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I have been confused as to the difference between a response element and an enhancer.
Wikipedia has the definition of response element as the following:
Response elements are short sequences of DNA within a gene promoter region that are able to bind specific transcription factors and regulate transcription of genes.
Wikipedia's definition of enhancers:
In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors.
They seem almost the same. What are the main differences?
The only difference I can see is that response elements can both halt transcription or allow for it. While enhancers only promote transcription if the transcription factor is present.
Is this the difference between the two, or is there something else that differentiates them?
Enhancers specifically bind transcription factors in an effort to obtain robust rates of transcription, in a very general fashion and may be upstream or downstream of a promoter. Remember that you don't need to receive a signal to produce housekeeping genes, regulated by general transcription factors, because they're always needed (in part). A response element can enhance or repress transcription depending on the stimulus.
Vitamin D response element (VDRE) is a fair example: In response to your extracellular calcitriol or 1,25(OH)2D, the vitamin D receptor will complex with a number of proteins that bind at the VDRE, controlling transcription of various vitamin D-controlled gene targets.
Vitamin D activity is mediated through binding of 1,25(OH)2D3 to the vitamin D receptor (VDR), which can regulate transcription of other genes involved in cell regulation, growth, and immunity. VDR modulates the expression of genes by forming a heterodimer complex with retinoid-X-receptors (RXR).
And just as well, other promoters such as that for pro-parathyroid hormone contain VDRE sequences that suppress it's transcription (ref).
What is the difference between a response element and a enhancer? - Biology
The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function are encoded together in blocks called operons. For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac) operon.
In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers. Repressors are proteins that suppress transcription of a gene in response to an external stimulus, whereas activators are proteins that increase the transcription of a gene in response to an external stimulus. Finally, inducers are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate.
- Understand the basic steps in gene regulation in prokaryotic cells
- Explain the roles of repressors in negative gene regulation
- Explain the role of activators and inducers in positive gene regulation
Imaging and Cancer
Shahriar S. Yaghoubi , Sanjiv Sam Gambhir , in The Molecular Basis of Cancer (Third Edition) , 2008
Reporter Gene Imaging
Imaging reporter genes (RGs) provide a powerful tool for studying molecular events in living subjects ( Figure 23-8 18 ). They have been used to study intracellular molecular interactions (for example, protein–protein interactions 19 ), image transgene expression ( 48 ), and endogenous gene expression ( 49 ), cell trafficking (e.g., metastasis or adoptively transferred cells for cancer immunotherapy 50,51 ) in living subjects. With the exception of RG coding for fluorescent proteins (e.g., green fluorescent protein) the expression of RG is usually detected by specific imaging probes. The reporter probes can be activatable, emitting signal after interaction with the reporter protein, or may be emitting constant signal and detecting reporter gene expression by accumulating in tissues containing the cells that are producing the reporter proteins. Bioluminescent ( Figure 23-8A ), fluorescent, and some MRI RGs ( Figure 23-8D ) are detected by activatable reporter probes. The detection of all nuclear imaging RGs and some MRI RGs is through interactions of the probes with the reporter enzymes, receptors, or transporters, resulting in their accumulation within or on the surface of cells expressing these RGs ( Figures 23-8B and 23-8C ). The MRI and nuclear imaging RGs offer the greatest potential for oncologic applications in human patients. In fact, the PET RG/suicide gene herpes simplex virus-1 thymidine kinase has been imaged in cancer patients and the clinical application of PET RG is expected to expand in other gene and cell therapy trials ( 52 ) however, more research is needed to improve delivery of PET RG into target cells, such that RG expression is sufficiently high with minimal effect on the cells.
What is the difference between ResponseEntity<T> and @ResponseBody?
ResponseEntity will give you some added flexibility in defining arbitrary HTTP response headers. See the 4th constructor here:
A List of possible HTTP response headers is available here:
Some commonly-used ones are Status, Content-Type and Cache-Control.
If you don't need that, using @ResponseBody will be a tiny bit more concise.
HttpEntity represents an HTTP request or response consists of headers and body.
ResponseEntity extends HttpEntity but also adds a Http status code.
