News Article | April 15, 2017
There are many efforts to identify dinosaurs excavated from sites in many parts of the world but being able to identify new species and seeing full-sized reconstructions of the ancient creatures are always exciting to experience. Now a new herbivorous dinosaur species has just been recognized. The Brigham Young University geologist and professor who discovered the bones in the 1970s has finally given it the name Moabosaurus utahensis, a nod to the location where he excavated the creature. The Moabosaurus utahensis, a relative of the Brontosaurus and Brachiusaurus, stands 32 feet long and has pillar-like legs and a long neck that allow it to reach leaves from high trees. It also has a long tail and a small brain, much like other sauropods. According to the paper published in University of Michigan's Contributions from the Museum of Paleontology, the creature is about 125 million years old, which dates it back to the early Cretaceous period. According to the study, the Moabosaurus utahensis is actually more closely related to the sauropod species found in Spain and Tanzania, leading researchers to believe that there were intermittent cross-continent connections during the cretaceous period. The first bits of the Moabosaurus utahensis were discovered by BYU professor of geology Brooks Britt at the Dalton Wells Quarry in Moab, Utah back when he was still a student in the 1970s. He continued the excavation with colleagues over the decades until they finally collected enough - about 5,500 pieces - of the creature's bones to put it together. "Most bones we find are fragmentary, so only a small percentage of them are usable. And that's why it took so long to get this animal put together: we had to collect huge numbers of bones in order to get enough that were complete," Britt said. Britt also said that analyzing dinosaur species relies heavily on differentiating it from samples of other specimens, which is why it took a while before they confirmed that their excavation revealed a new species. "It's like looking at a piece of a car ... You can look at it and say it belongs to a Ford sedan, but it's not exactly a Focus or a Fusion or a Fiesta," he explained. As mentioned earlier, the new sauropod species was named after the location of the excavation: Moab, Utah. According to Britt, the name is really a way of expressing gratitude to the city for its support toward his research team's excavation efforts. "We're honoring the city of Moab and the State of Utah because they were so supportive of our excavation efforts over the decades it's taken us to pull the animal out of the ground," he expressed. Watch the video below to get an up-close look at the Moabosaurus utahensis. © 2017 Tech Times, All rights reserved. Do not reproduce without permission.
News Article | April 17, 2017
In the United States alone, a half million babies are born preterm; worldwide, the number is an estimated 15 million. Complications associated with preterm birth are the no. 1 cause of death for children under 5, and those who live often face a range of health problems. But with help from a palm-sized plastic rectangle with a few pinholes in it, Brigham Young University researchers are hoping to minimize the problem of premature deliveries. The small chip -- integrated microfluidic device if you speak chemistry -- is designed to predict, with up to 90 percent accuracy, a woman's risk for a future preterm birth. "It's like we're shrinking a whole laboratory and fitting it into one small microchip," said BYU chemistry Ph.D. student Mukul Sonker, who is the lead author of a study recently published in Electrophoresis and funded in part by the National Institutes of Health. The goal for the device is to take a finger-prick's worth of blood and measure a panel of nine identified preterm birth biomarkers -- essentially biological flags that can tip people off to diseases or other conditions. There aren't any current biomarker-based diagnostics for preterm births, and doctors typically only keep tabs on women who have other clear risk factors. For the most part, "the symptom of preterm labor is a woman goes into labor, and at that point you're managing the outcome instead of trying to prepare for it," said Adam Woolley, BYU chemistry professor and study co-author. With their oldest child, Woolley's wife began having contractions early in her third trimester. With the help of hospital intervention, eventually her contractions stopped and she was able to carry their son full term. "Ours was only a glimpse into the potential problems of a preterm birth, but it is still really satisfying to know that the research my students and I are doing now could help others in some way with this important medical issue." There's still work to be done at the front end of the process, but for this study, Sonker and Woolley, along with BYU post-docs Radim Knob and Vishal Sahore, created the chip and a system for preconcentrating and separating biomarkers on it. That's important, explained Sonker, "because when you look at these proteins and peptides, they're present in such a trace amount, but if you preconcentrate them on the chip, you can get enough of a signal for prediction." Among other benefits, the device is cheap, small and fast: once fully developed, said Woolley, "it will help make detecting biomarkers a simple, automated task." Some peg the annual costs associated with preterm birth just in the United States at close to $30 billion, so one clear perk of such a screening tool, said Woolley, is economic. More significantly, he added, "there are a lot of preterm babies who don't survive: if we could get them to survive and thrive, it would be a huge gain to society."
News Article | April 17, 2017
FILE - In this Tuesday, Dec. 2, 2014 file photo, Brigham Young University paleontologist Brooks Britt, right, works to excavate a sauropod humerus from a hillside on the Fossil Discovery Trail at Dinosaur National Monument in Utah. The fossil was vandalized in September, 2014, making it necessary to remove it for safekeeping. In a paper published Tuesday, April 11, 2017, BYU officials say they've identified the fossil as that of a new dinosaur, named Moabosaurus, since it was found near Moab, Utah. (Geoff Liesik/Deseret News via AP, File) MOAB, Utah (AP) — In a story April 14 about a newly named dinosaur, The Associated Press erroneously attached photos from a different fossil dig in Utah. The photos have been removed. The story is below: Professors name dinosaur after digging up thousands of bones University officials say they've named a dinosaur that they found hidden in Utah MOAB, Utah (AP) — University officials say they've named a dinosaur that they found hidden in Utah. Brigham Young University professors have created a full picture of the sauropod from thousands of fossilized bones and published a paper Tuesday in the University of Michigan's Contributions from the Museum of Paleontology. The creature has been named Moabosaurus because it was found near Moab. Like other sauropods, researchers say it was an herbivore with a long neck and tail and a small brain but it was much smaller, at 32 feet. The paper says the Moabosaurus is 125 million years old and its skeleton was found in a quarry. Geologist Brooks Britt and his team have been excavating the bones since the late 1970s. The skeleton is on display at BYU's Museum of Paleontology.
