Intro. to Molecular biology (281)

 

Lecture 1: About the course (Readings: None, 281_Lec1)

Lecture 2: General introduction (Readings: Chapter 1, 281_Lec2)

Lecture 3: The identity and location of the genetic material (Readings: Chapter 2, 281_Lec3, Puzzle3)

Lecture 4: DNA: chemical composition (Readings: Chapter 2, 281_Lec4, Puzzle4)
VideoDNA building blocks

Lecture 5: DNA: the double helix structure (Readings: Chapter 2, 281_Lec5, Puzzle5)
VideoThe DNA double helix discovery
VideoPauling triplet helix
VideoJames Watson – Basepairing
VideoChargaff’s rule
VideoThe double strands

Lecture 6: DNA: genome organization (Readings: Chapter 2, 11, 281_Lec6)
VideoDNA packaging – Basic
VideoDNA packaging – Advanced

Lecture 7: DNA: replication experiments (Readings: Chapter 10, 281_Lec7)
VideoDNA structure and replication

Lecture 8: Prokaryotic replication: elements (Readings: Chapter 10, 281_Lec8, Puzzle6)
Lecture 9: Prokaryotic replication: process (Readings: Chapter 10, 281_Lec9, Puzzle7)
Lecture 10: Eukaryotic and phage replication (Readings: Chapter 10, 281_Lec10, Puzzle8)
VideoDNA replication – Basic
VideoDNA replication – Advanced

Lecture 11: Transcription (Readings: Chapters 4, 5, & 6281_Lec11 , Puzzle9)
Lecture 12: Transcription in prokaryotes (Readings: Chapters 4, 5, & 6281_Lec12 , Puzzle10)
Lecture 13: Transcription in eukaryotes (Readings: Chapters 4, 5, & 6281_Lec13 , Puzzle11)
VideoTranscription – Basic
VideoTranscription – Advanced
VideoEukaryotic mRNA splicing

Lecture 14: The genetic code (Readings: Chapter 7281_Lec14 , Puzzle12)
VideoThe Triplet Code

Lecture 15: Amino acids and proteins (Readings: Chapters 7 & 8281_Lec15 , Puzzle13)
Lecture 16: Translation: tRNA and rRNA (Readings: Chapters 5, 6, 7, & 8, 281_Lec16)
Lecture 17: Translation in prokaryotes (Readings: Chapters 7 & 8, 281_Lec17)
Lecture 18: Translation in eukaryotes (Readings: Chapters 7 & 8, 281_Lec18)
VideoTranslation – Basic
VideoTranslation – Advanced

Lecture 19: Regulation of gene expression: Generalities (Readings: Chapter 9, 281_Lec19)
Lecture 20: Lambda phage repressor (Readings: Chapter 9, 281_Lec20)
Lecture 21: Prokaryotic regulation (Readings: Chapter 9, 281_Lec21)
Lecture 22: Eukaryotic regulation (I) (Readings: Chapter 9, 281_Lec22)
Lecture 23: Eukaryotic regulation (II) (Readings: Chapter 9, 281_Lec23)
Lecture 24: Eukaryotic regulation (III) (Readings: Chapter 9, 281_Lec24)

Lecture 25: DNA mutation (Readings: Chapter 16, 281_Lec25)
VideoThe Fly Room
MovieMutation – The science of survival

Lecture 26: Point mutations (Readings: Chapter 16, 281_Lec26)

Lecture 27: Chromosomal mutations (Readings: Chapter 16, 281_Lec27)

Lecture 28: Sources of mutations (Readings: Chapter 16, 281_Lec28)

Lecture 29: DNA repair (Readings: Chapter 16, 281_Lec29)

Extra material not needed for exams but interesting to know!
Extra lecture 1: ModelOrganisms, Puzzle1.
Fun readsWhat are model organisms?
Extra lecture 2: MendelANDGenetics, Puzzle2.
Extra lecture 3: DNA_Extraction
VideoHow to extract DNA from strawberries
Extra lecture 4: DNA_Quality_Quantity
Extra lecture 5: PCR_DNAsequencing
VideoPolymerase Chain Reaction
VideoSanger Sequencing
VideoPCR song
VideoBio Rad GTCA song

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

UC Davis visit – 2019

January 9th 2019

It was a joy to return to my Ph.D. school (University of California, Davis) as the first destination of my one-year academic leave from Kuwait University. Beside reviving the memories and feelings associated with the place, I was eager to meet friends, colleagues, and mentors. I stayed, sadly, for only one day but had a chance to walk around the main campus and meet people despite the rainy weather.

