IUBMB

IUBMB Focused Meeting on Biochemistry & Molecular Biology of RNA Viruses

15th November, 2022- 18th November, 2022

Venue: Regional Centre for Biotechnology, Faridabad

About the Conference

The ongoing COVID19 pandemic has made it abundantly clear that infectious diseases due to pathogenic viruses with RNA genomes represents a global public health problem. Mortality and morbidity due to known RNA viruses are high and the problem is compounded due to the appearance of new viruses due to animal-human conflicts. RNA viruses such as SARS-CoV-2, Influenza, Japanese Encephalitis Virus, Dengue virus, Chikungunya virus and HIV may cause death or result in long-term sequelae in recovered patients. A number of laboratories in different parts of the world are engaged in research to identify critical intervention points in the life cycle of these viruses and exploit this knowledge to develop effective therapeutic and prophylactic strategies. To encourage a productive discussion and to disseminate knowledge about new advances in this area, we have organized, with support from the IUBMB, a focused meeting on the Biochemistry & Molecular Biology of RNA viruses. In addition to seminars by scientists, the meeting will also provide an opportunity for young researchers to present posters. Some of the poster abstracts will be selected for oral presentations.

About RCB

Regional Centre for Biotechnology (RCB) is an academic institution established by the Department of Biotechnology, Govt. of India with regional and global partnerships synergizing with the programmes of UNESCO as a Category II Centre. The primary focus of RCB is to provide world class education, training and conduct innovative research at the interface of multiple disciplines in biotechnology. A major aim of the institution is to create high quality human resource in disciplinary and interdisciplinary areas of biotechnology in a globally competitive research milieu. RCB is an integral founding component of the NCR Biotech Science Cluster, a large academic research campus located in the National Capital Region of India adjacent to New Delhi. In 2016, RCB was recognised as an Institution of National Importance by the Parliament of India.

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How to Choose a DNA and RNA Purification Kit

How to Choose a DNA and RNA Purification Kit

Looking to assure high-quality DNA and RNA for any downstream application including PCR and Next-Gen Sequencing? With the emergence of new purification technologies, the process has never been easier. Now, advanced purification technologies are suitable for even small input amounts of nucleic acids and low elution volumes, purifying DNA and RNA from gels, enzymatic reactions, and impure or diluted samples. However, with an abundance of options available, it can be tricky to navigate which kit will be the best fit. Explore each kit’s top features and what distinguishes them from similar options below.

Selecting the Right Purification Kit

Key Principles:

  • 1. Nucleic Acid Type
  • 2. Fragment Size
  • 3. Contaminants

These three principles dictate which kit is suitable. Protein and salt contamination can be prevalent in any sample. Purification kits are best if looking to remove any unwanted salts, proteins, unincorporated dyes/fluorescence and nucleotides, and phenol.

Alternatively, the OneStep PCR Inhibitor Removal Kits eliminate common contaminants in environmental samples that inhibit downstream applications. The categories for nucleic acid purification and their optimal applications for double-stranded and single-stranded DNA and RNA are listed in Table 1 and Table 2.

Purification Kits Based On Nucleic Acid Type

DNA Purification Kits:

DNA Clean & Concentrator (DCC) Kits and Genomic DNA Clean & Concentrator (gDCC) Kits are optimized for dsDNA but are capable of binding single-stranded nucleic acid types. However, the Oligo Clean & Concentrator Kit (OCC) utilizes a binding chemistry more favorable for smaller double-stranded or single-stranded fragments.

Zymo Research’s gel recovery kits and Select-a-Size DNA Clean & Concentrator Kits remove unwanted salts, proteins, and fragments as well as perform size selection. The Zymoclean Recovery Kits provide precise extraction of nucleic acids from agarose gels, while the Select-a-Size DCC Kits purify a desired, tunable range of DNA fragment sizes.

RNA Purification Kits:

The RNA Clean-Up kits, including RNA Clean & Concentrator (RCC) Kits and Oligo Clean & Concentrator (OCC) Kits are compatible with dsDNA, ssRNA, dsRNA, and ssDNA (including cDNA). The clean and concentrator kits in Table 2 are optimized to elute total RNA and other single-stranded fragments from impure or dilute extractions.

Whereas the RNA recovery kits provide precise size-selection of double-stranded and single-stranded nucleic acids. These kits remove unwanted salt, protein, and fragments from either agarose or PAGE isolated samples.

 

PCR Inhibitor Removal Kits:

OneStep PCR Inhibitor Removal Kits yield high-quality DNA or RNA and stand out for their ability to only bind PCR inhibitors and not nucleic acids. These kits consist of a fast, one-step procedure for cleaning impure samples prior to PCR, sequencing and reverse transcription (RT), with a 50 – 90% recovery rate. The column matrices efficiently remove contaminants that can inhibit downstream applications such as humic acids, tannins, polyphenolics, and melanin. These inhibitors are common in environmental samples like feces, soil, plants, and seeds.

