Alabama based scientists help secure the future of chocolate

People around the world consumed nearly 7.7 million tons of chocolate in the last year, but the cacao crop that supports the production of these sweets is under significant environmental threat.

Millions of cacao farmers in West Africa, Southeast Asia and Latin America feel the pressures of ever-increasing consumption, a changing climate and devastating fungal infections. In 2017, The New York Times declared that we have entered “a battle to save the world’s favorite treat.”

Scientists at the HudsonAlpha Institute for Biotechnology with the help of Mars Wrigley Confectionery have created the newest weapon in that battle — an improved reference genome to help researchers and farmers develop healthier, more productive cacao crops.

Sweets Under Siege

The production of one of the world’s favorite delicacies relies on a particularly delicate plant. Cacao can only be grown within 20 degrees of the equator, and global studies suggest that the effects of climate change will shrink the farmland currently suitable for production even further. Increasing temperature and decreasing humidity in the areas that currently produce cacao will mean the crop must be grown at higher elevations.

Cacao also proves particularly vulnerable to fungi and diseases. It suffers from a number of menacingly-named blights, including frosty pod rot, witches’ broom, black pod and cacao swollen-shoot virus. One fear is that if any of these blights spread from its native region, it could sweep through global crops, devastating worldwide production.

The Newest Weapon in the War to Save Cacao

HudsonAlpha scientists have completed and released an updated reference genome for Theobroma cacao, the tree that produces cacao beans. With the help of funding from Mars Wrigley, HudsonAlpha researchers generated this new resource using advanced long-read sequencers, producing a more modern reference genome than the first version, which was completed in 2010.

A reference genome allows you to identify parts of the genome you wish to see carried through to the next generation of plants, like genes that promote drought tolerance, increase yield or improve disease resistance. Then, researchers can sequence each generation of selectively bred plants to quickly find which ones carry the desirable traits.

This most recent effort was co-led by HudsonAlpha faculty investigators Jane Grimwood, PhD, and Jeremy Schmutz. Schmutz said of the project, “As our technology improves, we’re able to produce more detailed, versatile reference genomes, which are critical for the kind of rapid crop improvement you want to see with cacao.”

Farmers have used selective breeding to improve crops for centuries. The process works by crossbreeding two plants, hoping to combine desirable traits and make hardier plants. Then you take the offspring that show those traits and breed them again. This selective breeding process takes time though, as you have to wait for each crop to reach maturity. A cacao tree, for example, takes about five years to start generating fruit.

A Better “Chocolate Tree”

Cacao trees, like many modern crops, do not show a lot of genetic diversity. Most of the cacao trees worldwide come from a handful of clones selected in the 1940’s. Because the trees are so closely related, they have similar genetic weaknesses. If a disease reaches a group of cacao trees that doesn’t carry any genetic resistance to that disease, it can destroy the entire crop.

“Having so little genetic diversity leaves the cacao tree vulnerable,” noted HudsonAlpha Faculty Investigator Jane Grimwood, PhD. “However, it also means that genes can be exchanged between trees, which gives researchers and farmers an opportunity.”

Using this new reference genome, researchers will be able to guide crossbreeding and hybridization efforts more quickly. That means traits like drought tolerance can be bred into a population faster and disease resistances can be introduced more efficiently.

The “chocolate tree” remains under threat, but now scientists and farmers alike have a more complete toolkit to produce more robust cacao crops.

About HudsonAlpha: HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to developing and applying scientific advances to health, agriculture, learning, and commercialization.

6 hours ago

Coach Bill Clark: UAB ready for football season preparations to start

UAB football coach Bill Clark is like many fans who are waiting for a clear sign that the college football season is on the horizon this year.

With less than 90 days until the start of the season, that sign will be next week when UAB players report for voluntary individual workouts and training. Clark said that will progress into the more familiar pre-season camp between now and August.

“I’m excited to get them back, even in small numbers right now,” Clark said.

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Coach Bill Clark: UAB ready for football season preparations from Alabama NewsCenter on Vimeo.

It’s been a challenging few months for everyone because of the COVID-19 pandemic and football was not immune. It eliminated the normal spring training and spring football scrimmages for all collegiate teams, and officials from all schools and conferences have been weighing whether and how to proceed with preparations for a season that at one time seemed uncertain.

Clark said he is confident the plan UAB has in place is a good one and he has one of the premier institutions to draw on for medical expertise.