News Article | April 19, 2017
Radical Transformation May Be the Only Way to Save Some of Today's Most Successful Enterprises, Says New Book "Dual Transformation: How To Reposition Today's Business While Creating The Future" LEXINGTON, MA--(Marketwired - Apr 19, 2017) - They are household names, some more than a century old. Ford Motor Company, Aetna, Johnson & Johnson, Singtel, Adobe, Xerox, Netflix, Intuit, Brigham Young University-Idaho. They come from different industries and span the globe, but have one thing in common: each has confronted threats to its business model and the need to radically change its business in the face of major disruption. Big disruptions have upended markets for mobile handsets, personal computers, cameras, newspapers, books, magazines, music, broadcast television and so on -- felling a long list of well-known companies along the way. The most viable response to such radical disruption, according to the authors of the book Dual Transformation: How to Reposition Today's Business While Creating the Future (Harvard Business Review Press, April 2017), is a two-track process: transforming the core business to enhance and extend its life, while building a new and different business to power the future. This kind of "dual transformation" depends on leveraging an established company's unique difficult-to-replicate assets such as brand, scale, and decades of accumulated know-how. By sharing these capabilities and assets between the efforts, the established can come out on top, and help define the future. Consider the challenge facing automakers: autonomous vehicles and web-based ride-share services are threatening their traditional business model. In response, the 113-year-old Ford Motor Company is evolving from a "car company" into a "mobility services" business. "Cars" will be just one component of a very different business model. "In every mature industry, incumbent leaders are extremely vulnerable to competitors offering greater simplicity, convenience, and affordability," says Scott Anthony, managing partner at growth strategy consulting firm Innosight. "And those at the top of their game are most vulnerable." "Dual transformation offers a way to fortify a core business that has brought past success -- maximizing its relevance and resilience," says Anthony. "But it's also a way to leverage disruption and find strong growth in a new and under-served market. Growth that will power the company into the future." DUAL TRANSFORMATION: THE RIGHT RESPONSE TO DISRUPTION Dual Transformation helps executives spot the signs of unfolding disruption, devise a strategy to address it and manage the crises that arise during the transformation process. To demonstrate the challenge -- and the power of the dual transformation solution -- the authors tell the stories of companies that have transformed themselves, creating the next version of themselves that may ending up in a very different place from where they started, such as: "Dual transformation is very different from typical CEO challenges, like restructuring, or downsizing, or a new product innovation," says Clark Gilbert, co-author and president of Brigham Young University-Idaho. "It forces the CEO to work deep in an organization's culture to build two truly new business models simultaneously." DISRUPTION IS COMING -- AND NO ONE IS SAFE There is no such thing as a safe incumbent. Radical innovation is creating new markets, and new products and services, every day. The ripple effects will be felt in every corner of every enterprise, public and private, including some unexpected places: OPTIMIZE FOR THE FUTURE -- NOT THE PAST Dual transformation addresses one of the biggest mistakes that today's business leaders make: a present-forward view of strategy that is based on the assumption that the future will resemble the past. As a result, their growth strategy becomes rooted in today's business and today's data. When change is too incremental, businesses sooner or later end up defending an obsolete business model. Dual transformation builds on a "future-back" view of strategy, by contrast. This begins with the assumption that tomorrow will be different than today, involves looking at powerful trends that hold transformational potential, coming to consensus about the future environment, and developing shared aspirations about the company's future state. "Business leaders have to imagine the future and begin creating it, today, in both the core business and the new growth business," says Mark Johnson, co-founder and senior partner at Innosight. "They have to imagine what the company's markets will look like in five, or ten, or twenty years; design a company that can be successful in that future; and transform today's company right now, so it can still lead when that radically different future finally arrives." For more information, a copy of Dual Transformation: How to Reposition Today's Business While Creating the Future or an interview with Mark Johnson and Scott Anthony of Innosight or Clark Gilbert of BYU-Idaho, please contact Katarina Wenk-Bodenmiller of Sommerfield Communications at +1 (212) 255-8386 or Katarina@sommerfield.com. ABOUT SCOTT D. ANTHONY Scott D. Anthony is the Managing Partner of Innosight. Based in the firm's Singapore office, he leads its Asian consulting operations and its venture-capital investment activities (Innosight Ventures). He has worked with clients ranging from national governments to companies in industries as diverse as health care, telecommunications, consumer products and software. He is the author of The First Mile (Harvard Business Review Press, 2014), The Little Black Book of Innovation (Harvard Business Review Press, January 2012) and The Silver Lining (Harvard Business Review Press, 2009). He is the co-author of Seeing What's Next (Harvard Business Review Press, 2004) and The Innovator's Guide to Growth (Harvard Business Review Press, 2008). ABOUT MARK W. JOHNSON Mark W. Johnson is Cofounder and a Senior Partner of Innosight, which he co-founded with Harvard Business School professor Clayton M. Christensen. He has been a strategic advisor to both Global 1000 and start-up companies in a wide range of industries, including automotive, health care, aerospace/defense, enterprise IT, energy and consumer packaged goods. He has also advised Singapore's government on innovation and entrepreneurship. He is the author of the best-selling book Seizing the White Space: Business Model Innovation and Growth and Renewal (Harvard Business Review Press, 2010). ABOUT CLARK G. GILBERT Clark G. Gilbert is the 16th and current president of Brigham Young University-Idaho. He served previously as the CEO of both the Deseret News, Utah's longest running business and one of the nation's fastest growing businesses, and Deseret Digital Media. Clark is a former Professor of Entrepreneurial Management at Harvard Business School and an associate academic vice president at BYU-Idaho. He is also a founding partner of Innosight Ventures, where he has served as a founding director of several health care and media startups. ABOUT INNOSIGHT Innosight, the strategy and innovation business of global professional services firm Huron, helps organizations design and create the future, instead of being disrupted by it. Acquired by Huron in 2017, Innosight is the leading authority on disruptive innovation and strategic transformation. The company collaborates with clients across a range of industries to identify new growth opportunities, build new ventures and capabilities, and accelerate organizational change. Learn more at www.innosight.com and www.huronconsultinggroup.com.
