The Great Escape mRNA export

Transcription is the process through which the mRNA is synthesized form the DNA. The process of DNA transcription is similar to DNA replication but the enzymes involved are different. Transcription of DNA into an mRNA through a DNA template is mainly influenced by an enzyme called RNA polymerase. For the RNA polymerase to influence the transcription process, the enzyme must first recognize where the sequence of the gene begins. This will ensure that the enzyme knows where synthesis of the mRNA should start. The ability of the enzyme to recognize the site of initiation in the DNA is due to the presence of the promoter sequence, a sub-unit in the DNA. The promoter sequence which is located at one end of the DNA strands instructs the enzyme where and in what direction to start synthesizing the mRNA. This is followed by unwinding of the double helix strand by the enzyme and the mRNA strand is synthesized, complimentary to the DNA strands. This process is unidirectional. Although the transcription process is similar to the DNA replication which has been well studied, it is not clear what events or processes are responsible for instructing the enzyme to stop transcription process (Peters, pg 235).    

After DNA transcription is complete, the resultant RNA is not ready for export to the ribosome and the subsequent translation process. The mRNA produced undergoes a series of modification before it is exported to outside the nucleus. The modifications are called post transcription modification. However, this processes are absent in some non eukaryotic organisms whose mRNA is ready for export after transcription and may not require any modification. In the eukaryotic organisms, research indicates that a series of modification process takes place before the mRNA is exported to the ribosome. The export of the mRNA from the nucleus to the cytoplasm across the membrane takes place through the nuclear pore complex. It is essential for the transcript to be modified in a way that it will be recognized by the nuclear pore complex. (Grlich and Mattaj, pg 1515).

Post transcriptional modifications are series of processes through which the precursor mRNA is converted into a mature mRNA. These processes are essential for the correct translation of the genetic material in protein synthesis in eukaryotic cells. In these cells, the primary mRNA or the precursor mRNA contains the exons and the introns. The exons describe the coding segments of the mRNA precursor while the introns consist of the non coding segments. Before the mRNA molecule is exported for export, there are three main modifications that take place. These includes 5 capping, 3 polyadenylation and finally splicing.

The capping of the precursor mRNA is a process through which a 7- methylguanosine is added to the 5 end of the precursor. This is done by first removing the phosphate on the 5 end using the phosphatase enzyme followed by formation of disphosphate on the 5 terminal which is catalyzed by guanosyl transferase. The GTP molecule is then added to the diphosphate terminal leading to lose of the disphospate. This process is also catalyzed by the enzyme guanosyl transferase (Moore, M.S and Blobel, pg 662). The process leads to 5 to 5 linkage of between the triphosphate groups in the guanine residue. The nitrogen in the 7 position is then methylated using SAM (S-adenosyl methionine). Incase no other capping modification happens apart from the methyl group added on nitrogen at seventh terminal, the mRNA precursor is known as cap 0. Otherwise more capping can be done where SAM can be used to add methyl group on the ribose sugar groups of the neighboring nucleotides to form a cap 1 mRNA precursor. Subsequent methylation of the ribose groups of the nucleotides along the mRNA molecule leads to formation of cap 2, cap 3 cap 4 and so on. It should however be noted that these subsequent additions of methyl groups downstream are added at the hydroxyl groups at position 2 of the ribose sugar molecule. This capping at the fifth position introduces a protecting group in the mRNA to reduce the likelihood of attack by the 3 5 phosphodiesters in the ribonucleaseses which are found in the eukaryotic cells (Izaurralde, pp 710).    

Studies suggests that there exists a  capping enzyme complex, consisting of the enzyme units involved in the capping process, which is incorporated on the RNA polymerase and ensures that capping continues as the transcription goes on. The enzyme complex through a series of processes caps the first terminal as soon as it emerges. This capping enzyme complex can bind to an RNA polymerase only, the enzyme responsible for the transcription process, to ensure that only the transcripts are capped in the nucleus. Other than protecting the 5 terminal of the mRNA in the translation process, the capping regulates the export of the RNA by ensuring that only the capped mRNA is exported. The cap binding complex, which regulate the export of mRNA from the nucleus can only bind to mRNAs which are capped at the fifth terminal. This is very important because the nuclear pore can only recognize the cap binding complex. The nuclear pore then exports the mRNA to the cytoplasm and the position of the cap binding complex is taken by the translation factors (Peters, pg 236).

