• Hidden Microbiome

    bacteria-811861_1920The Center for Disease Control reported that lower respiratory tract infections (LRTI), otherwise known as Pneumonia, were responsible for approximately 53,000 deaths in 2013. In 2010, 37,000 patients with Pneumonia died while admitted in the hospital. According to the World Health Organization, Pneumonia was responsible for 15% of all deaths of children under 5 years old. In a study recently published by the journal MicrobiomeResearchers from the University of Pennsylvania describe in this study that approximately 15% of patients hospitalized with lower respiratory tract infections experience respiratory failure and are forced to undergo mechanical ventilation. Additionally, 15% of patients who are forced to undergo mechanical ventilation not as a result of (LRTI) will in fact develop a lower respiratory tract infection.

    Kelly et al. sought out to gain greater insight into the microbiota of the respiratory tract of intubated patients by way of 16s rRNA gene sequencing. In the past, researchers and diagnosticians would have to rely on their ability to grow certain bacteria using a growth culture in order to identify the bacteria present during infection. Unfortunately, this technique is often times inadequate as many bacteria are unable to grow under standard laboratory conditions. However, scientific advancements such as PCR and Next-generation sequencing have made 16s rRNA gene sequencing a more reliable tool to complete taxonomic studies. Kelly et al. state “16s ribosomal RNA (rRNA) gene sequencing has allowed culture-independent characterization of the bacterial communities in health and disease, termed the microbiome.” In many cases, 16s rRNA gene sequencing was able to confirm the results of traditional culture-based data, but in addition, 16s rRNA gene sequencing was also able to identify “unexpected bacteria”, according to Kelly et al. in relation to LRTI that had previously been unknown as LRTI pathogens.

  • Your Microbiome: An Early Indicator of Type II Diabetes?

    infographic-diabetes

    The National Diabetes Statistics Report (2014) put out by the Center for Disease Control indicates that 29.1 million people in the United States have diabetes. The number of individuals that are considered prediabetic are even more staggering, 86 million people, or 1 out of 3 adults are considered to be prediabetic. In adults, approximately 95% of all patients diagnosed with diabetes are diagnosed with type 2 diabetes. Fortunately, with proper measures, such as weight loss, increased exercise, and a healthy diet, individuals with prediabetes can delay or even prevent the onset of type 2 diabetes. However, 9 out of 10 individuals considered to be prediabetic do not know that they are at risk.

    MRDNA Shotgun Sequencing

    2 Million Reads: Metagenome Sequencing

    A team of researchers from The Broad Institute partnered with researchers from Seoul National University in order to investigate whether or not the associated imbalance of microbes within the gut microbiota of individuals with type 2 diabetes is present prior to disease onset. Yassour et al. recently published their findings in Genome Medicine, where they were able to perform shotgun metagenomic sequencing on 36 stool samples collected from 20 monozygotic Korean twins. While most metagenomic microbiome studies examine a diseased population and compare the detected microbial diversity with that of a healthy population, Yassour et al, concluded that this study design is unable to determine the relationship between the microbial ecology of the gut and the disease state, be it causal or responsive. Yassour et al. report both positive and negative correlations in biomarkers associated with type 2 diabetes, “functional changes in the gut microbiome at higher sub-clinical values of BMI, FBS, and triglycerides resembled the signatures found in patients with established IBD or T2D, suggesting a shared response to oxidative stress in the gut, induced even at low levels of inflammation or immune activation.” The results from this study and others exploring the host microbiota indicate the presence of a relationship between the gut response and disease state of the host.

     

  • Microbiome of Breast Milk

    newborn-659685_1920Researchers from the University of Western Ontario sought out to determine how the various factors that take place during birth affect the microbiome of human milk e.g. delivery vaginally or caesarean section, gender of the infant, delivery at term or preterm. Urbaniak et al. collected milk from 39 Caucasian Canadian women for DNA isolation and 16s rRNA sequencing. The microbial data for each sample was generated using the Illumina MiSeq platform.

