SAMPLE OF SCIENCE EDITORIAL

Doors and Pores

The awesome architecture of the gateways to the nucleus
By Mary Beth Aberlin | December 1, 2016
1839
Hobbit houses, jigsaw puzzles, and nuclear pores have a lot more in common than
you might think.

In 1937, J.R.R. Tolkien introduced his dearly beloved hobbits as a little people,
about half our height, and smaller than the bearded Dwarves. Their domiciles had
a perfectly round door like a porthole, painted green, with a shiny yellow brass knob
in the exact middle. The door opened on to a tube-shaped hall like a tunnel. Not
such a bad description of nuclear pore complexes either, those intricately
constructed portals that pierce the double membrane enveloping the nucleus and
control traffic into and out of the organelle. Of course, the aptness of the analogy
has a lot to do with the level of magnification (not to mention imagination). But you
can judge for yourself in this months issue, with illustrations that go from a 3-D
model pieced together from electron micrographs in 1992 (Foundations) to the
zoomed-in photo on this months cover and all the way down to the molecular twists
and turns derived from X-ray crystallography in Nuclear Pores Come Into Sharper
Focus.

While Tolkien enthusiasts can YouTube how to construct a hobbit door (very tricky to
hang, hinge-wise), structural biologists didnt design the object of their fascination
their task is to decode how it is built. Awe is the only appropriate response to the
architectural masterpiece that is emerging.

Which brings me to jigsaw puzzles. I love doing them, the bigger the better. But the
pieces I fit together are two-dimensional, and 3-D puzzles boggle my mind. Nuclear
pore complexes raise jigsawing to a far more rarified level. In their feature, Daniel
Lin and Andr Hoelz describe these massive molecular machines as put together
from more than 1,000 protein subunits with a total molecular mass of
approximately 120 million daltonsthe equivalent of more than 6.5 million water
molecules. The subunits self-assemble to form more than 30 types of nucleoporin
proteins, 17 of which constitute the beautifully symmetric three-ringed core of the
nuclear pore complex. Through the pores central channel smaller molecules enter
and exit by diffusion while proteins or ribosomal units in their native states hop a
ride on cargo ships known as karyopherins.
The study of another cellular envelope has been the research passion of Satyajit
Mayor, this months profilee (Pushing Boundaries). His fascination with the
organization and function of the plasma membrane began with his study of
glycoproteins tethered to the outer surface of a parasite. He now investigates the
nanoscale organization of such proteins and the role of the cytoskeleton in that
organization.

All of these exciting discoveries owe much to technical innovations, which we take
stock of in our ninth annual Top 10 Innovations competition. Assembled by Senior
Editor Bob Grant, this years panel of independent judges evaluated submissions of
products or techniques new to the market from fall 2015 to fall 2016. Given the
buzz surrounding CRISPR technology, its no surprise that several products that
facilitate the technique made the final list. Ditto for sequencing tools and methods
that enhance the evaluation of new drugs. But the number one spot goes to a
method for doing Western blots in single cells. (See Top 10 Innovations of 2016.)

Whether its zeroing in on single cells or individual nuclear pores, as more and more
life science puzzles are fit together, we look forward to covering the story.

-Mary Beth Aberlin Editor-in-Chief

SAMPLE OF SCIENCE NEWS

3-billion-year-old crystals hint at lost continents

fate
Volcanoes, shifting plates caused Mauritia to
crumble
BY THOMAS SUMNER 11:00AM, JANUARY 31, 2017
rocky outcrop on Mauritius

LOST WORLD Tiny crystals found inside rocky outcrops such as this one on the
Indian Ocean island of Mauritius are shards of a long-lost continent called Mauritia,
researchers propose.

SUSAN J. WEBB/UNIVERSITY OF THE WITWATERSRAND

Relics of a long-lost continent may lurk beneath the Indian Ocean.

Tiny zircon crystals coughed up by volcanic eruptions on the island of Mauritius are
around 2.5 billion to 3 billion years old. Thats billions of years older than the island
itself, researchers report January 31 in Nature Communications. The zircons, the
researchers propose, are remnants of an ancient continent called Mauritia that
formed part of the nexus of Madagascar and India before the two landmasses split
apart around 84 million years ago (SN: 1/21/17, p. 18).

