17 research outputs found
The Promoter of Rv0560c Is Induced by Salicylate and Structurally-Related Compounds in <i>Mycobacterium tuberculosis</i>
No full textPMCID: PMC3317779This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The emb proteins in Mycobacterium smegmatis
No full textMycobacterium tuberculosis, the causative agent of tuberculosis, was once thought to be a ghost of the past. However, the emergence of drug resistant strains has brought this bacterium back into the spot light. Ethambutol, a compound with structural similarity to D-arabinose, has been shown to have many inhibitory effects on M. tuberculosis and other mycobacterial species. Some of these activities include: inhibition of synthesis of the arabinan constituent of the cell wall arabinogalactan (AG), inhibition of RNA metabolism, and phospholipid synthesis. Likewise, this inhibition of arabinan synthesis extends to that of lipoarabinomannan (LAM). One of the most significant components of all mycobacterial cell walls is LAM; it has been implicated as a central molecule involved in the virulence and immunopathogenesis of tuberculosis. The arabinan of LAM is attached to a mannan backbone which extends from a phosphatidylinositol mannoside anchor at the reducing end. Recent research efforts have been directed towards showing that the Emb proteins are involved in arabinan synthesis. These proteins are conserved throughout all mycobacterial species, and through the use of computer program algorithms (such as SOSUI, TMPRED), it has been predicted that there are 11-13 transmembrane domains in the N-terminal region of the proteins. This correlates to approximately 670 amino acids. Also, these programs showed a soluble globular C-terminal domain accounting for approximately 430 amino acids. Specifically, it was found that EmbC targets the arabinan of LAM. This was made possible by the inactivation of the embA, embB, and embC genes individually, and subsequently looking at the resulting structural alterations on the arabinan component of cell wall AG and LAM. With this knowledge, the establishment of the catalytic site of the embC gene that specifically controls the arabinosylation of lipomannan to give mature lipoarabinomannan was necessary. Generation of hybrids with variation in the N-terminus of the EmbC protein is the current strategy being used to pursue this information. An EmbC/B hybrid was created by the fusion of the N-terminus of EmbC and the C-terminal domain of EmbB. This included 668 amino acids from the N-terminal of EmbC, fused with the last 407 amino acids of EmbB. This gene fusion was cloned into the pVV16 shuttle vector and electroporated into M. smegmatis ΔembC. LAM was then extracted from these hybrid cells, and analysis showed that the EmbC/B hybrid resulted in a shortened form of LAM. After further biochemical studies on this truncated LAM such as glycosyl compositional analysis, endoarabinase digestion followed by HPAEC (High-pH anion-exchange chromatography) profiling, and mass spectrometry analysis, it was shown that LAM was not only truncated, but had a structural alteration where the nonreducing end resembled that of the arabinan of AG. After such exciting results, current work continues with the generation of hybrids. The formation of the 50:50 EmbC/B hybrid containing approximately 580 amino acids of each of the EmbC and EmbB genes has been completed. This final construct has been transformed into the ΔembC mutant by electroporation and biochemical analysis is being performed. Results pertaining to the hybrids capacity to complement the LAM defect will be discussed in this poster presentation. This new 50:50 fusion will be essential in giving us the knowledge on the contribution of the first eight transmembrane domains of the EmbC protein in LAM biosynthesis.College Honors
The Late Pleistocene and Holocene Evolution of The North Caspian Plain
