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Wednesday, October 3, 2018

Most Recent 10 Nobel's Prizes for Medicine or Physiology


  1. 2018-  James P Allison and Tasuku Honjo for Immune checkpoint therapy to treatments for advanced, deadly cancers.
  2. 2017- Jeffrey Hall, Michael Rosbash and Michael Young for unravelling how bodies keep a circadian rhythm or body clock
  3. 2016 - Yoshinori Ohsumi for discovering how cells remain healthy by recycling waste.
  4. 2015 - William C Campbell, Satoshi Ōmura and Youyou Tu for anti-parasite drug discoveries.
  5. 2014 - John O'Keefe, May-Britt Moser and Edvard Moser for discovering the brain's navigating system.
  6. 2013 - James Rothman, Randy Schekman, and Thomas Sudhof for their discovery of how cells precisely transport material.
  7. 2012 - Two pioneers of stem cell research - John Gurdon and Shinya Yamanaka - were awarded the Nobel after changing adult cells into stem cells.
  8. 2011 - Bruce Beutler, Jules Hoffmann and Ralph Steinman shared the prize after revolutionising the understanding of how the body fights infection.
  9. 2010 - Robert Edwards for devising the fertility treatment IVF which led to the first "test tube baby" in July 1978.
  10. 2009 - Elizabeth Blackburn, Carol Greider and Jack Szostak for finding the telomeres at the ends of chromosomes.

2018 Nobel prize for medicine or Physiology goes to immune checkpoint therapy


Two scientists who discovered how to fight cancer using the body's immune system have won the 2018 Nobel Prize for physiology or medicine.
The work, by Professor James P Allison from the US and Professor Tasuku Honjo from Japan, has led to treatments for advanced, deadly skin cancer.
Immune checkpoint therapy has revolutionised cancer treatment, said the prize-giving Swedish Academy.
Experts say it has proved to be "strikingly effective".
Prof Allison, of the University of Texas, and Prof Honjo, of Kyoto University, will share the Nobel prize sum of nine million Swedish kronor - about $1.01 million or 870,000 euros.
Accepting the prize, Tasuku Honjo told reporters: "I want to continue my research ... so that this immune therapy will save more cancer patients than ever."
Prof Allison said: "It's a great, emotional privilege to meet cancer patients who've been successfully treated with immune checkpoint blockade. They are living proof of the power of basic science, of following our urge to learn and to understand how things work."
Treating the untreatable
Our immune system protects us from disease, but it has built-in safeguards to stop it from attacking our own tissue.
Some cancers can take advantage of those "brakes" and dodge the attack too.
Allison and Honjo, now both in their 70s, discovered a way to unleash our immune cells to attack tumours by turning off proteins that put the brakes on.
And that led to the development of new drugs which now offer hope to patients with advanced and previously untreatable cancer.
Immune checkpoint therapy is being used by the NHS to treat people with the most serious form of skin cancer, melanoma.
It doesn't work for everyone, but for some patients it appears to have worked incredibly well, getting rid of the tumour entirely, even after it had started to spread around the body.
Such remarkable results had never been seen before for patients like these.
Doctors have also been using the treatment to help some people with advanced lung cancer.
Prof Charles Swanton, from Cancer Research UK, congratulated the prize winners, saying: "Thanks to this groundbreaking work, our own immune system's innate power against cancer has been realised and harnessed into treatments that continue to save the lives of patients. For cancers such as advanced melanoma, lung, and kidney, these immune-boosting drugs have transformed the outlook for many patients who had run out of options.
"The booming field of immunotherapy that these discoveries have precipitated is still relatively in its infancy, so it's exciting to consider how this research will progress in the future and what new opportunities will arise."
Medicine is the first of the Nobel Prizes awarded each year.
The literature prize will not be handed out this year, after the awarding body was affected by a sexual misconduct scandal.

