Paired field and water measurements from drainage management practices in row-crop agriculture.

This paper describes a multi-site and multi-decadal dataset of artificially drained agricultural fields in seven Midwest states and North Carolina, USA. Thirty-nine research sites provided data on three conservation practices for cropland with subsurface tile drainage: saturated buffers, controlled drainage, and drainage water recycling. These practices utilize vegetation and/or infrastructure to minimize off-site nutrient losses and retain water in the landscape. A total of 219 variables are reported, including 90 field measurement variables and 129 management operations and metadata. Key measurements include subsurface drain flow (206 site-years), nitrate-N load (154 site-years) and other water quality metrics, as well as agronomic, soil, climate, farm management and metadata records. Data are published at the USDA National Agricultural Library Ag Data Commons repository and are also available through an interactive website at Iowa State University. These multi-disciplinary data have large reuse potential by the scientific community as well as for design of drainage systems and implementation in the US and globally.

The molecular landscape and associated clinical experience in infant medulloblastoma: prognostic significance of second-generation subtypes.

AIMS: Biomarker-driven therapies have not been developed for infant medulloblastoma (iMB). We sought to robustly sub-classify iMB, and proffer strategies for personalized, risk-adapted therapies. METHODS: We characterized the iMB molecular landscape, including second-generation subtyping, and the associated retrospective clinical experience, using large independent discovery/validation cohorts (n = 387). RESULTS: iMBGrp3 (42%) and iMBSHH (40%) subgroups predominated. iMBGrp3 harboured second-generation subtypes II/III/IV. Subtype II strongly associated with large-cell/anaplastic pathology (LCA; 23%) and MYC amplification (19%), defining a very-high-risk group (0% 10yr overall survival (OS)), which progressed rapidly on all therapies; novel approaches are urgently required. Subtype VII (predominant within iMBGrp4 ) and subtype IV tumours were standard risk (80% OS) using upfront CSI-based therapies; randomized-controlled trials of upfront radiation-sparing and/or second-line radiotherapy should be considered. Seventy-five per cent of iMBSHH showed DN/MBEN histopathology in discovery and validation cohorts (P < 0.0001); central pathology review determined diagnosis of histological variants to WHO standards. In multivariable models, non-DN/MBEN pathology was associated significantly with worse outcomes within iMBSHH . iMBSHH harboured two distinct subtypes (iMBSHH-I/II ). Within the discriminated favourable-risk iMBSHH DN/MBEN patient group, iMBSHH-II had significantly better progression-free survival than iMBSHH-I , offering opportunities for risk-adapted stratification of upfront therapies. Both iMBSHH-I and iMBSHH-II showed notable rescue rates (56% combined post-relapse survival), further supporting delay of irradiation. Survival models and risk factors described were reproducible in independent cohorts, strongly supporting their further investigation and development. CONCLUSIONS: Investigations of large, retrospective cohorts have enabled the comprehensive and robust characterization of molecular heterogeneity within iMB. Novel subtypes are clinically significant and subgroup-dependent survival models highlight opportunities for biomarker-directed therapies.

Endoscopic appearance and location dictate diagnostic yield of biopsies in eosinophilic oesophagitis.

