JA Negrón Berríos, Ph.D.Jan 17, 2017

MS Biotechnology Inter American University of Puerto Rico

Barranquitas Campus

Contents• Inter American University of PR - Barranquitas

– Science and Technology Department

– Institute of Sustainable Biotechnology (ISBiot)

• MS Biotechnology– Curriculum design

• Plant sciences

• Industrial biotechnology

– Procedures

• Thesis

• Comprehensive exams

– Research

– Internationalization

Institute of Sustainable Biotechnology

• ISBiot– Non-profit organization focused on sustainable use of modern

biotechnology through learning, research and development.

– Preparation of qualified professionals who will contribute to the progress of biotechnology as a key piece for the socio-economical development of our society.

– Learning, research, and development

• Issues related to intellectual property

Learning

Research

Development

MS in Biotechnology at Barranquitas Campus

• The Master of Science Program in Biotechnology with Specializations in Biotechnology of Plants and Industrial Biotechnology has as its goal the formation of professionals who possess the knowledge, skills, attitudes and the social commitment, which allow them to make responsible contributions to the scientific development for our society and to the advancement of biotechnology.

• It aims to facilitate the development of graduates that can handle the basic technologies of biosciences and emit judgments related to their area of specialization and to related areas.

REQUIREMENTS FOR THE MASTER OF SCIENCE DEGREE IN BIOTECHNOLOGY WITH SPECIALIZATIONS IN BIOTECHNOLOGY OF

PLANTS AND INDUSTRIAL BIOTECNOLOGY

• Curriculum Design– Core Course Requirements 18 credits

– Specialization Requirements 9 credits

– Prescribed Distributive Requirements 9 credits Total 36 credits

– Core Course Requirements - 18 credits

Course Num Course Tittle Credits

BIOT 5011 Cellular and Molecular Biotechnology 3

BIOT 5100 Molecular Genetics and Bioinformatics 3

BIOT 6100 Bio-security 2

BIOT 6115 Biotechnology of Plants 3

BIOT 6125 Instrumental Analysis of Biomolecules 3

BIOT 6200 Industrial and Commercial Biotechnology 3

BIOT 6970 Seminar 1

Specialization in Biotechnology of Plants

• Specialization Requirements in Biotechnology of Plants: - 9 credits

Course Num Course Tittle Credits

BIOT 6116 Micro-propagation of Plants 3

BIOT 6117 Plants as Biofactories 3

BIOT 6210 Biotechnology and Improvement of Cultures 3

Specialization in Industrial Biotechnology

• Specialization Requirements in Industrial Biotechnology : - 9 credits

Course Num Course Tittle Credits

BIOT 6120 Animal Biotechnology 3

BIOT 6117 Animal Tissue Culture in Industrial Biotechnology 3

BIOT 6230 Bioprocess 3

Prescribed Distributive Requirements - 9 credits• Students will have two (2) options to complete the 9

credits of the Prescribed Distributive Courses. – Option A: With a Research Project (Thesis)

– Option B: Without a Research Project (Thesis)• Student will approve 9 additional credits in biotechnology from either

of the specializations or from elective courses. In addition, they will take a comprehensive examination. They will not take the Research Methods and Thesis courses.

Course Num Course Tittle Credits

BIOT 6220 Research Methods in Biotechnology I 3

BIOT 6221 Research Methods in Biotechnology II 3

BIOT 6990 Thesis in Biotechnology 3

Course Num Course Tittle Credits

BIOT 6`240 Special Topics in Biotechnology 3

BIOT 6225 Marine Biotechnology 3

BIOT 6105 Biotechnology of Microorganisms 3

Research/Thesis Option

• Proposal– With the advice of faculty

– Selection of the Thesis Committee

– Presentation and defense

• Research– Between 1 and 1.5 years

– Under the supervision of Thesis Committee, specially the Chair of the Committee

• Thesis– After of concurrent with research

– It is expected a least a publication in peer-review journal

Thesis Committee

• The purpose is to maintain high standards of quality in the conduct of graduate student research and writing.

• It provides a vital role in the guidance and direction of graduate student research.

• Three graduate faculty members will constitute the thesis/research committee

– The chair, with more administrative responsibilities, must be a graduate faculty member from IAUPR BC.