By Michelle RobertsHealth editor, BBC News online

Sunday, March 25, 2018

Biodiversity worsens all over the world, in urgency to cope with

An intergovernmental ecological body said on Friday that the biodiversity, the essential variety of life forms on Earth, continued to decline in every region of the world, significantly reducing nature’s capacity to contribute to people’s well-being.
Those alarming trends are endangering economies, livelihoods, food security and the quality of life of people everywhere, according to four peer-reviewed regional reports released by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES).
Human-induced climate change, which affects temperature, precipitation and the nature of extreme events, is increasingly driving biodiversity loss and the reduction of nature’s contributions to people, said Jake Rice, a co-chair of the Americas assessment.
In the Americas, the populations of species are about 31 percent smaller than those was at the time of European colonization, according the report. With the growing effects of climate change added to the other drivers, this loss is projected to reach 40 percent by 2050, it says.
In Africa, by 2100, climate change could also result in the loss of more than half of African bird and mammal species, a 20 to 30 percent decline in the productivity of Africa’s lakes and significant loss of African plant species.
The most recent sad example went to the death of the world’s only remaining male northern white rhino in Kenya on Monday. Its death left only two female northern white rhinos on the planet.
There have been some good news in Asia, however. Over the past 25 years, marine protected areas in the region increased by almost 14 percent and terrestrial protected area by 0.3 percent. Its forest coverage increased by 2.5 percent, with the highest increases in North East Asia (22.9 percent) and by South Asia (5.8 percent).
But the report considered those efforts in Asia insufficient to halt the loss of biodiversity. Unsustainable aquaculture practices, overfishing and destructive harvesting, threaten coastal and marine ecosystems, with projections that, if current fishing practices continue, there will be no exploitable fish stocks in the region by 2048.
Also in Asia, intertidal zones are also rapidly deteriorating due to human activities as up to 90 percent of corals will suffer severe degradation by 2050, even under conservative climate change scenarios.
In the European Union, only 7 percent of marine species and 9 percent of marine habitat types have shown a “favorable conservation status.” Moreover 27 percent of species assessments and 66 percent of habitat types assessments show an “unfavorable conservation status.”
“One of the most important findings across the four IPBES regional assessments is that failure to prioritize policies and actions to stop and reverse biodiversity loss, and the continued degradation of nature’s contributions to people,” said Anne Larigauderie, the Executive Secretary of IPBES.
“Tools like these four regional assessments provide scientific evidence for better decision making and a path we can take forward to achieve the Sustainable Development Goals and harness nature’s power for our collective sustainable future,” said Achim Steiner, Administrator of United Nations Development Program.

Wednesday, February 14, 2018

Clues to aging found in stem cells' genomes

Stem cells that produce sperm use a genetic trick to stay perpetually young across generations, researchers at the University of Michigan (UM) Life Sciences Institute have discovered.
The results have been newly reported in the journal eLife.
Certain sections of the fruit fly genome get shorter with age. But remarkably, some reproductive cells can repair the shrinkage, and this genomic shrinkage may underlie aspects of aging and hint at ways that select cells might thwart it.
In the study, UM researchers focused on workhorse genes encoded in ribosomal DNA, or rDNA. These genes carry instructions for the parts that make up ribosomes, cellular machines that turn RNA molecules into every protein needed in the body.
In fruit flies, chains of rDNA genes are found on the X and Y chromosomes. Compared with young male fruit flies, old males had a shortage of rDNA genes on the Y chromosome, leaving them with a shrunken Y chromosome.

Moreover, this dearth of rDNA seems to be passed on from generation to generation. Geriatric fly fathers, those 40 days old, passed on their reduced number of rDNA genes to their sons, UM researchers found. These sons had considerably fewer copies of rDNA genes than sons born to younger fathers.
Then the researchers saw something surprising. In many cases, this rDNA loss reversed itself. At about 10 days of age, sons born to old fathers had recovered enough rDNA to be comparable to sons born to young fathers.
"This recovery was something we really didn't expect," said UM Life Sciences Institute faculty member Yukiko Yamashita.
The results suggest that rDNA rejuvenation in sons might be a crucial aspect of how stem cells persist from father to son. The researchers do not yet know whether such a reset can happen to female stem cells in the ovaries.
Until now, researchers had observed the phenomenon only in yeast. If the results hold true for humans, they could offer insight into how most cells deteriorate over time.
Being pushed, Yamashita would wager that some types of immortal cells in people can perform the same rejuvenating trick to prevent the rDNA declines that come with age.

