The full assembly of human chromosome 8 is reported this week in Nature. While on the outside this chromosome looks typical, being neither short nor long or distinctive, its DNA content and arrangement are of interest in primate and human evolution, in several immune and developmental disorders, and in chromosome sequencing structure and function generally.
This linear assembly is a first for a human autosome — a chromosome not involved in sex determination. The entire sequence of chromosome 8 is 146,259,671 bases. The completed assembly fills in the gap of more than 3 million bases missing from the current reference genome.
The Nature paper is titled “The structure, function and evolution of a complete chromosome 8.”
One of several intriguing characteristics of chromosome 8 is a fast-evolving region, where the mutation rate appears to be highly accelerated in humans and human-like species, in contrast to the rest of the human genome.
While chromosome 8 offers some insights into evolution and human biology, the researchers point out that the complete assembly of all human chromosomes would be necessary to acquire a fuller picture.
An international team of scientists collaborated on the chromosome 8 assembly and analysis. The lead author of the paper is Glennis Logsdon, a postdoctoral fellow in genome sciences at the University of Washington School of Medicine in Seattle.

Powerful algorithms used by Netflix, Amazon and Facebook can ‘predict’ the biological language of cancer and neurodegenerative diseases like Alzheimer’s, scientists have found.
Big data produced during decades of research was fed into a computer language model to see if artificial intelligence can make more advanced discoveries than humans.
Academics based at St John’s College, University of Cambridge, found the machine-learning technology could decipher the ‘biological language’ of cancer, Alzheimer’s, and other neurodegenerative diseases.
Their ground-breaking study has been published in the scientific journal PNAS today (April 8 2021) and could be used in the future to ‘correct the grammatical mistakes inside cells that cause disease’.
Professor Tuomas Knowles, lead author of the paper and a Fellow at St John’s College, said: “Bringing machine-learning technology into research into neurodegenerative diseases and cancer is an absolute game-changer. Ultimately, the aim will be to use artificial intelligence to develop targeted drugs to dramatically ease symptoms or to prevent dementia happening at all.”
Every time Netflix recommends a series to watch or Facebook suggests someone to befriend, the platforms are using powerful machine-learning algorithms to make highly educated guesses about what people will do next. Voice assistants like Alexa and Siri can even recognise individual people and instantly ‘talk’ back to you.

Pioneering research led by experts from the University of Exeter’s Living Systems Institute has provided new insight into formation of the human embryo.
The team of researchers discovered an unique regenerative property of cells in the early human embryo.
The first tissue to form in the embryo of mammals is the trophectoderm, which goes on to connect with the uterus and make the placenta. Previous research in mice found that trophectoderm is only made once.
In the new study, however, the research team found that human early embryos are able to regenerate trophectoderm. They also showed that human embryonic stem cells grown in the laboratory can similarly continue to produce trophectoderm and placental cell types.
These findings show unexpected flexibility in human embryo development and may directly benefit assisted conception (IVF) treatments. In addition, being able to produce early human placental tissue opens a door to finding causes of infertility and miscarriage.
The study is published in the leading international peer-review journal Cell Stem Cell on Wednesday, April 7th 2021.
Dr Ge Guo, lead author of the study from the Living Systems Institute said: “We are very excited to discover that human embryonic stem cells can make every type of cell required to produce a new embryo.”
Professor Austin Smith, Director of the Living Systems Institute and co-author of the study added, said: “Before Dr Guo showed me her results, I did not imagine this should be possible. Her discovery changes our understanding of how the human embryo is made and what we may be able do with human embryonic stem cells”
Human naïve epiblast cells possess unrestricted lineage potential is published in Cell Stem Cell. The research was funded by the Medical Research Council (MRC) .
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Scientists have made a pivotal breakthrough in understanding the way in which cells communicate with each other.
A team of international researchers, including experts from the University of Exeter’s Living Systems Institute, has identified how signalling pathways of Wnt proteins — which orchestrate and control many cell developmental processes — operate on both molecular and cellular levels.