“Rule No. 1 has always been athlete safety, so this is not something new for us,” Clark said. “Obviously, the COVID crisis was something new for us to deal with. The support of our athletic trainers obviously being at UAB with the medical school helps.”

(Courtesy of Alabama NewsCenter)

6 hours ago

Hero German Shepherd from Alabama vies to be country’s top dog in American Humane contest

A mom’s reaction to being reunited with her lost child – found by Küsse, a German Shepherd rescue dog – was to smother both with kisses and hugs.

Indeed, the name Küsse – German for “kisses” – fits Corey Speegle’s rescue dog to a “T.” With her innate ability to find lost people, Küsse has earned huge praise during her short career.

Nearly half a million dog lovers across the country have cast their votes for Küsse, one of three semifinalists for the American Humane Hero Dog prize in the Search and Rescue category. Other categories include Therapy Dogs; Service Dogs; Military Dogs; Law Enforcement Dogs; Shelter Dogs; and Guide/Hearing Dogs.

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Küsse and Speegle live in Sheffield, Alabama, and she’s the only dog representing the Yellowhammer State. Supporters can vote for Küsse once a day through July 16.

Training the nation’s ‘top dog’ 

Speegle got Küsse as a pup and began training her at a year old. Küsse’s innate ability to find individuals has primed her to win the national contest this fall, which concludes with a gala and a two-hour special on the Hallmark Channel.

“Küsse is a beautiful dog, and she loves to serve and help find missing people,” said Speegle, state coordinator for the Community United Effort Center for Missing Persons and a volunteer firefighter for Spring Valley and White Oak Volunteer Fire departments. “Her mother is a German Shepherd from the Czech Republic and the father is a second-generation explosives dog out of Fort Hood, Texas.”

Speegle has trained with the Federal Emergency Management Association, and he and Küsse have completed numerous search and rescue classes.

“I’ve taken advanced building search classes through detection services, and I’ve had boat training to locate bodies in the water,” Speegle said.

He’s accustomed to receiving calls for help from Colbert County Sheriff Frank Williamson. On March 4, Speegle and Küsse were called to work search and reconnaissance efforts in Cookeville, Tennessee, after a powerful EF4 tornado decimated the town in the early morning. Cookeville is the county seat of Putnam County, 79 miles east of Nashville.

“Küsse and I worked for hours on end to help find survivors and bring closure to families with missing loved ones,” said Speegle, who volunteers with the White Oak Volunteer Fire Department’s K-9 Search and Rescue crew. The team also uses highly trained cadaver dogs.

“It was like a bomb went off there,” he said. “We stayed until the last person was accounted for – it wasn’t pretty, as you can imagine.” Despite their round-the-clock search March 4-6, Küsse and Speegle found no survivors among the 27 people missing.

Speegle trained Küsse with the “recall/refind” method.

“I say, ‘show me,’ and she will return to me and lead me to the person,” he said. “When she finds somebody, she gets her purple kong wubba, her favorite toy in the whole world.”

“The new thinking is you don’t want the dog to bark at someone and scare them, so she’s trained to find them and, depending on the distance, she returns to me and makes me know she found them,” he said.

Speegle uses a handheld detection module linked to Küsse’s GPS-monitored collar, which can track her up to 9 miles.

“Occasionally, with small children, the dog won’t leave the child,” he said. “It will lay down and stay with the subject, so we can still track where the dog is.

“She also does scent article finds,” Speegle said. “Küsse locates a person using a scent article – a sock, hat or shirt, for instance.

“Küsse will work on- or off-lead,” he said. “If you have someone lost in a national forest, she can use that scent to find them.”

Küsse recently helped in the search for a 20-year-old marathon runner from Colbert County near Muscle Shoals, Alabama, whose family reported him missing.

“He’d gone running in the evening and it had stormed all night,” Speegle said. “We tracked him 200 to 300 yards but Küsse lost his scent because of the rain. But she assisted law enforcement to go in the right direction to find him.”

Using video, the sheriff tracked the man’s run. The marathoner had been caught in the storm and sheltered overnight in the field house at Muscle Shoals High School. He borrowed a phone the next morning to call his parents.

Honoring the past at LaGrange Cemetery

Colbert County Commissioner Darol Bendall asked Speegle to locate unmarked historic graves at the historic LaGrange Cemetery in Leighton, Alabama. He and Küsse volunteered a weekend in April.

“The descendants would like to know where they’re at – it’s rough terrain,” said Speegle, who assisted other members of the LaGrange Living History Association. “There are probably 100 graves that are unaccounted for, some of which date to 1815.”

