scholarly journals The past, present and future of ancient bacterial DNA

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Nicolas Arning ◽  
Daniel J. Wilson
Keyword(s):  
Demographic Transition ◽  
Dental Plaque ◽  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Industrial Revolution ◽  
Environmental Isolates ◽  
Bacterial Dna ◽  
Content Type ◽  
The Past ◽  
History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

scholarly journals Extensive introgression and mosaic genomes of Mediterranean endemic lizards

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Weizhao Yang ◽  
Nathalie Feiner ◽  
Catarina Pinho ◽  
Geoffrey M. While ◽  
Antigoni Kaliontzopoulou ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Mediterranean Islands ◽  
The Past ◽  
Island Endemics ◽  
Extant Species ◽  
Mediterranean Island ◽  
History Of ◽  
Entire History ◽  
The Mediterranean ◽  
The Mediterranean Basin

AbstractThe Mediterranean basin is a hotspot of biodiversity, fuelled by climatic oscillation and geological change over the past 20 million years. Wall lizards of the genus Podarcis are among the most abundant, diverse, and conspicuous Mediterranean fauna. Here, we unravel the remarkably entangled evolutionary history of wall lizards by sequencing genomes of 34 major lineages covering 26 species. We demonstrate an early (>11 MYA) separation into two clades centred on the Iberian and Balkan Peninsulas, and two clades of Mediterranean island endemics. Diversification within these clades was pronounced between 6.5–4.0 MYA, a period spanning the Messinian Salinity Crisis, during which the Mediterranean Sea nearly dried up before rapidly refilling. However, genetic exchange between lineages has been a pervasive feature throughout the entire history of wall lizards. This has resulted in a highly reticulated pattern of evolution across the group, characterised by mosaic genomes with major contributions from two or more parental taxa. These hybrid lineages gave rise to several of the extant species that are endemic to Mediterranean islands. The mosaic genomes of island endemics may have promoted their extraordinary adaptability and striking diversity in body size, shape and colouration, which have puzzled biologists for centuries.

Haunted by the past: transformations and daily challenges of China's prosthetics

2020 ◽  
Vol 10 (1) ◽  
pp. 115-124
Author(s):  
Chunchun Wang
Keyword(s):  
Design Methodology ◽  
Cross Cultural ◽  
Future Research ◽  
Institutional Pressures ◽  
Rehabilitation Center ◽  
Content Type ◽  
The Past ◽  
Daily Experiences ◽  
History Of ◽  
Depth Interviews

PurposeThe purpose of this paper is to examine the transformations of prosthetic practices in China, as well as the daily experiences and dilemmas arising from the everchanging practices since 1949. On the basis of materials, this paper explores an everyday perspective to review the history of technology.Design/methodology/approachEthnography was collected with the application of participant observations, informal interviews and in-depth interviews during a 13-months study at a rehabilitation center in Chengdu, China. The literature on prosthetic manufacturing was also reviewed for this paper.FindingsChina's prosthetic technology seems to evolve from traditional to modern. However, this progressive narrative – innovation-based timeline (Edgerton, 2006, xi) – has been challenged by daily practices. Due to institutional pressures, prosthetists are in a dilemma of selectively using their knowledge to create one kind of device for all prosthesis users with a certain kind of disability, thereby regulating the physical and social experiences of prosthesis users. Besides, prosthesis users are accustomed to prostheses made with old techniques, and must correct themselves from old experiences to the daily practices recognized by the selected techniques.Originality/valueThis paper provides a cross-cultural case to reexamine Edgerton's criticism of the progressive and orderly innovation-centric technological narrative. More importantly, it reviews the history and practices of China's prosthetics from daily experiences rather than Edgerton's concentration on technology; therefore, it provides an everyday perspective for future research on technological transformations.

History of forestry and forest management

1975 ◽  
Vol 271 (911) ◽  
pp. 69-80 ◽  
Keyword(s):  
Forest Management ◽  
Industrial Revolution ◽  
Environmental Benefits ◽  
National Forest ◽  
Private Landowners ◽  
Timber Production ◽  
Land Area ◽  
The Past ◽  
The Social ◽  
History Of

Britain possesses a forest area which is one of the smallest in Europe in relation to its population and land area. In the past, forests have been felled to make way for farming and to supply timber for ships, houses, fuel and metal smelting. Timber was a key to sea power, and repeatedly the availability of home timber supplies has proved crucial in time of war. The nation’s dwindling reserves of timber have been a source of anxiety since Tudor times and periodic surges of planting for timber production by private landowners took place until about 1850. Thereafter, interest faded with the advent of the iron ship, the Industrial Revolution and the availability of cheap timber imports. Govern­ ment activity was minimal until a national forest authority was formed in 1919 to create a strategic timber reserve. Since 1958 there have been frequent policy reviews to assess the changing needs of the nation for timber and the new values associated with the social and environmental benefits of forests.

scholarly journals The moral arc of the library: what are our duties and limitations after 45?

