Saturday, October 30, 2010

Wednesday, October 27, 2010

Practical: NUCLEIC ACIDS


Picture 2

Picture 1.



 
 

Picture 1 & 2: Students performing practical on  DNA Isolation And Partial Characterisation From Bacterial Cells.

Picture 3: Showing bands of Nucleic acids


Tuesday, October 26, 2010

FREEMAN CENTRE


The state-of-the-art building "FREEMAN CENTRE" is the new home for the university's research team SPRU (Science and Technology Policy Research) and for the University of Brighton's Centre for Research in Innovation Management (CENTRIM). It is named after SPRU's founding director, Professor Christopher Freeman.


   Thanks to the authorities for providing me a place to work in the same building.

Monday, October 25, 2010

ACCOMMODATION


Accommodation is one of the biggest problems that I faced here in Sussex University. As soon as I was awarded the title of Visiting fellow in June 2010, for a period of six months from 1st October, 2010 to 31st March 2011 in SPRU (Science and Technology Policy Research) by the School of Business, Management and Economics, University of Sussex,. I started  looking for accommodation at the University campus.
Majority of the first year undergraduate students live in the University Campus, The University has five accommodation blocks. The housing office of the University  also  helps those students who prefer to live outside the campus, as also in the University-owned accommodation across Brighton and Hove. The  housing office maintains a list of rented properties in the local area, and  also gives advice relating to getting property on rented basis. The university accommodation is self-catering, with cooking facilities in shared kitchens. Typically rooms you get with bed, wardrobe, shelves, desk and chair, desk lamp and easy chair. Bathroom facilities are normally shared, although most rooms do have their own sink. The majority of rooms are for one person although some are shared at slightly lower cost.
Since I had this information, I had written a mail to the housing office of the University of Sussex in July 2010.  I got an auto-generated reply saying "Please note that the closing date for housing applications for 2010/11 is 1st August 2010".
I continued my efforts. On 5th August 2010, I got a reply saying "Unfortunately we would not be able to provide accommodation for visitors at the time your request as our residences will be full of students and the guest rooms do not become available until mid December. We would recommend trying our private sector website www.yourstudentpad.co.uk password welcome and leaving a message for landlords to contact you if they can help with a 6 month tenancy. Alternatively you could try the host family list attached as they may be happy to help or perhaps contact a bed and breakfast/ hotel from the following link:
I kept my efforts on and meanwhile I wrote a mail to Dr. Parimal Patel, Sr. Research Fellow at SPRU and he suggested me to contact his colleague Neha Rai, regarding my accommodation problem. She guided me and gave me the website addresses of private accommodation letting agents like http://www.Rightmoves.co.uk and http://www.gumtree.com I visited all these websites from Goa.But in vain. Finally while sending my application for UK visa I was required to attach accommodation proof. I wrote back to Neha again. Realising my problem, she sent me an invitation letter to stay with her family.
Her letter helped me in getting the UK visa. Meanwhile I received a letter from the Institute of Development Studies (IDS) permitting me to stay for initial fifteen days, i.e., from 1st October, 2010 to 15th October 2010.

After coming over here on 2nd October, 2010, it took me  15 days to find out a furnished, single bed room flat at Brighton-Hove. Every day I used to check on the website the availability of flats. I experienced that within 24 hours of announcement on the website the flats are occupied.
Normally those who want to join the University of Sussex, particularly students and parents visit the university campus one year in advance on open days. On open days, the  students and parents come to see the facilities particularly, the  accommodation .
If I was to come here at least by 15th September, 2010 then probably I would have got the accommodation easily outside the university campus and not on the university campus. This year, the  number of students who joined for the various undergraduate courses of SU  is more than that of the previous years. Hence, the university could not provide accommodation to all the students. A large number of students had to go off the campus and by 25 th September,2010, accommodation outside campus was  also full. The Autumn term started from 4th October, 2010 for the academic year 2010-2011.

Saturday, October 23, 2010

UNIVERSITY OF SUSSEX LIBRARY

                      This is self return book machine. User is receives acknowledgement.

UNIVERSITY OF SUSSEX LIBRARY

                                                 Students are accessing the library catalogue

UNIVERSITY OF SUSSEX LIBRARY

Students and staff can use this machine to borrow, renew, reserve books and to pay fines if
any. Identity card is barr coded. By placing the ID card in the space provided,  one can
 open  their library account.

