaling. Subtype-specific gene signatures are proposed to identify these subtypes. Three subtypes have markedly better disease-free survival (DFS) after surgical resection, suggesting these patients might be spared from the adverse effects of chemotherapy when they have localized disease. One of these three subtypes, identified by filamin A expression, does not respond to cetuximab but may respond to cMET receptor tyrosine kinase inhibitors in the metastatic setting. Two other subtypes, with poor and intermediate DFS, associate with improved response to the chemotherapy regimen FOLFIRI in adjuvant or metastatic settings. Development of clinically deployable assays for these subtypes and of subtype-specific therapies may contribute to more effective management of this challenging disease.

Use of transgenic mice for the characterization of human alpha 1-acid glycoprotein (orosomucoid) variants.

Sera from transgenic mice (TM) carrying human genes of alpha 1-acid glycoprotein (orosomucoid or ORM) have been analyzed by isoelectrofocusing and subsequent immunoblotting with antihuman ORM antibodies. With this technique it is possible to reveal selectively the human protein secreted in the TM sera. Orosomucoid bands present in TM sera have been compared with those of the most common human ORM phenotypes to correlate the products of specific genes to previously identified genetic variants. In this paper, we report the identification of the genes encoding for variants ORM1 F1 and ORM2 A, which are genes AGP-A and AGP-B/B' respectively. The nucleotide sequences of these genes are known; therefore a direct correlation between variants and specific amino acid sequences can be established.

QUANTIDADE DE FÓSFORO EXTRAÍDO PELAS SOLUÇÕES DE MEHLICH-1 E MEHLICH-3 EM RAZÃO DE DIFERENTES VELOCIDADES DE AGITAÇÃO, TEMPOS DE CONTATO E TEMPERATURAS

A extração de fósforo do solo pode ser comprometida pelas condições em que a análise é realizada e isso pode explicar a variabilidade nos resultados encontrados. O objetivo deste trabalho foi verificar a influência de desvios na velocidade de agitação, no tempo de contato e na temperatura sobre a extração do P pelos extratores Mehlich-1 (M-1) e Mehlich-3 (M-3) em amostras de solo. O estudo foi conduzido por meio de três experimentos executados com 11 amostras de solo provenientes da camada arável de Latossolo, Neossolo, Argissolo, Cambissolo, Planossolo, que são representativas das regiões geomorfológicas do Planalto e da Depressão Central do Estado do Rio Grande do Sul. Para todos os experimentos, adotou-se o delineamento experimental inteiramente casualizado em esquema fatorial 2 × 5 × 11, sendo dois extratores, cinco velocidades, temperaturas ou tempos de contato solo/solução e 11 tipos de solo, com quatro repetições. No primeiro experimento, a mistura solo:solução foi agitada em 80, 100, 120, 140 e 160 oscilações por min (opm). No segundo, após a agitação por 5 min, a mistura solo:solução foi deixada em repouso por períodos de tempo de oito, 12, 16, 20 e 24 h para retirada dos extratos. No terceiro, a temperatura de execução de todo o protocolo de análises foi mantida constante em 15, 20, 25, 30 e 35 °C. O aumento na velocidade de agitação de 120 até 160 opm aumentou a quantidade de P extraído pelos extratores. O aumento no tempo de contato antes da extração da alíquota elevou as quantidades de P extraído pelo M-1 e diminuiu para o M-3. Variações na temperatura não influenciaram significativamente o extrator M-1, mas o M-3 foi mais sensível a variações. Uma padronização na velocidade de agitação, no tempo de repouso e uma climatização dos laboratórios tornam-se necessárias para diminuir a interferência causada sobre as quantidades de P extraído pelos métodos M-1 e M-3 em amostras de solo.