Various mechanisms exist for cells to communicate with each other, and many are essential for development. This information exchange between cells is often based on signalling proteins that activate specific intracellular signalling cascades to control cell behaviour at a distance.
Wnt proteins are produced by a relatively small group of cells and orchestrate cell proliferation and differentiation, but also cell movement and polarity of the neighbouring cells.
However, one of the most crucial functions of the Wnt signalling is patterning of the body axis — which essentially helps determine where the head and tail should form in in a developing tissue.
Previous research led by Professor Steffen Scholpp, from the Living Systems Institute, highlighted that thin finger-like protrusions, known as cytonemes, carry Wnts from the source cells to recipient cells.

A dysfunctional immune system significantly contributes to the development of cancer. Several therapeutic strategies to activate the immune system to target cancer cells have been approved to treat different types of cancer, including melanoma. However, some patients do not show beneficial clinical responses to these novel and very promising immunotherapies. In a new article published in Proceedings of the National Academy of Sciences of the United States of America, Moffitt Cancer Center researchers demonstrate how an important defect in STING gene expression in melanoma cells contributes to their evasion from immune cell detection and destruction.
Several different mechanisms have been discovered that allow cancer cells to avoid immune cell detection and destruction, including defective T cell function, losses in expression of key proteins on tumor cells and defective cell signaling in both immune and tumor cells. An important signaling pathway that contributes to interactions between tumor cells and immune cells is the interferon signaling pathway. The interferon pathway increases expression of molecules that allow tumor cells to be recognized and killed by immune cells. One of the key molecules in the interferon signaling pathway is STING, which is activated by the protein cGAS.
Moffitt researchers previously demonstrated that STING activity is commonly suppressed and altered in a subset of melanomas, which prevents the ability of these tumor cells to be targeted by the immune system. The research team wanted to further the understanding of the importance of alterations in STING signaling in melanoma and determine how STING expression becomes suppressed. They focused on a process called epigenetic modification during which methylation groups are added to the DNA regulatory regions of genes, resulting in genes being turned off.
The researchers performed a series of laboratory experiments and discovered that the DNA regulatory region of the STING gene is highly modified by methylation groups resulting in loss of STING gene expression in certain melanoma cell lines. Importantly, they confirmed these findings in patient clinical samples of early and late-stage melanomas and showed similar methylation events and loss of expression of the upstream STING regulator cGAS.
Next, the researchers demonstrated that it is possible to reactivate expression of STING and/or cGAS with a demethylating drug or genetic approaches that overcome methylation. These interventions successfully turned on STING functional activity, resulting in increased interferon levels when triggered by STING agonist drugs that enabled the melanoma cells to now be recognized by immune cells and targeted for destruction.
These findings demonstrate for the first time that a strategy to overcome STING gene methylation can restore interferon signaling and immune cell activity in melanoma and improve a cell-based immunotherapy when combined with STING agonist drugs.
“These studies show the critical importance of an intact STING pathway in melanomas for optimal T cell immunotherapy success, and how to overcome a notable STING defect in melanoma cases of gene hypermethylation by a combination therapy,” said James J. Mulé, Ph.D., senior author and associate center director for Translational Science at Moffitt. “Unless patients’ melanomas are pre-screened for intact versus defective STING, it is not at all surprising that clinical trials of STING agonists have, to date, uniformly failed.”
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Short pieces of DNA — jumping genes — can bounce from one place to another in our genomes. When too many DNA fragments move around, cancer, infertility, and other problems can arise. Cold Spring Harbor Laboratory (CSHL) Professor & HHMI Investigator Leemor Joshua-Tor and a research investigator in her lab, Jonathan Ipsaro, study how cells safeguard the genome’s integrity and immobilize these restless bits of DNA. They found that one of the jumping genes’ most needed resources may also be their greatest vulnerability.
The mammalian genome is full of genetic elements that have the potential to move from place to place. One type is an LTR retrotransposon (LTR). In normal cells, these elements don’t move much. But if something happens to allow them to move, say during sexual reproduction or in cancerous cells Joshua-Tor says:
“Sometimes they jump into very important spots, either genes themselves or in areas of the genome that is important for regulating genes.”
