scholarly journals DNA metabarcoding of forensic mycological samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Saverio Giampaoli ◽  
Elisabetta De Vittori ◽  
Filippo Barni ◽  
Anna Anselmo ◽  
Teresa Rinaldi ◽  
...  
Keyword(s):  
Deposition Time ◽  
Forensic Sciences ◽  
Molecular Tools ◽  
Fungal Population ◽  
Post Mortem Interval ◽  
Dna Metabarcoding ◽  
Forensic Samples ◽  
Identification Of Fungi ◽  
User Friendly

Abstract Background DNA metabarcoding and massive parallel sequencing are valuable molecular tools for the characterization of environmental samples. In forensic sciences, the analysis of the sample’s fungal population can be highly informative for the estimation of post-mortem interval, the ascertainment of deposition time, the identification of the cause of death, or the location of buried corpses. Unfortunately, metabarcoding data analysis often requires strong bioinformatic capabilities that are not widely available in forensic laboratories. Results The present paper describes the adoption of a user-friendly cloud-based application for the identification of fungi in typical forensic samples. The samples have also been analyzed through the QIIME pipeline, obtaining a relevant data concordance on top genus classification results (88%). Conclusions The availability of a user-friendly application that can be run without command line activities will increase the popularity of metabarcoding fungal analysis in forensic samples.

scholarly journals Application of Innovative TGA/Chemometric Approach for Forensic Purposes: The Estimation of the Time since Death in Contaminated Specimens

Diagnostics ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 121
Author(s):  
Roberta Risoluti ◽  
Giuseppina Gullifa ◽  
Vittorio Fineschi ◽  
Paola Frati ◽  
Stefano Materazzi
Keyword(s):  
Multidisciplinary Approach ◽  
Vitreous Humor ◽  
Classification Model ◽  
Forensic Sciences ◽  
Time Since Death ◽  
Time Of Death ◽  
Novel Approach ◽  
Chemometric Approach ◽  
Postmortem Examinations

Chronothanatology has always been a challenge in forensic sciences. Therefore, the importance of a multidisciplinary approach for the characterization of matrices (organs, tissues, or fluids) that respond linearly to the postmortem interval (PMI) is emerging increasingly. The vitreous humor is particularly suitable for studies aimed at assessing time-related modifications because it is topographically isolated and well-protected. In this work, a novel approach based on thermogravimetry and chemometrics was used to estimate the time since death in the vitreous humor and to collect a databank of samples derived from postmortem examinations after medico–legal evaluation. In this study, contaminated and uncontaminated specimens with tissue fragments were included in order to develop a classification model to predict time of death based on partial least squares discriminant analysis (PLS-DA) that was as robust as possible. Results demonstrate the possibility to correctly predict the PMI even in contaminated samples, with an accuracy not lower than 70%. In addition, the correlation coefficient of the measured versus predicted outcomes was found to be 0.9978, confirming the ability of the model to extend its feasibility even to such situations involving contaminated vitreous humor.

scholarly journals Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1338
Author(s):  
Morgan E. Meissner ◽  
Emily J. Julik ◽  
Jonathan P. Badalamenti ◽  
William G. Arndt ◽  
Lauren J. Mills ◽  
...  
Keyword(s):  
Error Rates ◽  
Maximum Depth ◽  
Sequencing Data ◽  
Background Error ◽  
High Background ◽  
Immunodeficiency Virus ◽  
User Friendly ◽  
Viral Mutagenesis ◽  
Hiv 1

Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

scholarly journals PIMBA: a PIpeline for MetaBarcoding Analysis

2021 ◽  
Author(s):  
Renato R. M. Oliveira ◽  
Raissa L S Silva ◽  
Gisele L. Nunes ◽  
Guilherme Oliveira
Keyword(s):  
Environmental Samples ◽  
Next Generation Sequencing Data ◽  
Ecological Studies ◽  
Sequencing Data ◽  
Monitoring Method ◽  
Computational Tools ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
User Friendly ◽  
Generation Sequencing

DNA metabarcoding is an emerging monitoring method capable of assessing biodiversity from environmental samples (eDNA). Advances in computational tools have been required due to the increase of Next-Generation Sequencing data. Tools for DNA metabarcoding analysis, such as MOTHUR, QIIME, Obitools, and mBRAVE have been widely used in ecological studies. However, some difficulties are encountered when there is a need to use custom databases. Here we present PIMBA, a PIpeline for MetaBarcoding Analysis, which allows the use of customized databases, as well as other reference databases used by the softwares mentioned here. PIMBA is an open-source and user-friendly pipeline that consolidates all analyses in just three command lines.

