August 12, 2020 - SciWriteGlobal

Aug, 2020

A quadruple helix DNA discovered in a healthy human cell for the first time

Yes, you heard it right for the first time ever, scientists find quadruple DNA in healthy human cells.

It’s been 67 years since Watson and Crick first established that DNA forms a double-stranded helix. Every now and then it is identified that the double-stranded DNA can double up, to form a special quadruple stranded helix form.

Previously, quadruple DNA has been developed synthetically but was only seen in a curious point of view. Around 2013, scientists for the first time noticed quadruple DNA in human cancer cells. Today another milestone was set, when scientists for the first time have identified the peculiar DNA in healthy human cells.

“We’ve undoubtedly demonstrated that the quadruple-strand DNA forms in living cells,” says Marco Di Antonio at Imperial College London. “This forces us to rethink the biology of DNA.”

How does quadruple DNA form?

The DNA molecule is made up of 4 nucleobases- guanine, adenine, cytosine, guanine, and thymine, which can configure themselves in multiple ways.

At times, it happens so that the DNA can double up to form quadruple helix DNA, formed by sequences rich in guanine. Guanine is the only known nucleobase that is capable of forming bonds with each other. The quadruple DNA usually occurs helically in nature and contains the guanine bases stacked on top of each other.

The unimolecular regions are usually seen at the ends of the chromosome/ telomeric regions. This is usually seen in microbes, oncogenes and now in healthy human cells.

Time to rethink the biology of DNA:

The DNA was viewed by Di Antonio and team from the University of Cambridge. The team viewed the DNA within the human cell by attaching a novel fluorescent marker.

Quadruplexes, in the primary region of the DNA, act as an “on” and “off” switch particularly for the genes associated with cancer. Previous research suggests that the quadruple DNAs can be used as molecular targets to diagnose cancer at early stages.

Although Di Antonio and the team are aware of the DNA function, it is still a mystery on how a cell knows where to express the gene or decrease its activity. The researchers hypothesize that the quadruple structure may hold the door open to facilitate the reading of the genetic code.

“There is a sort of crosstalk between the formation of quadruplex DNA and epigenetic markers,” says Di Antonio. “The quadruplex form is an epigenetic mark in its own right.”

Concluding remarks:

This recent discovery adds to the evidence that the quadruple portions are a normal part of DNA regulation and function. It has also made us realize that we need to rethink our whole biology and that our view of double-stranded DNA may be out of date.

Though the new discovery can be assumed to be a native state of DNA, it is another example proving that DNA is not a fixed shape or structure.

Aug, 2020

Discovery of ‘on-off’ switch in plant immune defense

Living systems are known to be equipped with self defense mechanisms, and plants are no exception. For the first time, experts find a novel “on-off switch” in plant defense.

The main purpose of an immune system is to protect the host from any harm. All living organisms are equipped with an immune system, and plants are no exception. Plants are home to rich sources of nutrients attracting many organisms including fungi, bacteria and vertebrates. Although plants lack an immune system as complex as humans, they do have stunning forms of chemical, structural and protein defense that experts are trying to understand.

Plant immune defense:

Plants immune defenses are designed to detect any living organism and stop them from causing any extensive damage. Plants are equipped with multi layers of surveillance mechanisms that are capable of recognising potentially dangerous pathogens.

The defense mechanisms are specifically programmed and operate through a complex network. They are timed for effective and rapid response against the predators, yet at the same time are controlled to avoid any damage to the host.

The novel discovery:

Keini Dressano, Alisa Huffaker and team from the University of California San Diego, have recently discovered a novel ‘on-off’ switch in the plant defense system.

The new switch mechanism is an RNA binding protein that can help turning on immune responses a few minutes after being attacked. They also observed that it was capable of switching off the immune response hours later, to prevent self inflicting damage.

“These findings have provided new insights into how the complex intricacies of plant immune responses are orchestrated to successfully fight off pathogens, and lay a path forward for improving plant disease resistance to ensure future food stability,” said Huffaker, an assistant professor in the Section of Cell and Developmental Biology.

Science behind the discovery:

The novel discovery was found in arabidopsis plants, and it was found to control splicing of the mRNA transcripts that encode signalling protein regulators if the plants defense system.

According to the researchers, a simple chemical modification of the RNA binding protein was seen to reverse mRNA splicing that usually keeps the immune response deactivated. To turn on the immune response, a second chemical modification returns the mRNA splicing to normal resuming the inactivation process.

“This work went beyond simply identifying a new regulator of plant immunity,” said Huffaker, of the detailed mechanisms uncovered. “We discovered specific chemical modifications that control regulatory function, transcriptional targets of the regulator, differential splicing of the targets and precise effects of splicing on both target function and overall plant immune responses and disease resistance.”

