Size Exclusion

Introduction: 

Size Exclusion chromatography is a useful method for separating molecules according their sizes and shapes. Stationary phase consists of beads with pores. Large molecules that has great volume than pore size can be excluded from solvent. Continue reading “Size Exclusion”

Differences between prokaryotic and eukaryotic genomes

This was written by Direncan Boyraz (Izmir Institute of Technology)

1)Genome structure: 

Prokaryotic genome has only one chromosome in the cytoplasm, but eukaryotic genome has multiple chromosomes inside a nucleus. Because of multiple number of chromosomes, eukaryotes can be haploid or diploid as difference than always diploid prokaryote. Also Prokaryotic genome own  a circular structure, but there are exceptions, besides always linear strands are present in the eukaryotic cells and linear DNA provide telomeres, non-coding DNA ends, for eukaryotic cells. The eukaryotic genome is more complex with longer gene, on the other hand, prokaryotic genome has up to 90% coding sequences than often around 3% in eukaryotic genome. Supercoiling of DNA exist in both, but patterns of them are different because of circular and linear genome. One replication site or Ori is found in prokaryotic genome and it serves quicker division rate more bidirectionally. Eukaryotes have long repeating nucleotides than rare prokaryotic genome (1).  

2)Gene Structure: 

Both of them have some common features about genes. Replication directions, DNA and RNA structures, principles of work of polymerases can be seen as examples. Eukaryotic genes have introns and exons. In mature eukaryotic mRNA, only exons exist. Also eukaryotic genes are clustered, so genes that are related to similar functions are on same region of chromosome and they are controlled independently. Operons or polycistronic mRNAs do not exist in eukaryotes and in prokaryotic gene, regulatory parts are on same place with actual gene (2,3).      

3)RNA polII-driven transcription initiation:  

In contrast, prokaryotes have simpler transcription. σ factors in prokaryotes attach to promoter with mostly RNA pol and start transcription. Different σ factors bind to different promoters for a responsible gene. In Eukaryotes, transcription initiation are quiet different and more complex. This complexity comes from supercoiled structure and regulator elements. RNA pol can’t initiate transcription. Some DNA binding proteins such as transcription factors and enhancers helps to change conformation of chromatin structure. RNA pol can bind to promoter with help of transcription factors and starts transcription (4).     

 References: 

[1]Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002. Chapter 2, Genome Anatomies. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21120/  

[2]Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002).Molecular Biology of the Cell(Fourth ed.). New York: Garland Science.  

[3]Shafee, Thomas; Lowe, Rohan (2017). “Eukaryotic and prokaryotic gene structure”.WikiJournal of Medicine.4(1).doi:10.15347/wjm/2017.002  

[4]Dvir, Arik & Conaway, Joan & C Conaway, Ronald. (2003). Assays for Investigating the Mechanism of Promoter Escape by RNA Polymerase II. Methods in enzymology. 370. 733-40. 10.1016/S0076-6879(03)70059-7.  

The best model organisms for chromatin studies

This was written by Direncan Boyraz (Izmir Institute of Technology)

1) Saccharomyces cerevisiae 

Saccharomyces is one of easier organisms to be analysed for isoforms of histones and histone modifications chromatin structure studies than other complex eukaryotes; additionally Saccharomyces has common modifications with mostly all eukaryotes (1). There are some key points for this. Firstly, promoters of yeast as enhancers can be activated by becoming nucleosome-depleted. Second, nucleosomes on chromatins are well located. Distances and bordering regulatory of nucleosome provide convenience. Third, highly transcribed genes own low nucleosome occupancy because of RNA polymerase II activity with its associated factors (2).  

2) Drosophila melanogaster 

Fruit fly as a model organism has some advantage in chromatin structure analysis such as DNA methylation. DNA methylation in flies are manageable than other animal or models. We have available data for the system of it and also existence of less methylated genome than human genome  with less number of gene is useful for epigenetic studies. More restrainable number of chromosomes form an easier environment for observations. Fruit fly is one of most model organism for those experiments. Easy observable and high similarity to human make it a good model(3).  