Another post transcription modification of the mRNA precursor is the addition of a 200 units of adenosine monosphospates tail. The process starts with cleavage at the 3 terminal of the strand which is followed by a process of adenylation. This process is triggered by the presence of a polyadenylation signal sequence near the 3 terminal of the precursor followed by a second signal. The first signal is designated by 5AAUAAA3 while the second signal is designated by 5CA3 on the precursor RNA strand. The cleavage always takes place at the second signal sequence. A strand rich in GU sequence downstream is also essential in the polyadenylation process. This process begins as the transcription process ends. Because the cleavage happened specifically at the 3 most position on the poly (A) chain, the transcripts formed are homogeneous. However, some cells have been found to exhibit alternate cleavage where adenylation takes place at other sites within the site producing a variety of transcripts from a single precursor (Segref, pg 3256).

Splicing is also a major process that takes place before triplicates are exported to the cytoplasm. It involves removing the introns, the non coding segments, on the precursor. This process leaves the exons which are reconnected into a single molecule with continuous proteins codes. This splicing process can occur at any point during the transcription process depending on the protein being synthesized. The process is catalyzed by an enzyme complex known as splicesome. Following this modifications, the pre mRNA molecule forms complexes with the export proteins to form RNP. The formation of these complexes is essential for the recognition of the mRNA by the nuclear pore complexes. The adapter proteins and the export receptor TAP are the most important components of the RNP complex. The Export receptor TAP component causes the export of the mRNA to the cytoplasm by interacting with the adaptor protein and the nuclear pore complex. The adaptor protein on the other hand binds directly to the mRNA being exported (Huang and Joan, pp 900).  

Summary of the article Muc2 Protects against Lethal Infectious Colitis by Disassociating pathogenic and Commensal Bacteria from the Colonic Mucosa

Investigation of the manner by which host cells evade the attack of attaching and effacing (AE) Escherichia coli pathogens was sought to be executed in this paper by analyzing the role of goblet cell-derived Muc2 in host-pathogen interactions. To accomplish the goal of this paper, Citrobacter rodentium, a murine AE pathogen related to AE coli, was inoculated to Muc2 deficient mice (Muc2--). Mice with Muc2 or the wild types were also infected with C. rodentium, and were used as control organisms. Physical and physiological changes were monitored, compared, and evaluated. Results showed that WT mice tend to release significant amount of Muc2 when exposed to pathogens as compared to Muc2-- mice thereby suggesting the importance of Muc2 in pathogen evasion. Further studies confirmed that Muc2 limits overall pathogen and commensal species in order to protect the host from prolonged bacterial AE infection.  

Enteropathogenic Escherichia coli (EPEC) and Enterohemorrhagic E. coli (EHEC), both of which are attaching and effacing (AE) types, are the main cause of mortality and morbidity in both developing and developed countries (Bergstrom et al., 2010). These microorganisms mainly target  the digestive system of patients and results to diarrhea, dehydration and a series of other complications. Aside from this, EHEC may also lead to the production of the highly lethal Shiga Toxin (Stx) if not properly treated. Main sources of these microorganisms are infected food and water supplies. Because of the profound significance of AE E. coli in public health, researchers are working hard to investigate the mechanisms by which hosts will be able to fight the detrimental to lethal effects of EHEC and EPEC. However, due to ethical reasons, actual tests on humans cannot be done so scientists opt to investigate the AE pathogen equivalent of E. coli on mice, Citrobacter rodentium (Bergstrom et al., 2010). This microorganism has been found to result to acute colitis, mucosal hyperplasia, barrier disruption and loose stools. Furthermore, a number of scientific studies have suggested that mucin production is one of the most important strategies of host cells when managing enteric bacterial infections.

