Архив метки: laboratory

Using urine samples to diagnose disease in preterm newborns

An interview with Skoltech Professor Evgeny Nikolaev, conducted by April Cashin-Garbutt, MA (Cantab), originally published on news-medical.net.

Which respiratory pathologies are preterm newborns at risk of, and how have these conditions traditionally been tested for?

The majority of patients in neonatal intensive care units are premature babies, who often have infectious (congenital pneumonia) or noninfectious (tachypnea, infant respiratory distress syndrome) respiratory pathologies.

Routine clinical and laboratory tests are not always good for fast and accurate identification of pathogens. Also, the invasiveness of examination and therapy methods is a serious problem for the intensive care and nursing of premature infants.

Left to right - Head of team Prof. Evgeny Nikovaev, Anna Bugrova, Olga Kechko, senior fellow Alexey Kononikhin

Left to right – Head of team Prof. Evgeny Nikovaev, Anna Bugrova, Olga Kechko, senior fellow Alexey Kononikhin

Why is it important to determine whether an infection or a failure in the development process is the underlying cause of the illness?

Identifying the cause of respiratory pathologies in preterm infants and providing them with the adequate treatment is crucial for nursing them back to health.

In particular, it is important to differentiate between the infectious and the noninfectious respiratory disorders, since the former require antibiotic treatment.

What sparked your research into the possibility of using urine samples for diagnosis?

Urine is a desirable material for the study and diagnostics of diseases. The urinary proteome of adults has been studied for more than 30 years, but studies of the urinary proteome in pediatrics, especially in neonatology, are limited.

It is worth noting that, to the best of our knowledge the urine proteome during the first week of life of premature infants with respiratory pathologies of infectious and noninfectious origin was not yet investigated.

How much information can be gained from the urinary proteome?

Urine contains proteins that are readily detectable in all studied individuals (adults, children, infants), also known as the core urine proteome, and infant-specific and disease-specific proteins.

In order to further specify the defined infant-specific dataset, the proteins were compared with the urinary proteome of healthy adults (men and pregnant women).

Which techniques did you use to determine whether respiratory pathologies were infectious or noninfectious?

Here we apply liquid chromatography coupled with high accuracy mass spectrometry to study the urine proteome of preterm neonates with respiratory disorders of infectious (pneumonia) and noninfectious (apnea, transient tachypnea, respiratory distress syndrome) origins.

Label-free proteomic data was compared for preterm neonates with respiratory disorders against term healthy newborns (control) and healthy adults (men and women) with the aim of defining the urine proteins that are disease-specific.

baby

Why have studies of the urinary proteome in pediatrics, and in particular neonatology, been limited in the past?

New technologies are currently being developed rapidly and implemented at the clinic, including its newly established labs.

The major setback for the research of that kind, promising as it may be, has to do with the ethical issues. Nevertheless, a few studies were performed, and potential biomarkers in the urine samples of infants were demonstrated for predicting such pathologies as obstructive nephropathy and necrotizing enterocolitis and for monitoring the development of the urinary system.

What impact do you think this research will have?

In our pilot study, we succeeded in defining the core urinary proteome and the proteins that are specific to infants and pathological conditions. We are pioneers in the noninvasive identification of urinary biomarkers diagnosing respiratory conditions in newborns. The results are optimistic and will serve as a platform to move forward in developing a method of monitoring conditions in newborns.

What are the next steps for your research?

Verification of our results requires further research with a bigger sampling group and the inclusion of additional comparison groups to assess the specificity and diagnostic value of the presented panel of proteins.

Where can readers find more information?

The findings have been published in the Journal of Proteomics.

Skoltech Establishes first Hands-on Biomed Lab

Basic Molecular Biology course at Skoltech: course book and lab equipment

Basic Molecular Biology course at Skoltech: course book and lab equipment

“There might be no word in English to describe what we are doing here”, Skoltech Professor Konstantin Severinov manages to furrow his forehead and chuckle at the same time. A student rushes by through the beige painted corridor at the Institute of Gene Biology, carrying a test-tube rack. A fluorescent purple liquid swirls inside the flask she is holding. The biomed professor glances at the Erlenmeyer and continues: “Skoltech has officially established its first Basic Cafedra. It has an important role in Russian science and academy, because it allows students to combine top notch education with hands-on experience in a real lab. But still, how is this basic cafedra model called in English?” he challenges two colleagues.