Performance of Strip Seals in Iowa Bridges, Project TR-437, January 2001

A pilot study was conducted on the premature failures of neoprene strip seals in expansion joints in Iowa bridges. In a relatively large number of bridges, strip seals have pulled out of the steel extrusions or otherwise failed well before the expected life span of the seal. The most serious consequence of a strip-seal failure is damage to the bridge substructure due to salt, water, and debris interacting with the substructure. A literature review was performed. Manufacturers’ specifications and recommendations, practices in the states bordering Iowa, and Iowa DOT design and installation guidelines were reviewed. Discussions were held with bridge contractors and the installation of a strip seal system was observed. Iowa DOT bridge databases were analyzed. A national survey was conducted on the use and performance of strip seals. With guidance from the Iowa DOT, twelve in-service bridges with strip-seal expansion joints were selected for detailed investigation. Effective bridge temperatures and corresponding expansion-joint openings were measured, DOT inspection reports were reviewed, and likely cause(s) of premature failures of strip seals were proposed. All of the seals used in the twelve bridges that had the most serious failures were in concrete girder bridges. Experimental results show that for a majority of these serious failures, the joint opening at 0° F predicted by the Iowa DOT design equations, the joint opening at 0° F extrapolated from the experimental data, or both, are larger than the movement rating of the strip seal specified on the bridge plans. Other likely causes of premature failures of seals in the twelve bridges include debris and ice in the seal cavity, a large skew and the corresponding decrease in the movement rating of the seal, improper installation, and improper setting of the initial gap.

Erosion Control for Highway Applications, Phase I: Review and Synthesis of Literature, Final Report, TR-464, May 2002

The project described herein has led to a convenient, computer-based expert system for identifying and evaluating potentially effective erosion- and sedimentation-control measures for use in roadway construction throughout Iowa and elsewhere in the Midwest. The expert system is intended to be an accessible and efficient practical resource to aid state, county, and municipal engineers in the selection of the best management practices for preventing unwanted erosion and sedimentation at roadway construction sites, during and after construction.

Evaluation of Safety Treatments for Roadside Culverts: TR-517, April 24, 2009

Roadside cross-drainage culverts have been found to impact vehicle accident injury levels. Designers have commonly used three safety treatments to protect errant drivers from culvert accidents. These treatments have included: culvert extension, guardrail installation and grating. In order to define which safety treatment is the most appropriate, benefit-cost analysis has used accident cost reduction to estimate societal gains earned by using any safety treatment. The purpose of this study was to estimate accident costs for a wide range of roadway and roadside characteristics so that designers can calculate benefit/cost ratios for culvert safety treatment options under any particular scenario. This study began with conducting a parametric study in order to find variables which have significant impact on accident cost changes. The study proceeded with highway scenario modeling which included scenarios with different values for combinations of roadway and roadside variables. These variables were chosen based upon findings from the parametric study and their values were assigned based upon highway classification. This study shows that the use of different culvert safety treatments should be flexible to roadway and roadside characteristics. It also shows that culvert extension and grating were the safety treatments found to produce the lowest accident costs for all highway scenarios modeled. Therefore, it is believed that the expanded adoption of culvert extension and culvert grates can improve overall highway safety.

Precast Concrete Elements for Accelerated Bridge Construction Final Report, Volume 1-1. Laboratory Testing of Precast Substructure Components: Boone County Bridge, January 2009

In July 2006, construction began on an accelerated bridge project in Boone County, Iowa that was composed of precast substructure elements and an innovative, precast deck panel system. The superstructure system consisted of full-depth deck panels that were prestressed in the transverse direction, and after installation on the prestressed concrete girders, post-tensioned in the longitudinal direction. Prior to construction, laboratory tests were completed on the precast abutment and pier cap elements. The substructure testing was to determine the punching shear strength of the elements. Post-tensioning testing and verification of the precast deck system was performed in the field. The forces in the tendons provided by the contractor were verified and losses due to the post-tensioning operation were measured. The stress (strain) distribution in the deck panels due to the post-tensioning was also measured and analyzed. The entire construction process for this bridge system was documented. Representatives from the Boone County Engineers Office, the prime contractor, precast fabricator, and researchers from Iowa State University provided feedback and suggestions for improving the constructability of this design.