News Article | July 21, 2016
Peak camping season is upon us, and this July and August millions of Americans will be loading the minivan, heading into our national parks and forests, and inevitably meeting some bears. Fortunately, most of these encounters will be uneventful. In almost every case, the bear will turn its tail and run. Take Yellowstone national park for example, a perfect grizzly bear habitat. In its 145-year history, with over 120 million visitors, only eight people have been killed by bears. You are far more likely to die of a tick bite or a bee sting. Indeed, you are more likely to be murdered in your own bed in America than you are to be killed by a grizzly while camping in Yellowstone. And yet our fear of America’s largest predator prevails (images of Leonardo DiCaprio being ripped apart in Alejandro Iñárritu’s The Revenant are hard to forget). If statistics cannot assuage our primeval fear, perhaps knowledge can. The fact of the matter is running into the continent’s largest predator is unlikely. But here’s what to do if you run into a yogi in the wild. If you come into contact with a bear, it’s important to know what you’re dealing with. There are three species in North America: the black bear, brown bear and polar bear. Unless you’re hiking above the Arctic Circle, you’ll likely only meet one of the first two. Weighing in at 200-500lbs, black bears can be white, blond, cinnamon, chocolate or jet black. The good news? Many are largely vegetarian. Brown bears are divided into two categories: brown bears and grizzlies. Grizzlies are smaller than brown bears, weighing 200-700lbs, where the coastal brown bear can easily weigh over 1,000lbs. Although they come in the same variety of colors as black bears, grizzlies/brown bears are easily distinguished from black bears by their greater size, large hump at the shoulders and massive head. Of the estimated 32,000 bruins, only a couple thousand inhabit Yellowstone and Glacier, the rest are in Canada and Alaska. The best way to handle a bear encounter is never to have one. Bears like thick brush, berry patches and parsnip thickets, but also regularly use hiking trails. The last thing you want to do is startle a bear. Here are five ways to avoid doing so. In this trigger-happy society where there are over 300m guns – one for every man, woman and child – the most common myth is that you can protect yourself from a bear with a gun. Forget it. According to research by the US Fish and Wildlife Service, of those who defended themselves against a bear attack with a weapon, 50% sustained serious injuries – compared to very few injuries incurred by those defending themselves with bear spray. In two studies published in 2008 and 2012 by bear researchers Tom Smith, a professor at BYU, and Stephen Herrero, professor emeritus at the University of Calgary and author of Bear Attacks: Their Causes and Avoidance, the profound efficacy of bear spray versus weapons has been proven beyond a doubt. “Nothing has changed over the past 20 years,” Herrero told me by phone from his home in Calgary. “Bear spray is the most effective deterrent in bear encounters.” Herrero, 76, explains that when a 500lb beast is charging you at 30 mph, a bullet is very small and can easily miss or injure rather than stop a bear. On the other hand, bear spray has a 20ft spread at a 25ft range. (Practice using bear spray before going into bear country.) “Bear spray is not a substitute for common sense and being cautious – looking around, making noise, avoiding dense bushes and berry patches – but it needs to be with you, always on your belt not inside your pack, whenever you’re hiking in bear country.” Now get out there and go camping.