Mucins are glycoproteins with high molecular weights and are embedded with serine, threonine, and proline-rich domains. One of its derivative, Muc1, was found to be active against Campylobacter jejuni infection by reducing the impact of the attack and prohibiting potential spread of the infectious agents (McAuley et al., (2007). In this study, Muc2, the major secretory mucin in both humans and mice, will be investigated. Muc2 forms polymers which become the basis of  two-distinct layers in the mammalian colon, inner and outer, where the former is sterile while the latter is heavily colonized by commensal bacteria (Bergstrom et al., 2010). Related researchers have confirmed the role of Muc2 in regulating commensal and gut homeostasis but its interaction with the mucosal pathogens is not yet established. In line with this, the authors of this study wanted to investigate the role of Muc2 in preventing the colonization of AE pathogens in the mucus layer by using C. rodentium in mice models.

Research DesignMethods
Experimental procedures made use of two groups of six to 11 weeks old mice where one group was composed of in vivo-altered Muc2 deficient (Muc2--) and the other included wild type (Muc2) mice. C. rodentium were inoculated to mice by oral gavage. Infected and uninfected tissues of the halothane-anesthetized and cervical dislocation-killed mice were collected and enumerated for bacterial counts. Histological staining and RNA extraction were performed on the tissues followed by cecal loop modeling, bioluminescent imaging, metabolic labeling, permeability and antimicrobial assay, DNA staining, and finally, statistical analysis of the measurements obtained.  

Results and Discussion
Results showed that Muc2-- mice exhibited increased susceptibility to C. rodentium, worsened mucosal damage, and elevated microcolony formation on their mucosal surface as compared to wild type mice. Also, mucus secretion was also significantly elevated in response to C. rodentium infection. These findings are consistent with the hypothesis that mucins play important role in the evasion of AE pathogens and it was discovered in this paper that the muc2 is the first line of defense of hosts against invading AE pathogens. It was also discovered that an array of non-pathogenic microorganisms have thrived in the gut of Muc2 deficient mice, an event that was not observed in wild type mice. Hence, the authors concluded that Muc2 in mammals serve an important role in effectively managing infectious and non-infectious agents by reducing commensal load on the mucosal surface.  

Presentation of my understanding of the paper
The findings presented in this paper offer a possible method of combating attaching and effacing EPEC and EHEC. Utilization of this knowledge may help researchers to finally devise a way to reduce, if not totally eliminate, the occurrence of digestive diseases related to E.coli infections in both developing and developed countries. Subsequent studies must be done to demonstrate Muc2 responses in humans. But at present, it can be said that this study, once perfected, will truly benefit humans and will offer a possible way of controlling disease proliferation. The authors must be commended for doing a detailed experiment and for presenting their results in a well-written report. Lastly, studies of this type must be executed more often in order to address the growing number of deaths due to bacterial infections.

Pathophysiology of Colon Cancer

According to the United States Cancer Statistics (2010), colorectal cancer is one of the most commonly diagnosed cancers in America as of 2006.  There are an estimated 70,270 men and 68,857 women who were diagnosed with colorectal cancer (cited in US Cancer Statistics Group 2010, web-based report).

The progression of colorectal cancer has been known to begin with may start as a benign polyp but may become malignant, invade, and destroy normal tissues, and extend into surrounding structures (cited in Brunner and Suddharths textbook of medical-surgical nursing 2008, p. 1070).  There are several disorders and preexisting conditions known to be linked to colorectal cancer, including familial adenomatous polyposis, such as Gardners syndrome and Peutz-Jeghers syndrome, ulcerative colitis, Crohns disease, Turcots syndrome, hereditary nonpolyposis colorectal carcinoma, and other pelvic cancers treated with abdominal radiation (ibid, p. 22).