In this study, Joshua-Tor and Ipsaro examined a mouse protein called Asterix/Gtsf1 that immobilizes LTRs. To understand how this protein locks down LTRs, Ipsaro used several techniques, including cryo-EM, to take a closer look at the protein structure. Joshua-Tor says:
“Structure just informs us in many ways, like how things work. If you can see something, you have a way better idea of how it works.”
Ipsaro found Asterix/Gtsf1 binds directly to a particular class of RNA called transfer RNA (tRNA). tRNAs normally are part of the cell’s protein manufacturing machinery. LTRs have borrowed that part of the protein-making machinery to replicate their genetic material. Asterix/Gtsf1 overrides what the LTRs are trying to do by freezing the otherwise mobile element in place, shutting down their ability to move. Ipsaro says:
“It’s trying to copy and paste itself all over the genome. A part of it evolutionarily has depended on tRNA binding in order to replicate.”
Instead of freezing the entire genome, scientists think Asterix/Gtf1 is using tRNAs to suppress small specific regions, like LTRs. Researchers are trying to figure out how cells protect themselves against these and other types of mobile genetic elements. They hope that someday they might tame an overly restless genome, preventing new mutations in the germline and in tumors.
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Multiple studies show that there are antibodies in a vaccinated mother’s milk. This has led some women to try to restart breastfeeding and others to share milk with friends’ children.As soon as Courtney Lynn Koltes returned home from her first Covid-19 vaccine appointment, she pulled out a breast pump. She had quit breastfeeding her daughter about two months earlier because of a medication conflict. But she was off those pills, and she had recently stumbled across research suggesting that antibodies from a vaccinated mother could be passed to her baby through milk.Getting the milk flowing again — a process known as relactation — would not be easy. She planned to pump on every odd-numbered hour from 7 a.m. to 11 p.m. But Ms. Koltes and her husband were eager to finally introduce their 4-month-old daughter to family members, and with children not yet eligible for vaccination, she was willing to try.“I am starting to see very slow progress, so it is all worth it if it means I can protect her,” Ms. Koltes, who lives in Orange County, Calif., said last week — nine days after receiving her first dose of the Pfizer-BioNTech vaccine.Partly because it’s so physically taxing, relactation is not common. (Medication is often also involved.) But over the past few weeks, online forums focused on relactation have been swarmed with newly vaccinated mothers like Ms. Koltes. Some had stopped breastfeeding their children more than a year earlier.“I’m glad I’m not the only one here trying to relactate for this reason!” one woman wrote in a lively thread in a private Facebook group.“Go team vaccine!” another wrote.In stark contrast, other parenting and breastfeeding forums have been simmering with worries that breast milk from a newly vaccinated mother could be dangerous. It’s not only vaccine skeptics who have been encouraging those fears, which researchers say are unfounded: Some pediatricians and vaccine administrators have been urging nursing mothers to dump their milk after they are vaccinated.So which is it? Is breast milk from a vaccinated person a sort of elixir capable of staving off Covid? And if so, are the newly vaccinated mothers sneaking breast milk into older children’s cereal or sharing their extra milk with friends’ babies onto something? Or should nursing mothers hold off on getting vaccinated?The answer, six researchers agreed, is that newly vaccinated mothers are right to feel as if they have a new superpower. Multiple studies show that their antibodies generated after vaccination can, indeed, be passed through breast milk. As with so much to do with the coronavirus, more research would be beneficial. But there is no concrete reason for new mothers to hold off on getting vaccinated or to dump out their breast milk, they said.Does ‘vaccinated breast milk’ contain antibodies?Yes, study after study shows it does contain antibodies. How exactly these antibodies protect the infant from Covid is not yet clear.Rebecca Powell, left, and her research team have collected breast milk samples for analysis at their Mount Sinai hospital lab.James Estrin/The New York TimesIn the first nine months of the pandemic, around 116 million babies were born worldwide, according to Unicef estimates. This left researchers scrambling to answer