Thesis/Research, General Guidelines

• Responsibilities and expectations– Planification– Safety – Laboratory notebook (belongs to ISBiot)

• It must be regularly updated!

– Disposing of chemical/biohazard materials– Equipment maintenance– Working areas – cleaned & organized– Laboratory consumables

• Solutions (for everybody)• Solutions (specifically for your experiments)

– Oral reports• At least every Friday

– You are expected to be in the lab from Mon-Friday• It may require additional time

– Every body is responsible for the own work, however, we are a team.

Comprehensive Exams

• Students who do not write a thesis are required to successfully pass a comprehensive exam and take three additional graduate courses in biotechnology. This should be coordinated with the Graduate Program Coordinator.

• It is required a cumulative grade point average of 3.0 to qualify to take the comprehensive exams.

• To be eligible for the comprehensive exam, the student must be within one semester of program completion.

Teaching/Laboratory/Research Assistantships

• Learning experience• Requirements

– Full time graduate student– Extra hours, therefore, it is expected not being employed– Discipline, compromise

• Teaching assistantships– In charge of an undergraduate laboratory course and under de supervision of

a faculty member

• Research assistantships– Intensive laboratory work either in the student’s research project or any other

laboratory work assigned– Under the supervision of the graduate faculty

• Laboratory assistant– Regular laboratory work as a laboratory assistant

• Stipends may be available

Research Projects-Alok Arun

1. Sequencing the complete chloroplast genome of a putative Scutellaria from Puerto Rico

2. Genome applications from chloroplast of the crop apio

3. Biochemical characterization of cytotoxic activity of apio extracts on cancerous cell lines

4. Biochemical characterization of cytotoxic activity of extracts of a bryophyte Marchantia on

cancerous cell lines

5. Tissue culture and micropropagation of Arracacia xanthorrhiza

6. Identification and characterization of microbiome of the commercially important brown

seaweed Gracilaria using NGS approach

7. De novo assembly and characterization of the apio transcriptome

8. Initiating the formation of insectarium to rear and study the morphology of Puerto Rican

butterrflies

9. Understanding the mechanism of salinity tolerance in Canavalia sp. from Puerto Rico

10. Effect of Seaweed Liquid Extract (SLE) on growth and protein content of beans

11. Molecular characterization of genes associated with secondary metabolite production in

Scutellaria

Research Projects-JA Negrón Berríos

1. Arracacia xanthorrihiza and Calathea allouia : Biochemical analysis

2. Polyphenols profile in tropical plants

3. Structure/function of non-muscle myosin

4. Commercial applications of molecular markers Theobroma cacao

5. Estrogenic disruptors of endocrine system in fresh water organisms

6. Heavy metal accumulation and Bryophyllum pinnatum

7. ncRNAs and heavy metals in mammalian cells• Pb, Cd, Se, Cu, As

8. ncRNAs in Bryophyllum pinnatum exposed to heavy metals

9. Methylation profile of actin/myosin from CHO cytoskeleton

10. Bioplastics from cacao wastes

Calathea allouia Arracacia xanthorrihiza : Biochemical analysis

Main objectives:Lipids compositionFlavonoids and other antioxidantsProcessed foods from these crops

The project involves, micropropagation, PCR techniques, GC MS, HPLC MS, UV spectrophometry, food processing techniquues, as well as writing the paper for publication

Project 1

Structure/function of non-muscle myosins

Main objectives:Proteomics of MYH9 in mammalian cells and MYOXI in plant cellsCellular role of these non-muscle myosinsRole of these non-muscle myosins in cancer

The project involves, purification of native proteins, cloning and PCR techniques, recombinant DNA techniques, 2D electrophoresis, enzymology, as well as writing the paper for publication

Project 2

Commercial applications of molecular markers Theobroma cacao

Main objectives:Identify molecular makers associated to commercial quality at the genomic and proteomic level of Theobroma cacao

The project involves, plant tissue culture, DNA fingerprinting, 2D electrophoresis,, cloning and PCR techniques, recombinant DNA techniques, 2D electrophoresis,, as well as writing the paper for publication

Project 3

Polyphenols profile in tropical plants

• Main objectives– Determination of

antioxidants content• Bryophyllum pinnatum

– Determination of the general profile of polyphenols by LC MS• Bryophyllum pinnatum

