Author Archives: Hasan

Fall 2023 – Molecular Evolution (410)

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Class time and location
Sun, Tue, Thur – 12:00-12:50 (Room: SCI-S Room 123)
Textbook, readings, and lecturing style
Fundamentals of Molecular Evolution 2nd edition, by Dan Graur and Wen-Hsiung Li. You do not have to buy the book. I will be handing parts of the book when needed. The lectures will be given using board. It is YOUR RESPONSIBILITY to come to the lectures and take notes. You will be tested on the material I give in class and the handouts I provide.
Attendance
I will not give points for attending my lectures. You are a RESPONSIBLE student and you want to learn. Missing lectures will significantly affect your performance and grade. I do not intend to give lectures during my office hours or photocopy my lecture notes for you!
Academic dishonesty
DO NOT CHEAT. You are smart and you can get the grade you want. Academic dishonesty will not be tolerated.
Tests and grading:
Exam1: 20%
Exam2: 20%
Exam3: 20%
(Drop lowest exam grade)
Project work: 10%
Project presentation: 10%
Final exam: 40%
Important dates:
Exam 1: Sunday 15/10/2023 (Lectures: 2-8)
Exam 2: Sunday 12/11/2023 (Lectures: 9-14)
Exam 3: Thursday 14/12/2023 (Lectures: 15-20)
Project Presentation: 17, 19, 21, 24/12/2023
Final Exam: Tuesday 2/1/2024 – 8:00-10:00
(X) Not performing tasks on time
Enrolled students:
  1. Reem Alsayegh – Project animal: Penguin (Paper)./
  2. Nour Alramadhan – Project animal: Seahorse (Paper)./
  3. Kafiah Alenezi – Project animal: Peafowl (Paper).X/
  4. Alla Alharbi – Project animal: Red Panda (Paper)./
  5. Hassen Esseyid – Project animal: Finches (Paper)./
  6. Fatemah Sadeq – Project animal: Dog (Paper)./
  7. Saad Almutairi – Project animal: Bear (Paper)./
  8. Rana Chami – Project animal: Cow (Paper)./
  9. Albandari Alshammeri – Project animal: Butterfly (Paper)./
  10. Lin Ataya – Project animal: Cat (Paper)./
  11. Mariam Chehade – Project animal: Zebra fish (Paper)./
  12. Jenna Almutawa – Project animal: Horse (Paper).X/
  13. Shaha Alfarhan – Project animal: Snake (Paper1, Paper2)./
Lec1: 410_lec1_General_introduction
Lec2: 410_lec2_GeneticsTraditions
Lec3: 410_lec3_NatureOfAlleles
Lec4: 410_lec4_PrinciplesOfGeology
Lec5: 410_lec5_FossilsInWithin
Lec6: 410_lec6_Homologies
Lec7: 410_lec7_DirectObservations
Lec8: 410_lec8_TheoryForEvolution
Lec9: 410_lec9_PopulationGenetics
Lec10: 410_lec10_TheBasicModel
Lec11: 410_lec11_FindingTheAllele1
Lec12: 410_lec12_FindingTheAllele2
Lec13: 410_lec13_FindingTheAllele3
Lec14: 410_lec14_FindingTheAllele4
Lec15: Sequence alignment 
Lec16: Alleles and allele frequencies
Lec17: Genotypes and genotype frequencies
Lec18: Testing HW equilibrium
Lec19: Haplotypes and haplotype frequencies
Lec20: 410_lec20_Phylogeny
Tasks:
  1. Make a folder on your desktop or in your flash-drive named “410 Material”.
  2. Choose an animal species or an animal group that you like.
  3. What is the class and order of your favourite animal?
  4. Why did you choose this animal?
  5. How many species does your class, order, and family have?
  6. Open a powerpoint and save it as (YOUR NAME_410).
  7. What is the subfamily of your selected animal species and how many species belong to that sub-family?
  8. What is the genus of your selected animal species and how many species belong to that genus?
  9. Visit NCBI and using the Taxonomy database, search for your taxonomic group.
  10.  

