News
The Kansas Intellectual and Developmental
Disabilities Research Center
(Formerly
the Kansas Mental Retardation and Developmental Disabilities Research Center)
Volume 8, No. 10, October-November 2007
Editor:
Karen Henry, Assistant Director for Communications, for Steven Warren, Director, KIDDRC, and Peter Smith, Co-Director, KIDDRC
Eighth Annual
NIH Summer Institute on Randomized Clinical Trials Involving Behavioral
Interventions
This
month, we get a refresher course on some of the excellent services the KIDDRC
Cores offer investigators - plus some news.
The
KUMC Microarray Facility
Clark Bloomer,
Project Manager
The
KUMC Microarray Facility would like to inform the KIDDRC community of some
recent additions to our personnel and offered services. In March the Microarray
Facility added Yafen Niu as a Research Associate to the facilities staff. Yafen
performs an integral role in the microarray services offered by the facility as
well as a lead role in the newly implemented RNA isolation service. The
facility is also servicing the new Gene Array and Exon Array expression
platforms for the Affymetrix GeneChip system. The Human SNP
5.0
(500k SNP) and 6.0 (1M SNP) are the latest genomic mapping arrays that will be
serviced by the Microarray Facility. In support of investigators conducting
genomic mapping projects, the facility has also added DNA isolation services.
For more information, see: http://www2.kumc.edu/siddrc/microarray.
The
Bioinformatics Core at KU Medical Center
Stan R. Svojanovsky, Ph.D.
Bioinformatics
Coordinator
New microarray technologies and data evaluation software
allow us to investigate many genes at once and determine which are expressed in
a particular cell type. We use this powerful technology to investigate which
genes are turned on and off in treated versus healthy tissues from various
organisms and to determine the biological relevance of the genes and the
biological pathway between different classes of genes.
The
KUMC Bioinformatics Core was established with funding
from NIH Grant Number P20 RR016475 from the INBRE Program of the National
Center for Research Resources (Kansas IDeA Network of Biomedical Research
Excellence (K-INBRE) and supported by The Smith Intellectual
Developmental Disabilities Research Center (SIDDRC)
NICHD HD 02528.
The primary goal of this core is to provide high quality collaborative services
for genomic, proteomic and biomedical data analysis to investigators at KUMC
other K-INBRE participants and KIDDRC investigators on either campus.
We
provide assistance in three phases of microarray data analysis. In the primary phase, data, including numerical
signal intensity and the probe accession number, are formatted, normalized and
transferred into Affymetrix Data Mining Tool. The data are saved in Microsoft
Excel format, which is compatible with Affymetrix, GeneSpring and StatMost
software. Data are archived as password-protected copies maintained in a CD
library, on computer hard drives and on the K-INBRE server. Databases are
created using Affymetrix GCOS (GeneChip Operating System) software and
populated via GCOS Data Transfer Tool into Affymetrix Data Mining Tool. Numbers
of genes present in the target samples are determined and ranked according to
fold change relative to control samples.
Statistical significance for changes in expression is determined using
StudentÕs t-test. Visual information on changes in gene expression for all
probe sets is represented via scatter plots, histograms and fold change graphs.
In
the secondary phase, additional data mining is conducted based on the specific
aspects of the experiment and the investigatorÕs requirements. This usually
includes reordering of the data, data filtration, additional plots, and cluster
analyses. We also provide information on protein descriptions and biological
pathways using Affymetrix NetAffx web site, GeneSpring GX, Ingenuity Pathway
Analysis and other relevant software platforms and databases.
Tertiary
analysis consists of more detailed analysis of the microarray data, including
mining a specific group (cluster) of genes of interest. Comparisons of different clusters of
genes and Principal Component Analysis (PCA) to reveal and quantify the impact
of the principal gene in a given cluster are conducted using GeneSpring GX
software. Location of sequences
and specific genes on the genome and the degree of sequence similarity is determined
using BLAST and BLAT analysis with publicly available genome databases.
For
more information, please visit our web page:
http://www2.kumc.edu/siddrc/bioinformatics/
Biobehavioral
Measurement: Rodent Behavioral
Testing
Jonathan Pinkston, Ph.D. Biobehavioral Core
Coordinator
The
Biobehavioral Measurement Core (BMC) provides KIDDRC investigators with a host
of resources related to behavioral measurement. In addition to experimental design, programming, and
instrumentation design, the BMC also manages and controls resources related to
rodent behavioral testing. Many
investigators trained in pharmacology, medicine, or molecular biology
underutilize behavioral procedures or, when they are applied, use procedures
that are less than the state of the art.