A malignant polyp contains cancerous cells and is invasive (cited in Madara  Denino 2008, p. 423).  The authors further expounded that the time it takes for a benign polyp to develop malignancy is 10 to 15 years with genetic mutations occurring in a predictable manner.  The epithelial lining of the intestine usually is the site of adenocarcinoma where 95 of the cancer of the colon and rectum begins to develop.   The effects of progression of colorectal cancer start locally in the area close to the anus.  The patient with colorectal cancer may experience a change on bowel habits and a feeling of incomplete defecation.  Thus, it is important to assess patients for a possible sign of colorectal cancer when there is lower gastrointestinal bleeding and increased presence of mucus.  When the cancer progress, the tumor can grow into a size large enough to obstruct the bowel thus leading to constipation, abdominal distention, and vomiting.  Based on my experience, my great aunt died of colorectal cancer lost a significant amount of weight, chronic anemia, jaundice, decreased appetite and abdominal pain.

 Kemeny  Dizon stated, sixty percent of patients diagnosed with colorectal cancer go on to develop hepatic metastases (Bleiberg  Kemeny 2002, p. 359).  Based on this finding, the abdominal pain experienced by my late aunt is due to the stretching of the capsule covering the liver.  The only site of colorectal cancer is the liver by as many as 30 of patients.  The authors elaborated that in general, the liver is a frequent site of metastatic involvement by a variety of tumors, including breast, colon, lung, stomach, and pancreas.  The portal circulation of the liver provides a rich, blood supply and changes how cancer calls originating from the colon.  When these cancer cells grow beyond 3 mm angiogenesis enables them to form their own system for the supply of blood, which they draw from the arterial circulation (ibid 2002, p. 360).  Furthermore, cases of colorectal cancer have a physiologic rationale for hepatic metastasis due to the drainage of the gastrointestinal tract by the portal system of the liver (ibid 2002, p. 359).

Fast Food Nation Summary

Fast Food Nation is a movie tie-in of the book with the same title by Eric Schlosser, and a film which tackles the topic of fast food and its steadily-growing industry, mostly about its ill-effects and how it has emerged to become a force to contend with among business enterprises on a global scale.

Some facts that can be ascertained from this film immediately follow.  Primarily, the movie attempts to tell the viewer that fast food is now inextricably linked to the American way of life.  Next, despite the lack of training, the immigrants, most of whom are Mexicans, are made to work in hazardous conditions where they are expected to keep the pace, make the required quota, stay away from drugs and take utmost care not to be injured.  The presence of cattle manure is traced back to the meat packing plants where the untrained workers sometimes make mistakes in gutting the cattle, hence the accidental spillage of manure on the meat, which, by the way, occurs on a regular basis.  Fast food chains in general capitalize on low production costs such as cheap labor and the low price of raw materials to maintain the low prices of the items on their menu.  Oftentimes, students from the poor communities are the ones hired in fast food chains, and it is quite notable that sanitation standards are left unchecked, where these underpaid workers rebel against the corrupt system by delivering products which are of the most unhygienic and inferior quality.

The film is a poor adaptation of the book by Schlosser mainly because the film failed to capture everything that the author wanted to share to the viewer.  The movie tried to present some sub-plots out of the different ideas imparted by Schlosser but it somehow fails to cohere or conjure a unified portrait of all of these ideas pertaining to fast food.  Still, it is an enlightening piece of art on its own since it gives a glimpse of the accurate situation or what really goes on behind the fast food counter and even farther behind that, into the other links to the business as well as the factual routes in food handling and preparation.  There is not much reference made to the problem of obesity and its continuing upsurge as related to consumption of fast food in the US although there is an essential link to these two issues.  Likewise, possible solutions should have been included to address the issues, or the film should have just adhered to the documentary format like Super Size Me so that all the authors ideas could have been included.  

Post-exercise Recovery Period for the Cardiopulmonary System Review of a related literature, a journal article entitled, A Practical Test for Predicting Maximum Oxygen Consumption by Jimmy H. Ishee

Although this research study is not very expressly measuring the post-exercise recovery period of the cardiopulmonary system itself it is a very relevant measure as it directly relates to VO2 measurements during a physical activity. The post-exercise state means one has to do the activity first, measure the VO2 level during that physical activity and similar variables are used when measuring the changed level when one is already done with the activity. Thus, this journal article is selected by yours truly. Below is the summary.