Ode to DNA

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Below is the creative work of my student Mariam Chehadeh, who took my Molecular Genetics course Spring 2023. A very surprising creative work.

My DNA, you inspire me to write!
I adore the way you conserve and express.
Invading my mind day and night.
Always dreaming about your work in progress.

Let me compare you to a unique bouquet.
You are very selfish, precious, and rare.
Your truthful breeze flaps the blueprint dancers of May.
And springtime has the singular spare.

How can I see you? I will count the ways.
Because you are highly intricate and complicated.
Oh, how your helical structure swirls my days!
Though my need for you is anticipated.

Now I must deal with a heavy heart.
Remember my warm words while we are apart.

Intro. to Genomics – Spring 2024

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Class time and location
Mon, Wed – 9:30-10:45 (Room: 1st floor, SCI-S-194)
Important dates:
Exam 1: Wednesday 28/2/2024 (10%)
Exam 2: Wednesday 20/3/2024 (10%)
Exam 3: Monday 8/4/2024 (10%)
Exam 4: Wednesday 8/5/2024 (10%)
Report due: Monday 15/4/2024 (10%)
Presentations due: 9/5/2024 (10%)
Final Exam: Thursday 23/5/2024 – 11:00-1:00 (40%)

Your report should be typed using Microsoft Word (no lower or upper limit to the report) and be named (YOUR NAME_485). The report should include (to the best of your ability) the following with respect to your organism:

  1. The common and scientific.
  2. The taxonomy.
  3. The closest relatives.
  4. The geographic distribution.
  5. Physical characteristics.
  6. Life cycle.
  7. Any unique information that fascinated you.
 Projects:
  1. Reem Alsayegh (Tuatara, Paper).*/
  2. Saad Almutairi (Asian vine snake, Paper)./
  3. Omar Rashdan (Green anole lizard, Paper).*/
  4. Fatmah Alsahly (Australian dragon lizard, Paper).*/
  5. Dana Altaher (King cobra, Paper)./
  6. Narjes Aleissa (Habu, Paper).*/
  7. Nutaila Almahfudhi (Tiger Rattlesnake, Paper)./
  8. Belqees Almutairi (Anguid lizard, Paper).*/
  9. Duaa Shaher (Leopard gecko, Paper)./
  10. Sara Alwohaib (Guatemalan Beaded Lizard, Paper).*/
  11. Amna Alrashid (Burmese python, Paper)./
  12. (Organism: Common Lizard, Paper)./
 Lecture 1: General Introduction
Lecture 2: History and Review (I)
Lecture 3: History and Review (II)
Lecture 4: The genome: the word and beyond
Lecture 5: Exploring the genome: workable pieces
Lecture 5.1: 485_lec5.1_DNAExtraction
Lecture 5.2: 485_lec5.2_DNAQualityQuantity
Lecture 6: DNA sequencing: the thing to the information (485_lec6_Sequencing)
Sequencing methods videos:
– Maxam and Gilbert Sequencing
– Sanger Sequencing, V2
– Pyrosequencing, V2
– Illumina Sequencing, V2
– SOLiD Sequencing
– Ion Torrent Sequencing, V2 
– Oxford Nanopore Sequencing, V2
– PacBio Sequencing, V2
Lecture 7: The sequence: Reading the reads
Sequencing strategies videos:
– Hierarchical Sequencing
– Whole-Genome Shotgun Sequencing (WGS)
– The race to the human genome
Lecture 8: Stitching the sequences: Genome assembly
– Sequence Alignment (Abdulatif Alfulaij + Hafsa Aziz)
Lecture 9: The meaning: Genome annotation
Lecture 10: Meaningful parts: coding regions
Lecture 11: Functional annotation
RNAi (Abdulatif Alfulaij, Malak Alrasabiya)
CRISPR-Cas9 (Abdulatif Alfulaij), CRISPR-Cas9 (Malak Alrasabiya)
 
Lecture 12 : Non-coding genomic elements
Lecture 13 : Genetic transfer
Lecture 14: Polymorphisms
Lecture 15: Population Genetics
 