 There are four machines at the entrance of the libray and there is no need of any assistance of library staff.

Friday, October 22, 2010

Seminar 1: Human Physiology


 Seminar is a very different learning environment from the lecture, and today the first year students were engaged in group discussion to develop ideas with their fellow students. What I find here is that, majority of the students take keen interest in the subjects they study. Around 150-200 students have registered for this core course -Human Physiology’. Eight groups are made to organise seminars. In each group there are 20-25 students. The seminars are conducted in smaller lecture halls. The duration of this seminar class is one hour. Today, all eight groups had seminars from 9:00 to 17:00.  
For today’s seminar, the topic given was ‘the use of oxygen’ (and to some extent the removal of CO2). The students were asked to read two papers and these papers were available for the students to download from the ‘Study Direct’ site.
1)Widmaier, E.P. (1998) “Oxygen – The Breath of Life”; Chapter 5 in Why Geese Don’t Get Obese; pp. 53-70; Freeman.
This is a chapter from a book, looking at different adaptations to oxygen needs in different environments. Among other aspects, it introduces the fact that many diving mammals can dive for extended time periods, without surfacing for air. The Weddell seal in particular is spectacular at this.
2) Kanatous et. al (2002) “Aerobic capacities in the skeletal muscles of Weddell seals : key to longer dive durations?” Journal of Experimental Biology; 205; 3601-8
This paper is more complex. It is an experimental scientific paper - studying diving in the Weddell seal again. The students are given two versions: the full, original paper, and a version which is only the discussion of the paper, with numbered paragraphs. It is the latter version which is considered for the seminar. However, the students are asked to read the full paper also, particularly the “abstract” (effectively a summary of the background and findings of the article).
 The students are asked to read both the papers at least two days before the seminar.
The students were given following information and the questions.
Background :
Oxygen is essential to our survival. We obtain it from the air, the exchange of gases take place in the lungs. Some bacteria can live anaerobically. In fact, for some oxygen is a potent poison. But we, and all other large animals, need oxygen to function. Various species have adapted in different ways, but oxygen requirement is a common thread.
Following Questions were given to the students to  answer before the seminar and were asked to bring the written answers.
1          How do O2 and CO2 interact with erythrocytes?
2          What is erythropoetin? Think about why the kidneys should be responsible for making it?
3          What is myoglobin? Compare it to haemoglobin? Why is it useful – and in particular to diving seals?
4          What do apnoea (or apnea), hypoxia, hypercapnia and acidosis mean? - and what role do these have in diving?

5         What does ADL mean?

6         Article 2 discusses various types of muscle fibre within the big swimming muscles. What are the main differences between Type I and Type  IIA muscle fibres – relevant to the article?
7         What is the significance of the mention of the penguin in article 2?
8          Why are the changes to blood pH so detrimental (for example lactic acid; article1, p.59 )?
9          Where does lactic acid come from? Why and how is it kept in the muscles of a diving seal? And why is pyruvic acid useful (article 1, p.60)?
10        What is the problem with nitrogen when diving, and how is it thought that diving mammals like seals and dolphins overcome the problem?
11        What are the adaptations of mountain people. Why is this necessary?
       Initially all these questions were discussed and the students improved their answers by adding additional points which they got after discussion.
       In the last half an hour or so, these 20-25 students were further grouped in to four still smaller (4-5 students in each) groups. Each group was given a paragraph from the second paper and were asked to discuss among themselves for five minutes to know what the paragraph means to them? One student from each of these smaller groups was asked to make presentation for a minute. All group leaders from each group made their presentations. The seminar lasted for an hour.

Thursday, October 21, 2010

Lecture on Plagiarism and Collusion

Since this is an important topic, I attended the lecture on Plagiarism and Collusion which was delivered by Dr. Simon Morley to the first year students. It is a part of their curriculum in the core course namely-‘Essential Skills in Biomedical Science’. He stated that a  significant number of students are submitting plagiarised work. He said a student from the School of life science was sent out of the Sussex University since he was found twice guilty. He advised the students to adopt good working practices. He said that the Essays/Dissertations/theses, Computer programs, Presentations, Reference lists/Bibliographies, Images/Figures/DataArguments/Debate, the ideas, thoughts and words must be of the writer , and not the work of other people.
The main objectives of this lecture were:
1.To clarify the meaning of plagiarism and collusion to the students.
2.To inform the students on the expectations of good academic conduct.
3.To introduce the students to the citation and referencing requirements for written work.
4.To guide them in the development of personal skills that underpins high quality academic work.