BACKGROUND: Acknowledging that eosinophilic esophagitis (EoE) is a disease with variable involvement throughout the oesophagus, studies have suggested a minimum of five biopsies to diagnose EoE. Although it is accepted that furrows and exudates appear to represent areas of inflammation, no research to date has looked specifically at EoE endoscopic findings to see if eosinophilic infiltrate correlates with specific endoscopic findings. AIM: To evaluate the distribution of eosinophils in EoE and determine whether endoscopic appearances predict the degree of eosinophilia at various locations of the oesophagus. METHODS: We performed a prospective cross sectional study of EoE (treated and untreated) patients to study the distribution of eosinophils according to endoscopic findings. The oesophagus of 10 EoE patients were biopsied up to 32 times in a circumferential manner. The mucosal changes were documented at the site of each biopsy. Histological determination of eosinophil counts and related histopathology of the oesophagus were then correlated with endoscopic findings. Similar biopsy assessments were made in treated (resolved) EoE patients (n = 6) to determine the permanence of specific endoscopic appearances. RESULTS: A total of 16 patients were biopsied (10 EoE, 6 treated EoE). A total of 432 biopsies were obtained in all with 294 biopsies from 10 EoE subjects. Eosinophil density was increased distally in the majority of EoE patients. Biopsies performed in areas of exudates and furrows demonstrated higher eosinophil counts. Lines and normal-appearing oesophagi in EoE subjects were not commonly associated with elevated eosinophil counts (>15 eos/HPF). Rings alone without associated furrows or plaques did not demonstrate elevated eosinophil counts and were seen in resolved EoE (Rx-EoE) as well as in active EoE patients. CONCLUSIONS: Eosinophilic esophagitis remains a variable disease with some patients manifesting extensive disease throughout the oesophagus. Characteristics of furrows and exudates found during endoscopy are associated with higher peak eosinophil counts, requiring fewer biopsies to make a diagnosis. Lines and otherwise normal appearances of the oesophagus suggest a milder mucosal eosinophilia, requiring substantial biopsies to adequately identify fields with diagnostic eosinophil counts.

Aggregation kinetics of colloidal particles measured by gas-phase differential mobility analysis.

We demonstrate the utility of electrospray gas-phase ion-mobility analysis as a new method to investigate nanoparticle flocculation, or aggregation. Au nanoparticle (Au-NP) solutions were sampled via electrospray (ES), followed by differential ion-mobility analysis (DMA) to determine the particle mobility distribution. Multimodal size distributions obtained with ES-DMA indicated the presence of single Au-NPs (monomer) as well as larger Au-NP clusters such as dimers, trimers, and tetramers under specific solution conditions. The fraction of each aggregate species as a function of time was quantitatively characterized, from which the degree of aggregation, aggregation rate, and stability ratio at different ionic strengths were determined. The latter enabled the extraction of a surface potential (or surface charge density) of 64 +/- 2 mV for 10 nm Au-NPs, which is in good agreement with values obtained from other methods, thus validating our approach. Our results show that ES-DMA is a valuable tool for quantitatively probing the early stages of colloidal aggregation or as a preparatory tool for the size election of aggregates.

Gas-phase ion-mobility characterization of SAM-functionalized Au nanoparticles.

We present results of a systematic examination of functionalized gold nanoparticles (Au-NPs) by electrospray-differential mobility analysis (ES-DMA). Commercially available, citrate-stabilized Au colloid solutions (10-60 nm) were sized using ES-DMA, from which changes in particle size of less than 0.3 nm were readily discerned. It was found that the formation of salt particles and the coating of Au-NPs by salt during the electrospray process can interfere with the mobility analysis, which required the development of sample preparation and data correction protocols to extract correct values for the Au-NP size. Formation of self-assembled monolayers (SAMs) of alkanethiol molecules on the Au-NP surface was detected from a change in particle mobility, which could be modeled to extract the surface packing density of SAMs. A gas-phase temperature-programmed desorption (TPD) kinetic study of SAMs on Au-NPs found the data to be consistent with a second-order Arrhenius-based rate law, yielding an Arrhenius factor of 1.0 x 10 (11) s (-1) and an activation energy approximately 105 kJ/mol. For the size range of SAM-modified Au-NP we considered, the effect of surface curvature on the energetics of binding of carboxylic acid terminated SAMs is evidently negligible, with binding energies determined by TPD agreeing with those reported for the same SAMs on planar surfaces. This study suggests that the ES-DMA can be added to the tool set of characterization methods used to study the structure and properties of coated nanoparticles.

Immunomodulation using the recombinant monoclonal human B7-DC cross-linking antibody rHIgM12.

