• The occurrence and potential health risk of microcystins in drinking water of rural areas in China.

      Zheng, Weiwei; Yang, Lan; Ma, Wuren; Huang, Yu; Crabbe, M. James C.; Qu, Weidong (Elsevier, 2018-12-26)
      Large-scale use of nitrogen and phosphorus fertilizers in agricultural production, environmental pollution and climate warming cause frequent algal blooms and the generation of algal toxins in water bodies in China. Algal pollution is increasing and microcystins (MCs) are detectable in both surface and ground water in China at sub- μg/L and μg/L levels. Toxicological studies show that microcystins have hepatic and  renal toxicity, genotoxicity, tumor-promoting effects, neurotoxicity, reproductive and developmental toxicity. Epidemiological evidence from China further reveals that chronic exposure to MCs through drinking water and liver cancer are positively correlated and demonstrate that MCs in drinking water are a main risk factor in liver cancer. Effectively controlled water pollution, reduced sewage discharge, and enhanced wastewater treatments are pivotal measures to control algal pollution and toxins in the drinking water of rural China.
    • On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae)

      Bellot, Sidonie; Bayton, Ross P.; Couvreur, Thomas L.P.; Dodsworth, Steven; Eiserhardt, Wolf L.; Guignard, Maite S.; Pritchard, Hugh W.; Roberts, Lucy; Toorop, Peter E.; Baker, William J. (Wiley, 2020-06-16)
      Seed size shapes plant evolution and ecosystems, and may be driven by plant size and architecture, dispersers, habitat and insularity. How these factors influence the evolution of giant seeds is unclear, as are the rate of evolution and the biogeographical consequences of giant seeds. We generated DNA and seed size data for the palm tribe Borasseae (Arecaceae) and its relatives, which show a wide diversity in seed size and include the double coconut (Lodoicea maldivica), the largest seed in the world. We inferred their phylogeny, dispersal history and rates of change in seed size, and evaluated the possible influence of plant size, inflorescence branching, habitat and insularity on these changes. Large seeds were involved in 10 oceanic dispersals. Following theoretical predictions, we found that: taller plants with fewer-branched inflorescences produced larger seeds; seed size tended to evolve faster on islands (except Madagascar); and seeds of shade-loving Borasseae tended to be larger. Plant size and inflorescence branching may constrain seed size in Borasseae and their relatives. The possible roles of insularity, habitat and dispersers are difficult to disentangle. Evolutionary contingencies better explain the gigantism of the double coconut than unusually high rates of seed size increase.
    • Opening of the outer membrane protein channel in tripartite efflux pumps is induced by interaction with the membrane fusion partner

      Janganan, Thamarai K.; Zhang, Li; Bavro, Vassiliy N; Matak-Vinkovic, Dijana; Barrera, Nelson P.; Burton, Matthew F.; Steel, Patrick G.; Robinson, Carol V.; Borges-Walmsley, Maria Ines; Walmsley, Adrian R.; et al. (American Society for Biochemistry and Molecular Biology, 2011-02-18)
      The multiple transferable resistance (MTR) pump, from Neisseria gonorrhoeae, is typical of the specialized machinery used to translocate drugs across the inner and outer membranes of Gram-negative bacteria. It consists of a tripartite complex composed of an inner-membrane transporter, MtrD, a periplasmic membrane fusion protein, MtrC, and an outer-membrane channel, MtrE. We have expressed the components of the pump in Escherichia coli and used the antibiotic vancomycin, which is too large to cross the outer-membrane by passive diffusion, to test for opening of the MtrE channel. Cells expressing MtrCDE are not susceptible to vancomycin, indicating that the channel is closed; but become susceptible to vancomycin in the presence of transported substrates, consistent with drug-induced opening of the MtrE channel. A mutational analysis identified residues Asn-198, Glu-434, and Gln-441, lining an intraprotomer groove on the surface of MtrE, to be important for pump function; mutation of these residues yielded cells that were sensitive to vancomycin. Pull-down assays and micro-calorimetry measurements indicated that this functional impairment is not due to the inability of MtrC to interact with the MtrE mutants; nor was it due to the MtrE mutants adopting an open conformation, because cells expressing these MtrE mutants alone are relatively insensitive to vancomycin. However, cells expressing the MtrE mutants with MtrC are sensitive to vancomycin, indicating that residues lining the intra-protomer groove control opening of the MtrE channel in response to binding of MtrC.
    • Optimising the release rate of naproxen liqui-pellet: a new technology for emerging novel oral dosage form