3) Arabidopsis thaliana 

Histone modification and DNA methylation are to key for studying chromatin structure and natural changes Arabidopsis lives brought it to rapid modifications evolutionary.  Also epigenetic variation is proved with some ways such as modifications and the presence of repeated sequences or transposons within the promoters. First and most known plant on the earth is Arabidopsis, and this makes it a good model organism for that (4). 

References: 

[1] Rando, Oliver J., and Howard Y. Chang. “Genome-Wide Views of Chromatin Structure.” Annual review of biochemistry 78 (2009): 245–271. PMC. Web. 28 Feb. 2018.  

(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811691/) 

[2] Rando Lab Biochemistry and Molecular Pharmacology, Umass Medical School, Chromatin Structure and Function,  

(https://www.umassmed.edu/randolab/research/chromatin-structure-and-function/) 

[3] Lyko F., Beisel C., Marhold J., Paro R. (2006) Epigenetic Regulation in Drosophila. In: Doerfler W., Böhm P. (eds) DNA Methylation: Development, Genetic Disease and Cancer. Current Topics in Microbiology and Immunology, vol 310. Springer, Berlin, Heidelberg  

[4] Turck, F. and Coupland, G. (2014), Natural Variation in Epigenetic Gene Regulation and Its Effects on Plant Developmental Traits. Evolution, 68: 620–631. doi:10.1111/evo.12286  

Reverse Sorusu

“void reverse(char s[])”  tanımında bir fonksiyon yazın. Bu fonksiyona bir string geçirildiğinde, fonksiyonunuz kendisine geçirilmiş harfleri tersine çevirsin.
Yani,  fonksiyonu çağırmadan önce  string’in içinde  “merhaba dünya” varsa, fonksiyondan dönünce string’in içinde artık  “aynüd abahrem” olsun.

Çözümü

#include<stdio.h>
#include<conio.h>

int i,n,birincibardak,ikincibardak,bosbardak;

void reverse(char yazi[100])
{
for(i=0;yazi[n]!=’\0′;n=n+1) ;
for(i=0;i<n/2;i=i+1)
{
/*
bosbardak = birincibardak;
birincibardak = ikincibardak;
ikincibardak = bosbardak;
*/
bosbardak = yazi[n-i-1];
yazi[n-i-1] = yazi[i];
yazi[i] = bosbardak;
}

printf(“%s”,yazi);

}
main()
{ char yazi[100];
printf(“Bir cumle yaz: “); gets(yazi);
reverse(yazi);

getch();
}

Pointer Sorusu

1. Bir karakter dizisi tanımlayın, ve içine “strcpy” ile bilgi koyun. Bir
döngü ve pointer ile diziyi harf-harf (teker teker) ekrana yazın. Programın
başında pointer’i dizinde ilk elemanına atayın, daha sonra çift artı
işareti ile pointer’in değerini arttırın. Ayrı bir tamsayi değişkeni
ile kaç karakter yazılacağını kontrol edin..

Çözümü

#include<stdio.h>
#include<string.h>
#include<conio.h>

main() {

int i=0;
char characterArray[100],*pointer;

strcpy(characterArray,”TEST”);

pointer = &characterArray[0];

for(i;characterArray[i] != ‘\0’;i++) {

printf(“%s \n”,pointer);

pointer++;
}

getch();
}

2. 1. deki programı, pointeri dizinin sonuna atayıp, çift eksi işaretini
kullanarak sondan basa doğru yazması için değiştiriniz.

