scholarly journals Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kelsey E. Witt ◽  
Karthik Yarlagadda ◽  
Julie M. Allen ◽  
Alyssa C. Bader ◽  
Mary L. Simon ◽  
...  
Keyword(s):  
Mississippi River ◽  
Pathogenic Bacteria ◽  
Intestinal Parasites ◽  
Dna Amplification ◽  
Late Woodland ◽  
Integrative Analysis ◽  
Archaeological Sites ◽  
Human Diet ◽  
Saint Louis ◽  
Fecal Microbiome

AbstractPaleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600–1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.

scholarly journals Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhen Han ◽  
Peter S. Thuy-Boun ◽  
Wayne Pfeiffer ◽  
Vincent F. Vartabedian ◽  
Ali Torkamani ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Human Microbiome ◽  
Host Immunity ◽  
Rrna Gene ◽  
Metabolic Labeling ◽  
Selective Labeling ◽  
Fecal Microbiome ◽  
Acetylneuraminic Acid ◽  
Intestinal Mucus ◽  
Microbial Systems

AbstractN-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.

scholarly journals Bakteri Simbion Gastropoda Pleuroploca trapesium Dari Perairan Ternate, Sebagai Alternatif Antibakteri MDR (Bacterial Symbiont Gastropoda Pleuroploca trapezium from Ternate, as Alternative Antibacterial MDR)

2014 ◽  
Vol 19 (1) ◽  
pp. 55
Author(s):  
Delianis Pringgenies ◽  
Person Pesona Renta
Keyword(s):  
16S Rdna ◽  
Pathogenic Bacteria ◽  
Dna Amplification ◽  
Sensitivity Test ◽  
Symbiotic Bacteria ◽  
Drug Resistant ◽  
16S Rdna Sequence Analysis ◽  
Close Relationship ◽  
Antibiotic Compounds ◽  
Bacterial Sensitivity

Bakteri yang resisten terhadap beberapa jenis antibakteri ini dikenal dengan bakteri multi drug resistant (MDR).Untuk mengatasi permasalahan tersebut, perlu dilakukan pencarian senyawa antibiotik baru yang lebih efektif dan efisien dalam mengatasi permasalahan bakteri MDR. Penelitian bertujuan untuk mengetahui potensi bakteri yang bersimbiosis dengan gastropoda Pleuroploca trapezium sebagai sumber antibakteri MDR. Sampel Moluska dikoleksi dari perairan Ternate, Maluku. Tahapan penelitian meliputi isolasi bakteri, skrining  bakteri simbion yang potensi sebagai anti bakteri MDR, uji antibakteri, isolasi bakteri patogen klinis MDR; uji sensitivitas anti-bakteri, ekstraksi, amplifikasi dan sekuensing DNA. Hasil 16S urutan r-DNA dianalisis dan diedit menggunakan program Genetix dan diikuti dengan analisis urutan 16S rDNA. Hasil menunjukkan bahwa terdapat 19 isolat bakteri dengan 5 bakteri aktif yang berasosiasi dengan Pleuroploca trapezium. Berdasarkan besarnya zona hambat yang dibentuk dan konsistensi munculnya zona hambatan, isolat terbaik adalah TPT 4.7. Isolat ini memiliki hubungan yang dekat dengan Paracoccus  sp. MBIC4019 dengan homologi sebesar 95% yang menunjukkan kekerabatan ditingkat genus. Hasil penelitian ini memberikan harapan adanya potensi besar sebagai bahan antibakteri baru. Kata kunci: antibakteri, simbion, Pleuroploca trapezium, multi drugs resistantThe bacteria resistant to some antibiotics are known as multi drug resistant (MDR). To overcome the problem, it is needed to search for a new antibiotic compounds more effectively and efficiently. This study aims to identify potential from symbionts of Pleuroploca trapezium as a source of antibacteria MDR and identifying the bacteria that were active against the MDR. Samples were collected from Ternate, Maluku. Isolation of symbiotic bacteria, screening for bacteria which producing secondary metabolites as anti-MDR bacteria, antibacterial test, isolation of clinical pathogenic bacteria of MDR. Conducting anti-bacterial sensitivity test,  sensitivity test for antibacterial,  DNA exctraction, DNA amplification based on PCR method, DNA sequencing.  Result of 16S r-DNA sequence was then analyzed and edited using GENETYX program and followed by 16S rDNA sequence analysis. Screening of bacteria associated with P. trapezium resulted in 19 isolates with 5 active bacteria. Based on the size of the zone forming and the consistency of zone, so the best isolate is TPT 4.7. The identification shows that TPT 4.7 has a close relationship with the Paracoccus sp. MBIC4019 with homologi of 95%, which shows the relationship at the genus level. Its suggest that these results are very promising as a new antibacterial material. Keywords: antibacterial, symbiotic bacteria, Pleuroploca trapezium, multi drugs resistant

