scholarly journals Bacillus anthracis Phylogeography: New Clues From Kazakhstan, Central Asia

2021 ◽  
Vol 12 ◽  
Author(s):  
Alexandr Shevtsov ◽  
Larissa Lukhnova ◽  
Uinkul Izbanova ◽  
Jean-Philippe Vernadet ◽  
Marat Kuibagarov ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Central Asia ◽  
Tandem Repeats ◽  
Epidemiological Data ◽  
Variable Number ◽  
Technical Institute ◽  
The Past ◽  
Independent Events ◽  
The Common ◽  
Common Era

This article describes Bacillus anthracis strains isolated in Kazakhstan since the 1950s until year 2016 from sixty-one independent events associated with anthrax in humans and animals. One hundred and fifty-four strains were first genotyped by Multiple Locus VNTR (variable number of tandem repeats) Analysis (MLVA) using 31 VNTR loci. Thirty-five MLVA31 genotypes were resolved, 28 belong to the A1/TEA group, five to A3/Sterne-Ames group, one to A4/Vollum and one to the B clade. This is the first report of the presence of the B-clade in Kazakhstan. The MLVA31 results and epidemiological data were combined to select a subset of seventy-nine representative strains for draft whole genome sequencing (WGS). Strains from Kazakhstan significantly enrich the known phylogeny of the Ames group polytomy, including the description of a new branch closest to the Texas, United States A.Br.Ames sublineage stricto sensu. Three among the seven currently defined branches in the TEA polytomy are present in Kazakhstan, “Tsiankovskii”, “Heroin”, and “Sanitary Technical Institute (STI)”. In particular, strains from the STI lineage are largely predominant in Kazakhstan and introduce numerous deep branching STI sublineages, demonstrating a high geographic correspondence between “STI” and Kazakhstan, Central Asia. This observation is a strong indication that the TEA polytomy emerged after the last political unification of Asian steppes in the fourteenth century of the Common Era. The phylogenetic analysis of the Kazakhstan data and of currently available WGS data of worldwide origin strengthens our understanding of B. anthracis geographic expansions in the past seven centuries.

Advancing community-led research into the climate of the Common Era

2021 ◽  
Author(s):  
Sarah S. Eggleston ◽  
Steven Phipps ◽  
Oliver Bothe ◽  
Helen V. McGregor ◽  
Belen Martrat ◽  
...  
Keyword(s):  
Climate Science ◽  
Global Changes ◽  
Present Climate ◽  
The Third ◽  
The Past ◽  
Third Phase ◽  
The Common ◽  
Common Era ◽  
Scientific Questions ◽  
New Phase

<p>The past two thousand years is a key interval for climate science. This period encompasses both the era of human-induced global warming and a much longer interval when changes in Earth’s climate were governed principally by natural drivers and unforced variability. Since 2009, the Past Global Changes (PAGES) 2k Network has brought together hundreds of scientists from around the world to reconstruct and understand the climate of the Common Era using open and collaborative approaches to palaeoclimate science, including virtual meetings. The third phase of the network will end in December 2021. Here we highlight some key outputs of PAGES 2k and present the major themes and scientific questions emerging from recent surveys of the community. We explore how these might boost a new phase of PAGES 2k or a successor project(s). This year we will further reach out to the community through Town Hall consultations, vEGU and other meetings, and a PAGES 2k global webinar series. The aim of these activities is to foster development of post-2021 community-led PAGES initiatives that connect past and present climate.</p>

scholarly journals Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Anna Engström ◽  
Uladzimir Antonenka ◽  
Abdylat Kadyrov ◽  
Gulmira Kalmambetova ◽  
Katharina Kranzer ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Population Structure ◽  
Central Asia ◽  
Tandem Repeats ◽  
Relative Size ◽  
Multidrug Resistant ◽  
Variable Number ◽  
Health Concern ◽  
Drug Resistant ◽  
Recent Emergence

Abstract Background Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. Methods The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. Results The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94–32 (n = 145) and 100–32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. Conclusions Beijing clusters 94–32 and 100–32 are the dominant MTB genotypes in Central Asia. The relative size of 100–32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.

scholarly journals Millennial-to-centennial patterns and trends in the hydroclimate of North America over the past 2000 years