Hence used to fully configure the HTTP response.
@ResponseBody indicates that return value of method on which it is used is bound to the response body (Mean the return value of method is treated as Http response body)
React vs Respond – 4 Differentiating Points
Apart from the time involved, there are a few key traits that can help you understand the difference between reaction and response. In the article that follows, we will help you do so.
1. Reaction is emotion-driven, response is well-thought
Unlike response, reaction is heavily driven by the emotions that you experience while in the middle of the situation. We are not saying that response is an emotion-less action. Of course not! Just that response is the result of thorough evaluation so when you respond, you can calmly keep aside all the emotion.
2. Reaction is aggressive, response is calm
Imagine a situation when you are arguing with your colleague and he abuses you. You are most likely going to experience an impulse to hurl back an abuse. But ask yourself, would that be the right thing to do? Your unconscious mind may fuel your anger through pre-judged notions. However, once you sit back and evaluate, you get a chance to step into the other person’s shoes and understand their actions. This gives you an opportunity to respond more accurately.
3. Reaction fuels disagreement, response helps resolve it
The instant reaction that we give can lead to a lot of discomfort in a relationship. Since it is usually based on assumptions, you will find it difficult to justify your actions in this phase. The response, on the other hand, is more likely to help you resolve a conflict.
4. Reaction weakens you but response empowers you
The minute you start taking into consideration the well being of everyone around, there is a higher possibility of taking empowered decisions. Needless to say, these decisions are beneficial in the professional as well as personal life. On the other hand, the reaction can usher the consequences that you are likely to regret later.
The urge to react is always strong and instant. The first step to learn to respond accurately is to control this urge.
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The Nobel Prize in Physiology or Medicine for 2019 is awarded to William Kaelin, Jr., Sir Peter Ratcliffe, and Gregg Semenza. The need for oxygen to sustain life has been understood since the onset of modern biology but the molecular mechanisms underlying how cells adapt to variations in oxygen supply were unknown until the prize-winning work described here. Animal cells undergo fundamental shifts in gene expression when there are changes in the oxygen levels around them. These changes in gene expression alter cell metabolism, tissue re-modeling, and even organismal responses such as increases in heart rate and ventilation. In studies during the early 1990’s, Gregg Semenza identified, and then in 1995 purified and cloned, a transcription factor that regulates these oxygen-dependent responses. He named this factor HIF, for Hypoxia Inducible Factor, and showed that it consists of two components: one a novel and oxygen-sensitive moiety, HIF-1α, and a second, previously identified and constitutively expressed and non-oxygen-regulated protein known as ARNT. William Kaelin, Jr. was in 1995 engaged in the study of the von Hippel-Lindau tumor suppressor gene, and after isolation of the first full-length clone of the gene showed that it could suppress tumor growth in VHL mutant tumorigenic cell lines. Ratcliffe then demonstrated in 1999 that there was an association between VHL and HIF-1α, and that VHL regulated HIF-1α post-trans-lational and oxygen-sensitive degradation. Finally, the Kaelin and Ratcliffe groups simultaneously showed that this regulation of HIF-1α by VHL depends on hydroxylation of HIF-1α, a covalent modification that is itself dependent on oxygen. Through the combined work of these three laureates it was thus demonstrated that the response by gene expression to changes in oxygen is directly coupled to oxygen levels in the animal cell, allowing immediate cellular responses to occur to oxygenation through the action of the HIF transcription factor.
Oxygen and Animal Life
In the early 1770’s, the Swedish scientist Carl Scheele determined that, from his calculations, approximately one fourth of the volume of air was ‘feuer luft’, or ‘fire air’, as he called it that is to say, the component of the atmosphere that allows substances to burn. This was eventually published in 1777 (Scheele, 1777). At essentially the same time in England, Joseph Priestley also found a method to purify this previously unknown gas, calling it de-phlogisticated air (Priestley, 1775). Antoine Lavoisier was simultaneously with Scheele and Priestley carrying out experiments to isolate this substance in Paris, and Lavoisier gave the gas the name we know it by today: oxygen (Lavoisier, 1777).