News Article | April 27, 2017
LAIE, Hawaii--(BUSINESS WIRE)--The Polynesian Cultural Center (PCC), today announced it will launch a Million Visitor Per Year Initiative, as part of a transformative strategy crafted by the management team which is led by P. Alfred Grace, president and CEO. The initiative will enable the PCC to advance its mission which includes preserving and portraying the cultures of Polynesia and providing jobs for international students from the Asia Pacific region who attend Brigham Young University (BYU) – Hawaii. The Polynesian Cultural Center is one of the largest employers on the North Shore of Oahu with 1,200 employees including 750 students and 200 community members working part-time. The Polynesian Cultural Center is a non-profit organization that has been affiliated with BYU-Hawaii since its inception 54 years ago and provides education and employment opportunities for students through the I-WORK program. “Many of our student employees come from the pacific islands and countries where they have limited opportunities for employment experience and education. Some students working part time at a minimum wage job will still be the most significant wage earner in their family,” said Grace. The I-WORK program, which stands for International Work Opportunity Returnability Kuleana, supplements up to 100% of the individual costs for students’ attendance and is funded by donations, family contributions and work opportunities at the PCC. Part of the program is a commitment from the student to return home with the goal that they are better able to contribute to their family, their community and their local economy, creating a positive ripple effect that can have a significant impact. Grace stated, “By launching this million visitor initiative, we will make the turnstiles turn and that will enable us to hire and positively impact the lives of more students. We are all about providing more opportunities for more students. That is the heart of our mission and purpose. That is our reason for being.” “Our student employees gain experience that will contribute to any employment they seek in the future,” said Eric Workman, executive vice president for the Polynesian Cultural Center. “When they leave us, the combination of an excellent education and engagement with visitors from all over the world, along with leadership opportunities that come as a result of working at the PCC, prepares them to be better global citizens and positions them to make significant contributions to their native culture when they return home.” Through new marketing efforts in China and Japan, coupled with greater promotional efforts to attract visitors from the Northeast, East Coast, and the Southern United States, the new initiative will allow the Polynesian Cultural Center to create more jobs and expand the positive influence of the ancient cultures and customs of Polynesia to a growing number of visitors from around the world. “Our mission is dear to us and this initiative could not come at a more relevant time,” Grace continued. “There is a growing body of research that documents millennials’ interest in changing the world and looking for authentic purpose-driven work and experiences. Everything we do at the PCC matches up with their priorities. We know the time is right to increase visitors to the PCC by showing the world the beautiful, ancient cultures of Polynesia and providing new opportunities for its progeny.” The management team of the PCC is staffed with former students and performers whose insights stem from their collective decades of involvement with the organization. With growth initiatives that are in place, the PCC has already driven a record rise in visitors through 2016 when guest traffic increased by 30 percent. Growth initiatives have included the opening of The Hukilau Marketplace, which is a collection of nine dining venues, including the flagship restaurant, Pounders, and twelve shopping venues which has contributed to the recent uptick in guest traffic. The marketplace celebrated its 2nd anniversary on March 11th. To date, more than 39 million people have been to the Polynesian Cultural Center and over 20,000 BYU-Hawaii students in total have been employed over its 54-year history. Located on Oahu’s beautiful North Shore, the Polynesian Cultural Center (PCC), owned by The Church of Jesus Christ of Latter-day Saints, is the only cultural tourist attraction of its kind in the world and a favorite of visitors to Hawaii. An engaging, interactive celebration showcasing the people, culture, arts and crafts of Polynesia, the PCC has entertained more than 39 million visitors from around the world in its first 50 years (1963-2013). A non-profit organization, 100 percent of PCC’s revenue goes to daily operations and to support the education of its student-employees from neighboring Brigham Young University-Hawaii.
News Article | April 17, 2017
The Best Response to Disruption: A Dual Transformation of Your Business. But That Brings with It Crises of Commitment, Identity and Conflict that CEOs Must Now Learn to Navigate and Resolve, Says Innosight NEW YORK, NY--(Marketwired - Apr 12, 2017) - Most business leaders tend to avoid crises, like a shareholder revolt or PR disaster, whenever they can. But in order to avoid the ultimate crisis -- extinction -- many of the best CEOs will need to engage with and overcome three others: crises of commitment, identity and conflict. Disruption is wreaking havoc on America's leading companies: Average company tenure in the S&P 500 is forecast to fall to 14 years in 2026, from 33 years in 1965. The best way to respond is with a two-track, "dual transformation" of the company: repositioning today's business to fortify it, while launching a separate venture to create the growth business of tomorrow. But to transform successfully, leaders will need to deal with three new types of crisis, according to growth strategy consulting firm Innosight. "Real, authentic transformation is a monumental challenge, and one that more and more CEOs recognize is critical to their company's survival," says Innosight Managing Partner Scott Anthony, co-author of the new book Dual Transformation: How to Reposition Today's Business While Creating the Future (Harvard Business Review Press, April 2017). "When leaders commit to what we call dual transformation -- making their core business more resilient while at the same time building new growth engines -- they will inevitably encounter three crises, and how they respond will make or break their effort." Anthony and his co-authors, Mark Johnson, Innosight Co-Founder and Senior Partner, and Clark Gilbert, BYU-Idaho President, cite examples of CEOs currently leading dual transformation initiatives. For example, Aetna Chairman and CEO Mark Bertolini has managed crises of commitment, identity and conflict in transforming Aetna's business model away from "insurance," and toward population health management, disease prevention and consumer affordability. To transform successfully in response to market disruption, business leaders will need to guide their companies through three kinds of demanding challenges unlike any others they face: "Major companies, across many different industries, are using dual transformation to anticipate disruption and craft a long-term, strategic approach for dealing with it," says BYU-Idaho President, and Dual Transformation co-author, Clark Gilbert. "But these kinds of transformations bring their own set of challenges, which most CEOs have never dealt with before. Those are challenges CEOs must learn to solve if their companies are to go beyond mere survival, and become leaders in a radically changed world." ABOUT INNOSIGHT Innosight, the strategy and innovation business of global professional services firm Huron, helps organizations design and create the future, instead of being disrupted by it. Acquired by Huron in 2017, Innosight is the leading authority on disruptive innovation and strategic transformation. The company collaborates with clients across a range of industries to identify new growth opportunities, build new ventures and capabilities, and accelerate organizational change. Learn more at www.innosight.com and www.huronconsultinggroup.com.