2017 ◽  
Author(s):  
Bryan N. Shuman ◽  
Cody Routson ◽  
Nicholas McKay ◽  
Sherilyn Fritz ◽  
Darrell Kaufman ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Ice Age ◽  
The Arctic ◽  
Medieval Period ◽  
The Past ◽  
Past 2000 Years ◽  
Annual Range ◽  
The Common ◽  
Common Era ◽  
Millennial Scale

Abstract. A synthesis of 93 hydrologic records from across North and Central America, and adjacent tropical and Arctic islands, reveals centennial to millennial trends in the regional hydroclimates of the Common Era (CE; past 2000 years). The hydrological records derive from materials stored in lakes, bogs, caves, and ice from extant glaciers, which have the continuity through time to preserve low-frequency (> 100 year) climate signals that may not be well represented by other shorter-lived archives, such as tree-ring chronologies. The most common pattern, represented in 46 (49 %) of the records, indicates that the centuries before 1000 CE were drier than the centuries since that time. Principal components analysis indicates that millennial-scale trends represent the dominant pattern of variance in the southwest and northeast U.S., the mid-continent, Pacific Northwest, the Arctic, and the tropics, although not all records within a region show the same direction of change. The Pacific Northwest, Greenland, and the southernmost tier of the tropical sites tended to dry toward present, as many other areas became wetter than before. Twenty-two records (24 %) indicate that the Medieval period (800–1300 CE) was drier than the Little Ice Age (1400–1900 CE), but in many cases the difference was part of the longer millennial-scale trend, and, in 25 records (27 %), the Medieval period represented a pluvial (wet) phase. Where quantitative records permitted a comparison, we found that centennial-scale fluctuations over the Common Era represented changes of 3–7 % of the modern inter-annual range of variability in precipitation, but the accumulation of these long-term trends over the entirety of the Holocene caused recent centuries to be significantly wetter, on average, than most of the past 11 000 years.

Brucella ceti from two striped dolphins stranded on the Apulia coastline, Italy

2014 ◽  
Vol 63 (2) ◽  
pp. 325-329 ◽  
Author(s):  
Giuliano Garofolo ◽  
Katiuscia Zilli ◽  
Pasquale Troiano ◽  
Antonio Petrella ◽  
Francesca Marotta ◽  
...  
Keyword(s):  
Marine Mammals ◽  
Tandem Repeats ◽  
Variable Number ◽  
Sequence Type ◽  
Epidemiological Investigation ◽  
Stenella Coeruleoalba ◽  
First Case ◽  
Microbiological Methods ◽  
The Common ◽  
Common Sequence

Since 1994, when Brucella ceti was first isolated from an aborted dolphin fetus, several cases have been reported worldwide. The first case of B. ceti in the Mediterranean (and in Italy), however, was recorded only in 2012, off the coast of Tuscany. Extensive studies, using serological and microbiological methods, have documented this bacterium in dolphins and demonstrated its zoonotic potential. We describe the typing of two B. ceti strains isolated from striped dolphins (Stenella coeruleoalba) stranded on the southern Apulia coastline. B. ceti isolates were conventionally typed, and then genotyped by both the multilocus sequence typing (MLST) and the multilocus variable number of tandem repeats typing (MLVA) methodologies to infer phylogeny and potential epidemiological links between the two cases. The two isolates were identified through MLST analysis as belonging to the common sequence type 26 (ST26), while MLVA analysis, having established that the two isolates have identical profiles, assigned them to a novel genotype within cluster A – a unique representative of a new Mediterranean subcluster. The results thus revealed a link between the two cases studied, demonstrating the usefulness of MLST and MLVA for the epidemiological investigation of brucellae among marine mammals.

scholarly journals Placing the Common Era in a Holocene context: millennial to centennial patterns and trends in the hydroclimate of North America over the past 2000 years

2018 ◽  
Vol 14 (5) ◽  
pp. 665-686 ◽  
Author(s):  
Bryan N. Shuman ◽  
Cody Routson ◽  
Nicholas McKay ◽  
Sherilyn Fritz ◽  
Darrell Kaufman ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Ice Age ◽  
Medieval Climate Anomaly ◽  
Climate Anomaly ◽  
The Holocene ◽  
The Past ◽  
Past 2000 Years ◽  
The Common ◽  
Common Era ◽  
Millennial Scale

