Text Annotating and Resume

English Class D1

Ghaitsa Zahira Shofa

183221051

Biology-Faculty of Science and Technology

Text 1

What Makes a Carrot Orange?

New Findings Could Lead to
Improved Health Benefits
TOPICS:AgricultureGeneticsNorth Carolina State UniversityPlants
By NORTH CAROLINA STATE UNIVERSITY NOVEMBER 26, 2023

A new study has uncovered that three recessive genes are responsible for the orange color in
carrots, offering insights into carrot breeding and health benefits. The research traces the
carrot’s journey from its Asian origins in the 9th century to the prevalence of orange carrots
in Europe from the 15th century, emphasizing their appealing color and flavor.

A study of the genome provides insights into pigmentation

and domestication.

A recent study analyzing the genetic sequences of over 600 carrot varieties has
revealed that the orange color in carrots is determined by three specific genes.
Interestingly, for carrots to display this orange hue, these genes must be in a
recessive state, essentially switched off. This discovery offers valuable insights into
key traits for enhancing carrots, potentially leading to improved health benefits from
this vegetable.

“Normally, to make some function, you need genes to be turned on,” said Massimo
Iorizzo, an associate professor of horticultural science with North Carolina State
University’s Plants for Human Health Institute and co-corresponding author of a
paper describing the work, published in Nature Plants. “In the case of the orange
carrot, the genes that regulate orange carotenoids – the precursor of vitamin A that
have been shown to provide health benefits – need to be turned off.”

Carrots and Health: A Colorful Connection

Carrots, especially orange carrots, contain high quantities of carotenoids, which can
help reduce the risk of diseases like eye disease. The orange carrot is the most
abundant plant source of pro-vitamin A in the American diet.

NC State researchers worked with colleagues from the University of Wisconsin-

Madison to sequence 630 carrot genomes in a continuing examination of the history
and domestication of the orange carrot; a 2016 study published in Nature Genetics by
these researchers provided the first carrot genome sequence and uncovered the gene
involved in the pigmentation of yellow carrot.

Massimo Iorizzo examines orange carrots to learn more about their pigmentation and
domestication. Credit: Photo courtesy of Massimo Iorizzo

The researchers performed so-called selective sweeps – structural analyses among

five different carrot groups to find areas of the genome that are heavily selected in
certain groups. They found that many genes involved in flowering were under
selection – mostly to delay the flowering process. Flowering causes the taproot, the
edible root that we consume, to turn woody and inedible.

Selection and Domestication of the Orange Carrot

“We found many genes involved in flowering regulation that were selected in
multiple populations in orange carrot, likely to adapt to different geographic
regions,” Iorizzo said.
The study also adds further evidence that carrots were domesticated in the 9th or
10th century in western and central Asia.

“Purple carrots were common in central Asia along with yellow carrots,” Iorizzo said.
“Both were brought to Europe, but yellow carrots were more popular, likely due to
their taste.”

Orange carrots made their appearance in Western Europe in about the 15th or 16th
century. The orange carrot may have resulted from crossing a white and yellow
carrot, Iorizzo said.

“This study basically reconstructed the chronology of when carrot was domesticated
and then orange carrot was selected,” he said. “Orange carrot could have resulted
from white and yellow carrot crosses, as white and yellow carrots are at the base of
the phylogenetic tree for the orange carrot.”

The Rise of the Orange Carrot

The color and sweeter flavor of the orange carrot drove its popularity and farmers
selected for those traits. Different types of orange carrots were developed in northern
Europe in the 16th and 17th centuries, which matches the appearance of different
shades of orange carrots in paintings from that era. Orange carrots later grew in
popularity as a greater understanding of alpha- and beta-carotenes, the precursor of
vitamin A in the diet, progressed in the late 19th and early 20th centuries.

“Carotenoids got their name because they were first isolated from carrots,” Iorizzo
said.

Reference: “Population genomics identifies genetic signatures of carrot

domestication and improvement and uncovers the origin of high-carotenoid orange
carrots” by Kevin Coe, Hamed Bostan, William Rolling, Sarah Turner-Hissong, Alicja
Macko-Podgórni, Douglas Senalik, Su Liu, Romit Seth, Julien Curaba, Molla Fentie
Mengist, Dariusz Grzebelus, Allen Van Deynze, Julie Dawson, Shelby Ellison, Philipp
Simon and Massimo Iorizzo, 28 September 2023, Nature Plants.
DOI: 10.1038/s41477-023-01526-6

Philipp Simon from the University of Wisconsin-Madison is the paper’s co-

corresponding author. Kevin Coe, Hamed Bostan, William Rolling, Sarah Turner-
Hissong, Alicja Macko-Podgórni, Douglas Senalik, Su Liu, Romit Seth, Julien
Curaba, Molla Fentie Mengist, Dariusz Grzebelus, Allen Van Deynze, Julie Dawson
and Shelby Ellison co-authored the paper.

