scholarly journals Metagenomic analysis through the extended Burrows-Wheeler transform

2020 ◽  
Vol 21 (S8) ◽  
Author(s):  
Veronica Guerrini ◽  
Felipe A. Louza ◽  
Giovanna Rosone
Keyword(s):  
Human Microbiome ◽  
Simulated Data ◽  
High Sensitivity ◽  
Human Microbiome Project ◽  
Positive Control ◽  
Negative Control ◽  
Microbial Composition ◽  
Combinatorial Properties ◽  
Burrows Wheeler Transform ◽  
Ngs Data

Abstract Background The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxonomic classification of metagenomic reads, i.e., identifying the microorganisms that are present in a sample collected directly from the environment. The analysis of environmental samples (metagenomes) are particularly important to figure out the microbial composition of different ecosystems and it is used in a wide variety of fields: for instance, metagenomic studies in agriculture can help understanding the interactions between plants and microbes, or in ecology, they can provide valuable insights into the functions of environmental communities. Results In this paper, we describe a new lightweight alignment-free and assembly-free framework for metagenomic classification that compares each unknown sequence in the sample to a collection of known genomes. We take advantage of the combinatorial properties of an extension of the Burrows-Wheeler transform, and we sequentially scan the required data structures, so that we can analyze unknown sequences of large collections using little internal memory. The tool LiME (Lightweight Metagenomics via eBWT) is available at https://github.com/veronicaguerrini/LiME. Conclusions In order to assess the reliability of our approach, we run several experiments on NGS data from two simulated metagenomes among those provided in benchmarking analysis and on a real metagenome from the Human Microbiome Project. The experiment results on the simulated data show that LiME is competitive with the widely used taxonomic classifiers. It achieves high levels of precision and specificity – e.g. 99.9% of the positive control reads are correctly assigned and the percentage of classified reads of the negative control is less than 0.01% – while keeping a high sensitivity. On the real metagenome, we show that LiME is able to deliver classification results comparable to that of MagicBlast. Overall, the experiments confirm the effectiveness of our method and its high accuracy even in negative control samples.

scholarly journals Computational Modeling of the Human Microbiome

2020 ◽  
Vol 8 (2) ◽  
pp. 197
Author(s):  
Shomeek Chowdhury ◽  
Stephen S. Fong
Keyword(s):  
Computational Modeling ◽  
Human Health ◽  
Large Scale ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Microbial Composition ◽  
Site Specific ◽  
Microbiome Research ◽  
High Level ◽  
The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

Label-Free and Immobilization-Free Immunoassay

2007 ◽  
Author(s):  
Island Pinnick ◽  
Kieseok Oh ◽  
Chen-Ling Chang ◽  
Kyong-Hoon Lee ◽  
Jae-Hyun Chung
Keyword(s):  
Analytical Model ◽  
High Sensitivity ◽  
Positive Control ◽  
Negative Control ◽  
Measured Signal ◽  
Label Free ◽  
Particle Counter ◽  
Fluid Resistance

This paper presents an immunoassay capable of detecting an antigen without labeling or immobilization. By measuring a change in fluid resistance, the immunoassay successfully differentiates a positive control from a negative control. The same device can also act as a particle counter due to its high sensitivity. It is capable of detecting differences in concentrations as low as 104 particles per milliliter. An analytical model is developed to analyze the measured signal.

scholarly journals ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 103 ◽  
Author(s):  
Subina Mehta ◽  
Marie Crane ◽  
Emma Leith ◽  
Bérénice Batut ◽  
Saskia Hiltemann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Human Health ◽  
Genetic Material ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Taxonomic Composition ◽  
Sequencing Technologies ◽  
The Galaxy ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

scholarly journals Squeegee: de-novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes

2021 ◽  
Author(s):  
Yunxi Liu ◽  
R. A. Leo Elworth ◽  
Michael D. Jochum ◽  
Kjersti M. Aagaard ◽  
Todd J. Treangen
Keyword(s):  
Computational Analysis ◽  
De Novo ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Negative Control ◽  
Control Data ◽  
Detection Tool ◽  
Health And Disease ◽  
Microbial Contaminants ◽  
Negative Controls

Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic bread crumbs across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, a de novo contamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision. Squeegee is open-source and available at: https://gitlab.com/treangenlab/squeegee

scholarly journals The Anticaries Effect of a Food Extract (Shiitake) in a Short-Term Clinical Study

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Peter Lingström ◽  
Egija Zaura ◽  
Haidar Hassan ◽  
Mark J. Buijs ◽  
Pamie Hedelin ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Dental Plaque ◽  
Weight Fraction ◽  
Edible Mushroom ◽  
Positive Control ◽  
Negative Control ◽  
Controlled Clinical Trial ◽  
Low Molecular Weight ◽  
Microbial Composition ◽  
Double Blind