Dr. Simon Morley explained the meaning of plagiarism as follows.
“Plagiarism is the use, without acknowledgement, of the intellectual work of other people, and the act of representing the ideas or discoveries of another as one's own in written work submitted for assessment. To copy the sentences, phrases or even striking expressions without acknowledgement of the source (either by inadequate citation or failure to indicate verbatim quotations), is plagiarism; to paraphrase without acknowledgement is likewise plagiarism. Where such copying or paraphrase has occurred the mere mention of the source in the bibliography shall not be deemed sufficient acknowledgement; each such instance must be referred specifically to its source. Verbatim quotations must be either in inverted commas, or indented, and directly acknowledged.”

Complete plagiarism is when a piece of work is copied entirely from one or more sources. Even if the source(s) are acknowledged, and even properly referenced, it is still considered to be plagiarism as it contains no original work, or interpretation of the information, from the student.

Partial plagiarism involves inserting sections of directly copied and unacknowledged source(s) within an assignment.
 ‘Copy and paste’: The availability of information on the internet & electronic journals means that it is now easy to 'copy and paste' information for assignments. It is important that if such information is included in assignments that it is included in quotation marks ("....") and that it is properly referenced.
 ‘Word switch’: If you copy a sentence or paragraph for the assignment and change a few words it will still be considered to be plagiarism. It is better to paraphrase than to quote, and if one copies a phrase he/she should copy it word by word and use quotation marks.

Dr. Simon also gave some suggestions to the students on ‘how to avoid avoid plagiarism’.
The lecture also covered reference lists. I would like to place before you some of his views on referencing and citation.
How to write Reference List? (This is useful for everybody).
The reference list must contain all the relevant information to enable another reader to find the original source. Date of publication by the author, title of chapter or article, Journal title and publisher, page and volume numbers must be given.
The text and reference list: single author
e.g. Harvard format –where you use the name and date in the text (Morley, 2003 ), and a reference list at the end.
Morley, S.J. (2003) Phosphorylation of initiation factor (eIF) 4E is resistant to SB203580 in cells expressing a drug-resistant mutant of stress-activated protein kinase2a/p38.Cell. Signalling15, 741-749.
The text and reference list: two authors
e.g. Harvard format –where you use the name and date in the text (Naegele and Morley, 2004 ), and a reference list at the end.
Naegele, S., and Morley, S.J.(2004)Molecular cross-talk between MEK1/2 and mTORsignaling during recovery of 293 cells from hypertonic shock.J. Biol. Chem.279, 46023-46034.
The text and reference list: multiple authors
e.g. Harvard format –where you use the name and date in the text (Coldwell et al., 2004), and a reference list at the end.
Coldwell, M.J., Hashemzadeh-Bonehi, L., Hinton, T.M., Morley, S.J., and Pain, V.M.(2004).Expression of fragments of translation initiation factor eIF4GI reveals a nuclear localisation signal within the N-terminal apoptotic cleavage fragment N-FAG. J. Cell Sci.117, 2545-2555.

Referencing on-line sources
Web sites must be referenced in a similar fashion to journals and books. Author (s), Publisher (copyright holder), Date of publication (copyright date), Title PLUS: URL (web address) accession date (date you read the material.)

What is a Bibliography?
A bibliography is not a reference list. It is a list of sources that provide general background information or further develop the ideas presented. It is not the specific list of articles, which you refer to in your writing, and use to directly support your work.
It is not the specific list of articles, which you refer to in your writing, and use to directly support your work.
Unless you are specifically asked to provide a bibliography as well, a reference list and in text citations are all that are necessary.