Coring Archaeological Sites

1986 ◽  
Vol 51 (3) ◽  
pp. 505-527 ◽  
Author(s):  
Julie K. Stein
Keyword(s):  
Mississippi River ◽  
River Sediments ◽  
Radiometric Dating ◽  
Archaeological Sites ◽  
New Device ◽  
Culture History ◽  
Lower Mississippi River ◽  
History Of ◽  
River Deposits ◽  
Relationship Of

The history of coring and augering at archaeological sites is traced to two periods in the twentieth century. In the first period, Period I (1935-1955), the technique was used primarily to correlate archaeological deposits with river sediments for dating purposes. Rarely were the deposits containing artifacts cored or augered; rather the stratigraphic relationship of cultural to non-cultural deposits was sought. Most of this work was done in the Lower Mississippi River Delta where geologists had calculated absolute dates for river deposits. This period seems to have ended with the availability of radiometric dating and was followed by Period II (1964-present). After 1964 there is a renewed interest in coring and augering, mostly following a shift in archaeological research interests from culture history toward ecological questions. This shift coincides with the availability of a new device: a mechanical corer. During Period II, coring is utilized in many different projects, including reconstructing the environment surrounding sites, collection of samples from subsurface deposits, and locating buried archaeological sites. Following the discussion of the history of coring and augering, a description of equipment, techniques, and data potential is presented.

scholarly journals Burden of Enteropathogens Associated Diarrheal Diseases in Children Hospital, Nepal

1970 ◽  
Vol 7 (7) ◽  
pp. 71-75 ◽  
Author(s):  
Jeevan B Sherchand ◽  
Michiyo Yokoo ◽  
Ojaswee Sherchand ◽  
Arun R Pant ◽  
Osamu Nakogomi
Keyword(s):  
Public Health ◽  
Pathogenic Bacteria ◽  
Diarrheal Disease ◽  
Intestinal Parasites ◽  
Significant Proportion ◽  
Culture Method ◽  
Institute Of Medicine ◽  
Shigella Species ◽  
Causative Agents ◽  
Stool Samples

Diarrheal disease caused by bacteria, parasites or viruses continues to be an important cause of morbidity and mortality among young children in developing countries. Methods currently used in public health laboratories do not allow for the identification of rotavirus, Cyclospora and pathogenic E.coli infection though they represent as an etiology in large proportion of patients with diarrhea, the possibility exists that a portion of the undiagnosed illness may be attributable to one or more of the above enteropathogens. In a view to determine the causative agents of diarrhoea, the current study described the various enteropathogens associated with diarrhoea in hospitalized children. Stool samples were collected from children under 11 years of age who developed diarrhoea and were admitted to Kanti Children's Hospital between May to October 2007 and investigated in Tribhuvan University, Institute of Medicine, Health Research Laboratory; by using both the combination of microbiological and immunological tools ( EIA for rotavirus detection, standard parasitological procedure for Cyclospora and other intestinal parasites, and selective culture method and serotyping were used to differentiate the species of bacteria). A total of 440 diarrhoeal stool samples were collected and 285 (64.8%) enteropathogens were identified. The highest infection was due to intestinal parasites 104/285 (36.5%) followed by rotavirus 92/285 (32.3%); pathogenic bacteria 57/285 (20%) and Cyclospora 32/285 (11.2%). Among the pathogenic bacteria (20%) isolated, the predominant bacteria were Shigella species (36.8%); Vibrio species (26.3%); Escherichia coli (22.8%) and Salmonella species (14.03%) respectively. Various enteropthogens responsible for diarrhoea especially rotavirus, different pathogenic bacteria and Cyclospora infection, which are not examined routinely in public health laboratories, were found in significant proportion as a cause of diarrhoeal illness in children. The infection was peak in children under 2 years of age and was highest in rainy season. Key words: Burden; Diarrhea; Enteropathogens; Children; Nepal. DOI: 10.3126/sw.v7i7.3830Scientific World Vol.7(7) 2009 pp.71-75