Comparing the crystals ages with those of nearby landmasses, petrologist Lewis
Ashwal of the University of the Witwatersrand, Johannesburg and colleagues
retraced Mauritias fate. Volcanic eruptions and shifting tectonic plates fragmented
Mauritia, the researchers say, and the land was eventually buried under thick layers
of lava. Some of that land, including the zircon crystals, was recycled into the rising
plume of magma that fueled the eruptions that eventually built Mauritius.

A handful of zircons dating back nearly 2 billion years had already been uncovered
in the islands sands. Some scientists raised concerns that those crystals were
brought to the island from elsewhere as part of ship ballast or construction material.
Ashwal and colleagues pried the newfound crystals from rocky outcrops on the
island, erasing any doubts of the zircons origins.

SAMPLE OF SCIENCE FEATURE

DNA sequencing in the palm of your hand
22 January 2017
Posted by KERSTIN GPFRICH.

It is
smaller
and
lighter than your smartphone, it plugs into your laptop with a standard USB cable
and its been to space. What is it? A new DNA sequencer. I tried it out with a bunch
of schoolkids in a classroom an experiment which would have been carried out in
large sequencing centres at an unaffordably high cost until just a few years ago.

Think of a technology that has been improved tremendously over the course of your
own lifetime. I wouldnt be surprised if computers came to your mind. A room-filling
apparatus used mainly by the army has been transformed into an omnipresent
consumer product. Your smartphone can do what large computers were struggling
with just a decade ago. After all, computing power is doubling every two years. And
yet, computers are outpaced by DNA sequencers in many respects.

How DNA sequencing started

DNA stores the information of life in the form of the bases A, T, C and G a bit like
computers store information in a string of the numbers 0 and 1. Volumes of natural
history are written in the ancient alphabet of life, which we are starting to decipher
with DNA sequencers.

DNA sequencing means reading the order of the letters A, T, C and G of the genetic
code. It started in the 1960s, soon after the discovery of the iconic double helix. The
scientific efforts were fuelled by the hope that a better understanding of our
genomes would open up an era of personalised medicine, allowing unprecedented
opportunities to diagnose and treat disease. It wasnt until 2003 that the first
complete human genome, the three billion bases of our own genetic code, were
read. This mammoth project required 13 years of work carried out by 150 scientists
with a budget of three billion dollars. Today, just 13 years later, the same task can
be carried out in about a day for just a thousand dollars. DNA sequencers now fit
into my back pocket! The technology that enabled this sudden miniaturisation is
shortlisted for the Breakthrough of the Year 2016 award by the Science magazine.

DNA my smoothie!

I had the chance to try a DNA sequencer out with Kim Judge from the Wellcome
Trust Sanger Institute. Together, we set out to challenge the kids at the Perse School
in Cambridge to sequence some real DNA. But what were we going to sequence?
DNA is in every living creature we know, so choices were vast. The kids? Ethically
questionable. Some bacteria? Too boring. Then Kim suggested sequencing a fruit
smoothie!

In the morning I prepared a smoothie with some mystery ingredients. Before Kim
arrived, the kids helped me to get the DNA out of the smoothie. In a laboratory, we
would carefully follow a refined procedure, but in the classroom, a quick and dirty
method with household ingredients and equipment had to do the job.

What we ended up with looked, quite frankly, like a bit of whitish, stringy snot.
Thats the DNA from the fruit in the smoothie. It should contain all the information
we need to recover what went into the drink. Kim helped us dissolve the DNA in
water and added some chemicals necessary for the sequencing process. With a
pipette, we squirted some of the DNA into an opening on the DNA sequencer, which
was plugged into a laptop.

What we couldnt see is that, inside the sequencing device, there is an array of
invisibly small channels called nanopores. When a strand of DNA is pulled through
these nanopores, the DNA blocks part of the current which flows across it. Since the
bases A, T, C and G are all slightly different, they cause slightly different blockades,
which directly appear as different levels on the computer screen. A bit like different
levels in sheet music correspond to different notes, these levels correspond to
different combinations of DNA bases. This data is analysed on the Cloud and then
sent back to the user as a spreadsheet full of the letters A, T, C and G. Depending
on how much DNA there is to read, this can take anywhere from minutes to days.
We left the sequencer to run overnight.

My PhD has taught me that experiments dont often work the first time you try, but I
was pleasantly surprised. Some of our DNA sequences we got back were of high
enough quality that we could copy them into an online DNA database to compare it
to the DNA of plants that have previously been sequenced. So what was in our
smoothie? Thats for you to find out! Click here to have a go for yourself. Just to set
your expectations the school kids did get it right!