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Monday, February 12, 2018

DNA Cloning


In biology a clone is a group of individual cells or organisms descended from one progenitor. This means that the members of a clone are genetically identical, because cell replication produces identical daughter cells each time. The use of the word clone has been extended to recombinant DNA technology, which has provided scientists with the ability to produce many copies of a single fragment of DNA, such as a gene, creating identical copies that constitute a DNA clone. In practice the procedure is carried out by inserting a DNA fragment into a small DNA molecule and then allowing this molecule to replicate inside a simple living cell such as a bacterium. The small replicating molecule is called a DNA vector (carrier). The most commonly used vectors are plasmids (circular DNA molecules that originated from bacteria), viruses, and yeast cells. Plasmids are not a part of the main cellular genome, but they can carry genes that provide the host cell with useful properties, such as drug resistance, mating ability, and toxin production. They are small enough to be conveniently manipulated experimentally, and, furthermore, they will carry extra DNA that is spliced into them.

Recombinant DNA technology


Recombinant DNA technology, joining together of DNA molecules from two different species that are inserted into a host organism to produce new genetic combinations that are of value to science, medicine, agriculture, and industry. Since the focus of all genetics is the gene, the fundamental goal of laboratory geneticists is to isolate, characterize, and manipulate genes. Although it is relatively easy to isolate a sample of DNA from a collection of cells, finding a specific gene within this DNA sample can be compared to finding a needle in a haystack. Consider the fact that each human cell contains approximately 2 metres (6 feet) of DNA. Therefore, a small tissue sample will contain many kilometres of DNA. However, recombinant DNA technology has made it possible to isolate one gene or any other segment of DNA, enabling researchers to determine its nucleotide sequence, study its transcripts, mutate it in highly specific ways, and reinsert the modified sequence into a living organism.

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Friday, February 9, 2018

Isolating DNA fragments


Materials:
0.8 % agarose gel in 1x TAE
Digested DNA
Glass Milk
NaI solution
New Wash

Procedure:
1) Run digested DNA out on agarose gel slowly (70 V on BioRad gel)
2) Use long wave UV lamp to visualize bands. Cut out band with scalpel. Cut smallest possible piece.
3) Put gel slice in an eppendorf tube and weigh to figure out volume of gel slice. (empty tube approx. 1 g).
4) Add 3 vol of NaI solution (gel slice is usually ~200 mg, therefore, add 600 ul NaI).
5) Melt gel slice in 55 degree water bath.
6) Add 5 ul glass milk and mix (vortex glass milk vigorously to resuspend before adding to DNA mx). Incubate on ice ~5 min.
7) Spin down glass milk quickly. Decant. Add 1 ml New Wash and vortex. Do a total of 3 washes.
8) Spin down hard to pellet glass milk. Aspirate off liquid and air dry.
9) Resuspend pellet in 30-50 ul TE pH 7.5. Heat at 55degrees for 5 min.
10) Spin down glass milk and save supernatant. This is your DNA.

NaI solution
Mix 90.8 g NaI and 1.5 g Na2SO3 (note: sulfite!) to a final volume of 100 ml (cover with foil while stirring, light sensitive). Filter through #1 Whatman paper add 0.5 g Na2SO3. Store in dark at 4degreesC.
New Wash for 500 ml
50% EtOH 250 ml
0.1 M NaCl 2.92 g
10 mM Tris 7.5 5 ml 1M
1 mM EDTA 1 ml 0.5 M


E. coli Transformation


Long
1) Get 200ul aliquots of E. coli (DH5a for normal transformation or DE3 for expression) from -80C freezer and let thaw on ice.
2) Add DNA
For plasmid: 1ul DNA desired
For ligation: 10ul ligation reaction
-Also include a negative control with no DNA.
3) Incubate for 30min on ice.
4) Heat shock for 90sec at 42C.
5) Incubate for 1min on ice.
6) Add 1ml LB.
7) Agitate at 37C for 45min – 2hrs (1hr is good).
8) Spin down and pour off LB leaving ~100ul.
9) Resuspend cells in the ~100ul.
10) Plate the entire suspension on appropriate prewarmed plates.
11) Incubate at 37C overnight.