      Lam, Matthew; Ghafourian, Taravat; Nokhodchi, Ali; (Springer, 2019-07-08)
      Liqui-pellet is a new dosage form stemming from pelletisation technology and concept from liquisolid technology. In spite of liqui-pellet overcoming a major hurdle in liquisolid technology through achieving excellent flow property with high liquid load factor, the formulation requires to be optimised in order to improve drug release rate. Liqui-pellets of naproxen containing Tween 80, Primojel, Avicel and Aerosil were extruded and spheronised. Flowability test confirmed that all liqui-pellet formulations have excellent-good flow property (Carr’s index between 3.9–11.17%), including liqui-pellets with a high liquid load factor of 1.52, where 38% of the total mass is co-solvent. This shows a relatively high liquid load factor can be achieved in liqui-pellet without compromising the flowability, which is one of the key novelty of this work. It was found that the improved drug release rate was due to the remarkably improved disintegration of the supposedly non-disintegrating microcrystalline-based pellet; the optimised liqui-pellet seems to explode into fragments in the dissolution medium. At pH 1.2, the optimised formulation had ~ 10% more drug release than non-optimised formulation after 2 h, and at pH 7.4, the drug release of the optimised pellet was nearing 100% at ~ 15 min, whereas the none-optimised pellet only achieved ~ 79% drug release after 2 h. DSC and XRPD indicated an increase in the dissolution rate could be due to molecularly dispersion of naproxen in the pellets. Overall results showed that liqui-pellet exhibited an enhanced drug release and the capacity for high liquid load factor whilst maintaining excellent flowability, rendering it a potentially commercially feasible drug delivery system.
    • Oral ingestion of bacterially expressed dsrna can silence genes and cause mortality in a highly invasive, tree-killing pest, the emerald ash borer

      Leelesh, Ramya Shanivarsanthe; Rieske, Lynne K.; University of Kentucky; University of Bedfordshire (MDPI, 2020-07-14)
      RNA interference (RNAi) is a naturally occurring process inhibiting gene expression, and recent advances in our understanding of the mechanism have allowed its development as a tool against insect pests. A major challenge for deployment in the field is the development of convenient and efficient methods for production of double stranded RNA (dsRNA). We assessed the potential for deploying bacterially produced dsRNA as a bio-pesticide against an invasive forest pest, the emerald ash borer (EAB). EAB feeds on the cambial tissue of ash trees (Fraxinus spp.), causing rapid death. EAB has killed millions of trees in North America since its discovery in 2002, prompting the need for innovative management strategies. In our study, bacterial expression and synthesis of dsRNA were performed with E. coli strain HT115 using the L4440 expression vector. EAB-specific dsRNAs (shi and hsp) over-expressed in E. coli were toxic to neonate EAB after oral administration, successfully triggering gene silencing and subsequent mortality; however, a non-specific dsRNA control was not included. Our results suggest that ingestion of transformed E. coli expressing dsRNAs can induce an RNAi response in EAB. To our knowledge, this is the first example of an effective RNAi response induced by feeding dsRNA-expressing bacteria in a forest pest.
    • The origin and diversification of the hyperdiverse flora in the Chocó biogeographic region

      Pérez-Escobar, Oscar Alejandro; Lucas, Eve; Jaramillo, Carlos; Monro, Alexandre; Morris, Sarah K.; Bogarín, Diego; Greer, Deborah; Dodsworth, Steven; Aguilar-Cano, José; Sanchez Meseguer, Andrea; et al. (Frontiers, 2019-12-06)
      Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil’s Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth’s ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry’s [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry’s hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American–Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots.
    • The Ov20 protein of the parasitic nematode Onchocerca volvulus - A structurally novel class of small helix-rich retinol-binding proteins

