Introduction
Herein we present details of the standard procedures and operations of the Leukemia Sample Bank (LSB) as a guide to others desiring to establish their own bank. The availability of ...primary tissue samples to evaluate the molecular biology and pathogenesis of leukemia, as well as to develop and evaluate novel therapeutic strategies, has been instrumental to advances in the leukemia field. The Department of Leukemia at the University of Texas M. D. Anderson Cancer Center (MDACC) improves the treatment of patients with leukemias by providing basic, translational, and clinical scientists access to clinically annotated fresh and frozen primary tissue samples to test and validate their hypotheses. The LSB was created to collect, process, and maintain tissue specimens from patients with known or suspected hematologic malignancies, and also maintains a comprehensive, prospective, interactive database with detailed clinical and pathologic data and facilitates distribution of samples to various investigators.
Bank Design and Activity
An MDACC protocol was IRB approved in 2001 to facilitate primary leukemia tissue collection, storage, and distribution. The protocol serves as a "front door" consent to the Leukemia Department for approaching all new patients that come to the Leukemia Center. The protocol allows for use of tissue samples for current and future research projects related to researching hematological malignancies. Investigators utilize a separate IRB approved "back door" protocol, with a waiver of consent, to obtain samples for various projects. The LSB protocol thus serves as a single-sign research consent for patients, avoiding consent "fatigue" and ennui. A bank usage committee reviews request for samples and determines which to approve, including collaborations that are intra departmental, intra institution, inter academic institutional and with pharmaceutical institutions. A priority of usage is given to MDACC leukemia department investigators, other academic departments inside and outside MDACC, and finally to pharmaceutical institutions. Our policy is not to release the last vial of material for any particular patient. In the past year, these efforts have resulted in 93% of patients being approached, 82% providing consent, and only 11% declining. While most patients are motivated to consent to help advance research and improve treatments, hematology banks are unique in that they experience barriers to consent that solid tissue banks may not. Once blood and bone marrow samples are obtained, samples are processed per disease specific algorithms on the same day of collection to yield disease enriched material such as DNA, RNA, protein, serum or viable cells. Same day processing removes cryopreservation effects on labile analytes (mRNA, miRNA, protein) that could arise from a freeze thaw cycle. Material is distributed fresh to investigators or cryopreserved for later use. Samples are collected serially at the time of diagnosis, during therapy, in remission, or at relapse. The LSB provides annotated clinical data for any distributed samples. In support of the bank, a database records sample collection and archive details, and provides "chain of custody". A query tool was also developed allows for searching sample inventory by demographic, clinical, and sample characteristics, which also links to the Leukemia Clinical Data Repository (LCDR), to allow for searching of samples by leukemia specific characteristics such as diagnosis, prior treatments, and cytogenetic abnormalities.
Results
The LSB is one of the world's largest leukemia repositories and serves as a valuable local and national resource. The very high levels of patients consenting to participate make the holdings truly representative of all leukemias. The serial samples collected from patients allow for comparison between diagnosis and relapse states of disease. The ability to provide detailed annotation of clinical, laboratory, and outcome data further increases the value of research done with these samples. The LSB continues to collect valuable samples for use in research related to improving patient outcomes for patients with hematological malignancies.
No relevant conflicts of interest to declare.
Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been ...investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions.
Through microarray analysis of exponential- and stationary-phase cultures with low and high domoic acid production, respectively, we identified candidate reference genes whose transcripts did not vary across conditions. We tested eleven potential reference genes for stability using RT-qPCR and GeNorm analyses. Our results indicated that transcripts encoding JmjC, dynein, and histone H3 proteins were the most suitable for normalization of expression data under conditions of silicon-limitation, in late-exponential through stationary phase. The microarray studies identified a number of genes that were up- and down-regulated under toxin-producing conditions. RT-qPCR analysis, using the validated controls, confirmed the up-regulation of transcripts predicted to encode a cycloisomerase, an SLC6 transporter, phosphoenolpyruvate carboxykinase, glutamate dehydrogenase, a small heat shock protein, and an aldo-keto reductase, as well as the down-regulation of a transcript encoding a fucoxanthin-chlorophyll a-c binding protein, under these conditions.