#include<stdio.h>
#include<string.h>
#include<conio.h>

main() {

int i=3;
char characterArray[100],*pointer;

strcpy(characterArray,”TEST”);

pointer = &characterArray[3];

for(i;characterArray[i] != ‘\0’;i–) {

printf(“%s \n”,pointer);

pointer–;
}

getch();
}

 

Fonksiyonlar ve Değişkenler hakkında Çözülmüş Sorular

1. Daha önce yazdığımız Santigrad’dan Fahrenheit’a karşılık tablosundaki derece hesaplamasını bir fonksiyona geçiriniz.
2. Ekrana isminizi 10 kere yazan bir program yazınız. Yazma isini yapmak için bir fonksiyon çağırınız. Daha sonra bu fonksiyonu main() in başına alarak, derleyicinin bunu kabul edip etmediğini kontrol ediniz.

Çözümler

#include<stdio.h>
#include<conio.h>

/*
. Ekrana isminizi 10 kere yazan bir program yazınız. Yazma isini yapmak için bir fonksiyon çağırınız.
Daha sonra bu fonksiyonu main() in başına alarak, derleyicinin bunu kabul edip etmediğini kontrol ediniz.

1.sorunun cevabı

*/

char printString() {

printf(“Denisa Nanushaj \n”);

}

main() {

for(int i=0;i<=9;i++) printString();

getch();
}

2.sorunun cevabı

#include<stdio.h>
#include<conio.h>

/*
Daha önce yazdığımız Santigrad’dan Fahrenheit’a karşılık tablosundaki derece hesaplamasını bir fonksiyona geçiriniz.

*/

float centigradeToFahrenheit(float centigradeValue) {

return centigradeValue*9/5+32;
}

main() {

float centigradeValue;

printf(“Santigrad degerini girin : “); scanf(“%f”,&centigradeValue);
printf(“Fahrenheit degeri : %f “,centigradeToFahrenheit(centigradeValue));

getch();
}

Tam Sayı Atama Çözülmüş Sorular

1. Birden on ikiye sayacak bir program yazın. Bu program, sayarken rakamları
ve bu rakamların karelerini ekrana yazsın

1 1
2 4
3 9
gibi..

2. Birden on ikiye sayan programı biraz değiştirerek , sayımı yazan, ve 1 in
inversini, beş haneli alan bir program yazın. Yani:

1 1.00000
2 .50000
3 .33333
4 .25000
gibi..

3. Birden yüze kadar sayan, fakat 32 ila 39 arasındaki değerleri yazan bir
program yazın. Her satıra bir rakam yazılsın..

1.sorunun cevabı

#include<stdio.h>
#include<conio.h>

/*
Birden yüze kadar sayan, fakat 32 ila 39 arasındaki değerleri yazan bir
program yazın. Her satıra bir rakam yazılsın..
*/

main() {

for(int i=1;i<=100;i++) {

if(i>=32 && i<=39) {

printf(“%d – %d \n”,i,i);

} else printf(“%d \n”,i);

}

getch();
}

2.sorunun cevabı

#include<stdio.h>
#include<conio.h>

/*
Birden on ikiye sayacak bir program yazın. Bu program, sayarken rakamları
ve bu rakamların karelerini ekrana yazsın
*/

main() {

for(int i=1;i<=12;i++) {

printf(“%d : %d \n”,i,i*i);

}

getch();
}

3.sorunun cevabı

#include<stdio.h>
#include<conio.h>

/*
Birden on ikiye sayan programı biraz değiştirerek , sayımı yazan, ve 1 in
inversini, beş haneli alan bir program yazın. Yani:

1 1.00000
2 .50000
3 .33333
4 .25000
gibi..

*/

main() {

for(int i=1;i<=12;i++) {

printf(“%d %f \n”,i,(1/(float)i));

}

getch();
}

C soruları

  1. soru-Birden yüze kadar olan sayıları ekrana döken bir program yazınız
  2. soru-Programı değiştirip, sayıları ikişer ikişer atlayarak ekrana dökmesini sağlayınız.
  3. soru-2. ödevdeki programı değiştirip, sadece 50 den büyük sayıları (ikişer ikişer) ekrana dökmesini sağlayınız

1.sorunun cevabı

#include<stdio.h>
#include<conio.h>

main() {

// 1den 100’e kadar

for(int i=1;i<=100;i++){

printf(“%d \n”,i);
}

getch();