Freshwater Mussels as a Prehistoric Food Resource

1974 ◽  
Vol 39 (3) ◽  
pp. 421-434 ◽  
Author(s):  
Paul W. Parmalee ◽  
Walter E. Klippel
Keyword(s):  
Mississippi River ◽  
Freshwater Mussels ◽  
Food Resource ◽  
Food Resources ◽  
Archaeological Sites ◽  
Eastern North America ◽  
Subsistence Economies ◽  
Level Data ◽  
Food Potential ◽  
Prehistoric Subsistence

AbstractThe explication of prehistoric subsistence economies has been of increasing interest to archaeologists. This emphasis is reflected, in part, by the considerable attention afforded faunal analyses in the recent archaeological literature. However, little effort has been made toward developing methods that permit meaningful comparisons of food resources at the interspecies level. Data pertinent to the calculation of both quantitative and qualitative food potential of many of the vertebrate animals represented in archaeological contexts are extant. These data are lacking for freshwater mussels, frequently found in archaeological sites in eastern North America. Information relevant to determining the food energy provided by freshwater mussels common to much of the Mississippi River drainage is presented. Results are applicable to more credible interpretations of prehistoric subsistence as related to animal food resources.

Other-Than-Human Persons, Mishipishu, and Danger in the Late Woodland Inland Waterway Landscape of Northern Michigan

2020 ◽  
Vol 85 (2) ◽  
pp. 347-366
Author(s):  
Meghan C. L. Howey
Keyword(s):  
Social Economic ◽  
Late Woodland ◽  
Early Spring ◽  
Woodland Period ◽  
Archaeological Sites ◽  
Late Woodland Period ◽  
Inland Lakes ◽  
Significant Relationships ◽  
Inland Waterway ◽  
Northern Michigan

Other-than-human persons and the role they play in transforming social, economic, and ideological material realities is an area of expanding interest in archaeology. Although the Anishinaabeg were an early and vital focus of cultural anthropological studies on nonhumans given their significant relationships with other-than-human persons, known to them as manitou, emerging archaeologies advancing this topic are not largely centered on ancestral Anishinaabeg sites and artifacts. This article analyzes a set of nonvessel ceramic artifacts from Late Woodland archaeological sites in the Inland Waterway in northern Michigan, which are interpreted to be ceramic renderings of manitou. I argue that these were manitou-in-clay, vibrant relational entities that are brought into being for and through use in ceremonial perspective practices related to Mishipishu—a complexly powerful, seductive, and dangerous nonhuman being known as the head of all water spirits. I contextualize the making and breaking of Mishipishu manitou-in-clay as acts of petition by hunter-fishers who had been seduced by this manitou in dreams, as they headed out on necessary but high-risk early-spring resource harvesting in the inland lakes of the Inland Waterway. This case advances insights into how relationships with other-than-human persons were coproductive of the world in the northern Great Lakes region during the Late Woodland period.

scholarly journals Fatal canine adenovirus type 1 acute infection in a Yorkshire Terrier puppy in Portugal: a case report

2014 ◽  
Vol 59 (No. 4) ◽  
pp. 210-220
Author(s):  
MD Duarte ◽  
AM Henriques ◽  
C. Lima ◽  
C. Ochoa ◽  
F. Mendes ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Mdck Cells ◽  
Intestinal Parasites ◽  
Acute Infection ◽  
Diagnostic Algorithm ◽  
Adenovirus Type ◽  
Infectious Hepatitis ◽  
Rapid Progression ◽  
Sequencing Analysis