Short
Note: Use for amplifying AmpR plasmids only.
1) Get 200ul aliquots of E. coli (DH5a) from -80C freezer and let thaw on ice.
2) Aliquot 50ul of cells into tubes.
3) Add 1ul DNA desired.
4) Incubate on ice 5min-30min.
5) Plate on prewarmed LB-Amp plates. (Plate the whole thing--no spinning, no nothing).
6) Incubate at 37C overnight.
Blue/White Selection
-Used for plasmids like Bluescript.
-No insert=Blue. Insert=White.
-Do long transformation of ligations basically as described above.
-While cells are agitating,
A) Spread X-Gal and IPTG on plates.
X-Gal (50mg/ml): 20ul
IPTG (1M): 10ul
B) Incubate at 37C to dry (about 30min).

E. coli Miniprep


1) Grow 2ml culture o/n.
2) Spin down. Pour off all but ~100ul of sup. Resuspend cells in the ~100ul.
3) Add 130ul P1. Resuspend.
4) Add 130ul P2. Mix immediately.
5) Add 182ul N3. Mix immediately.
6) Spin 10 min at 4C. (Removes genomic DNA and debris).
7) Transfer sup to a fresh eppendorf.
8) Add 900ul ice-cold 100% EtOH (bottom shelf in door of -20C freezer). Mix thoroughly.
9) Spin 15min at 4C. Discard sup.
10) Wash pellet once with ~400ul ice-cold 70% EtOH.
11) Dry pellet on rack or in speedy-vac.
12) Resuspend in 50ul water. Use 3-10ul for digest.

Molecular Biology Protocols Online




One-Tube Isolation of DNA from Mouse Tails
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot093534
   
   
Buffers
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.top098210
   
   
Caring for Escherichia coli
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot101337
   
   
Protein Immunodepletion and Complementation in Xenopus laevis Egg Extracts
Christopher Jenness, 

David J. Wynne, 

and Hironori Funabiki
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot097113
   
Analysis of Mitotic Checkpoint Function in Xenopus Egg Extracts
Yinghui Mao
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot099853
   
Transformation of Schizosaccharomyces pombe in a 96-Well Format
Assen Roguev, 

Jiewei Xu, 

and Nevan J. Krogan
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot091942
   
   
DNA Preparation from Schizosaccharomyces pombe
Assen Roguev, 

Jiewei Xu, 

and Nevan J. Krogan
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot091959
   
   
Preparation of Plasmid DNA by Alkaline Lysis with Sodium Dodecyl Sulfate: Maxipreps
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot093351
   
   
A Single-Step Method for the Simultaneous Preparation of DNA, RNA, and Protein from Cells and Tissues
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot093500
   
   
Gateway Recombinational Cloning
John S. Reece-Hoyes
   
and Albertha J.M. Walhout
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.top094912
   
   


Propagating Gateway Vectors

John S. Reece-Hoyes
   
and Albertha J.M. Walhout
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot094920
   
   
Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone
John S. Reece-Hoyes
   
and Albertha J.M. Walhout
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot094938
   
   
Using Multisite LR Cloning to Generate a Destination Clone
John S. Reece-Hoyes
   
and Albertha J.M. Walhout
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot094946
   
   
Preparation of DNA from Embryonic Stem Cells or Other Cultured Cells
Richard Behringer, 

Marina Gertsenstein, 

Kristina Vintersten Nagy, 

and Andras Nagy
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot092718
   
   
Analysis of DNA Methylation in Mammalian Cells
Paul M. Lizardi, 

Qin Yan, 

and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.top094821
   
   
Methylation-Specific Polymerase Chain Reaction (PCR) for Gene-Specific DNA Methylation Detection
Paul M. Lizardi, 

Qin Yan, 

and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094847
   
   
Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis
Paul M. Lizardi, 

Qin Yan, 

and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094854
   
   
High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation
Paul M. Lizardi, 

Qin Yan, 

and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094862
   
   
Preparation of Single-Stranded Bacteriophage M13 DNA by Precipitation with Polyethylene Glycol
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot093419
   
   
Growing Bacteriophage M13 in Liquid Culture
Michael R. Green
   
and Joseph Sambrook
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot093435
   
   