scholarly journals Prevalence and Molecular Epidemiological Data onDirofilaria immitisin Dogs from Northeastern States of India

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Sonjoy Kumar Borthakur ◽  
Dilip Kumar Deka ◽  
Saidul Islam ◽  
Dilip Kumar Sarma ◽  
Prabhat Chandra Sarmah
Keyword(s):  
Epidemiological Data ◽  
Elisa Test ◽  
Molecular Techniques ◽  
Diagnostic Methods ◽  
Molecular Tools ◽  
Stray Dogs ◽  
Concentration Technique ◽  
Working Dogs ◽  
Polymerase Chain

The aim of the present study was to determine the prevalence ofDirofilaria immitisin stray, pet, and working dogs (n=413, 266, and 103, resp.) from Guwahati (Assam) and Aizawl (Mizoram), areas located in two Northeastern States of India. Diagnostic methods applied were microscopy (wet film and Knott’s concentration technique), immunological test (Ag ELISA by SNAP 4Dx ELISA kit), and molecular tools (polymerase chain reaction and sequencing), which evidenced 11.38, 18.03, and 13.93% of positive animals, respectively. No significant differences were observed by area (18.23% versus 17.68%) nor by sex (18.1% versus 17.9%), whereas stray dogs proved more infected than other groups (P<0.05). ELISA test evidenced an overall 22.69% of occult infections, mainly in working dogs (60%), and molecular techniques detectedDirofilaria (Nochtiella) repensin 4 stray dogs from Guwahati. Characterization ofD. immitisisolates for ITS-2 region showed close identity with South Asian isolates.

scholarly journals A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Simon Roux
Keyword(s):  
Cell Metabolism ◽  
Ecosystem Functions ◽  
Biological Knowledge ◽  
Viral Sequence ◽  
Molecular Tools ◽  
Microbial Cells ◽  
Health And Disease ◽  
Virus Genomes ◽  
Do So

ABSTRACTMicrobes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection. While the majority of viruses and their associated impacts remain poorly characterized, a number of mechanisms by which viruses alter microbial cells and ecosystems have already been revealed. Here I outline how a comprehensive host-resolved mapping of viral sequence space will enable a thorough characterization of virus-encoded mechanisms for microbial manipulation. With soon-to-be millions of virus genomes obtained from metagenomes, one of the major challenges resides in the development of methods for high-throughput and high-resolution virus-host pairing, before multi-omics approaches can be leveraged to fully decipher virus-host dynamics in nature. Beyond novel fundamental biological knowledge, these studies will likely provide new molecular tools enabling a precise engineering of microbial cells and communities.

scholarly journals Characterization of Cobalt Sulfide Thin Films Synthesized from Acidic Chemical Baths

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Tizazu Abza ◽  
Dereje Gelanu Dadi ◽  
Fekadu Gashaw Hone ◽  
Tesfaye Chebelew Meharu ◽  
Gebremeskel Tekle ◽  
...  
Keyword(s):  
Thin Films ◽  
Crystallite Size ◽  
Deposition Time ◽  
Average Crystallite Size ◽  
Cobalt Sulfide ◽  
Face Centered Cubic ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
Face Centered

Cobalt sulfide thin films were synthesized from acidic chemical baths by varying the deposition time. The powder X-ray diffraction studies indicated that there are hexagonal CoS, face-centered cubic Co3S4, and cubic Co9S8 phases of cobalt sulfide. The crystallite size of the hexagonal CoS phase decreased from 52.8 nm to 22.5 nm and that of the cubic Co9S8 phase increased from 11 nm to 60 nm as the deposition time increased from 2 hrs to 3.5 hrs. The scanning electron microscopic images revealed crack and pinhole free thin films with uniform and smooth background and few large polygonal grains on the surface. The band gap of the cobalt sulfide thin films decreased from 1.75 eV to 1.3 eV as the deposition time increased from 2 hrs to 3.5 hrs. The photoluminescence (PL) spectra of the films confirmed the emission of ultraviolet, violet, and blue lights. The intense PL emission of violet light at 384 nm had red shifted with increasing deposition time that could be resulted from the increase in the average crystallite size. The FTIR spectra of the films indicated the presence of OH, C-O-H, C-O, double sulfide, and Co-S groups. As the deposition time increased, the electrical resistivity of the cobalt sulfide thin films decreased due to the increase in both the crystallite size and the films’ thickness.

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