Oxygen is necessary for animal life during the oxidation reactions that drive the conversion of nutrients in food to ATP. Indeed, calibrating cellular conditions to the amount of available oxygen is a critical aspect of controlling meta-bolism. This has been known for more than a century for example, in 1858 Louis Pasteur was the first to show that there is a complex balance of oxygen use in animal cells, and that cells use multiple pathways to accomplish energy con-version (Pasteur, 1858). The mechanisms under-lying oxygen sensing in animals have been previously marked by two Nobel Prizes from more than 75 years ago: to Otto Warburg in 1931 for his discoveries concerning the enzymatic basis for cellular respiration, and to Corneille Heymans in 1938 for his findings on the role of the nervous system in the respiratory response to oxygen. However, for most of the 20 th century, it was not clear how adaptations to oxygen flux were regulated at the fundamental level of gene expression.
Adaptation to variations in oxygen
In almost all animal cells, the ability to rapidly respond and adapt to variations in oxygen availability is essential. It is clear from studies of molecular taxonomy that during evolution, as animal cells began organizing themselves into multicellular three-dimensional structures, this response to oxygen flux became more than a cell-autonomous reaction allowing metabolic adaptations within individual cells it also allowed the development of complex physiological responses. Cells need to adapt in many auto- nomous ways to variations in oxygen levels, in particular by adjusting their metabolic rates. When we examine this response at the level of tissues and organs, we find that multi-cellular organisms need to both remodel tissues to adapt to altered oxygen levels (for example, by reconstructing vasculature following injury) and adapt the whole organism to compensate for changes in oxygenation (e.g., the increased ventilatory responses seen during exercise, or at exposure to high altitude).
As an example: in humans at high altitude, variations in oxygen levels in the blood are sensed by specialized cells in our kidneys that make and release the hormone erythropoietin (EPO). This hormone activates red blood cell synthesis (erythropoiesis) in the bone marrow. One way of triggering this reaction is to be exposed to the low oxygen levels of high altitude: living at high altitudes boosts EPO production by the kidney, leading to increased concentration of erythrocytes in our blood, which in turn helps us adapt to lower oxygen partial pressures.
Animals can be exposed to low oxygen environments, but importantly, oxygen levels vary in tissues as well. Tissue oxygen levels in animals vary both spatially and temporally and this variation occurs during normal physiological events (drops in available oxygen in skeletal muscle during exertion, for example) as well as in pathological processes such as cancer and infection. It became clear from research in the 1970’s and 1980’s that these local and transient variations in oxygen partial pressure regulate critical adaptive responses in both cells and tissues through changes in gene transcription. These gene regulatory responses alter cellular metabolism, and control fundamental develop-mental, regenerative and defense processes, including those as diverse as angiogenesis, inflammation, and development.
This ability of animal cells to sense different concentrations of oxygen and, as a result, re-wire their gene expression patterns, is essential for the survival of virtually all animals. The oxygen-activated signaling pathways that are controlled by these pathways affect at least 300 genes, belonging to a wide variety of regulatory networks. These molecular pathways pervade numerous physiological processes, ranging from organ development and metabolic homeostasis to tissue regeneration and immunity, and play important roles in many diseases, including cancer.
Oxygen and the erythropoietic response
Any signaling pathway of profound importance to animal life will almost certainly turn out to involve numerous layers of fine-tuning and points of intersection with other molecular pathways. The oxygen response pathway is no exception. As expected, therefore, the molecular details of oxygen response regulation did not stop unfolding once the discoveries now awarded with the 2019 Nobel Prize had been made. On the contrary, these key discoveries opened the field, and led to an explosion of work that has uncovered an immense molecular complexity to the response to oxygen flux.
The fundamental discoveries of Gregg Semenza, William Kaelin and Sir Peter Ratcliffe all revolve around the actions of the HIF (hypoxia inducible factor) transcription factor. The discovery of this factor had its roots in the work done by a number of people in 1986 and 1987, including Maurice Bondurant, Mark Koury, and Jaime Caro their work showed that hypoxia causes increases in the transcriptional expression of the erythropoietin hormone (EPO) in kidney (Bondurant and Koury, 1986 Jelkmann and Hellwig-Burgel, 2001 Schuster et al., 1987). This finding in turn had its roots in experiments going back to 1882 and the French physiologist Paul Bert, who first demon-strated the cardiovascular effects of hypoxia (Bert, 1878), and was the first to show that exposure to high altitude increased red blood cell counts (Bert, 1882).
