Biochemistry and Molecular Biology Official Blog

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Friday, 18 January 2019

Mitochondrial DNA can be inherited from fathers, not just mothers

The DNA of eukaryotic organisms (such as animals, plants and fungi) is stored in two cellular compartments: in the nucleus and in organelles called mitochondria, which transform nutrients into energy to allow the cell to function. The nucleus harbours most of our genes, tightly packaged into 46 chromosomes, of which half are inherited from our mother’s egg and half from our father’s sperm. By contrast, mitochondrial DNA (mtDNA) was thought to derive exclusively from maternal egg cells, with no paternal contribution1Writing in Proceedings of the National Academy of Sciences, Luo et al.2 challenge the dogma of strict maternal mtDNA inheritance in humans, and provide compelling evidence that, in rare cases, the father might pass on his mtDNA to the offspring, after all.
Human eggs contain more than 100,000 copies of mtDNA, whereas sperm contain approximately 100 copies3. Early hypotheses suggested that paternal mtDNA molecules became diluted in number relative to maternal mtDNA ones in the fertilized egg, but these ideas were replaced when evidence from various organisms, such as the uni-cellular alga Chlamydomonas reinhardtii4 and medaka fish5, showed that paternal mtDNA is rapidly eliminated after fertilization. For decades, researchers have speculated on why healthy organisms obtain their cellular powerhouses from just one parent and on the possible evolutionary advantages conferred by mitochondrial genes inherited in this fashion.
A healthy individual’s mtDNA molecules are mostly identical. But in people with diseases caused by mtDNA mutations, normal and mutant mtDNA molecules typically coexist in a single cell — a situation termed heteroplasmy6. Disease severity is often associated with the amount of mutant mtDNA in cells, which is in turn determined by events that occurred when the person’s mother was still an embryo7. The developing eggs in the female embryo go through an ‘mtDNA bottle-neck’, in which the number of mtDNA copies is first reduced and then amplified to more than 100,000 copies8,9. Accordingly, variable amounts of mutant and normal mtDNA are present in the mature eggs of an individual woman, and, therefore, in the cells of her offspring. This phenomenon influences the severity of diseases caused by mtDNA mutations, and can lead to very different manifestations between individuals from the same family7.
Luo and colleagues identified three families with mtDNA heteroplasmy that could not be explained by maternal inheritance. The story started with a young boy suspected of having a mitochondrial disease. The authors performed high-resolution mtDNA sequencing, but did not identify any disease-causing mtDNA mutations. However, their analysis uncovered unusually high levels of mtDNA heteroplasmy. Intriguingly, the same unusual pattern of mtDNA variation was found in the boy’s mother and in his two healthy sisters (Fig. 1).


Figure 1 | Family tree revealing paternal inheritance of mitochondrial DNA (mtDNA). Luo et al.2 sequenced the mtDNA of several members of a family in which many individuals had a high level of mtDNA heteroplasmy (the presence of distinct genetic variants in the same cell). This mtDNA variability is denoted by two colours in the same silhouette of an individual. The analysis showed that some of the individuals with heteroplasmy had inherited mtDNA from both of their parents, breaking the usual pattern of exclusive maternal inheritance of mtDNA. Luo et al. suggest that the ability to inherit paternal mtDNA is a genetic trait.

