New Mexico INBRE Specific Aims in Brief

(NM-INBRE 2014 – 2019)

1. Network leadership, organization, oversight, and communication

2. Student-focused experiences in biomedical and biobehavioral research

3. Sequencing & Bioinformatics Core (SBC)

4. Faculty development and scientific research projects (DRPP)

5. Collaboration

    a. multi-disciplinary collaborative and community-based research, and

    b. cooperate synergistically with NIGMS IDeA and

    c. other related programs at the state, regional and national level

 

New Mexico INBRE Specific Aims, Complete

 

1. Network leadership, organization, oversight, and communication

Aim 1a: The continuing successful management and operation and achievement of progress towards the long-term goals of the program will be accomplished through an experienced leadership team and highly capable staff.

Aim 1b: The established organizational structure and framework of formal policies, procedures and agreements in place will support continuing development and effective management of NM-INBRE as a dynamic and functional network.

Aim 1c: The Steering Committee will provide governance of the program through implementation of policies and operating procedures with effective representation of the priorities, interests, and internal perspectives of the individual participating network institutions.

Aim 1d: The External Advisory Committee will contribute scientific expertise in the thematic focus areas with direct responsibilities for the admission of investigators, assessment of progress, and guidance to ensure effective operation and longitudinal progress of the network towards achieving the goals of the program.

Aim 1e: Cohesive relationships and dissemination of information between network participants and institutions will be fostered through effective communications, organized meetings and conferences.

Aim 1f: Systematic program evaluation of the processes and outcomes will enable further development and improvements and contribute to the overall success of NM-INBRE. The Evaluation Plan will consist of both internal and external evaluation components, which combined will provide a comprehensive and systematic approach to assessing the effectiveness of the NM-INBRE in developing an institutional and statewide scientific network. Benchmarks and specific measures of assessment will be defined for each of the Aims 1-5 in this plan.

 

2. Student-focused experiences

Aim 2a: Student research experiences will be available through Developmental Research Projects.

Aim 2b: Formal programmatic undergraduate summer research experiences will be available for promising and highly qualified undergraduates.

Aim 2c: Inter-programmatic coordination of activities and effective partnering with other Training Workforce Development and Diversity (TWD) programs will facilitate the research training objectives.

 

3. Sequencing & Bioinformatics core (SBC)

Aim 3a: Advance cutting-edge knowledge discovery through innovative bioinformatics analysis techniques, resources, and tools. NGS is the first step in unlocking biologically-relevant discoveries. Mining and interpretation of the data are paramount. We will apply our robust array of bioinformatics resources, experience and skills to advance research in the network.

Aim 3b: Deliver and develop ground-breaking next-generation sequencing technologies and resources. NGS is transforming the genomics and transcriptomics landscape. We will leverage these resources, and use our knowledge and expertise to develop new techniques to accelerate research possibilities for the network.

Aim 3c: Engage the network in education and training through outreach, mentorships, internships, and symposia. There is great importance in training students in this rapidly developing field. Scientists and health professionals need to understand these emerging technologies in order to advance research and to deliver new prognostic and diagnostic techniques in the new field of personalized medicine. Our education plan is to develop bioinformatics-based pipeline initiatives for K-12, colleges, universities and teachers in the state of New Mexico and throughout the INBRE network, including seminars, workshops, consulting, mentorships and internships for faculty and students.

Aim 3d: Build and maintain research-enabling IT Infrastructure and mechanisms for communication within the network and to the public. The foundation of computationally-intensive bioinformatics, voluminous sequence data generation, remote collaboration and information sharing is a robust IT infrastructure. We will leverage and develop this resource to support the research goals of the network.

 

4. Faculty development, DRPP

Aim 4a:  The Developmental Research Project Program (DRPP) will support projects within the thematic research focus areas to address important biomedical questions and critical health problems. The thematic and crucial basic and translational research health focus areas targeted by the NM-INBRE Developmental Research Project Program (Brain and Behavioral Health; Cancer; Cardiovascular and Metabolic Diseases; Child Health; Environmental Health; Infectious Disease and Immunity) are strategic and enable inclusive participation from all of the network institutions to engage in research that benefits the health of our citizens and underserved communities.

Aim 4b:  The DRPP will use an efficient process for project application submission and review. A stepwise application process, with clear instructions and convenient web-based system for submission, will support participation from eligible faculty across the network. The selection process will involve a study section panel and NIH review criteria to identify the most promising scientific studies, strengthen the research capacity of the network, and increase the competitiveness of NM investigators for NIH research and training programs.

Aim 4c:  The DRPP mentoring program will facilitate faculty professional development. The scientific capabilities, academic progress and overall career development of Full Project Investigators will be fostered by through a formal mentoring program.

Aim 4d:  The DRPP will engage students and promote opportunities for research experiences. The portfolio of Full and Focus research projects will provide research experiences for undergraduate and graduate students in basic, clinical, translational and community based participatory research.

Aim 4e:  The maturation of scientific projects, professional development of investigators, and participation in the network will be assisted through annual assessment of progress. A process for annual reporting and progress review of research projects will be implemented to recognize accomplishments and achievements, identify challenges, needs, and areas for improvement, and enable programmatic interventions that maximize the potential for development of research capacity and training.

