New technique can reconstruct history of every mature cell’s development 08-11

All humans begin life as a single cell that divides repeatedly to form two, then four, then eight cells, all the way up to the 26 billion or so that make up a newborn. Tracing how and when those 26 billion cells arise from one zygote is the grand challenge of developmental biology, a field that so far has only been able to capture and analyze snapshots of the development process.

Now, a new method developed by scientists at the Wyss Institute and Harvard Medical School (HMS) brings that task into the realm of possibility using evolving genetic barcodes that record the process of cell division in developing mice, enabling the lineage of every cell in a mouse’s body to be traced back to its single-celled origin.

The research is published today in Science as a First Release article.

“Current lineage-tracking methods can only show snapshots in time, because you have to physically stop the development process to see how the cells look at each stage, almost like looking at individual frames of a motion picture,” said senior author George Church, who is a core faculty member at the Wyss Institute, professor of genetics at HMS, and professor of health sciences and technology at Harvard and MIT. “This barcode recording method allows us to reconstruct the complete history of every mature cell’s development, which is like playing the full motion picture backwards in real time.”

The genetic barcodes are created using a special type of DNA sequence that encodes a modified RNA molecule called a homing guide RNA (hgRNA), which was described in a previous paper. The hgRNA molecules are engineered such that when the enzyme Cas9 (of CRISPR-Cas9 fame) is present, the hgRNA will guide the Cas9 to its own hgRNA sequence in the genome, which Cas9 then cuts. When the cell repairs that cut, it can introduce genetic mutations in the hgRNA sequence, which accumulate over time to create a unique barcode.

The researchers implemented the hgRNA-Cas9 system in mice by creating a “founder mouse” that had 60 different hgRNA sequences scattered throughout its genome. They then crossed the founder mouse with mice that expressed the Cas9 protein, producing zygotes whose hgRNA sequences started being cut and mutated shortly after fertilization.

“Starting with the zygote and continuing through all of its progeny, every time a cell divides there’s a chance that its daughter cells’ hgRNAs will mutate,” explained first author Reza Kalhor, a postdoctoral research fellow at the Wyss Institute and HMS. “In each generation, all the cells acquire their own unique mutations in addition to the ones they inherit from their mother cell, so we can trace how closely related different cells are by comparing which mutations they have.”

Each hgRNA can produce hundreds of mutant alleles; collectively, they can generate a unique barcode that contains the full developmental lineage of each of the approximately 10 billion cells in an adult mouse.

The ability to continuously record cells’ development also allowed the researchers to resolve a longstanding question regarding the embryonic brain: Does it distinguish its front from its back end first, or its left from its right side? By comparing the hgRNA mutation barcodes present in cells taken from different parts of two mice’s brains, they found that neurons from the left side of each brain region were more closely related to neurons from the right side of the same region than to neurons from the left side of neighboring regions. This result suggested that front-back brain patterning emerges before left-right patterning in central nervous system development.

“This method allows us to take the final developmental stage of a model organism and from there reconstruct a full lineage tree all the way back to its single-cell stage. It’s an ambitious goal that will certainly take many labs several years to realize, but this paper represents an important step in getting there,” said Church.

The researchers are now focusing on improving their readout techniques so that they can analyze the barcodes of individual cells and reconstruct the lineage tree that has been recorded.

“Being able to record cells continuously over time is a huge milestone in developmental biology that promises to exponentially increase our understanding of the process by which a single cell grows to form to an adult animal and, if applied to disease models, it could provide entirely new insights into how diseases, such as cancer, emerge,” said Donald Ingber, director of the Wyss Institute. Ingber is also the Judah Folkman Professor of Vascular Biology at HMS and the vascular biology program at Boston Children’s Hospital, and professor of bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences.

Additional authors of the paper include Kian Kalhor from Sharif University of Technology in Tehran, Iran; Leo Mejia from HMS; Kathleen Leeper and Amanda Graveline from the Wyss Institute; and Prashant Mali, associate professor at the University of California, San Diego.

This research was supported by the National Institutes of Health and the Intelligence Advanced Research Projects Activity.