To trace the origin of this mysterious mtDNA pattern, Luo et al. extended their investigation to the previous generation. Sequencing of the mtDNA of the boy’s maternal grandparents revealed an unexpected contribution: his unusual mtDNA pattern seemed to be the product of mtDNA from both grandparents. The authors went on to identify two additional and unrelated families that had biparental mitochondrial transmission. A similar scenario was previously observed in an individual with mitochondrial disease who had a paternally inherited mtDNA variant10. Together, these reports provide evidence for biparental mitochondrial inheritance in humans.
Human disease-causing mtDNA mutations were originally reported in 1988 (refs 6, 11)6,11, and more than 200 such mutations (see go.nature.com/2fucdqt) have been discovered since then, most of them occurring in a hetero-plasmic context7. More-over, the estimated frequency of mutations of matrilineal mtDNA has made it a useful and often-used tool in studies of ancestry and evolution, as well as in forensic identification12. Human mtDNA has also been a valuable tool in archaeology, because its small size (16,569 base pairs) and circular form make it more resistant to degradation than is nuclear DNA (which has around 3 billion base pairs)13.
Given this long and multifaceted research history, why would paternal mtDNA have remained undetected? Luo et al. suggest that mtDNA heteroplasmy is often overlooked in diagnostics when it does not involve a disease-causing variant. Although this might be true to some extent, it is a rather unsatisfactory explanation in this era of deep DNA sequencing. Nevertheless, Luo and colleagues’ findings should provoke a re-assessment of the extensive global mtDNA sequencing data available, for those wishing to unearth further instances of atypical heteroplasmy. If the paternal contribution to mtDNA is more common than previously realized, this could alter some estimated timings of human evolution, because these are often based on predictions of mtDNA sequence variation under the assumption of exclusive maternal inheritance.
Although biparental inheritance of mtDNA and heteroplasmy coincided with disease symptoms in some of the individuals studied by Luo et al., the authors’ data do not demonstrate a causal link with disease. In fact, we cannot be certain that the study participants have mitochondrial disease, because no specific examinations to confirm this diagnosis are reported. Further study is needed to identify more cases of potential paternal mtDNA inheritance, and to determine the functional consequences of such heteroplasmy. Notably, this knowledge is relevant to mitochondrial-donation therapy (“three-parent babies”), which aims to prevent the transmission of disease-causing mtDNA to offspring14, but which can also potentially generate individuals with two types of mtDNA, one from the donor and another from the mother.
Could the amount of paternal mtDNA in a fertilized egg or developing embryo be deliberately boosted to diminish the adverse effects of mutant maternal mtDNA when this is present? This is an interesting option, but still far from reality. In addition to evading elimination, paternal mtDNA molecules would need to have a considerable replicative advantage over maternal ones to reach meaningful proportions.
Will Luo and colleagues’ findings affect the counselling of individuals carrying disease-causing mtDNA mutations who are considering having children? Not greatly, because paternal mitochondrial transmission seems to be exceedingly rare in humans. At present, this discovery represents an interesting conceptual breakthrough, rather than one that will directly influence clinical practice.
Previous work15 has shown that mitophagy, the process by which cells ‘eat’ their own mitochondria, has a role in the selective elimination of paternal mitochondria. Given our rapidly expanding knowledge of mammalian mitophagy in vivo16, these rare instances of paternal mtDNA transmission might be attributed to defective mitochondrial turnover. The inheritance pattern of paternal mtDNA in Luo and colleagues’ study suggests that a yet unidentified gene on one of the autosomes (non-sex chromosomes) is involved in eliminating paternal mitochondria. The families in whom paternal mtDNA inheritance was observed provide an exciting opportunity to decipher the signalling pathways that modulate paternal mitochondrial elimination and prevent biparental mitochondrial transfer.
Nature 565, 296-297 (2019)
doi: 10.1038/d41586-019-00093-1


Monday, 14 January 2019

Protein modification fine-tunes the cell’s force producers

Actin is one of the most abundant proteins in our cells. It assembles into filaments that produce force for many processes that are essential to the life of animals, plants and fungi — including cell migration and division, and muscle contraction1. The organization and dynamics of actin filaments in cells are regulated by a large array of actin-binding proteins. Moreover, post-translational modifications of actin — the addition of certain chemical groups to its amino-acid residues, or their removal — is thought to have a role in controlling the cellular functions of actin filaments. However, the proteins that catalyse these changes have been elusive. Writing in Nature, Wilkinson et al.2 report the identification of the long-sought enzyme that catalyses the methylation (addition of a methyl group) of actin, and shed light on the biological role of this post-translational modification in animals.


Some post-translational modifications of actin are present in all isoforms (structural variants) of the protein, whereas others are more specific. 