 

5. Collaboration

Aim 5a:  In partnership with other NIH programs in the State, the qualified personnel, resources and unique characteristics of the NM-INBRE network will be leveraged to increase the competitiveness of investigators, and enable productive multi-disciplinary clinical, translational and community-based research collaborations.

Aim 5b:  Inter-programmatic cooperation through the Mountain West Regional Research Consortium will provide opportunities for productive interactions, training and collaboration that contribute to the development of clinical and translational research capacity that benefits the health of our citizens and underserved communities.

 

 

2015 PUBLICATIONS

 

Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration. Full Text

Dziewanowska K, Settles M, Hunter S, Linquist I, Schilkey F, Hartzell PL.

PLoS One. 2014;9(4):e95189. PubMed PMID: 24733297; PubMed Central PMCID: PMC3986340.

 

Dissecting regulation mechanism of the FMN to heme interdomain electron transfer in nitric oxide synthases.  Full Text

Feng C, Chen L, Li W, Elmore BO, Fan W, Sun X.

J Inorg Biochem. 2014 Jan;130:130-40. PubMed PMID: 24084585; PubMed Central PMCID: PMC3844001.

 

DETERMINATION OF OXALATE ION DOPANT LEVEL IN POLYPYRROLE USING FT-IR.  Full Text

Miller ET, Benally KJ, GreyEyes SD, McKenzie JT.

J Undergrad Chem Res. 2014;13(1)PubMed PMID: 25598749; PubMed Central PMCID: PMC4295657.

 

Lipophilic prodrug conjugates allow facile and rapid synthesis of highloading capacity liposomes without the need for post-assembly purification.  Full Text

Mikhalin AA, Evdokimov NM, Frolova LV, Magedov IV, Kornienko A, Johnston R, Rogelj

S, Tartis MS.

J Liposome Res. 2014 Dec 23;PubMed PMID: 25534989; PubMed Central PMCID: PMC4478286.

 

Expanding our understanding of sequence-function relationships of type II polyketide biosynthetic gene clusters: bioinformatics-guided identification of Frankiamicin A from Frankia sp EAN1pec.  Full Text

Ogasawara Y, Yackley BJ, Greenberg JA, Rogelj S, Melançon CE 3rd.

PLoS One. 2015;10(4):e0121505. PubMed PMID: 25837682; PubMed Central PMCID: PMC4383371.

 

A Home-Based Educational Intervention Improves Patient Activation Measures and Diabetes Health Indicators among Zuni Indians.  Full Text

Shah VO, Carroll C, Mals R, Ghahate D, Bobelu J, Sandy P, Colleran K, Schrader R, Faber T, Burge MR.

PLoS One. 2015;10(5):e0125820. PubMed PMID: 25954817; PubMed Central PMCID: PMC4425648.

 

Modulation of flavivirus population diversity by RNA interference.  Full Text

Brackney DE, Schirtzinger EE, Harrison TD, Ebel GD, Hanley KA.

J Virol. 2015 Apr;89(7):4035-9. PubMed PMID: 25631077; PubMed Central PMCID: PMC4403385.

 

High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio Technologies.   Full Text

Ogasawara Y, Torrez-Martinez N, Aragon AD, Yackley BJ, Weber JA, Sundararajan A, Ramaraj T, Edwards JS, Melançon CE 3rd.

Genome Announc. 2015 Apr 2;3(2)PubMed PMID: 25838474; PubMed Central PMCID: PMC4384478.

 

Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics.  Full Text

Cotton TB, Nguyen HH, Said JI, Ouyang Z, Zhang J, Song M.

Sci Rep. 2015 Apr 28;5:9634. PubMed PMID: 25921728.

 

ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. Full Text

Zhang Y, Liu ZL, Song M.

Nucleic Acids Res. 2015 May 19;43(9):4393- 407. PubMed PMID: 25897127; PubMed Central PMCID: PMC4482087.

 

Allometry of animal-microbe interactions and global census of animal-associated microbes.  Full Text

Kieft TL, Simmons KA.

Proc Biol Sci. 2015 Jul 7;282(1810)PubMed PMID: 26108631; PubMed Central PMCID: PMC4590480.

 

Epigenetic profiles of pre-diabetes transitioning to type 2 diabetes and nephropathy.  Full Text

VanderJagt TA, Neugebauer MH, Morgan M, Bowden DW, Shah VO.

World J Diabetes. 2015 Aug 10;6(9):1113-21. PubMed PMID: 26265998; PubMed Central PMCID: PMC4530325.

 

R-Ketorolac Targets Cdc42 and Rac1 and Alters Ovarian Cancer Cell Behaviors Critical for Invasion and Metastasis.   Full Text

Guo Y, Kenney SR, Muller CY, Adams S, Rutledge T, Romero E, Murray-Krezan C, Prekeris R, Sklar LA, Hudson LG, Wandinger-Ness A.

Mol Cancer Ther. 2015 Oct;14(10):2215-27. PubMed PMID: 26206334; PubMed Central PMCID: PMC4596774.