Quoting a certain part of the article, it states that according to the American College of Sports Medicine, VO.sub.2 max tests are costly and time-consuming. In this regard, it can be assumed that normal individuals may not perfectly measure the VO.sub.2  ( VO2 for brevity) but this measure can of course be closely estimated or at least predicted. However, there is no harm in trying to experiment in real situation with at least hundred individuals to simulate the reality of it and at the same time lower the cost of this expensive process and at the same time compare it with the predicted VO2 max or base the predicted value from a test or a study. According to the journal article, VO2 measurement tests are usually administered in university laboratories or medical settings, which are not available to the average practitioner. Submaximal prediction tests that have been developed are capable of predicting VO2 max outside a clinical setting with large groups of people. This method is less expensive and in some ways a safer way to measure VO2 max. Since submaximal tests do not require maximum effort, they are more suitable for a wider range of the population.

The main purpose of the research study, as stated in the journal was to develop a submaximal endurance test for college students through various physical activities such as walking, jogging, or running. The authors wanted to eliminate the reliance on heart rate as a measurement for predicting VO2max and provide a test that had a comfortable pace suited for individuals at different fitness levels. There were a hundred and one (101) participants to the study, consisting of 54 males and 47 females. There were 3 exercise tests composed of a two 1.5 mile endurance tests and a maximal GXT, which was given in a laboratory and these tests were completed not on the same day allowing the participants to relax or rest in between. The article emphasized that the 1.5 mile run is on a somewhat hard level of activity.

Based on the 1.5-mile data that the study gathered from the activities, two VO2 max regression models were generated by multiple linear regression. It was hypothesized that in order to assess the concurrent validity of the VO2 max equations, correlation coefficients and standard error of estimates were computed. Various measures and statistical factors were presented in the article and sample computations were given in order to arrive at the conclusion of the study.

According to the journals final note, it was concluded by the study that the activity, which was the 1.5-mile endurance test, that the VO2  max from submaximal exercise without measuring the heart rate or requiring an all out effort allowing those who participated to do their exercises such as walking, jogging or running to be accommodated, can be predicted. It was concluded that these different levels of fitness activity is a practical way in predicting VO2 max.

Feedback Inhibition

Feedback inhibition also known as end product inhibition refers to an important mechanism in the biosynthetic pathways involving enzymes. The synthesis of molecules such as amino acids and pyrimidines in the human body is tightly regulated and most of the steps controlled enzymatically. Usually, in feedback inhibition, the end products in biosynthetic pathways inhibit the first enzymatic step and hence controlling the synthesis of the end products themselves (Khanna, 289).

The first enzyme in the pathway which is inhibited is known as the allosteric enzyme. This mechanism takes advantage of the preexisting enzymes already in the cells to control various biosynthetic processes. An interesting example of allosteric or feedback inhibition is what happens in the biosynthesis of pyrimidine nucleotide bases which are important components of nucleic acids. The allosteric enzyme involved in the first step catalysis in the synthesis of cytidine triphosphate (CTP) is aspartate transcarbamoylase (ATCase) which catalyzes the condensation of carbamoyl phosphate and aspartate to produce orthophosphate and form N-carbamoylaspartate (Berg, Tymoczko  Stryer, 402). The CTP which is the final product of pyrimidine synthesis acts as an inhibitor to the enzyme ATCase. It is observed that the increased accumulation of CTP greatly reduces the speed (Vmax) of the enzyme ACTase (Berg, Tymoczko  Stryer, 402).

The process of feedback inhibition such as that which takes place in CTP biosynthesis is crucial in the synthesis of nucleic acids, the molecules that regulate all the life processes. In the absence of the CTP, the rate of ATCase is faster but this rate decreases when more CTP accumulates. This process is critical as it ensures that more CTP molecules are sent in the biosynthetic pathway to produce more and more pyrimidine bases. The more bases synthesized, the faster the growth process of organisms and the faster the wound healing process or DNA repair.


The food that we eat cannot be assimilated into the body in the same manner that we ingest it. It needs to be broken down through various processes aided by chemicals and anatomical structures in the human body. This paper discusses the process of digestion in the alimentary tract until it is absorbed into the body.