For lunch, I was invited by the Grahns (Robert and Jennifer Grahn) to eat at Sophia’s. It is the best Thai restaurant in Davis, in my opinion. The lunch special of shrimp curry hasn’t changed over the years and my taste buds haven’t forgotten the delicious flavors. Rob and Jen Grahn are a couple of my dearest friends in Davis. I have shared the office with Dr. Robert Grahn throughout my Ph.D. years and shared much of my general and scientific thoughts as well as my feelings and frustrations. It was unusual for me and for them that our lunch extended for nearly two hours but I enjoyed every second of it and I hope they did.

Although not sure that walking would assist in the digestion of my tasty lunch, I walked around the nice small downtown of Davis and to my surprise I saw the Framers Market, which takes place Wednesday afternoon and Saturday morning of every week. The Farmers Market was one of the frequently visited locations of my family where we can try and buy different food items in addition to fruits and vegetables. My son, Ali, also has enjoyed the playgrounds and the company of other kids. On my way to the main campus, I passed by the 3rd and U Cafe where I used to join REHAB journal club on Fridays afternoon for a free learning experience. 

A visit to UCD always starts with the Memorial Union. The place has changed a little since my graduation with more spacious foodcourts and a newly renovated larger bookstore. Drowning in my memories, it was a challenge for me to avoid all the bikers on campus. Davis is known to be the bicycle capital city in the United States and the campus is almost car free on its internal roads. Everyone rides a bike at UCD including faculty and if one decides to walk instead, a class or a meeting will definitely be missed. I remember re-learning how to ride a bike when I first joined the Ph.D. program of the Genetics Graduate Group (now known as the Integrative Genetics and Genomics – IGG – Graduate Group). When you are in Davis, do what Davisians do and ride a bike.

I walked my way to the office of my dissertation committee member and mentor, Jeffery Ross-Ibarra, at Robbins Hall. Jeff, as we call him, has been an inspiration for me as a scientist. He is a population geneticist and in love with studying corn. He taught me population genetics and was one of the many reasons why I love the topic. Also, He has been my inspiration to establish a journal club at Kuwait University (EHRAB) based on his entertaining and intellectually valuable REHAB. Two things stand out as the most memorable lessons that I learned from Jeff. The first lesson was scientific humility. I learned that by his ungarnished comments and questions, which were at the time quite hurtful but much needed on the long run and for a true scientific maturity. The second lesson was to be in love with the organism one studies. I still remember vividly my last conversation with him before my return to Kuwait after my graduation. He asked me “why camels?” His question was in reference to a statement that I made during my exist seminar that I am interested in studying camels when I return home. The first answer that came to my mind was “the camel has waited a long time for me to study it”. Of course my answer wasn’t along the lines of the first lesson that he taught me, humility, but it was may be a reflection of my determination and passion to study the camel and just like his passion to study corn. Without any prior appointment, I walked into Jeff’s office to see him standing in a chair-less room. Yes, he has a standing desk with two large computer screens. He told me that this was his treat for becoming a full professor. Nothing in the office changed. The nice vertical chalk-board is still in the same location and the corn samples and photos decorate the office elegantly. We chatted for about half an hour before I handed him a little gift from my camel lab. The gift was T-shirts and keychains/car mirror hanging accessory with a camel design.

