A state of independents: rationalising the high <em>Z</em>\u27 crystal structures of shikimate esters

Zˈ is a parameter used to denote the number of symmetry-independent molecules in the asymmetric unit of a crystal structure. High Zˈ (&gt;1) crystal structures are relatively uncommon and are thought to arise through competition between intermolecular interactions of similar strength. As such high Zˈ crystal structures are challenging to predict, new examples are valuable in improving understanding in the field. Herein, we report the X-ray crystal structures of a series of shikimate esters, the asymmetric units of which exhibit high Zˈ values. Of special interest is the crystal structure of methyl shikimate, the asymmetric unit of which comprises 12 independent molecules; Zˈ = 12. This uncommonly large Zˈ value arises through a combination of factors, including the intrinsic homochirality of the molecule, the conformational inflexibility of the cyclohexene ring, the presence of multiple hydrogen bonding motifs, and both the cis- and trans-conformers of the ester moiety. Comparison of the X-ray crystal structures of shikimic acid, methyl shikimate, ethyl shikimate, and iso-propyl shikimate suggests that instances of high Zˈ in this series correlate with specific hydrogen bonding motifs influenced by the steric bulk of the ester. The results of this study provide important insights into factors that influence the formation of organic crystal structures where the value of Zˈ is greater than 1

Alkali Metal Complexes of Phosphine-Borane-Substituted Benzyl Ligands and Their Application in the Synthesis of B-H\ub7\ub7\ub7Sn Stabilized Dialkylstannylenes

\ua9 2024 The Authors. Published by American Chemical Society.The benzyl-substituted phosphine-boranes PhCH2P(BH3)R2 [R = iPr (1H), Ph (2H), Cy (3H)] are accessible through either the reaction between R2PCl and PhCH2MgBr, followed by treatment with BH3\ub7SMe2 or the reaction between R2P(BH)3Li and PhCH2Br. Treatment of 1H, 2H, or 3H with nBuLi, PhCH2Na, or PhCH2K gave the corresponding alkali metal complexes [{iPr2P(BH3)CHPh}Li(THF)]2 (1Li), [{Ph2P(BH3)CHPh}Li(OEt2)2] (2Li), [{Cy2P(BH3)CHPh}Li(TMEDA)] (3Li), [iPr2P(BH3)CHPh]Na (1Na), [{Ph2P(BH3)CHPh}Na(THF)2]2 (2Na), [Cy2P(BH3)CHPh]Na(THF)0.5 (3Na), [{iPr2P(BH3)CHPh}K]∞ (1K), [{Ph2P(BH3)CHPh}K(THF)]∞ (2K), and [{Cy2P(BH3)CHPh}K.0.5PhMe]∞ (3K). X-ray crystallography revealed that, while 2Li and 3Li crystallize as monomers, 1Li and 2Na crystallize as borane-bridged dimers. The potassium complexes 1K, 2K, and 3K all crystallize with polymeric structures, in which the monomer units are linked to each other through a range of both bridging BH3 groups and multihapto interactions between the potassium cations and the aromatic rings. The reactions between two equivalents of either 1Li or 3Li and Cp2Sn gave the corresponding dialkylstannylenes [{R2P(BH3)CHPh}2Sn] [R = iPr (1Sn), Cy (3Sn)]. These compounds were isolated as mixtures of the rac and meso diastereomers. X-ray crystallography reveals that rac-1Sn and rac-3Sn crystallize as discrete monomers each exhibiting two agostic-type B-H\ub7\ub7\ub7Sn contacts

Patterns of deep-sea genetic connectivity in the New Zealand region : implications for management of benthic ecosystems

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e49474, doi:10.1371/journal.pone.0049474.Patterns of genetic connectivity are increasingly considered in the design of marine protected areas (MPAs) in both shallow and deep water. In the New Zealand Exclusive Economic Zone (EEZ), deep-sea communities at upper bathyal depths (<2000 m) are vulnerable to anthropogenic disturbance from fishing and potential mining operations. Currently, patterns of genetic connectivity among deep-sea populations throughout New Zealand’s EEZ are not well understood. Using the mitochondrial Cytochrome Oxidase I and 16S rRNA genes as genetic markers, this study aimed to elucidate patterns of genetic connectivity among populations of two common benthic invertebrates with contrasting life history strategies. Populations of the squat lobster Munida gracilis and the polychaete Hyalinoecia longibranchiata were sampled from continental slope, seamount, and offshore rise habitats on the Chatham Rise, Hikurangi Margin, and Challenger Plateau. For the polychaete, significant population structure was detected among distinct populations on the Chatham Rise, the Hikurangi Margin, and the Challenger Plateau. Significant genetic differences existed between slope and seamount populations on the Hikurangi Margin, as did evidence of population differentiation between the northeast and southwest parts of the Chatham Rise. In contrast, no significant population structure was detected across the study area for the squat lobster. Patterns of genetic connectivity in Hyalinoecia longibranchiata are likely influenced by a number of factors including current regimes that operate on varying spatial and temporal scales to produce potential barriers to dispersal. The striking difference in population structure between species can be attributed to differences in life history strategies. The results of this study are discussed in the context of existing conservation areas that are intended to manage anthropogenic threats to deep-sea benthic communities in the New Zealand region.This work was funded in part by a Fulbright Fellowship administered by Fulbright New Zealand and the U.S. Department of State, awarded in 2011 to EKB. Funding and support for research expedition was provided by Land Information New Zealand, New Zealand Ministry of Fisheries, NIWA, Census of Marine Life on Seamounts (CenSeam), and the Foundation for Research, Science and Technology. Other research funding was provided by the New Zealand Ministry of Science and Innovation project “Impacts of resource use on vulnerable deep-sea communities” (FRST contract CO1X0906), the National Science Foundation (OCE-0647612), and the Deep Ocean Exploration Institute (Fellowship support to TMS)

