Perspectives on the Delta Waterfowl Research Station-Ducks Unlimited Canada Marsh Ecology Research Program

Present wetland management has been developed largely on a trial and error basis (Figure 1 ). The effects of many important environmental variables on wetland productivity 253 are not known, consequently management results have not been predictable with a high degree of accuracy (Weller 1981 ). Many marsh management techniques have been described; however, consistently successful marsh management requires a more comprehensive understanding of the structure and function of wetland systems. Although there have been numerous observational studies, major advances in our understanding will result from tightly controlled experimentation which permits the integration of simultaneous research efforts by a number of different scientific disciplines (Reichle 1975, Weller 1978). Because wetlands are temporally dynamic, this type of multi-disciplinary ecosystem analysis must also span a number of years to document the annual and long-term variability within the system. By better understanding the structure and function of wetlands, managers will be better able to design management techniques and strategies suited to their particular situation and therefore realize greater success in manipulating the productivity of these systems (Figure I)

A dynamic model of gene expression in monocytes reveals differences in immediate/early response genes between adult and neonatal cells

Neonatal monocytes display immaturity of numerous functions compared with adult cells. Gene expression arrays provide a promising tool for elucidating mechanisms underlying neonatal immune function. We used a well-established microarray to analyze differences between LPS-stimulated human cord blood and adult monocytes to create dynamic models for interactions to elucidate observed deficiencies in neonatal immune responses. We identified 168 genes that were differentially expressed between adult and cord monocytes after 45 min incubation with LPS. Of these genes, 95% (159 of 167) were over-expressed in adult relative to cord monocytes. Differentially expressed genes could be sorted into nine groups according to their kinetics of activation. Functional modelling suggested differences between adult and cord blood in the regulation of apoptosis, a finding confirmed using annexin binding assays. We conclude that kinetic studies of gene expression reveal potentially important differences in gene expression dynamics that may provide insight into neonatal innate immunity

Evidence for chronic, peripheral activation of neutrophils in polyarticular juvenile rheumatoid arthritis

Although strong epidemiologic evidence suggests an important role for adaptive immunity in the pathogenesis of polyarticular juvenile rheumatoid arthritis (JRA), there remain many aspects of the disease that suggest equally important contributions of the innate immune system. We used gene expression arrays and computer modeling to examine the function in neutrophils of 25 children with polyarticular JRA. Computer analysis identified 712 genes that were differentially expressed between patients and healthy controls. Computer-assisted analysis of the differentially expressed genes demonstrated functional connections linked to both interleukin (IL)-8- and interferon-γ (IFN-γ)-regulated processes. Of special note is that the gene expression fingerprint of children with active JRA remained essentially unchanged even after they had responded to therapy. This result differed markedly from our previously reported work, in which gene expression profiles in buffy coats of children with polyarticular JRA reverted to normal after disease control was achieved pharmacologically. These findings suggest that JRA neutrophils remain in an activated state even during disease quiescence. Computer modeling of array data further demonstrated disruption of gene regulatory networks in clusters of genes modulated by IFN-γ and IL-8. These cytokines have previously been shown to independently regulate the frequency (IFN-γ) and amplitude (IL-8) of the oscillations of key metabolites in neutrophils, including nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and superoxide ion. Using real-time, high-speed, single-cell photoimaging, we observed that 6/6 JRA patients displayed a characteristic defect in 12% to 23% of the neutrophils tested. Reagents known to induce only frequency fluctuations of NAD(P)H and superoxide ion induced both frequency and amplitude fluctuations in JRA neutrophils. This is a novel finding that was observed in children with both active (n = 4) and inactive (n = 2) JRA. A subpopulation of polyarticular JRA neutrophils are in a chronic, activated state, a state that persists when the disease is well controlled pharmacologically. Furthermore, polyarticular JRA neutrophils exhibit an intrinsic defect in the regulation of metabolic oscillations and superoxide ion production. Our data are consistent with the hypothesis that neutrophils play an essential role in the pathogenesis of polyarticular JRA

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)

Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were subsequently replaced with a randomized trinucleotide sequence donated by the DNA cassette termed SubSeqNNN. The bla gene encoding TEM-1 β-lactamase was used as a model to demonstrate the effectiveness of TriNEx. Sequence analysis revealed that the mutations were distributed throughout bla, with variants containing single, double and triple nucleotide changes. Many of the resulting amino acid substitutions had significant effects on the in vivo activity of TEM-1, including up to a 64-fold increased activity toward ceftazidime and up to an 8-fold increased resistance to the inhibitor clavulanate. Many of the observed amino acid substitutions were only accessible by exchanging at least two nucleotides per codon, including charge-switch (R164D) and aromatic substitution (W165Y) mutations. TriNEx can therefore generate a diverse range of protein variants with altered properties by combining the power of site-directed saturation mutagenesis with the capacity of whole-gene mutagenesis to randomly introduce mutations throughout a gene