2020 ◽  
Vol 48 (2) ◽  
pp. 219-225
Author(s):  
Kelsey Cheshire ◽  
Jennifer Stout
Keyword(s):  
Design Methodology ◽  
White Privilege ◽  
White Supremacy ◽  
Code Of Ethics ◽  
Past Century ◽  
Political Climate ◽  
Content Type ◽  
Critical Thought ◽  
The Past ◽  
History Of

Purpose This study aims to explore the question of whether or not librarians can ethically remain politically neutral in the wake of the 45th administration. The authors take a critical look at the American Library Association’s Code of Ethics, as well as the concept of vocational awe, and recommend challenging the “sacredness” of neutrality as a core tenet of the profession. Additionally, the authors describe the history of white privilege within libraries and argue that it is time to actively fight white supremacy and disavow the profession’s history of replicating racist social structures. Design/methodology/approach This study is a researched think piece designed to encourage critical thought about long-held idealistic beliefs in the profession. Findings This study suggests that despite the profession’s history of outwardly valuing “neutrality,” libraries are not and have never been neutral. Libraries have chosen, time and again, to value white privilege and a white frame of reference to the detriment of librarians and patrons of color. Because many librarians also see the profession as upholding “sacred” ideals like neutrality, we fall into the trap of being unable to criticize our own profession and practices and, therefore, are unable to make much needed changes. Research limitations/implications This study is based on the opinions of the authors and on the opinions of authors they have cited. It contains no original quantitative or qualitative research. Originality/value This study challenges the long-held assumptions that the profession has taken for granted over the past century. The authors argue that it is good and necessary to question the Code of Ethics, vocational awe and neutrality with the goal of improving the profession in light of the current cultural and political climate.

scholarly journals The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Meghan M. Pearce ◽  
Evann E. Hilt ◽  
Amy B. Rosenfeld ◽  
Michael J. Zilliox ◽  
Krystal Thomas-White ◽  
...  
Keyword(s):  
Urinary Incontinence ◽  
Urinary Tract ◽  
High Throughput Sequencing ◽  
Urgency Urinary Incontinence ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Content Type ◽  
Urinary Microbiome ◽  
Live Bacteria ◽  
Tract Infections

ABSTRACTBacterial DNA and live bacteria have been detected in human urine in the absence of clinical infection, challenging the prevailing dogma that urine is normally sterile. Urgency urinary incontinence (UUI) is a poorly understood urinary condition characterized by symptoms that overlap urinary infection, including urinary urgency and increased frequency with urinary incontinence. The recent discovery of the urinary microbiome warrants investigation into whether bacteria contribute to UUI. In this study, we used 16S rRNA gene sequencing to classify bacterial DNA and expanded quantitative urine culture (EQUC) techniques to isolate live bacteria in urine collected by using a transurethral catheter from women with UUI and, in comparison, a cohort without UUI. For these cohorts, we demonstrated that the UUI and non-UUI urinary microbiomes differ by group based on both sequence and culture evidences. Compared to the non-UUI microbiome, sequencing experiments revealed that the UUI microbiome was composed of increasedGardnerellaand decreasedLactobacillus. Nine genera (Actinobaculum,Actinomyces,Aerococcus,Arthrobacter,Corynebacterium,Gardnerella,Oligella,Staphylococcus, andStreptococcus) were more frequently cultured from the UUI cohort. AlthoughLactobacilluswas isolated from both cohorts, distinctions existed at the species level, withLactobacillus gasseridetected more frequently in the UUI cohort andLactobacillus crispatusmost frequently detected in controls. Combined, these data suggest that potentially important differences exist in the urinary microbiomes of women with and without UUI, which have strong implications in prevention, diagnosis, or treatment of UUI.IMPORTANCENew evidence indicates that the human urinary tract contains microbial communities; however, the role of these communities in urinary health remains to be elucidated. Urgency urinary incontinence (UUI) is a highly prevalent yet poorly understood urinary condition characterized by urgency, frequency, and urinary incontinence. Given the significant overlap of UUI symptoms with those of urinary tract infections, it is possible that UUI may have a microbial component. We compared the urinary microbiomes of women affected by UUI to those of a comparison group without UUI, using both high-throughput sequencing and extended culture techniques. We identified statistically significant differences in the frequency and abundance of bacteria present. These differences suggest a potential role for the urinary microbiome in female urinary health.

scholarly journals Human Origin for Livestock-Associated Methicillin-Resistant Staphylococcus aureus

mBio ◽  
2012 ◽  
Vol 3 (2) ◽  
Author(s):  
J. Ross Fitzgerald
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary History ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Agricultural Practices ◽  
Methicillin Resistant ◽  
Content Type ◽  
Zoonotic Infections ◽  
Ancestral Origin ◽  
Important Study ◽  
History Of

