Nanopore sequencing enables high-resolution analysis

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome

High-resolution analysis of resistant determinants and mobile elements in the human gut microbiome is quite difficult with the existing technologies. However, in the present research study, the authors highlight the effectiveness of Nanopore sequencing in getting the desired results. The analysis of genomic data derived from mobile elements in the human gut microbiome can often be limited due to the fragmented assembly from short-read sequencing.

One can overcome the limitations of fragmented assembly by using third-generation sequencing technology, which helps in getting long-reads. However, it is noted that third-generation based sequencing technologies give high-error rates and very poor throughput rates. This has resulted in limited use of technology in metagenomic related studies. The researchers in the present study have found a new way to overcome the exiting challenges by developing the first hybrid metagenomic assembler which will combine the properties of both long and short-read technologies. This will surely be considered to give high improvement when compared with the older version of assemblies along with high base par accuracy.

The approach includes a metagenome clustering technique which will be unique. It will include a scaffolding algorithm that can repeat-rich sequences with high accuracy and low error rates. Based on the numerous analysis done, the researchers identified that near-complete genomes from metagenomes can be assembled with as little as 9x long read coverage. This can enable the high-quality assembly of less abundant species. To take this understanding further, the researchers applied the concept of nanopore sequencing to analyze the gut microbiome of patients under antibiotic treatment. It was found in the study that long reads can be obtained from the samples to create accurate and efficient assemblies.

A critical review on quantum dots

A critical review on quantum dots: From synthesis toward applications in electrochemical biosensors for determination of disease-related biomolecules

Nanoscience or nanotechnology is a very fast-growing field of science, which has introduced various new transforming technology in the present era. One such technology is fluorescent quantum dots (QDs), which have been a part of nanotechnology since the very beginning of the field. Fluorescent quantum dots are very small nanocrystals, defines by a diameter of about 2-10 nanometers i.e. around 10-50 atoms. The most unique property of quantum dots is the resultant fluorescence of distinctive colors produced, which is highly dependent on the size of the nanocrystal.

Quantum dots are known to be consisting of a variety of structural, photochemical, and electrochemical properties also, which can be exploited to use them as a very promising technology in the field of sensing applications. The use of quantum dots as a nanomaterial in these sensing applications can increase the performance of biosensors in the market, specifically in terms of overcoming the existing issues such as detection limit, selectivity, and sensor sensitivity. The applications of quantum dots is not only limited to this, instead, it also expands to their high-level functionalization with bioreceptors. In this review article, the authors highlight how fluorescent quantum dots function and their core knowledge along with a detailed explanation of their applications in sensors to receptors.

The potential of quantum dots is immense, one of the reason is their enhanced capability to associate nanotechnology and biotechnology together. They indeed possess a huge potential to set a new paradigm in the research field to give a comprehensive view of zero-dimensional nanoparticles. These nanoparticles can be effectively used in the designing of electrochemical sensors which can be used in the diagnosis of diseases. This can specifically include identifying biomolecules such as tumor markers, depression markers, inflammatory markers, and more. Considering the huge application of quantum dots, the researcher highlights more in-depth research in the field. Detailed insight about quantum dots can help in understanding their electronic and magnetic properties in more detail. One can understand how they can be synthesized in labs efficiently for further large scale production to be used effectively at the industrial scale for biomolecule diagnosis and other related applications.

Serum- and glucocorticoid- inducible kinase 2, SGK2, is a novel autophagy regulator and modulates platinum drugs response in cancer cells

Serum- and glucocorticoid- inducible kinase 2, SGK2, is a novel autophagy regulator and modulates platinum drugs response in cancer cells

Many cases of ovarian cancers arise from the epithelial cells of the ovary and fallopian tube. The epithelial ovarian cancer is not a single entity disease but rather are several subtypes, each with its distinct genetic and biological backgrounds. This diversity determines the clinical outcome of the disease, where the patients respond differently to the same treatment and sometimes even different prognosis. 

For the past three decades, the standard treatment for advanced epithelial ovarian cancer is chemotherapy, commonly used platinum-based drugs (PT). Though the majority of the patients achieve complete remission, there are cases who might experience recurrence due to acquired resistance to platinum-based drugs. Cellular diversity in tumors and the microenvironment can lead to chemoresistance. Overcoming PT resistance is one of the major challenges faced in ovarian cancer research. 