To Do:
Make a folder on your desktop named “485 material”.
Do you know what your organism looks like?
Download a high quality photo of your organism.
Visit the wikipedia page of your organism and send a link of the page to your instructor.
14/2/23
Learn the different forms of communication in science.
Learn the different forms of printed scientific communication and their levels of scientific details.
Learn the process of publishing scientific papers.
Learn the difference between scientific journals and news journals.
Learn to do a mindful search for genome papers using keywords and search engines.
How do I know that a scientific journal is a good journal?
Can you search for the genome sequence paper of your organism?
Did you find the same article that your instructor assigned to you?
16/2/23
Download the pdf of your article into your folder.
Download the supplementary files of your paper into your folder.
Print your article and keep it with you everyday.
DO NOT print your supplementary material.
23/2/2023
Identify (1) the journal that your paper was published in, (2) the publisher, (3) year published, (4) authors, (5) volume, (6) issue, (7) doi.
How many individuals authored your paper?
Circle the name of the first author.
Circle the name of the last author.
Was your paper authored by a consortium?
Why genome papers are authored by many authors? 
How many words are used in the title?
Circle the following words in the title if present: genome, sequence, organism name.
What is the common name of your organism?
Is the common name of your organism present in the title?
What is the scientific name of your organism?
Is the scientific name of your organism present in the title?
When titles include scientific names and when titles include a common name?
 
Does the title of your paper reveal the objective of the study?
Read the abstract and locate the objective sentence.
Does the abstract of your paper contain an introductory sentence?
Can you locate the methods sentence(s) in the abstract of your paper?
Can you locate the results sentence(s) in the abstract of your paper?
Does the abstract of your paper highlight the significance of the study?
30. Can you identify the major components of you scientific paper (Abstract, Intro, M&M, Results, Discussion, and Refs)?
31. In the introduction of your paper, locate the summary paragraph of the study and the detailed objectives (if present).
32. Can you from the introduction of your assigned paper find general information of the organism under investigation?
33. Make a list of the general information regarding your organism that you extracted from the introduction?
34. Are there any information regarding the number of chromosomes and genome architecture of your organism in the introduction?
35. What is the source of DNA used to sequence your organism?
36. What is the sequencing method(s) used in your assigned paper?
37. Make sure that you understand all sequencing methods and specifically the methods in your paper.
38. Send links of YouTube videos of the sequencing methods (your choice) to your instructor.
39. Identify the sequencing strategy used in your paper
40. Send links of YouTube videos of the sequencing strategies to your instructor
41. Identify wether the sequencing single-end or paired-end sequencing was performed in you paper.
42. What is the sequence coverage or sequence depth in your paper
43. What is the total number of reads of your genome?
44. What is the number of contigs in your genome assembly?
45. What is the number of scaffolds in your genome assembly?
46. What is the N50 contig of your genome assembly?
47. What is the N50 scaffold of your genome assembly?
48. What is the size of the largest contig?
49. What is the size of the largest scaffold?
50. Send a draft of your powerpoint presentation to your instructor.
51. What is the number of predicted genes in your organism’s genome? 
52. What is the number of operons in your organism’s genome? (if reported and applicable). 
53. What is the GC content of  your organism’s genome? 
54. What is the average gene size in your organism’s genome? (mention minimum and maximum).
55. What % of your organism’s genome is represented by genes?
56. What is the average number of exons per gene  in your organism’s genome?
57. What is the average number of introns per gene  in your organism’s genome?
58. What is the gene density in your organism’s genome?
59. How many rRNA genes are present in your organism’s genome?
60. How many tRNA genes are present in your organism’s genome?
61. What % of your organism’s genome is represented by repeat elements?
62. What % of your organism’s genome is represented by simple repeats?
63. What % of your organism’s genome is represented by tandem repeat elements?
64. What % of your organism’s genome is represented by psuedo-genes?
65. What % of your organism’s genome is represented by transposable elements?
66. What % of your organism’s genome is represented by LINE elements?
67. What % of your organism’s genome is represented by SINE elements?
68. Send your final summary of data collection Excel file (Fall2020_genomic_data_YourName).
Data collection (YourName_485_data)
Presentation template (PresentationTemplate_485)

