Genetic Variant Key To Fighting MRSA

The world wide mortality due to drug-resistant infections such as tuberculosis, HIV and malaria has reached 700,000 each year. It’s estimated that this figure will jump to 10 million people per year by 2050. The antibiotic resistance is a growing menace. The resistance crisis has caused reduction in effective antibiotics available in the market and at same time there are fewer drugs in the development pipeline.  Antibiotics are used in medical procedures such as C-sections, hip replacements and cancer treatments. These procedures would become extremely difficult and risky without antibiotics. To combat this resistance crisis, one can boost the antibiotic pipeline. The other measures could be to identify host factors associated with antibiotic resistance. Scientist at Duke university have uncovered that people with genetic mutation in a DNA methyltransferase gene called DNMT3A have greater chance to resolve methicillin-resistant Staphylococcus aureus (MRSA) infections. This study enhances the understanding of the genetic factors underlying predisposing to persistent MRSA bacteremia and may help researchers to discover better treatment options in future. Furthermore, this study highlights the impact of next generation sequencing in identifying potentially influential variants.

Staphylococcus aureus (staph) is a common bacteria present on people’s skin. These bacteria are harmless but can cause serious infection if it gets into the body. Once in the body, it can cause blood stream infection, sepsis and even death due to the reactions triggered in the body resulting in tissue damage and multiple organ failure. What is MRSA? methicillin-resistant Staphylococcus aureus (MRSA) is a staph infection and difficult to treat because of resistance to methicillin, an antibiotic. Anyone can get infected with MRSA. Greater risks are associated with those who work in hospitals and deal with patients and contaminated equipments.  These bacteria can survive on equipments for weeks. Risks are also associated with activities or places that involve crowd and skin to skin contact. Open wound such as abrasion or incisions are the sites of MRSA infection. In community these bacteria usually spread through infected people or things that carry the bacteria. The severity and duration of MRSA bacteremia varies widely between individuals. The role of the host in development of persistent MRSA bacteremia is not clear.





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How to Optimize qPCR Analysis Using a Melt Curve

When choosing a qPCR procedure there are two basic methods: the use of probes or intercalating dyes.  The use of intercalating dyes such as SYBR® Green only uses primers and binds to any double stranded DNA.  The dye absorbs blue light and emits green, which is then detected by the instrument.  The use of probes and primers introduces a third sequence and adds specificity to the reaction.  Although the use of intercalating dyes generates signal from non specific PCR products and primer dimmers, it is more widely used because it is far more affordable and can be used with a wide range of primers without the need of a specific probe per assay.  The use of a melt curve and controls can be implemented in quality control procedures to insure proficiency of quantitative PCR experiments using intercalating dyes.


 A melt curve is used after the amplification cycles have been completed.  The temperature is incrementally increased usually around 0.5°C per cycle starting at 60 to 65°C.  As the temperature is increased, the fluorescence will gradually decrease evenly as the dye is pulled off the double stranded DNA.  There will be a sharp drop off of fluorescence when dissociation of the double stranded DNA occurs.  This slope is recorded as Tm, or melting temperature.  It is interesting to note that a melt curve will not work with qPCR experiments that use probes because the initial fluorescence recorded by the instrument is not due to the fluorophore binding to the amplicon, but rather the probe being cleaved after amplification.  Typically, the presence of one Tm indicates specific amplification. However, further investigation is required to validate this assumption.



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What's in My Mouth? The Oral Microbiome

While our oral cavity is the initiating point of food digestion process, it is also the habitat for hundreds of microorganisms Those microorganisms found in the oral cavity include bacteria, fungi, viruses and protozoa. Although most of the microorganisms are beneficial to the human body, certain oral microbes can cause diseases such as tooth cavities, gum diseases, bad breath etc.  Within the oral cavity, there are various microenvironments, e.g. cheek, gingiva, lower and upper mouth floors, throat, tongue, saliva, and teeth.  Identification of the microbiome present in the oral cavity is vital to understand the role of those microorganisms on human health and diseases.  Oral microbiomes are the most studied group of microorganisms in human body because of ease of sampling. Like in other human body part, the oral cavity also possesses core and variable microbiomes. The core microbiomes are found in all individuals, while the variable microbiomes are unique to individuals.


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Ferocious Whole Genome Sequencing

Tiger (Panthera tigris) is a ferocious, but at the same time a majestic wildlife species which is found in habitats ranging from Siberian temperate forest to subtropical and tropical forests of South and South-East Asia. Although there were earlier nine subspecies of tigers, currently, there are six subspecies, i.e. Bengal, Indochinese, Malayan, South-china, Siberian, and Sumatran. Three subspecies of the tiger (Bali, Caspian, and Java) have already been extinct mainly due to poaching and habitat loss.  Although there are about 150 individuals of South-China tiger in captivity, they have already been extinct from the wild habitat. Tiger is listed as an endangered species because of its rapid decline in populations as a result of loss of habitats, hunting and poaching. Currently, the global tiger population is estimated to be in between 3000 and 4000 individuals.