Science Priorities for Seamounts: Research Links to Conservation and Management

Seamounts shape the topography of all ocean basins and can be hotspots of biological activity in the deep sea. The Census of Marine Life on Seamounts (CenSeam) was a field program that examined seamounts as part of the global Census of Marine Life (CoML) initiative from 2005 to 2010. CenSeam progressed seamount science by collating historical data, collecting new data, undertaking regional and global analyses of seamount biodiversity, mapping species and habitat distributions, challenging established paradigms of seamount ecology, developing new hypotheses, and documenting the impacts of human activities on seamounts. However, because of the large number of seamounts globally, much about the structure, function and connectivity of seamount ecosystems remains unexplored and unknown. Continual, and potentially increasing, threats to seamount resources from fishing and seabed mining are creating a pressing demand for research to inform conservation and management strategies. To meet this need, intensive science effort in the following areas will be needed: 1) Improved physical and biological data; of particular importance is information on seamount location, physical characteristics (e.g. habitat heterogeneity and complexity), more complete and intensive biodiversity inventories, and increased understanding of seamount connectivity and faunal dispersal; 2) New human impact data; these shall encompass better studies on the effects of human activities on seamount ecosystems, as well as monitoring long-term changes in seamount assemblages following impacts (e.g. recovery); 3) Global data repositories; there is a pressing need for more comprehensive fisheries catch and effort data, especially on the high seas, and compilation or maintenance of geological and biodiversity databases that underpin regional and global analyses; 4) Application of support tools in a data-poor environment; conservation and management will have to increasingly rely on predictive modelling techniques, critical evaluation of environmental surrogates as faunal “proxies”, and ecological risk assessment

RNAseq Analyses Identify Tumor Necrosis Factor-Mediated Inflammation as a Major Abnormality in ALS Spinal Cord

ALS is a rapidly progressive, devastating neurodegenerative illness of adults that produces disabling weakness and spasticity arising from death of lower and upper motor neurons. No meaningful therapies exist to slow ALS progression, and molecular insights into pathogenesis and progression are sorely needed. In that context, we used high-depth, next generation RNA sequencing (RNAseq, Illumina) to define gene network abnormalities in RNA samples depleted of rRNA and isolated from cervical spinal cord sections of 7 ALS and 8 CTL samples. We aligned \u3e50 million 2X150 bp paired-end sequences/sample to the hg19 human genome and applied three different algorithms (Cuffdiff2, DEseq2, EdgeR) for identification of differentially expressed genes (DEG’s). Ingenuity Pathways Analysis (IPA) and Weighted Gene Co-expression Network Analysis (WGCNA) identified inflammatory processes as significantly elevated in our ALS samples, with tumor necrosis factor (TNF) found to be a major pathway regulator (IPA) and TNFα-induced protein 2 (TNFAIP2) as a major network “hub” gene (WGCNA). Using the oPOSSUM algorithm, we analyzed transcription factors (TF) controlling expression of the nine DEG/hub genes in the ALS samples and identified TF’s involved in inflammation (NFkB, REL, NFkB1) and macrophage function (NR1H2::RXRA heterodimer). Transient expression in human iPSC-derived motor neurons of TNFAIP2 (also a DEG identified by all three algorithms) reduced cell viability and induced caspase 3/7 activation. Using high-density RNAseq, multiple algorithms for DEG identification, and an unsupervised gene co-expression network approach, we identified significant elevation of inflammatory processes in ALS spinal cord with TNF as a major regulatory molecule. Overexpression of the DEG TNFAIP2 in human motor neurons, the population most vulnerable to die in ALS, increased cell death and caspase 3/7 activation. We propose that therapies targeted to reduce inflammatory TNFα signaling may be helpful in ALS patients

Borrelia burgdorferi BBK32 Inhibits the Classical Pathway by Blocking Activation of the C1 Complement Complex