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of human morbidity and mortality worldwide. The emergence in the last decade of a livestock-associated MRSA (LA-MRSA) clone which also has the capacity to cause zoonotic infections in humans has raised important questions regarding its origin and its potential to cause human epidemics. An important study by L. B. Price et al. [mBio 3(1):e00305-11, 2012] provides evidence for a human ancestral origin for LA-MRSA, raising concerns about agricultural practices that may have contributed to its emergence and expansion. The study highlights the potential for comparative whole-genome sequencing of closely related strains to provide valuable insights into the evolutionary history of bacterial pathogens.

scholarly journals Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131

mSphere ◽  
2016 ◽  
Vol 1 (4) ◽  
Author(s):  
Timothy J. Johnson ◽  
Jessica L. Danzeisen ◽  
Bonnie Youmans ◽  
Kyle Case ◽  
Katharine Llop ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Single Molecule ◽  
Convergent Evolution ◽  
Evolutionary History ◽  
Gene Clusters ◽  
Content Type ◽  
E Coli ◽  
History Of ◽  
Evolutionary Success

ABSTRACT A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success. The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B− plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B− plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success.

scholarly journals Tongue Microbiota Composition and Dental Caries Experience in Primary School Children

mSphere ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Daixi Zhang ◽  
Toru Takeshita ◽  
Michiko Furuta ◽  
Shinya Kageyama ◽  
Mikari Asakawa ◽  
...  
Keyword(s):  
Dental Caries ◽  
Primary School ◽  
School Children ◽  
Dental Plaque ◽  
Primary School Children ◽  
Caries Experience ◽  
Microbiota Composition ◽  
Elderly Adults ◽  
Content Type ◽  
History Of

ABSTRACT The tongue microbiota of elderly adults is composed of two cohabiting commensal groups and their ratios are related to the number of teeth with dental caries experience. In this study, the variation in the tongue microbiota of primary school children and its relationship with the dental caries experience were investigated. We examined the tongue microbiota of 138 children aged 6 to 7 years and 11 to 12 years (61 and 77 children, respectively) who underwent annual dental examinations. The bacterial composition was determined by sequencing the V1-V2 region of the 16S rRNA gene. Cooccurrence network analysis indicated two groups of cohabiting predominant commensals in the tongue microbiota of children. The microbiota in children without a history of dental caries showed significantly higher relative abundances of one of the cohabiting groups, primarily composed of Neisseria subflava, Porphyromonas pasteri, and Fusobacterium periodonticum, compared to that in children with a history of dental caries, which is consistent with that of elderly adults with fewer teeth with dental caries experience. Linear discriminant analysis effect size (LEfSe) further identified Streptococcus oralis subsp. dentisani, belonging to the aforementioned commensal group, as a discriminant species in children without dental caries experience aged 6 to 7 years and 11 to 12 years. Our results describe the tongue microbiota composition of primary school children without history of dental caries and support the possibility that dental caries experience is accompanied by a shift in the tongue microbiota. IMPORTANCE Dental caries is now considered to be caused by acids produced by the overall dental plaque microbiota rather than by specific pathogens. This study focused on the relationship between dental caries experience and the variations in tongue microbiota, which is adjacent but separate from the dental plaque microbiota. Our results demonstrated that the tongue microbiota of primary school children with no history of dental caries experience was composed of predominant commensals with different relative abundances compared to those present in children with dental caries experience, suggesting that dental caries experience is accompanied by a shift in the tongue microbiota. The maintenance of a healthy tongue microbiota may indirectly contribute to the prevention of dental caries.

The Measure of the Machine: How Exposure to Current Technology Can Upgrade a Student’s Education

2004 ◽  
Author(s):  
Robert Conger ◽  
Amanda Blum ◽  
Paul A. Erickson
Keyword(s):  
Computer Technology ◽  
Evolutionary History ◽  
The Internet ◽  
Technology In Education ◽  
Computing Power ◽  
Educational Benefits ◽  
The Past ◽  
History Of ◽  
Design Projects ◽  
Remarkable Progress

Over the past decade there has been a distinct trend toward implementing computer technology in education. The advent of affordable, student accessible computing power has allowed engineering curricula to follow the trends of computer technology in the engineering workplace. The developments in hardware and software, combined with the explosive entrance of the Internet, have allowed design projects to evolve into elaborate and imaginative endeavors. The enhanced speed at which projects can now be completed allows students the opportunity to undertake tasks of greater magnitude, while the advanced tools now available permit students to solve more sophisticated and lifelike problems. The examination of a senior-level design course, in which students must design and build a maze-solving robot, serves to highlight the educational benefits that stand to be gained through the judicious application of technology. The evolutionary history of this design course demonstrates the remarkable progress that computer technology has allowed in educational settings.

scholarly journals Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

2020 ◽  
Vol 59 (1) ◽  
pp. e02198-20
Author(s):  
N. Effelsberg ◽  
M. Stegger ◽  
L. Peitzmann ◽  
O. Altinok ◽  
G. W. Coombs ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary History ◽  
De Novo ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Invasive Disease ◽  
Phylogenetic Groups ◽  
Content Type ◽  
Global Epidemiology ◽  
History Of

ABSTRACTStaphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.

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