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Heat Stress Responsive Genes in Wheat

Climate change and global warming has introduced new challenges for modern agriculture.  Wheat is a staple food worldwide and it is crucial to gain further understanding of how heat stress is effecting wheat production and wheat biology.  High temperature during the reproductive stage decreases yield by 15%.  Heat stress causes drying of fluid on stigmatic surface, reduces enzymatic activity critical for photosynthesis and starch biosynthesis pathways, and overexpression of heat shock proteins.  Next Generation Sequencing has been utilized for transcriptome study and has provided useful data on the regulatory pathway networks operating in plants under different conditions.  At the Indian Agriculture Research Institute in New Delhi, India, a study was performed in which the whole transcriptome of wheat in the flowering stage at control temperature and heat stress temperature.  Sequencing was done using Illumina HiSeq and Roche GS-FLX 454 platforms.


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Whole Genome Sequencing for Predicting Cancer

Cancer is the second most cause of the death worldwide. According to World Health Organization (WHO) around 10 million deaths were caused by cancer globally. There are more than 120 types of cancers. The most common types of cancers are: bladder, breast, colon and rectal, kidney, leukemia, lung, pancrease, prostate, skin and thyroid. Many of the cancers are genetically inherited from one generation to the next. Therefore, sequencing and comparing of genomes will help to predict the probability of occurrence of cancer. If cancer responsible genes are detected, this will help patient to be alert in advance and take preventive measures.


With the rapid advancement in next generation sequencing technology, genome sequencing is getting more accessible and cheaper every year...


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Do left-handers have genetic advantage?

In your daily life, you may have seen some of your relatives or friends or colleagues that are left-handed and have wondered what makes them left-handed while the vast majority of the people around us are right-handed. Researchers from the University of Oxford also wondered about the same issue and conducted a research study, published in Brain, to see if there is an association between the genetic characteristics and left-handedness. To conduct this study, the researchers used the data from the UK Biobank. Brain imaging phenotypes were identified after analyzing about 9,000 brain imaging data, which included 721 left-handers. Genome-wide association studies were performed in approximately 400,000 individuals that included 38,332 left-handers. Each individual was genotyped across 547,011 single nucleotide polymorphisms (SNPs). SNP-based enrichment analyses were performed to determine the biological pathways. Average expression analyses of mapped genes were performed in 53 tissue types. Estimation of heritability of SNPs according to the right-handed versus left-handed individuals was completed to find out if there is any correlation between genotypes and the neurological and psychiatric diseases.



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How can a C-Section affect the baby’s gut?

Learning about our baby’s gut at time of birth gives researchers an opportunity to study the development and colonization of the infants’ gut microbiome as they get exposed to a variety of microorganisms in the early stage of life. The neo-natal period (first 21 days of life) is crucial for the infants’ microbiome in terms of shaping the future of their gut flora expansion depending on the type of microorganisms encountered.

This Baby Biome Study (BBS) involved the participation of 596 healthy, carried to full term babies 314 of which were vaginally born and 282 births by ceasarean section. Fecal samples were retrieved at least once from all babies during the first month of life and 302 babies went through another round of sample collection as they approached their first year of life (8.75 ± 1.98 months). Fecal samples from 175 mothers were also collected in coupling with 178 babies. With the help of next generation whole genome sequencing a total of 1679 fecal samples were processed and analyzed to show how a “blank canvas” of gut microbiota is adapting and progressing with age. As one would suspect no individual gut flora is the same considering millions of various bacteria are involved; the results presented high diversity and instability within the same group. As much as 57% of diversity in the bacterial communities was found when comparing vaginal versus caesarian mode of birth.



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DNA In My Belly Button?

Behold, the great umbilicus, most commonly referred to as the belly button. Whether you are sporting an “innie” or an “outie”; one fact remains. Found within the human naval cavity is an incredible number of bacterial phylotypes (or “species”) and even on the very rare occasion, archaea, that has captured the attention of many scientific minds.

There are several groups of scientists that have decided to sample and research what could exist in the folds and wrinkles of this shared physical trait, and to elucidate the bacterial phylogenetics using both microbial techniques and next generation sequencing.  One such group published their findings in a paper titled “A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable,” in which scientists studied the next generation sequencing results of over 500 belly button swabs, including a sample swab from an individual’s belly button who had not showered or bathed for several years.




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Sequencing Bones in the Himalayas

The Himalayas are a mountain range in Asia and it separates the plains of the Indian subcontinent from the Tibetan Plateau. It includes over fifty mountains exceeding 23,600 ft in elevation. Bones of mysterious human beings are buried in a site in the Himalayan region named "Skeleton Lake". These bones emerge from the ice during summer time and puzzle scientists about how they migrated there. Who were these individuals? A recent study published in Nature communications about the skeletons of Roopkund Lake in the Himalayan region of northern India uncovers the mystery of Mediterranean migrants in India. The genetic profiling using next generation sequencing tools explains the mystery behind those individuals. The study suggests that Roopkund Lake in Himalayan region has been visited by diverse populations over the past 1,000 years. Migrants from the Mediterranean or South Asia visited this region and died there within the last few centuries. The lake is located around 5000 meters above the sea level in India. Migration from Mediterranean region means a trip of 5000 kilometers from Greece to skeleton lake.

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