Source

Aug, 2020

Use of nanoparticles in drug carrier systems

Since ancient times, plant-based natural products have been commonly used as medicines. Nearly as much as 25% of major pharmaceutical compounds are derived from natural resources. They exhibit fascinating chemical diversity and biological properties with minimal toxicity.

Despite the advantages, companies are hesitant to invest more in natural delivery systems, due to concerns such as size, shape, and biocompatibility. The use of large materials in drug delivery includes many risks such as solubility and poor absorption. Such problems gave rise to nanotechnology, currently revolutionizing the field of medicine.

Nanotechnology is an advanced field of nanoparticles being used in the science field at a molecular level. Nanoparticles are as small as 10nm to 1000nm, usually preferred to be less than 200nm. This helps them to move freely inside an organism when compared to other materials. Lately, the use of nanoparticles in drug delivery systems is speculating a lot of discussions.

Nanoparticles in drug delivery:

Currently, one of the challenges faced by researchers is to deliver a drug to an accurate site without causing any potential side effects to other healthy organs. This is especially important for cancer treatment, where the tumor is a distant metastasis in various organs. Nanoparticles employed, have specific properties to overcome the above limitation. These include their small size, ability to penetrate cell membranes, binding and stabilizing proteins. Nanoparticle entrapment of drugs is performed to make sure the drug is delivered to the target tissue supported with a controlled release.

The idea of using nanoparticles with natural compounds is very attractive in recent times. Natural compounds have a lot of properties that are enhanced by combining with nanoparticles. These properties include targeting a specific tissue and controlled release of the drug.

Metallic, inorganic, and polymeric nanoparticles are some of the frequently used types in performing a target-specific drug delivery system. In particular, drugs with poor solubility need the aid of these nanoparticles.

The efficacy of the use of nanoparticles varies according to the material, size, and other biodegradability properties. Due to their biocompatibility properties, various synthetic polymers such as polyvinyl alcohol and poly-L-lactic acid, and natural polymers such as chitosan and alginate are broadly used in fabricating nanoparticles.

Polymeric nanoparticles can be divided into nanocapsules and nanospheres, both of which are proven to be attractive drug delivery systems. The use of an optimal nano-drug delivery system is based upon the properties of the drugs chosen for the treatment.

Possible hazards:

When combining nanotechnology in medicine, toxicity exhibited by nanoparticles cannot be ignored. For pharmaceuticals, specific drug formulations can be put in place for clinical efficacy and minimizing toxicity.

Nanoparticles are known for their unique surface properties, and since it is the contact layer with the body tissue, it should be evaluated from a toxicology standpoint. Although a lot of tests and procedures are available to evaluate the material, it cannot be assumed that these tests will be precise in detecting all risks. This will most likely depend on the origin of the materials- biological or non-biological.

Recently, researchers are exploring the ideas of combining nanoparticles and natural products to minimize toxicity. Both individually have already been in use for several years, but have their own limitations. The greenway of formulating nanoparticles is widely encouraged as it lowers the hazardous constituents during the synthesis process. By using green nanoparticles, the chances of side effects can be minimized. Furthermore, by changing the shape, size, and hydrophobicity we can further enhance the bioactivity of nanoparticles.

Future of nanoparticles in the medicinal field:

Nanoparticles in the medicinal field is currently one of the fascinating areas of research out there. In the future, by the looks of it, the field of cancer looks to benefit the most from nanoparticles. By using various types of nanoparticles, it is possible to transport an accurate amount of drug to the tumor cells without causing harm to other cells. The application of nanoparticles in medicine will definitely be the future trend in diagnosis and treatment research.

More research needs to be performed to achieve a more consistent drug loading and release capacity. , progress is being made in the use of metal-based nanoparticles like gold and silver in diagnosis and therapy areas of research.

Nanotechnology is truly a multidisciplinary science beneficial to drug delivery systems. Despite the overwhelming advantages, its actual impact on the healthcare system is quite limited. In the future, a more conceptual understanding of biological response to nanoparticles must also be studied. Ultimately researchers should be able to deliver drugs for a long period of time with great precision and controlled release.

Aug, 2020

What does it mean when an article is peer-reviewed?

A top-quality research paper is always a combination of original research and good writing. Whether a student or a renowned research scientist, writing and submitting a research paper is not an easy task. It goes through several rounds of editing and review, both time-consuming and exhausting.

What is a peer review?

Reviewers are known to play an important role in any scholarly publishing. Peer review is a long, arduous process of subjecting a scholarly or research work to the scrutiny of others who are fellow experts in the field. The concept of the peer review was conducted long before the first known scholarly journal. For centuries the process has been used as a method to evaluate written work.

