Cross-subtype neutralizing antibodies induced in baboons by a subtype E gp120 immunogen based on an R5 primary human immunodeficiency virus type 1 envelope

Global human immunodeficiency virus type 1 (HIV-1) diversity may require engineering vaccines to express antigens representing strains prevalent in the target population of vaccine testing. The majority (90%) of incident infections in Thailand are genetic subtype E, with a small percentage of subtype B infections in the intravenous drug user populations. We have evaluated and compared the binding and HIV-1 neutralizing properties of serum antibodies induced in baboons by CHO cell-expressed monomeric gp120 derived from a CCR5-using (R5) subtype E primary HIV-1CM235 or a CXCR4-using (X4) subtype B T-cell line-adapted (TCLA) HIV-1SF2 isolate. In contrast to the subtype-specific HIV-1 neutralizing antibodies induced with recombinant HIV-1SF2 gp120 (rgp120SF2), rgp120CM235 immunization induced antibodies capable of neutralizing both subtype E and subtype B TCLA HIV-1 isolates. However, neither immunogen induced antibodies capable of neutralizing primary HIV-1 isolates. Antibody induced by rgp120CM235 preferentially bound natively folded gp120 and retained strong cross-reactivity against multiple gp120 strains within subtype E as well as subtype B. In contrast, antibody responses to rgp120SF2 were directed predominantly to linear epitopes poorly exposed on native gp120 and had more limited cross-recognition of divergent gp120. Fine epitope mapping revealed differences in antibody specificities. While both rgp120CM235 and rgp120SF2 induced antibodies to regions within C1, V1/V2, V3, and C5, unique responses were induced by rgp120CM235 to multiple epitopes within C2 and by rgp120SF2 to multiple epitopes within C3, V4, and C4. These data demonstrate that strain and/or phenotypic differences of HIV-1 subunit gp120 immunogens can substantially alter antibody binding specificities and subsequent HIV-1 neutralizing capacity.     

Origin and relationships of New Zealand chestnut (Castanea sp.Fagaceae) selections reflect patterns of graft failure

Graft failure that occurs in the clonal propagation of chestnuts is a practical problem which has arisen in recent years. Several hypotheses have been put forward to explain reasons for the failure but none have focused on origin and relationships of cultivars. This study was carried out to determine whether relationships of New Zealand chestnut selections and their origin reflect patterns of graft failure within the selections. Two different character data sets, random amplified polymorphic DNA (RAPD) and morpho-nut, were employed for the analyses of the relationships between the chestnut selections. Four different analyses were done to generate trees depicting the relationships of the selections. These were: morpho-nut character, RAPD character, taxonomic congruence (combination of morpho-nut and RAPD trees), and character congruence (combination of morpho-nut and RAPD data sets). When graft failure data were mapped onto the majority rule consensus tree constructed from character congruence analysis, it was found that self graft incompatibility was reflected in the origin and relationships of the chestnut selections. Information on the affinities of the chestnut selections to introduced chestnut species showed that the selections that were mostly implicated in graft failure which are from the North Island had affinities with theCastanea crenata species. But the selections (from the South Island) that were placed withCastanea sativa as well as hybrids (1002 and 1007 from the North Island) ofCastanea mollissima andC. crenata had no failed grafts. This finding indicates that graft failure in New Zealand chestnut selections does not occur by chance but is dependent on the origin and/or evolutionary history of the selections.     

AluElements: Repetitive DNA as Facilitators of Chromosomal Rearrangement

Alu repeats are the most common type of repetitive DNA sequences dispersed throughout the human genome. Technical advances in the field of cytogenetics and molecular biology have facilitated the analysis of epithelial tumors and hematologic malignancies which has led to the observation of Alu elements in and near sites often involved in chromosomal rearrangements. Repair mechanisms of double strand breaks (DSB) such as homol-ogous recombination (HR) may rely on the sequence homology of Alu repeats, potentially leading to chromosomal rearrange-ments. Databases have confirmed the strong association between Alu repeats, specifically the 26 bp consensus sequence and chro-mosomal regions involved in deletions and translocations. Although the Alu repetitive sequence is a potential "hotspot" during homologous recombination, there are other cellular mech-anisms that may play a more prominent role in the initiation of chromosomal rearrangements.     

Severe CD4+ T-cell depletion in gut lymphoid tissue during primary human immunodeficiency virus type 1 infection and substantial delay in restoration following highly active antiretroviral therapy

Gut-associated lymphoid tissue (GALT) harbors the majority of T lymphocytes in the body and is an important target for human immunodeficiency virus type 1 (HIV-1). We analyzed longitudinal jejunal biopsy samples from HIV-1-infected patients, during both primary and chronic stages of HIV-1 infection, prior to and following the initiation of highly active antiretroviral therapy (HAART) to determine the onset of CD4(+) T-cell depletion and the effect of HAART on the restoration of CD4(+) T cells in GALT. Severe depletion of intestinal CD4(+) T cells occurred during primary HIV-1 infection. Our results showed that the restoration of intestinal CD4(+) T cells following HAART in chronically HIV-1-infected patients was substantially delayed and incomplete. In contrast, initiation of HAART during early stages of infection resulted in near-complete restoration of intestinal CD4(+) T cells, despite the delay in comparison to peripheral blood CD4(+) T-cell recovery. DNA microarray analysis of gene expression profiles and flow-cytometric analysis of lymphocyte homing and cell proliferation markers demonstrated that cell trafficking to GALT and not local proliferation contributed to CD4(+) T-cell restoration. Evaluation of jejunal biopsy samples from long-term HIV-1-infected nonprogressors showed maintenance of normal CD4(+) T-cell levels in both GALT and peripheral blood. Our results demonstrate that near-complete restoration of mucosal immune system can be achieved by initiating HAART early in HIV-1 infection. Monitoring of the restoration and/or maintenance of CD4(+) T cells in GALT provides a more accurate assessment of the efficacy of antiviral host immune responses as well as HAART.     