Often the dearth in behavioral procedures is the consequence of training
that has de-emphasized behavioral research and many researchers simply are not
familiar with the complexities of behavioral experimentation. After all, one cannot be a specialist
in everything.
And
that is where the BMC comes in: we have a staff of behavior specialists with
backgrounds in animal learning, psychopharmacology, and behavioral neuroscience
to provide expertise in these areas and aid in adding behavior dimensions to
your research. The BMC is a unique
opportunity for KIDDRC investigators.
Currently,
the BMC manages two resources for rodent behavioral testing. At the KU campus in Lawrence,
renovations have been completed for the Complex Behavior and Learning Facility,
located in Malott Hall. At
present, equipment is being moved into the new facility. The various apparatuses and testing
batteries will be made available as they come online. The full suite of equipment will provide for experimentation
with transgenic and knockout mice to examine a broad range of brain and
psychological processes.
The
BMCÕs rodent testing aspect also has a presence at KUMC. The Rodent Behavior
Facility (RBF) counterpoints the facility in Lawrence. Over the past several years,
investigator usage of the rodent testing resources has greatly increased for
the RBF. The swell of requests has
prompted a new addition to the capabilities at the KUMC campus. The new addition will occupy a 500
square-foot laboratory space in the new KLSIC building and will be dedicated
solely to the examination of rat behavior. The existing facility in the LAR building will continue to
service the interests of researchers using mouse models.
Together,
the two facilities currently support investigations of rodent models in several
areas of research, including schizophrenia, stereotypy, HuntingtonÕs Disease,
AlzheimerÕs Disease, diabetes, spinal injury and recovery, ALS,
nutritional-related cognitive impairments, and impulse-control disorders. The breadth of research projects speaks
to the range of domains to which our skills are applicable. So, when it comes time to consider
systems-level experimentation, the BMC stands ready. We look forward to helping our investigators meet the needs
of their projects and to the generation of collaborative research
enterprise. Those interested in
adding state-of-the-art behavioral testing to their existing projects should
visit the BMC website at http://kiddrc.kumc.edu/coreb.html
for more information.
Raymond Cheung,
Assistant Director for Information Technology, Life Span Institute
The Ticket Tracker System, an online system that tracks the
service requests of KIDDRC affiliated investigators, has been in use by Core B
– Biobehavioral Measurement staff for more than 2 months. The system for Core C - Research Design
and Analysis - will go live by the end of fall semester. The Core C staff is currently learning
the process and reviewing details.
Core D, Integrative Imaging, is still
working with the software developer to customize their forms and reports and
will have the system ready to use soon.
Stay tuned for the progress. You can access Ticket Tracker online at the
following URLs or you can simply call the core coordinators as usual and they
will initiate the request for you.
Core B: http://www2.ku.edu/~lsi/cgi-bin/tracker/newrequest.php
Core C: http://www2.ku.edu/~lsi/cgi-bin/CoreCtracker/newrequest.php
A one-time administrative supplement to our P30
will support the dissemination of the highly successful program of LSI Peruvian
affiliate, Centro Ann Sullivan del Per, across
Peru and to other third world countries. CASP, directed by Liliana Mayo, who
received her doctorate from KU, and Judith LeBlanc, KU Professor Emeritus, is a
comprehensive model program for children and adults with developmental
disabilities and their families.
CASP has received international awards and
recognition for its highly sustainable family-based holistic approach grounded
in evidence-based practices. CASP attracts faculty and students from KU and
other universities who teach and learn in the school set in urban Lima. Several
KIDDRC investigators have consulted with CASP in recent years including Steve
Warren, Steve Schroeder, Matt Reese, and Eva Horn.
The supplement will support the development,
testing and evaluation of an online system to allow CASPÕs video-based training
modules to be accessible through the Internet via technologies that can
function in regions with very low bandwidth infrastructure based on the
University of IowaÕs Global Campus Network.
Karen Henry, LSI Assistant Director for
Communications and a Core A staff member, will serve as project coordinator
working with a CASP counterpart.
Eighth
Annual Summer Institute on Randomized Clinical Trials Involving Behavioral
Interventions
The Eighth Annual Summer Institute on Randomized Clinical Trials Involving
Behavioral Interventions, organized by the NIH Office of Behavioral and Social
Sciences Research, is scheduled for July 13 - 25, 2008, the Airlie Conference
Center in Airlie Virginia, about 60 minutes driving time from Washington, DC
and surrounding airports.