    There is a gaining interest in the correlation between the microbiome of infants and the onset of certain diseases and/or health issues such as asthma, types I and II diabetes, and obesity. It is well known that newborns receive a boost in their immune system from breast feeding, but how the microbiome is affected by various stages of gestation is still unknown.

    This study employed the use of barcoded primers to sequence the V6 hypervariable region and was able to determine that despite the differing physiological and hormonal factors between the 39 women there was no alteration to the bacterial composition found in the breast milk.

  • Whole-Transcriptome Sequencing (RNA-Seq)

    ARNm-Rasmol.gif (353×423)Whole transcriptome analysis is important to understand genome-wide differences in RNA expression which allows Scientists to understand how altered genetic variants changes in gene expression. RNA-seq method can help to sequence different types of RNAs such as total RNA, small RNA (miRNA, tRNA and rRNA). The RNA-seq can contribute to understand the complexity of diseases such as cancer, diabetes, and heart disease.  MR DNA provides low cost Whole-Transcriptome Sequencing service to Scientists around the world. Scientists at MR DNA routinely carry out the Whole-Transcriptome sequencing using Illumina (HiSeq or MiSeq), 454 and Ion Torrent platforms. For more information please visit www.mrdnalab.com.

     

     

     

     

     

    Next Generation Sequencing | MR DNA

    MR DNA can perform whole-genome or de novo sequencing, resequencing … in one flow cell lane, reducing the cost of this service for small genomic libraries. …transcriptome analysis using mRNA sequencing on the HiSeq platform.

    Price List | MR DNA

    TruSeq RNA/small RNA sample library prep, per sample … Illumina HiSeq 2000/2500sequencing (high-output mode) 7 lanes run with samples, 1 phiX lane

     

    Next Generation Sequencing Facility – MR DNA

    The DNA Sequencing Facility offers all-inclusive next generation sequencing, DNA extraction and SNP genotyping services on a … We work with our customers to prepare DNA, RNA, ChIP, GBS, metagenomic, exome, and other sequencing … Run Charges – HiSeq 2000/2500 High Throughput  …

    RNA-Seq (Quantification) | MR DNA

    Powered by our unique bioinformatics capabilities, MR DNA RNASeq services deliver …RNASeq based on Hiseq: high-throughput and a wide  …

     

    Sequencing – Genome Technology | MR DNA

    https://mrdnalab.com

    … instructions. Below you will find more information about our sequencing services: library preparation, sequencing, and analyses. … mRNASeq · ChIP-Seq …Sequencing. GTAC operates four Illumina HiSeq 2500 sequencing instruments.

     

     

     

     

    MR DNA: HiSeq 2500 & MiSeq – Next Generation Sequencing

    www.mrdnalab.com

     

    The MR DNA Facility houses an Illumina HiSeq 2500 and an … such as ChIP-Seq, transcript counts, SNP detection, and small RNA analysis, the … the mate-pair protocol and should contact the facility regarding this service.

     

     

     

  • Genome Sequencing Service

    Genome sequencing is described as the process of determining the order of the nucleotide bases within a certain length strand of DNA. You can sequence a short piece, the whole genome, or parts of the genome (exomes – parts of the genome that contain genes).

    The knowledgeable team at MR DNA Lab (also known as Molecular Research) have been helping hundreds of researchers from around the world get the next-generation sequencing (NGS) services they need. We are one of the most reputable NGS labs providing high-quality data, and have fast turn-around without compromising quality. Our genome sequencing services are a cost-effective solution, and we try to beat anyone’s quoted pricing.

    MR DNA scientists have more than 20 years of continuous experience (not combined) developing new and novel molecular methods, systematics, microsatellite screening, MHC assays, viral assays, protozoan assays and much more. Our team’s goal is to take advantage of each new technology as it arrives and leverage it to develop unique, improved and more cost effective molecular methods and tools.

    Our highly-trained scientists are ready to help you with your research goals. We always try and understand the focus of your research to best provide you with the analysis you are looking for. Your results are always confidential.