Over the years, many experiments have been conducted to identify the particular genes responsible for the mechanism directly associated with the PT resistance. PT resistance is linked to several alterations such as drug inactivation, transport, DNA repair, and apoptosis. Among the general pathways, researchers have also observed autophagy has shown to confer with the metabolic plasticity which is necessary to grow and survive in therapy-induced stress. 

Autophagy is a dynamic catabolic process that aids in the formation of double-membrane vesicles also known as autophagosomes. They help in engulfing cellular proteins and organelles and deliver them to the lysosome. When  autophagosomes merge with lysosomes, the contents are degraded and help in fueling the metabolic pathways. 

In this study, the authors began a mission to find the genes responsible for the PT- chemoresistance. A loss of function screening was performed and unveiled that serum- glucocorticoid- kinase 2 (SGK2) as a novel modulator of platinum-based drug sensitivity. SGK family constitutes three isoforms: SGK1, SGK2, and SGK3. Most of the studies revolving around the SGK family, mention its role in the development of human diseases in cancer and in cellular physiology. SGKs were initially identified as regulators, and pumps in the context of epithelial cells ion transport. The study further demonstrates the previously unrecognized role of SGK2 in platinum based drug sensitivity exerted by the autophagic reflux. 

Starting from identifying SGK2 as a druggable modulator, the study characterized the role of autophagy as an escaping strategy activated by the cancer cells to resist PT treatment. The study later demonstrated that pharmacological or genetic inhibition of the isotype SGK2 could potentially block the autophagic process stimulated by the PT treatment. This evidence throws light on the possibility of developing new anticancer strategies on drug repositioning. Overall the study proves that SGK2 kinase controls the PT induced cell death in epithelial ovarian cancer by inhibiting autophagy.

Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model

Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model

For the past few months, there has been a global spread and toll of COVID-19. So far, humanity has been able to eradicate only one other human infectious disease- smallpox. The novel infectious disease- COVID-19 has had its devastating share of lives globally and currently there is no cure or licensed vaccine. 

Many studies lately have been discussing in-depth about neutralizing antibodies. They represent therapeutic and prophylactic options that could help guide potential vaccine designs. Neutralizing antibodies (nAbs) in terms of another respiratory virus- respiratory syncytial virus (RSV) is widely used clinically, usually to protect vulnerable infants prophylactically. Generally, nAbs with good potency also known as super antibodies can supersize antiviral therapeutic efficiency. Along with the help of bioengineering, the nAbs half-life can be prolonged bringing down the cost considerably. 

In this study, the authors try to present potent nAbs to the COVID-19 virus and further demonstrate their efficacy in-vivo using small animal models. The researchers of this paper, isolated and characterized the required monoclonal antibodies from recovering convalescent donors and developed neutralizing assays to investigate the antibody responses. In parallel, the researchers also developed both live attenuated and pseudovirus neutralization assays using HeLa- ACE2 (Angiotensin-converting enzyme) cell line. The collected convalescent plasma was evaluated against COVID-19 by using 8 donors. The antigen-specific B cells were sorted and corresponding genes were identified and cloned to enable antibody expression and characterization. The promising monoclonal antibodies were progressed for further testing in-vivo using a small animal model. 

The study further isolated the potent neutralizing antibodies to two epitopes- the receptor-binding domain (RBD) and the non RBD- Spike (S) protein. The data showed that the passive transfer of neutralizing antibodies provides distinct protection against the novel- COVID-19 virus as seen in Syrian hamsters. The animal model throughout the infection maintained the same weight and showed low lung abnormalities. Nevertheless, as for any animal model, there were a few limitations, including the difference in receptor cells between the hamster and humans.

The results from the study suggest a focus on the RBD and a string neutralizing antibody responses were seen by immunizing mice with a multivalent RBD. The few weak preponderances of neutralizing antibody to S protein may be due to the result of the study using recombinant S protein. In conclusion, the data from the study potentially open up to the idea of the very rapid generation of neutralizing antibodies to a newly emerged novel virus. The antibodies can open up to the possibilities of finding a clinical application and will aid in vaccine manufacturing or design.

