Proteomics in Forensic Analysis: Applications for Human Samples

Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.

Download Full-text

Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process

DNA Research ◽

10.1093/dnares/dsaa014 ◽

2020 ◽

Vol 27 (3) ◽

Cited By ~ 1

Author(s):

Rei Kajitani ◽

Dai Yoshimura ◽

Yoshitoshi Ogura ◽

Yasuhiro Gotoh ◽

Tetsuya Hayashi ◽

...

Keyword(s):

High Resolution ◽

Large Scale ◽

De Novo ◽

Bacterial Genomes ◽

Long Reads ◽

Wide Range ◽

Long Read ◽

Phylogenomic Analyses ◽

Error Removal ◽

Iterative Error

Abstract De novo assembly of short DNA reads remains an essential technology, especially for large-scale projects and high-resolution variant analyses in epidemiology. However, the existing tools often lack sufficient accuracy required to compare closely related strains. To facilitate such studies on bacterial genomes, we developed Platanus_B, a de novo assembler that employs iterations of multiple error-removal algorithms. The benchmarks demonstrated the superior accuracy and high contiguity of Platanus_B, in addition to its ability to enhance the hybrid assembly of both short and nanopore long reads. Although the hybrid strategies for short and long reads were effective in achieving near full-length genomes, we found that short-read-only assemblies generated with Platanus_B were sufficient to obtain ≥90% of exact coding sequences in most cases. In addition, while nanopore long-read-only assemblies lacked fine-scale accuracies, inclusion of short reads was effective in improving the accuracies. Platanus_B can, therefore, be used for comprehensive genomic surveillances of bacterial pathogens and high-resolution phylogenomic analyses of a wide range of bacteria.

Download Full-text

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.689797 ◽

2021 ◽

Vol 9 ◽

Author(s):

Li-Fu Song ◽

Zheng-Hua Deng ◽

Zi-Yi Gong ◽

Lu-Lu Li ◽

Bing-Zhi Li

Keyword(s):

Data Storage ◽

Large Scale ◽

De Novo ◽

Special Focus ◽

Oligonucleotide Synthesis ◽

Phosphoramidite Chemistry ◽

Challenges And Opportunities ◽

The Status ◽

Remarkable Progress ◽

Enzymatic Methods

Over the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications. Among them, de novo genome synthesis and DNA data storage are striking. However, to make these two applications more practical, the synthesis length, speed, cost, and throughput require vast improvements, which is a challenge to be met by the phosphoramidite chemistry. Harnessing the power of enzymes, the recently emerged enzymatic methods provide a competitive route to overcome this challenge. In this review, we first summarize the status of large-scale oligonucleotide synthesis technologies including the basic methodology and large-scale synthesis approaches, with special focus on the emerging enzymatic methods. Afterward, we discuss the opportunities and challenges of large-scale oligonucleotide synthesis on de novo genome synthesis and DNA data storage respectively.

Download Full-text

Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis

10.1101/077511 ◽

2016 ◽

Cited By ~ 2

Author(s):

Alan Medlar ◽

Laura Laakso ◽

Andreia Miraldo ◽

Ari Löytynoja

Keyword(s):

Comparative Analysis ◽

Large Scale ◽

De Novo ◽

Sequence Data ◽

Model Organism ◽

Model Organisms ◽

Rna Seq ◽

Reference Species ◽

Wide Range ◽

The Impact

AbstractHigh-throughput RNA-seq data has become ubiquitous in the study of non-model organisms, but its use in comparative analysis remains a challenge. Without a reference genome for mapping, sequence data has to be de novo assembled, producing large numbers of short, highly redundant contigs. Preparing these assemblies for comparative analyses requires the removal of redundant isoforms, assignment of orthologs and converting fragmented transcripts into gene alignments. In this article we present Glutton, a novel tool to process transcriptome assemblies for downstream evolutionary analyses. Glutton takes as input a set of fragmented, possibly erroneous transcriptome assemblies. Utilising phylogeny-aware alignment and reference data from a closely related species, it reconstructs one transcript per gene, finds orthologous sequences and produces accurate multiple alignments of coding sequences. We present a comprehensive analysis of Glutton’s performance across a wide range of divergence times between study and reference species. We demonstrate the impact choice of assembler has on both the number of alignments and the correctness of ortholog assignment and show substantial improvements over heuristic methods, without sacrificing correctness. Finally, using inference of Darwinian selection as an example of downstream analysis, we show that Glutton-processed RNA-seq data give results comparable to those obtained from full length gene sequences even with distantly related reference species. Glutton is available from http://wasabiapp.org/software/glutton/ and is licensed under the GPLv3.