    At MR DNA, we offer a wide variety of genome sequencing services. Below is a general list of the different types of services we provide:

    Metagenomics

    ALLinONE

    Whole Genome Resequencing

    Exome Sequencing

    Target Region Sequencing

    de novo Sequencing

    Whole Genome Mapping

    Genotyping

    Sanger Sequencing

    Oligo Synthesis

    Single-cell DNA Sequencing

    Epigenomics

    Bisulfite Sequencing

    RRBS

    MeDIP-Seq

    Chip-Seq

    Transcriptomics

    RNA-Seq (Transcriptome)

    RNA-Seq (Quantification)

    Whole Transcriptome Sequencing

    Single-cell RNA sequencing

    Here is a small sample of the organisms in our database:

    Aerococcus viridans

    Aerococcus viridans zf-68-I

    Aeroglyphus robustus

    Aeromicrobioides flava

    Aeromicrobium alkaliterrae

    Aeromicrobium erythreum

    Aeromicrobium fastidiosum

    Aeromicrobium flavum

    Aeromicrobium ginsengisoli

    Aeromicrobium kwangyangensis

    Aeromicrobium marinum

    Aeromicrobium panaciterrae

    Aeromicrobium ponti

    Aeromicrobium spp.

    Aeromicrobium tamlensis

    Aeromonadaceae spp.

    Aeromonas allosaccharophila

    Aeromonas aquariorum

    Aeromonas bestiarum

    Aeromonas bv. veronii

    Aeromonas caviae

    Aeromonas culicicola

    Aeromonas encheleia

    Aeromonas enteropelogenes

    Aeromonas eucrenophila

    Aeromonas guangheii

    Aeromonas hydrophila

    Aeromonas hydrophila ayu-Ah0201

    Aeromonas hydrophila HL060811-1

    Aeromonas hydrophila HL060811-3

    Aeromonas hydrophila PC IW 38

    Aeromonas hydrophila PC IW 39

    Aeromonas hydrophila PC IW 40

    Aeromonas hydrophila SBRD9

    Aeromonas hydrophila subsp. dhakensis

    Aeromonas hydrophila subsp. ranaei

    Aeromonas hydrophila TS IW 32

    Aeromonas ichthiosmia

    Aeromonas jandaei

    Aeromonas jandaei sf3-14

    Aeromonas media

    Aeromonas media 1

    Aeromonas media 2

    Aeromonas media 3

    Aeromonas media 4

    Aeromonas media 6

  • Microbial Communities: Microbiome, Metagenome, Microbiota

    What consists of microbial communities analysis? Microbiome and microbiota explain the collective genomes of the microorganisms that inhabit an environmental niche or the microorganisms themselves. Microbiota are the microorganisms present within a particular environment. The approach to describe microbial diversity relies on analyzing the gene diversity 16S ribosomal RNA (16S rRNA) through next-generation sequencing. The “S” in 16S rRNA genes sequencing represents a Svedberg unit. Microbiome refers to the entire habitat; including the microorganisms, their genes, and the surrounding environmental setting. Metagenome is the collection of genomes and genes from the members of a microbiota.

    MR DNA Lab offers microbial sequencing. Microbial sequencing is the focused sequencing of a single microbe or relatively small group of microbes, in contrast with metagenomics. It can assist in the discovery of genetic variations that support the designing of antimicrobial compounds, vaccines, and even engineered microbes for industrial applications. (1)

  • Next-Generation Sequencing Services (DNA)

    Scientists are now able to elucidate the microbiome of human diseases, agricultural and other natural, environments. Especially at MR DNA Lab, scientists are dedicated to microbiome research. Their method development has opened doors to research around the world.