This study reports the diagnostic algorithm followed for the identification of a fatal canine adenovirus type 1 (CAdV-1) infection in an unvaccinated 56 day-old puppy to overcome the limitations imposed by inconclusive histopathology hampered by body freezing. The animal was submitted to necropsy after a clinical history of lethargy, dehydration, vomiting and haemorrhagic diarrhoea. Pathological features, suggestive of infectious illness, included generalised gelatinous subcutaneous oedema, petechial, ecchymotic haemorrhages of the subcutaneous tissues and a friable uniformly yellow mottled liver. Differential diagnosis based on PCR ruled out the presence of most common gastrointestinal canine viruses and bacteriology and coprology confirmed that pathogenic bacteria and intestinal parasites did not account for the puppy’s death. Strong amplification of CAdV-1 DNA was obtained from liver samples. Isolation of CAdV-1 in MDCK cells was subsequently demonstrated and sequencing analysis showed high similarity with CAdV-1 isolates from Europe. In the absence of serum, antibodies against CAdV-1 were investigated in lung tissue extracts. The presence of CAdV-1 infectious particles and absence of immune response was consistent with rapid progression of the infection and death of the animal two days after the onset of clinical signals, allowing a final diagnosis of the acute form of ICH. Antibodies against CAdV-1 were detected in sera collected from clinically healthy dogs from the same premises, 14-months after the index case, suggesting that the virus had circulated in the breeding kennel. We believe this to be the first report of CAdV-1 in Portugal where canine infectious hepatitis is considered a rare infection.  

scholarly journals Modeling Regional Radiocarbon Trends: A Case Study from the East Texas Woodland Period

Radiocarbon ◽  
2012 ◽  
Vol 54 (02) ◽  
pp. 239-265 ◽  
Author(s):  
Robert Z Selden
Keyword(s):  
Probability Distributions ◽  
Late Woodland ◽  
Woodland Period ◽  
Archaeological Sites ◽  
Middle Woodland ◽  
East Texas ◽  
Data Set ◽  
Early Woodland ◽  
Resultant Data

The East Texas Radiocarbon Database contributes to an analysis of tempo and place for Woodland era (∼500 BC–AD 800) archaeological sites within the region. The temporal and spatial distributions of calibrated14C ages (n= 127) with a standard deviation (ΔT) of 61 from archaeological sites with Woodland components (n= 51) are useful in exploring the development and geographical continuity of the peoples in cast Texas, and lead to a refinement of our current chronological understanding of the period. While analysis of summed probability distributions (SPDs) produces less than significant findings due to sample size, they are used here to illustrate the method of date combination prior to the production of site- and period-specific SPDs. Through the incorporation of this method, the number of14C dates is reduced to 85 with a ΔTof 54. The resultant data set is then subjected to statistical analyses that conclude with the separation of the east Texas Woodland period into the Early Woodland (∼500 BC–AD 0), Middle Woodland (∼AD 0–400), and Late Woodland (∼AD 400–800) periods.

Different Methods for Molecular and Rapid Detection of Human Novel Coronavirus

2021 ◽  
Vol 27 ◽  
Author(s):  
Mohamad Hesam Shahrajabian ◽  
Wenli Sun ◽  
Qi Cheng
Keyword(s):  
Nucleic Acid ◽  
Rapid Detection ◽  
Pathogenic Bacteria ◽  
Scientific Information ◽  
Meat Products ◽  
Lamp Assay ◽  
Dna Amplification ◽  
Digital Pcr ◽  
Recombinase Polymerase Amplification ◽  
Nucleic Acid Amplification

Introduction: While PCR has been recognized as one of the appropriate ways to diagnosis of infectious diseases, Loop-mediated isothermal amplification (LAMP), which is a nucleic acid amplification method, can be considered as an alternative to PCR, and it is faster, cost-effective, and easier to perform than nested PCR. Patients and Methods: Keywords were searched in PubMed/MEDLINE, Scopus and Institute for Scientific Information Web of Science, as well as the search engine of Google Scholar. Keywords were PCR, LAMP, RAA, RPA, Virus and COVID-19. Results: LAMP technology has been extensively applied for the detection of human pathogenic bacteria, crop pests, pathogenic organisms and components in meat products. A new isotheral method, Recombinase polymerase amplification (RPA), can amplify the DNA as well as RPA. RPA has benefited from isothermal PCR and both simplicity and rapid amplification. Recombinase aided amplification (RAA) assay has been favorably used in the detection of bacterial and viral pathogens and solved the technical difficulties posed by DNA amplification methods because it does not need thermal denaturation of the template and employs at a low and constant temperature. Conclusions: Reverse transcription polymerase chain reaction, digital PCR, LAMP, nicking endonuclease amplification reaction, recombinase polymerase amplification, and clustered regularly interspaced short palindromic repeats are different nucleic acid amplification tests of COVID-19. LAMP methods can be more specific than qPCR and immunoassays. The LAMP assay can be applied for rapid detection of SARS-CoV, MERS-CoV, SARS-CoV-2, and influenza, because LAMP is a highly sensitive and specific DNA/RNA amplification technique.

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