No full textThe rapid rates of sea level change in the Caspian Sea since its formation (Proterozoic) have resulted in unique sedimentary sequences, including many oil and gas reservoirs. An important hydrocarbon province is the fine grained-sandstone of the Productive Series in the South Caspian Basin that consist for at least some part of sheetflood sandstones. Their sedimentology and reservoir architecture remain uncertain. This study reconstructs the chrono-stratigraphic framework of the low-gradient North-East Caspian plain between the Ural and Emba Rivers, and its potential as a reservoir analogue for Productive Series. Because of the similarities between the sedimentary systems, like rapid sea level changes and the absence of a shelf break. The data for this study consist of 26 shallow core- and 10 outcrop-descriptions and include the analyses of selected samples for Optically Stimulated Luminescence dating, radiocarbon dating and grain-size distribution analyses. Three sea-level cycles (I-III) were identified depositing four different sedimentary sequences (a-d): (I-a) marine clays (41 ka BP) followed by a regression resulting in an erosional surface, (II-b) transgressive shallow marine silty clays and sandy barrier deposits (16-17 ka BP) (locally identified as ‘Khvalynian chocolate clays’), (II-c) Terminal Splay Complex consisting of clayey sands (9-11 ka BP) related to a major regressive event, that are eroded into a deflation landscape (e.g. yardangs), locally known as ‘Baer-hills’ and Sors’ and (III-d) present day inter-yardang deposits lagoonal- and playa- like deposits consisting of fine silty clays. Preservation of these fines is closely related to sea-level oscillations. Possibly a fourth sea-level cycle occurred before 41 ka BP depositing marine clays. The identification of a Holocene terminal splay complex and yardang-formation gives new insight in the regional sedimentary processes. More importantly this complex could serve as a new analogue for the Productive Series, giving alternative insights in reservoir architecture and internal connectivity, e.g. the Productive Series could be more terrestrial of origin despite the absence of evidence for sub-aerial exposure.Applied GeologyApplied Earth SciencesCivil Engineering and Geoscience
Author correction:Mapping peat thickness and carbon stocks of the central Congo Basin using field data
No full textCorrection to: Nature Geoscience https://doi.org/10.1038/s41561-022-00966-7, published online 21 July 2022
Politeness in Diplomatic Talk: A Thai Case Study
No full textThis research starts from the assumption that there are goal-oriented politeness strategies in diplomatic talk. The case study analyses Thai-foreign diplomatic events during Thailand’s national crisis, the massive demonstrations across the country in the years of
2009-2011, in which the colours of the protesters’ clothing signified divergent political allegiances (so-called “colorized politics”). The research aims are threefold: firstly, to characterise politeness strategies in the Thai-foreign diplomatic talks conducted in English; secondly, to examine the extent to which culture-specific values inform the conversational performance of Thai speakers; and thirdly, to explore potential causes of misunderstandings arising from cross-cultural mismatches which occur during these social interactions. The research data are real-time conversations in courtesy calls and international meetings between foreign diplomatic representatives and the leaders of the Thai state and government agencies. My study is influenced by Brown and evinson’s theory along with intercultural communication theories for analysing the ethnographically observed talk-in-action events and transcribed conversational discourse. The research frames a conclusive argument that the diplomatic speakers use both conventional politeness and
unconventional politeness strategies. The latter includes what I term ‘lexical politeness’, ‘interactive politeness’, and ‘intercultural politeness’. The Thai party’s politeness strategies in pursuit of diplomatic goals carry an implication of Thai cultural values, specifically: fun-orientation, interdependence, and non-confrontation. Potential pragmatic failures in Thai cultural-oriented politeness are intimacy and directness. The research reveals the suppositions and entailments of English utterances by non-native speakers (Thais) and develops linguistic politeness strategies from the evidence of the diplomatic conversations
The C-Terminal Domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC Is a Lectin-Like Carbohydrate Binding Module