    This initiative is one component of the MR DNA program and constitutes a major NIH effort to broaden access to rapid assay technologies. This program will fund the development and adaptation of biological assays for use in automated high throughput molecular screening (HTS). It is intended that this initiative promote the development of automated screening projects. High throughput molecular screening (HTS) is the automated, simultaneous testing of thousands of distinct molecular signatures in models of biological mechanisms. Active compounds identified through HTS can provide the starting point in the design of powerful research tools that allow pharmacological probing of basic biological mechanisms, and which can be used to establish the role of a molecular target in a disease process, or, its ability to alter the metabolism or toxicity of a therapeutic. The immense potential of HTS to impact our understanding of biological mechanisms is largely untapped because access to automated screening facilities and large compound libraries is limited in academic, government and non-profit research sectors. Many in vitro biological models are currently used to study biological pathways, the effects of genetic perturbations and to establish a disease association. These can be adapted to high throughput formats for the purpose of screening large collections of biologically active compounds. There are a number of characteristics that make an assay suitable for high throughput approaches. The assay must be robust, reproducible and have a readout that is amenable to automated analysis. In addition, it must be possible to miniaturize the assay, for example; to a 96-well plate (or higher density) format or flow-cytometric approach. Further, the assay protocol should be simple enough for automated handling. A broad range of models share many of these features, including; biochemical assays, cellular models and certain model organisms such as yeast or C. elegans. This initiative will support the development of innovative assays for use in both basic research and in therapeutics development programs, with an emphasis on novelty of assay approach and/or novel targets and mechanisms. (1)

    The following list is a basic description of the sequencing services provided by Molecular Research, LP (MR DNA).

    Genome Sequencing

    Genome sequencing is the process through which we can elucidate the the core information (genes) of the DNA or RNA of the sample, or in the case of whole genome sequencing, the entirety of the information (genes and non-coding sequences).

    Metagenomics

    Metagenomics is a rapidly evolving field through which scientists can elucidate some of the previously hidden insights into the vast array of microscopic life on the planet. Every day, scientists are gaining a better understanding of ecology, evolution, diversity, and functions of the microbial universe thanks to metagenomics, which seeks to help sequence microorganisms in large groups that are often difficult to culture.

    Microbial Sequencing

    Microbial sequencing is the focused sequencing of a single microbe or relatively small group of microbes, in contrast with metagenomics. It can assist in the discovery of genetic variations that support the designing of antimicrobial compounds, vaccines, and even engineered microbes for industrial applications.

    Genotyping

    Genotyping is the technique through which the variations in an organisms DNA are determined by comparing that organisms DNA to a reference sequence. Genoptyping of an organism also reveals its alleles, the various alternative forms of genes or groups of genes. It plays a very important part in the study of diseases, and in combination with next-generation sequencing technology will help improve treatment methods.

    Exome Sequencing

    Selective sequencing of coding regions of the genome is an effecient and effective alternative to whole genome sequencing. Exons are the parts of coding regions which control the translation of proteins.

    Transcriptome Sequencing

    Transcriptome sequencing focuses on the complete array of RNA molecules, which include transfer RNA, messenger RNA, ribosomal RNA, and non-coding RNA. Transcriptome sequencing can help answer questions about gene expression, discovery of novel genes and their functions, classification of diseases, or to help identify targets for drug treatment development.

    Amplicon Sequencing

    Amplicon sequencing targets relatively small, specific regions of the genome usually in the hundreds of base pairs. Amplicon sequencing combined with next-generation sequencing allows for thousands of amplicons across many samples to be prepared simultaneously and indexed within hours and often within a single-run.

    Bacterial/Viral Typing

    Bacterial and virus typing is used in the accurate and fast identification and discrimination of strains. Enhancements in bacterial and viral typing can also assist in outbreak identification, surveillance, and in the understanding of transmission, pathogenesis, and evolutionary relationships of the target. Often specific isolates can be sequenced within a day using next-generation sequencing techniques.

    De novo Sequencing

    De novo is a latin expression meaning “from the beginning”. Hence, de novo sequencing is primarily focused on the sequencing of a novel genome for the first time, or genomes in which large variations are expected, such as genomes with high plasticity. It often requires specialized assembly of sequencing reads, and can be very computationally intensive, though next-generation sequencing has largely reduced the overhead associated with it.

    Targeted DNA Sequencing

    Targeted DNA sequencing allows the researcher to utilize the specificity of PCR in order to target the genes of their choosing. Targeted DNA sequencing provides the ability to acheive deeper sequencing coverage in order to identify those genes expressed at lower levels that may possibly have been missed by other sequencing methods.