The isolation of HIF
Once it was realized that the EPO gene showed a hypoxia-induced transcriptional response, the next step was to determine the actual DNA sequence in the EPO gene regulatory region that was responsible for the oxygen sensitivity. Semenza decided to trace the transcriptional regulatory elements of the EPO gene in transgenic mice, using clones of different size DNA fragments encompassing the human EPO gene. Semenza and colleagues first demonstrated that a 4 kilobase region covering the EPO-coding sequence, plus some small 5’ and 3’ flanking sequences, led to EPO production in all transgenic tissues analyzed, and caused increased circulating EPO levels and a resultant polycythemia, i.e., increased red blood cell counts (Semenza et al., 1989). He next showed that a longer EPO gene construct containing 6 kilobases of 5’ flanking DNA was able to confer inducible EPO expression in the kidney (Semenza et al., 1990). This work pointed to a complex transcriptional regulation of EPO response to oxygen, including both positive and negative regulatory elements.
A year later, in 1991, Semenza published two additional studies that added significant infor mation about the regulation of the EPO gene: 1) a DNAse hypersensitivity study pinpointed a small region in the EPO 3’ flanking DNA that bound several nuclear factors, at least two of which were induced in liver and kidney by anemia this small region was able to function as a hypoxia-inducible enhancer in transient expression assays in vitro (Semenza et al., 1991b) 2) a study that further characterized the transcriptional regulation of EPO in transgenic models (Semenza et al., 1991a). At about the same time, work from Sir Peter Ratcliffe’s and Jaime Caro’s laboratories reported on the presence of a cis-acting DNA element 3’ of the EPO gene that conferred oxygen-responsiveness to reporter constructs transfected to cultured hepatoma cells (Beck et al., 1991 Pugh et al., 1991).
The work summarized above led Semenza in 1992 to identify an approximately 50 base pair enhancer at the 3’ end of the EPO gene that could be used to elicit hypoxia-inducible reporter gene expression in cultured cells. This enhancer, which Semenza termed a hypoxia response element (HRE), bound several nuclear factors in hepatoma cells: one that was constitutive, and one that was induced by low oxygen levels (hypoxia). The latter factor was consequently termed the hypoxia-inducible factor (HIF) by Semenza (Semenza and Wang, 1992).
Both Ratcliffe and Semenza were able to demonstrate that the EPO 3’ enhancer could drive hypoxia-induced reporter expression in a wide range of mammalian cell types (Maxwell et al., 1993 Wang and Semenza, 1993). This showed that the molecular mechanism involved in oxygen regulation of the EPO gene was active in a diverse range of animal cells, a finding that opened up the possibility that this new factor represented part of a common cellular machinery for oxygen sensing.
The notion that hypoxic HIF induction could be observed in many types of mammalian cells, and not only the EPO-producing cells in the kidney and liver, sparked the interest and attention of a wider community of scientists. The discovery of HIF indicated the potential existence of a universal molecular machinery underlying metabolic adaptation and the induction of tissue remodeling in response to tissue oxygen flux.
At this point, Semenza took a biochemical approach to purify the protein from large quantities of cell extracts. As the functional assay for HIF during its purification, he used electrophoretic mobility shift assays (EMSA) applied to the 3’ enhancer element of the EPO gene (Wang et al., 1995 Wang and Semenza, 1995). Amino acid sequencing and subsequent cDNA cloning of the purified proteins revealed that HIF itself was a heterodimer, composed of two different gene products. The first of these components was the oxygen sensitive part of the HIF factor, termed by Semenza HIF-1α and the second component was a constitutively expressed gene that was initially termed HIF-1β, until it became evident that this second component had been previously cloned and described, as the Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT) (Wang et al., 1995). The ARNT protein heterodimerizes with a number of other factors, and since its expression was not oxygen-sensitive, it quickly became clear that HIF-1α was the regulator of oxygen responsiveness in the HIF complex.