The food that is ingested needs to go through several processes in the body before it is assimilated into the body. These processes occur in the alimentary tract which is a long structure beginning from the mouth to the anus. There are also other important chemicals, hormones and digestive juices which are involved in this whole process. These are found in specific portions of the tract and each food is digested or broken down in specific region. Therefore, the breakdown of food is either mechanical or chemically carried out. The end result is the division of the food into very small components or sizes that can pass through into the cells (Insel, Turner and Ross, 2004).

Everyone has at one time embarked on a journey in their lifetime. In addition to this, you hope to have a smooth trip and reach your destination safely. Herbert the hamburger has prepared to go through a very long and tortuous journey of his life. Everything is in place and he only hopes to have a safe trip. The main purpose of this trip is to deliver very vital documents that are needed to a company known as Body Builders. If these documents do not reach their destination, the company dies. These documents includes Fats, Carbohydrates, Proteins and Minerals.

The journey begins in the mouth where Herbert goes through some rough machines known as the teeth. This breaks it down into small forms through mastication. The document known as carbohydrate starts to be processed in the mouth and it involves a good friend known as saliva who is the boss in this department. Saliva does this with the help of amylase. This breaks it down into simple forms. From the mouth, permission is anted to move to the next level. To do this, Herbert is rolled into a bolus by the tongue and thrown at the back of the mouth. The epiglottis prevents Herbert from going through the trachea which is a wrong route. Herbert moves down in a smooth wave known as peristalsis into the esophagus until it reaches the gate of another department known as the stomach. This gate is known as the cardiac sphincter (Insel, Turner and Ross, 2004).

In the stomach, enzymes are also involved in the digestion process. Protein digesting enzymes are known as proteases. Amino acids are the building blocks of proteins. The bonds existing between them are broken down by hydrochloric acid from gastric wall. This is followed by breakdown of amino acids by the enzyme pepsin (Insel, Turner and Ross, 2004).

The food enters the small intestines through the pyloric sphincter. In the small intestine, pancrease produces amylase which further breaks carbohydrates to lactose, sucrose and maltose. These are broken down by lactase, sucrase and maltase enzymes respectively. These three are converted to an important form known as glucose which is absorbed via the villi on the walls of the intestines and finally find its way into blood circulation. Glucose is necessary for cell metabolism and function. However, the amount of glucose is regulated by the liver with the help of hormones. Too much glucose (hyperglycemia) is transformed into glycogen and stored in the liver through the help of insulin. In cases where glucose levels are low in the blood (hypoglycemia), the reverse happens i.e. conversion of glycogen to glucose with the help of the hormone glucagon. In cases where there is no glycogen, the hormone glucagons initiate formation of glucose from amino acids or fats. This process is known as gluconeogenesis (Insel, Turner and Ross, 2004).

The digestion of fats is with the help of enzymes known as lipases. Fats are complex molecules and should be turned into small molecules. This happens with the help of lipase enzyme from the pancrease and the end result is glycerol and fatty acid molecules. In addition to this process, bile from liver enters through the bile duct and emulsifies the fat. This makes it easy for the enzyme (lipase) to break down the fats starting from the surface. Storage of the bile usually occurs in the gall bladder. The body absorbs fats through the villi that cover the small intestines. The structure of the villus is such that it has capillaries and lacteals (lymph vessels). Fatty acids and glycerol enter into the lacteals into lymphatic system and finally bloodstream. Fatty acids find its way into adipose cells for storage or as source of energy (Insel, Turner and Ross, 2004).  

Protein digestion also continues in the small intestines in duodenum. The pancrease produces protease enzyme namely trypsin. In addition, chymotrypsin is also secreted. It works in a similar manner as pepsin. The end result of breakdown of protein by trypsin is amino acids. This is done through hydrolysis with insertion of water molecule between the bonds of amino acids. This helps in separation of the bonds that hold the amino acids together. The amino acids can thus pass through the intestinal wall into bloodstream. Their importance is in the repair of structures of the body. The waste products and undigested material move to the large intestines where water is re-absorbed. From there, it moves to the cecum and out through the anus (Insel, Turner and Ross, 2004).