What can we do with a portable sequencer?

I certainly had fun with our DNA smoothie experiment, but to be fair, our taste buds
may have given a quicker answer. So what difference is a portable, real-time DNA
sequencer really going to make? Think of the horsemeat scandal. There is no better
way to find out and to be absolutely certain what is in your food than to look at the
DNA. Think of all the food you throw away because it might have gone bad. A DNA
test would easily reveal if your soup is still safe to eat or, in remote places, if water
is safe to drink. The same sequencer we had for our smoothie experiment is
currently used to monitor the Zika epidemic in Brazil. The kids had their own ideas:
I would go to the jungle because theres loads of different species and you could
just find their origins. Ecologists are using nanopore sequencing for precisely this
purpose. But in 2016 DNA sequencers have made it even further away from our
laboratories. For the first time, DNA has been sequenced in space on the
International Space Station. Again, an experiment that worked the first time it was
attempted. Sequencing in space what sounds like an expensive marketing gag -
may actually be extremely useful, according to Dr. Aaron Burton who is involved in
the NASA project.

For the crew health standpoint, if you have a sequencer you can identify microbes
in air, surfaces, and water and make sure that everythings safe. he states.

Sounds sensible. But what about more alien endeavours? In the future we may even
be able to look for DNA on other planets. All life we know has DNA, so it will be
interesting to discover if DNA is really the blueprint of life across the universe. And
even if it isnt, nanopore sequencers cannot only sequence DNA. They have been
used to determine the sequence of DNAs cousin RNA and even of proteins.
You can imagine that if you had alien life that used a different alphabet you would
still be able to pass those molecules through the nanopore and get that the change
in current would be diagnostic of an informational molecule going through it, says
Aaron.

What will the future bring?

DNA sequencing has come on a long way: from a billion dollar multinational project
into the palm of your hand within 20 years. But where will this technology take us?
It could open up the ability to sequence your own DNA, which opens up a can of
ethical dilemmas and uncertainty. Would you like to know about a genetic problem
with no cure? And could employers or insurance companies demand this
information? Sequencing, however, could also change our ability to monitor food
production, and track disease outbreaks, which could save lives. Like computers,
DNA sequencers have the power to change our world we just need to make sure
its for the best.

SAMPLE OF SCIENCE COLUMN

Gazing Into Danakil Depressions Mirror, and Seeing Mars Stare Back
By AMY YEEJAN. 30, 2017
In pools of water in the Danakil Depression, the combination of heat, high acidity
and sulfur concentrations causes bright yellow chimneys to form. Credit Carl
Court/Getty Images

DANAKIL DEPRESSION, Ethiopia In oppressively dry heat and a miasma of sulfur

and chlorine, the rocky landscape sprouts patches of neon green and yellow that
resemble oozing scrambled eggs.

Near-boiling pools of acidic water bubble between odd formations of rocks and
minerals: white beehive-shaped mounds of salt, yolk-colored lattices of sulfuric
crust, purplish-red crumbles. Nearby, iron-rich rock fans out into flat mushroom
shapes. The ground crackles hollowly underfoot and emits the hiss of bubbling
liquid. Cones and small mineral chimneys babble from one-holed spouts in alien
whispers.

Though it looks like an extraterrestrial scene, this landscape belongs to the Danakil
Depression, in a remote northeast region of Ethiopia aptly named Afar, near Eritrea.

About 100 meters below sea level, the Danakil Depression is one of the worlds
lowest places. It is also one of the hottest places on Earth, with average daily
temperatures of 34.4 degrees Celsius (93.9 degrees Fahrenheit) and only about 100
millimeters of rain each year.

This volcanic region is known as a geological wonder. Indeed, most of the relatively
scant scientific research on the Danakil Depression involves its fantastical geology,
not its biology. Now, scientists are studying this area to understand the possibilities
of life on other planets and moons, despite the regions political volatility and
sporadic violence between Ethiopia and Eritrea. This month, a team of
astrobiologists from Europlanet, a consortium of research institutions and
companies doing planetary research, returned to study the depressions geology,
mineralogy and especially its biology, as an analogue to Mars.