From Robbins Hall I walked to the haunted building (a claim or a joke) Storer Hall where the office of my other dissertation committee member and my dear mentor, Bruce Rannala, resides. I knew before my arrival that Dr. Rannala would be in town. However, I wanted to walk to his office just like I used to when I was a student. Bruce, as he likes me to call him, has taught me statistics and was the first to introduce me to R programming. I still remember setting behind my friend Carolyn Yrigollen and leaning to the right wall of the classroom. When Bruce plotted a histogram using R, my first question was “is it possible to change the colors?”. He smiled and replied that a lot of things can be modified. I laugh when I remember this incident because for all the statistics that he was introducing to us, my only question was to the plotting, much to my love and fascination with visualization.

At about 4 o’clock, I drove to UC Davis Veterinary Genetics Laboratory (VGL). I had an appointment with my friend Rob (Robert Grahn) to meet old friends at the testing lab, to get introduced to the director (Dr. Rebecca Bellone), and to get a quick tour to the facilities, and equipments of the lab. I was familiar with the lab in general when I did the genotyping and sequencing aspects of my Ph.D. projects using their machines. Beside all the new machines and the automated systems for DNA extraction etc., I was particularly amazed by the number of samples that the lab houses and the way these samples are organized. Thousand and thousands of biological samples are stored from several species. I discussed the setup of my camel biobank (Cdrom Archive) with Rob who provided me with valuable suggestions and recommendations. I hope that my visit to the VGL puts the seeds for future camel specific collaborations.

Scientific Posters – my philosophy and design

I had the pleasure of giving a workshop on scientific poster design at the University of Florida, Gainesville (Feb 8th 2019) where I was hosted by the Dr. Samantha Brooks and Brooks Equine Genetics Laboratory. Below are the general guidelines that I prepared for the participants of the workshop.


