"She went from being a perfect little girl to the total other side of the spectrum," said Johnson. "The hopelessness that you feel as a parent when you see your child declining – I don't know how to describe it."
"The grief cycle just runs over and over again every time there is another loss of a function – the ability to walk or talk – the cycle starts over again," he said.
Johnson, who had once dreamed of becoming the president of the Ohio railroad he worked at, said that his daughter's diagnoses changed his path. Instead, he joined the Batten Disease Support and Research Association and helped it become the leading distributor of information about the disease as well as a fundraiser for research into treatments.
In addition to the gene therapy trials, a stem-cell therapy trial is also underway, said Johnson. The treatment is pending FDA approval before it can proceed.
"Just like gene therapy is looking for funding, we're looking for the FDA to approve us before anything else can be done," he said.
"I am optimistic," said Johnson. "We don't know which therapy will be the one that will work; it's possible that it could be a combination of therapies."
Rochester Medical Center's Pearce said that despite parents' dedication to development of treatments, because so few children are affected by the disease recruiting scientists to research it is not easy.
"The families work incredibly hard [to bring attention to the disorder], but there are still only a few of us in the world working on the research," said Pearce.
"Unfortunately science is like any business – the more dollars we throw at it the more likely we'll be able to fix it," adds Pearce.
Competing with more well-known diseases such as AIDS and cancer for funding and attention is difficult.
But Pearce argues that researchers and doctors wary to get involved are overlooking the fact that breakthroughs for Batten disease will likely be used to understand other neurological disorders.
"Anything we discover for Batten disease will be applicable for many other diseases too," said Pearce.
"We don't understand how the brain works in its normal sense so while studying it in terms of Batten disease we may find something that might be applicable to Parkinson's or Alzheimer's – I'm sure of it."
While their parents continue to try to find funding for the gene therapy treatment, Nathan and P.J. sit together in their shared room and listen to DVDs.
The boys require around-the-clock care, said their mother, who has recently begun to worry that Nathan may not have much longer to live.
"Every day is getting harder," said Tricia Milto. "I do feel like with Nathan I'm playing tug of war right now. I feel like someone tugging him one way saying its almost time and I'm saying I'm not ready."
The Miltos have accepted that Nathan and P.J.'s conditions are too advanced to respond to any of the pending treatments, but say that the way the disease has affected their sons has changed the way they look at life.
They hope their hard work will one day result in a cure for the hundreds of other children suffering from Batten disease.
"I want no one to imagine what we're going through," said Phil Milto. "It was my dream to raise our kids and coach them in sports."