News Article | February 15, 2017
No statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. We sequenced Chenopodium quinoa Willd. (quinoa) accession PI 614886 (BioSample accession code SAMN04338310; also known as NSL 106399 and QQ74). DNA was extracted from leaf and flower tissue of a single plant, as described in the “Preparing Arabidopsis Genomic DNA for Size-Selected ~20 kb SMRTbell Libraries” protocol (http://www.pacb.com/wp-content/uploads/2015/09/Shared-Protocol-Preparing-Arabidopsis-DNA-for-20-kb-SMRTbell-Libraries.pdf). DNA was purified twice with Beckman Coulter Genomics AMPure XP magnetic beads and assessed by standard agarose gel electrophoresis and Thermo Fisher Scientific Qubit Fluorometry. 100 Single-Molecule Real-Time (SMRT) cells were run on the PacBio RS II system with the P6-C4 chemistry by DNALink (Seoul). De novo assembly was conducted using the smrtmake assembly pipeline (https://github.com/PacificBiosciences/smrtmake) and the Celera Assembler, and the draft assembly was polished using the quiver algorithm. DNA was also sequenced using an Illumina HiSeq 2000 machine. For this, DNA was extracted from leaf tissue of a single soil-grown plant using the Qiagen DNeasy Plant Mini Kit. 500-bp paired-end (PE) libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina. Sequencing reads were processed with Trimmomatic (v0.33)42, and reads <75 nucleotides in length after trimming were removed from further analysis. The remaining high-quality reads were assembled with Velvet (v1.2.10)43 using a k-mer of 75. High-molecular-weight DNA was isolated and labelled from leaf tissue of three-week old quinoa plants according to standard BioNano protocols, using the single-stranded nicking endonuclease Nt.BspQI. Labelled DNA was imaged automatically using the BioNano Irys system and de novo assembled into consensus physical maps using the BioNano IrysView analysis software. The final de novo assembly used only single molecules with a minimum length of 150 kb and eight labels per molecule. PacBio-BioNano hybrid scaffolds were identified using IrysView’s hybrid scaffold alignment subprogram. Using the same DNA prepared for PacBio sequencing, a Chicago library was prepared as described previously10. The library was sequenced on an Illumina HiSeq 2500. Chicago sequence data (in FASTQ format) was used to scaffold the PacBio-BioNano hybrid assembly using HiRise, a software pipeline designed specifically for using Chicago data to assemble genomes10. Chicago library sequences were aligned to the draft input assembly using a modified SNAP read mapper (http://snap.cs.berkeley.edu). The separations of Chicago read pairs mapped within draft scaffolds were analysed by HiRise to produce a likelihood model, and the resulting likelihood model was used to identify putative mis-joins and score prospective joins. A population was developed by crossing Kurmi (green, sweet) and 0654 (red, bitter). Homozygous high- and low-saponin F lines were identified by planting 12 F seeds derived from each F line, harvesting F seed from these F plants, and then performing foam tests on the F seed. Phenotyping was validated using gas chromatography/mass spectrometry (GC/MS). RNA was extracted from inflorescences containing a mixture of flowers and seeds at various stages of development from the parents and 45 individual F progeny. RNA extraction and Illumina sequencing were performed as described above. Sequencing reads from all lines were trimmed using Trimmomatic and mapped to the reference assembly using TopHat44, and SNPs were called using SAMtools mpileup (v1.1)45. For linkage mapping, markers were assigned to linkage groups on the basis of the grouping by JoinMap v4.1. Using the maximum likelihood algorithm of JoinMap, the order of the markers was determined; using this as start order and fixed order, regression mapping in JoinMap was used to determine the cM distances. Genes differentially expressed between bitter and sweet lines and between green and red lines were identified using default parameters of the Cuffdiff function of the Cufflinks program46. A second mapping population was developed by crossing Atlas (sweet) and Carina Red (bitter). Bitter and sweet F lines were identified by performing foam and taste tests on the F seed. DNA sequencing was performed with DNA from the parents and 94 sweet F lines, as described above, and sequencing reads were mapped to the reference assembly using BWA. SNPs were called in the parents and in a merged file containing all combined F lines. Genotype calls were generated for the 94 F genotypes by summing up read counts over a sliding window of 500 variants, at all variant positions for which the parents were homozygous and polymorphic. Over each 500-variant stretch, all reads with Atlas alleles were summed, and all reads with the Carina Red allele were summed. Markers were assigned to linkage groups using JoinMap, with regression mapping used to obtain the genetic maps per linkage group. The Kurmi × 0654 and Atlas × Carina Red maps were integrated with the previously published quinoa linkage map13, with the Kurmi × 0654 map being used as the reference for the positions of anchor markers and scaling. We selected markers from the same scaffold that were in the same 10,000-bp bin in the assembly. The anchor markers on the alternative map received the position of the Kurmi × 0654 map anchor marker in the integrated map. This process was repeated with anchor markers at the 100,000-bp bin level. The assumption is that at the 100,000-bp bin level recombination should essentially be zero. On this level, a regression of cM position on both maps yielded R2 values >0.85 and often >0.9, so the regression line can easily be used for interpolating the positions of the alternative map towards the corresponding position on the Kurmi × 0654 map. All Kurmi × 0654 markers went into the integrated map on their original position. Pseudomolecules were assembled by concatenating scaffolds based on their order and orientation as determined from the integrated linkage map. An AGP (‘A Golden