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Arctic river turns red again - two years after ‘pollution problem' supposedly fixed 08-11

Shocking : Water  turns red,as nearby nickel processing plant says cause is decades of contamination in Soviet times which company is working to overcome.

The ‘river of blood’ has appeared again, two years after the plant was fined by an eco-watchdog.

Nornickel, owner of Nadezhdinsky factory, also known as Nadezhda Metallurgical Plant, says it has taken major action to clean-up the environment around Norilsk and in particular around the controversial Daldykan River.

Nikolay Utkin, director of the Polar Division of Norilsk Nickel, told The Siberian Times: 'The reason why the water in the Doldykan River got the reddish-brown colour is the active melting of snow, a powerful flood, which washes off the stuff that had been gathering here for decades.

'Unfortunately, during the Soviet era, the environmental issues were resolved on a residual basis. 

'At present, Norilsk Nickel is making serious efforts to solve this problem.'

Critics have suggested a dammed slurry lake appears to be leaking again into the Daldykan River, so much so that the sight is visible from space satellites, but this is denied by the company. 

In the lake are ‘tailings’, the residue of ore after processing, it has been reported. 

The red tinge of the Arctic river, in the north of Krasnoyarsk region, is also seen on a video that has appeared on local news sites.

The press service of the plant said there was 'no emergency' but initially did not comment further, said local reports. 

Nornickel empire, better known as Norilsk Nickel, has $16.5 billion in assets.

Dammed slurry lake appears to be leaking again into the Daldykan River, so much so that the sight is visible from space satellites. 

In 2016 ecological watchdog - Rosprirodnadzor - announced an 'administrative fine' had 

been imposed over the ‘river of blood’.

The exact amount of the fine was not divulged but it could not be higher than 40,000 roubles - or $650. 

The fine was criticised at the time as too small but there were also understandings that the problem of pollution leaking into the river would be solved. 

Sergey Dyachenko, Chief Operating Officer of Nornickel, was on record saying: ‘We hope that it will not happen in future.’

Now Mr Uktin has revealed: 'In 2016, the slurry pipeline from Nadezhdinsky Metallurgical Plant to tailings was completely replaced, which helped to eliminate the main cause of the (problem).

'Daily monitoring of this facility allows us to say that there are no leaks. 

'For two years of intensive use the pipeline has proved its reliability.

'The results of environmental monitoring of the territory, both visual and in the lab, confirm a significant improvement compared to the situation during the flood in the past year.

'In 2017, as part of the implementation of the three-year plan for the containment and cleaning of the spills, Norilsk Nickel began to clean up the area adjacent to the pipeline. 

'In total, 84,000 tons of spills, a considerable amount of scrap metal and various garbage were removed. 

'Totally more than 2 million square metres (227.89 hectares) was cleared. 

'The cost of the cleaning in 2017 amounted to about 150 million roubles ($2.4 million).

'In the years 2018-2019  more than 220 million roubles ($3.5 million) will be allocated to the cleaning of the long-term pollution. 

'We expect that, after carrying out all the planned works, the colouring of the Doldykan River in the period of heavy rains or high water will be minimised.' 

Regional deputy leader Anatoly Samkov warned in 2016: ‘Such violations are one of the facts of environmental mismanagement. 

'The administrative sanctions imposed on the company cannot serve as a serious preventive measure and we will demand the tightening of existing legislation for such cases. 

'We will keep the situation under control.'

Previously Alexei Kiselyov, of Greenpeace Russia, blamed iron salts.

'It was impossible to say if there was damage to local fauna without investigating the site, he said. 

'Results of the tests are needed,' he said.

Locals say the river frequently turned red in Soviet times, but there were no eco-campaigners then to point to environmental damage. 

'It spring, that means the Daldykan turns red', said one longtime resident. 

Others questioned the company's claims that the water was clean.

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Rewiring STEM education 08-09

The idea that science skills are innate and great discoveries are made only by “lone geniuses” is losing traction in STEM. 