What is collusion and how do you avoid it?
Collusion is when the students work together on assignments which should be completed alone. For some assignments the students may be required to work together and even submit joint / group work for assessment. Usually a student must submit his/her work which is entirely his/her own. A student who helps another to produce work is guilty of collusion, along with the student who has benefited from  the help by other student.
The course documentation should clearly state which assignments, if any, can be done in collaboration with others and whether that requires producing a joint piece of work or only the preparation for it. The students must only work together on producing an assignment if the course specifically allows it, otherwise this is collusion and is an offence .

Wednesday, October 20, 2010

Human Physiology – Histology practical

Mammalian tissue histology slides for the light microscope.
This pratical was of three hours, i.e. 9:00-12:00 in John Maynard Smith (JMS) building in 1A1 Laboratory. Nearly fifty students had gathered out side the lab. before the scheduled time. The lab. was already set up and two demonstrators were waiting inside the to receive the students. The main person to conduct the practical is none other than Dr. Camilla Tornoe who delivered two lectures   earlier on the same topic. As soon as she entered the lab., she asked all students whether they have come with the practical hand out or not. All students had brought. She told students what they are going to do today and what is expected from them. In this practical they will be looking at thin sections of material which have been given a general stain, either Haematoxylin and Eosin (H&E) or Massons Trichrome both of which show the basic structure of tissue. For this assignment rat tissue was used.
The procedure for the preparation of microtome slides, staining was mentioned in the practical hand out. The  first year students are not expected to do this step.
Students were asked to collect pre-stained, permanent microtome slides of tissues of different organs like, liver, pacreas,kidney,heart,small intestine. Surprisingly all students could get one set of all slides. A4 size plain white sheets were kept on the teachers table. Students are expected to draw maximum two diagrams on each paper. Each sheet should bear the name of the student. Student should draw neatly, label, write the name of the stain used and magnification of the diagram (10 x 40) = 400x.
Simultaneously teacher projected the slide one at a time over the T V screen. The purpose is to give you an insight into the structure of these organs. it is intended to make students to think about how structure and function are linked.
On a separate sheet of paper, students are expected to write their name and answer the questions (answers should be typed, not hand-written).
Students have to do a literature search for the answer to some of the questions. Sources of information should be appropriately included in a bibliography at the end.
 They are also need to go through the online tutorials on the Human Physiology
course website in order to answer.
Important:
The answers to the questions constitute 60% of the assignment. However, students cannot pass the assessment without decent drawings with correct labelling and magnification, even if they have perfect answers to the questions. Students are expected to submit this assignment on 7th week of the autumn term. 

Tuesday, October 19, 2010

Essential Skills in Biomedical Science

 This course is for first year B.Sc. students (level 1) and of 12 credits.



Course Outline:
This course is made up of two components, data handling and essential skills. The main purpose of the data handling part of the course is to help the students to acquire the calculation skills and  to interpret the results from frequently used biochemical techniques. This will provide  the  foundation for practical work which they will do, not just during the first year, but also for several other courses they will opt during their degree program, and, particularly, in their final year research project. The essential skills component aims to introduce the students to the basic skills needed for life at the University. It includes significant transferable basic skills, which promote personal development and academic performance. The Key under-pinning skills for success include how to extract information from journal articles, citation and referencing, annotated bibliographies, mind maps/outlines and scientific writing.
Learning Outcomes:
By the end of the course, a successful student should be able to:
1. Carry out basic biochemical calculations
2. Write an annotated bibliography
3. Carry out a literature search using PubMed
4. Understand the concept of good academic practice
5. Demonstrate proficiency in the use of Excel.
In the previous two lectures the students were taught the techniques of notes making, time-management and also discussion on the work sheet which is available as a course material. These work sheets provide information on units of measurement (molecules, moles & other units) required in a laboratory, abbreviations used, their meaning, solutions and dilutions with worked out examples.
Today there was a ‘Open Book Test’ 1. This test was on Molecules and Moles and the duration of the test was 2 hrs. This is a formative test. All the students were given the test paper cum answer sheet. They  have to do the calculations on a separate sheet and this sheet is to be enclosed to the test paper. This is annotated and will be returned to the students. This test was conducted in a lecture theatre and appeared to me that all the students (150) were present at 9:00.