Path’) file was made that describes the positions of the scaffold-based assembly in coordinates of the pseudomolecule assembly, with 100 ‘N’s inserted between consecutive scaffolds. Based on these coordinates, custom scripts were used to generate the pseudomolecule assembly and to recoordinate the annotation file. DNA was extracted from C. pallidicaule (PI 478407) and C. suecicum (BYU 1480) and was sent to the Beijing Genomic Institute (BGI, Hong Kong) where one 180-bp PE library and two mate-pair libraries with insert sizes of 3 and 6 kb were prepared and sequenced on the Illumina HiSeq platform to obtain 2 × 100-bp reads for each library. The generated reads were trimmed using the quality-based trimming tool Sickle (https://github.com/najoshi/sickle). The trimmed reads were then assembled using the ALLPATHS-LG assembler47, and GapCloser v1.1248 was used to resolve N spacers and gap lengths produced by the ALLPATHS-LG assembler. Repeat families found in the genome assemblies of quinoa, C. pallidicaule and C. suecicum (see Supplementary Information 3) were first independently identified de novo and classified using the software package RepeatModeler49. RepeatMasker50 was used to discover and identify repeats within the respective genomes. AUGUSTUS51 was used for ab initio gene prediction, using model training based on coding sequences from Amaranthus hypochondriacus, Beta vulgaris, Spinacia oleracea and Arabidopsis thaliana. RNA-seq and isoform sequencing reads generated from RNA of different tissues were mapped onto the reference genome using Bowtie 2 (ref. 52) and GMAP53, respectively. Hints with locations of potential intron–exon boundaries were generated from the alignment files with the software package BAM2hints in the MAKER package54. MAKER with AUGUSTUS (intron–exon boundary hints provided from RNA-seq and isoform sequencing) was then used to predict genes in the repeat-masked reference genome. To help guide the prediction process, peptide sequences from B. vulgaris and the original quinoa full-length transcript (provided as EST evidence) were used by MAKER during the prediction. Genes were characterized for their putative function by performing a BLAST search of the peptide sequences against the UniProt database. PFAM domains and InterProScan ID were added to the gene models using the scripts provided in the MAKER package. The following quinoa accessions were chosen for DNA re-sequencing: 0654, Ollague, Real, Pasankalla (BYU 1202), Kurmi, CICA-17, Regalona (BYU 947), Salcedo INIA, G-205-95DK, Cherry Vanilla (BYU 1439), Chucapaca, Ku-2, PI 634921 (Ames 22157), Atlas and Carina Red. The following accessions of C. berlandieri were sequenced: var. boscianum (BYU 937), var. macrocalycium (BYU 803), var. zschackei (BYU 1314), var. sinuatum (BYU 14108), and subsp. nuttaliae (‘Huauzontle’). Two accessions of C. hircinum (BYU 566 and BYU 1101) were also sequenced. All sequencing was performed with an Illumina HiSeq 2000 machine, using either 125-bp (Atlas and Carina Red) or 100-bp (all other accessions) paired-end libraries. Reads were trimmed using Trimmomatic and mapped to the reference assembly using BWA (v0.7.10)55. Read alignments were manipulated with SAMtools, and the mpileup function of SAMtools was used to call SNPs. Orthologous and paralogous gene clusters were identified using OrthoMCL28. Recommended settings were used for all-against-all BLASTP comparisons (Blast+ v2.3.056) and OrthoMCL analyses. Custom Perl scripts were used to process OrthoMCL outputs for visualization with InteractiVenn57. Using OrthoMCL, orthologous gene sets containing two copies in quinoa and one copy each in C. pallidicaule, C. suecicum, and B. vulgaris were identified. In total, 7,433 gene sets were chosen, and their amino acid sequences were aligned individually for each set using MAFFT58. The 7,433 alignments were converted into PHYLIP format files by the seqret command in the EMBOSS package59. Individual gene trees were then constructed using the maximum likelihood method using proml in PHYLIP60. In addition, the genomic variants of all 25 sequenced taxa (Supplementary Data 5) relative to the reference sequence were called based on the mapped Illumina reads in 25 BAM files using SAMtools. To call variants in the reference genome (PI 614886), Illumina sequencing reads were mapped to the reference assembly. Variants were then filtered using VCFtools61 and SAMtools, and the qualified SNPs were combined into a single VCF file which was used as an input into SNPhylo62 to construct the phylogenetic relationship using maximum likelihood and 1,000 bootstrap iterations. To identify FT homologues, the protein sequence from the A. thaliana flowering time gene FT was used as a BLAST query. Filtering for hits with an E value <1 × e−3 and with RNA-seq evidence resulted in the identification of four quinoa proteins. One quinoa protein (AUR62013052) appeared to be comprised of two tandem repeats which were separated for the purposes of phylogenetic analysis. For the construction of the phylogenetic tree, protein sequences from these five quinoa FT homologues were aligned using Clustal Omega63 along with two B. vulgaris (gene models: BvFT1-miuf.t1, BvFT2-eewx.t1) and one A. thaliana (AT1G65480.1) homologue. Phylogenetic analysis was performed with MEGA64 (v6.06). The JTT model was selected as the best fitting model. The initial phylogenetic tree was estimated using the neighbour joining method (bootstrap value = 50, Gaps/ Missing Data Treatment = Partial Deletion, Cutoff 95%), and the final tree was estimated using the maximum likelihood method with a bootstrap value of 1,000 replicates. The syntenic relationships between the coding sequences of the chromosomal regions surrounding these FT genes were visualized using the CoGE65 GEvo tool and the Multi-Genome Synteny Viewer66. The alignment of bHLH domains was performed with Clustal Omega63, using sequences from Mertens et al.39. The phylogeny was inferred using the maximum likelihood method based on the JTT matrix-based model67. Initial trees for the heuristic search