“A university department”, one of them attempts cross cultural translation.

“A chair,” another suggests.

“Maybe,” the professor says, “let it be both. What’s important is that our biomedicine students would feel comfortable and confident entering any molecular biology lab in the world.”

Professor Konstantin Severinov with biomedicine technology students at  the Institute of Gene Biology, Msocow. Skoltech and the IGB finalized an agreement to create a "basic cafedra" - a unit combining fundamental studies and hands-on experiences and similar to a department in western research institutes.

Professor Konstantin Severinov with biomedicine technology students at the Institute of Gene Biology, Moscow. Skoltech and the IGB finalized an agreement to create a “basic cafedra” – a unit combining fundamental studies and hands-on experiences and similar to a department in western research institutes.

One of Skoltech’s key targets is to build a community of scientists in collaboration with research centers worldwide. Thus, this specific molecular biology course is modeled after the one designed by Cold Spring Harbor lab in the US. Anna Pavlova, a biomedicine technology PhD student, is a medical doctor and an experienced physician. And still, she says, the establishment of a new biomedicine department and lab experience are a “great opportunity to get a sense of whether you are ready and willing to spend every day over the next three years in a lab.”

Pavlova pours droplets of solution into a Microtiter plate. “We are practicing things such as PCR, point mutations, restriction, knockouts, and designing primers, which are strands of nucleic acid that serve as a starting point for DNA synthesis. These skills allow us to feel much more comfortable in a foreign lab and develop a deeper understanding of theoretical courses.” She puts the pipette aside.

“Wednesday has become so exhausting since we have begun working here. But it’s my favorite day of the week. It slowly dawns on me that a mixture of something with something could knockout genes or give E.coli bacteria absolutely new features.”

Like what?

“Like antibiotic resistance or the ability to produce fluorescent proteins. Interesting, right?”

The molecular biology Skoltehc course is modeled after a hands-on experience designed by Cold Spring Harbor lab in the US.

The hands-on modular molecular biology Courses at Skoltech are modeled after the Cold Spring Harbor laboratory courses in the US.

Brendan Wilcox, a Canadian PhD student who joined Skoltech this year, oversees the proceedings at the laboratory. A graduate of Penn State university, he is experienced in lab techniques and was appointed teaching assistant (TA) for this course.

“My role in this particular class is to help oversee the students as they go through the laboratory procedures, and answer any technical questions they may have. I also do my best to instill some English speaking lab lingo”, he smiles.

“But mind you, the course is as good as any class taught in an American university. Except there is more Russian being spoken here.”

 While planners and builders rush to complete the construction of the Skoltech campus, interim solutions must be devised. The eight students work and study at a lab located at the Institute of Gene Biology in Moscow, a division of the Russian Academy of Science, which signed an agreement with Skoltech.

“Our PhD students get to do proper lab rotations and research projects here,” explains Severinov, a Russian expat who returned from the US to live in the Russian capital and heads five labs worldwide.  “We followed a hugely successful strategy developed by the Moscow Institute of Physics and Technology (also known as Phystech) in the 1950’s. They are the ones who originally created the ‘basic cafedra’ (‘базовая кафедра’ in Russian). We stand on the shoulders of some very serious people.”

 

 

Skoltech biomedicine technology MSc and PhD students at a molecular biology class.

Skoltech biomedicine technology MSc and PhD students at a molecular biology class.

Course instructor Inna Zukher takes students through the intricacies of molecular biology research methods.

Course instructor Inna Zukher takes students through the intricacies of molecular biology research methods.

Brendan Wilcox, a Penn State graduate is a PhD student and teaching assistant (TA) at Skoltech: "The course is as good as any class taught in an American university."

Brendan Wilcox, a Penn State graduate is a PhD student and teaching assistant (TA) at Skoltech: “The course is as good as any class taught in an American university.”

 

 

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