Pre-Practical session in Cell and Molecular Biology


The Pre-Practical session was conducted today for a group of around 150 students in a Lecture Theatre (LT) between 17:00 to 18:00 by Prof. Trevor Beebee. He had come with the copies of the manual for the practical to be conducted after two days and had placed them on the table. Students collected these copies as soon as they entered the LT. This practical is based on the two lectures delivered by him last week on Nucleic Acids.
The session was on Nucleic Acids: ‘ DNA Isolation and Partial Characterisation from Bacterial cells’. The instructions in the manual says that the students are expected to read these carefully before they come for the practicals. This will help them to understand better and enable them to work faster. This practical session is going to be 3 hours on Thursday either 9:00 -12:00 or 14:00 to 17:00 in four groups depending on the degree programme. The students will work in pairs.
The three hours practical is divided in to three Parts:
Part I: How to isolate and purify DNA from Bacteria (1½ hours)...first half of the practical.
Part II: Investigate the size of the DNA and RNA ,and
PartIII: Estimate yield and purity.
The Solutions, apparatus, instruments and procedure required to carry out this practical is given and was explained with the help of power point slides.
After the practical (i.e. at home) the students are expected to draw  graph, calculate the yield and concentration.
After this the students should look at the questions at the end of the schedule. Once they are ready with the answers then should log on to ‘Study Direct and complete’- the on-line quiz.
At the end of this practical the students should be able to:
  1. Understand how to isolate and purify DNA from Bacteria.
  2. Investigate the size of DNA and measure how much RNA is present.
  3. Know how to estimate yield and purity of DNA.
From this pre-practical session what I understand is that the aims, objectives, procedure, time management and assessment are clearly defined and the students will not have any confusion during the practical .

Thursday, October 14, 2010

COURSE IN CELL AND MOLECULAR BIOLOGY


 Autumn Term 2010/11
Course code:C7004
This course is of 24 credits spread over autumn and spring terms.
Faculty:
Course Organizers:
Dr. Mark Paget (Chemistry and Biochemistry)
Room 5.17 CRPC
Phone extension: 7764

Dr. Robert Ray (Biology and Environmental Science)
Room 4C10 John Maynard Smith Building
Phone extension: 7634

 The Lecturers are:
                                    Prof. Trevor Beebee (T.J.C.Beebee@sussex.ac.uk)
                                    Dr. Mark Paget (m.paget @sussex.ac.uk)
                        Dr. Louise Serpell L.C.Serpell@sussex.ac.uk)
Practical Leaders are:
                                    Prof. Trevor Beebee (T.J.C.Beebee@sussex.ac.uk)
                        Dr Alexander Van Aken (A.van-Aken@sussex.ac.uk)
                        Dr Neil Crickmore (n.crickmore@sussex.ac.uk)
Course Meetings are:
Lectures (weekly):
Monday (weeks 3, 5, & 7 only)          17:00 - 18:00               CHICH-1LT
Tuesday                                               15:00 - 16:00               CHICH-1LT
Wednesday                                         09:00 - 10:00               CHICH-1LT

Tutorials (weeks 3, 6, & 9):
Tutor assignments are available on Sussex Direct. Students and tutors should organize tutorials during the first week of the  term.
Practicals:       
Practicals will be held in Weeks 3-8 on Thursdays. Practicals are half-day sessions running .Thursday mornings 9:00-12:00 or Thursday afternoons 14:00-17:00.
 All this information in more details was sent to me by the course coordinator, Dr. Mark Paget. Absolutely no confusion of finding out the place Chichester I building (CHICH I) and Lecture Theatre (LT).
Yesterday (Tuesday) I attended the lecture on the topic “Nucleic Acids – the basics” and today on the topic “Primary and secondary structures of Nucleic acids.” These two lectures were delivered by one of the most senior faculty members, Prof. Trevor Beebee.  Both the days he reached the lecture theatre 15 minutes before the scheduled lecture time . The students including me were also waiting before the scheduled time of the lecture. Since LT was occupied by the other faculty we could enter just five minutes before 15:00. The LT has multimedia facility including POD casting. Prof. Trevor entered the class with his pen drive. Within few seconds he was ready with the power point presentation on the topic. Exactly at 15:00 he started his lecture by introducing himself . He also told us where he will be  available .This was his first slide. He delivered  lecture for 45minutes. In between once or twice he asked the students if they had  any doubts or any questions. The students did ask him some questions and he answered. After the lecture,  he was available for  discussion  with  the students  for 15 minutes . The students  lined up and got their doubts cleared. The class had nearly 150 well behaved and good students. Some students had come to class with the printouts of Prof. Trevor's  power point presentation slides and some used to take down. Two students had laptop with them.
Today (Wednesday) I reached  the LT at 8.40. And Prof. Trevor reached at 8.45. The lecture was at 9.00. Again as usual he was ready for his lecture 10 minutes before the scheduled time. He started exactly at 9.00. He said that he felt sorry because his  yesterday’s  lecture could not get recorded.
 Today also his lecture was very systematic and informative. The manner in which he delivered was same like yesterday.
Yesterday,  I have sent a mail to the course coordinator as per the guidance and discussion which I had with Prof. Trevor regarding my tutorial and practical batch.
I also would like to attend some more courses and  will  write to the course coordinators.         