The main objective was to investigate whether low-molecular-weight fraction of edible mushroom shiitake extract (Lentinus edodes) possesses caries-preventive properties. The study was designed as a double-blind, three-leg, cross-over, randomized, controlled clinical trial carried out on two series of volunteers at the University of Gothenburg, and the Academic Centre for Dentistry Amsterdam. Volunteers rinsed twice daily with a solution containing low-molecular-weight fraction of edible mushroom, placebo (negative control without active ingredients), or Meridol (positive control, AmF-SnF2) for two weeks, with a two-week washout period between each rinsing period. Changes in the acidogenicity of dental plaque before and after a sucrose challenge, shifts in microbial composition, and plaque scores were determined. Frequent rinses with shiitake reduced the metabolic activity of dental plaque. No reduction of plaque scores and no inhibition of the production of organic acids in plaque was found. Minor differences in microbial composition between test sessions were found. To conclude, the results indicate that shiitake extract has anticariogenic potential, but not to the same extent as the positive control.

scholarly journals Modeling of Urinary Microbiota Associated With Cystitis

2021 ◽  
Vol 11 ◽  
Author(s):  
Marina Ceprnja ◽  
Damir Oros ◽  
Ena Melvan ◽  
Ema Svetlicic ◽  
Jasenka Skrlin ◽  
...  
Keyword(s):  
Urinary Tract ◽  
16S Rdna ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Protective Role ◽  
Genetic Profile ◽  
Microbial Composition ◽  
Rdna Sequencing ◽  
Tract Infections

A decade ago, when the Human Microbiome Project was starting, urinary tract (UT) was not included because the bladder and urine were considered to be sterile. Today, we are presented with evidence that healthy UT possesses native microbiota and any major event disrupting its “equilibrium” can impact the host also. This dysbiosis often leads to cystitis symptoms, which is the most frequent lower UT complaint, especially among women. Cystitis is one of the most common causes of antimicrobial drugs prescriptions in primary and secondary care and an important contributor to the problem of antimicrobial resistance. Despite this fact, we still have trouble distinguishing whether the primary cause of majority of cystitis cases is a single pathogen overgrowth, or a systemic disorder affecting entire UT microbiota. There are relatively few studies monitoring changes and dynamics of UT microbiota in cystitis patients, making this field of research still an unknown. In this study variations to the UT microbiota of cystitis patients were identified and microbial dynamics has been modeled. The microbial genetic profile of urine samples from 28 patients was analyzed by 16S rDNA Illumina sequencing and bioinformatics analysis. One patient with bacterial cystitis symptoms was prescribed therapy based on national guideline recommendations on antibacterial treatment of urinary tract infections (UTI) and UT microbiota change was monitored by 16S rDNA sequencing on 24 h basis during the entire therapy duration. The results of sequencing implied that a particular class of bacteria is associated with majority of cystitis cases in this study. The contributing role of this class of bacteria – Gammaproteobacteria, was further predicted by generalized Lotka-Volterra modeling (gLVM). Longitudinal microbiota insight obtained from a single patient under prescribed antimicrobial therapy revealed rapid and extensive changes in microbial composition and emphasized the need for current guidelines revision in regards to therapy duration. Models based on gLVM indicated protective role of two taxonomic classes of bacteria, Actinobacteria and Bacteroidia class, which appear to actively suppress pathogen overgrowth.

Aktivitas Antifungi Air Perasan Bawang Merah (Allium ascalonicum L.) Terhadap Candida albicans Secara In Vitro

2017 ◽  
Vol 9 (2) ◽  
pp. 71
Author(s):  
Nurhasanah Nurhasanah ◽  
Fauzia Andrini ◽  
Yulis Hamidy
Keyword(s):  
Candida Albicans ◽  
Antifungal Activity ◽  
Allium Sativum ◽  
Fungicidal Activity ◽  
Positive Control ◽  
Negative Control ◽  
Randomized Design ◽  
Significant Difference ◽  
Completely Randomized Design

Shallot (Allium ascalonicum L.) has been known as traditional medicine. Shallot which has same genus with garlic(Allium sativum L.) contains allicin that is also found in garlic and has been suspected has fungicidal activity toCandida albicans. It is supported by several researches. Therefore, shallot is suspected has antifungal activity too.The aim of this research was to know antifungal activity of shallot’s water extortion againsts Candida albicans invitro. This was a laboratory experimental research which used completely randomized design, with diffusion method.Shallot’s water extortion was devided into three concentrations, there were 50%, 100% and 200%. Ketoconazole 2%was positive control and aquadest was negative control. The result of this research based on analysis of varians(Anova), there was significant difference between several treatments and was confirmed with Duncan New MultipleRange Test (DNMRT) p<0,05, there was significant difference between 100% shallot’s water extortion with othertreatments, but there was no significant difference between 50% shallot’s water extortion with 200% shallot’s. Theconclusion was shallot’s water extortion had antifungal activity againsts Candida albicans with the best concentration100%, but it was lower than ketoconazole 2%.