Laboratory Performance Evaluation of CIR-Emulsion and it Comparison Against CIR-Form Test Result from Phase II, Final Report TR-578 Phase III, December 2009

Currently, no standard mix design procedure is available for CIR-emulsion in Iowa. The CIR-foam mix design process developed during the previous phase is applied for CIR-emulsion mixtures with varying emulsified asphalt contents. Dynamic modulus test, dynamic creep test, static creep test and raveling test were conducted to evaluate the short- and long-term performance of CIR-emulsion mixtures at various testing temperatures and loading conditions. A potential benefit of this research is a better understanding of CIR-emulsion material properties in comparison with those of CIR-foam material that would allow for the selection of the most appropriate CIR technology and the type and amount of the optimum stabilization material. Dynamic modulus, flow number and flow time of CIR-emulsion mixtures using CSS-h were generally higher than those of HFMS-2p. Flow number and flow time of CIR-emulsion using RAP materials from Story County was higher than those from Clayton County. Flow number and flow time of CIR-emulsion with 0.5% emulsified asphalt was higher than CIR-emulsion with 1.0% or 1.5%. Raveling loss of CIR-emulsion with 1.5% emulsified was significantly less than those with 0.5% and 1.0%. Test results in terms of dynamic modulus, flow number, flow time and raveling loss of CIR-foam mixtures are generally better than those of CIR-emulsion mixtures. Given the limited RAP sources used for this study, it is recommended that the CIR-emulsion mix design procedure should be validated against several RAP sources and emulsion types.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the 'intermediate phenotype' nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.

Inflammatory role of ASC in antigen-induced arthritis is independent of caspase-1, NALP-3, and IPAF.

Because IL-1beta plays an important role in inflammation in human and murine arthritis, we investigated the contribution of the inflammasome components ASC, NALP-3, IPAF, and caspase-1 to inflammatory arthritis. We first studied the phenotype of ASC-deficient and wild-type mice during Ag-induced arthritis (AIA). ASC(-/-) mice showed reduced severity of AIA, decreased levels of synovial IL-1beta, and diminished serum amyloid A levels. In contrast, mice deficient in NALP-3, IPAF, or caspase-1 did not show any alteration of joint inflammation, thus indicating that ASC associated effects on AIA are independent of the classical NALP-3 or IPAF inflammasomes. Because ASC is a ubiquitous cytoplasmic protein that has been implicated in multiple cellular processes, we explored other pathways through which ASC may modulate inflammation. Ag-specific proliferation of lymph node and spleen cells from ASC-deficient mice was significantly decreased in vitro, as was the production of IFN-gamma, whereas IL-10 production was enhanced. TCR ligation by anti-CD3 Abs in the presence or absence of anti-CD28 Abs induced a reduction in T cell proliferation in ASC(-/-) T cells compared with wild-type ones. In vivo lymph node cell proliferation was also significantly decreased in ASC(-/-) mice, but no effects on apoptosis were observed either in vitro or in vivo in these mice. In conclusion, these results strongly suggest that ASC modulates joint inflammation in AIA through its effects on cell-mediated immune responses but not via its implication in inflammasome formation.

T cells maintain an exhausted phenotype after antigen withdrawal and population reexpansion.

During chronic infection, pathogen-specific CD8(+) T cells upregulate expression of molecules such as the inhibitory surface receptor PD-1, have diminished cytokine production and are thought to undergo terminal differentiation into exhausted cells. Here we found that T cells with memory-like properties were generated during chronic infection. After transfer into naive mice, these cells robustly proliferated and controlled a viral infection. The reexpanded T cell populations continued to have the exhausted phenotype they acquired during the chronic infection. Thus, the cells underwent a form of differentiation that was stably transmitted to daughter cells. We therefore propose that during persistent infection, effector T cells stably differentiate into a state that is optimized to limit viral replication without causing overwhelming immunological pathology.

Role of HIV-1-specific CD4 T cells.