were obtained automatically by applying Neighbour-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. All positions containing gaps and missing data were eliminated. Trimmed PE Illumina sequencing reads that were used for the de novo assembly of C. suecicum and C. pallidicaule were mapped onto the reference quinoa genome using the default settings of BWA. For every base in the quinoa genome, the depth coverage of properly paired reads from the C. suecicum and C. pallidicaule mapping was calculated using the program GenomeCoverage in the BEDtools package68. A custom Perl script was used to calculate the percentage of each scaffold with more than 5× coverage from both diploids. Scaffolds were assigned to the A or B sub-genome if >65% of the bases were covered by reads from one diploid and <25% of the bases were covered by reads from the other diploid. The relationship between the quinoa sub-genomes and the diploid species C. pallidicaule and C. suecicum was presented in a circle proportional to their sizes using Circos69. Orthologous regions in the three species were identified using BLASTN searches of the quinoa genome against each diploid genome individually. Single top BLASTN hits longer than 8 kb were selected and presented as links between the quinoa genome assembly (arranged in chromosomes, see Supplementary Information 7.3) and the two diploid genome assemblies on the Circos plot (Fig. 2a). Sub-genome synteny was analysed by plotting the positions of homoeologous pairs of A- and B-sub-genome pairs within the context of the 18 chromosomes using Circos. Synteny between the sub-genomes and B. vulgaris was assessed by first creating pseudomolecules by concatenating scaffolds which were known to be ordered and oriented within each of the nine chromosomes. Syntenic regions between these B. vulgaris chromosomes and those of quinoa were then identified using the recommended settings of the CoGe SynMap tool70 and visualized using MCScanX71 and VGSC72. For the purposes of visualization, quinoa chromosomes CqB05, CqA08, CqB11, CqA15 and CqB16 were inverted. Quinoa seeds were embedded in a 2% carboxymethylcellulose solution and frozen above liquid nitrogen. Sections of 50 μm thickness were obtained using a Reichert-Jung Frigocut 2800N, modified to use a Feather C35 blade holder and blades at −20 °C using a modified Kawamoto method73. A 2,5-dihydroxybenzoic acid (Sigma-Aldrich) matrix (40 mg ml−1 in 70% methanol) was applied using a HTX TM-Sprayer (HTX Technologies LLC) with attached LC20-AD HPLC pump (Shimadzu Scientific Instruments). Sections were vacuum dried in a desiccator before analysis. The optical image was generated using an Epson 4400 Flatbed Scanner at 4,800 d.p.i. For mass spectrometric analyses, a Bruker SolariX XR with 7T magnet was used. Images were generated using Bruker Compass FlexImaging 4.1. Data were normalized to the TIC, and brightness optimization was employed to enhance visualization of the distribution of selected compounds. Individual spectra were recalibrated using Bruker Compass DataAnalysis 4.4 to internally lock masses of known DHB clusters: C H O = 273.039364 and C H O = 409.055408 m/z. Accurate mass measurements for individual saponins and identified compounds were run using continuous accumulation of selected ions (CASI) using mass windows of 50–100 m/z and a transient of 4 megaword generating a transient of 2.93 s providing a mass resolving power of approximately 390,000 at 400 m/z. Lipids were putatively assigned by searching the LipidMaps database74 (http://www.lipidmaps.org) and lipid class confirmed by collision-induced dissociation using a 10 m/z window centred around the monoisotopic peak with collision energy of between 15–20 V. Quinoa flowers were marked at anthesis, and seeds were sampled at 12, 16, 20 and 24 days after anthesis. A pool of five seeds from each time point was analysed using GC/MS. Quantification of saponins was performed indirectly by quantifying oleanolic acid (OA) derived from the hydrolysis of saponins extracted from quinoa seeds. Derivatized solution was analysed using single quadrupole GC/MS system (Agilent 7890 GC/5975C MSD) equipped with EI source at ionisation energy of 70 eV. Chromatography separation was performed using DB-5MS fused silica capillary column (30m × 0.25 mm I.D., 0.25 μm film thickness; Agilent J&W Scientific), chemically bonded with 5% phenyl 95% methylpolysiloxane cross-linked stationary phase. Helium was used as the carrier gas with constant flow rate of 1.0 ml min−1. The quantification of OA in each sample was performed using a standard curve based on standards of OA. Specific, individual saponins were identified in quinoa using a preparation of 20 mg of seeds performed according a modified protocol from Giavalisco et al.75. Samples were measured with a Waters ACQUITY Reversed Phase Ultra Performance Liquid Chromatography (RP-UPLC) coupled to a Thermo-Fisher Exactive mass spectrometer, which consists of an electrospray ionisation source and an Orbitrap mass analyser. A C18 column was used for the hydrophilic measurements. Chromatograms were recorded in full-scan MS mode (mass range, 100 −1,500). Extraction of the LC/MS data was accomplished with the software REFINER MS 7.5 (GeneData). SwissModel76 was used to produce homology models for the bHLH region of AUR62017204, AUR62017206 and AUR62010677. RaptorX77 was used for prediction of secondary structure and disorder. QUARK78 was used for ab initio modelling of the C-terminal domain, and the DALI server79 was used for 3D homology searches of this region. Models were manually inspected and evaluated using the PyMOL program (http://pymol.org). The genome assemblies and sequence data for C. quinoa, C. pallidicaule and C. suecicum were deposited at NCBI under BioProject codes PRJNA306026, PRJNA326220 and PRJNA326219, respectively. Additional accessions numbers for deposited data can be found in Supplementary Data 9. The quinoa genome can also be accessed at http://www.cbrc.kaust.edu.sa/chenopodiumdb/ and on the Phytozome database (http://www.phytozome.net/).