The Comparison of Ostecyte in the Pressure area and Tension area on Tooth Movement Because of Hyperbaric Oxygen Therapy

DENTA ◽  
2018 ◽  
Vol 12 (1) ◽  
pp. 34
Author(s):  
Arya Barahmanta ◽  
Muhammad Faizal Winaris ◽  
Pambudi Raharjo
Keyword(s):  
Hyperbaric Oxygen ◽  
Oxygen Therapy ◽  
Tooth Movement ◽  
Bone Remodelling ◽  
Orthodontic Tooth Movement ◽  
Negative Control Group ◽  
Positive Control ◽  
Negative Control ◽  
Control Group ◽  
Pressure Area

<p><strong><em>Background:</em></strong><em> Orthodontic tooth movement is a </em><em>interaction prosess</em><em> of resorption and deposition of bone remodeling. Orthodontic tooth movement by mechanical strength causes changes in alveolar bone. Osteocyte is an essential cell to respond bone remodelling. Hyperbaric Oxygen Therapy affects production of osteocyte because it can release Reactive Oxygen Species (ROS) and Nitrid Oxide (NO).  <strong>Purpose: </strong>To determine the difference number  of osteocyte in pressure and tension area during tooth movement by adjuvant of Hyperbaric Oxygen 2,4 ATA during 7 days starting on day 8 to day 14. <strong>Materials and Methods</strong>: This research used Completery Randomized Control Group Post Test Only Design. 36 cavia cobaya (male)  were divided into 3 groups randomly : the negative control groups, positive control group, and treatment group. Preparat staining used Hematoxylin Eosin (HE) and calculated on microscop 1000x with 20 field of view. Data analyses used one way ANOVA and LSD test then compared each area by using paired T test. <strong>Result:</strong> The data showed that the treatment group (P=10,67) tension area has the highest number of osteocyte than  negative control group (K-=3,67), positive control (K+=7,42). In the pressure area showed that negative control group (K-=5,00) has the highest  than positive control group (K+=3,83) and treatment (P=3,25). <strong>Conclusion: </strong>Therapy HBO 2,4 ATA 7 days starting on day 8 to day 14 is could increase osteocyte in the tissue to stimulate process of bone remodelling.</em></p><pre><strong> </strong></pre><p><strong><em>Keywords:</em></strong><em> Hyperbaric Oxygen, Tooth movement, Bone remodeling, </em><em>Osteocyte</em><em></em></p><p><em> </em></p><p><strong><em>Correspondence:</em></strong><em> </em><em>Arya Brahmanta</em><em>, Department of Orthodonty, Faculty of Dentistry, Hang Tuah University, Arif Rahman Hakim 150, Surabaya, Phone 031-5945864, Email:</em><em> </em><a href="mailto:[email protected]"><em>arya.brahmanta</em><em>@</em><em>hangtuah.ac.id</em></a></p>

UJI AKTIVITAS HEPATOPROTEKTOR KOMBINASI EKSTRAK ETANOL DAUN PANDAN WANGI (Pandanus amaryllifolius roxb) DAN KAYU MANIS (Cinnamomum burmanii) TERHADAP KADAR MDA YANG DIINDUKSI PARASETAMOL

2020 ◽  
pp. 68-73
Author(s):  
Yuni Asri Mulatsih Agami ◽  
Eka Wisnu Kusuma
Keyword(s):  
Oxidative Stress ◽  
Ethanol Extract ◽  
Optimal Dose ◽  
Experimental Methods ◽  
Positive Control ◽  
Negative Control ◽  
Male Rats ◽  
Negative Group ◽  
Ic50 Value ◽  
Dose Combination