No full textThe D-arabinan-containing polymers arabinogalactan (AG) and lipoarabinomannan (LAM) are essential components of the unique cell envelope of the pathogen Mycobacterium tuberculosis. Biosynthesis of AG and LAM involves a series of membrane-embedded arabinofuranosyl (Araf) transferases whose structures are largely uncharacterised, despite the fact that several of them are pharmacological targets of ethambutol, a frontline drug in tuberculosis therapy. Herein, we present the crystal structure of the C-terminal hydrophilic domain of the ethambutol-sensitive Araf transferase M. tuberculosis EmbC, which is essential for LAM synthesis. The structure of the C-terminal domain of EmbC (EmbCCT) encompasses two sub-domains of different folds, of which subdomain II shows distinct similarity to lectin-like carbohydrate-binding modules (CBM). Co-crystallisation with a cell wall-derived di-arabinoside acceptor analogue and structural comparison with ligand-bound CBMs suggest that EmbCCT contains two separate carbohydrate binding sites, associated with subdomains I and II, respectively. Single-residue substitution of conserved tryptophan residues (Trp868, Trp985) at these respective sites inhibited EmbC-catalysed extension of LAM. The same substitutions differentially abrogated binding of di- and penta-arabinofuranoside acceptor analogues to EmbCCT, linking the loss of activity to compromised acceptor substrate binding, indicating the presence of two separate carbohydrate binding sites, and demonstrating that subdomain II indeed functions as a carbohydrate-binding module. This work provides the first step towards unravelling the structure and function of a GT-C-type glycosyltransferase that is essential in M. tuberculosis. Author Summary Top Tuberculosis (TB), an infectious disease caused by the bacillus Mycobacterium tuberculosis, burdens large swaths of the world population. Treatment of active TB typically requires administration of an antibiotic cocktail over several months that includes the drug ethambutol. This front line compound inhibits a set of arabinosyltransferase enzymes, called EmbA, EmbB and EmbC, which are critical for the synthesis of arabinan, a vital polysaccharide in the pathogen's unique cell envelope. How precisely ethambutol inhibits arabinosyltransferase activity is not clear, in part because structural information of its pharmacological targets has been elusive. Here, we report the high-resolution structure of the C-terminal domain of the ethambutol-target EmbC, a 390-amino acid fragment responsible for acceptor substrate recognition. Combining the X-ray crystallographic analysis with structural comparisons, site-directed mutagenesis, activity and ligand binding assays, we identified two regions in the C-terminal domain of EmbC that are capable of binding acceptor substrate mimics and are critical for activity of the full-length enzyme. Our results begin to define structure-function relationships in a family of structurally uncharacterised membrane-embedded glycosyltransferases, which are an important target for tuberculosis therapy
Current knowledge on the Cuvette Centrale peatland complex and future research directions
No full textCongoPeat Early Careers Researchers Group is a group of early career researchers who work directly or in partnership with the NERC funded CongoPeat project (NERC reference no.: NE/R016860/1; https://congopeat.net), which has provided the authors with full or partial financial and academic support.The Cuvette Centrale is the largest tropical peatland complex in the world, covering approximately 145,000 km2 across the Republic of Congo and the Democratic Republic of Congo. It stores ca. 30.6 Pg C, the equivalent of three years of global carbon dioxide emissions and is now the first trans-national Ramsar site. Despite its size and importance as a global carbon store, relatively little is known about key aspects of its ecology and history, including its formation, the scale of greenhouse gas flows, its biodiversity and its history of human activity. Here, we synthesise available knowledge on the Cuvette Centrale, identifying key areas for further research. Finally, we review the potential of mathematical models to assess future trajectories for the peatlands in terms of the potential impacts of resource extraction or climate change.Peer reviewe
Mapping peat thickness and carbon stocks of the central Congo Basin using field data
No full textThe world’s largest tropical peatland complex is found in the central Congo Basin. However, there is a lack of in situ measurements to understand the peatland’s distribution and the amount of carbon stored in it. So far, peat in this region has been sampled only in largely rain-fed interfluvial basins in the north of the Republic of the Congo. Here we present the first extensive field surveys of peat in the Democratic Republic of the Congo, which covers two-thirds of the estimated peatland area, including from previously undocumented river-influenced settings. We use field data from both countries to compute the first spatial models of peat thickness (mean 1.7 ± 0.9 m; maximum 5.6 m) and peat carbon density (mean 1,712 ± 634 MgC ha−1; maximum 3,970 MgC ha−1) for the central Congo Basin. We show that the peatland complex covers 167,600 km2, 36% of the world’s tropical peatland area, and that 29.0 PgC is stored below ground in peat across the region (95% confidence interval, 26.3–32.2 PgC). Our measurement-based constraints give high confidence of globally significant peat carbon stocks in the central Congo Basin, totalling approximately 28% of the world’s tropical peat carbon. Only 8% of this peat carbon lies within nationally protected areas, suggesting its vulnerability to future land-use change