A patient with Waldenstrom's macroglobulinaemia expresses a high titre IgM antibody in serum that binds both mouse and human dendritic cells (DC) in a B7-DC (PD-L2)-dependent manner. We have reported previously that purified antibody from patient serum activates immature and mature DC in vitro, enhancing the ability of these professional antigen-presenting cells to activate naive T cells, take up antigen, resist a cytokine-depleted environment and secrete immunomodulatory cytokines, such as interleukin (IL)-6 and tumour necrosis factor (TNF)-alpha. Systemic treatment of experimental animals with this antibody induces potent anti-melanoma immunity and modulates protectively the recall response against antigen challenge through the airway in an experimental model of inflammatory airway disease. Here we describe a monoclonal IgM antibody derived from this serum immunoglobulin that recapitulates each of these earlier observations, providing direct evidence that M protein from the Waldenstrom's patient mediates these potent immunomodulatory effects. Furthermore, cell lines expressing this recombinant form of the human antibody provide the basis for developing this reagent for clinical application.

Differential protein acetylation induced by novel histone deacetylase inhibitors.

Histone deacetylase (HDAC) inhibitors induce the hyperacetylation of nucleosomal histones in carcinoma cells resulting in the expression of repressed genes that cause growth arrest, terminal differentiation, and/or apoptosis. In vitro selectivity of several novel hydroxamate HDAC inhibitors including succinimide macrocyclic hydroxamates and the non-hydroxamate alpha-ketoamide inhibitors was investigated using isolated enzyme preparations and cellular assays. In vitro selectivity for the HDAC isozymes (HDAC1/2, 3, 4/3, and 6) was not observed for these HDAC inhibitors or the reference HDAC inhibitors, MS-275 and SAHA. In T24 and HCT116 cells these compounds caused the accumulation of acetylated histones H3 and H4; however, the succinimide macrocyclic hydroxamates and the alpha-ketoamides did not cause the accumulation of acetylated alpha-tubulin. These data suggest "selectivity" can be observed at the cellular level with HDAC inhibitors and that the nature of the zinc-chelating moiety is an important determinant of activity against tubulin deacetylase.

The effect of molluscan glue proteins on gel mechanics.

Several molluscs have been shown to alternate between a non-adhesive trail mucus and a similar gel that forms a strong glue. The major structural difference between the two secretions is the presence of specific proteins in the adhesive mucus. The present study identifies similar proteins from the glue of the slug Arion subfuscus and the land snail Helix aspersa. To investigate the role played by these proteins in adhesion, the proteins were isolated from the adhesive mucus of different molluscs and added to commercial polymer solutions. The effect was observed qualitatively, and quantified using a dynamic rheometer. The isolated proteins triggered gelling or visible stiffening of agar, pectin and polygalacturonic acid. The effect was stronger on more negatively charged polymers. The effect of the proteins was concentration dependent with an optimal concentration of 1-1.5 mg ml(-1), and was weakened when their structure changed. Other proteins and carbohydrates found in the adhesive mucus had no clear mechanical effect on gels. These findings show that the addition of these proteins to large, anionic polymers plays a central role in the formation of a glue from a mucus-like secretion. Such a mechanism may be common among invertebrates, and it may guide biomimetic approaches in the development of glues and gels.

Enhanced binding of low-affinity antibodies interacting simultaneously with targeted cell surface molecules and Fc receptor.

The possibility that different forms of class I molecules might be expressed on the cell surface of lymphocytes has been investigated periodically over the past several decades. A series of major histocompatibility complex (MHC) class I-specific monoclonal antibodies, including the commonly used antibodies 64-3-7 and 25-D1.16, bind B cells differentially, suggesting the existence of differentially expressed class I-associated cell surface determinants on B lymphocytes. However, the ability of antibodies to bind cells is determined by the sum of interactions between the antibodies and the molecules expressed on the cell surface. The interactions of class I-specific antibodies with B cells were dissected, revealing dual specificity of the antibodies for the targeted class I molecules, as well as to Fc receptors preferentially expressed by B cells. We demonstrate that antibodies simultaneously bind targeted class I molecules and Fc receptors expressed on the surface of B cells. Simultaneous binding to two cell surface structures significantly enhances the class I-specific binding pattern of certain antibodies by increasing their avidity, leading to apparent cell-specific differences in MHC expression patterns. We conclude that no differences in MHC structures need be postulated to account for the observed binding patterns.