The protein’s amino-terminal region can be modified by acetylation (addition of an acetyl group) and arginylation (addition of an arginine amino-acid residue)3. Recent studies identified the enzyme responsible for amino-terminal acetylation of actin and demonstrated that this modification affects the elongation and depolymerization of actin filaments4,5.
Most actin isoforms are also methylated at a particular histidine amino-acid residue known as His73, which is close to the site to which one of two nucleotides, ATP or ADP, binds. Hydrolysis of ATP to ADP plus one free phosphate molecule is essential for the turnover of actin filaments, and hence for their ability to produce force in cells. Although methylation of His73 was identified more than five decades ago6, the enzyme responsible and the biological functions of this modification have remained unknown.
The study by Wilkinson et al. and a related study published in eLife7 report that the SETD3 protein is the enzyme that methylates actin at His73 (Fig. 1). This is the first time an actin methyltransferase (an enzyme that catalyses methylation) has been identified, and also the first time a histidine methyltransferase has been identified in animals. Earlier work suggested that SETD3 methylates lysine amino-acid residues in histone H38, a protein associated with DNA, but Wilkinson et al. convincingly demonstrate that SETD3 is not a methyltransferase for histones. The authors provide extensive biochemical and cell-biological evidence showing that, at least in mammals, SETD3 is the only enzyme that catalyses the His73 methylation of actin, and that actin is the only substrate of SETD3. They also show that SETD3 and His73 methylation of actin are present in a wide range of organisms, including plants and animals, but that SETD3 is not present in budding yeast, which also lacks His73-methylated actin.
Figure 1 | Methylation of actin by the SETD3 protein.Wilkinson et al.2 show that SETD3 catalyses the addition of a methyl chemical group (methylation) to a histidine amino-acid residue (His73) of the protein actin, and that this modification fine-tunes the protein’s function. His73 is close to a site to which either an ATP or an ADP nucleotide binds. The switch between ATP and ADP is essential to allow actin filaments to produce force in cells. Other evolutionarily conserved post-translational modifications of actin, including the addition of an acetyl chemical group (acetylation) to its amino-terminal region, are distant from the nucleotide-binding pocket of actin.
Why does SETD3 methylate actin, but not other proteins? To answer this question, Wilkinson et al. determined the atomic structure of SETD3 in complex with a short chain of amino acids (a peptide) that has the same amino-acid sequence as the region of actin around His73. They found that this peptide occupies an extended groove in the domain of SETD3 that is responsible for the enzyme’s methyltransferase activity. The interface between SETD3 and the actin peptide has many specific interactions, which explain why SETD3 binds to and methylates only actin.
To examine the biological functions of this post-translational modification, Wilkinson et al. generated ‘knockout’ mice and cell lines in which the gene encoding SETD3 was inactive. They observed that actin is no longer methylated in these models. Surprisingly, the mice lacking SETD3 seemed to be healthy, which demonstrates that methylation of actin at His73 is not essential in mammals. However, female mice lacking SETD3 took longer to give birth than did mice in which this protein was present. The delay resulted from defective contraction of certain muscles of the uterus during labour. Moreover, the migration of SETD3-knockout cells in culture was slower than that of wild-type cells. Finally, non-methylated actin purified from the SETD3-knockout cells polymerized slightly more slowly than did methylated actin, and had a faster rate of exchange of nucleotides on single actin molecules than did actin purified from wild-type cells.
These experiments provide evidence that, despite being evolutionarily conserved across a broad group of organisms, methylation at His73 is not essential for the normal functioning of actin. Instead, this modification seems to fine-tune the protein’s biochemical properties and cellular roles.
Future studies should investigate the SETD3-knockout mice in more detail for possible additional differences from wild-type mice, and should examine the effects of SET
D3 deletion in other model organisms. Also, the effects of His73 methylation on actin biochemistry should be studied more precisely. Previously, analysing these effects was possible only by mutating the His73 residue in actin or by producing human actin in yeast, in which this protein cannot be methylated9,10. The new findings will enable careful side-by-side comparison of wild-type actin and actin that lacks methylation only at His73. 
Because His73 is close to the nucleotide-binding site of actin, it will be especially interesting to study how this modification affects the functions of proteins that catalyse nucleotide exchange on actin11and that rely on ATP hydrolysis and subsequent release of free phosphate for their interactions with actin filaments12.
Nature 565, 297-298 (2019)
doi: 10.1038/d41586-018-07882-0

Friday, 21 December 2018

Call for Microsoft Imagine Cup 2019 Pakistan

The Higher Education Commission & Microsoft are collaborating to bring to faculty, students and academia Microsoft’s Imagine Cup - the world’s most prestigious student technology competition, bringing together student innovators from all over the world. 
Each year, a team is chosen from Pakistan that completes against the best from around the world, to get a chance to win $100,000 USD.
This is an amazing opportunity for you to participate and utilize your potential by bringing your imagination and their passion towards creating technological solutions and compete to win great prizes! 
Microsoft along with the HEC is striving for nurturing innovation and transforming technology among the youth of Pakistan. It is hoped that the platform made available through this collaborated effort will help students of Pakistan in recognition of their innovative ideas and relative projects. 
To ensure quality output, the competing teams from Pakistan are initially evaluated in Regional finals that are held in different cities. The winning teams compete for National Finals to select a National winner. A mix of judges from both academia (as directed by HEC) and industry evaluates the solutions during both rounds. Both regional finals as well as National Finals evaluations are made based over team’s deliverables submitted online on the Imagine Cup portal using the criterion listed in 2019 Imagine Cup Competition Official Rules and Regulations (attached with this email).
Regional & National Finals detailed per team plan and relative winner’s announcements will be made on Official MSDN Pakistan Community Blog: https://blogs.msdn.microsoft.com/pakistan/.
The deadline for the project submission for the Regional Finals is 15 January 2019.
All interested students are requested to contact their faculty members concerned as early as possible to participate in the Imagine Cup 2019 with reference of this email. 
Please click onto https://imaginecup.microsoft.com/en-us/pakistan for further details. 