a critical question: Could the virus be transmitted through breast milk? Some people assumed it could. But as several groups of researchers tested the milk, they found no traces of virus, only antibodies — suggesting that drinking the milk could protect babies from infection.The next big question for breast milk researchers was whether the protective benefits of a Covid vaccine could be similarly passed to babies. None of the vaccine trials included pregnant or breastfeeding women, so researchers had to find lactating women who qualified for the first vaccine rollout.Through a Facebook group, Rebecca Powell, a human milk immunologist at the Icahn School of Medicine at Mount Sinai in Manhattan, found hundreds of doctors and nurses willing to periodically share their breast milk. In her most recent study, which has not been formally published, she analyzed the milk of six women who had received the Pfizer-BioNTech vaccine and four who had received the Moderna vaccine, 14 days after the women had received their second shots. She found significant numbers of one particular antibody, called IgG, in all of them. Other researchers have had similar results.“There is reason to be excited,” said Dr. Kathryn Gray, a maternal fetal medicine specialist at Brigham and Women’s Hospital in Boston, who has conducted similar studies. “We’d presume that could confer some level of protection.”But how do we know for sure? One way to test this — exposing those babies to the virus — is, of course, unethical. Instead, some researchers have tried to answer the question by studying the antibodies’ properties. Are they neutralizing, meaning they prevent the virus from infecting human cells?In a draft of a small study, one Israeli researcher found that they were. “Breast milk has the capacity to prevent viral dissemination and block the ability of the virus to infect host cells that will result in illness,” Yariv Wine, an applied immunologist at Tel Aviv University, wrote in an email.Research is too premature for vaccinated mothers who are breastfeeding to act as if their babies can’t get infected, however, said Dr. Kirsi Jarvinen-Seppo, the chief of pediatric allergy and immunology at the University of Rochester Medical Center. Dr. Jarvinen-Seppo has been conducting similar studies. “There is no direct evidence that the Covid antibodies in breast milk are protecting the infant — only pieces of evidence suggesting that could be the case,” she said.How long might protection last?As long as the baby is consuming the antibody-containing breast milk.Destiny Burgess’s twins were born prematurely. Ms. Burgess and her husband are back at work in Asheville, N.C. One of their older children is in kindergarten. Two are in day care. All of that makes Ms. Burgess worried for her now 3-month-old babies.When a vaccinated friend offered to share some of her milk with the twins, she accepted.“I feel like I have this newfound superpower,” that friend, Olivia de Soria, said. Along with feeding her own 4-month-old and sneaking a bit of her milk into her 3-year-old’s chocolate milk, Ms. de Soria is now sharing her milk with five other families.“They can’t get the shot, so this is giving me a little peace of mind,” said Ms. Burgess. She does wonder, though, how much “vaccinated milk” would be needed to make a dent.The unsatisfying answer is that it’s not clear. What researchers agree on is that a baby who consumes breast milk all day long is more likely to be protected than one who gets just an occasional drop e. But none scoffed at the idea of giving a bit to older children if it’s not a hassle.They also agree that breast milk’s protective benefits work more like a pill that you must take every day than a shot that lasts a decade. This short-term defense — known as “passive protection” — may only last hours or days from the baby’s last “dose,” Dr. Powell said.“It’s not the same as the baby getting vaccinated,” she added.That means “as soon as you stop feeding that breast milk, there is no protection — period,” said Antti Seppo, another breast milk researcher at the University of Rochester Medical Center. Dr. Seppo also found that it took about two weeks after the first shot for the antibodies to show up in the milk and that they peaked after the second shot.How do we know ‘vaccinated breast milk’ is safe?Researchers say they know enough about how vaccines generally affect breast milk not to be concerned.Multiple researchers involved in research on breast milk and the Covid vaccine offered slight variations of the same opinion. “There is no reason to think there is anything about this vaccine that would cause it to be harmful, and there’s reason to believe it would be beneficial,” said Christina Chambers, co-director of the Center for Better Beginnings at the University of California, San Diego.So why are parenting forums brimming with anecdotes about pediatricians telling mothers to wait to get vaccinated until their baby is older or to dump their milk after vaccination? Mostly because lactating mothers were not included in vaccine trials, so researchers have not been able to concretely study risks.But researchers’ confidence that breast milk from Covid-19-vaccinated mothers is safe comes from what is known broadly about how vaccines work.