The
objective of the Institute is to provide a thorough grounding in the
conduct of randomized clinical trials to researchers and health professionals
interested in developing competence in the planning, design, and execution of
clinical trials involving behavioral or social interventions.
APPLICATIONS DUE JANUARY 31, 2008:
Applications for 2008 must be submitted electronically. The
application instructions are posted at http://www.blsweb.net/app2attend/
General Information at
http://obssr.od.nih.gov/Content/Training_and_Career_Development/Annual_RCT_Course/RCT_2008/2008_RCT.htm
FREQUENTLY ASKED QUESTIONS:
http://obssr.od.nih.gov/Content/Training_and_Career_Development/Annual_RCT_Course/RCT03_QA.htm
LISTSERV for Course Information:
For periodic updates, join the electronic mailing list for forthcoming
announcements and instructions by sending an e-mail message to
listserv@list.nih.gov. The
body of the message should read
SUBscribe RCT-L [your full name]. The message is case sensitive; so
capitalize as indicated! Don't include the brackets.
The subject line should be blank.
CONTACTS
Ronald P. Abeles, Ph.D.
Special Assistant to the Director
Office of Behavioral and Social Sciences Research
National Institutes of Health
Bldg. 31C, Rm. B1C19, MSC 2027
Bethesda, MD 20892-2027
Telephone: 301.496.7859
Email: abeles@nih.gov
Funded
by NICHD HD048528
Kate Saunders, Ph.D., Principal
Investigator, LSI Senior Scientist
and KIDDRC Investigator
Many
individuals with mental retardation (MR) read at levels below what might be
expected based on other cognitive skills. Further, reading instruction
historically has emphasized sight words, and this emphasis limits reading vocabulary
to words that have been taught directly. There is a critical need for effective
methods to teach word-attack, or decoding, skills to this difficult-to-teach
population. Word-attack skills enable reading words that have not been taught
directly.
In
the literature on reading instruction for normally developing children, the major scientific development of
the last few decades has been the identification of prerequisite and component
skills that help to make decoding instruction successful. There is now
incontrovertible evidence that phonological awareness, especially the ability
to perceive sounds that make up spoken syllables, facilitates the acquisition
of word-attack skills. Examples of phonological awareness include recognizing
rhyming words, and recognizing that several words begin with the same sound. Phonemes are the smallest
within-syllable units of sound that make a difference to meaning. It is
important to note that learning to produce individual phonemes to corresponding
printed letters (a part of phonics instruction) does not automatically ensure
the awareness of phonemes within syllables. This is because phonemes within
syllables are Ōsmeared together,Ķ they do not have discrete boundaries (this
characteristic is called coarticulation).
Our
long-term goal is to develop computerized instructional programming to teach
foundational skills for reading to individuals with MR. The current project
will take a step towards that goal by addressing the most neglected area of
instruction for this population: the critical early reading skills of
phonological awareness and the related concept that print maps the sounds that
comprise syllables. The scientific foundation for our work lies in the
conclusion of the National Reading Panel (2000) that phonological-awareness
training that involves linking letters to sub-syllable sounds is more effective
than training that is conducted only in the auditory mode. Thus, we plan to
study the development of these skills using a word-construction task, in which
the participants build words that they hear by touching individual letters in a
pool of letters on a touch-sensitive computer screen. The word-construction
procedures have several benefits. They promote left-to-right scanning and
attention to each letter in a word. Further, if carefully composed sets of
words that have subsyllable components in common are taught, these procedures
can simultaneously promote the development of generalized sound-print relations
and phonological awareness.
We
will know that a participant has learned generalized skills when the
participant can construct words that are composed of new combinations of
sound-letter relations contained in words that the participant has learned to
construct. For example, if a participant learns to construct the words cat,
rat, and ran, and then proves able to construct can, even
though can has not been taught, s/he has demonstrated generalization of
the sound-letter relations across words. Further, our work has shown that it is
not necessary for participants to be able to read words before learning to
construct them. Given that the word construction task teaches component skills
of individual-word reading, it is important that word-construction training can
occur prior to or in conjunction with learning to read the words. This is an
unstudied approach to establishing foundational skills in individuals with MR.
The
project is being carried out with adults served by Community Living
Opportunities and by Cottonwood, in Lawrence. Children participants come from
the Educare preschool in the Dole building and we are planning for an expansion
to children with intellectual disabilities in the Lawrence Public Schools. Four
graduate students within the Department of Applied Behavioral Sciences are
working on the project: Janna Skinner, Tanya Bayhnam, Katey Schmidt, and Megan
Weaver.
SEASONS
GREETINGS!