Thursday, 13 December 2018

Brain tumor related epileptic disorders


Diagnostic monitoring and modern technology based therapeutic strategies to manage the adverse effects


Tumor is a multifaceted, genetically complex disorder and the complications are further increased, when couple with some serious neural disturbances. 20-40% patients with brain tumor have been reported to suffer from different types of seizures.

Brain tumor related epilepsy (BTRE) are the most complicated neurological disorders for neuro-scientists and oncologists that demand intense molecular strategies and therapies to tackle the entangled cascade of neural network and at the same time there is need to understand the abnormal cellular architecture of cancerous cells in the brain. BTRE has also acquired multiple drug resistance (MDR) behavior, thus makes a challenge-able choice of anti-epileptic drug for physicians and also has adverse effect on the quality of life of the patients.

With the emergence of technological revolution in the modern clinical world, the onset of Nano-biotechnology and artificial intelligence has gain lot of interest and practical acceptance among scientific community. 

Recently couple of studies have been reported to use artificial neural network (ANN) for more precise diagnosis of epilepsy and to understand the clinical impact of human mutations with deep neural network system. There is a need to get maximum benefits from these emerging fields in parallel with biological advancements for the implication of treatment.


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STEM CELLS AND AGING


Stem cells have potential to differentiate into all types of cells depending upon need of the cell. Therefore , stem cells are considered main source for regeneration and replacement of damaged cells. But it is confirmed that aging has negative impact on development of stem cells.

Skeletal muscle cells have capacity to regenerate and replace damaged parts of muscle cells.The potential of satellite cells deminishes with the onset of aging. It disturbs the normal function of B and T cells.

The process of aging reduces the stem cells function. Neural stem cells (NSCs) which are responsible for replenishment of new neurons i.e maintaining brain function , starts to cause neurodegenerative diseases within the onset of aging.


Aging of skin:-

 There are various reasons of aging specifically when it relates to molecular and cellular level. The factors are supposed to involve in aging of skin are genetration of ROS , utraoviolet rays, smoking ,contamination and due to disturbace in metabolism. ROS promotes mechanism of gene expression resulting in collagen degeneration and aggre gation of elastin.moreover, ROS enhances the activation of matrix degenerating metalloproteases while suppresses the TIMP .

Stem cells have potential to differentiate into all types of cells depending upon need of the cell.

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Wednesday, 12 December 2018

Environmental biotechnology

Envoirmental biotechnology


Introduction:
 Environmental Biotechnology has come up at present time in its efforts to clean up our environment because our environment over the year has become a repository for dozen of chemical and the main purpose of this technology is to introduce Eco-friendly techniques which involve the use of microorganism. 

Environmental Biotechnology is extremely important constituent of the scientific and engineering tools which are required to handle environmental issues. This technology absorbs additional elucidation of biological principles that are bases of environmental engineering. 

Environmental biotechnology hang on a systematized overlook of dozen factors having a part in when organism used to resolve our environmental issues. For example, fungus is used for the treating unhealthy waste that comes from industries specifically paper making industry. By using this technology, we can more fruitfully clean up unhealthy chemical instead of using prevailing methods which greatly dis-rate our dependence for clean up on methodology which is burning process or waste dump sites.

We can say biotechnology is not a new technique to treat waste material. Most of the population already depends upon microbes, bacteria and microorganism to treat waste. Much of the bacteria survive on chemical material and few organism feed on toxic material. Environmental engineer apply different techniques to treat waste one of them is to add bacteria at hazardous place bacteria then eat waste and produce harmless byproduct (bioremediation)

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EPIGENETICS The heart of future biology


EPIGENETICS The heart of future biology

Epigenetic is the modern technique which involves the changes in the expression of the gene without change in the basic DNA sequence that determines the correct order of nucleotides with chromosomes and genome. Epigenetics research includes the appliance of strong alteration techniques for DNA.

Epigenetics is associated with DNA modification or protein modification. It includes histone modification, DNA methylation as well as chromatin modification. These modification effects the regulation of gene expression. 