      Kennedy, Malcolm W.; Garside, Lisa H.; Goodrick, Lucy E.; McDermott, Lindsay C.; Brass, Andrew; Price, Nicholas C.; Kelly, Sharon M.; Cooper, Alan; Bradley, Jannette E.; University of Glasgow; et al. (American Society for Biochemistry and Molecular Biology, 1997-11-21)
      Ov20 is a major antigen of the parasitic nematode Onchocerca volvulus, the causative agent of river blindness in humans, and the protein is secreted into the tissue occupied by the parasite. DNA encoding Ov20 was isolated, and the protein was expressed in Escherichia coli. Fluorescence-based ligand binding assays show that the protein contains a high affinity binding site for retinol, fluorescent fatty acids (11-((5-dimethylaminonaphthalene-1-sulfonyl)amino)undecanoic acid, dansyl-DL-alpha-aminocaprylic acid, and parinaric acid) and, by competition, oleic and arachidonic acids, but not cholesterol. The fluorescence emission of dansylated fatty acids is significantly blue-shifted upon binding in comparison to similarly sized beta-sheet-rich mammalian retinol- and fatty acid-binding proteins. Secondary structure prediction algorithms indicate that a alpha-helix predominates in Ov20, possibly in a coiled coil motif, with no evidence of beta structures, and this was confirmed by circular dichroism. The protein is highly stable in solution, requiring temperatures in excess of 90 degrees C or high denaturant concentrations for unfolding. Ov20 therefore represents a novel class of small retinol-binding protein, which appears to be confined to nematodes. The retinol binding activity of Ov20 could possibly contribute to the eye defects associated with onchocerciasis and, because there is no counterpart in mammals, represents a strategic target for chemotherapy.
    • Peptide-specific, TCR-alpha-driven, coreceptor-independent negative selection in TCR alpha-chain transgenic mice

      Furmanski, Anna L.; Bartok, Istvan; Chai, Jian-Guo; Singh, Yogesh; Ferreira, Cristina; Scott, Diane; Holland, Stephen J.; Bourdeaux, Christophe; Crompton, Tessa; Dyson, Julian (American Association of Immunologists, 2010-01-06)
      As thymocytes differentiate, Ag sensitivity declines, with immature CD4-CD8- double-negative (DN) cells being most susceptible to TCRsignaling events. We show that expression of alphabetaTCR from the DN3 stage lowers the threshold for activation, allowing recognition of MHC peptides independently of the TCR beta-chain and without either T cell coreceptor. The MHC class I-restricted C6 TCR recognizes the Y-chromosome-derived Ag HYK(k)Smcy. Positive selection in C6 alphabetaTCR females is skewed to the CD8 compartment, whereas transgenic male mice exhibit early clonal deletion of thymocytes. We investigated the effect of the HYK(k)Smcy complex on developing thymocytes expressing the C6 TCR alpha-chain on a TCR-alpha(-/-) background. On the original selecting haplotype, the skew to the CD8 lineage is preserved. This is MHC dependent, as the normal bias to the CD4 subset is seen on an H2b background. In male H2k C6 alpha-only mice, the presence of the HYK(k)Smcy complex leads to a substantial deletion of thymocytes from the DN subset. This phenotype is replicated in H2k C6 alpha-only female mice expressing an Smcy transgene. Deletion is not dependent on the beta variable segment of the C6 TCR or on a restricted TCR-beta repertoire. In contrast, binding of HYK(k)Smcy and Ag-specific activation of mature CD8+ T cells is strictly dependent on the original C6 beta-chain. These data demonstrate that, in comparison with mature T cells, alphabetaTCR+ immature thymocytes can recognize and transduce signals in response to specific MHC-peptide complexes with relaxed binding requirements.
    • Petal, sepal, or tepal? B-genes and monocot flowers

      Dodsworth, Steven; Royal Botanic Gardens, Kew (Elsevier Ltd, 2016-11-25)
      In petaloid monocots expansion of B-gene expression into whorl 1 of the flower results in two whorls of petaloid organs (tepals), as opposed to sepals in whorl 1 of typical eudicot flowers. Recently, new gene-silencing technologies have provided the first functional data to support this, in the genus Tricyrtis (Liliaceae).
    • Pharmacokinetics of radioimmunotherapeutic agent of direct labeling mAb 188Re-HAb18