Peer review is primarily conducted for two reasons. Firstly, it acts as a filtered process to ensure only high standard research and content are published by validating the originality and significance of the study. Secondly, it is intended to encourage the authors to meet the high standards and to ensure any unwarranted claims or personal views are not published.

An overview of the peer-review process:

The process usually begins right after the author has completed the research and has finished the manuscript. A manuscript usually contains the purpose of the study, design, results, and conclusions. The paper is then submitted to a suitable journal of choice usually relevant to the field of study. The paper is then reviewed by the journal editors to ensure the subject matter is in the same line as the journal.

As the next step, the paper is sent to certain experts in the field related to the study for a peer-review process. Peer reviewers are also popularly known as referees. Editors work includes that the peer review process takes place fairly and in a timely and effective manner. Additionally, they must also monitor if there are any conflicts of interest involved during the review process.

As a first step, the reviewer first reads the whole paper thoroughly to carefully scrutinize the validity of the science, the quality of the study, and the methods used. Additionally, the findings from the study are evaluated and its contribution to the field advancement.

Furthermore, the reviewers also identify any scientific flaws or if any references are missing or inappropriate. They later give recommendations to the editor whether the paper should be accepted or not. If the paper is good enough with minute errors, the editor acts as a mediator between the referee and the author to make the required corrections if any.

If accepted, as per the referees’ recommendation the after goes to the production stage, where it is properly formatted by the editors according to the journal standards.

Types of peer-review:

The peer-review process takes many forms. It must, therefore, be checked which type is employed by a journal before working on a paper.

Single-blind review:

In this type of review, the reviewers/referees’ name is usually hidden to prevent any impartial decisions or influence by the authors. It is a traditional method of reviewing and is most popularly used. Sometimes, reviewers may misuse their anonymity and portray unnecessary criticisms when reviewing work.

Double-blind review:

In this process, both the author and the reviewer are hidden. This way there is no bias like the author’s sexuality, academic status, or country of origin. This type of review is conducted to make sure that articles written by renowned scientists or authors are considered on the basis of their content research rather than their reputation.

Triple blind review:

In this peculiar case, all three people involved: editor, reviewer, and author are unknown to each other. The paper is anonymized even before the submission stage and is handled this way to keep away any bias towards the author.

Peer review has become an essential tool in assisting the journal editor in selecting high quality, credible, novel, and highly interesting scientific papers. Though not all peer-reviewed processes are smooth or accurate, a more suitable and tedious process hasn’t been discussed or developed.

A more transparent review:

As the name suggests, this type of review process has full transparency. Both the authors and the reviewer’s names are open. It is popularly believed that this is the best way to prevent any plagiarism, malicious comments, and to encourage honest, open reviewing. A few of them feel it is a less honest process, which may cause the reviewer to hold back his comments due to fear or politeness.

It is high time journals start looking at options to make this process automated. This ensures a foolproof system ensuring to release high quality and error-free papers into the scientific community.

Aug, 2020

MYC Drives Temporal Evolution of Small Cell Lung Cancer subtypes by reprogramming Neuroendocrine Fate

Small Cell Lung Cancer (SSLC) is a very particular lethal malignant cancer type for which effective therapies are urgently needed. Small cell carcinomas are usually centrally located, arising from the bronchus, with a small number of peripheral lesions. They obstruct most of the airways through circumferential compression.

Around 15% of lung cancers are classified under SCLC. Recent studies indicate that SCLC can be split into 4 major subtypes, based on the expression YAP1, ASCL1, NEUROD1, or POU2F3. Treatments for these subtypes are not yet standardized, due to the lack of information on their physiology.

Now scientists have summarised their new findings “MYC Drives Temporal Evolution of Small Cell Lung Cancer subtypes by reprogramming Neuroendocrine Fate” in Cancer Cell about the physiology of SCLC subtypes, which could potentially pave the way to study and treat the disease.

Historically SCLC has been treated as a single disease. The disease exhibits genetic loss of tumor suppressors along with the expression of MYC, MYCL, or MYCN. Large scale gene expression analyses suggest that SCLC subtypes have distinct vulnerabilities which need to be understood to improve treatment. Subtype SCLC-ASCL1 which comprises 70% of the tumors is a regulator of neuroendocrine (NE) fate. Using genetically engineered mouse models (GEMM) it was found that ASCL1 is important for tumor development and that MYCL was highly expressed in this subtype. Contrastingly the other SCLC subtypes constituting 30% found to overexpress MYC and exciting low non-NE cell fate. Research shows that Myc expression drives a non-NE SCLC in GEMMs, however, the relationship between the subtypes SCLC-A and ACLC-N and involvement of MYC in driving other subtypes is still unknown.