Suggested reading material

My Genomics teaching style: Laying a string NOT filling a vessel.
“What is a genome?” by Aaron David Goldman1 and Laura F. Landweber
Evolution of DNA Sequencing by Jonathan Eisen
Figures, photos, and graphs in my lectures are collected using google searches.  I do not claim to have personally produced the material (except for some). I do cite only articles or books used. I thank all owners of the visual aid that I use and apologize for not citing each individual item.  If anybody finds the inclusion of their material in my lectures a violation of their copy rights, please contact me via email.

hhalhaddad@gmail.com

Crick’s Dogma

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Once again Amna Alrashid shares with us a very nice portrait of Francis Crick with a touch related his idea of the central dogma of molecular biology. Very nice!

Mother of DNA

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This is a wonderful artwork by a very talented student in my Introduction to Mol. Genetics class. Ms. Amna Alrashid made this portrait of Rosalind Franklin. You can see Amna’s artwork in her social media (Amna Alrashid).

Scientific Report – Fall 2022

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Meetings: Wednesdays @ 9am and @ 1pm in my office.

* Absent
? No task received
Students:
  1. Hanan Alfoudari – paper.*/
  2. Asmaa Alghanem – paper./
  3. Hassen Esseyid.?*/
  4. Nouf Aldhafiri – paper.??*/
  5. Lulwah Alsenan./
  6. Fatmah Abdullah – paper./
Activity:
12/10/22:
  • Discussing a blog post.
  • Communication in science: print, poster, talk, video, tweets, blog posts etc.
  • Task after meeting: Write a one page summary of what you learned in Arabic or English and send it to your instructor.
19/10/22:
  • The process of publishing peer-reviewed scientific articles.
  • Task after meeting: Write a one page summary of what you learned in Arabic or English and send it to your instructor.
26/10/22:
  • Searching for scientific papers.
  • Accessing scientific papers.
  • Task after meeting: Find a good scientific paper related to camels and send a pdf to your instructor (paper should be a research peer-reviewed article not published by your instructor).
2/11/22:
  • The structure of a scientific paper
  • How to efficiently read a scientific paper.
  • Reading – Your selected paper from last week.
  • Task after meeting: identify and highlight the discussed sections in your paper and send a pdf to your instructor.
9/11/22:
  • Referencing primary literature.
  • What parts of scientific articles is used as a reference?
  • How to cite scientific communication (articles, books etc.) in your reports? (e.g., Reference managers)
  • Reading – Your selected paper from last week.
  • Task after meeting: From your selected paper, highlight the parts that you want cite and send a pdf copy to your instructor. Send an APA formate of your paper to your instructor. 
16/11/22:
  • Writing scientific material (e.g., writing an abstract and an introduction)
  • Task after meeting: Re-writing (1) the abstract of your paper, (2) outline of the introduction’s paragraphs and (3) the last paragraph of the introduction. Send your writings to your instructor.
23/11/22:
  • Writing scientific material (e.g., writing materials & methods, results and discussion).
  • Task after meeting: Highlight how can the writing of the paper that you selected can be improved. Send a pdf copy to your instructor.
30/11/22:
  • Reading – Cdrom Archive: A Gateway to Study Camel Phenotypes.
  • Task after meeting: Write a one page summary of what you learned in Arabic or English and send it to your instructor. Make sure to explain what parts you can cite from the paper.
7/12/22:
  • Reading – SamplEase: a simple application for collection and organization of biological specimen data in the field.
  • Task after meeting: Write a one page summary of what you learned in Arabic or English and send it to your instructor. Make sure to explain what parts you can cite from the paper.
14/12/22:
  • Reading – Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair.
  • Task after meeting: Write a one page summary of what you learned in Arabic or English and send it to your instructor. Make sure to explain what parts you can cite from the paper.
21/12/22:
  • Reading – FGF5 missense mutation is associated with dromedary hair length variation.
  • Task after meeting: Write a one page summary of what you learned in Arabic or English and send it to your instructor. Make sure to explain what parts you can cite from the paper.

