Sunday, March 25, 2018

Biodiversity worsens all over the world

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

Another Inoutscripts Scamming Script? Inout Scripts Adserver's 1 error and 134 warnings


I checked the Inout Scripts Adserver script with http://infohound.net/tidy/. To my surprise, there are still 1 error and 134 warnings with it after 15 months troubleshooting with Inoutscripts supporters Nair and Saranya.

In addition, most of the addons are not working at all.

The inoutscripts software has security vurnerability. It had been attacked 3 times.

These Inout Scripts Scammers had never got these bug fixed. They just took cash and left me nothing working.

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.

Friday, February 9, 2018

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

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      • Propagating Gateway Vectors