The HIF family broadens
A protein that is highly related to HIF-1α was cloned independently by four different groups, i.e., those of Yoshiaki Fujii-Kuriyama, Werner Risau, Christopher Bradfield, and Steven McKnight, all in 1997 (Ema et al., 1997 Flamme et al., 1997 Hogenesch et al., 1997 Tian et al., 1997) it had a number of names initially, including one still commonly used (HIF-2a), but the gene is properly designated EPAS1. The EPAS1 gene encodes a protein that has a high degree of sequence homology to HIF-1α, and also binds to ARNT as a heterodimer, it shares HIF-1α’s sensitivity to hypoxia, and has essentially all of the same regulatory motifs as those described below for HIF-1α.
There are, however, significant differences in function between HIF-1α and EPAS1. The HIF-1α gene deletion in mice gives rise to a clear phenotype, i.e., mid-gestational lethality (Iyer et al., 1998 Ryan et al., 1998) but Epas1 gene deletions have highly varying phenotypes, likely due to variations in genetic background (Compernolle et al., 2002 Peng et al., 2000 Tian et al., 1998). Additionally, there is a wealth of evidence that some hypoxic responses are exclusively controlled by one or the other oxygen-sensitive HIF isoform erythropoiesis, for example, appears primarily controlled by EPAS1 (Fandrey, 2004).
Regulation of HIF is post-translational and involves VHL
Data obtained by a number of laboratories, including Ratcliffe’s, showed that HIF-1α levels were themselves regulated by changes in protein stability, and not by changes in gene transcription or protein synthesis (Huang et al., 1998a Kallio et al., 1999 Pugh et al., 1997 Salceda and Caro, 1997 Srinivas et al., 1999). It was further demon strated by a number of groups, including those of Caro and H. Frank Bunn, that HIF-1α was degraded through the ubiquitin-proteasome pathway, and that this occurred in an oxygen-dependent manner (Huang et al., 1998b Salceda and Caro, 1997). This work also identified the specific structural domain in HIF-1α responsible for its oxygen-dependent degradation (termed the ODD region of the protein, and present in both HIF-1α and EPAS1).
At approximately this point, in 1995, Kaelin’s group published the first full-length sequence of the VHL tumor suppressor gene, and showed that re-introducing a wild type version of VHL into a renal carcinoma cell line prevented the cell line from forming tumors (Iliopoulos et al., 1995). Kaelin and a number of other groups had been studying the VHL gene and its link to a number of families with a genetic predisposition to certain cancers. The paper from Kaelin established that VHL is a tumor suppressor gene, whose activity can act to inhibit tumor growth of cells from patients with VHL mutations. In 1996, during the course of the characterization of the VHL gene, collaborative work between Kaelin’s group and the group of Mark Goldberg showed that a number of HIF target genes were over-expressed in VHL mutant cell lines (Iliopoulos et al., 1996). This finding suggested that the two pathways, of HIF response and VHL-linked tumorigenesis, could be linked in some fashion.
An important clue regarding VHL function next came with the identification of binding partners to the VHL protein. Richard Klausner and colleagues, as well as Kaelin and his group, had found in 1995 that VHL interacts with the transcriptional elongation factors elongins B and C (Duan et al., 1995 Kibel et al., 1995), and in 1997, Klausner, W. Marston Linehan, and colleagues showed that VHL is found in a complex with the Cul-2 protein (Pause et al., 1997), a factor involved in protein ubiquitination a finding subsequently replicated by Kaelin (Lonergan et al., 1998). Since elongin C and Cul-2 show structural similarity to Skp1 and Cdc53, factors that were known to target specific proteins for ubiquitin-dependent proteolysis, these observations revealed a potential link between VHL and protein degradation.