Antibodies Targeting Influenza Viruses – A Hope for Universal Vaccine

Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication

Ever since its first eruption late last year, the number of COVID-19 has surged to millions around the world in a matter of a few months. The novel virus has claimed thousands of lives and is spreading fast and furious. For months now, experts around the world are working in harmony to find a solution for the deadly virus. One quick solution is maybe reworking the already existing antiviral drugs. However, it is not an easy task, due to an incomplete biological understanding of the virus and how the host cells react when encountered by it. 

To judiciously repurpose drugs, experts are working around the clock to understand the molecular process of the infection and the changes in the host to accommodate the viral replication. By finding the exact viral targets in the host cells, a potential drug can be selected for further testing to avoid patients from exposure to unnecessary drugs lacking validation. 

Growth Factor Receptor (GFR) is known to play a crucial role in many viral infections. The GFR signalling activation leads to a change in many cellular processes like adhesion, replication, and differentiation. In the past, various viruses like hepatitis C and influenza have shown to activate GFR signaling to replicate in the host cells. Currently, though COVID-19 is suspected to fall under the same category there is no solid evidence. The authors of this paper tried to establish that COVID-19 infections do activate GFR signaling which in turn aids in the viral replication process. While monitoring the above signalling changes in the host cells, the experts also observed that the activation of GFR signalling was consistent with other viruses relying on the receptors themselves. 

The study employed an in-vitro COVID-19 infection model replicating a human cell environment, to study the signalling changes within the host cell to accommodate viral replication. Well into the experiments the authors observed that the changes in the viral protein phosphorylation and phosphorylation driven host signalling was caused upon infection. Both the GFR signalling and downstream pathways were activated. 

On further experimentation, by performing drug-protein network analysis experts revealed that GFR signaling pathways is the key for viral replication. The GFR signalling further activates EGFR or PDGFR signalling with a profusion of RhoGTPase associated signalling molecules. 

The study does portray a few limitations. The authors had used cancer cells lines to study the virus in-vitro which does not completely speak for other cell lines. The kinetics of infection may be different for different cell lines and needs to be studied further. But taken together the results from the study provides potential novel insights into the molecular process of the viral infection. The proteomic analysis performed by the authors also revealed that several pathways are rearranged when the host cells are infected. By targeting these particular pathways a valid therapy can be found to inhibit the viral replication upon infection.

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

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.


COVID-19 patients with hypertension have more severe disease: a multicenter retrospective observational study

COVID-19 patients with hypertension have more severe disease: a multicenter retrospective observational study

Late last year, a number of unexplained pneumonia cases surfaced in Wuhan, China. Later scientists revealed that it is caused by a familiar group of pathogens, coronavirus. The WHO later named this virus, COVID-19. The virus is highly contagious, infecting millions in the last couple of months.

From previous studies, it is considered that angiotensin-converting enzyme (ACE2) is the receptor for the COVID-19 virus to enter the host cell. ACE2 is a widely expressed receptor in several organ systems of the human body, including cardiovascular and respiratory systems. The enzyme helps in catalyzing angiotensin II to angiotensin 1-7, which is the peptide counteracting proinflammation caused by Angiotensin II. 

Studies have proven that hypertension is a common condition that co-occurs in patients with COVID-19. A previously conducted study, involving 1099 COVID-19 patients reported that 23.4% of the population also suffered from hypertension. Due to the coexisting status of hypertension and COVID-19 and the involvement of ACE2 in hypertension, the authors of this study speculate that hypertension may directly be involved with the pathogenesis of COVID-19. 

To confirm if hypertension affects the progress and prognosis of COVID-19, the published study was conducted. The study involved 310 patients from the Central Hospital of Wuhan and Wuhan Jinyintan Hospital. All the participants according to the WHO were tested positive for COVID-19. The study was later divided according to high blood pressure (hypertensive and non-hypertensive group). To avoid unwanted complications, the hypertension group was further segregated to exclude patients with other complications other than hypertension. 

All the participants were monitored closely and the entire course of the disease was recorded. The median age of the participants in the study was 62 years and the prevalence rate of hypertension was 36.5%. The authors speculate that the high prevalence rate of hypertension in the study group could be due to the high median age. The study also revealed that COVID-19 patients with high blood pressure showed higher mortality. 

Evidence suggests that an imbalance of cytokines could be a possible correlation between COVID-19 and hypertension. An increase in cytokines like IL-6, IL-7, and tumor necrosis factor is associated with the development of hypertension. It should also be noted that the increased levels of cytokines, may potentially activate excessive inflammatory reactions, resulting in cell and lung damage. 

