Deletion of nef slows but does not prevent CD4-positive T-cell depletion in human immunodeficiency virus type 1-infected human-PBL-SCID mice.

The pathogenicity of four human immunodeficiency virus type 1 (HIV-1) isolates with nef deleted for SCID mice repopulated with human peripheral blood leukocytes (hu-PBL-SCID mice) was studied. Deletion of nef led to a substantial reduction in CD4-positive T-cell depletion and delayed kinetics of plasma viremia in infected hu-PBL-SCID mice. Deletion of the nef gene impacts both the efficiency of primary infection and the cytopathicity of virus for infected CD4-positive T cells in this animal model of HIV-1 infection.     

Induction of B cell priming by neonatal injection of mice with thymic-independent (type 2) antigens.

Mice injected at birth with the thymus-independent type 2 antigen TNP-AECM-Ficoll have augmented anti-TNP antibody responses when their spleen cells subsequently are challenged in vitro with TNP-coupled thymic independent or thymic dependent antigens. This neonatal priming effect was shown to occur in neonatal nu/nu mice and thus does not appear to require T lymphocytes. The primary explanation for the priming effect seems to be an increase of approximately 10-fold in the numbers of TNP-specific precursors of antibody-forming cells. The neonatal injection of TNP-AECM-Ficoll induces little or no antibody formation directly. It appears, therefore, that some thymic independent antigens can deliver a signal to immature B cells, which causes clonal expansion, but is unable to induce differentiation into antibody-forming cells.     

Inhibition of cellulases by phenols

Enzyme hydrolysis of pretreated cellulosic materials slows as the concentration of solid biomass material increases, even though the ratio of enzyme to cellulose is kept constant. This form of inhibition is distinct from substrate and product inhibition, and has been noted for lignocellulosic materials including wood, corn stover, switch grass, and corn wet cake at solids concentrations greater than 10 g/L. Identification of enzyme inhibitors and moderation of their effects is of considerable practical importance since favorable ethanol production economics require that at least 200 g/L of cellulosic substrates be used to enable monosaccharide concentrations of 100 g/L, which result in ethanol titers of 50 g/L. Below about 45 g/L ethanol, distillation becomes energy inefficient. This work confirms that the phenols: vanillin, syringaldehyde, trans-cinnamic acid, and hydroxybenzoic acid, inhibit cellulose hydrolysis in wet cake by endo- and exo-cellulases, and cellobiose hydrolysis by β-glucosidase. A ratio of 4 mg of vanillin to 1 mg protein (0.5 FPU) reduces the rate of cellulose hydrolysis by 50%. β-Glucosidases from Trichoderma reesei and Aspergillus niger are less susceptible to inhibition and require about 10× and 100× higher concentrations of phenols for the same levels of inhibition. Phenols introduced with pretreated cellulose must be removed to maximize enzyme activity.     

Synthesis and biological evaluation of [D-lysine]8cyclosporin A analogs as potential anti-HCV agents

An efficient synthesis of [D-lysine](8)cyclosporin A has been developed. Several analogs of [D-lysine](8)cyclosporin A have been synthesized and show promising anti-HCV activity, particularly compounds 39 and 43, which each exhibit an anti-HCV EC(50)<200 nM, and are each ≥50-fold less immunosuppressive than cyclosporin A.     

9-Aminomethyl-9,10-dihydroanthracene (AMDA) analogs as structural probes for steric tolerance in 5-HT2A and H1 receptor binding sites

Synthesis, radioligand binding and molecular modeling studies of several 9-aminomethyl-9,10-dihydroanthracene (AMDA) analogs were carried out to determine the extent of the steric tolerance associated with expansion of the tricyclic ring system and amine substitution at 5-HT_2A and H₁ receptors. A mixture of (7,12-dihydrotetraphene-12-yl)methanamine and (6,11-dihydrotetracene-11-yl)methanamine in a 75–25% ratio was found to have an apparent K_i of 10 nM at the 5-HT_2A receptor. A substantial binding affinity for (7,12-dihydrotetraphene-3-methoxy-12-yl)methanamine at the 5-HT_2A receptor (K_i = 21 nM) was also observed. Interestingly, this compound was found to have 100-fold selectivity for 5-HT_2A over the H₁ receptor (K_i = 2500 nM). N-Phenylalkyl-AMDA derivatives, in which the length of the alkyl chain varied from methylene to n-butylene, were found to have only weak affinity for both 5-HT_2A and H₁ receptors (K_i = 223 to 964 nM). Our results show that large rigid annulated AMDA analogs can be sterically accommodated within the proposed 5-HT_2A binding site.     

Surprising negative association between IgG1 allotype disparity and anti-adalimumab formation: a cohort study

Introduction

The human monoclonal antibody adalimumab is known to induce an anti-globulin response in some adalimumab-treated patients. Antibodies against adalimumab (AAA) are associated with non-response to treatment. Immunoglobulins, such as adalimumab, carry allotypes which represent slight differences in the amino acid sequences of the constant chains of an IgG molecule. Immunoglobulins with particular IgG (Gm) allotypes are racially distributed and could be immunogenic for individuals who do not express these allotypes. Therefore, we investigated whether a mismatch in IgG allotypes between adalimumab and IgG in adalimumab-treated patients is associated with the development of AAA.