Continue reading the main story

RELATED COVERAGE

Visions of Life on Mars in Earths Depths SEPT. 12, 2016

interactive
Mars Curiosity Rover Tracker AUG. 5, 2013
Felipe Gmez Gmez of the Centro de Astrobiologa in Madrid led the teams first
expedition last spring to study Danakils extremophiles, microbes that live in
extreme conditions. Researchers from Madrid and the University of Bologna and the
International Research School of Planetary Sciences, both in Italy, assisted by
scientists from the University of Mekelle in Ethiopia, are isolating and identifying the
hardy bacteria that thrive in this hostile environment of heat, acidity and salinity.
A camel caravan in the Danakil Depression in Ethiopia last week. Credit Carl
Court/Getty Images
The aim is to try to know the limits of life and the possibility of such forms of life in
other planets like Mars, said Dr. Gmez, who is part of the science team of
Curiosity, the NASA exploration rover that landed on Mars over four years ago.

He has also studied other extremophiles, such as microbes that thrive in the acidic
iron-rich Ro Tinto in southwestern Spain. For that research, he and his colleagues
exposed an acidophile to simulated Mars conditions, described in a 2010 paper in
the journal Icarus.

Knowledge from Danakil could be applied to Mars missions. Studying Danakils

microbes is a way to train ourselves to identify different forms of life for
astrobiological exploration, Dr. Gmez said. While Mars today has subfreezing
temperatures, its origins are volcanic and might be similar to the early history of
Earth.

There is also a broader goal of exploring ways to identify signs of life in extreme
environments. What is life? What are the limits of life? Scientists dont agree on
what is life, Dr. Gmez said. If we find life on Mars, would we be able to recognize
it? We dont know.
The Danakil Depression, a rift valley stretching from the Dallol volcano in Ethiopia to
the salt plains of Lake Assal in Djibouti, lies at the convergence of three tectonic
plates that are slowly separating. As the earth pulls apart and thins over
millenniums, the land sinks.

Thousands of years ago, the larger Danakil Desert was part of the Red Sea. But
volcanic eruptions formed rock barriers and created an inland sea that eventually
evaporated in the intense heat. Vast salt flats and salt lakes remain and are still
mined by the nomadic Afar tribes, who transport salt slabs from Danakil by camel
caravan.

Dallol, which means disintegration in the Afar language, is the section that is home
to colorful, otherworldly formations. Here, magma heats groundwater, which wells
up and dissolves salt, potash and other minerals when emerging through hot
springs. Brine evaporates, leaving crusty formations colored by minerals, iron and
salt-thriving halophile algae to create this multicolored scenery.

Some pools of water reach 90 degrees Celsius. The combination of heat, high acidity
and sulfur concentrations causes bright yellow chimneys to form. Other pools of
water heated to 40 degrees Celsius take on a turquoise hue from copper salts.

Europlanet researchers last year took water samples from salt chimneys, blue and
red pools, and yellow and brown crust. Although halophiles microbes that thrive
in saline conditions have been identified in Dallol, this new research is the first to
focus on microbes thriving in extreme acidity and heat, in addition to salinity, Dr.
Gmez said.

Researchers are isolating bacteria and their DNA and also doing genetic sequencing
to identify the bacteria. Among them are chemolithotrophs micro-organisms that
acquire energy from inorganic compounds that were found in the hot water on
the mineral chimneys. These microbes do not require sunlight for energy and are
usually found in extreme environments like hydrothermal vents on the seafloor.

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These simple organisms can survive with a very small battery, and were probably
among the first bacteria on Earth, Dr. Gmez said. That is what makes them so
interesting from an astrobiological point of view.

Chemolithotrophs can use inorganic reduced compounds like sulfide, elemental

sulfur, hydrogen and ammonia as energy sources, and can grow without organic
compounds and light. Scientists believe this kind of metabolism happens only with
prokaryotes, microbes without a nucleus.

Sulfur is abundant in Dallol because the area was covered by the sea ages ago.
Here, sulfur vapor steams from chimneys on the ground. In dark submarine depths,
sulfur can be the main energy source for certain bacteria living far from sunlight. In
Dallol, these sources of sulfur are within arms reach on the Earths surface.

Scientists are still studying their first samples from Danakil, but we know there is
life, Dr. Gomez said.

This winters expedition will focus on bacterias relationship with the atmosphere.
Researchers will set up weather stations to record wind, temperature, humidity and
more, to study the environment completely, like what Curiosity does on Mars, Dr.
Gmez said. In this case, though, scientists will not have to leave Earth to do so.