• A. xanthorrihiza

• Other

https://openi.nlm.nih.gov/detailedresult.php?img=PMC2835915_omcl0205_0270_fig001&query=&req=4&npos=-1

Project 4

Estrogenic disruptors of endocrine system in fresh water organisms

• Main objectives– Assessment of steroids

disruptors of reproductive endocrine system in fresh water in P.R.• GC MS/LC MS

– In vitro calibration of [estrogenic disruptors] that induce disruption of endocrine system in fresh water fishes• Anatomical characterization• qPCR vitellogenin

– Exposition of fresh water fishes to effluents from water treatment facilities from PR

Project 5

Heavy metal accumulation and Bryophyllumpinnatum

• Main objectives

– In vitro exposition of Bryophyllum pinnatum to various heavy metals (Cd, As, Pb, Cu, Se, others)

• Measure accumulation of heavy metals by AAS/ICP OES

• Correlation of heavy metal accumulation with molecular markers associated to hyperacumulation

Project 6

ncRNAs and heavy metals in mammalian cellsand Bryophyllum pinnatum

• Main objectives

– Preparation of a literature/bioinformatics analysis of the current status of mammalian ncRNAs and heavy metals

– Preparation of cDNA library of mammalian cells exposed to Cd and other heavy metals• Analysis of the transcriptome

http://www.exosome-rna.com/microguards-and-micromessengers-of-the-genome/

Project 6

Bioplastics

• Main objectives

– Adaptation of industrial processes to obtain plastics from T. cacao

– Chemical processeses

Project 7

Chloroplast genome sequencing of Puerto Rican crop Calathea allouia

The project would involve tissue culture, micropropagation, chloroplast isolation, chloroplast DNA isolation, PCR techniques, Next Generation Sequencing, bioinformatic analysis and drafting as well as writing the paper for publication

Broader objective: Identify and characterize the genes associated with photosynthesis efficiency in Calathea.

Project 8

De novo high-throughput transcriptome sequencing of Puerto Rican crop Calathea allouia

The project would involve tissue culture, micropropagation, RNA extraction, cDNA synthesis, PCR and real time PCR techniques, Next Generation Sequencing, bioinformatic analysis and drafting as well as writing the paper for publication

Broader objective: Study and characterize the genes controlling developmental processes in Calathea

Project 9

Estimation of fatty acid and biochemical constitutes of PuertoRican seaweeds to characterize their potential for biofuel andfine chemicals

The project would involve algal collection and culture, PCR and real timePCR techniques, HPLC, GC/MS analyses, statistics, possible two monthsvisit to India on field trip and drafting as well as writing the paper for

publication

Broader objective: Study and characterize the Puerto Rican seaweedsfor identifying sources of biofuel and fine chemicals.

Project 10

Biochemical and field characterization of Apio leaves to identify it as a potential source for biofuel and secondary metabolite production.

The project would involve tissue culture, micropropagation, DNA extraction, biochemical assays, and drafting as well as writing the paper for publication.

Broader objective: Propose apio as an alternative source for biofuel and secondary metabolite production.

Project 11

Bioinformatic analysis of the transcriptome sequence from four different tissues of apio plant.

The project would involve analyzing the NGS data already available in the lab to write the paper for publication.

Broader objective: Identify genes/proteins involved in various developmental and infection processes in apio cultivation.

Project 12

De novo high-throughput transcriptome sequencing of Puerto Rican crop Apio flowers.

The project would involve tissue culture, micropropagation, RNA extraction, cDNA synthesis, PCR and real time PCR techniques, Next Generation Sequencing, bioinformatic analysis and drafting as well as writing the paper for publication

Broader objective: Study and characterize the genes controlling flowering time in apio.

Project 13

Studying the effect of temperature and stress on the growth and reproductive behaviors of Puerto Rican butterflies.

The project would involve catching, rearing and reproducing butterflies for their further intensive studies.

Broader objective: The aim of the study is to create a butterfly center of its kind in our university.

Project 14

Internationalization

• Institute of Bioresources and Sustainable Development

– Manipur, India

• Catholic University of Louvain

– Louvain, Belgium

• Hindu College- Univ. of Delhi

– New Delhi, India