Abstract. A synthesis of 93 hydrologic records from across North and Central America, and adjacent tropical and Arctic islands, reveals centennial to millennial trends in the regional hydroclimates of the Common Era (CE; past 2000 years). The hydrological records derive from materials stored in lakes, bogs, caves, and ice from extant glaciers, which have the continuity through time to preserve low-frequency ( > 100 year) climate signals that may extend deeper into the Holocene. The most common pattern, represented in 46 (49 %) of the records, indicates that the centuries before 1000 CE were drier than the centuries since that time. Principal component analysis indicates that millennial-scale trends represent the dominant pattern of variance in the southwestern US, northeastern US, mid-continent, Pacific Northwest, Arctic, and tropics, although not all records within a region show the same direction of change. The Pacific Northwest and the southernmost tier of the tropical sites tended to dry toward present, as many other areas became wetter than before. In 22 records (24 %), the Medieval Climate Anomaly period (800–1300 CE) was drier than the Little Ice Age (1400–1900 CE), but in many cases the difference was part of the longer millennial-scale trend, and, in 25 records (27 %), the Medieval Climate Anomaly period represented a pluvial (wet) phase. Where quantitative records permitted a comparison, we found that centennial-scale fluctuations over the Common Era represented changes of 3–7 % in the modern interannual range of variability in precipitation, but the accumulation of these long-term trends over the entirety of the Holocene caused recent centuries to be significantly wetter, on average, than most of the past 11 000 years.

scholarly journals Low-resolution Australasian palaeoclimate records of the last 2000 years

2017 ◽  
Author(s):  
Bronwyn C. Dixon ◽  
Jonathan J. Tyler ◽  
Andrew M. Lorrey ◽  
Ian D. Goodwin ◽  
Joëlle Gergis ◽  
...  
Keyword(s):  
Climate Variability ◽  
A Priori ◽  
High Quality ◽  
Bayesian Techniques ◽  
The Past ◽  
Past 2000 Years ◽  
Dating Methods ◽  
The Common ◽  
Common Era ◽  
Australasian Region

Abstract. Non-annually resolved palaeoclimate records in the Australasian region were compiled to facilitate investigations of decadal to centennial climate variability over the past 2000 years. A total of 661 lake/wetland, geomorphic, marine, and speleothem records were identified and then assessed against a set of a priori criteria based on temporal resolution, record length, dating methods, and confidence of the proxy-climate relationship over the Common Era. A high quality subset of 22 records across Australasia met the criteria and they are endorsed for subsequent analyses. New chronologies based on progressive Bayesian techniques were constructed for the high quality records to ensure a consistent approach to age modelling and quantification of age uncertainties. Chronological uncertainty was the primary reason why records did not meet the selection criteria. Despite present limitations, existing proxies and reconstruction techniques that successfully capture climate variability in the region show potential to address spatial gaps and expand the range of climate variables covering the last 2000 years from the Australasian region.

scholarly journals Comparison of Minisatellite Polymorphisms in the Bacillus cereus Complex: a Simple Assay for Large-Scale Screening and Identification of Strains Most Closely Related to Bacillus anthracis

2005 ◽  
Vol 71 (11) ◽  
pp. 6613-6623 ◽  
Author(s):  
Samina Valjevac ◽  
Valérie Hilaire ◽  
Olivier Lisanti ◽  
Françoise Ramisse ◽  
Eric Hernandez ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Large Scale ◽  
Tandem Repeats ◽  
Low Cost ◽  
Point Mutations ◽  
Variable Number ◽  
Virulence Plasmids ◽  
Screening And Identification ◽  
Genetic Events ◽  
Large Scale Screening

