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New imaging technique can capture entire plant tissues in 3D

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Whole-mount spatial mapping of root tip cell-type marker genes with PHYTOMap. a, In fixed whole-mount tissue, target mRNA molecules are hybridized by pairs of DNA probes (SNAIL probes) that harbor mRNA species-specific barcode sequences (pink bars). Barcode-containing DNA probes are circularized by ligation (red star) and amplified in situ by RCA. During amplification, amine-modified nucleotides are incorporated into the DNA amplicons (RCPs) and stably cross-linked with the cellular protein matrix using a non-reversible amine cross-linker. Amplified DNA barcodes are detected by SBH chemistry through multiple rounds of imaging. b, SBH chemistry. Before each imaging round, four types of bridge probes are hybridized to a set of four DNA barcodes. Each bridge probe is then targeted by one of four fluorescent probes to be imaged. After imaging, bridge probes and fluorescent probes are stripped away, keeping RCPs in place. These steps are repeated until all the DNA barcodes are read. c, Representative images at different imaging rounds. The maximum exposure of 60 z planes of the same position in the tissue is displayed. Scale bar, 30 μm. d, Schematic representation of the root tip and UMAPs displaying root tip scRNA-seq data18 used in this study. In the UMAPs, cells are labeled with cell types (left) and regions (right). LRC, lateral root cap; QC, quiescent center. e,f, Representative results from the imaging rounds 2 (e) and 3 (f). Left, UMAPs showing expression patterns of target genes. The colors of the gene name labels correspond to the colors in the images below. Middle, 3D projections (upper) and optical sections (2D, lower) of whole-mount tissue images. Right, representative cross-section views of the middle part of the samples (transition/elongation zone). Scale bar, 25 μm. Credit: Nature Plants (2023). DOI: 10.1038/s41477-023-01439-4

The cellular life inside a plant is as vibrant as the blossom. In each plant tissue—from root tip to leaf tip—there are hundreds of cell types that relay information about functional needs and environmental changes. Now, a new technology developed by Salk scientists can capture this internal plant world at an unprecedented resolution, opening the door for understanding how plants respond to a changing climate and leading to more resilient crops.

The method, called PHYTOMap, can capture entire (like the whole root tip), instead of a small slice and provides insight into the complex biological conversations between cells that is difficult in two dimensions.

The method was detailed in Nature Plants on June 12, 2023, and the researchers expect PHYTOMap to be quickly popularized by the global scientific community.

“PHYTOMap allows us to examine dozens of plant and see which cells express those genes, how cells influence each other, and how tissue architecture influences those cells,” says Salk Professor Joseph Ecker, director of the Genomic Analysis Laboratory and Howard Hughes Medical Institute investigator. “We can then use those answers to improve crops, predict plant reactions to climate change, and more.”

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PHYTOMap enables scientists to see plant genes in three dimensions. Each dot (purple, green, blue, and red) represents a different gene. Credit: Salk Institute

Existing imaging techniques can only view a small number of genes in one type of and requires altering the plants’ genetic makeup (creating transgenic lines). PHYTOMap (short for plant hybridization-based targeted observation of gene expression map) allows researchers to study dozens of genes simultaneously without any time-consuming genetic manipulation of the plant.

“PHYTOMap was able to map various cell-type-specific genes in expected locations of root tips in 3D,” says Tatsuya Nobori, a postdoctoral researcher in Ecker’s lab. “Now, we can use PHYTOMap to ask more complex questions, like how do different respond and react to each other and their environment?”

In addition to being powerful, PHYTOMap is also accessible—the technique used is relatively standard and the associated cost is relatively minimal.

“With PHYTOMap, we will be able to ask so many new biological questions. I can’t wait to use the method to see how plants interact with surrounding microorganisms,” says Nobori.

“PHYTOMap makes visualizing cells in plant tissues so much easier—no need to alter the plant’s genetic makeup, no need to flag cells with colorful markers,” says Ecker, who is also the Salk International Council Chair in Genetics. “I’m excited to see how PHYTOMap propels efforts to understand plant gene regulation during and under various environmental conditions as well as how it may inform the optimization of agriculture.”

In the future, the Ecker lab will use PHYTOMap to better understand the regulation of cell populations in various plant tissues to eventually engineer crops that are more resilient to climate change.

More information:
Tatsuya Nobori et al, Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap, Nature Plants (2023). DOI: 10.1038/s41477-023-01439-4

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The body of a Ugandan Olympic athlete who was set on fire by her partner is received by family

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NAIROBI, Kenya (AP) — The body of Ugandan Olympic athlete Rebecca Cheptegei — who died after being set on fire by her partner in Kenya — was received Friday by family and anti-femicide crusaders, ahead of her burial a day later.

Cheptegei’s family met with dozens of activists Friday who had marched to the Moi Teaching and Referral Hospital’s morgue in the western city of Eldoret while chanting anti-femicide slogans.

She is the fourth female athlete to have been killed by her partner in Kenya in yet another case of gender-based violence in recent years.

Viola Cheptoo, the founder of Tirop Angels – an organization that was formed in honor of athlete Agnes Tirop, who was stabbed to death in 2021, said stakeholders need to ensure this is the last death of an athlete due to gender-based violence.