Citation: Garcia, B. L., Zhi, H., Wager, B., Hook, M., & Skare, J. T. (2016). Borrelia burgdorferi BBK32 Inhibits the Classical Pathway by Blocking Activation of the C1 Complement Complex. Plos Pathogens, 12(1), 28. doi:10.1371/journal.ppat.1005404Pathogens that traffic in blood, lymphatics, or interstitial fluids must adopt strategies to evade innate immune defenses, notably the complement system. Through recruitment of host regulators of complement to their surface, many pathogens are able to escape complement-mediated attack. The Lyme disease spirochete, Borrelia burgdorferi, produces a number of surface proteins that bind to factor H related molecules, which function as the dominant negative regulator of the alternative pathway of complement. Relatively less is known about how B. burgdorferi evades the classical pathway of complement despite the observation that some sensu lato strains are sensitive to classical pathway activation. Here we report that the borrelial lipoprotein BBK32 potently and specifically inhibits the classical pathway by binding with high affinity to the initiating C1 complex of complement. In addition, B. burgdorferi cells that produce BBK32 on their surface bind to both C1 and C1r and a serum sensitive derivative of B. burgdorferi is protected from killing via the classical pathway in a BBK32-dependent manner. Subsequent biochemical and biophysical approaches localized the anti-complement activity of BBK32 to its globular C-terminal domain. Mechanistic studies reveal that BBK32 acts by entrapping C1 in its zymogen form by binding and inhibiting the C1 subcomponent, C1r, which serves as the initiating serine protease of the classical pathway. To our knowledge this is the first report of a spirochetal protein acting as a direct inhibitor of the classical pathway and is the only example of a biomolecule capable of specifically and noncovalently inhibiting C1/C1r. By identifying a unique mode of complement evasion this study greatly enhances our understanding of how pathogens subvert and potentially manipulate host innate immune systems

TNFR1 inhibition with a nanobody protects against EAE development in mice

TNF has as detrimental role in multiple sclerosis (MS), however, anti-TNF medication is not working. Selective TNF/TNFR1 inhibition whilst sparing TNFR2 signaling reduces the pro-inflammatory effects of TNF but preserves the important neuroprotective signals via TNFR2. We previously reported the generation of a Nanobody-based selective inhibitor of human TNFR1, TROS that will be tested in experimental autoimmune encephalomyelitis (EAE). We specifically antagonized TNF/TNFR1 signaling using TROS in a murine model of MS, namely MOG(35-55)-induced EAE. Because TROS does not cross-react with mouse TNFR1, we generated mice expressing human TNFR1 in a mouse TNFR1-knockout background (hTNFR1 Tg), and we determined biodistribution of Tc-99m-TROS and effectiveness of TROS in EAE in those mice. Biodistribution analysis demonstrated that intraperitoneally injected TROS is retained more in organs of hTNFR1 Tg mice compared to wild type mice. TROS was also detected in the cerebrospinal fluid (CSF) of hTNFR1 Tg mice. Prophylactic TROS administration significantly delayed disease onset and ameliorated its symptoms. Moreover, treatment initiated early after disease onset prevented further disease development. TROS reduced spinal cord inflammation and neuroinflammation, and preserved myelin and neurons. Collectively, our data illustrate that TNFR1 is a promising therapeutic target in MS

Clinical presentation of abdominal tuberculosis in HIV seronegative adults

BACKGROUND: The accurate diagnosis of abdominal tuberculosis usually takes a long time and requires a high index of suspicion in clinic practice. Eighty-eight immune-competent patients with abdominal tuberculosis were grouped according to symptoms at presentation and followed prospectively in order to investigate the effect of symptomatic presentation on clinical diagnosis and prognosis. METHODS: Based upon the clinical presentation, the patients were divided into groups such as non-specific abdominal pain & less prominent in bowel habit, ascites, alteration in bowel habit, acute abdomen and others. Demographic, clinical and laboratory features, coexistence of pulmonary tuberculosis, diagnostic procedures, definitive diagnostic tests, need for surgical therapy, and response to treatment were assessed in each group. RESULTS: According to clinical presentation, five groups were constituted as non-specific abdominal pain (n = 24), ascites (n = 24), bowel habit alteration (n = 22), acute abdomen (n = 9) and others (n = 9). Patients presenting with acute abdomen had significantly higher white blood cell counts (p = 0.002) and abnormalities in abdominal plain radiographs (p = 0.014). Patients presenting with alteration in bowel habit were younger (p = 0.048). The frequency of colonoscopic abnormalities (7.5%), and need for therapeutic surgery (12.5%) were lower in patients with ascites, (p = 0.04) and (p = 0.001), respectively. There was no difference in gender, disease duration, diagnostic modalities, response to treatment, period to initial response, and mortality between groups (p > 0.05). Gastrointestinal tract alone was the most frequently involved part (38.5%), and this was associated with acid-fast bacteria in the sputum (p = 0.003). CONCLUSION: Gastrointestinal tract involvement is frequent in patients with active pulmonary tuberculosis. Although different clinical presentations of patients with abdominal tuberculosis determine diagnostic work up and need for therapeutic surgery, evidence based diagnosis and consequences of the disease does not change