      Lou, Chao; Chen, Zhi-Nan; Bian, Hui-Jie; Li, Jie; Zhou, Shaobo; (Baishideng Publishing Group, 2002-02-15)
      AIM:To label anti-hepatoma monoclonal antibody (mAb) fragment HAb18 F(ab')2 was labeled with 188Re for the pharmacokinetic model of 188Re-HAb18 F(ab')2 and to evaluate its pharmacokinetic parameters in hepatoma-bearing nude mice. METHODS:HAb18 F(ab')2 was directly labeled with 188Re using 2-mercaptoethanol (2-ME) as reducing agents. Labeling efficiency and immunoreactivity of 188Re-HAb18 F(ab')2 were evaluated by Whatman 3MM paper chromatography and live cell assay, respectively. Biodistribution analysis was also conducted in nude mice bearing human hepatoma in which animals were sacrificed at different time points (1, 4, 18, 24 and 24h) after 188Re-HAb18 F(ab')2 was injected through tail-vein into hepatoma-bearing nude mice. The blood and radioactivity of organs and mass were measured. The concentrations of (188)Re-HAb18 F(ab')2 were evaluated with a pharmacokinetic 3P97 software. RESULTS:The optimum labeling efficiency and immunoreactive fraction were 91.7% and 0.78% respectively. The parameters of 188Re-HAb18 F(ab')2 were: T (1/2),2.29 h;Vd,1.49 x 10(-9)L x Bq(-1);AUC, 20.49 x 10(9)Bq x h x L(-1);CL, 0.45 x 10(-3)L x h(-1). 188Re-HAb18 F(ab')2 could locate specially in hepatoma with high selective reactivity of HAb18 F(ab')2. 188Re-HAb18 F(ab')2 was mainly eliminated by kidney. The maximal tumor to blood ratio was at 48 h,and maximal tumor to liver ratio was at 18 h. CONCLUSION:The pharmacokinetics of 188Re-HAb18 F(ab')2 fit a l-compartment model. 188Re-HAb18 F(ab')2 can be uptaken selectively at the hepatoma site.
    • Phenotype of striatofugal medium spiny neurons in parkinsonian and dyskinetic nonhuman primates: a call for a reappraisal of the functional organization of the basal ganglia

      Nadjar, Agnes; Brotchie, Jonathan M.; Guigoni, Celine; Li, Qin; Zhou, Shaobo; Wang, Guijie; Ravenscroft, Paula; Georges, François; Crossman, Alan R.; Bezard, Erwan; et al. (Society for Neuroscience, 2006-08-23)
      The classic view of anatomofunctional organization of the basal ganglia is that striatopallidal neurons of the "indirect" pathway express D2 dopamine receptors and corelease enkephalin with GABA, whereas striatopallidal neurons of the "direct" pathway bear D1 dopamine receptors and corelease dynorphin and substance P with GABA. Although many studies have investigated the pathophysiology of the basal ganglia after dopamine denervation and subsequent chronic levodopa (L-dopa) treatment, none has ever considered the possibility of plastic changes leading to profound reorganization and/or biochemical phenotype modifications of medium spiny neurons. Therefore, we studied the phenotype of striatal neurons in four groups of nonhuman primates, including the following: normal, parkinsonian, parkinsonian chronically treated with L-dopa without exhibiting dyskinesia, and parkinsonian chronically treated with L-dopa exhibiting overt dyskinesia. To identify striatal cells projecting to external (indirect) or internal (direct) segments of the globus pallidus, the retrograde tracer cholera toxin subunit B (CTb) was injected stereotaxically into the terminal areas. Using immunohistochemistry techniques, brain sections were double labeled for CTb and dopamine receptors, opioid peptides, or the substance P receptor (NK1). We also used HPLC-RIA to assess opioid levels throughout structures of the basal ganglia. Our results suggest that medium spiny neurons retain their phenotype because no variations were observed in any experimental condition. Therefore, it appears unlikely that dyskinesia is related to a phenotype modification of the striatal neurons. However, this study supports the concept of axonal collateralization of striatofugal cells that project to both globus pallidus pars externa and globus pallidus pars interna. Striatofugal pathways are not as segregated in the primate as previously considered.
    • Phenotype of striatofugal medium spiny neurons in parkinsonian and dyskinetic nonhuman primates: a call for a reappraisal of the functional organization of the basal ganglia