The project was an excellent training opportunity. Speegle, Küsse and his other dogs located nine lost gravesites. During the years, headstones for a man and his wife, dating to the 1800s, had been moved about 50 yards from their resting place. Volunteers reset the headstones properly. Other graves were found outside the cemetery.

“My cadaver dog found an unmarked grave in a wooded area,” he said.

During the work, a volunteer’s child went missing.

“This little 6-year-old girl had wandered off 200 to 300 yards,” Speegle said. “Küsse found her at the back of the cemetery, at the wood line. It was a little scary for all of us.”

Speegle finds a lot of satisfaction in helping others.

“There was no happy ending in Tennessee, but finding the little girl was a good one,” he said. “Küsse is at the beginning of her career. I hope she serves her community well. If she wins in her overall category, I will be one proud daddy.”

(Courtesy of Alabama NewsCenter)

8 hours ago

Florists decorate Birmingham Rotary Trail in an act of beauty and healing

Flowers bring joy, and they can heal the soul.

On Friday morning about 25 florists joined in decorating the Rotary Trail in Birmingham. As a beautiful start to the weekend, said Cameron Pappas, florists swathed the trail in greenery, roses and colorful blooms of all sorts. People even brought flowers from their yards.

The effort was to bring “light and joy” to Birmingham residents. And the 46-foot-tall sign with the words “Rotary Trail in the Magic City” was the perfect place to begin.

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“I was laying in bed Sunday night, watching these scenes unfold where Birmingham was in chaos. Seeing this was so sad,” said Pappas, owner of Norton’s Florist in Birmingham.

When Carolyn Chen called Pappas later, an idea was born. The owner of Wild Things Flowers & Curiosities in Homewood, Chen thought that decorating the entrance of the Rotary Trail could be a start to bringing emotional healing to the Magic City.

Area florists put Birmingham’s Rotary Trail in full bloom from Alabama NewsCenter on Vimeo.

Random acts of botany

“Carolyn wanted to figure out how to help the city heal after this past weekend and the coronavirus,” said Pappas, owner of Norton’s Florist for more than four years. Between the two, giving flowers in a difficult time is a natural response: “Flowers bring joy. Whether it’s a sad time like a funeral or a happy occasion like a birthday, flowers bring happiness,” he said.

Pappas and Chen invited more than 50 florists from a 40-mile area around the city to help. Three wholesale flower distributors in Birmingham – DavisR&W Wholesale Inc. and Hall’s Birmingham Wholesale Florist – donated flowers and greenery.

“It’s cool to have everyone in an industry come together,” he said. “We want to make people happy, and give them something to look at besides broken glass and boarded up windows.”

What started as a simple gesture bloomed into something memorable. Several of the participating florists were livestreaming to Facebook. Several people from outside of Birmingham saw the videos and posts on social media, and came to take their own pictures.

Pappas said that seeing people join together to help was an amazing sight.

“People were cutting flowers, using their talents to help,” he said. “Everyone was busy beautifying the Rotary Trail with one thought: We love Birmingham. We love this city and our people.”

(Courtesy of Alabama News Center)

8 hours ago

Auburn University expert discusses COVID-19’s impact on sales projections, consumer costs

Brian Gibson, the Wilson Family Professor and executive director of the Center for Supply Chain Innovation in Auburn University’s Harbert College of Business, recently commented on the impact of coronavirus on sales projections for retailers and suppliers, how supply chains are adapting and how consumer costs will be affected.

Gibson leads multiple industry studies, including the Logistics 2030 project, the annual State of the Retail Supply Chain Report and the Council of Supply Chain Management Professionals’ talent management project. He has published numerous articles in supply chain journals, co-wrote “The Definitive Guide to Integrated Supply Chain Management” and co-produces the “Supply Chain Essentials” video series.

Q: How is coronavirus affecting sales projections for retailers and suppliers?

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Gibson: The COVID-19 pandemic has created quite the challenge in the retail sector. U.S. retail sales plunged nearly 9 percent in March as shoppers began to follow shelter-in-place measures. The situation has created a “Tale of Two Cities” scenario. For many retailers it has been the worst of times, with all stores closed due to state government emergency orders. Small retailers lacking the resources to support online selling, and large discounters like TJ Maxx and Ross Stores with minimal e-commerce operations are generating no sales. Retailers with a large online presence are generating e-commerce sales, but it is not enough to make up the loss of in-store revenues. Only the small group of retailers selling essential products like groceries and household goods items are in the best-of-times category, relatively speaking. In March, Kroger and Walmart experienced double-digit growth of same-store sales due to consumers stocking up on essentials. AmazonCostcoTarget and other select retailers also generated higher revenues.