Overall the comparative study conducted using COVID-19 patients with and without hypertension showed that patients who were hypertensive were more likely to be severely affected with COVID-19 compared to the non-hypertensive group. It must be brought to light that there might be a small number of people with hypertension not recorded because the diagnosis of hypertension in this study was extracted from medical history data. 

Finally, the authors conclude that much larger groups need to be studied since the current result could be due to the higher aged participants. In the future, additional complications also need to be analyzed like ARDS, renal injury focusing on its risks associated with hypertension and COVID-19. 


Risk Factors and Biomarkers of Ischemic Stroke in Cancer Patients

Risk Factors and Biomarkers of Ischemic Stroke in Cancer Patients

Numerous types of cancer are associated with ischemic stroke and are popularly known to be co-morbid conditions. They are two of the most frequent causes of death among the elderly population. A previous report of autopsies on cancer patients indicated that around 7.4% of the population suffered from stroke symptoms. With further analysis it was noticed that about 3.5% of the cancer patients were paralysed from strokes. 

The causes of ischemic stroke in cancer and non-cancer patients are highly different. Reports suggest, most of the cancer patients suffer from stroke mainly due to hypercoagulation. The blood clot formed restricts the blood flow to the brain, causing the cells in the brain to perish. This in turn paralyses the parts of the body controlled by the dead cells. While on the other hand, some reports suggest that stroke and cancer pathogenesis may be due to coagulopathy and atherosclerosis. The aim of this study is to study ischemic stroke in cancer patients using relevant biomarkers and compare it with non cancer patients with stroke. 

The study involved cancer patients with ischemic stroke from General Hospital in Busan, Korea. All the patients had active cancer with an onset of stroke symptoms. The control group used were patients from the same hospital, non cancer patients suffering from ischemic stroke. For examining the biomarkers, patients’ blood was collected and serum was assessed. 

The study found that biomarkers such as D-dimer levels, erythrocyte sedimentation rate (ESR), fibrinogen and Brain natriuretic peptide (BNP) were significantly higher in the cancer patients when compared to non cancer patients with stroke. 

D-dimer are one of the basic bio-markers for stroke due to their discovery as by-products of fibrinolysis. As a fibrin degradation product, dimer is directly associated with coagulation and plays a major role in hypercoagulation. Compared to non cancer ischemic stroke patients, D-dimer levels were found to be higher in cancer patients diagnosed with stroke. 

Blood coagulation in cancer patients is activated by inflammation. In this study, the authors used ESR, because of its well known use as a marker for infection and inflammation. An increased level of ESR indicating fibrinolysis was noticed in cancer stroke patients when compared to the control group.

From previous papers, it is well known that fibrinogen plays a major role in inflammation and platelet aggregation. An increase in fibrinogen is directly associated with increased risk of stroke in patients. In the current study cancer patients with ischemic stroke had a significant increase in fibrinogen than non cancer patients. 

Cancer patients with ischemic stroke portrayed high levels of stroke biomarkers when compared to the non cancer patients with ischemic stroke- control group. The above results showcase a strong relationship between the cancer patients and conditions like hypercoagulation and inflammation, which could possibly explain the frequency of paralysis in aged cancer patients leading to death. Therefore, in order to reduce any incidence of ischemic stroke in cancer patients, doctors should focus on reducing inflammation and platelet coagulation. 


Adapting to survive: How Candida overcomes host-imposed constraints during human colonization

Adapting to survive: How Candida overcomes host-imposed constraints during human colonization

The human body is well known to host a large number of microbes, mostly harmless but when triggered might turn virulent. A large fungal ecosystem resides inside a human body mainly including Candida species, constituting a large part of the human body’s microbial flora. Usually asymptomatic, Candida forms small colonies, but when triggered such as environmental change, can potentially help the microbes to break barriers and cause life-threatening diseases.

Though multiple numbers of antifungal drugs are available, it is recently found that Candida species is capable of building resistance against the drugs by forming biofilms. The article further talks about the environment within the host body paving way to such resistance. 

Within the human host, Candida is capable of changing morphology and functions according to the change in the environment it resides in. Several factors play a role including temperature, ph, and oxygen supply. Candida depending on the environment can take forms such as hyphae, budding, or even pseudohyphae. 