ABSTRACT Polymorphism of five tandem repeats that are monomorphic in Bacillus anthracis was investigated in 230 isolates of the B. cereus group and in 5 sequenced B. cereus genomes in search for markers allowing identification of B. cereus and B. thuringiensis strains most closely related to B. anthracis. Using this multiple-locus variable number of tandem repeat analysis (MLVA), a cluster of 30 strains was selected for further characterization. Eventually, six of these were characterized by multilocus sequence type analysis. One of the strains is only six point mutations (of almost 3,000 bp) away from B. anthracis and was also proposed to be closest to B. anthracis by MLVA analysis. However, this strain remains separated from B. anthracis by a number of significant genetic events observed in B. anthracis, including the loss of the hemolysin activity, the presence of four prophages, and the presence of the two virulence plasmids, pXO1 and pXO2. One particular minisatellite marker provides an efficient assay to identify the subset of B. cereus and B. thuringiensis strains closely related to B. anthracis. Based on these results, a very simple assay is proposed that allows the screening of hundreds of strains from the B. cereus complex, with modest equipment and at a low cost, to eventually fill the gap with B. anthracis and better understand the origin and making of this dangerous pathogen.

scholarly journals Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates.

1997 ◽  
Vol 63 (4) ◽  
pp. 1400-1405 ◽  
Author(s):  
P J Jackson ◽  
E A Walthers ◽  
A S Kalif ◽  
K L Richmond ◽  
D M Adair ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Tandem Repeats ◽  
Variable Number ◽  
Variable Number Tandem Repeats

Perfections (Six and Ten) of Bodhisattvas in Buddhist Literature

2016 ◽  
Author(s):  
James B. Apple
Keyword(s):  
Southeast Asia ◽  
The Other ◽  
Past Participle ◽  
Sanskrit Literature ◽  
Buddhist Literature ◽  
Loving Kindness ◽  
The Past ◽  
The Common ◽  
Common Era ◽  
Standard List

The etymology of the Sanskrit and Pāli term pāramitā was a contested issue in classical India. One representation considered that the term was derived from pāram, “other (side),” plus the past participle ita, “gone.” This derivation is later preserved in the standard Tibetan translation pha-rol-tu phyin-pa, “gone to the other shore,” implying that such virtues lead to the blissful shore of nirvāṇa and away from the side of saṃsāra, the conditioned world of repeated rebirth and redeath. Other interpretations advocated that this etymology was misguided, and derived pāramitā from the term parama, “excellent, supreme.” The noun pāramitā is translated in early Chinese through “double translation” composed by tu wu-chi, meaning “crossed over” (tu) plus “limitless” (wu-chi), which brings together both of the traditional etymologies. The conception of the perfections as a specific set of practices is not found in the earliest layers of Buddhist literature. Rather, the perfections as a set of practices developed sometime before the common era as an alternative group of spiritual practices in conjunction with revised notions of buddhahood as well as newly considered notions of what constitutes the path leading to buddhahood. The lists of perfections varied according to the genre of literature in which they appeared. What practices constituted the varied lists of perfections and how the perfections were conceived differed not only among groups but also among scholarly authors. The perfections appear in Buddhist literature as a group in varying lists, but the lists of perfections are notoriously unfixed, with six and ten perfections being the most common. The Theravāda tradition recognizes ten, although only eight are listed in the Buddhāpadāna and seven in the Cariyāpiṭaka. The ten perfections in the Theravāda tradition are (1) generosity (dāna), (2) morality (sīla), (3) renunciation (nekhamma), (4) insight (pañña), (5) energy (viriya), (6) patience (khanti), (7) truthfulness (sacca), (8) resolution (adhiṭṭhāna), (9) loving-kindness (metta), and (10) equanimity (upekkhā). This list differs from the list of ten perfections found in Buddhist Sanskrit literature. A set of six perfections became common among some genres of mainstream Buddhist literature and developed into a standard list in a number of Mahāyāna sūtras. However, other lists of four, five, or seven perfections also occurred. In time, a set of six perfections became standard in Mahāyāna sūtras. The six are (1) generosity (dāna), (2) morality (śīla), (3) patience (kṣānti), (4) vigor (vīrya), (5) concentration (dhyāna), and (6) wisdom (prajñā). This list was expanded to complement the ten stages (bhūmi) traversed by a bodhisattva in the course leading to full buddhahood. The additional perfections were (7) skill-in-means (upāya-kauśalya), (8) resolution (praṇidhāna), (9) strength (bala), and (10) knowledge (jñāna). The manner in which the perfections were understood in different Buddhist cultures, such as in East Asia, Tibet, or Southeast Asia, was dependent on the Buddhist literature that was accessible or acceptable to the particular culture and the interpretative attention given to that literature.

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