HIF is targeted for ubiquitination and proteo-lysis by VHL
While during the period between 1996 and 1998 it was made clear that HIF-1α and EPAS1 get rapidly eliminated by proteasomal degradation at normoxia, it was still unknown how this process was inhibited during hypoxia. A missing piece of the puzzle was the ubiquitin E3 ligase suspected to be involved in targeting HIF-1α for degradation. Here, Ratcliffe and colleagues provided a key breakthrough in 1999, in a landmark paper where they showed that the VHL complex is involved in HIF-1α proteolysis (Maxwell et al., 1999). They and others subsequently showed that VHL acts as a recognition component of a ubiquitin E3 ligase complex in this process (Cockman et al., 2000 Kamura et al., 2000 Krieg et al., 2000 Ohh et al., 2000 Tanimoto et al., 2000).
A critical and remaining piece of the puzzle at that point was how VHL-HIF-1α interaction and subsequent HIF-1α degradation was regulated by oxygen. Importantly, the Maxwell et al., paper from 1999 points out that VHL-HIF-1α interaction requires an activity that is both oxygen and iron-dependent. This finding initiated the search for the mechanism: both for the oxygen-dependent chemical modification of HIF-1α that enables VHL binding, and the enzyme(s) that catalyze that reaction.
At that time, oxygen-dependent protein hydroxylation was known to occur in collagen proteins, and was known to be mediated by collagen prolyl-4-hydroxylase. Thus, it was suspected that oxygen-dependent hydroxylation of proline residues in HIF-1α might confer the conformational change required to allow VHL binding. This turned out to be the case. In 2001, the Ratcliffe and Kaelin laboratories simul-taneously reported that oxygen-dependent 4-hydroxylation of two proline residues within the ODD domain of HIF-1α increased the affinity for VHL-complex binding of the HIF transcription factor. The two papers describing this were published back-to-back (Ivan et al., 2001 Jaakkola et al., 2001).
The oxygen-dependent switches
Proline hydroxylation requires oxygen, and thus the elegant mechanism of post-translational regulation of HIF-1α and EPAS1 proteins was revealed: in the absence of oxygen, no hydroxylation can occur, and VHL does not recognize HIF-1α because of this, HIF-1α is not ubiquitinated, and so avoids proteasomal degradation and remains intact. It can then accumulate, and transcriptionally activate the hypoxia-induced gene α program (see Figure 1).
Figure 1. When oxygen levels are low (hypoxia), HIF-1α is protected from degradation and accumulates in the nucleus, where it associates with ARNT and binds to specific DNA sequences (HRE) in hypoxia-regulated genes (1). At normal oxygen levels, HIF-1α is rapidly degraded by the proteasome (2). Oxygen regulates the degradation process by the addition of hydroxyl groups (OH) to HIF-1α (3). The VHL protein can then recognize and form a complex with HIF-1α leading to its degradation in an oxygen-dependent manner (4).
Ratcliffe’s group and McKnight’s group independently identified the prolyl hydroxylase (PHD) genes involved in hydroxylating HIF-1α and EPAS1 these papers, describing the genetic isolation of the PHDs, were published in 2001 (Bruick and McKnight, 2001 Epstein et al., 2001). The Kaelin group also isolated the PHD genes, in their case using biochemical methods, and published that work in 2002 (Ivan et al., 2002). The identification of these hydroxylases gave rise to the possibility of creating specific PHD inhibitors to increase HIF activity e.g., to increase EPO levels in patients with anemia.
A second oxygen-dependent mechanism, this time not for HIF-1α degradation but for inhibition of its activity as a transcription factor was discovered in 2001. Semenza and his group were the first to identify the factor involved, termed FIH-1 (for “factor inhibiting HIF”) (Mahon et al., 2001). FIH is also an oxygen-dependent hydroxylase, in this case one that hydroxylates an asparagine residue in the N-terminal activation domain (NTAD) of HIF-1α and EPAS1 this hydroxylation was found by Murray Whitelaw and Richard Bruick to interfere with the recruitment of the p300 transcriptional co-activator (Lando et al., 2002a Lando et al., 2002b). In this way, oxygen not only promotes HIF-1α degradation via prolyl-hydroxylation of its ODD domain, but also can inhibit the transcriptional function of any HIF-1α or EPAS1 that has escaped VHL-dependent degradation. Thus, HIF activity has not one, but two independent mechanisms for oxygen-dependent post-translational inhibition. This indicates that keeping HIF levels properly and exactly regulated by cellular oxygen levels is necessarily a very finely tuned process.