Mapping water levels across a region of the Cuvette Centrale peatland complex
No full textInundation dynamics are the primary control on greenhouse gas emissions from peatlands. Situated in the central Congo Basin, the Cuvette Centrale is the largest tropical peatland complex. However, our knowledge of the spatial and temporal variations in its water levels is limited. By addressing this gap, we can quantify the relationship between the Cuvette Centrale’s water levels and greenhouse gas emissions, and further provide a baseline from which deviations caused by climate or land-use change can be observed, and their impacts understood. We present here a novel approach that combines satellite-derived rainfall, evapotranspiration and L-band Synthetic Aperture Radar (SAR) data to estimate spatial and temporal changes in water level across a sub-region of the Cuvette Centrale. Our key outputs are a map showing the spatial distribution of rainfed and flood-prone locations and a daily, 100 m resolution map of peatland water levels. This map is validated using satellite altimetry data and in situ water table data from water loggers. We determine that 50% of peatlands within our study area are largely rainfed, and a further 22.5% are somewhat rainfed, receiving hydrological input mostly from rainfall (directly and via surface/sub-surface inputs in sloped areas). The remaining 27.5% of peatlands are mainly situated in riverine floodplain areas to the east of the Congo River and between the Ubangui and Congo rivers. The mean amplitude of the water level across our study area and over a 20-month period is 22.8 ± 10.1 cm to 1 standard deviation. Maximum temporal variations in water levels occur in the riverine floodplain areas and in the inter-fluvial region between the Ubangui and Congo rivers. Our results show that spatial and temporal changes in water levels can be successfully mapped over tropical peatlands using the pattern of net water input (rainfall minus evapotranspiration, not accounting for run-off) and L-band SAR data.Remote Sensin
Francis Quarles: a study of his literary ancestry and contemporary setting as a religious poet.
No full textPhDIn his choice of biblical material, in his attitude
towards biblical matter in poetry, in his efforts to
supplant secular poetry with divine poetry, and in his
style and metre, Francis Quarles is in an established
tradition of religious poetry which dates from the
mid-sixteenth century. He used this poetry to support
the Established Church and a Monarchy based on Divine
Right when these institutions were being attacked. He
criticized particularly Roman Catholics, Arminians, Puritans,
and Separatists. However, his poetry is not purely
propagandist. He shared a contemporary interest in the
vocabulary of the language and made many additions to it,
and in his syncretizing of classical mythology with
Christianity he followed contemporary practice. He
favoured the Authorized Version of the Bible, and he
satisfied demands for moralistic and didactic literature
in his poetic renderings of biblical material, which is
developed through the use of long speeches, long similes,
descriptive action, and exegesis. In Emblemes, where the
poems are but extended paraphrases of biblical text, the
same techniques of development are used.In his invocations Quarles follows prevailing
practices in addressing the Holy Spirit, God, or Christ.
There was contemporary confusion concerning the muse
Urania, but she retains her primary classical
associations and is never more than the Christian poet's
tutelary spirit or a personification of his poetic genius.
The high esteem in which Quarles' works were held
is shown in the comments of many of his contemporaries.
In Cowley's criticism his lack of artistry in handling
biblical material is pointed out.
Quarles shows more poetic powers in his occasional
lyrics and his satirical ability is at times suggested.
Had be concentrated on these powers, quite possibly he
would today hold a higher place as a poet in English
literature