      Nadjar, Agnes; Brotchie, Jonathan M.; Guigoni, Celine; Li, Qin; Zhou, Shaobo; Wang, Guijie; Ravenscroft, Paula; Georges, François; Crossman, Alan R.; Bezard, Erwan; et al. (Society for Neuroscience, 2006-08-23)
      The classic view of anatomofunctional organization of the basal ganglia is that striatopallidal neurons of the “indirect” pathway express D2 dopamine receptors and corelease enkephalin with GABA, whereas striatopallidal neurons of the “direct” pathway bear D1 dopamine receptors and corelease dynorphin and substance P with GABA. Although many studies have investigated the pathophysiology of the basal ganglia after dopamine denervation and subsequent chronic levodopa (l-dopa) treatment, none has ever considered the possibility of plastic changes leading to profound reorganization and/or biochemical phenotype modifications of medium spiny neurons. Therefore, we studied the phenotype of striatal neurons in four groups of nonhuman primates, including the following: normal, parkinsonian, parkinsonian chronically treated with l-dopa without exhibiting dyskinesia, and parkinsonian chronically treated with l-dopa exhibiting overt dyskinesia. To identify striatal cells projecting to external (indirect) or internal (direct) segments of the globus pallidus, the retrograde tracer cholera toxin subunit B (CTb) was injected stereotaxically into the terminal areas. Using immunohistochemistry techniques, brain sections were double labeled for CTb and dopamine receptors, opioid peptides, or the substance P receptor (NK1). We also used HPLC-RIA to assess opioid levels throughout structures of the basal ganglia. Our results suggest that medium spiny neurons retain their phenotype because no variations were observed in any experimental condition. Therefore, it appears unlikely that dyskinesia is related to a phenotype modification of the striatal neurons. However, this study supports the concept of axonal collateralization of striatofugal cells that project to both globus pallidus pars externa and globus pallidus pars interna. Striatofugal pathways are not as segregated in the primate as previously considered.
    • Phylogenetic signal from genomic repeat abundances of hominid primates

      Martín-Peciña, María; Ruiz-Ruano, Francisco J.; Camacho, Juan Pedro M.; Dodsworth, Steven (2018-11-25)
    • Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates

      Martín-Peciña, Maria; Ruiz-Ruano, Francisco J.; Camacho, Juan Pedro M.; Dodsworth, Steven (Oxford University Press (OUP), 2019-02-11)
      The genomic abundance of different types of repetitive DNA elements contains a phylogenetic signal useful for inferring the evolutionary history of different groups of organisms. Here we test the reliability of this approach using the Hominidae family of primates, whose consensus phylogeny is well accepted. We used the software RepeatExplorer to identify the different repetitive DNA clusters and quantify their abundances. With these data, we performed phylogenetic analyses by maximum parsimony, including one, two or three individuals per species, technical replicates, and including or discarding two clusters of repetitive elements (i.e. a satellite DNA and an endogenous retrovirus) that generated random homoplasy, because they were abundant in Pan and Gorilla but almost absent in Homo and Pongo. The only phylogenetic tree congruent with the accepted topology for hominids, thus coinciding with that obtained from the mitogenomes of the same individuals, was the one built after filtering out the libraries for the two homoplasious clusters and using three individuals per species. Our results suggest some caution in the use of repeat abundance for phylogenetic studies, because some element abundances are homoplasious, which severely distorts the phylogenetic signal owing to their differential amplification among evolutionary lineages.
    • Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

      Serna-Sánchez, Maria Alejandra; Pérez-Escobar, Oscar A.; Bogarín, Diego; Torres-Jimenez, María Fernanda; Alvarez-Yela, Astrid Catalina; Arcila-Galvis, Juliana E.; Hall, Climbie F.; de Barros, Fábio; Pinheiro, Fábio; Dodsworth, Steven; et al. (SpringerNature, 2021-03-25)
      Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
    • The polyprotein and FAR lipid binding proteins of nematodes: shape and monomer/dimer states in ligand-free and bound forms

