Lifeboat Foundation

While carrying out high-throughput chromosome conformation capture (Hi-C) analysis on stage 8 (s8) X. tropicalis embryos, we noticed that chromatin interactions plotted at 100-kilobase (kb) resolution using the reference genome v.9.1 showed inversions, misplacements and gaps in nearly every chromosome (Fig. 1a and Extended Data Fig. 1). Thus, to accurately characterize the genome folding patterns in X. tropicalis, we conducted a de novo genome assembly of X. tropicalis using Hi-C and single-molecule sequencing^42,43,44 (Fig. 1b). The newly assembled genome fixed most misplacements, inversions and gaps (Fig. 1c, d, Extended Data Fig. 2 and Supplementary Fig. 1). This new version of the genome was also longer (Supplementary Table 1 and Fig. 1e) and centromere interactions can now be detected (Supplementary Fig. 2). During the preparation of this work, v.10.0 of the X. tropicalis genome was released. While both v.10.0 and our assembly fixed major errors, both versions are still flawed with visually identifiable errors (Supplementary Fig. 1; blue and green arrows). A comparison of the three versions is shown in Supplementary Table 1. Conclusions from the following analyses are the same whether we used v.10.0 or our assembled genome.

To examine when the 3D chromatin architecture is established in X. tropicalis, we generated in situ Hi-C maps on hand-picked s8 embryos (Fig. 2a). A high-resolution (5-kb) inspection of chromatin contact heatmaps failed to reveal any distinct patterns (Fig. 2b), indicating the lack of structural organization before MBT. Next, we determined whether chromatin structures will emerge when rapid synchronized cell division ends by carrying out in situ Hi-C on s9 embryos. Although weak, TAD-like structures appeared across chromatin contact heatmaps (Fig. 2b), suggesting that TAD structures start forming as MBT begins in X. tropicalis.

We continued to examine the changes in chromatin conformation at later developmental stages (stages 10, 11, 12, 13, 15, 17, and 23) after major ZGA (Fig. 2b). TAD boundaries increased progressively from 2471 at s9 to 3000 at s11 (Extended Data Fig. 3a, b). This level was maintained throughout the later developmental stages and with relatively stable median TAD sizes (Extended Data Fig. 3a, b). Consistent with this pattern, the percentage of the genome folded into TADs positively correlated with the number of TADs established at each stage (Extended Data Fig. 3c). Overall, TAD borders were stable during development (Fig. 2c) and contained a high level of gene expression (Extended Data Fig. 3D, e).

The study found that children following vegan diets were on average 3 cm (1.2 inches) shorter, had 4–6% lower bone mineral content and were more than three times more likely to be deficient in vitamin B-12 than the omnivores.

Children on vegan diets have a healthier cardiovascular profile and less body fat than their omnivore peers, but the diets may affect growth, bone mineral content and micronutrient status, according to researchers from UCL Great Ormond Street Institute of Child Health and the Children’s Memorial Health Institute in Warsaw, Poland.

The peer-reviewed study, published in the American Journal of Clinical Nutrition, also found that children following vegetarian diets had a lower risk of nutritional deficiencies compared to the omnivores, but a less healthy cardiovascular profile.

Continue reading “Vegan diets in children may bring heart benefits but pose growth risks” »

The landmark decision has been eagerly awaited by millions but will be hotly contested by some experts doubt the drug’s effectiveness.

Human chromosomes weigh about 20 times heavier than the DNA within them. So where’s all this extra mass coming from?

Rutgers engineers have created a highly effective way to paint complex 3D-printed objects, such as lightweight frames for aircraft and biomedical stents, that could save manufacturers time and money and provide new opportunities to create “smart skins” for printed parts.

The findings are published in the journal ACS Applied Materials & Interfaces.

Conventional sprays and brushes can’t reach all nooks and crannies in complex 3D-printed objects, but the new technique coats any exposed surface and fosters rapid prototyping.

A dozen states — many of them in the Northeast, including Maine, Massachusetts and Connecticut — have already reached a benchmark of at least 70 percent of adults with at least one vaccine dose, a goal President Biden has set for the nation to make by July 4. But in the South, that marker is nowhere in sight for several states.

In 15 states — including Arkansas, the Carolinas, Georgia and Louisiana — about half of adults or fewer have received a dose, according to a New York Times analysis. In two states, Alabama and Mississippi, it would take about a year to get one dose to 70 percent of the population at the current pace of distribution.

Public-health experts and officials in states with lower vaccination rates say the president’s benchmark will help reduce cases and deaths but is somewhat arbitrary — even if 70 percent of adults are vaccinated, the virus and its more contagious variants can spread among those who are not.

Summary: Study identifies genes that become activated in the brain prior to the initiation of severe repetitive behaviors associated with addiction, ASD, and schizophrenia.

Source: MIT

Extreme repetitive behaviors such as hand-flapping, body-rocking, skin-picking, and sniffing are common to a number of brain disorders including autism, schizophrenia, Huntington’s disease, and drug addiction. These behaviors, termed stereotypies, are also apparent in animal models of drug addiction and autism.

Mark my words. When the first real treatment happens people will change their tune. They need to see it work and see that it’s safe.

A new study of about 900 U.S. adults has found that only 33% would use a hypothetical life extension treatment that would allow them “to live forever,” even if it were available today. About 42% said they would not use it, and 25% said they were unsure.

The study, published by University of Texas researchers Michael Barnett and Jessica Helphrey, appeared in the Journal of Aging Studies on April 21.

Continue reading “New study finds most adults would not take a life extension pill, even if it existed” »

Circa 2019

Several recent studies have claimed that cancer cells can be reprogrammed into induced pluripotent stem cells (iPSCs). However, in most cases, cancer cells seem to be resistant to cellular reprogramming. Furthermore, the underlying mechanisms of limited reprogramming in cancer cells are largely unknown. Here, we identified the candidate barrier genes and their target genes at the early stage of reprogramming for investigating cancer reprogramming.

We tried induction of pluripotency in normal human fibroblasts (BJ) and both human benign (MCF10A) and malignant (MCF7) breast cancer cell lines using a classical retroviral reprogramming method. We conducted RNA-sequencing analysis to compare the transcriptome of the three cell lines at early stage of reprogramming.

Continue reading “Reprogramming of Cancer Cells into Induced Pluripotent Stem Cells Questioned” »