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Tuesday, February 6, 2018

Tailed spider trapped in 100-million-year old amber offers insight in evolution

A spider-like creature bearing a long tail has been discovered in an amber from Myanmar dating back about 100 million years.
"There's been a lot of amber being produced from northern Myanmar and its interest stepped up about ten years ago when it was discovered this amber was mid-Cretaceous," said Paul Selden, a palaeontologist at the University of Kansas and an author of a paper on the ancient arachnid.
"Therefore, all the insects found in it were much older than first thought," Selden told the university in an interview.
The finding is published Monday in a paper in Nature Ecology & Evolution by an international team of researchers from the United States, China, Germany and the United Kingdom.
According to the paper, the creature shares many similarities with modern spiders including fangs, eight legs and silk-producing spinners.
Moreover, it also bears a long flagellum, or a tail, at its rear, which is not commonly seen among modern spiders.
Thought the ancient arachnid has a tiny body, only about 2.5 millimeters long, it had a tail nearly twice of its body length.
"Any sort of flagelliform appendage tends to be like an antenna," Selden said, "It's for sensing the environment. Animals that have a long whippy tail tend to have it for sensory purposes."
The tailed arachnid, named Chimerarachne after the Greek mythological Chimera, documents a key transition stage in spider evolution.
Previously, Selden and his colleagues had found similar insects without spinnerets from the much older Devonian and Permian periods.
"That's why the new one is really interesting, apart from the fact that it's much younger -- it seems to be an intermediate form," Selden said.
"In our analysis, it comes out sort of in between the older one that hadn't developed the spinneret and modern spider that has lost the tail," he added.

Cloned monkeys could help development of drugs for human brain diseases

Chinese scientists' successful cloning of monkeys could eventually help the development of new drugs to treat human diseases, like brain and nervous system problems, a leading Chinese neuroscientist said.
At the end of 2017, a non-human primate research facility under the Beijing-based Chinese Academy of Sciences (CAS) produced two cloned macaques.
Allaying fears that cloning monkeys for research could ultimately lead to human cloning, Poo Muming, director of the Institute of Neuroscience at CAS, told Xinhua, "We have no intention to clone humans."
The macaque cloning was done for a humane reason, he said: "Because this is the species that will really help human health and cure human disease."
The cloning will reduce the use of large numbers of primates for research, especially in the West.
In 2016, the United States used over 71,000 primates for research or experimentation, according to the U.S. Department of Agriculture's animal and plant health inspection service.
U.S. pharmaceutical companies import at least 50,000 monkeys every year to test the efficacy of different drugs and determine safe doses for human clinical trials, Poo said.
"That is a huge number of monkeys used, which you should consider unethical," he said.
Since these monkeys have diverse genetic backgrounds, researchers must use a large number to make sure that the observed effects are due to treatment and not because of the genetic variation.
"Cloning is really the way to go," Poo said. "Because it reduces the interference (of) the diversity of genetic background on drug development. So it is for (that) ethical reason that we (have cloned) monkeys."
Darren Griffin, genetics professor at the University of Kent, holds the same view.
"If they can produce these cloned animals that means that you could use fewer animals for ... research, rather than the number being used at the moment," he said in a previous interview with Xinhua.
At present, the medical community mostly uses mice as a model to research cures for human diseases. But for many diseases, especially brain diseases, drugs that are developed using mice as model have failed clinical trials in humans, Poo said.
"Basically all big pharmas have given up developing neuro drugs," he said, citing two decades of drug development failure, with hundreds of billions of dollars spent on each drug.
"Next, we want to develop clones of animals that carry brain disorders," he said, especially degenerative or development diseases that have clear genetic causes.
Poo said he would like to focus on Alzheimer's, Parkinson's, autism and ALS, a nervous system disorder that causes disability.
Regarding the debate on the ethics of non-human primate cloning, he said every new technology is a two-edged sword: "There will be discussions and we'll see how the society deals with it."
In the 1970s, when genetic engineering technology first came out, he said everybody was worried about its harmful effect on humans.
"But so far, it has been 40 to 50 years and you don't see any real problem yet," he said.
"Cloned monkeys could be very valuable in studying specific aspects of human disease," said Tom Holder, director of Speaking of Research, an international organization that supports the use of animals in scientific labs.
"The breakthrough has shown that it is possible," Holder said in an emailed interview to Xinhua. "But it is too early to make any conclusions on whether the method will be able to be repeated efficiently and reliably."
Holder also said non-human primate research is subject to increased ethical and welfare considerations and is generally used only when other species are unsuitable for the research.

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