Discovery of selective hydroxamic acid inhibitors of tumor necrosis factor-alpha converting enzyme.

Modification of the P(1)' substituent of macrocyclic matrix metalloproteinase (MMP) inhibitors provided compounds that are selective for inhibition of tumor necrosis factor-alpha converting enzyme (TACE) over MMP-1 and MMP-2. Several analogues potently inhibited the release of TNF-alpha in a THP-1 cellular assay. Compounds containing a trimethoxyphenyl group in the P(1)' substituent demonstrated TACE selectivity across several series of hydroxamate-based inhibitors.

Immunoglobulin-mediated CNS repair.

Our view of the immune system continues to evolve from a system dedicated primarily to defense against pathogens to a system that monitors the integrity of the organism and aids in repair following damage. Repair following injury to the central nervous system (CNS) is facilitated by both cellular and humoral components of the immune system. Transfer of macrophages or T cells activated against CNS antigens promote axon regrowth and protect axons from further damage. Animals immunized with spinal cord antigens and subsequently challenged with demyelination or transection of the spinal cord demonstrate better repair than animals without prior immunization. In both experimental systems, antibodies are the biologically active immune component. Human mAbs reactive to oligodendrocytes that arise in the absence of neurologic injury promote remyelination. These data support the hypothesis that B-cell clones producing mAbs reactive to CNS epitopes are a normal part of the human antibody repertoire. They challenge the assertion that an immune response to CNS antigens is pathogenic. Treatment with CNS-reactive human mAbs following CNS disease may facilitate CNS regeneration.

Preservation of motor function by inhibition of CD8+ virus peptide-specific T cells in Theiler's virus infection.

Central nervous system-infiltrating CD8+ T cells are potential mediators of neuropathology in models of multiple sclerosis induced by Theiler's murine encephalomyelitis virus (TMEV) infection. C57BL/6 mice mount a vigorous cytotoxic T lymphocyte (CTL) response against the immunodominant virus peptide VP2121-130 and clear TMEV infection. Interferon-g (IFN-g)R-/- mice also mount a strong CTL response against the VP2121-130 epitope, but because of genetic deficiencies in critical IFN-g signaling pathways, they do not clear TMEV infection and develop prominent neurological deficits within 6 wk. This pronounced disease process, coupled with a defined CTL response, provides an ideal model for evaluating the importance of antiviral CTL activity in the development of severe demyelination and loss of motor neuron function. By administering the VP2121-130 peptide before and during TMEV infection, 99% of the VP2121-130-specific CD8+ T cell response was inhibited. No decrease in virus infection was observed. Peptide treatment did result in significantly less motor dysfunction, even when no differences in levels of demyelination were observed. Although most investigators focus on the role of CD4+ T cells in demyelinating disease, these studies are the first to demonstrate a clear contribution of antiviral CD8+ T cells in neurological injury in a chronic-progressive model of multiple sclerosis.

Monomeric class I molecules mediate TCR/CD3 epsilon/CD8 interaction on the surface of T cells.

Both CD8 and the TCR bind to MHC class I molecules during physiologic T cell activation. It has been shown that for optimal T cell activation to occur, CD8 must be able to bind the same class I molecule that is bound by the TCR. However, no direct evidence for the class I-dependent association of CD8 and the TCR has been demonstrated. Using fluorescence resonance energy transfer, we show directly that a single class I molecule causes TCR/CD8 interaction by serving as a docking molecule for both CD8 and the TCR. Furthermore, we show that CD3epsilon is brought into close proximity with CD8 upon TCR/CD8 association. These interactions are not dependent on the phosphorylation events characteristic of T cell activation. Thus, MHC class I molecules, by binding to both CD8 and the TCR, mediate the reorganization of T cell membrane components to promote cellular activation.

Theiler's virus-infected L-selectin-deficient mice have decreased infiltration of CD8(+) T lymphocytes in central nervous system but clear the virus.