Before Lauren Aguilar began her freshman year of college, she had dreams of becoming a neuroscientist. She remembers sitting in a lecture hall for her very first course, Chemistry 101. The professor had required the students to read the first chapter of the textbook before arriving. As someone with a passion for STEM who had excelled in high school, Aguilar had been confident the course was going to go well.

But then she, a Latina woman, looked around the room. She didn’t see many people who looked like her, either women or men or women of color. “The seed of doubt was planted right then,” she says. “If there aren’t people like me here, then maybe this field isn’t for people like me.”

The professor began the class with a demand: Anyone who didn’t understand everything in the first chapter perfectly should immediately drop the class.

“I said, well, I didn’t understand everything perfectly, so this isn’t for me,” she says. “And right then and there I dropped that course and dropped that major. That one experience absolutely changed the course of my career.” 

This out-of-place feeling is not uncommon in STEM and contributes to the lack of diversity in STEM fields. The NSF’s 2018 STEM Inclusion Study showed that women and racial and ethnic minorities, as well as those who identify as LGBTQ and those with disability status, report more feelings of marginalization and experiences of exclusion in STEM fields compared to white men. 

The experience didn’t derail Aguilar’s dreams of a career in STEM. Instead, it propelled her into another field: social psychology. She wanted to try to understand what leads some people to feel like they belong in certain fields where others don’t, and how that leads to things like career engagement, learning outcomes, teamwork and innovation. Aguilar is now a diversity and inclusion consultant, helping organizations, many of them STEM related, create cultures of inclusion and belonging.

Breaking the mindset

According to Micha Kilburn, director of Outreach and Education at the National Science Foundation’s Joint Institute for Nuclear Astrophysics Center for the Evolution of the Elements, people have been studying STEM education for as long as we’ve been doing science. But it wasn’t until recent decades that these studies became more formal. Since then, the field of STEM education studies has been on the rise, with studies done both in academia and in industry, many dealing with diversity, inclusion and intervention. 

As part of her postdoctoral research at Stanford University, Aguilar collaborated with her advisor, Greg Walton, an associate professor in the department of psychology, and Nobel Laureate Carl Wieman, a professor in the department of physics and in the Graduate School of Education, to bring insights about STEM education to the field of physics and give educators tools to increase diversity in the field. In 2014, they published a paper called “Psychological insights for improved physics teaching” in Physics Today.

One important insight drawn in the paper, Aguilar says, is the idea of a “growth mindset,” which originated with Stanford psychology professor Carol Dweck in her book Mindset. 

“Growth mindset is a set of beliefs that talent, intelligence and skill can be grown and exercised like a muscle, rather than being fixed or innate, like eye color,” she says. “If you have a fixed mindset, the most important goal is to prove your intelligence at all costs. When you run up against dead ends or are struggling and putting a lot of effort into something, it threatens your view of your intelligence and makes you fear that other people might find you out. 

“For people who have a growth mindset, effort is an exciting opportunity to learn and grow. It means you’re building that talent.”

In her research, Dweck found that these two mindsets lead to different learning processes and outcomes, causing people to engage in learning in very different ways. 

“Dweck has shown how different types of praise can produce different mindsets in children,” Wieman says. “A strong fixed mindset in a learner, teacher or parent is very much a self-fulfilling prophecy if nothing is done to intervene. The belief that you cannot succeed, and prominent authority figures telling you that you cannot succeed, is very effective at ensuring most people will not be successful at a challenging task. Even relatively small interventions can shift students of all ages from a fixed to a more growth mindset, and their performance improves accordingly.”

Genius culture

According to Aguilar, studies have shown that fixed mindsets are much more prevalent in STEM fields than in liberal arts.

“Something that’s problematic for STEM is this idea of a lone genius scientist,” she says. “It’s a stereotype about how work gets done that really leads people who don’t fit that stereotype to feel like they don’t belong.”

In more mathematical sciences such as physics, Wieman says, the idea that the skills required to succeed are innate is particularly persistent. 

“These beliefs are most strongly linked to math in our society,” Wieman says. “At some point it became fashionable to be ‘stupid’ in math and science. Rather than saying you or your child isn’t working hard enough and that’s why they’re doing poorly in math, you can say ‘he just doesn’t have a brain that is good for math.’”