PURPOSE OF REVIEW: Most of the studies investigating antiviral immunity have predominantly focused on CD8 T cells. However, numerous recent studies have highlighted the importance of HIV-1-specific CD4 T cells in the antiviral immune response, and have also revealed the high level of complexity and heterogeneity of the virus-specific CD4 T-cell responses. An understanding of the role of these key players in the antiviral immune response is of fundamental importance.RECENT FINDINGS: A comprehensive investigation of several features of virus-specific CD4 T-cell responses, including the magnitude, breadth, function and phenotype, has recently been performed. In particular, HIV-1-specific CD4 T-cell responses have been studied in different stages of HIV-1 infection, i.e. acute and chronic phase, under conditions of spontaneous (long-term non-progressors) or antiviral therapy-mediated control of virus replication or uncontrolled virus replication. Different phenotypical and functional patterns of HIV-1-specific CD4 T-cell responses were associated with different conditions of controlled versus uncontrolled virus replication, thus allowing the identification of signatures of protective immune responses. Robust and diverse virus-specific CD4 T-cell responses have been observed. These responses, however, were not predictive of nonprogressive versus progressive HIV-1-associated disease.SUMMARY: There is an urgent need to delineate the immune correlates of protective T-cell responses in order to develop novel immunological markers to evaluate the degree of immune restoration of antiviral therapy as well as the potential effectiveness of HIV vaccine-induced T-cell immune responses.

A Candidate HIV/AIDS Vaccine (MVA-B) Lacking Vaccinia Virus Gene C6L Enhances Memory HIV-1-Specific T-Cell Responses.

The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, involved in regulation of host immune responses, but its role is unknown. Here, we have characterized the C6 protein and its effects in virus replication, innate immune sensing and immunogenicity in vivo. C6 is a 18.2 kDa protein, which is expressed early during virus infection and localizes to the cytoplasm of infected cells. Deletion of the C6L gene from the poxvirus vector MVA-B expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (MVA-B ΔC6L) had no effect on virus growth kinetics; therefore C6 protein is not essential for virus replication. The innate immune signals elicited by MVA-B ΔC6L in human macrophages and monocyte-derived dendritic cells (moDCs) are characterized by the up-regulation of the expression of IFN-β and IFN-α/β-inducible genes. In a DNA prime/MVA boost immunization protocol in mice, flow cytometry analysis revealed that MVA-B ΔC6L enhanced the magnitude and polyfunctionality of the HIV-1-specific CD4(+) and CD8(+) T-cell memory immune responses, with most of the HIV-1 responses mediated by the CD8(+) T-cell compartment with an effector phenotype. Significantly, while MVA-B induced preferentially Env- and Gag-specific CD8(+) T-cell responses, MVA-B ΔC6L induced more Gag-Pol-Nef-specific CD8(+) T-cell responses. Furthermore, MVA-B ΔC6L enhanced the levels of antibodies against Env in comparison with MVA-B. These findings revealed that C6 can be considered as an immunomodulator and that deleting C6L gene in MVA-B confers an immunological benefit by enhancing IFN-β-dependent responses and increasing the magnitude and quality of the T-cell memory immune responses to HIV-1 antigens. Our observations are relevant for the improvement of MVA vectors as HIV-1 vaccines.

A novel method of dynamic culture surface expansion improves mesenchymal stem cell proliferation and phenotype.

Repeated passaging in conventional cell culture reduces pluripotency and proliferation capacity of human mesenchymal stem cells (MSC). We introduce an innovative cell culture method whereby the culture surface is dynamically enlarged during cell proliferation. This approach maintains constantly high cell density while preventing contact inhibition of growth. A highly elastic culture surface was enlarged in steps of 5% over the course of a 20-day culture period to 800% of the initial surface area. Nine weeks of dynamic expansion culture produced 10-fold more MSC compared with conventional culture, with one-third the number of trypsin passages. After 9 weeks, MSC continued to proliferate under dynamic expansion but ceased to grow in conventional culture. Dynamic expansion culture fully retained the multipotent character of MSC, which could be induced to differentiate into adipogenic, chondrogenic, osteogenic, and myogenic lineages. Development of an undesired fibrogenic myofibroblast phenotype was suppressed. Hence, our novel method can rapidly provide the high number of autologous, multipotent, and nonfibrogenic MSC needed for successful regenerative medicine.