Shoots of recovery

C&I Issue 11, 2008

‘It looked like an absolute disaster. On the ground level floors there was mud, spilled chemicals, damaged equipment, mould growing on the walls. There were even dead fish in the hallway.’

This was the scene that greeted Pat Jordan, then director of the US Department of Agriculture’s Southern Regional Research Center (SRRC), in early October 2005 when he was finally able to get back to survey the damage inflicted by Hurricane Katrina.

The storm hit New Orleans several weeks earlier, on the morning of Monday 29 August 2005. While most of the city’s residents – including SRRC staff – had already fled the area after the order to evacuate at the weekend, the real ‘catastrophe of Katrina,’ says Al French, a researcher in the SRRC’s cotton, structure and quality research unit, ‘was the unprecedented destruction of the levees and floodwalls’ surrounding the city.

Designed and built by the US Army Corps of Engineers, the storm surge caused more than 50 breaches in these drainage and navigational canals – dubbed the ‘worst engineering disaster in US history’.

Located in the Lakeview area of the city, SRRC was flooded to a depth of roughly 1.5m, creating havoc with electrical, heating, ventilation and air conditioning units located on the ground floor. ‘Because of the flooding, even the emergency power stopped, causing loss of precious refrigerated and frozen samples,’ French says. ‘Research termites expired. Our textile building lost its large-scale warping and sizing equipment that prepared yarns for weaving, as well as the dyeing and finishing equipment for processing the woven fabric. A number of research offices and laboratories were located at ground level, where normal office and laboratory equipment was lost.’

Most of the chemicals in the chemical storeroom in the basement also had to be discarded. ‘Temperatures reached the upper 90s for weeks after the storm and mould grew with great enthusiasm with all the humidity from the flood waters in the building.’

With the building out of action, Jordan’s most immediate priority was to take care of his staff. In all, more than $5m was spent on relocation and support for staff, assigned to 22 locations including other USDA sites and universities across the US. French himself was relocated to the USDA laboratories in Athens, Georgia, and was offered a spare room in the house of one of his research colleagues at the University of Georgia. ‘We received an allowance for being at a temporary duty location, so there was little feeling of deprivation as far as I was concerned. Still, I was very sympathetic for colleagues who had lost their homes or sustained major damage, as well as those who didn’t have the freedom to travel so much. Many had to put their home repairs on hold while they were away.’

Work to repair the damaged SRRC buildings started in October 2005, with funding from the USDA-Agricultural Research Service (ARS), which operates SRRC. Once the debris and chemical and biological materials were cleaned away, the next priority was to restore power supply and get the air conditioning back in action as soon as possible to control mould growth So far about $24m has been spent to get the SRRC operating and to replace equipment. Another $20m is being spent on protection against future flooding and on long-term recovery.

Ten months after Katrina, and one year earlier than experts had predicted, SRRC reopened and all employees were recalled by 3 July 2006. Employees who did not have housing were assigned a standard trailer provided by the Federal Emergency Management Agency. A village of 50 trailers was set up in the parking lot behind the SRRC, where employees could stay for up to a year while repairing their home or making new arrangements.

But perhaps the biggest indication of the success of the overall operation was the fact that most of the Center’s staff came back, Jordan says. Compared with other US federal agencies in the region, which lost roughly a quarter of employees on average, SRRC lost only 3-4% of net staff.

Cotton picking ideas
Knowing when exactly to pick cotton is a skilled business, says James Rodgers, head of the SRRC’s cotton structure and quality (CSQ) research unit. If picked too early, the cotton will be immature, which can impact downstream quality and processing, but leave it too late and it may be ‘off-quality’.

To do away with this uncertainty, CSQ scientists have now developed a portable technique for testing the state of readiness of cotton plants in the field, by assessing the quality of the growing cotton boll. The method, Rodgers says, is one of the first applications of near infrared (NIR) spectroscopy for field-testing cotton plants. It works by measuring the cellulose content of the cotton fibre, in turn a measure of a key cotton quality parameter called ‘micronaire’, which represents the combination of the fibre’s maturity and size (‘fineness’).

The traditional way of assessing cotton quality is by using a laboratory-based High Volume Instrument (HVI), Rodgers explains, which gives a readout of six parameters including length, strength, length uniformity, colour, trash content and micronaire, in just under one minute. However, ‘it costs over $200 000 and requires trained operators and very consistent laboratory conditions and control’.

The new NIR analyser is intended to complement rather than replace the HVI, Rodgers notes. It costs under $30 000, is easy to use and requires minimum training to operate. Total analysis time is less than a minute and can be performed at-line during ‘ginning’ on a fibre-production plant as well as in the field.

Tests of the portable analysers to measure micronaire in the lab have already proved successful, Rodgers says. ‘Investigations in the field are still ongoing, but initial results are encouraging.’

Wiping out aflatoxin
Farmers around the world could one day have SRRC scientists to thank for wiping out one of their most deadly enemies: aflatoxin. That day may now have come a step closer with the sequencing by SRRC and other US scientists of the fungus Aspergillus flavus that produces the toxin, a known carcinogen that renders crops unsafe for consumption and un-saleable.

In as yet unpublished work, researchers in the SRRC’s food and food safety unit, and their collaborators at North Carolina State University and the J Craig Venter Institute, claim to have deduced for the first time the complete genome sequence of the fungus – information that they believe could lead to new weapons by which to combat and one day possibly even eradicate the toxin.