      Solovyova, Alexandra S.; Meenan, Nicola; McDermott, Lindsay C.; Garofalo, Antonio; Bradley, Jannette E.; Kennedy, Malcolm W.; Byron, Olwyn; University of Glasgow; National Academy of Science of the Ukraine; University of Nottingham (Springer, 2003-08-31)
      Nematodes produce two classes of small, helix-rich fatty acid- and retinol-binding proteins whose structures and in vivo functions remain to be elucidated. These are the polyprotein allergens (NPA) and the FAR proteins. The solution properties of recombinant forms of these proteins from parasitic [Ascaris suum (As) and Onchocerca volvulus (Ov)] and free-living [Caenorhabditis elegans (Ce)] nematodes have been examined. Analytical ultracentrifugation (AUC) showed that, contrary to previous findings, the rAs-NPA-1A polyprotein unit (approximately 15 kDa) is a monomer, and this stoichiometry is unaltered by ligand (oleic acid) binding. The rOv-FAR-1 and rCe-FAR-5 proteins differ in that the former forms a tight dimer and the latter a monomer, and these oligomeric states are also unaffected by ligand binding or protein concentration. Sedimentation equilibrium experiments showed that the partial specific volume v of the unliganded proteins agree well with the value calculated from amino acid composition extrapolated to experimental temperature, and was unaffected upon ligand binding. Data from small-angle X-ray scattering (SAXS) indicated that both of the monomeric proteins rAs-NPA-1A and rCe-FAR-5 are globular, although slightly elongated and flattened. These data are in good agreement with shapes predicted from sedimentation velocity experiments and hydrodynamic bead modelling. On the basis of functional and secondary structural homology with the ligand-binding domain of the retinoic acid receptor RXRalpha, de novo atomic resolution structures for rAs-NPA-1A and rCe-FAR-5 have been constructed which are consistent with the SAXS and hydrodynamic data.
    • Potential of herbariomics for studying repetitive DNA in angiosperms

      Dodsworth, Steven; Guignard, Maite S.; Christenhusz, Maarten J.M.; Cowan, Robyn S.; Knapp, Sandra; Maurin, Olivier; Struebig, Monika; Leitch, Andrew R.; Chase, Mark W.; Forest, Felix; et al. (Frontiers Media, 2018-10-29)
      Repetitive DNA has an important role in angiosperm genomes and is relevant to our understanding of genome size variation, polyploidisation and genome dynamics more broadly. Much recent work has harnessed the power of high-throughput sequencing (HTS) technologies to advance the study of repetitive DNA in flowering plants. Herbarium collections provide a useful historical perspective on genome diversity through time, but their value for the study of repetitive DNA has not yet been explored. We propose that herbarium DNA may prove as useful for studies of repetitive DNA content as it has for reconstructed organellar genomes and low-copy nuclear sequence data. Here we present a case study in the tobacco genus (Nicotiana; Solanaceae), showing that herbarium specimens can provide accurate estimates of the repetitive content of angiosperm genomes by direct comparison with recently-collected material. We show a strong correlation between the abundance of repeat clusters, e.g., different types of transposable elements and satellite DNA, in herbarium collections versus recent material for four sets of Nicotiana taxa. These results suggest that herbarium specimen genome sequencing (herbariomics) holds promise for both repeat discovery and analyses that aim to investigate the role of repetitive DNAs in genomic evolution, particularly genome size evolution and/or contributions of repeats to the regulation of gene space.
    • The prediction of miRNAs in SARS-CoV-2 genomes: hsa-miR databases identify 7 key miRs linked to host responses and virus pathogenicity-related KEGG pathways significant for comorbidities

      Arisan, Elif Damla; Dart, Alwyn; Grant, Guy H.; Arisan, Serdar; Cuhadaroglu, Songul; Lange, Sigrun; Uysal-Onganer, Pinar; ; Gebze Technical University; St George’s University of London; et al. (MDPI, 2020-06-04)
      Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the betacoronavirus family, which causes COVID-19 disease. SARS-CoV-2 pathogenicity in humans leads to increased mortality rates due to alterations of significant pathways, including some resulting in exacerbated inflammatory responses linked to the "cytokine storm" and extensive lung pathology, as well as being linked to a number of comorbidities. Our current study compared five SARS-CoV-2 sequences from different geographical regions to those from SARS, MERS and two cold viruses, OC43 and 229E, to identify the presence of miR-like sequences. We identified seven key miRs, which highlight considerable differences between the SARS-CoV-2 sequences, compared with the other viruses. The level of conservation between the five SARS-CoV-2 sequences was identical but poor compared with the other sequences, with SARS showing the highest degree of conservation. This decrease in similarity could result in reduced levels of transcriptional control, as well as a change in the physiological effect of the virus and associated host-pathogen responses. MERS and the milder symptom viruses showed greater differences and even significant sequence gaps. This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments. Therefore, patterns of mutation, occurring during sequence divergence from the longer established human viruses to the more recent ones, may have led to the emergence of sequence motifs that can be related directly to the pathogenicity of SARS-CoV-2. Importantly, we identified 7 key-microRNAs (miRs 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways linked to viral pathogenicity and host responses. According to Bioproject data (PRJNA615032), SARS-CoV-2 mediated transcriptomic alterations were similar to the target pathways of the selected 7 miRs identified in our study. This mechanism could have considerable significance in determining the symptom spectrum of future potential pandemics. KEGG pathway analysis revealed a number of critical pathways linked to the seven identified miRs that may provide insight into the interplay between the virus and comorbidities. Based on our reported findings, miRNAs may constitute potential and effective therapeutic approaches in COVID-19 and its pathological consequences.
    • Proteomic analysis of age-related changes in ovine cerebrospinal fluid