The situation is much the same for suppliers. It all depends on the type of product being produced. Manufacturers of essential food, paper and cleaning products are working overtime to handle demand surges. In contrast, the apparel and automobile industries are largely shut down due to lack of demand, key parts or available labor. Some of these companies are now making personal protective equipment, ventilators and other necessary products that are in short supply.

Q: How have coronavirus-affected supply chains adapted to this situation?

Gibson: The news headlines and stories certainly paint a bleak picture of a broken supply chain that is plagued by product shortages. The reality is that there is no single supply chain. Products flow through different channels from their raw material sources to manufacturers to retailers and distributors. As consumption patterns for certain products have spiked to historic highs, there have been temporary shortages while companies work to restock their inventories. It is an ongoing challenge. If a meat processor shuts down for two weeks, that link in the supply chain is broken temporarily, but the whole supply chain is not broken.

Supply chains are resilient; they bend but typically don’t break. Adjustments are being made by companies to continue serving demand. Distribution centers and grocery stores are working overtime to fulfill orders. Product is being redirected from commercial channels to consumer channels. Production lines are being modified and alternate sources of supply are being tapped to alleviate inventory shortages. Collectively, these solutions from organizations along the supply chain will bring supply and demand back into sync.

Q: Will supply chain costs increase and, thus, increase the cost of consumer goods?

Gibson: Without question, supply chain costs are rising. Retailers are paying front-line store and distribution center associates an hourly wage premium. It costs more to fill and deliver an e-commerce order than to have consumers do their own shopping. Facilities are going through expensive deep-cleaning protocols on a regular basis. And the cost of some commodities is rising. It’s logical to expect that some of these costs will be passed along to consumers in the form of higher product prices. How much they will go up and for how long is the tricky question.

Q: Will we see changes in supply chains and will this actually help certain companies?

Gibson: In the wake of COVID-19 disruptions, “Massive Shifts in Supply Chains Forthcoming” is a popular headline but one that is almost clickbait status. Change will happen, but in a more methodical and incremental fashion than is currently being predicted by pundits. Production will continue to shift from China to other low-cost countries. We will possibly see more domestic production with flexible capacity built in. Some companies will increase safety stock inventories of key materials. And companies will likely cultivate additional strategic supplier relationships. Companies that succeed with these initiatives will achieve greater supply chain agility and resiliency without dramatically increasing their costs. They will be the ultimate winners.

This story originally appeared on Auburn University’s website.

(Courtesy of Alabama NewsCenter)

9 hours ago

Snapper season opener shows pent-up demand

While the second weekend of the private recreational red snapper season in Alabama saw near perfect conditions, the opening weekend proved why state management of the red snapper is so important to ensure maximum access to this treasured fishery.

Pent-up demand from a variety of reasons, including the COVID-19 restrictions, placed the May 22 opening day of snapper season in record territory.

“On opening day, that was the most people I’ve ever seen on a Friday,” said Alabama Marine Resources Director Scott Bannon. “Even though the weather was a little rougher, the harvest was almost the same as the 2018 numbers. People were just glad to have the opportunity to get out. They were tired of being at home. They felt this was a safe and enjoyable outdoor activity. And we agree. When I got to Dauphin Island at 8 o’clock on opening day, the trailers parked alongside the road were already backed up 7/10ths of a mile from the ramp (Billy Goat Hole). Saturday was another busy day. With the winds picking up Sunday and Monday, the activity was down a good bit.”

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The 2018 and 2019 seasons were conducted under an EFP (exempted fishing permit) to allow state management and significantly increased the number of days private recreational anglers were allowed to catch red snapper over recent years.

With the approval of regional management beginning in 2020 for the five states on the Gulf of Mexico, each state sets its season, bag and size limits under certain parameters.

Because Alabama closely monitors the red snapper harvest through its Red Snapper Reporting System, Snapper Check, Marine Resources can adjust the seasons to allow anglers to catch as many fish as possible while staying within the state’s quota. Alabama’s private recreational season is set to run each Friday through Monday with a closing date tentatively set for July 19. The closing date may be adjusted to ensure the state’s quota of 1,122,662 pounds is met but not exceeded. Snapper Check numbers indicated 176,782 pounds of red snapper were harvested opening weekend.