Research Topics and Seminar I: Fall 2022

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Class time and location
Wednesdays 2:00-3:00 (Room: SCI-S Room 179)
* No self-evaluation
* No peer-evaluation
* No response to peer evaluation
* Absence
* No presentation
Participants:
  1. Sara Alsrayea./
  2. Raghad Alrefaei./
  3. Ali Garashi./

Seminar Topics: Medical Biotechnology.

HA selected examples:
Your presentation should include:
  1. Title, student name, course, presentation date-slide.
  2. Paper front page and abstract-slide.
  3. General info about the organism-slide(s).
  4. General info about the problem/goal of the study-slide(s).
  5. General description about the methods used-silde(s).
  6. Result (each figure or table in a separate slide).
  7. Discussion slide about the usefulness of the study.
  8. A final slide about your ideas/suggestions/ethical issues for implementing such studies in Kuwait.
To Do:
  1.  Search for a biotechnology research paper that is related to the seminar topic and send a pdf to your instructor for approval.
  2. Make a powerpoint file named (YourName_501).
  3. Send a copy of your presentation a day before your actual presentation.
  4. Non-presenters should read the paper and prepare to engage in discussion.
  5. If it is possible, we will repeat the process with a second publication.
Useful files:
  1. Powerpoint presentation template ().
  2. Self evaluation template ().
  3. Peer evaluation template ().
  4. Response of peer evaluation template ().
Topics:
Seminar 1 – 5/10/22: Course planning, scientific publications, finding good ones
– HA
Seminar 2 – 12/10/22: How to read a scientific paper? – HA
Seminar 3 – 19/10/22: Making a good presentation – HA
Seminar 4 – 26/10/22: Hematopoietic Stem Cell Gene Therapy with a Lentiviral Vector in X-Linked Adrenoleukodystrophy – Sara Alsrayea
Seminar 5 – 2/11/22: Development of small interfering RNA delivery system using PEI-PEG-APRPG polymer for antiangiogenic vascular endothelial growth factor tumor-targeted therapy – Raghad Alrefaei
Seminar 10 – 7/12/22: Studies on the immunogenic potential of plant-expressed cholera toxin B subunit – Sara Alsrayea
Seminar 11 – 14/12/22: Tumor selective uptake of drug-nanodiamond complexes improves therapeutic outcome in pancreatic cancer – Raghad Alrefaei 

Intro. to Genomics – Fall 2022

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Class time and location
Sun, Tue, Thur – 12:00-12:50 (Room: SCI-S-119)
 
 
Projects:
Group 1: Felis catus, Presentation:
  1. Bedour Almutairi, Paper, Sup.material.**/
  2. Dalal Almayas, Paper, Sup.material./
  3. Sarah Alresheedy, Paper, Sup.material.*********/
  4. Noor Khanafer, Paper, Sup.material./
Group 2: Canis familiaris, Presentation:
  1. Ghaleya Aldhafeeri, Paper, Sup.material.*****/
  2. Asmaa Alghanem, Paper, Sup.material.*/
  3. Zenab Bahman, Paper, Sup.material.****/
  4. Fatemah Alhusain, Paper, Sup.material./
Group 3: Equus caballus, Presentation:
  1. Maryam Alhajri, Paper, Sup.material.***/
  2. Shahah Alkharafi, Paper, Sup.material.*/
  3. Haya Alshammari, Paper, Sup.material.*/
  4. Rawan Abdulaziz, Paper, Sup.material.*/
Group 4: Bos taurus, Presentation:
  1. Rana Chami, Paper, Sup.material.*/
  2. Shaha Farhan, Paper, Sup.material./
  3. Shouq Alhazaa, Paper, Sup.material.*********/
  4. Belqees Almutairi, Paper, Sup.material.******/
Group 5: Camelus sp., Presentation:
  1. Nazek Haydar, Paper, Sup.material./
  2. Lin Ataya, Paper, Sup.material.*/
  3. Hajer Alshammari, Paper, Sup.material./
  4. Fatmah Abdullah, Paper, Sup.material.*/