Download Full-text

PDV: an integrative proteomics data viewer

Bioinformatics ◽

10.1093/bioinformatics/bty770 ◽

2018 ◽

Vol 35 (7) ◽

pp. 1249-1251 ◽

Cited By ~ 24

Author(s):

Kai Li ◽

Marc Vaudel ◽

Bing Zhang ◽

Yan Ren ◽

Bo Wen

Keyword(s):

Large Scale ◽

De Novo ◽

Source Code ◽

Peptide Identification ◽

Supplementary Information ◽

Visualization Tool ◽

Command Line ◽

Proteomics Data ◽

Desktop Computers ◽

Wide Range

Abstract Summary Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation of peptide identification results. Herein, we present PDV, an integrative proteomics data viewer that can be used to visualize a wide range of proteomics data, including database search results, de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from public proteomics repositories. PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes. Availability and implementation PDV software and the user manual are freely available at http://pdv.zhang-lab.org. The source code is available at https://github.com/wenbostar/PDV and is released under the GPL-3 license. Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

PLoS Pathogens ◽

10.1371/journal.ppat.1010036 ◽

2021 ◽

Vol 17 (11) ◽

pp. e1010036

Author(s):

Paulo Vieira ◽

Roxana Y. Myers ◽

Clement Pellegrin ◽

Catherine Wram ◽

Cedar Hesse ◽

...

Keyword(s):

Gene Transfer ◽

Large Scale ◽

De Novo ◽

Economic Damage ◽

Radopholus Similis ◽

Effector Genes ◽

Wide Range ◽

Burrowing Nematode ◽

Generation Sequencing

The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.

Download Full-text

Identification of myelodysplastic syndrome–specific genes by DNA microarray analysis with purified hematopoietic stem cell fraction

Blood ◽

10.1182/blood.v98.2.422 ◽

2001 ◽

Vol 98 (2) ◽

pp. 422-427 ◽

Cited By ~ 113

Author(s):

Akira Miyazato ◽

Shuichi Ueno ◽

Ken Ohmine ◽

Masuzu Ueda ◽

Koji Yoshida ◽

...

Keyword(s):

Stem Cell ◽

Myelodysplastic Syndrome ◽

Hematopoietic Stem Cell ◽

Microarray Analysis ◽

Myeloid Leukemia ◽

Large Scale ◽

De Novo ◽

Hematopoietic Stem ◽

Wide Range ◽

Specific Manner

Myelodysplastic syndrome (MDS) is a slowly progressing hematologic malignancy associated with a poor outcome. Despite the relatively high incidence of MDS in the elderly, differentiation of MDS from de novo acute myeloid leukemia (AML) still remains problematic. Identification of genes expressed in an MDS-specific manner would allow the molecular diagnosis of MDS. Toward this goal, AC133 surface marker–positive hematopoietic stem cell (HSC)-like fractions have been collected from a variety of leukemias in a large-scale and long-term genomics project, referred to as “Blast Bank,” and transcriptome of these purified blasts from the patients with MDS were then compared with those from AML through the use of oligonucleotide microarrays. A number of genes were shown to be expressed in a disease-specific manner either to MDS or AML. Among the former found was the gene encoding the protein Delta-like (Dlk) that is distantly related to the Delta-Notch family of signaling proteins. Because overexpression of Dlk may play a role in the pathogenesis of MDS, the disease specificity of Dlk expression was tested by a quantitative “real-time” polymerase chain reaction analysis. Examination of the Blast Bank samples from 22 patients with MDS, 31 with AML, and 8 with chronic myeloid leukemia confirmed the highly selective expression of the Dlk gene in the individuals with MDS. Dlk could be the first candidate molecule to differentiate MDS from AML. The proposal is made that microarray analysis with the Blast Bank samples is an efficient approach to extract transcriptome data of clinical relevance for a wide range of hematologic disorders.