Elevated temperature effects on the oxidant/antioxidant balance in submerged batch cultures of the filamentous fungus Aspergillus niger B1-D

In the present study the relationship between oxidative stress and elevated culture temperature was examined in an industrially relevant fungal culture, Aspergillus niger B1-D. For the first time, both the intracellular levels of the main stressor species (superoxide radical [O(2) (.-)]) and activities of cellular defensive enzymes (superoxide dismutase [SOD], catalase [CAT], and glutathione peroxide [GPx]) were quantified at varying temperature (25, 30, 35, 40 degrees C) to more fully characterize culture response in different growth phases. Elevated culture temperature led to increased O(2) (.-) levels in various culture phases. In the exponential phase this was due to an enhanced generation of O(2) (.-), whereas in stationary phase a decreased dismutation rate may also have contributed. CAT activities generally increased with culture temperature, whereas GPx activity changed little as temperature rose, indicating that GPx played only a minor role in destroying H(2)O(2) in this A. niger. The combination of elevated temperature (35 degrees C) and increased O(2) supply (50% enrichment) led to decreased levels of O(2) (.-) compared to the cultivation at 35 degrees C gassed with air, probably due to enhanced activity of the alternative fungal respiratory pathway. Our findings indicate that while elevated cultivation temperature does clearly induce oxidative stress events, mechanistically, it does so by a rather more complex route than previous studies indicate. Elevated temperature caused a marked disparity in the activities of SOD and CAT, very distinct from the integrated increase in activity of these enzymes in response to oxidative stress.     

In-situ near infrared spectroscopy to monitor key analytes in mammalian cell cultivation

The use of in-situ near infrared spectroscopy (NIRS) as a tool for monitoring four key analytes in a CHO-K1 animal cell culture was investigated. Previous work using on-line NIRS to monitor bioprocesses has involved its application ex-situ where the analyzer is physically outside the fermentor, or to microbial bioprocesses. This novel application of NIRS to monitor analytes within an animal cell culture using a steam sterilizable in-situ fiber optic probe is very important for furthering the use of NIRS within the bioprocessing industry. The method of calibration used to develop the models involved the use of large data sets so that all likely variation in stoichiometry was incorporated within the models. Successful models for glucose, lactate, glutamine, and ammonia were built with Standard Error of Predictions (SEP's) of 0.072 (g/L), 0.0144 (g/L), 0.308 (mM), and 0.036 (mM), respectively of the total concentration range.     

Use of at-line and in-situ near-infrared spectroscopy to monitor biomass in an industrial fed-batch Escherichia coli process

One of the key goals in bioprocess monitoring is to achieve real-time knowledge of conditions within the bioreactor, i.e., in-situ. Near-infrared spectroscopy (NIRS), with its ability to carry out multi-analyte quantification rapidly with little sample presentation, is potentially applicable in this role. In the present study, the application of NIRS to a complex, fed-batch industrial E. coli (RV308/PHKY531) process was investigated. This process undergoes a series of temperature changes and is vigorously agitated and aerated. These conditions can pose added challenges to in-situ NIRS. Using the measurement of a key analyte (biomass) as an illustration, the details of the relationship between the at-line and in-situ use of NIRS are considered from the viewpoint of both theory and practical application. This study shows that NIRS can be used both at-line and in-situ in order to achieve good predictive models for biomass. There are particular challenges imposed by in-situ operation (loss of wavelength regions and noise) which meant the need for signal optimisation studies. This showed that whilst the at-line modelling process may provide some useful information for the in-situ process, there were distinct differences. This study shows that the in-situ use of NIRS in a highly challenging matrix (similar to those encountered in current industrial practice) is possible, and thus extends previous works in the area.     

Disposable tyrosinase-peroxidase bi-enzyme sensor for amperometric detection of phenols

A new disposable amperometric bi-enzyme sensor system for detecting phenols has been developed. The phenol sensor developed uses horseradish peroxidase modified screen-printed carbon electrodes (HRP-SPCEs) coupled with immobilized tyrosinase prepared using poly(carbamoylsulfonate) (PCS) hydrogels or a poly(vinyl alcohol) bearing styrylpyridinium groups (PVA-SbQ) matrix. Optimization of the experimental parameters has been performed with regard to buffer composition, pH, operating potential and storage stability. A co-operative reaction involving tyrosinase and HRP occurs at a potential of -50 mV versus Ag/AgCl without the requirement for addition of extraneous H(2)O(2), thus, resulting in a very simple and efficient system. Comparison of the electrode responses with the 4-aminoantipyrine standard method for phenol sample analysis indicated the feasibility of the disposable sensor system for sensitive "in-field" determination of phenols. The most sensitive system was the tyrosinase immobilized HRP-SPCE using PCS, which displayed detection limits for phenolic compounds in the lower nanomolar range e.g. 2.5 nM phenol, 10 nM catechol and 5 nM p-cresol.