      Chen, Carl P.C.; Preston, Jane E.; Zhou, Shaobo; Fuller, Heidi R.; Morgan, David G.A.; Chen, Ruoli; King’s College London; Chang Gung University; University of Bedfordshire; RJAH Orthopaedic Hospital; et al. (Elsevier, 2018-04-21)
      Cerebrospinal fluid (CSF) circulates through the brain and has a unique composition reflecting the biological processes of the brain. Identifying ageing CSF biomarkers can aid in understanding the ageing process and interpreting CSF protein changes in neurodegenerative diseases. In this study, ovine CSF proteins from young (1-2 year old), middle aged (3-6 year old) and old (7-10 year old) sheep were systemically studied. CSF proteins were labelled with iTRAQ tagging reagents and fractionated by 2-dimensional high performance, liquid chromatography. Tryptic peptides were identified using MS/MS fragmentation ions for sequencing and quantified from iTRAQ reporter ion intensities at m/z 114, 115, 116 and 117. Two hundred thirty one peptides were detected, from which 143 proteins were identified. There were 52 proteins with >25% increase in concentrations in the old sheep compared to the young. 33 of them increased >25% but <50%, 13 increased >50% but <1 fold, 6 increased >1 fold [i.e. haptoglobin (Hp), haemoglobin, neuroendocrine protein 7B2, IgM, fibrous sheath interacting protein 1, vimentin]. There were 18 proteins with >25% decrease in concentrations in the old sheep compared to the young. 17 of them decreased >25% but <50%, and histone deacetylase 7 (HDAC7) was gradually decreased for over 80%. Glutathione S-transferase was decreased in middle aged CSF compared to both young and old CSF. The differential expressions of 3 proteins (Hp, neuroendocrine protein 7B2, IgM) were confirmed by immunoassays. These data expand our current knowledge regarding ovine CSF proteins, supply the necessary information to understand the ageing process in the brain and provide a basis for diagnosis of neurodegenerative diseases.
    • Public T cell receptor beta-chains are not advantaged during positive selection

      Furmanski, Anna L.; Ferreira, Cristina; Bartok, Istvan; Dimakou, Sofia; Rice, Jason; Stevenson, Freda; Millrain, Maggie M.; Simpson, Elizabeth; Dyson, Julian (American Association of Immunologists, 2008-01-04)
      Studies of human and murine T cells have shown that public TCR beta-chain rearrangements can dominate the Ag-specific and naive repertoires of distinct individuals. We show that mouse T cells responding to the minor histocompatibility Ag HYDbSmcy share an invariant Vbeta8.2-Jbeta2.3 TCR gene rearrangement. The dominance of this rearrangement shows that it successfully negotiated thymic selection and was highly favored during clonal expansion in all animals examined. We hypothesized that such beta-chains are advantaged during thymic and/or peripheral selection and, as a result, may be over-represented in the naive repertoire. A sequencing study was undertaken to examine the diversity of Vbeta8.2-Jbeta2.3 CDR3 loops from naive T cell repertoires of multiple mice. Public TCR beta-chain sequences were identified across different repertoires and MHC haplotypes. To determine whether such public beta-chains are advantaged during thymic selection, individual chains were followed through T cell development in a series of novel bone marrow competition chimeras. We demonstrate that beta-chains were positively selected with similar efficiency regardless of CDR3 loop sequence. Therefore, the establishment and maintenance of public beta-chains in the periphery is predominantly controlled by post-thymic events through modification of the primary, thymus-derived TCR repertoire.