 

Wittig derivatization of sesquiterpenoid polygodial leads to cytostatic agents with activity against drug resistant cancer cells and capable of pyrrolylation of primary amines.  Full Text

Dasari R, De Carvalho A, Medellin DC, Middleton KN, Hague F, Volmar MN, Frolova LV, Rossato MF, De La Chapa JJ, Dybdal-Hargreaves NF, Pillai A, Kälin RE, Mathieu V, Rogelj S, Gonzales CB, Calixto JB, Evidente A, Gautier M, Munirathinam G, Glass R, Burth P, Pelly SC, van Otterlo WA, Kiss R, Kornienko A.

Eur J Med Chem. 2015 Oct 20;103:226-37. PubMed PMID: 26360047; PubMed Central PMCID: PMC4617783.

 

Total synthesis and absolute stereochemistry of the proteasome inhibitors cystargolides A and B.

 Full Text

Tello-Aburto R, Hallada LP, Niroula D, Rogelj S.

Org Biomol Chem. 2015 Oct 28;13(40):10127-30. PubMed PMID: 26400369; PubMed Central PMCID: PMC4629797.

 

A Novel Pharmacologic Activity of Ketorolac for Therapeutic Benefit in Ovarian Cancer Patients.

 Full Text

Guo Y, Kenney SR, Cook L, Adams SF, Rutledge T, Romero E, Oprea TI, Sklar LA, Bedrick E, Wiggins CL, Kang H, Lomo L, Muller CY, Wandinger-Ness A, Hudson LG.

Clin Cancer Res. 2015 Nov 15;21(22):5064-72. PubMed PMID: 26071482; PubMed Central PMCID: PMC4644688.

 

Development of an Unnatural Amino Acid Incorporation System in the Actinobacterial Natural Product Producer Streptomyces venezuelae ATCC 15439.   Full Text

He J, Van Treeck B, Nguyen HB, Melançon CE 3rd.

ACS Synth Biol. 2015 Nov 18;PubMed PMID: 26562751; NIHMSID: 755024.

 

RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM(®) genes for hereditary disorders of hearing and balance.  Full Text

Ramírez-Gordillo D, Powers TR, van Velkinburgh JC, Trujillo-Provencio C, Schilkey F, Serrano EE.

BMC Res Notes. 2015 Nov 18;8:691. PubMed PMID: 26582541; PubMed Central PMCID: PMC4652436.

 

Tetraspanin CD82 regulates bone marrow homing of acute myeloid leukemia by modulating the molecular organization of N-cadherin.  Full Text

Marjon KD, Termini CM, Karlen KL, Saito-Reis C, Soria CE, Lidke KA, Gillette JM.

Oncogene. 2015 Nov 23;PubMed PMID: 26592446.

 

Synthetic and Biological Studies of Sesquiterpene Polygodial: Activity of 9-Epipolygodial against Drug-Resistant Cancer Cells.  Full Text

Dasari R, De Carvalho A, Medellin DC, Middleton KN, Hague F, Volmar MN, Frolova LV, Rossato MF, De La Chapa JJ, Dybdal-Hargreaves NF, Pillai A, Mathieu V, Rogelj S, Gonzales CB, Calixto JB, Evidente A, Gautier M, Munirathinam G, Glass R, Burth P, Pelly SC, van Otterlo WA, Kiss R, Kornienko A.

ChemMedChem. 2015 Dec;10(12):2014-26. PubMed PMID: 26434977; NIHMSID: 741864.

 

GPER1-mediated IGFBP-1 induction modulates IGF-1- dependent signaling in tamoxifen-treated breast cancer cells.  Full Text

Vaziri-Gohar A, Houston KD.

Mol Cell Endocrinol. 2015 Dec 13;PubMed PMID: 26690777; NIHMSID: 746929.

 

Composition, Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes.

 Full Text

Lambeth SM, Carson T, Lowe J, Ramaraj T, Leff JW, Luo L, Bell CJ, Shah VO.

J Diabetes Obes. 2015 Dec 26;2(3):1-7. PubMed PMID: 26756039; PubMed Central PMCID: PMC4705851.

 

Development and Application of a High Throughput Protein Unfolding Kinetic Assay.  Full Text

Wang Q, Waterhouse N, Feyijinmi O, Dominguez MJ, Martinez LM, Sharp Z, Service R, Bothe JR, Stollar EJ.

PLoS One. 2016;11(1):e0146232. PubMed PMID: 26745729; PubMed Central PMCID: PMC4706425.

 

Detection and Quantification of Ribosome Inhibition by Aminoglycoside Antibiotics in Living Bacteria Using an Orthogonal Ribosome- Controlled Fluorescent Reporter.  Full Text

Huang S, Zhu X, Melançon CE 3rd.

ACS Chem Biol. 2016 Jan 15;11(1):31-7. PubMed PMID: 26514081; NIHMSID: 755021.

 

Clotrimazole as a Cancer Drug: A Short Review. Full Text

Kadavakollu S, Stailey C, Kunapareddy CS and White S*

Medicinal chemistry. NIHMSID: 723253.