Allison Olshefke, a recent physics graduate from the University of Notre Dame, believes that the idea that physics skills are innate has a lot to do with the history of the field. 

“I think there’s just this historical idea that the people who have made it really big in physics and have lasted through the ages were just inherently brilliant,” Olshefke says. “So that became what was valued as what was needed to make those kinds of contributions. 

“And that just reinforces itself. The people who show promise earlier on in physics without having to work as hard for whatever reason are going to be encouraged more from the beginning, and that encouragement is going to keep them going. And then we learn from that experience to encourage those same types of people in the next generation.”

But despite the pervasiveness of the idea that STEM skills are innate, discoveries in science are more often than not a product of hard work and collaboration, as evidenced by the recent discoveries of gravitational waves and the Higgs boson by experiments made up of thousands of scientists each. And, Olshefke adds, it’s not as if people are born with the ability to do calculus.

“The idea that math is language you need to learn to speak goes along with the growth mindset,” Olshefke says. “If you’re learning a new language, it’s going to look and sound completely unintelligible to you when you begin, but then as you work and practice, it’s going to get easier to understand.”

In an article called ‘The cult of genius,’ Julianne Dalcanton of the University of Washington says that in physics, there’s no more damning phrase than saying someone is a “hard worker.” In general, Kilburn says, our society is much more likely to view white and Asian men as brilliant, and women and other underrepresented minorities as hardworking.

“This idea that you have to be born a genius or born with talent hits the fields that are more mathematically inclined, in particular physics,” Kilburn says. “Physics, in particular particle theory, is at the far edge of the mindset that innate brilliance is the most important quality required to succeed. There have been published studies that show the more the field values brilliance or innate talent over dedication, the fewer women and underrepresented minorities that they have.”

Hidden biases and combatting stereotypes

Olshefke, who will soon begin a graduate program at Notre Dame to become a high school math teacher, spent a lot of her undergraduate career doing physics education research. Olshefke met Kilburn at a luncheon and found that the questions she was asking about gender diversity in physics and STEM resonated with her own experiences as a woman pursuing physics.

Olshefke became involved with a study Kilburn was doing in which they evaluated letters of recommendation written by high school teachers. They had seen in previous research that in academic letters of recommendation, there are language differences based on the gender of the applicant. 

“We wanted to find out if these implicit biases extended into high school letters of recommendation as well, since these letters of recommendation are written at a crucial time when students are applying to colleges and programs,” Olshefke says. “We wanted to make sure that everybody is getting recommended in a way that’s going to create an equal playing field for admittance into programs for STEM.”

They looked at letters of recommendation high school teachers had written for Notre Dame’s high school programs from 2013 to 2017. They looked through more than 1700 applications, pulling out words from categories that had been pointed out in previous research to try to identify differences between letters written for men and women. 

“We ended up really only focusing on two of the categories: grindstone words and ability words,” Olshefke says. “Grindstone words describe students as working hard, putting in a lot of effort, while ability words describe natural talent and innate skill. This idea that women are described as working hard more often and men were more likely to be described as innately talented was reflected in the letters that we read. 

“Yet when we looked at the quantitative portion of the recommendation where teachers rated students in different categories, women and men were rated identically throughout all of those. So we saw this disconnect between how teachers are quantitatively rating their students and how they're qualitatively describing their students.”

A fixed mindset can keep programs from admitting a diverse pool of candidates, and it can also drive candidates away, Aguilar says. When a STEM field or a particular STEM department, research center or firm espouses a fixed mindset, research shows that women and underrepresented minorities feel less trust in that organization. 

“They’re worried about not belonging,” she says. “They’re worried that they're going to be seen through the lens of a stereotype. Stereotypes are really just fixed perceptions of people.”

This sentiment resonates strongly with Olshefke, who was one of only three women physics majors in her year.