“Unlike pregnancy, where there are theoretical safety concerns, there really aren’t concerns about lactation and vaccination,” said Dr. Kathryn Gray, a maternal fetal medicine specialist at Brigham and Women’s Hospital in Boston.Both the Moderna and the Pfizer-BioNTech products are mRNA vaccines. “The ingredients in the vaccine are mRNA molecules that have a short lifetime and have no way of making their way into milk,” Dr. Seppo said.So is relactation really worth all the effort?Maybe not, one initially enthusiastic mother decides.Nearly two weeks in, Ms. Koltes of Orange County was managing to pump only a few drops of breast milk each session. An email exchange with her pediatrician reinforced that she could not be sure — even if she got the milk flowing — that allowing unmasked, unvaccinated relatives to hold her daughter was safe. She applauded other women having more success with relactation. But for her, that was it.“It does feel like a weight is lifted,” she said of quitting her rigorous pumping schedule. Now all that’s left to do is wait for an actual vaccine for her daughter, she said. Both Pfizer and Moderna have recently begun testing their vaccines on babies as young as 6 months old.

When a new drug is being developed, the first question is, “Does it work?” The second question is, “Does it do harm?” No matter how effective a therapy is, if it harms the patient in the process, it has little value.
Doctoral student Robert Skolik and Associate Professor Michael Menze, Ph.D., in the Department of Biology at the University of Louisville, have found a way to make cell cultures respond more closely to normal cells, allowing drugs to be screened for toxicity earlier in the research timeline.
The vast majority of cells used for biomedical research are derived from cancer tissues stored in biorepositories. They are cheap to maintain, easy to grow and multiply quickly. Specifically, liver cancer cells are desirable for testing the toxicity of drugs for any number of diseases.
“You like to use liver cells because this is the organ that would detoxify whatever drug for whatever treatment you are testing,” Menze said. “When new drugs are being developed for diabetes or another disease, one of the concerns is whether they are toxic to the liver.”
The cells do come with limitations, however. Since they are cancer cells, they may not be as sensitive to toxins as normal cells, so they may not reveal issues with toxicity that can appear much later in the drug testing process.
Skolik and Menze have discovered that by changing two components of the media used to culture the cells, they can make liver cancer cells behave more like normal liver cells. Rather than using standard serum containing glucose, they used serum from which the glucose had been removed using dialysis and added galactose — a different form of sugar — to the media. The tumor cells metabolize galactose at a much slower rate than glucose. This changes the metabolism of the cells making them behave more like normal liver cells.

When cells are stressed, chemical alarms go off, setting in motion a flurry of activity that protects the cell’s most important players. During the rush, a protein called Parkin hurries to protect the mitochondria, the power stations that generate energy for the cell. Now Salk researchers have discovered a direct link between a master sensor of cell stress and Parkin itself. The same pathway is also tied to type 2 diabetes and cancer, which could open a new avenue for treating all three diseases.
“Our findings represent the earliest step in Parkin’s alarm response that anyone’s ever found by a long shot. All the other known biochemical events happen at one hour; we’ve now found something that happens within five minutes,” says Professor Reuben Shaw, director of the NCI-designated Salk Cancer Center and senior author of the new work, detailed in Science Advances on April 7, 2021. “Decoding this major step in the way cells dispose of defective mitochondria has implications for a number of diseases.”