    Targeted RNA Sequencing

    Targeted RNA sequencing allows the researcher to utilize the specificity of PCR in order to target the genes of their choosing. Targeted RNA sequencing provides the ability to acheive deeper sequencing coverage in order to identify those transcripts expressed at lower levels that may possibly have been missed by other sequencing methods.

    Aneuploidy and CNV Analysis

    Aneuploidy and Copy-umber variations (CNV) are important factors in the study of genetic disorders, disease, and phylogenetics. Next-generation sequencing has made the study and analysis of aneuploidy and CNV much easier than with previous methods.

    Small RNA and miRNA Sequencing

    This type of sequencing uses high-throughput methods to sequence miRNA and small RNA, which are important to tissue expression patterns, isoforms, and disease associations.

    (Source)

  • Organic Molecules: Nucleic Acids (RNA and DNA)

    Organic molecules are classified in four classes: carbs, lipids, proteins, and last but not least nucleic acids. There are two principle nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

    DNA is a double polymer of nucleotides, whereas RNA is only once strand. RNA strands are substantially shorter than DNA. The reason why DNA strands are longer is because they contain the code for many different proteins.

    There are four nitrogeneous bases in DNA, divided into two types. The first type is a double ring structure, consisting of purine’s adenine and guanine. The second type only has a single ring structure, and includes pyrimidine’s thymine and cytosine.

    The four bases in RNA are similar than in DNA, however when DNA is transcribed to RNA, all the T bases (thymine) are changed to U (uracil). RNA can be transcribed in three types:

    · Messenger RNA (mRNA) – transcribed from structural genes

    · Ribosomal RNA (rRNA) – transcribed from rDNA, component of the structure of ribosomes

    · Transfer RNA (tRNA) – transcribed from tDNA, key player in translation

    Ribosomal RNA, rRNA, is present in all cells. Consequently, rRNA genes are sequenced for the purposes like indentifying taxonomic groups, assessing related groups, and judging rates of species divergence.

    Sequencing for rRNA can be processed in small subunits like 16S. 16S rRNA sequencing can be performed by labs like MR DNA Lab. To find more information on 16S rRNA and other genomic sequencing, visit MR DNA or find them on Twitter and Facebook.

  • DNA Gets Social

    With over 200 million users, Twitter has emerged as a viable medium for determining influence in many fields – including the field of science. Scientists from all over the world are taking to Twitter to spread the ideas and information to followers.

    Social media teams, like the one at MR DNA Lab, have added Twitter to their platform. Followers use @mrdna_lab as their resource to science-related news and keep their clients updated. Connecting with @mrdna_lab is useful for those interested in learning more about updates or advancements in biological sciences, such as latest discoveries in genotyping or genome sequencing. Join the conversation today by following @mrdna_lab on Twitter.

    Whether it’s fungal genome or ion proton sequencing, MR DNA Lab can help with your next-generation sequencing. Need it fast? They can provide rush-orders if eligible! To learn more about the services they can offer, please visit their website.

  • Understanding the 454 Method

    A DNA strand is prepared by cutting the sample into small fragmented pieces (Fig 1). Attached to the ends of these fragments are oligonucleotide adaptors (Fig 2). These allow the fragments to individually attach to primer-coated beads. The goal is to have one fragment per bead. Amplification essentially copies fragments on each bead (Fig 3). Beads are then filtered, ridding of unattached DNA fragments. For sequencing, a single bead is placed into a picotiter-volume well on a plate accompanied with an enzyme bead to be incubated. Nucleotide bases are released in waves. A light signal is generated when each base is incorporated. The intensity of light is proportional to the number of repeated nucleotides of the same type.

    Many DNA and genome sequencing laboratories can provide services like this. MR DNA Lab is a next generation sequencing service provider and bioinformatics service provider specializing from 454 pyrosequencing to the new Ion Proton sequencing platform. They have over 20 years of continuous experience (rather than combined experience) developing new and novel molecular methods. Sytematics, microsatellite screening, MHC assays, viral assays, protozoan assays and etc. Visit www.mrdnalab.com for more information, or find them on Facebook and Twitter.