In this paper, the author and his team investigate MYC origins and its relationship with the SCLC subtypes. Functional data from the study suggest that MYC is behind the evolution of SCLC subtypes. In context to the times’ suppressor loss, MYC promotes temporal evolution from SCLC-A to SCLC-N to SCLC-Y in-vivo. The results from the study also revealed that MYC does not work alone and requires the help of the NOTCH signaling pathway to drive tumor progression.

The study further revealed that both MYCL and MYC are not functionally redundant in SCLC. They correlate with distinct gene expression and localize to super-enhancers. MYC and MYCL have the ability to change a cell morphology fate, molecular subtype, and influence drug sensitivity.

Different SCLC subtypes inhibit different targeting drugs and considering this, dynamically evolving tumors are termed as moving therapeutic targets. Over the years many targeted therapies have failed to treat SCLC like chemotherapy. The authors of this study speculate that chemotherapy has remained the most effective due to its non-specificity among subtypes that evolve. The findings from these studies demonstrate that SCLC and other similar cancer types would benefit from a combination or customized therapies.

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Aug, 2020

Small interfering RNA (siRNA) Technology

In the past two decades, there has been increasing awareness of the role RNAs play in the regulation of gene expression. The field of RNA was revolutionized with the discovery of RNA interference (RNAi).

RNAi is a regulatory mechanism seen in most of the eukaryotic cells that contain double-stranded RNA (dsRNA) which in turn triggers direct homology dependent control of gene activity. Popularly known as small interference RNAs (siRNA), dsRNA is usually 21–22 bp long and has characteristics 2 nt 3’ overhangs which helps them to be recognized by the mechanism of RNAi.

Targeting and manipulating RNAi pathways can be a potential tool to change any biological process post-transcriptionally in many health conditions including g autoimmune diseases and cancer among others. RNAi was described as “Breakthrough of the year” by the journal Science in the year 2002, having the potential to be a powerful drug for several diseases. Optimum designing of siRNA can enhance the stability and specificity of the RNAi process and prevent off-target effects.

Design:

When considering siRNAs for therapeutics, it is essential for the selection of appropriate designs that have good potency, stability, and specificity. Over the years, protocols have been put in place to assist in designing an ideal siRNA, based on the target of interest. Once synthesized these siRNAs should be experimentally evaluated to determine its effects in gene silencing. Though tested to be effective, at times siRNAs have off-target effects, where unrelated genes tend to be altered. Furthermore, siRNAs may also induce an unnecessary innate immune response which could potentially initiate a harmful inflammatory response in patients.

Stability:

When using siRNA technology for therapeutics in in-vivo models, the stability of the molecule plays an important factor. When unprotected, siRNA is highly unstable and can easily be degraded in the human plasma, with very minimal half-life. At times like these, siRNA is chemically modified to increase the half-life without altering the efficacy. Such chemical modifications usually happen in the phosphate group of the molecules hat confers exonuclease resistance or alterations in the sugar residues that confer endonuclease resistance. A right balance between increased stability and efficacy is the right way to configure a siRNA for in-vivo use.

Delivery:

It is safe to say that no matter the efficacy or stability it is most challenging to deliver the right siRNA to the targeted tissues/ cells. Due to its negative charge, siRNA molecules are incapable of penetrating cell membranes easily. For this reason, many strategies have been developed like lipid-based formulations. Most of these strategies are non-specific and are build into delivery agents.

Recently, study results showed that single-stranded siRNA is capable of performing gene silencing in-vivo. This finding is particularly significant since single-stranded siRNA has multiple advantages over double-stranded siRNA. The lack of second passenger strands makes it more potent and reduces the risk of uncalled alterations.

Applications in medicinal fields:

Due to the effective gene silencing, siRNA is popular among medicinal fields. The degree of specificity is also an added advantage, as is its ability to utilize numerous RNA sequences to target specific cells and deliver drugs or medicines. The ultimate goal for scientists is to find an optimal way to kill or slow down the disease without affecting the surrounding tissues. In addition, the ability to specifically target genes that cause cellular damage or destruction enables pharmaceutical experts to specifically target those genes by the use of siRNA interference.

The progression from the initial discovery of siRNA technology to clinical applications has been groundbreaking. Understanding the fundamentals behind the technology has led to its widespread application in both basic research and clinical applications of treating a disease.

Despite the significant progress made in the field of RNAi technology, there is still a lot of more research that needs to be conducted to perfect the design Before siRNA becomes a common commercial therapeutic technology in the clinical field, a number of major hurdles need to be addressed. Lately, the difficulties associated with inefficient delivery to target cells have been brought into the light. There are also problems associated with the reduced biostability of unmodified RNA.

Regardless of certain setbacks, the hope still remains that with the time, siRNA technology will prove to be the next “Superdrug” against many destructive diseases. In addition, RNAi has proven to be an important tool and has opened a new world of basic investigation.

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