Another crucial role played in a microbial existence within the human host is nutrients availability. It is reported that microbes thrive in the area of high glucose content. When deprived of glucose is when microbes turn to another source of nonfermentable nutrients. Research performed in labs using Candida flora has reported that in the presence of glucose the microbe is known to morph into hyphae and promote antifungal resistance. 

The limitations of micronutrients such as iron magnesium, and copper are known to limit the growth of invading microbes. But this is quite tricky as micronutrients are needed both by the host and microbes in functioning such as biochemical and cellular functions. 

It is very well known that oxygen and ph levels vary within every niche in the human body. While some are alkaline and high on oxygen concentration others are hypoxic and acidic. Candida microbes being versatile they are, can adapt their cell walls according to the change in ph. It is also interesting to note that Candida microbes thrive under hypoxic conditions, inducing their hyphal growth and causing immune evasion. 

The above has described the flexibility of the microbes to overcome multiple constraints faced in the host body. This ability of Candida helps it to form colonies and invade niches around the body. Another strategy imparted by the microbes is biofilm formation against the host body or biomedical devices. Biofilms consist of a 3D community of adherent cells with different biological properties. These cells are embedded in the ECM, which helps in maintaining the overall integrity of the biofilm. The ECM also acts as a protective barrier against any drug invasion. These features play a crucial role in Candida microbes resistance against antifungals and biomedical devices. 

With the emergence of resistant Candida species, the need to develop new antifungals is inevitable. Research using an in vivo model to mimic the host conditions is giving close insights to unravel the mysteries of the microbes. These approaches are paving the way to novel therapeutic vaccines and anti-fungal treatments, enhancing the body’s ability to fight off the infections. 


Artificial intelligence-enabled rapid diagnosis of patients with COVID-19

Artificial intelligence-enabled rapid diagnosis of patients with COVID-19

Since December 2019, multiple cases of pneumonia due to unknown reasons have emerged in Wuhan, China. Through testing multiple patient samples, scientists extrapolated a new coronavirus termed COVID-19. With no FDA approved therapeutics or treatment available for the disease, diagnosis plays an important role in containing COCVID-19, giving a path to the rapid implementation of control measures to limit the spread. With the disease spreading to almost 100 countries, a million cases have been confirmed worldwide to date. Imaging is one of the main principles used in diagnosing and evaluating the disease, with the final diagnosis depending on reverse transcriptase-polymerase chain reaction (RT-PCR). 

In response to the growing number of COVID-19 cases, there is currently a shortage of diagnostic kits worldwide. Multiple industries are coming forward to develop rapid, easy to use diagnostic kits to facilitate testing. However before these kits can be commercialized, they must be tested and validated. With the current available tests taking almost 2 days to complete and produce a result, serial testing is required to rule out any negative cases. Additionally, it is a mystery as to whether an RT-PCR is a gold standard and whether a false positive/ negative result is common. The above reasons highlight the need for alternative testing methods to produce rapid and accurate results to identify, isolate, and treat the affected people. 

Chest computed tomography is also a much-used valuable component in testing COVID-19. With some of the patients showing early-stage symptoms in radiological finding, limits the CT ability to differentiate between a positive and negative case. In this current study, the authors have used Artificial Intelligence (AI) algorithms to help in integrating CT scanning in finding the symptoms of the virus, exposure history and reliable lab testing to rapidly diagnose the patients affected with COVID-19. 

A trial was performed on 905 patients diagnosed using RT-PCR and next-generation RT-PCR and around 46% (419) people were declared positive for COVID-19. Parallelly in a test set of 279 participants, the AI system managed to achieve accuracy to about 92% of the population and had equal or even better sensitivity than a senior radiologist. The AI system also improved the detection of COVID-19 positive patients with negative CT scans, identifying 17 out of 25 participants who were tested positive via RT-PCR but negative with normal CT scans. In comparison, the radiologists’ declared the said 17 participants to be COVID negative. 

AI shows signs of analyzing huge amounts of data quickly, a quality that is much needed in the current pandemic. A major limitation of the above study is the small sample size, with available CT scans and clinical history data, the AI system can help in diagnosing COVID-19 patients rapidly. Though a promising tool, further data collection is required to test the generalization of AI mapping on other patient populations.