Parkin’s job is to clear away mitochondria that have been damaged by cellular stress so that new ones can take their place, a process called mitophagy. However, Parkin is mutated in familial Parkinson’s disease, making the protein unable to clear away damaged mitochondria. While scientists have known for some time that Parkin somehow senses mitochondrial stress and initiates the process of mitophagy, no one understood exactly how Parkin was first sensing problems with the mitochondria — Parkin somehow knew to migrate to the mitochondria after mitochondrial damage, but there was no known signal to Parkin until after it arrived there.
Shaw’s lab, which is well known for their work in the fields of metabolism and cancer, spent years intensely researching how the cell regulates a more general process of cellular cleaning and recycling called autophagy. About ten years ago, they discovered that an enzyme called AMPK, which is highly sensitive to cellular stress of many kinds, including mitochondrial damage, controls autophagy by activating an enzyme called ULK1.
Following that discovery, Shaw and graduate student Portia Lombardo began searching for autophagy-related proteins directly activated by ULK1. They screened about 50 different proteins, expecting about 10 percent to fit. They were shocked when Parkin topped the list. Biochemical pathways are usually very convoluted, involving up to 50 participants, each activating the next. Finding that a process as important as mitophagy is initiated by only three participants — first AMPK, then ULK1, then Parkin — was so surprising that Shaw could scarcely believe it.
To confirm the findings were correct, the team used mass spectrometry to reveal precisely where ULK1 was attaching a phosphate group to Parkin. They found that it landed in a new region other researchers had recently found to be critical for Parkin activation but hadn’t known why. A postdoctoral fellow in Shaw’s lab, Chien-Min Hung, then did precise biochemical studies to prove each aspect of the timeline and delineated which proteins were doing what, and where. Shaw’s research now begins to explain this key first step in Parkin activation, which Shaw hypothesizes may serve as a “heads-up” signal from AMPK down the chain of command through ULK1 to Parkin to go check out the mitochondria after a first wave of incoming damage, and, if necessary, trigger destruction of those mitochondria that are too gravely damaged to regain function.
The findings have wide-ranging implications. AMPK, the central sensor of the cell’s metabolism, is itself activated by a tumor suppressor protein called LKB1 that is involved in a number of cancers, as established by Shaw in prior work, and it is activated by a type 2 diabetes drug called metformin. Meanwhile, numerous studies show that diabetes patients taking metformin exhibit lower risks of both cancer and aging comorbidities. Indeed, metformin is currently being pursued as one of the first ever “anti-aging” therapeutics in clinical trials.
“The big takeaway for me is that metabolism and changes in the health of your mitochondria are critical in cancer, they’re critical in diabetes, and they’re critical in neurodegenerative diseases,” says Shaw, who holds the William R. Brody Chair. “Our finding says that a diabetes drug that activates AMPK, which we previously showed can suppress cancer, may also help restore function in patients with neurodegenerative disease. That’s because the general mechanisms that underpin the health of the cells in our bodies are way more integrated than anyone could have ever imagined.”
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Expressive language sampling (ELS) is a useful tool for measuring communication development in youth with Down syndrome, a new multi-site study has found.
The study, co-led by Angela Thurman and Leonard Abbeduto from the UC Davis MIND Institute and the Department of Psychiatry and Behavioral Sciences, focused on language as an outcome measure to detect meaningful changes in communication skills of individuals with Down syndrome. It successfully tested and validated ELS as a reliable set of procedures for collecting, measuring and analyzing the spoken language of participants interacting in a naturalistic setting.
Down syndrome and language delays
Down syndrome is the leading genetic cause of intellectual disability. Approximately one in every 700 babies in the United States is born with Down syndrome. Individuals with Down syndrome frequently have speech and language delays that might severely affect their independence and successful community inclusion.
“Interventions leading to improvements in language would have great impacts on the quality of life of individuals with Down syndrome,” said Abbeduto, director of the UC Davis MIND Institute, professor of psychiatry and behavioral sciences and senior author of the study. “To develop and evaluate such interventions, we need a validated measurement tool and ELS provides that.”
The ELS procedure
During the ELS procedure, researchers collect samples of participants’ speech during two types of natural interactions: conversation and narration.