Download Full-text

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1616736114 ◽

2017 ◽

Vol 114 (20) ◽

pp. 5213-5218 ◽

Cited By ~ 73

Author(s):

Arun Durvasula ◽

Andrea Fulgione ◽

Rafal M. Gutaker ◽

Selen Irez Alacakaptan ◽

Pádraic J. Flood ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Large Scale ◽

Molecular Model ◽

Genomic Analysis ◽

Geographic Region ◽

Early History ◽

Sub Saharan Africa ◽

Last Interglacial ◽

Wide Range ◽

History Of

Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa. Moreover, we show that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Our results also reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral A. thaliana population began to split by 120–90 kya, during the last interglacial and Abbassia pluvial, and Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for diverse species, including humans, implying a key role for climatic events during interglacial and pluvial periods in shaping the histories and current distributions of a wide range of species.

Download Full-text

Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity

Journal of Virology ◽

10.1128/jvi.00738-06 ◽

2006 ◽

Vol 80 (19) ◽

pp. 9687-9696 ◽

Cited By ~ 245

Author(s):

Steffen Mueller ◽

Dimitris Papamichail ◽

J. Robert Coleman ◽

Steven Skiena ◽

Eckard Wimmer

Keyword(s):

Large Scale ◽

De Novo ◽

Synonymous Codon ◽

Direct Analysis ◽

Synonymous Codon Usage ◽

Wild Type ◽

Coding Region ◽

Virus Particles ◽

Viral Virulence ◽

Wide Range

ABSTRACT Exploring the utility of de novo gene synthesis with the aim of designing stably attenuated polioviruses (PV), we followed two strategies to construct PV variants containing synthetic replacements of the capsid coding sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon position changes of the existing wild-type (wt) poliovirus codons (PV-SD). Despite 934 nucleotide changes in the capsid coding region, PV-SD RNA produced virus with wild-type characteristics. In contrast, no viable virus was recovered from PV-AB RNA carrying 680 silent mutations, due to a reduction of genome translation and replication below a critical level. After subcloning of smaller portions of the AB capsid coding sequence into the wt background, several viable viruses were obtained with a wide range of phenotypes corresponding to their efficiency of directing genome translation. Surprisingly, when inoculated with equal infectious doses (PFU), even the most replication-deficient viruses appeared to be as pathogenic in PV-sensitive CD155tg (transgenic) mice as the PV(M) wild type. However, infection with equal amounts of virus particles revealed a neuroattenuated phenotype over 100-fold. Direct analysis indicated a striking reduction of the specific infectivity of PV-AB-type virus particles. Due to the distribution effect of many silent mutations over large genome segments, codon-deoptimized viruses should have genetically stable phenotypes, and they may prove suitable as attenuated substrates for the production of poliovirus vaccines.

Download Full-text

GAAP: A Genome Assembly + Annotation Pipeline

BioMed Research International ◽

10.1155/2019/4767354 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 2

Author(s):

Jinhwa Kong ◽

Sun Huh ◽

Jung-Im Won ◽

Jeehee Yoon ◽

Baeksop Kim ◽

...

Keyword(s):

Genome Analysis ◽

De Novo ◽

Transcriptome Assembly ◽

Genomic Analysis ◽

Whole Genome ◽

High Throughput Analysis ◽

Whole Genome Analysis ◽

A Genome ◽

Base Sequences ◽

Wide Range

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

Download Full-text

Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits

10.21203/rs.3.rs-57915/v1 ◽

2020 ◽

Author(s):

Xinxin Yi ◽

Jing Liu ◽

Shengcai Chen ◽

Hao Wu ◽

Min Liu ◽

...

Keyword(s):

Reference Genome ◽

De Novo ◽

Agronomic Traits ◽

Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Wide Range ◽

Breeding Research ◽

High Quality Genome

Abstract BackgroundCultivated soybean (Glycine max) is an important source for protein and oil. Each soybean strain has its own genetic diversity, and the availability of more soybean genomes may enhance comparative genomic analysis of soybean.ResultsIn this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with high contiguity, completeness, and accuracy. We annotated 59,629 gene models and reconstructed 235,109 high-quality full-length transcripts. We have molecularly characterized the genotypes of some important agronomic traits of JD17 by taking advantage of these newly established genomic resources.ConclusionsWe reported a high-quality genome and annotations of a wide range of cultivars, and used them to analyze the genotypes of genes related to important agronomic traits of soybean in JD17. We have demonstrated that high-quality genome assembly can serve as a valuable reference for soybean genomics and breeding research community.

Download Full-text