Methods

This cohort study consisted of 250 adalimumab-treated rheumatoid arthritis (RA) patients. IgG allotypes were determined for adalimumab and for all patients. Anti-idiotype antibodies against adalimumab were measured with a regular radio immunoassay (RIA), and a newly developed bridging enzyme linked immunosorbent assay (ELISA) was used to measure anti-allotype antibodies against adalimumab. The association between AAA and the G1m3 and the G1m17 allotypes was determined. For differences between groups we used the independent or paired samples t-test, Mann-Whitney test or Chi square/Fisher's exact test as appropriate. To investigate the influence of confounders on the presence or absence of AAA a multiple logistic regression-analysis was used.

Results

Adalimumab carries the G1m17 allotype. No anti-allotype antibodies against adalimumab were detected. Thirty-nine out of 249 patients had anti-idiotype antibodies against adalimumab (16%). IgG allotypes of RA patients were associated with the frequency of AAA: patients homozygous for G1m17 had the highest frequency of AAA (41%), patients homozygous for G1m3 the lowest frequency (10%), and heterozygous patients' AAA frequency was 14% (P = 0.0001).

Conclusions

An allotype mismatch between adalimumab and IgG in adalimumab-treated patients did not lead to a higher frequency of AAA. On the contrary, patients who carried the same IgG allotype as present on the adalimumab IgG molecule, had the highest frequency of anti-adalimumab antibodies compared to patients whose IgG allotype differed from adalimumab. This suggests that the allotype of adalimumab may not be highly immunogenic. Furthermore, patients carrying the G1m17-allotype might be more prone to antibody responses.     

Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

Background  

The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T ²-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other.     

Water relations in grassland and desert ecosystems exposed to elevated atmospheric CO2

Atmospheric CO₂ enrichment may stimulate plant growth directly through (1) enhanced photosynthesis or indirectly, through (2) reduced plant water consumption and hence slower soil moisture depletion, or the combination of both. Herein we describe gas exchange, plant biomass and species responses of five native or semi-native temperate and Mediterranean grasslands and three semi-arid systems to CO₂ enrichment, with an emphasis on water relations. Increasing CO₂ led to decreased leaf conductance for water vapor, improved plant water status, altered seasonal evapotranspiration dynamics, and in most cases, periodic increases in soil water content. The extent, timing and duration of these responses varied among ecosystems, species and years. Across the grasslands of the Kansas tallgrass prairie, Colorado shortgrass steppe and Swiss calcareous grassland, increases in aboveground biomass from CO₂ enrichment were relatively greater in dry years. In contrast, CO₂-induced aboveground biomass increases in the Texas C₃/C₄ grassland and the New Zealand pasture seemed little or only marginally influenced by yearly variation in soil water, while plant growth in the Mojave Desert was stimulated by CO₂ in a relatively wet year. Mediterranean grasslands sometimes failed to respond to CO₂-related increased late-season water, whereas semiarid Negev grassland assemblages profited. Vegetative and reproductive responses to CO₂ were highly varied among species and ecosystems, and did not generally follow any predictable pattern in regard to functional groups. Results suggest that the indirect effects of CO₂ on plant and soil water relations may contribute substantially to experimentally induced CO₂-effects, and also reflect local humidity conditions. For landscape scale predictions, this analysis calls for a clear distinction between biomass responses due to direct CO₂ effects on photosynthesis and those indirect CO₂ effects via soil moisture as documented here.     

Policy implications of human-accelerated nitrogen cycling

The human induced input of reactive N into the globalbiosphere has increased to approximately 150 Tg N eachyear and is expected to continue to increase for theforeseeable future. The need to feed (125 Tg N) andto provide energy (25 Tg N) for the growing worldpopulation drives this trend. This increase inreactive N comes at, in some instances, significantcosts to society through increased emissions of NO_x,NH₃, N₂O and NO₃ ^– and deposition of NO_y and NH_x.In the atmosphere, increases in tropospheric ozone andacid deposition (NO_y and NH_x) have led toacidification of aquatic and soil systems and toreductions in forest and crop system production. Changes in aquatic systems as a result of nitrateleaching have led to decreased drinking water quality,eutrophication, hypoxia and decreases in aquatic plantdiversity, for example. On the other hand, increaseddeposition of biologically available N may haveincreased forest biomass production and may havecontributed to increased storage of atmospheric CO₂ inplant and soils. Most importantly, syntheticproduction of fertilizer N has contributed greatly tothe remarkable increase in food production that hastaken place during the past 50 years.The development of policy to control unwanted reactiveN release is difficult because much of the reactive Nrelease is related to food and energy production andreactive N species can be transported great distancesin the atmosphere and in aquatic systems. There aremany possibilities for limiting reactive N emissionsfrom fuel combustion, and in fact, great strides havebeen made during the past decades. Reducing theintroduction of new reactive N and in curtailing themovement of this N in food production is even moredifficult. The particular problem comes from the factthat most of the N that is introduced into the globalfood production system is not converted into usableproduct, but rather reenters the biosphere as asurplus. Global policy on N in agriculture isdifficult because many countries need to increase foodproduction to raise nutritional levels or to keep upwith population growth, which may require increaseduse of N fertilizers. Although N cycling occurs atregional and global scales, policies are implementedand enforced at the national or provincial/statelevels. Multinational efforts to control N loss tothe environment are surely needed, but these effortswill require commitments from individual countries andthe policy-makers within those countries.