Kasus penyakit hati semakin meningkat seiring penggunaan senyawa hepatotoksin salah satunya karena penggunaan parasetamol dengan dosis berlebih. Hal tersebut dapat meningkatkan produksi radikal bebas sehingga memicu terjadinya stress oksidatif yang dapat menimbulkan kerusakan jaringan yang ditandai dengan peningkatan kadar Malondialdehyde (MDA). Stress oksidatif dapat diatasi dengan antioksidan dari berbagai tanaman. Kulit kayu manis memiliki aktivitas antioksidan dengan nilai IC50 53ppm dan daun pandan wangi 39,7%  Penelitian ini bertujuan untuk mengetahui aktivitas kombinasi ekstrak etanol daun pandan wangi dan kayu manis dalam menurunkan kadar MDA. tikus yang diinduksi parasetamol. Penelitian menggunakan metode eksperimental, dilakukan selama 9 hari dengan 30 ekor tikus jantan dibagi menjadi 6 Kelompok, yaitu: Normal diberi aquadest, Kontrol Positif diberi silimarin 100 mg/kgBB, Kontrol Negatif diberi CMC-Na 0,05%, serta 3 kelompok lainnya diberi kombinasi ekstrak daun pandan wangi:kayu manis berturut-turut dosis I (25:75), dosis II (50:50), dosis III (75:25). Semua kelompok diinduksi parasetamol 2,5 g/kgBB pada hari ke-7  setelah 30 menit perlakuan, kecuali kelompok normal. Pada hari ke 9 dilakukan pengukuran kadar MDA dengan metode TBARs menggunakan spektrofotometri. Pemberian kombinasi ekstrak etanol daun pandan wangi dan kayu manis dapat menurunkan kadar MDA dengan kombinasi dosis yang paling optimal adalah 75:25 berdasarkan statistik dengan nilai signifikan 0,000<0,05 dibandingkan dengan kelompok negatif.    Cases of liver disease have increased with the use of hepatotoxin compounds, one of which is due to the use of paracetamol with excessive doses. This can increase the production of free radicals so that it triggers oxidative stress which can cause tissue damage which is characterized by increased levels of Malondialdehyde (MDA). Oxidative stress can be overcome with antioxidants from various plants. Cinnamomum burmanii has antioxidant activity with IC50 value of 53ppm and Pandanus amarrylifolius 39.7%. This study aims to determine the combined activity of ethanol extract of Pandanus amarrylifolius and Cinnamomum burmanii  in reducing MDA levels. Paracetamol-induced rats. Research using experimental methods, conducted for 9 days with 30 male rats divided into 6 groups, namely: Normal given aquadest, Positive Control were given silimarin 100 mg / kgBB, Negative Control was given CMC-Na 0.05%, and 3 other groups were given a combination of Pandanus amarrylifolius extract: Cinnamomum burmanii dose I (25:75), dose II (50:50), dose III (75:25). All groups induced paracetamol 2.5 g / kgBB on the 7th day after 30 minutes of treatment, except the normal group. On the 9th day MDA levels were measured using the TBARs method using spectrophotometry. Giving a combination of Pandanus amarrylifolius and Cinnamomum burmanii ethanol extract can reduce MDA levels with the most optimal dose combination is 75:25 based on statistics with a significant value of 0,000<0.05 compared with the negative group.

UJI IMUNOMODULATOR DARI EKSTRAK ETANOL DAUN WARU (HIBISCUS TILIACEUS) DENGAN METODE HIPERSENSITIVITAS TIPE LAMBAT

2019 ◽  
Vol 1 (2) ◽  
pp. 11-16
Author(s):  
Yanna Rotua Sihombing ◽  
Debi Dinha Sitepu
Keyword(s):  
Treatment Group ◽  
Leaf Extract ◽  
Positive Control ◽  
Negative Control ◽  
Delayed Type Hypersensitivity ◽  
Hypersensitivity Response ◽  
Delayed Type Hypersensitivity Response

Immunomodulator is a compound that can increaase the imuno system. One of the plants that have immunomodulator’s activity is Waru Leaf (Hibiscus tiliaceus). the purpose of this research was to test the effect of immunomodulator by extract of Waru Leaf ethanol on rat male. The activity of immunomodulator was determined by using digital pletysmometer by measuring the differences between the last leg swelling’s volume and the first leg swelling’s volume. The treatment group were divided into 5 groups. Each group consistof 5 rats CMC-Na 0,5% (negative control), Stimuno®  32,5 mg/kgBW (positive control), dose of EEDW 50, 100 and 200 mg/kgBW, and bacteria E.coli as antigen. The results slowed that distribution of EEDW dose 200 mg/kgBW can give the effect of immunostimulant by swelling enthancement compared by CMC-Na 0,5 %. EEDW 200 mg/kgBW that have activity comparable with Stimuno®  32,5 mg/kgBW. Thus, it is concluded that of Waru Leaf extract has immunomodulator effects on delayed-type hypersensitivity response of rat male.

Sign in / Sign up

Export Citation Format

Share Document