The research was supported by National Institute of Food and Agriculture, U.S.
Department of Agriculture (NIFA-USDA), under award numbers 2016-51181-25400,
2022-51181-38321 and Hatch project 1008691.
Resume Text:

Carrot is well-known as a vegetable that have an orange color. This orange color is
from a pigment named carotenoid (first time detected in carrot, so they named it caroten), that
also known have a great benefits for our eyes. But appearently, carrot is not just exist in one
color-that is orange-, but some varieties has other color like purple. It means there are some
genes in carrot that affected to the color of carrots. After in some research, finally found that
the color of an orange carrot is affected by three recessive genes sequences. We have to turn
off the dominant genes, so the orange color of carotenoid will appeared. Some researcher
estimated that orange carrots was exist after a crossing a white and yellow carrot, so it made
new varieties, that have an intermediet color between white and yellow parental.
Text 2

Scientists Discover That Worms

May Have “Emotions”
TOPICS:BrainGeneticsNeuroscience
By NAGOYA CITY UNIVERSITY NOVEMBER 17, 2023

Recent research on Caenorhabditis elegans suggests that even simple organisms can exhibit
basic emotions. This study, which combines behavioral observations and genetic analysis,
offers significant insights into the genetic basis of emotions, potentially aiding in the
understanding and treatment of human emotional disorders.

Insights into how short-term stimulation can alter sustained

brain activities and their underlying processes.

Brain research is one of the most crucial fields in modern life sciences, and “emotion”
is one of its major topics. Traditionally, the study of emotions in animals has been a
complex area, predominantly examining fear responses in mice and rats.

However, since the 2010s, it has been increasingly reported in scientific papers that
even crayfish and flies may have brain functions resembling emotions by focusing on
several characteristics of their behavior, such as persistence and valence.

For instance, when an animal experiences a dangerous situation like being attacked
by a predator (a negative valence) even for a short period, the animal’s behavior may
be to stay in a safe place, ignoring normally attractive smells of food even if hungry,
for a certain length of time (persistence), which can be regulated by a primitive form
of emotion.

However, the details of these fundamental “emotion mechanisms” remain largely

undisclosed.

Research on Emotions in Roundworms

An international research team from Nagoya City University (Japan) and Mills
College at Northeastern University (USA) has revealed the possibility that the
roundworm Caenorhabditis elegans possesses basic “emotions.”

They used the worms because worms have been used for detailed analysis of basic
functions such as perception, memory, and even decision-making at cellular and
genetic levels. The team initially discovered that when worms are subjected to
alternating current stimulation, worms start moving at an unexpectedly high speed.

Illustration of behavioral responses of worms to electric stimulus. Credit: Kristina Galatsis

Interestingly, the team also found that this “running” response persisted for 1-2
minutes even after the electrical stimulation for a few seconds was terminated.

In animals in general, when a stimulus is stopped, the response to that stimulus

usually ceases immediately. (Otherwise, the perception of stimuli such as sounds or
visual scenes would linger.) Therefore, the reaction of “continuing to run even after
the stimulus stops” is exceptional.

Behavioral and Genetic Analysis of Emotional Responses in Worms

Furthermore, during and after the electric stimulation, the team found that the
worms ignore their food bacteria, which provide crucial environmental information.
This suggests that while the presence or absence of their food bacteria is usually
crucial, the danger posed by electrical shocks, a survival-threatening stimulus, is
even more important.

In other words, when worms sense the dangerous stimulus of an electrical shock,
their highest survival priority is to escape from that location. To achieve this, the
brain’s functioning seems to persistently change, including ignoring the usually
significant “food” in order to escape danger.

This suggests that the phenomenon of “worms continuing to run due to short-term
electrical stimulation” reflects basic “emotions.”

Implications for Understanding Human Emotions

Furthermore, through genetic analysis, particularly leveraging the advantages of

worms, the team revealed that mutants unable to produce neuropeptides, equivalent
to our hormones, exhibited a longer duration of continuous running in response to
electrical stimulation compared to normal worms.

This result indicates that the continuous state in response to danger is regulated to
end at the appropriate time.

Indeed, if we experience excitement or fear that persists for a very long period, it
disrupts our daily lives. Therefore, the findings suggest that our emotions, such as
“excitement,” “happiness,” or “sadness,” induced by stimuli, may not be naturally
destined to fade away with time, but are controlled by an active mechanism involving
genes.