  1. Keep in mind:
  • Science is communicated by different ways such as peer-reviewed scientific articles, review papers, book chapters, books, scientific talks, or scientific posters. Each mean of scientific communication targets a specific audience and aims to deliver/report different scientific content.
  • The scientific content of your poster may not be as developed and complete as that of your future scientific papers. Your poster can be as simple as the layout of future experiments.
  • Scientific posters are not scientific papers and do not need to follow the standard sections (Abstract, Introduction, M&M etc.). You may be tempted to follow such model of scientific layout due to its wide usage in poster design.
  • The text content of your poster does not need to be in a paragraph format. As mentioned above, your poster is not a scientific paper. I highly suggest that you use bullet points of concise short sentences rather than long and complicated paragraphs.
  • Too much text in your poster is not attractive and is not a sign of sophistication or a high-quality work. On the contrary, in many cases it is both repulsive to the audience and a sign of desperation to fill the poster area.
  • The general audience (people out of your specialized field) will only glance at your poster and will likely spend ~15-20s (if you are lucky) looking at your poster whereas colleagues within your specialized field will be familiar with your work and will likely seek you to engage in lengthy scientific discussion. In both cases a lot of text material is a deterrent from any short or long scientific discussion.
  • Large scientific conferences display hundreds if not thousands of posters. Your goal is to catch the eye and mind of as many scientists as possible, which may initiate future collaborations or simply enhance your science with ideas and constructive criticism.
  1. Poster design software: Many softwares can be used for the design of your poster. I recommend using Microsoft Powerpoint due to its wide usage at academic institutions by faculty and students.
  2. Poster layout: Both landscape and portrait layouts are used to design scientific posters. However, a portrait layout is preferred especially in large scientific conferences since the posters’ display area is limited and more portrait than landscape posters can be displayed in the same area.
  3. Poster size: 46 inches height x 34 inches width (~100cm height, 80 cm width).
  4. Poster margins: Leave ½ inch (1cm) margins from all sides of the poster. Your poster material will be placed in 45inx33in design area (98cmx78cm).
  5. Font type: Use a basic font that can be easily read (ex. Arial).
  6. Font color: You need a font color that provides the greatest color contrast with the poster background color (see below). I suggest using black font color for most of the written content of your poster. You can use other colors for certain words/sentences to emphasize importance or a specific relationship to graphical content.
  7. Font size: The font size will vary depending on the poster section. However, with the exception of the authors’ affiliations, figure/table legends, acknowledgments, and possibly the references, all sections should be typed with font size at least 28pt. This will make the poster readable form ~5 feet away. Remember you don’t want to get people very close to the poster because it will reduce their interaction with you and may block other interested individuals from having visual access to your poster.
  8. Poster background: Avoid having a colored background or a background photo. Consider leaving the background white. This will concentrate the focus of the eye on the material of the poster (both writing and figures) rather than the background. This will also provide you with a lot of freedom in the design process.
  9. Title: Use a short catchy title in a large font size (>60pts). Your scientific poster is not a scientific paper to be titled with details and does not need to be easily searched and cited. The title should be attractive to individual passing by the poster or glancing at the conference’s program.
  10. Authors: Write the names of the authors in the order agreed upon by the research team (font size 36pt). Underline the name of the presenter. The presenter may not be the first author. This may happen when your advisor takes your work to large scientific conferences. After each of the authors’ names place a number in a superscript. The superscripted numbers will be the reference for the affiliations of the authors (font size ~24pt). You can be creative with the display of the affiliations. You do not need to give every institution/department a separate line under the author line. You can simply separate the numbered affiliations with a comma.
  11. Logos: Choose good quality logos of your institution or lab. It is preferred to choose a logo with a transparent back ground. There is no standard location to place the logos and it all depends on the design. I suggest that you scale the size of the logo proportionally to the height of the title lines.
  12. Abstract: Most scientific conferences require the submission of a ~ 250 words abstract for your poster, which will be printed in the conferences program or uploaded to the conference’s webpage. Thus, there is no need to include the abstract in your poster. You can use part of your submitted abstract in the poster but not in its entirety and not in a paragraph format.
  13. Objectives: The objectives section is the first most important section of your poster. You need to pay extra attention to the formulation of your sentences and the writing of concise and clear objectives. The entire poster will be focused on the various ways to achieve the objectives. I suggest that you highlight this section with an attractive color and make the font bold (font size 32-36 pts).
  14. Hypotheses: Your hypotheses may be included in the objectives section and highlighted. The inclusion of a hypothesis (if you have one) makes your poster easier to explain from your side and easier to read and understand by the audience.
  15. Figures: Your figures are the second most important part of your poster. Unlike your scientific papers which represent your work in written words or your oral presentations which are largely aided by your spoken words, your posters are largely visual representations of your science. Your audience will mostly look at your poster rather than read it and in many cases you will not be around to explain the content verbally. Thus, it is essential to present your work in clear figures and diagrams that are both attractive to the eye and self-explaining to the mind. Your figures may have different forms (plots, diagrams, pictures etc.). I recommend that you generate the plots and diagrams with a transparent or white background. This will ensure the perfect blend of your figures with the overall background of your poster (see poster background above).
  16. Tables: I suggest that you avoid inserting tables in your poster. Tables are generally detailed summary of your work or your scientific findings. The location of such details is not your poster but your scientific papers. Also tables generally occupy a large area of the poster (if displayed with a reasonable font size) which can alternatively be used for more important graphical or written content.
  17. Photos: If you study an organism and you do not have a good quality photo, you can obtain one from sources that authorize the photo usage for non-commercial use such as Flickr creative commons images (https://www.flickr.com/creativecommons/) or Wikimedia Commons (https://commons.wikimedia.org/wiki/Main_Page)). Make sure to mention the name/account of the owner of the photo in you acknowledgments or in the figures’ legend.
  18. Conclusion: The conclusion(s) section is the third most important section of the poster. It should give a general summary of the findings in a concise sentence or few sentences. The conclusions should include the general take home message of your scientific work.
  19. 30 seconds summary: I highly recommend that you include a section that provides a 30 seconds summary of the entire content of your poster in few words or a sentence. This may need some experimenting and activating or over-expressing most of your creativity genes.

See the implementation of these guidelines in our posters

If you found this workshop helpful and enhanced your scientific poster design experience, please share a pdf file of your future poster design with me (hhalhaddad@gmail.com).

 

Arabic calligraphy and DNA

This is a very nice creative work one of my former students, Fahad Alenizi.  Fahad is a very talented Arabic calligrapher especially in Dewani style.  This work was a collaboration between Fahad and my graduate student Huda Alaskar, a promising English calligrapher and the person who digitized the work.