The wide significance of the HIF pathway of control
Work by many groups have since shown the robustness of the HIF pathway, and its central role in modulating oxygen-influenced gene expression. Semenza, Ratcliffe, and Kaelin have remained central figures in this work since their original pathfinding discoveries. They have been involved in the further elucidation of the molecular biology of the HIF pathway, and have as well increased our understanding of the physiological roles played by hypoxic response in health and disease.
The discovery of the proline hydroxylases that regulate HIF-1α stability enabled a search for hydroxylase inhibitors to increase HIF levels and this has now opened up new pathways for pharmacologic discovery (Giaccia et al., 2003). In fact, a number of potential drugs that increase HIF function by inhibiting the PHD enzymes are already far along in clinical trials, with a recent series of publications demonstrating their clinical efficacy in treatment of anemia (Chen et al., 2019a Chen et al., 2019b).
Future applications to inhibit the HIF pathway are also on the horizon these are envisioned as a means to slow the progression of some cancers that are induced by VHL mutations. One of these is a specific blocker of EPAS1 function that was recently described by Kaelin and colleagues as capable of slowing tumor growth of VHL mutant cells in animal models (Cho et al., 2016).
Pharmacologically increased HIF function may aid in the treatment of a wide range of diseases, as HIF has been shown to be essential for phenomena as diverse as immune function, cartilage formation, and wound healing. Conversely, inhibition of HIF function could also have many applications: increased levels of HIF are seen in many cancers as well as in some cardiovascular diseases, including stroke, heart attack, and pulmonary hypertension. It is thus likely that we are only at the beginning of applications of these Nobel Prize-winning discoveries, since it is clear that the response to oxygen in cells, tissues and organisms is one of the most central and important physiological adaptations that animals have.
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Randall S. Johnson
Professor of Hypoxia Biology, Karolinska Institutet
Professor of Molecular Physiology and Pathology, University of Cambridge
Member of the Nobel Assembly
Karolinska Institutet, Stockholm, October 7, 2019
Correspondence: [email protected]
Illustration: Mattias Karlén
The Nobel Assembly, consisting of 50 professors at Karolinska Institutet, awards the Nobel Prize in Physiology or Medicine. Its Nobel Committee evaluates the nominations. Since 1901 the Nobel Prize has been awarded to scientists who have made the most important discoveries for the benefit of humankind.
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The RNA polymerase(s)
RNA is transcribed from DNA using an RNA polymerase (RNAP). In bacteria this is done by a single enzyme however, eukaryotes have muliple polymerases which are each responsible for a specific subset of RNAs. To gain this specificity, the eukaryotic RNAP can recognize and bind to specific promoter elements. This means that the promoter present in your plasmid backbone must to be compatible with the type of RNA that needs to be made: if you want mRNA (for gene expression) you need to use an RNAP II promoter, whereas small RNAs (such as shRNA) are transcribed from the RNAP III promoters. This post features promoters for general RNAP II and RNAP III transcription however, using viral LTRs as RNAP II promoters is commonly employed in lentiviral and retroviral constructs and we will discuss these in a future post on viral vector parts.
Anytime a person returns communication it can be called a response or a reply, while an answer is a form of response which is a solution to a problem or question. So response and reply are generic and can be used in any situation, while answer is more specific in its usage.
So if you asked a question or asked for a solution to a problem, and the person gave it to you, then you can say "Thanks for your quick answer". If it was not in one of these categories, then use response or reply since these are both generic.
And if you are still in doubt, remember that because response is generic you can use it in any situation.
Why you should use the luciferase reporter assay…
This reporter assay can be used to study gene expression as well as other cellular components and events that are involved in gene regulation. Its extreme sensitivity allows quantification of even small changes in transcription, and the availability of results within minutes of completing your experiment makes it even more appealing. All in all, the luciferase reporter assay may be just the thing you need to shed some light on your project from hell!