My First Week Experiences


Today I realized that I should have come to the University of Sussex one week before, i.e., in the last week of September, 2010. The Autumn Term for the academic year 2010-2011 started on 4th October, 2010.  This term is a ten weeks programme and will end on 10th December, 2010.
I reached here on Saturday, 2nd October, 2010 late in the evening. Next day was Sunday, 3rd October, 2010. So I could not meet anyone in the SU. However, I had sent an e-mail to Dr. Parimal Patel asking for an appointment to meet him on Monday, 4th October, 2010. On 4th October, 2010 Dr. Patel took me to the IT Services of Sussex and the School of Life Sciences as well as the faculty of Business, Management and Economics. There I met Dr. Maria Savona and others.
Let me remind  you that I was given accommodation at the IDS (Institute of Development Studies) till 16th October, 2010. So from 5th Oct. onwards till 9th Oct. I was busy searching for advertisements for accommodation on the websites of 'Gumtree' and 'Rightmoves' every day and every hour .Whenever I found the opportunity to view the flat I went to Brighton city personally to view the same. It so happened that  either I could  not get or when I got some flat I was advised by friends here not to take the same as that area is not safe. At the same time I started searching for the courses so that  I can attend the lectures and practicals . It was through Dr. Pari’s good contacts, I was able to write a mail to the course coordinators of Life Sciences, Dr. Mark Paget and Dr. Robert Ray. Dr Mark Paget not only directed me to Prof. Trevor Beebee but also sent me the entire course outline, contents, names of the lecturers with their e-mail IDs, course meetings, organisation of the course, reading materials, assessment (theory), time table, lecture synopsis, practical and assessment (practical). Thus by the end of the first week at Sussex I came to know what I have to attend in the second week of October, 2010.
Dr. Patel and his colleague were worried about my accommodation since only one week more was left for me to stay at the IDS as per earlier sanction. Pari suggested that I could ask for extension of my stay at IDS. When I met Mr. Gabriel who had helped me on the first day of arrival to IDS was kind enough to accommodate me for another week till 23 rd October, 2010. The University of Sussex got a large number of students for this academic year (2010-2011) particularly for the first years of  the undergraduate courses. So the university could not provide accommodation to everybody on the campus. All those students who did not get accommodation had to move out of the University campus.   
On Sunday i.e., on 11th October, 2010 Dr. Pari took me to Brighton city in the evening to the offices of accommodation letting agencies. I went to meet these accommodation letting agencies on Monday morning. I was told that no accommodation was available because the students had already occupied the dwelling units. My search continued further. Neha sent me a SMS for viewing the flat at 13.40 at Brunswick square. I went to that place at 13.15. Exactly at 13.35 two ladies entered the house number 6. I thought this time also. I may not get the flat.But when both  the ladies came out of the house one of them asked me whether I  had come for viewing the flat. When I said yes, she showed me the flat and told me to give a call by 15.00. since there was no other option left for me, I agreed and the procedures of ‘agreement of letting’ are going on. By tomorrow, 14th October, 2010, I will be able to get the house key. It is going to be six months contract. It is difficult to get accommodation for six months. Finally  my accommodation problem is solved. Luckily today 13th October, 2010 morning I met Mr. Gabriel . I requested him to cancel the extension given to me to stay  at the  IDS for another week.