It generally takes information from the nucleus of eukaryotic cells (having the nucleus in the cells) and packed that information. One of the examples of the epigenetic is the DNA methylation which is done by adding a methyl group to the cytosine. Methylation is a controlled process because of an enzyme that is methyltransferase in cell division
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Gut Microbiome and Dementia


Dementia basically a sort of symptoms that corresponding thinking skills, everyday performance of person and memory. It is infect a neuro-cognitive disorder. Alzheimer’s disease is almost its common cause. It is said that Dementia can’t be cure completely.

Role Of Gut Microbiome in Dementia:-

1.Nervous system disease, Neuro-inflammation and gut microbiome are closely related.

2. Neurotoxic metabolites D-lactic Acid and Ammonia processed by bacterial enzymes.

3.Human antigen and bacterial proteins cross-react with each other to vitalizing defective reactions of adaptive Immune Response.

4.The neurotransmittors and harmones made from gut microbes are similar to humans. Becterial growth for Harmones developed virulence and growth of microbes.

5. Clostridium difficile increased the chances of infections.



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Artificial skin for burn patients


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The skin is a complex organ that is difficult to replace when it is irreversibly damaged by burns, trauma or disease. These are now a number of commercially available. Skin is our body largest organ. Skin serve as a external barrier that protects unwanted substances from entering the body. Skin have three layers; epidermis, dermis, and hypodermis.


In the united states maximum 12,000 deaths annually are caused by thermal injury. Major contributors to mortality immediately following severe burn trauma are excessive fluid loss and rampant infection. It’s failure to achieve skin coverage within three to seven days increase the risk of death.

Since one of the main challenges in treating acute burn injuries is preventing infection, early excising of the eschar and covering of the wound becomes critical. Non-viable tissue is removed by initial aggressive surgical debridement. Many surgical options for covering the wound bed have been described, although split-thickness skin grafts remain the standard for the rapid and permanent closure of full-thickness burns.

Significant advances made in the past decades have greatly improved burns patient care, as such that major future improvements in survival rates seem to be more difficult. Research into stem cells, grafting, biomarkers, inflammation control, and rehabilitation will continue to improve individualized care and create new treatment options for these patients.

Engineering of biologic skin substitutes has progressed over time from individual applications of skin cells, or biopolymer scaffolds, to combinations of cells and scaffolds for treatment, healing, and closure of acute and chronic skin wounds. Skin substitutes may be categorized into three groups: acellular scaffolds, temporary substitutes containing allogeneic skin cells, and permanent substitutes containing autologous skin cells.

According to new research if artificial grafting is used from buffalo and cows is a cheap grafting procedure now a days research is going on this method in Pakistan in Lahore. So modern technique can prevents lives which oocur due to burns




Genetic Engineering


Introduction.


Genetic engineering also termed as genetic modification or genetic manipulation is the process which involves the direct manipulation of DNA of an organism to alter the organism’s characteristics to either produce novel or improved traits. In simple words, it can be defined as: the science of manipulating and cloning the genes for the production of new trait or biological substances like proteins. The organism produced through genetic engineering are termed as GMOs: Genetically Modified Organisms.

genetic engineering

The organisms into which foreign DNA has been inserted are called transgenic organisms. Along with inserting the genes, genetic engineering can be used to remove or knock out a specific gene. The exigency of genetic engineering owes to its promising results. Human insulin was first time possible to obtain from non-animal cells by genetic engineering. The modification in DNA of an organism for a desired outcome and its success has led to the new ways in modern science.

The term ‘Genetic Engineering’ was used by Jack Williamson in his novel named ‘Dragon Island’ in 1951. Paul Berg is considered as the pioneer in genetic engineering. In 1972, he paved the ways to possibility of rDNA formation by experimentally combining the DNA from lambda virus with that of monkey virus SV40.After one year, Herbert Boyer and Stanley Cohen created first transgenic bacterium.

In 1973, Rudolph Jaenisch introduced the foreign DNA into the mouse embryo thus creating a transgenic mouse. In 1976, Herbert Boyer and Robert Swanson led the foundation of first genetic engineering company, Genentech. In 1982, FDA approved the insulin production by bacteria. In 1987, first genetically modified organism was released in environment. 

In 1994, first genetically modified food, a tomato (Falvr Savr), was approved for commercial use. In 1995, a genetically modified pesticide producing crop was approved by FDA for plantation in USA. In 2009, 25 different companies grew transgenic crops. Jennifer Doudna and Emmanuelle Charpentier developed a technique, CRISPR/Cas9 system in 2012, to specifically alter the genome of almost any of the organism.





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