This study demonstrates that using worms can offer detailed insights into the genetic
mechanisms underlying primitive “emotions”. Many of the genes at work in worms
are known to have counterparts in humans and other organisms, so studying worms
can offer significant clues about the genes involved in the basis of “emotions.”

Specifically, conditions like depression, classified as mood disorders, can be

interpreted as states where negative emotions are excessively and persistently
maintained due to the inability to effectively process experienced stimuli. If novel
genes related to emotions are discovered through worm research, these genes could
potentially become targets for new treatments of emotional disorders.

Reference: “Electric shock causes a fleeing-like persistent behavioral response in the

nematode Caenorhabditis elegans” by Ling Fei Tee, Jared J Young, Keisuke
Maruyama, Sota Kimura, Ryoga Suzuki, Yuto Endo and Koutarou D Kimura, 18
August 2023, Genetics.
DOI: 10.1093/genetics/iyad148

The study was funded by the Japan Society for the Promotion of Science, Grant-in-
Aid for Research in Nagoya City University, the National Institutes of Natural
Sciences, the Toyoaki Scholarship Foundation, the Japanese Government (MEXT)
Scholarship, and the RIKEN Center for Advanced Intelligence Project (to K.D.K).

Resume Text:

Worm may have a condition that equal with their emotions. The emotions of worm is
a respons to a ccondition. From text, the research of worm’s emotions is studied about
worm’s behaviour about additional stimulus.
Text 3

Like Humans – Scientists Discover

That Rats Have an Imagination
TOPICS:BrainHoward Hughes Medical InstituteNeurosciencePopularProstheticsRats

By HOWARD HUGHES MEDICAL INSTITUTE NOVEMBER 4, 2023

Researchers have demonstrated that rats, through a novel brain-machine interface and virtual
reality system, can activate hippocampal activity patterns to imagine and navigate to
locations, similar to human imagination. This finding reveals animals’ ability to voluntarily
control their thoughts and could advance the study of memory and the development of
prosthetic devices.

As human beings, our lives are intertwined with our thoughts, whether we’re
contemplating dinner options or indulging in memories of our recent beach getaway.

Interestingly, scientists at HHMI’s Janelia Research Campus have discovered that

animals also have an imagination.
A group of researchers from the Lee and Harris laboratories devised an innovative
approach that fuses virtual reality with a brain-machine interface to explore the inner
thoughts of rats.

They found that, like humans, animals can think about places and objects that aren’t
right in front of them, using their thoughts to imagine walking to a location or
moving a remote object to a specific spot.

A team from HHMI’s Janelia Research Campus has developed a novel system combining
virtual reality and a brain-machine interface to probe the rat’s inner thoughts. The rat is
harnessed in the VR system. As the rat walks on a spherical treadmill, its movements are
translated on the 360-degree screen. The rat is rewarded when it navigates to its goal.
Credit: Chongxi Lai

Like humans, when rodents experience places and events, specific neural activity
patterns are activated in the hippocampus, an area of the brain responsible for
spatial memory. The new study finds rats can voluntarily generate these same
activity patterns and do so to recall remote locations distant from their current
position.

“The rat can indeed activate the representation of places in the environment without
going there,” says Chongxi Lai, a postdoc in the Harris and Lee Labs and first author
of a paper describing the new findings. “Even if his physical body is fixed, his spatial
thoughts can go to a very remote location.”

This ability to imagine locations away from one’s current position is fundamental to
remembering past events and imagining possible future scenarios. Therefore, the
new work shows that animals, like humans, possess a form of imagination, according
to the study’s authors.

At the same time that the rat is navigating in the VR arena, the BMI system records the rat’s
hippocampal activity. The researchers can see which neurons are activated when the rat
navigates the arena to reach each goal. These signals provide the basis for a real-time
hippocampal BMI, with the brain’s hippocampal activity translated into actions on the
screen. Credit: Chongxi Lai

“To imagine is one of the remarkable things that humans can do. Now we have found
that animals can do it too, and we found a way to study it,” says Albert Lee, formerly
a Group Leader at Janelia and now an HHMI Investigator at Beth Israel Deaconess
Medical Center.

A novel brain-machine interface

The project began nine years ago when Lai arrived at Janelia as a graduate student
with an idea to test whether an animal could think. His advisor, Janelia Senior
Fellow Tim Harris, suggested Lai walk down the hall to chat with Lee, whose lab had
similar questions.
Together, the labs worked to develop a system to understand what animals are
thinking – a real-time “thought detector” that could measure neural activity and
translate what it meant.