‘Our research partners are using the genetic information to see how the fungus reacts to environmental stress, ie conditions under which aflatoxins are produced by the fungus,’ explains Deepak Bhatnagar. ‘For the first time we have the tools to study how the fungus survives in the field, how it interacts with the crop plants it invades. So, we have the potential of finding some weaknesses in the toxin contamination process so that we can interrupt it from happening.’

Crucially as well, Bhatnagar continues, the SRRC researchers have recently identified a gene that controls the switching on and off of the entire suite or cluster of genes responsible for aflatoxin synthesis. Earlier work by the group has already pinpointed all of the genes in the cluster, as well as the entire biosynthetic pathway by which the toxin is produced.

‘The volume of data is so large that it will take us a while to sort through all of this,’ Bhatnagar says. However, he notes that the team hopes ‘to have some answers’ about how to develop useful strategies for combating aflatoxin in the next two to three years.

Methods to eradicate the toxin are urgently sought after. It has been estimated, for example, that cotton, maize, peanut and tree nut farmers can lose $100m crops in drought periods as a result of aflatoxin contamination, says SRRC interim director Ed Cleveland.

Low allergy peanuts
‘There are roughly 14 000 varieties of peanuts in the US germplasm collection,’ says Soheila Maleki, in the SRRC’s food processing & sensory qualities unit.  ‘We have screened over 900 of these and found a variety that lacks one of the Ara h2 isoforms, the most potent allergen in peanut, and other varieties that lack Ara h3 isoforms or have reduced levels of Ara h1, other major allergens.’

The ultimate aim of this work, Maleki explains, is to cross-breed these various peanut varieties to produce a new nut with a lower allergy potential compared with the ones commonly on supermarket shelves. ‘At the very least we are aiming to increase the threshold for a severe reaction, so that more of a nut containing food has to be eaten to cause a severe reaction. This will give individuals a chance to recognise peanut presence, ie mouth tingling, before they have a severe or fatal reaction by ingesting a large dose.’

The other possibility, she says, is to use the new peanut in desensitisation protocols to try to reduce the sensitivity of allergy sufferers.
With the help of a breeder at North Carolina State University, Maleki and coworkers have already shown that it is possible to produce a nut lacking both Ara h 3 and Ara h 2 proteins. Unfortunately, ‘due to Katrina all of the peanut  progeny were destroyed,’ Maleki says, ‘but not without leaving us with the knowledge that it is possible to incorporate those two traits (so far) into one  peanut.’

Now that the new breeding programmes are under way, the new nuts could be ready for human food tests in the next couple of years or so, the researchers say. Until then, it remains unclear how allergenic they may be. However, allergens Ara h 2 is recognised by more than 90% of the allergic population, and Ara h 3 by more than 50% of these individuals, Maleki points out. Ara h1 is another important target of recent breeding programmes, recognised by 90% of people with peanut allergy in the US.

Depending on the success of the programme, the new nuts could be on the marketplace in the next five to 10 years, Maleki says. Producing a totally allergy-free peanut is probably not possible, she adds, because many of these proteins also perform a critical function as seed storage materials.

Banishing bedsores
About 5m Americans, mostly the elderly, suffer from chronic and occasionally fatal open wounds also known as bedsores. The annual healthcare costs associated with treating them is estimated at around $7bn. Now, however, Vince Edwards and colleagues in SRRC’s cotton, chemistry & utilisation unit, believe they may have a solution in the form of super-smooth hospital bedsheets that could banish bedsores by preventing them before they even begin.

Widespread adoption of the new sheets, which could be available within the next five years, could see a ‘significant reduction’ in the number of cases of bedsores, according to Edwards – and could save lives. More than 30 000 people die in the US as a result of bedsores every year, particularly as a result of infections in the sores spreading to the underlying bone tissue.

The trick to making the new sheets, Edwards explains, lies in targeting two key risk factors known to promote the onset of the sores: friction and shear. Friction when the body slides across the bedsheet leads to the sloughing off of the outer layers of skin, while shear forces inside skin tissue occur as a result of gravity, for example, when a patient sits up in bed. And in addition to their super-softness, the new sheets are also designed to be wrinkle-free and possess antibacterial properties to ward off infection.

Traditional hospital bedsheets are typically made of a mixture of 50% cotton and 50% polyester, Edwards explains, but although this improves durability the sheets are not as soft as cotton alone. The novelty of the new sheets lies in using polyethylene glycol (PEG) polymers as the linker by which to graft the antimicrobial reagent – chitosan – onto the fabric and thereby improve the softness or ‘hand’ of the cotton, he says. In addition, the cotton is also treated with citric acid to produce a wrinkle-free effect not unlike that achieved in non-iron shirts.

The team is currently working with Louisiana State University engineers to incorporate the fabric in a multilayer cotton bedsheet that can also wick away moisture and keep the skin dry and cool. Moisture on the skin – often a problem with elderly patients who may be incontinent – softens skin and leads to the more rapid development of sores, Edwards explains.

The sheets will be designed for use alongside new foam mattresses increasingly used in some hospitals to alleviate bedsores by reducing downward forces that are another critical factor in their formation.

‘The real trick is to get approval from the US Food & Drug Administration to label the sheets as a medical device or “Bedsore Prevention Bedsheet”,’ Edwards says. While this could take five years to achieve, he points out that the FDA backing would help to bolster support among medical insurance companies which could put pressure on hospitals to adopt the technology.

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