Membrane-Associated RING-CH Proteins Associate with Bap31 and Target CD81 and CD44 to Lysosomes

Membrane-associated RING-CH (MARCH) proteins represent a family of transmembrane ubiquitin ligases modulating intracellular trafficking and turnover of transmembrane protein targets. While homologous proteins encoded by gamma-2 herpesviruses and leporipoxviruses have been studied extensively, limited information is available regarding the physiological targets of cellular MARCH proteins. To identify host cell proteins targeted by the human MARCH-VIII ubiquitin ligase we used stable isotope labeling of amino-acids in cell culture (SILAC) to monitor MARCH-dependent changes in the membrane proteomes of human fibroblasts. Unexpectedly, we observed that MARCH-VIII reduced the surface expression of Bap31, a chaperone that predominantly resides in the endoplasmic reticulum (ER). We demonstrate that Bap31 associates with the transmembrane domains of several MARCH proteins and controls intracellular transport of MARCH proteins. In addition, we observed that MARCH-VIII reduced the surface expression of the hyaluronic acid-receptor CD44 and both MARCH-VIII and MARCH-IV sequestered the tetraspanin CD81 in endo-lysosomal vesicles. Moreover, gene knockdown of MARCH-IV increased surface levels of endogenous CD81 suggesting a constitutive involvement of this family of ubiquitin ligases in the turnover of tetraspanins. Our data thus suggest a role of MARCH-VIII and MARCH-IV in the regulated turnover of CD81 and CD44, two ubiquitously expressed, multifunctional proteins

Antibody, not cellular, immune Responses to SARS-CoV-2 vaccination outperform infection in inflammatory bowel disease patients

Following the successful development of the first vaccines to protect against SARS-CoV-2 infection, the International Organization for the Study of Inflammatory Bowel Disease (IOIBD) recommended full vaccination of all patients with inflammatory bowel disease (IBD) already early in the pandemic.1 Subsequent studies have reported the effects of immunosuppressive medications on immune responses to SARS-CoV-2 infection and vaccination in patients with IBD. The most consistent findings are of reduced serological responses in patients on infliximab and an uncoupling of cellular and humoral responses.2–5 Although previous studies assessed aspects of the immune response in IBD, a direct longitudinal comparison of immunity induced by primary SARS-CoV-2 infection compared with vaccination in patients with IBD has not been reported. As part of the ICARUS-IBD study at the Icahn School of Medicine at Mount Sinai, patients with IBD were followed from early in the pandemic (May 2020) prior to vaccine development through March 2022 when full vaccination schedules, including booster doses, were available. We prospectively obtained clinical data, serum, and peripheral blood mononuclear cells (PBMCs; Supplementary Figure 1). This biobank allows the first detailed examination of the relative immune response to naturally acquired infection compared with vaccination-induced immunity

Perspectives on the Delta Waterfowl Research Station-Ducks Unlimited Canada Marsh Ecology Research Program

Present wetland management has been developed largely on a trial and error basis (Figure 1 ). The effects of many important environmental variables on wetland productivity 253 are not known, consequently management results have not been predictable with a high degree of accuracy (Weller 1981 ). Many marsh management techniques have been described; however, consistently successful marsh management requires a more comprehensive understanding of the structure and function of wetland systems. Although there have been numerous observational studies, major advances in our understanding will result from tightly controlled experimentation which permits the integration of simultaneous research efforts by a number of different scientific disciplines (Reichle 1975, Weller 1978). Because wetlands are temporally dynamic, this type of multi-disciplinary ecosystem analysis must also span a number of years to document the annual and long-term variability within the system. By better understanding the structure and function of wetlands, managers will be better able to design management techniques and strategies suited to their particular situation and therefore realize greater success in manipulating the productivity of these systems (Figure I).This is a proceeding from Murkin, H. R., B. D. J. Batt, C. B. Davis, J. A. Kadlec, and A. G. van der Valk. 1984. Perspectives on the Delta Waterfowl Research Station ‐‐ Ducks Unlimited Canada marsh ecology research program. Transactions of the Forty-ninth North American Wildlife and Natural Resources Conference, March 23-28, 1984, Boston, Massachusetts. Posted with permission.</p