“We are here to say that enough is enough, we are tired of burying our sisters due to GBV,” she said.

It was a somber mood at the morgue as athletes and family members viewed Cheptegei’s body which sustained 80% of burns after she was doused with gasoline by her partner Dickson Ndiema. Ndiema sustained 30% burns on his body and later succumbed.

Ndiema and Cheptegei were said to have quarreled over a piece of land that the athlete bought in Kenya, according to a report filed by the local chief.

Cheptegei competed in the women’s marathon at the Paris Olympics less than a month before the attack. She finished in 44th place.

Cheptegei’s father, Joseph, said that the body will make a brief stop at their home in the Endebess area before proceeding to Bukwo in eastern Uganda for a night vigil and burial on Saturday.

“We are in the final part of giving my daughter the last respect,” a visibly distraught Joseph said.

He told reporters last week that Ndiema was stalking and threatening Cheptegei and the family had informed police.

Kenya’s high rates of violence against women have prompted marches by ordinary citizens in towns and cities this year.

Four in 10 women or an estimated 41% of dating or married Kenyan women have experienced physical or sexual violence perpetrated by their current or most recent partner, according to the Kenya Demographic and Health Survey 2022.

The Canadian Press. All rights reserved.

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The ancient jar smashed by a 4-year-old is back on display at an Israeli museum after repair

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TEL AVIV, Israel (AP) — A rare Bronze-Era jar accidentally smashed by a 4-year-old visiting a museum was back on display Wednesday after restoration experts were able to carefully piece the artifact back together.

Last month, a family from northern Israel was visiting the museum when their youngest son tipped over the jar, which smashed into pieces.

Alex Geller, the boy’s father, said his son — the youngest of three — is exceptionally curious, and that the moment he heard the crash, “please let that not be my child” was the first thought that raced through his head.

The jar has been on display at the Hecht Museum in Haifa for 35 years. It was one of the only containers of its size and from that period still complete when it was discovered.

The Bronze Age jar is one of many artifacts exhibited out in the open, part of the Hecht Museum’s vision of letting visitors explore history without glass barriers, said Inbal Rivlin, the director of the museum, which is associated with Haifa University in northern Israel.

It was likely used to hold wine or oil, and dates back to between 2200 and 1500 B.C.

Rivlin and the museum decided to turn the moment, which captured international attention, into a teaching moment, inviting the Geller family back for a special visit and hands-on activity to illustrate the restoration process.

Rivlin added that the incident provided a welcome distraction from the ongoing war in Gaza. “Well, he’s just a kid. So I think that somehow it touches the heart of the people in Israel and around the world,“ said Rivlin.

Roee Shafir, a restoration expert at the museum, said the repairs would be fairly simple, as the pieces were from a single, complete jar. Archaeologists often face the more daunting task of sifting through piles of shards from multiple objects and trying to piece them together.

Experts used 3D technology, hi-resolution videos, and special glue to painstakingly reconstruct the large jar.

Less than two weeks after it broke, the jar went back on display at the museum. The gluing process left small hairline cracks, and a few pieces are missing, but the jar’s impressive size remains.

The only noticeable difference in the exhibit was a new sign reading “please don’t touch.”

The Canadian Press. All rights reserved.

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B.C. sets up a panel on bear deaths, will review conservation officer training

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VICTORIA – The British Columbia government is partnering with a bear welfare group to reduce the number of bears being euthanized in the province.

Nicholas Scapillati, executive director of Grizzly Bear Foundation, said Monday that it comes after months-long discussions with the province on how to protect bears, with the goal to give the animals a “better and second chance at life in the wild.”

Scapillati said what’s exciting about the project is that the government is open to working with outside experts and the public.

“So, they’ll be working through Indigenous knowledge and scientific understanding, bringing in the latest techniques and training expertise from leading experts,” he said in an interview.

B.C. government data show conservation officers destroyed 603 black bears and 23 grizzly bears in 2023, while 154 black bears were killed by officers in the first six months of this year.

Scapillati said the group will publish a report with recommendations by next spring, while an independent oversight committee will be set up to review all bear encounters with conservation officers to provide advice to the government.

Environment Minister George Heyman said in a statement that they are looking for new ways to ensure conservation officers “have the trust of the communities they serve,” and the panel will make recommendations to enhance officer training and improve policies.

Lesley Fox, with the wildlife protection group The Fur-Bearers, said they’ve been calling for such a committee for decades.

“This move demonstrates the government is listening,” said Fox. “I suspect, because of the impending election, their listening skills are potentially a little sharper than they normally are.”

Fox said the partnership came from “a place of long frustration” as provincial conservation officers kill more than 500 black bears every year on average, and the public is “no longer tolerating this kind of approach.”

“I think that the conservation officer service and the B.C. government are aware they need to change, and certainly the public has been asking for it,” said Fox.

Fox said there’s a lot of optimism about the new partnership, but, as with any government, there will likely be a lot of red tape to get through.

“I think speed is going to be important, whether or not the committee has the ability to make change and make change relatively quickly without having to study an issue to death, ” said Fox.

This report by The Canadian Press was first published Sept. 9, 2024.

The Canadian Press. All rights reserved.

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