Next, the researchers disconnected the treadmill and reward the rat for reproducing the
hippocampal activity pattern associated with a goal location. In this “Jumper” task – named
after a 2008 movie of the same name — the BMI translates the animal’s brain activity into
motion on the virtual reality screen. Essentially, the animal uses its thoughts to navigate to
the reward by first thinking about where they need to go to get the reward. Credit: Chongxi
Lai

The system uses a brain-machine interface (BMI), which provides a direct

connection between brain activity and an external device. In the team’s system, the
BMI produces a connection between the electrical activity in the rat’s hippocampus
and its position in a 360-degree virtual reality arena.

The hippocampus stores mental maps of the world involved in recalling past events
and imagining future scenarios. Memory recall involves the generation of specific
hippocampal activity patterns related to places and events. But no one knew whether
animals could voluntarily control this activity.

The BMI allows the researchers to test whether a rat can activate hippocampal
activity to just think about a location in the arena without physically going there –
essentially, detecting if the animal is able to imagine going to the location.

A new brain-machine interface and virtual reality system for rats. In this experiment, a rat
uses this system to navigate to a goal solely by thinking about where it wants to go.
According to the rules of this system, physical movement by the rat does not affect the rat’s
location in the virtual environment. Only by controlling its hippocampal brain activity can
the rat control where it goes. Specifically, in this system the animal is virtually moved toward
the ‘decoded location’ that the hippocampal activity represents. Credit: Lai et al. DOI:
10.1126/science.adh5206

Probing the rat’s inner thoughts

Once they developed their system, the researchers had to create the “thought
dictionary” that would allow them to decode the rat’s brain signals. This dictionary
compiles what activity patterns look like when the rat experiences something – in
this case, places in the VR arena.

The rat is harnessed in the VR system, designed by Shinsuke Tanaka, a postdoc in the
Lee Lab. As the rat walks on a spherical treadmill, its movements are translated on
the 360-degree screen. The rat is rewarded when it navigates to its goal.

At the same time, the BMI system records the rat’s hippocampal activity. The
researchers can see which neurons are activated when the rat navigates the arena to
reach each goal. These signals provide the basis for a real-time hippocampal BMI,
with the brain’s hippocampal activity translated into actions on the screen.
Next, the researchers disconnect the treadmill and reward the rat for reproducing the
hippocampal activity pattern associated with a goal location. In this “Jumper” task –
named after a 2008 movie of the same name — the BMI translates the animal’s brain
activity into motion on the virtual reality screen. Essentially, the animal uses its
thoughts to navigate to the reward by first thinking about where they need to go to
get the reward. This thought process is something humans experience regularly. For
example, when we’re asked to pick up groceries at a familiar store, we might imagine
the locations we will pass along the way before we ever leave the house.

Normally, hippocampal brain activity is like a GPS that reflects one’s current location. But,
using a new brain-machine interface + virtual reality system, a rat can control its
hippocampal activity to reflect remote locations (‘decoded locations’) and use this to move
an object to where it wants the object to go. These experiments could reveal how our
hippocampus allows us to recall memories of places we have visited before and how we can
imagine being in different places. This work could also lead to new hippocampal-based
neuroprosthetic devices. Credit: Lai et al. DOI: 10.1126/science.adh5206
In the second task, the “Jedi” task – a nod to Star Wars – the rat moves an object to a
location by thoughts alone. The rat is fixed in a virtual place but “moves” an object to
a goal in the VR space by controlling its hippocampal activity, like how a person
sitting in their office might imagine taking a cup next to the coffee machine and
filling it with coffee. The researchers then changed the location of the goal, requiring
the animal to produce activity patterns associated with the new location.

The team found that rats can precisely and flexibly control their hippocampal
activity, in the same way humans likely do. The animals are also able to sustain this
hippocampal activity, holding their thoughts on a given location for many seconds —
a timeframe similar to the one at which humans relive past events or imagine new
scenarios.

“The stunning thing is how rats learn to think about that place, and no other place,
for a very long period of time, based on our, perhaps naïve, notion of the attention
span of a rat,” Harris says.

The research also shows that BMI can be used to probe hippocampal activity,
providing a novel system for studying this important brain region. Because BMI is
increasingly used in prosthetics, this new work also opens up the possibility of
designing novel prosthetic devices based on the same principles, according to the
authors.

Reference: “Volitional activation of remote place representations with a hippocampal

brain–machine interface” by Chongxi Lai, Shinsuke Tanaka, Timothy D. Harris and
Albert K. Lee, 2 November 2023, Science.
DOI: 10.1126/science.adh5206
Review:

Based on a research, the scientists discover that animal, in this research were a rat, is
also have an imagination. This research is using a brain machine. The imagination of the rat
have function to memorize and imaginating a location. This also discover that rat able to
remember some places, and it used a brain part called hippocampus, by some neural
activities.