Bannon and Chris Blankenship, the Commissioner of the Alabama Department of Conservation and Natural Resources, ventured out on opening weekend with old friends Brian and Daniel Rowe and crew and came back with a box full of red snapper.

“I had some concerns that the seas were going to be a little choppy,” Bannon said. “We had been talking to some boats that were struggling, so they stayed close and came back pretty early. In the afternoon, the wind died down. The bite was not hard and fast, but we caught big fish. We only caught a few undersized fish that had to go back. We caught everything from just over legal (16 inches total length) to a few just over 20 pounds. It was a real good trip.”

From a management perspective, Bannon said that’s what marine scientists like to see on a reef, a variety of sizes of snapper. He also said some of the relatively small reefs held good-sized fish.

On opening day, Bannon said the anglers used a variety of baits to target the red snapper and definitely saw a preference.

“They seemed to like the whole pogeys (menhaden) better than cigar minnows on that day,” he said. “People caught a lot of big fish that opening weekend, which generally happens in a season. People reported catching legal-size fish relatively quick. They didn’t have to throw many undersized fish back.”

By the time the seas got rough on that opening weekend, Bannon could see how the state management of the season was paying dividends.

“That Monday of opening weekend, we only had a handful of reports through Snapper Check,” he said. “I think that was honest. People really paid attention to the weather and didn’t put themselves in harm’s way. People now realize it’s about the pounds caught and there will be more opportunities to catch snapper later. Of course, that all goes back to the reporting through Snapper Check and getting accurate numbers.”

One thing Bannon did on that opening Friday was to check to see if anglers had the Snapper Check app loaded on their smartphones.

“I, along with other Division employees, helped the ones that didn’t have it get the app loaded on their phones,” he said.

Bannon also discovered that many people are still unaware of the Reef Fish Endorsement that went into effect for the 2020 season. Anglers who catch any fish that are considered a reef fish species are required to purchase the $10 endorsement.

Visit www.outdooralabama.com/saltwater-fishing/saltwater-reef-fish-endorsement for a list of fish species the endorsement covers.

“Nobody seemed overly concerned the endorsement was in place, but they were unaware they needed it,” Bannon said. “Some people purchased it on the Outdoor Alabama app while they were launching the boat.”

The reef fish endorsement provides a source of funding to continue to maintain the research and monitoring for populations in Alabama’s artificial reef zones that is required to continue state management of the red snapper fishery.

“We had been using federal funds,” Bannon said. “We needed a source of funds to continue that work. Also, other than Snapper Check, we didn’t have way to determine how many people are participating in the reef fish fishery. The endorsement helps us to determine the effort.”

Bannon pointed out that if you’re fishing for saltwater species on the Causeway and you don’t catch reef fish, you don’t need to purchase the Reef Fish Endorsement.

“But if you’re participating in the fishery offshore, these funds help us pay for Snapper Check and the monitoring through Dauphin Island Sea Lab and the University of South Alabama,” he said. “Now that we do have state management, we are obligated to manage the fishery to the best of our ability. The endorsement helps provide funds to do that.”

Because the reef fishing endorsement is new, Bannon said Marine Resources Enforcement will issue warnings right now. On opening weekend, 11 warnings were issued for no reef endorsements.

“Our Enforcement staff wrote 12 citations for not reporting their snapper harvests,” he said. “We only had one over-the-limit case. We had no undersized fish citations and only one over-the-limit of all the people that were checked on opening weekend. I consider that a successful weekend. And people used good judgement for the smaller boats to not go on Sunday and Monday. I am a little concerned that our (Snapper Check) reporting is down just a little bit. That is the driving force of our management goal to give people the most opportunities to catch red snapper.”

Meanwhile, the charter-for-hire season opened Monday for a straight 62-day run through August 1, 2020. The charter boat section is still under federal management.

“A couple of different charter captains I’ve spoken with said bookings are up,” Bannon said.

Bannon is excited that it appears the red snapper season will be successful now that restrictions on Alabama’s beaches have been lifted.

“Alabama is definitely a fishing destination,” he said. “I’ve talked to folks who used to go to Destin to go fishing until they discovered Alabama. Now they make plans to go charter fishing in Alabama.”

David Rainer is an award-winning writer who has covered Alabama’s great outdoors for 25 years. The former outdoors editor at the Mobile Press-Register, he writes for Outdoor Alabama, the website of the Alabama Department of Conservation and Natural Resources.