}

2.sorunun cevabı

#include<stdio.h>
#include<conio.h>

main() {

// Sadece 50’den büyük sayıları ikişer ikişer 100’e kadar döken

for(int i=50;i<=100;i=i+2){

printf(“%d \n”,i);

}

getch();

}

3.sorunun cevabı

#include<stdio.h>
#include<conio.h>

main() {

// Sayıları ikişer ikişer döken

for(int i=1;i<=100;i=i+2){

printf(“%d \n”,i);
}

getch();

}

Referans

1.http://www.kalfaoglu.com/c-dili/3.html

 

 

 

Brief Explanation of Soft Microfabrication

Until recently the most favorable materials for photolithography were crystalline silicon, amorphous silicon, glass, quartz and metals which have several disadvanatges, such as the fact they are expensive, can be brittle and opaque. Soft materials include PDMS; PMMA; Polyimide; Hydrogel etc. Soft materials tend to be cheap, flexible, transparent to the visible light and UV and in most of the cases show improved biocompatibility. The main advantage of the soft materials is that they do not necessarily need a clean room for fabrication process. A cleanroom is the term that stands for a room environment where the concentrations of the different particles on the air is highly controlled and they are not able to change the parameters that need to stay constant such as temperature of the room, pressure and humidity. The source of particles that need to be controlled are most of the times: skin, scales, hair, clothing lint, paper, boxes, bare wood products, abrading actions. The person that needs to work on such rooms, is obligated to wear head cover, safety glasses, mask, shoe cover, sticky mat and gloves.


Soft lithography includes soft lithography, micromolding, 3-D Photopolymerization, 3-D Printing and Laser Prototyping. Soft term stands for the absence of energetic particles , such as electrons, ions or radiation particles, such as UV or X rays. Soft lithography can be differently called as molding, printing or transferring. Its prototype material is cheap and it garantuees a fast method. It is a highly applied method in microfluidics and biomedical engineering. One of the main advantages it provides is the high resolution nearly 10 nm resolution, while the biggest disadvantage is because of the complexity of the master mold. The mostly used techniques of the soft lithography include: Replica Molding (REM), Micro-contact printing, Micro-molding in capillaries (MIMIC) and solvent assisted micromolding (SAMIM). PDMS or polydimethylsiloxane is a silicon based elastomer with a hydrophobic surface, which results from the mixing of siloxane oligomers and siloxane cross-linkers. Some of the advantages that PDMS garantuees are its flexibility, elasticity, optical transparence, chemical inertness, its low surface energy, durability, low thermal expansion, biocompatibility, good resolution and the ability to seal to flat and clean surfaces. In the case the PDMS is treated on the oxygen plasma, PDMS becomes able to seal to itself, glass, silicon, silicon nitride or plastic materials.
PDMS Preparation
The gold ratio of the Silicon Elastomer Base to the Silicon Elastomer Curing Agent is 10:1 Those 2 materials are taken by a pipette and the mixing is done till the mixture turns to a white color from the clear apperarance it had initially. The mixture is put on the photoresist mold and afterwards the bubble air present should be removed by vacuum usage. Then, the PDMS is cured by being heated for 1 hour at a hot plate(100 degree Celcius). Sometimes it is more preferrable to cure on lower temperatures such as 60 for longer periods of time. After te curing the process the cooling process occurs . When PDMS turns on solid after being cured, it is cut by a knife and the parts are mounted on different glass slides.
Micro-Contact Printing
A PDMS stamp is used about formation of the self assembled monolayers over thte surfaces of substrates. Inking is important for this process as the PDMS stamp is coated and pressed over the surface due to an ink of molecules. Elastomers usage is important for the micropatterned surfaces to confront with over sized areas.
3-D Photopolymerization is a process where the layers are assembled over each other and is used for the products needed on modeling and prototyping.

References

1- lbms.iyte.edu.tr

2-https://en.wikipedia.org/wiki/Photolithography