Mice with targeted deletion of L-selectin gene (L-sel(-/-)) were used to investigate the role of adhesion molecule in immunologic responses following virus infection in the central nervous system (CNS). L-Sel(-/-) mice from a resistant H-2(b) genetic background and parental wild-type H-2(b) (C57BL/6) mice were infected with Theiler's murine encephalomyelitis virus (TMEV) intracerebrally and the kinetics of virus replication and infiltration of immune cells in the CNS determined. The levels of infectious TMEV, as measured by plaque assay at 3, 7, 14, and 28 days after infection were between 4 and 6 log(10) PFU of virus per gram of CNS tissues at days 3 and 7 post-infection, and then decreased to undetectable levels by day 14 after infection in both strains of mice. The L-sel(-/-) mice had decreased numbers of CD8(+) T lymphocytes (17.72%+/-2.4) infiltrating into the CNS at 7 days post-infection when compared to wild-type mice (31.02%+/-7.5). In addition, the L-sel(-/-) mice had significantly lower levels of TMEV-specific serum IgG resulting in lower virus neutralizing activity of the serum when compared to wild-type mice. However, the L-sel(-/-) mice had 2.5-fold increase in B lymphocytes in the CNS (8.29%+/-1.1) when compared to wild-type mice (3.2%+/-0.4). Taken together, these data indicate that L-selectin plays a role in recruitment of B and CD8(+) T lymphocytes into the CNS following virus infection, which, however, did not affect the ability of the mice to clear TMEV infection.

Thermal stability of MHC class I-beta 2-microglobulin peptide complexes in the endoplasmic reticulum is determined by the peptide occupancy of the transporter associated with antigen processing complex.

Once MHC class I heavy chain binds beta(2)-microglobulin (beta(2)m) within the endoplasmic reticulum, an assembly complex comprising the class I heterodimer, TAP, TAPasin, calreticulin, and possibly Erp57 is formed before the binding of high affinity peptide. TAP-dependent delivery of high affinity peptide to in vitro translated K(b)beta(2)m complexes within microsomes (TAP(+)/TAPasin(+)) was studied to determine at which point peptide binding becomes resistant to thermal denaturation. It was determined that the thermal stability of K(b)-beta(2)m-peptide complexes depends on the timing of peptide binding to K(b)beta(2)m relative to TAP binding high affinity peptide. Premature exposure of the TAP complex to high affinity peptide before its association with class I heavy chain results in K(b)beta(2)m-peptide-TAP complexes that lose peptide upon exposure to elevated temperature after solubilization away from microsome-associated proteins. These findings suggest that the order in which class I heavy chain associates with endoplasmic reticulum-resident chaperones and peptide determines the stability of K(b)beta(2)m-peptide complexes.

Clonal evolution in Waldenstrom macroglobulinemia highlights functional role of B-cell receptor.

The course of clonal evolution of 2 related clones in the blood of a patient with Waldenstrom macroglobulinemia (WM) indicates the functional importance for the expression of the B-cell receptor for the survival of these malignant cells. Protein and nucleotide sequencing of the paraproteins' variable regions revealed 2 predominant Vlambda and 2 VH sequences, each set comprised in the ratio 1:1.5. The 2 VH sequences and 2 Vlambda sequences shared the same VDJ and VJ junctional sequences, respectively, indicating that 2 malignant clones had evolved from a common ancestor. This is the first report on intraclonal heterogeneity in WM. Comparison of the Vlambda and VH sequences with the closest matching known germline genes showed that they contained approximately 10 somatic mutations each. The distribution and type of mutations demonstrate that mutations have continued to accumulate in the malignant clones and that selection has been operating to preserve immunoglobulin structure.

Humoral autoimmunity as a mediator of CNS repair.

Autoimmune responses directed against the central nervous system (CNS) have generally been considered pathogenic in nature. Although there are several well understood conditions in which this is the case, there is also a growing body of experimental evidence to show that both the cellular and humoral immune responses can promote tissue repair following CNS injury and disease. Our laboratory has used a mouse model of chronic demyelinating disease to characterize a class of polyreactive IgM autoantibodies that react with oligodendrocyte surface antigens and promote myelin repair. By screening a large number of human monoclonal antibodies, we have found that IgM antibodies that react with CNS tissue are relatively common. Autoreactive IgM antibodies might constitute an endogenous system for tissue repair, and therefore these antibodies could be of value as therapeutic reagents.