Choosing Between Similar Kits

DNA Clean & Concentrator vs. Genomic DNA Clean & Concentrator Kit

DNA Clean & Concentrator (DCC) Kits and Genomic DNA Clean & Concentrator (gDCC) Kits are both optimized for dsDNA samples, but they can also bind single-stranded or cDNA fragments with protocol modifications.

If the DNA fragment is < 10 kb, then DCC is optimal. DCC provides better DNA recovery of smaller fragments, 50 bp – 10 kb, at a 70 – 90% yield

If the DNA fragment is > 10 kb, then gDCC is the best kit to achieve the greatest sample recovery. The gDCC provides optimal recovery of larger DNA fragments, > 10 kb, at 70 – 95%.

Although both kits are scalable to increase the sample processed per prep, the DCC kit also has automation capabilities with an optional magnetic bead format.

Zymoclean Gel DNA Recovery vs. Select-a-Size DNA Clean & Concentrator Kit

When it comes to recovering precise size selection dsDNA fragments from agarose gels the Zymoclean DNA Kits are best. The Zymoclean gel DNA Recovery Kit optimally recovers the desired dsDNA isolated fragment from 50 bp – 10 kb with a typical recovery of 70 – 90%, while the Zymoclean Large Fragment DNA Recovery Kit best recovers isolated samples from 10 kb up to > 200kb.

On the other hand, Select-a-Size DNA Clean and Concentrator Kits are optimized for size selection over a broad range of dsDNA fragments without the need for gel excisions. Manipulating titration cutoffs allows customization for selectively isolating the fragment range of interest. This kit can manipulate a size selection range cutoff for ≥ 50 bp dsDNA and is automation ready with a magnetic bead format available.

RNA Clean & Concentrator vs. Oligo Clean & Concentrator Kit

RNA Clean & Concentrator (RCC) Kits and Oligo Clean & Concentrator (OCC) Kits are both shown to work with all nucleic acids. However, the OCC kit is best suited for DNA and short RNA oligonucleotides. Whereas the RCC kit is optimal for total RNA, cDNA, and other single-stranded fragments and can be scaled to process larger sample inputs per prep; it is also automation ready with a magnetic bead format available.

When it comes to yield, the OCC kit will yield ssDNA/RNA or dsDNA ≥ 16 nucleotides, while the RCC kit will yield total RNA ≥ 17 nucleotides. Both kits provide a yield with > 90% recovery, respectively.

Zymoclean Gel RNA Recovery vs. ZR Small-RNA Page Recovery Kit

The Zymoclean Gel RNA Recovery Kit is optimal for larger fragments that are effectively isolated in agarose gels with high resolution. While the ZR Small-RNA PAGE Recovery Kit purifies RNA from polyacrylamide gels. Whereas Zymoclean Gel RNA Recovery Kit extracts RNA resolved in TAE, TBE, and MOPS buffered agarose gels and provides ≥ 80% recovery for fragments ≥ 500 nucleotides.

On the contrary, the ZR Small-RNA PAGE Recovery Kit allows for the recovery of small RNA (and DNA) fragments, 17 – 200 nucleotides, from up to 20% (w/v) polyacrylamide gels stained with ethidium bromide or ssRNA-specific dyes (native or denatured). Additionally, this kit can bind small fragments, 17 – 28 nucleotides, with ≥ 50% recovery.

Fragment size and isolation effectiveness per gel composition are two key factors to consider when deciding between these gel recovery kits.

LEARN MORE ABOUT THE DNA AND RNA PURIFICATION KITS MENTIONED IN THIS BLOG:

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ZYMO RESEARCH’S DNA/RNA SHIELD INACTIVATES MONKEYPOX FOR THE COLLECTION & TRANSPORTATION OF SAMPLES

ZYMO RESEARCH’S DNA/RNA SHIELD INACTIVATES MONKEYPOX FOR THE COLLECTION & TRANSPORTATION OF SAMPLES

IRVINE, Calif., (July 14, 2022) — Zymo Research, in collaboration with the Institute of Virology, University Medical Center Freiburg, Germany, demonstrated data showing their DNA/RNA Shield inactivating transport medium (ITM) completely inactivated recent Monkeypox virus isolates.

This data comes at a critical time as Monkeypox cases continue to climb worldwide and scientists are seeking methods to safely collect and transport samples without compromising the genetic integrity. Monkeypox testing is primarily performed via PCR from a swabbed lesion.

The DNA/RNA Shield product line includes sample collection, preservation, and transportation devices for specimens used in research and infectious disease testing workflows. DNA/RNA Shield has enabled researchers to conduct infectious disease research and testing over the past decade, including throughout the COVID-19 pandemic.

Zymo Research offers several devices that can be filled with DNA/RNA Shield, including the popular SafeCollect Swab Collection Kit. The SafeCollect Swab Collection Kits contain a collection swab and a patented tube that features a safety seal to prevent accidental spillage, contact, and/or ingestion of the sample stabilization medium, making it ideal for at-home sample collection.