“As a woman in STEM,” she says, “you’d be less likely to raise your hand and ask a question during lecture because you didn’t want to reflect badly on women in physics. You’d be more afraid to go to office hours. You’d be worried people would think, ‘Oh, women don't understand things as quickly as men.’ Even though nobody is blatantly excluding you from doing anything, there’s still a little bit more fear because you’re different from everyone else.”

Olshefke remembers a time in high school when she was passed up for an “outstanding physics student” award because her teacher felt she didn’t ask enough questions in class. 

“I was the only girl in my class, so I wasn’t comfortable asking questions,” she says. “There was just a lack of understanding of what I was feeling in the class. I think it speaks to the same kind of lack of knowledge about how women and men are experiencing different worlds as they go through physics.”

Changing the face of STEM

One way to confront the issue of inequalities in STEM is by having conversations about the experiences of women and underrepresented minorities in physics. 

“There needs to be a discussion of experiences and what the issues actually are,” Olshefke says. “Having an open classroom and a supportive teacher who’s willing to talk about the issues that their students are going through will make a huge difference. It matches up really well with the growth mindset.”

When organizations have this growth mindset, Aguilar says, individuals from underrepresented backgrounds feel like they are going to be seen as individuals, not stereotypes, and respected and valued for their own contributions. They feel like they’ll have a chance to learn and grow.

“Decades of research has shown us that a growth mindset leads us to be more effective learners, teachers and managers, as well as creates a culture of inclusion and diversity in our STEM education centers,” she says. “Our brains develop and grow new neuronal connections every day. So if we believe in neuroplasticity, we need to believe in the growth mindset.”

Aguilar adds that the research has shown that diversity leads to better decision-making and more innovation. She cites a research study done with juries that compared one jury of all white jurors to another of mixed races. The juries had been asked to listen to a case and make a decision at the end. The researchers found that the more racially diverse juries actually considered more of the facts of the case in their deliberation and reached a more accurate or fair decision. 

“The reason was that each person felt like they couldn’t assume the perspective of everyone in the room,” she says. “They had to really think about each piece of information from all different angles and not make assumptions about what people would think or believe. It not only brings more ideas to the table, but it helps us challenge our own assumptions, be better thinkers and argue our points more clearly. It’s not just a nice-to-have, diversity is a must have to ensure that we make the best decisions and create the most innovative science.”

Learning to appreciate physics

In physics in particular, Kilburn says, having more diversity and inclusion could lead to new frames of thought and revolutions in our understanding of the universe.

“We think of physics as a very objective science, but for something to be truly objective, you have to ask all the questions and look at it from all perspectives,” she says. “If you’re training everybody through the same system and choosing the same types of people, then you’re going to ask the same types of questions. You might miss out on some of those left-field questions that lead to huge breakthroughs. If we want to be a really objective science, we have to ask questions from all angles, which requires people from all different backgrounds.”

Kilburn adds that creating a more inclusive culture in STEM will not just increase diversity in the fields but will also enable others to have an appreciation for it as well. 

“As soon as you tell somebody that you’re a physicist,” she says, “some of the most common responses are ‘I hated that class,’ or ‘I could never do that, you’re so smart.’ All students enter and leave the field with different proficiencies, but they all are capable of learning and appreciating the subject more. 

“The arts do this: Just because you couldn’t play the flute doesn’t mean you stopped listening to and appreciating music. I think that we don’t focus on physics appreciation as much as we could to combat that socially awkward loner genius stereotype.”

According to Wieman, everyone, regardless of their career, will be able to make better decisions if they have some understanding of STEM and how to use it. 

“Our way of life is so based on technology that one is regularly confronted by issues at work and home where STEM can help a person make better decisions,” he says. 

“More importantly, mankind is faced with critical decisions about things like energy sources and use of resources that will impact our world and species far into the future. These issues are fundamentally technical at their heart, so a person cannot make wise decisions on these issues without a grasp of STEM.  If we want to preserve democracy and our world, we must have all students learn STEM better, which research shows is quite possible if we improve the way we teach.”

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Please also read Shyam's article on STEM education.....

STEM (Science,Technology,Engineering,& Math) education in USA, The initiative, The interest, The action.