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After superstorm Sandy flooded New York University's medical research laboratories, first accounts were of Herculean rescue efforts. Animal-care staffers spent the night watching over their furry charges and, the next morning, a bucket brigade of scientists and others hauled dry ice up 15 flights to save tissue samples and human organs kept on ice for research.

But a week later a different pictures has emerged. Critics are asking whether the laboratories did everything they could – and whether they followed government guidelines – to protect the research animals.

Thousands of animals, mostly mice housed in the basement of one NYU Langone Medical Center building on the East River in Manhattan, died during the storm. The hospital also evacuated over 200 patients that night when it lost power; none was reported injured.

All told, said NYU spokeswoman Jessica Guenzel, the biomedical facility lost 7,660 cages of mice and 22 cages of rats. Each cage houses between one and seven animals, she said.

"This happens again and again and (research labs) never learn," said Fran Sharples, director of the Board on Life Sciences at the congressionally chartered National Academy of Sciences (NAS).

"Anybody with half a brain knows you do a site-specific analysis" to understand the risk of disasters, she said, "and it's really stupid to put your animals in the basement if you're in a flood zone."

It's not as if scientists didn't have recent lessons in the risk of natural disasters to biomedical research, she said. In 2001, tens of thousands of mice and scores of monkeys and dogs were lost when Hurricane Allison struck Houston; and in 2005, some 10,000 lab animals drowned when hurricane Katrina hit New Orleans.

The National Institutes of Health, the nation's primary funder of biomedical research, requires its grantees to follow the NAS animal-care guidelines. Scientists who fail to do so can have their grants revoked. Animal-use committees at universities also make sure scientists adhere to the guidelines, said Paul Locke, associate professor at the Johns Hopkins Bloomberg School of Public Health, who served on the NAS panel that wrote the 2011 guide.

NIH did not respond to questions about the guidelines, and it is not clear whether NYU in any way breached them.

In a statement, NYU noted that "a vast majority of our animals used for biomedical research were unharmed during Hurricane Sandy," and that the building where thousands did die was built according to code to withstand a storm surge of 20 per cent over the worst flood of the past century.

"Animal resource staff was on site continuously to mitigate the damage from the storm, but due to the speed and force of the surge, animal rescue attempts were unsuccessful," the statement said.

Some scientists who lost years of work praised the university for organizing the rescue efforts. "The amount of effort that went into saving what we could was enormous," said Bruce Cronstein, professor of medicine at NYU and director of its division of translational medicine; he lost an unknown number of mice to Sandy.

NYU officials are also still trying to determine how events unfolded in the lab as the storm blasted New York City.

Scientists say there was a double whammy. Flooding that overwhelmed the basements drowned some animals, while toxic fumes from breaches in the diesel fuel tank and lines that supplied back-up generators killed others.

Driving in from his home in the New York City suburbs last Tuesday morning, NYU neurobiologist Gordon Fishell had reached a bridge into Manhattan when his cellphone rang. A colleague had good news and bad news: "All our reagents [lab chemicals] were safe," said Fishell. "And all our mice were dead."

The Guide for the Care and Use of Laboratory Animals, produced by NAS's Institute for Laboratory Animal Research, states that facilities using animals in research must "have a disaster plan. The plan should define the actions necessary to prevent animal pain, distress, and deaths due to loss of systems such as those that control ventilation, cooling, (or) heating."

The Guide does not prohibit housing lab animals in basements and does not specifically address the threat of floods.

In California and other seismic zones, basements are relatively safe during earthquakes. The natural dark of a basement also lets animal caretakers control their charges' day-night cycle. And when animals are in the basement, any disease-causing microbes they might carry are less likely to enter the main air-circulation system.

But biomedical research facilities also choose basements to keep their animals out of sight, said NAS's Dr. Sharples, partly out of fear of animal rights activists who have been known to raid labs and threaten scientists' lives.

The issue is so sensitive that "the [NYU] administration is very clear that faculty are not to speak directly with the media," one NYU scientist said. "I know there's a concerted effort to not discuss the issues related to research animals. We are being contacted by folks claiming to be reporters, but who are actually PETA activists."

Scientists whose research has been set back years have not publicly criticized NYU but are assessing what they lost.

It took biologist Ryan Branski years to amass the collection of human larynxes and cells growing in lab dishes that he uses to study wound healing and damage to the airways.

"The lab is uninhabitable from a scientific perspective," he said. "We had a great team of graduate students and others shoving dry ice into the freezers" trying to preserve tissue samples. And although he is keeping the freezers closed to keep out any hint of warmth, he fears the larynxes – "irreplaceable human samples" – might be a total loss.

Many of the mice, tissue samples and other tools of the biologists' trade can be replaced, but it could take months to resume the research at pre-Sandy levels.

The mice Dr. Fishell lost were crucial to his studies of how the brain develops and creates a representation of the outside world, as well as how that development goes awry in autism, schizophrenia, epilepsy and other diseases. Many of the mice carried genes that have been linked to one or more of these illnesses and were mutated only in certain brain cells.

Experts on lab animals are quick to say that NYU has good company when it comes to its inability to protect lab animals in a disaster.

"This is just a guess," said the NAS's Dr. Sharples, "but if you did a survey of the universities doing biomedical research you'd find a fair number of animals that are by no means out of harm's way."