Learn more about Zymo Research’s DNA/RNA Shield SafeCollect Sample Collection Kits. here

View datasheet


A viral plaque assay demonstrating the inactivation of Monkeypox virus after exposure to Zymo Research’s DNA/RNA Shield reagent.

Please reference this link to the press release (PRNewswire) discussing this data and the use of DNA/RNA Shield to inactivate Monkeypox.

Highly Contagious Influenza Virus

Highly Contagious Influenza Virus

As of May 2022, a highly contagious influenza virus continues to wreak havoc on domestic bird flocks across the United States. Millions of chickens and other fowl are dying or being killed to stop the spread of an HPAI (highly pathogenic avian influenza) – to date, the H5N1 variant has been detected as the dominant strain.

 

 

 

There are four species of influenza viruses: A, B, C, and D.

Human influenza A and B viruses cause seasonal epidemics of disease (known as the flu season). Influenza A viruses are the only influenza viruses known to cause flu pandemics and are responsible for most cases of severe illness of “the flu”. Influenza A viruses are divided into subtypes based on the two surface proteins of the virus: hemagglutinin (H) and neuraminidase (N) with different combinations of subtypes of H and N, such as H5N1, H1N1, and H3N2.

Influenza outbreaks are cyclical and are known to peak and subside with time. The outbreak of the HPAI in the U.S. right now is peaking and growing to be the worst on record.  According to Food Safety News (1), the 2015 outbreak affected 48 million poultry birds where three variants were detected, the H5N1, H5N2, and the H5N8 (2).  The 2022 H5N1 outbreak is showing to be quite virulent spreading rapidly through flocks in multiple States. In an already unstable food and supply chain network that is recovering from the impacts of the COVID pandemic, the 2022 avian flu outbreak can have negative impacts on an already stressed system as death and culling numbers continue to climb.

These outbreaks are not limited to the U.S. and are seen regularly worldwide. They affect more than poultry and humans as swine-specific viruses (H1N1) have been known to impact food supplies and cross over to infect humans. The H5N1 avian flu virus along with several other variants have been reported by the Agriculture and Consumer Production Department throughout the world (3). The Global AIV with Zoonotic Potential Situation Update is primarily limited to livestock and wild animals, while the influenza virus in humans continues to be closely monitored and surveilled weekly by organizations such as the CDC (4)

Detection and surveillance of these HPAI strains continue to be at the forefront of virology and infectious disease research. From bench to diagnostics to antiviral therapies, the development of more sensitive and sophisticated detection systems and more effective therapies in both humans and animals will become increasingly important.

For  17 years ProSci has been providing researchers with several tools to help aid in the research and detection of influenza virus and their respective structural components:

Antibodies are raised against specific strains to match the characterization of surface proteins, utilizing recombinant proteins or corresponding peptides of the hemagglutinin and neuraminidase proteins.  Antibodies, detection sets, recombinant proteins, and custom antibody services are available to push your research forward.

Explore ProSci’s catalog of influenza reagents or get in contact with Prosci’s antibody experts to help you find the right reagent for your project.

Monkeypox Virus: A breakthrough in Scientific News

Monkeypox Virus: A breakthrough in Scientific News

The monkeypox virus that has been reported in mainstream and scientific news is part of the Orthopoxvirus genus that closely resembles smallpox (variola) virus. (1) The genetic code of monkeypox is similar enough to smallpox that known vaccines, such as those developed against the vaccinia virus, as well as anti-viral treatments are found to be effective in dampening its spread and adverse physiological effects. (2)

As reported by Nature on May 28th(3),  the impact on human health is concerning but it is the unusual spread of the disease that is perking curiosity amongst researchers. For decades this virus had been contained to animal populations with limited transmission to humans in Central and Eastern Africa. It has been recently identified to be spreading in humans and in countries around the world where the virus was not previously identified. Epidemiologists are working diligently to determine the causes of the abnormal distribution of the virus.

The poxviruses are interesting research targets. The risk of viruses evolving is always present, and as reported by Nature even small outbreaks (in comparison to the SARS-CoV-2 pandemic) present some risk of a virus mutating. “The monkeypox genome is enormous relative to that of many other viruses — it is more than six times as large as the genome for the SARS-CoV-2 coronavirus. That means they’re at least “six times harder to analyze”, says Rachel Roper, a virologist at East Carolina University in Greenville, North Carolina.” (2) Andrea McCollum, an epidemiologist from the CDC added “All of the new attention on monkeypox has laid bare just how much scientists have yet to understand about the virus, McCollum says. “When this has all settled down, I think we’ll have to think long and hard about where the research priorities are.”

ProSci supports infectious disease researchers with several tools to help advance discoveries and breakthroughs.

Looking for custom antibodies for your infectious disease targets? Contact ProSci antibody design specialists for your research, therapeutic, and diagnostic projects