News Article | February 23, 2017
Submission of kits improves to a rate of 75 percent from 38 percent in Utah with BYU nursing professor's in-depth involvement Since 2011, BYU nursing professor Julie Valentine has been researching the issues surrounding sexual assault kit processing and has been working with law enforcement agencies to improve the process. Nearly one year ago, in a press conference at BYU, Valentine spoke to a room full of media about the results of her groundbreaking study, looking at the processing of 1,874 sexual assault kits, commonly called rape kits, in seven Utah counties between 2010 and 2013. This was the most comprehensive study ever conducted on sexual assault kits in the United States. Valentine has worked to build upon her initial research and recently released a study that includes another year of data; the results now span from 2010--2014 and include 2,317 fully collected sexual assault kits. She found some encouraging results from the 2014 numbers. "We are seeing a significant increase in kit submission rates throughout the state," Valentine said. "Law enforcement agencies are to be commended for this substantial improvement." The big finding from the new study is that in 2014, 75 percent of sexual assault kits in Utah were submitted by law enforcement to the state crime laboratory for analysis. From 2010 to 2013, only 38 percent of kits were submitted. Washington County saw the most significant improvement. The submission rate of kits there increased to 93 percent in 2014 from only 18 percent in 2010 to 2013. Considerable variability still exists among jurisdictions on kit submission rates, and length of time between assault and submission date remains an issue. Submission rates of kits submitted to a crime lab within a month of the assault ranges from 2 percent in Washington County to 21 percent in Salt Lake County. In a review of 525 sexual assault kits submitted to the Utah Bureau of Forensic Services from Salt Lake County, Valentine discovered nine kits did not include the DNA of the suspect. Of the other 516 some of the kits did not have enough DNA to complete the analysis, some had DNA that matched the suspect, and some had DNA of an unknown assailant which has been entered into CODIS. "Generally, people tend to think of kit submissions as only benefitting victims," Valentine said. "This is important, but only part of the story. Testing kits benefits both victims and suspects. It helps to establish the truth." This most recent study of Valentine's is currently published in the Journal of Interpersonal Violence. Valentine's role in helping improve sexual assault kit processing is not just in crunching the numbers and sharing her research. She has been on the front lines. Last year she worked extensively with West Valley City's police department, where she helped train the department on the impact that trauma has on sexual assault victims. That led to implementing new protocols, meant to ensure compassionate treatment and support for sexual assault victims. The results of Valentine's work with West Valley City showed that sexual assault prosecution jumped from 6 percent to 24 percent. Valentine's work is currently front-and-center in the Utah legislature. House Bill 200 (HB200) mandates the submission and testing of all rape kits, development of trauma informed training for law enforcement and development of a tracking system allowing victims to track their own rape kits through the process. The bill is getting a substantial amount of media attention in Utah and is being watched throughout the US. "The passage of HB200 will be a victory for sexual assault victims, but also a victory in applying the scientific advancements of DNA analysis in establishing truth and justice in these cases," Valentine said. "The end result will be improved identification of serial perpetrators, thereby making Utah a safer state. A safer state is a healthier state."
News Article | February 17, 2017
The ancient art of origami has been inspiring engineers and designers for decades. The principles behind this Japanese folding technique have been appropriated by everyone from solar array designers for implementation in space to medical engineers creating ingestible robotics. Now a team at Brigham Young University (BYU) has created a lightweight bulletproof shield inspired by a Yoshimura origami crease pattern. After consulting with law enforcement and several federal departments, professor of mechanical engineering Larry Howell and his BYU team realized that current bulletproof shields and barriers, which are heavy, cumbersome and lack portability, were well overdue for an update. In the quest for something lighter and more compact that would still provide protection from bullets, the team developed an innovative new shield design made of 12 layers of bulletproof kevlar that takes only fives seconds to deploy. At only 55 lb (25 kg) the barrier is almost half the weight of current steel-based shields and can safely protect two to three people at once. "It goes from a very compact state that you can carry around in the trunk of a car to something you can take with you, open up and take cover behind to be safe from bullets," says Terri Bateman, BYU adjunct professor of engineering. "Then you can easily fold it up and move it if you need to advance your position." During testing, the researchers found the shield to be even more successful than they had initially predicted, stopping bullets from 9mm, .357 Magnum and .44 Magnum handguns. "Those are significant handguns with power," says Howell. "We suspected that something as large as a .44 Magnum would actually tip it over, but that didn't happen." Currently still in prototype form, the team is continuing to work with law enforcement agencies and has tested it with officers on site who have been impressed. The team also believes the barrier could have broader uses, such as for safety in schools or protecting the wounded in emergencies. Check out the team explaining and testing the design in the video below.