Human monoclonal antibodies reactive to oligodendrocytes promote remyelination in a model of multiple sclerosis.

Promoting remyelination, a major goal of an effective treatment for demyelinating diseases, has the potential to protect vulnerable axons, increase conduction velocity, and improve neurologic deficits. Strategies to promote remyelination have focused on transplanting oligodendrocytes (OLs) or recruiting endogenous myelinating cells with trophic factors. Ig-based therapies, routinely used to treat a variety of neurological and autoimmune diseases, underlie our approach to enhance remyelination. We isolated two human mAbs directed against OL surface antigens that promoted significant remyelination in a virus-mediated model of multiple sclerosis. Four additional OL-binding human mAbs did not promote remyelination. Both human mAbs were as effective as human i.v. Ig, a treatment shown to have efficacy in multiple sclerosis, and bound to the surface of human OLs suggesting a direct effect of the mAbs on the cells responsible for myelination. Alternatively, targeting human mAbs to areas of central nervous system (CNS) pathology may facilitate the opsonization of myelin debris, allowing repair to proceed. Human mAbs were isolated from the sera of individuals with a form of monoclonal gammopathy. These individuals carry a high level of monoclonal protein in their blood without detriment, lending support to the belief that administration of these mAbs as a therapy would be safe. Our results are (i) consistent with the hypothesis that CNS-reactive mAbs, part of the normal Ig repertoire in humans, may help repair and protect the CNS from pathogenic immune injury, and (ii) further challenge the premise that Abs that bind OLs are necessarily pathogenic.

T cell receptor interactions with class I heavy-chain influence T cell selection.

The interaction of the T cell receptor (TCR) with peptide in the binding site of the major histocompatibility complex molecule provides the basis for T cell recognition during immune surveillance, repertoire development, and tolerance. Little is known about the extent to which repertoire selection is influenced directly by variation of the structure of the class I heavy chain. We find that the 2C TCR, normally positively selected in the context of the K(b) molecule, is minimally selected into the CD8 lineage in the absence of antigen-processing genes. This finding underscores the importance of peptides in determining the positive-selecting class I ligands in the thymus. In contrast, K(bm3), a variant class I molecule that normally exerts a negative selection pressure on 2C-bearing T cells, positively selects 2C transgenic T cells into the CD8 lineage in an antigen-processing gene-deficient environment. These findings indicate that structural changes in the heavy chain can have direct influence in T cell recognition, from which we conclude that the nature of TCR interaction with class I heavy chain influences the array of TCRs selected during development of the functional adult repertoire.

TAP association influences the conformation of nascent MHC class I molecules.

The influence of TAP-MHC class I interactions on peptide binding to the class I heavy chain is assessed during TAP-dependent assembly using Kb-specific Abs that recognize conformational changes induced by assembly with beta2-microglobulin (beta2m) and by peptide binding. A significant portion (45%) of Kb molecules in TAP+, RMA-derived microsomes are associated with the TAP complex as measured by coimmunoisolation of Kb using anti-TAP1 Abs, while only 20% of the Kb heavy chain molecules are isolated as Kbbeta2m complexes with the alpha-Kb-specific Abs, Y-3 or K-10-56. The amount of Kb isolated with Y-3 and K-10-56 increases in proportion to transport and binding of peptide to the Kb molecules within the RMA microsomes. In contrast, less than 5% of the Kb within TAP2-RMA-S microsomes associated with the remaining TAP1 subunit. However, greater than 60% of Kb heavy chain is isolated as K-10-56- and Y-3-reactive Kbbeta2m complexes. We propose that a TAP-MHC class I interaction serves to stabilize the MHC class I:beta2m complex in an immature conformation (Y-3 and K-10-56 nonreactive) prior to high affinity peptide binding, preventing the export of class I molecules complexed with low affinity peptide ligands from the ER.