Our results provide a strong basis for further studies of RNA expression levels in Ps-n, which will contribute to our understanding of genes involved in the production and release of domoic acid, an important neurotoxin that affects human health as well as ecosystem function.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Course-based research pedagogy involves positioning students as contributors to authentic research projects as part of an engaging educational experience that promotes their learning and persistence ...in science. To develop a model for assessing and grading students engaged in this type of learning experience, the assessment aims and practices of a community of experienced course-based research instructors were collected and analyzed. This approach defines four aims of course-based research assessment—(1) Assessing Laboratory Work and Scientific Thinking; (2) Evaluating Mastery of Concepts, Quantitative Thinking and Skills; (3) Appraising Forms of Scientific Communication; and (4) Metacognition of Learning—along with a set of practices for each aim. These aims and practices of assessment were then integrated with previously developed models of course-based research instruction to reveal an assessment program in which instructors provide extensive feedback to support productive student engagement in research while grading those aspects of research that are necessary for the student to succeed. Assessment conducted in this way delicately balances the need to facilitate students’ ongoing research with the requirement of a final grade without undercutting the important aims of a CRE education.
Genetic markers identifying women at an increased risk of developing breast cancer exist, yet the majority of inherited risk remains elusive. While numerous
BRCA1
coding sequence mutations are ...associated with breast cancer risk,
BRCA1
mutations account for less then 5% of breast cancer risk. Since 3′ untranslated region (3′UTR) polymorphisms disrupting microRNA (miRNA) binding can be functional and can act as genetic markers of cancer risk, we tested the hypothesis that such polymorphisms in the 3′UTR of
BRCA1
and haplotypes containing these functional polymorphisms may be associated with breast cancer risk. We sequenced the
BRCA1
3′UTR from breast cancer patients to identify miRNA disrupting polymorphisms. We further evaluated haplotypes of this region including the identified 3′UTR variants in a large population of controls and breast cancer patients (
n = 221
) with known breast cancer subtypes and ethnicities. We identified three 3′UTR variants in
BRCA1
that are polymorphic in breast cancer populations, and haplotype analysis including these variants revealed that breast cancer patients harbor five rare haplotypes not generally found among controls (9.50% for breast cancer chromosomes, 0.11% for control chromosomes, p = 0.0001). Three of these rare haplotypes contain the rs8176318
BRCA1
3′UTR functional variant. These haplotypes are not biomarkers for
BRCA1
coding mutations, as they are found rarely in
BRCA1
mutant breast cancer patients (1/129 patients = 0.78%). These rare
BRCA1
haplotypes and 3′UTR SNPs may represent new genetic markers of breast cancer risk.
Genetic markers identifying women at an increased risk of developing breast cancer exist, yet the majority of inherited risk remains elusive. While numerous BRCA1 coding sequence mutations are ...associated with breast cancer risk, BRCA1 mutations account for less then 5% of breast cancer risk. Since 3' untranslated region (3'UTR) polymorphisms disrupting microRNA (miRNA) binding can be functional and can act as genetic markers of cancer risk, we tested the hypothesis that such polymorphisms in the 3'UTR of BRCA1 and haplotypes containing these functional polymorphisms may be associated with breast cancer risk. We sequenced the BRCA1 3'UTR from breast cancer patients to identify miRNA disrupting polymorphisms. We further evaluated haplotypes of this region including the identified 3'UTR variants in a large population of controls and breast cancer patients (n=221) with known breast cancer subtypes and ethnicities. We identified three 3'UTR variants in BRCA1 that are polymorphic in breast cancer populations, and haplotype analysis including these variants revealed that breast cancer patients harbor five rare haplotypes not generally found among controls (9.50% for breast cancer chromosomes, 0.11% for control chromosomes, p=0.0001). Three of these rare haplotypes contain the rs8176318 BRCA1 3'UTR functional variant. These haplotypes are not biomarkers for BRCA1 coding mutations, as they are found rarely in BRCA1 mutant breast cancer patients (1/129 patients= 0.78%). These rare BRCA1 haplotypes and 3'UTR SNPs may represent new genetic markers of breast cancer risk.
PDF
