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"Dodson, J. R"
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Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis
The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
Journal Article
Complete Genome Sequence of the Q-Fever Pathogen Coxiella burnetii
The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.
Journal Article
The Brucella suis Genome Reveals Fundamental Similarities between Animal and Plant Pathogens and Symbionts
The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1 and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.
Journal Article
Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae
The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
Journal Article
A vegetation and fire history in a subalpine woodland and rain-forest region, Solomons Jewel Lake, Tasmania
Solomons Jewel Lake occurs in an area of subalpine woodland with patches of cool temperate rain forest and the conifer Athrotaxis cupressoides, which is found mainly along stream channels. A pollen record shows that the main vegetation types have not varied throughout the last 4000 years but subtle changes are evident in some elements. Apart from a reduction in Eucalyptus for about 300 years, beginning around 3500 BP, the sclerophyll vegetation has remained relatively unchanged. A small decline in rainforest taxa began around 1700 BP, followed by an expansion of Sphagnum from 1200 BP, then Athrotaxis cupressoides and Cyperaceae from 800-900 BP. These trends probably represent a chain of events associated with a cooling which reduced rain forest and allowed wetland areas to expand. These then provided additional habitat for Athrotaxis cupressoides which expanded because the wetlands provided additional protection from fire.
Journal Article
A perspective from the past in conservation of plant biodiversity in central China
Biodiversity has increasingly come under threat from human activity everywhere on Earth. China, with over 33,000 species of vascular plants, is a megadiverse region, in part because of its diversity in topography and climates. One of its most extensive biomes is broadleaved evergreen/warm mixed forest which dominates eastern Asia and Central China. There is some debate about how glacial/interglacial cycles across the Quaternary had an impact on this biome. There were certainly broad scale changes in distribution of many key species. Here, we examine the four palaeoecological records from Central China that contain both LGM and Mid-Holocene vegetation records and consider the degree of biodiversity in Central China with the aim of developing a broad overview of the history on plants in the region. It is clear that in the mountainous regions of Central China, many taxa survived the LGM in situ, showing that there was enough stable habitat to support key species. Some mountainous areas have high degrees of endemism which suggests that fragmentation of populations across glacial/interglacial cycles may have been an important component in favoring speciation. The consideration of past records and modern species distributions have significance in selecting conservation areas.
Journal Article
Quantitative Holocene climatic reconstructions for the lower Yangtze region of China
Quantitative proxy-based and high-resolution palaeoclimatic datasets are scarce for the lower reaches of the Yangtze River (LYR) basin. This region is in a transitional vegetation zone which is climatologically sensitive; and as a birthplace for prehistorical civilization in China, it is important to understand how palaeoclimatic dynamics played a role in affecting cultural development in the region. We present a pollen-based and regionally-averaged Holocene climatic twin-dataset for mean total annual precipitation (PANN) and mean annual temperature (TANN) covering the last 10,000 years for the LYR region. This is based on the technique of weighted averaging-partial least squares regression to establish robust calibration models for obtaining reliable climatic inferences. The pollen-based reconstructions generally show an early Holocene climatic optimum with both abundant monsoonal rainfall and warm thermal conditions, and a declining pattern of both PANN and TANN values in the middle to late Holocene. The main driving forces behind the Holocene climatic changes in the LYR area are likely summer solar insolation associated with tropical or subtropical macro-scale climatic circulations such as the Intertropical Convergence Zone (ITCZ), Western Pacific Subtropical High (WPSH), and El Niño/Southern Oscillation (ENSO). Regional multi-proxy comparisons indicate that the Holocene variations in precipitation and temperature for the LYR region display an in-phase relationship with other related proxy records from southern monsoonal China and the Indian monsoon-influenced regions, but are inconsistent with the Holocene moisture or temperature records from northern monsoonal China and the westerly-dominated region in northwestern China. Overall, our comprehensive palaeoclimatic dataset and models may be significant tools for understanding the Holocene Asian monsoonal evolution and for anticipating its future dynamics in eastern Asia.
Journal Article
Holocene vegetation change in the mediterranean-type climate regions of Australia
In Australia mediteranean-type climates occur in southwestern Australia and in near coastal South Australia and adjacent western Victoria. These regions support species-rich sclerophyllous heaths and shrublands with the biodiversity particularly high in the southwest. Palynological records show that around the timne of the Last Glacial Maximum the climate was sufficiently severe that the vegetation of the southeastem regions was of a different character compared to today with grasses and Asteraceae more common everywhere. In the southwest the differences between Last Glacial Maximum and the Holocene were less pronounced and the tree and shrub genera Casuarina and Allocasuiarina were more prominent, and heathland and shrubland remaining the main vegetation type. Most of the records from the Last Glacial Maximun verify that common taxa in mediterranean-type climate environments today were present through that period in low niumbers. The modem chairacter of the vegetation developed arounid two key periods: the Pleistocene/Holocene boundary, and, to a much smaller degree, from the mid-Holocene, with the chaniges somewhat less in the southwest. The mid-Holocene period was mnarked by slightly wetter and waimer conditionis than present across all of southeastem Australia, yet most palynological records show little if any response in terrestrial vegetation in relation to this climate. The most significant Holocene changes appear to be a gradual decline in the importance of Casuarina, and changes in the abundance of Corymbia calophylla in the southwest. Many of the palynological records also have fossil charcoal histories and it is clear that, while there has been some regional variation. fire has been an important environmental feature of the regions throughout the Holocene. However, there are few indications that fire had any major role in vegetation change. What is clear is that European settlement, from about 150-180 years ago, wrought the greatest changes on vegetation, and possibly because of the parallel climate and environmental conditions the main invasive species have come from other mediterranean-type climate regions.
Journal Article
The 9.2 ka event in Asian summer monsoon area: the strongest millennial scale collapse of the monsoon during the Holocene
Numerous Holocene paleo-proxy records exhibit a series of centennial-millennial scale rapid climatic events. Unlike the widely acknowledged 8.2 ka climate anomaly, the likelihood of a significant climate excursion at around 9.2 cal ka BP, which has been notably recognized in some studies, remains to be fully clarified in terms of its magnitude and intensity, as well as its characteristics and spatial distributions in a range of paleoclimatic records. In this study, a peat sediment profile from the Dajiuhu Basin in central China was collected with several geochemical proxies and a pollen analysis carried out to help improve understanding of the climate changes around 9.2 cal ka BP. The results show that the peat development was interrupted abruptly at around 9.2 cal ka BP, when the chemical weathering strength decreased and the tree-pollen declined. This suggests that a strong drier regional climatic event occurred at around 9.2 cal ka BP in central China, which was, in turn, probably connected to the rapid 9.2 ka climate event co-developing worldwide. In addition, based on the synthesis of our peat records and the other Holocene hydrological records from Asian summer monsoon (ASM) region, we further found that the 9.2 ka event probably constituted the strongest abrupt collapse of the Asian monsoon system during the full Holocene interval. The correlations between ASM and the atmospheric 14C production rate, the North Atlantic drift ice records and Greenland temperature indicated that the weakened ASM event at around 9.2 cal ka BP could be interpreted by the co-influence of external and internal factors, related to the changes of the solar activity and the Atlantic Meridional Overturning Circulation (AMOC).
Journal Article