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Authority on Microbiological Definitions

Authority on Microbiological Definitions


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Is there an authority on definitions for molecular microbiology concepts, like an IUPAC book for chemical definitions?

The particular definition I am debating is chromatin. Some say it encompasses DNA, RNA and protein, whilst others say that it contains DNA and only during the mitotic interphase can it transcribe to produce RNA and protein.


So in a very broad definition, yes, chromatin encompasses DNA, RNA and protein. The primary function of chromatin is to provide a method to effectively package all the DNA in a cell. This packaging is dynamic, and it's constantly regulated in a cell type-specific manner. We can see the broad interactions of protein and DNA in this cartoon representation from wikipedia:

Combined with histone-modifying complexes, and chromatin remodeling complexes, we obtain the aforementioned mode of regulation. Histone protein can be modified (acetylation, methylation, glycosylation, phosphorylation, etc.), they can also be moved, substituted in their subunits for specific pruposes (think H3.3 or H2A.X). We can also end up with varying regions of dsDNA, 10nm or 30nm fiber.

The RNA comes in as a structural and functional components of the chromatin, participating in many controls as noncoding RNAs.

I believe most of the method in defining chromatin comes in very much as the amassed literature on the subject to-date. You'd even consider it "common knowledge" entering the field (i.e. a quick google search can return you the right definition).

"only during the mitotic interphase can it transcribe to produce RNA and protein."

Transcription halts entering M phase or mitosis, transcription may occur during G1, S, G2, or "interphase."


Microbiology

Finney, originally from Delaware, graduated this May from the University of Pittsburgh with a bachelor’s degree in microbiology .

Studies in non-medical areas of microbiology also recognized that microbes played important roles in ecosystems such as oceans, forests, or soils, according to Lita Proctor, program coordinator at the Human Microbiome Project.

“It does challenge dogma that was previously held,” said Samantha Dando, a lecturer in clinical microbiology at the Queensland Institute of Technology in Australia.

“It’s a very obvious progression given the success of the covid-19 vaccine to move right to flu,” said Andrew Pekosz, a professor of microbiology at the Johns Hopkins Bloomberg School of Public Health.

Eric Alm, a professor of microbiology at MIT, has an idea: use the sewers.

Go back to Adam and Eve, or wait for that thing to come out of the ocean, or do the microbiology thing.

My book has all these detours into microbiology and the science of flavor because truly amazing things are going on when you cook.

But other scientists counter that basic skills in microbiology and biotechnology can get you a bioweapon.

For this reason the term pathogenic Microbiology has been introduced to include all these organisms.

The case is similar to that of the rotation of crops in its relation to scientific microbiology .

In fact, I am assured that nothing exists which gives anything like so full a study of microbiology .


The Diagnostic Scheme

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.

Learning Objectives

Outline the various types of diagnostic methods used to diagnose a microbial infection

Key Takeaways

Key Points

  • Diagnosis of infectious disease is nearly always initiated by medical history and physical examination.
  • Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype.
  • Diagnostic methods include: Microbial culture, microscopy, biochemical tests and molecular diagnostics.

Key Terms

  • Diagnosis: Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation.
  • infectious: Infectious diseases, also known as transmissible diseases or communicable diseases, comprise clinically evident illness (i.e., characteristic medical signs and/or symptoms of disease) resulting from the infection, presence, and growth of pathogenic biological agents in an individual host organism.
  • pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.

The Challenge of Diagnosis

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified. The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is benign.

Primary and Opportunistic Pathogens

Among the almost infinite varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen depends upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. Clinicians therefore classify infectious microorganisms or microbes according to the status of host defenses – either as primary pathogens or as opportunistic pathogens.

An Orderly Process

Diagnosis of infectious disease is nearly always initiated by taking a medical history and performing a physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype. Other techniques, such as X-rays, CAT scans, PET scans or NMR, are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone abscess or a spongiform encephalopathy produced by a prion.

Diagnostic methods include microbial culture, microscopy, biochemical tests and molecular diagnostics:

  • Microbiological culture is a principal tool used to diagnose infectious disease. In a microbial culture, a growth medium is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium.
  • Microscopy may be carried out with simple instruments, such as the compound light microscope, or with instruments as complex as an electron microscope. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with biochemical staining techniques, and can be made exquisitely specific when used in combination with antibody based techniques.
  • Biochemical tests used in the identification of infectious agents include the detection of metabolic or enzymatic products characteristic of a particular infectious agent. Since bacteria ferment carbohydrates in patterns characteristic of their genus and species, the detection of fermentation products is commonly used in bacterial identification. Acids, alcohols and gases are usually detected in these tests when bacteria are grown in selective liquid or solid media.
  • Molecular diagnostics using technologies based upon the polymerase chain reaction ( PCR ) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease essentially it must amplify its own nucleic acids in order to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known, if they are not already.

Subdisciplines of Microbiology

Bacteriology

This is the study of bacteria.

Environmental Microbiology

This is the study of the function and diversity of microbes in their natural environments.

Evolutionary Microbiology

This is the study of the evolution of microbes.

Food Microbiology

This is the study of microorganisms causing food spoilage as well as those involved in creating foods such as cheese and beer.

Industrial Microbiology

This is the exploitation of microbes for use in industrial processes, such as industrial fermentation and wastewater treatment. This subdiscipline is linked closely to the biotechnology industry.

Medical (or Clinical) Microbiology

This is the study of the role of microbes in human illness. It includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology.

Microbial Genetics

This is the study of how genes are organized and regulated in microbes in relation to their cellular functions. This subdiscipline is related closely to the field of molecular biology.

Microbial Physiology

This is the study of how the microbial cell functions biochemically. It includes the study of microbial growth, microbial metabolism and microbial cell structure.


7.19B: Attenuation

  • Contributed by Boundless
  • General Microbiology at Boundless

Attenuation is a regulatory mechanism used in bacterial operons to ensure proper transcription and translation. In bacteria, transcription and translation are capable of proceeding simultaneously. The need to prevent unregulated and unnecessary gene expression can be prevented by attenuation, which is characterized as a regulatory mechanism.

Figure: Attenuation of the Tryptophan Operon: An example of attenuation is the tryptophan operon. This schematic represents transcriptional-attenuation as the formation of mRNA stem-loops prevents the continuance of transcription based on the levels of tryptophan in the metabolic environment.

The process of attenuation involves the presence of a stop signal that indicates premature termination. The stop signal, referred to as the attenuator, prevents the proper function of the ribosomal complex, stopping the process. The attenuator is transcribed from the appropriate DNA sequence and its effects are dependent on the metabolic environment. In times of need, the attenuator within the mRNA sequence will be bypassed by the ribosome and proper translation will occur. However, if there is not a need for a mRNA molecule to be translated but the process was simultaneously initiated, the attenuator will prevent further transcription and cause a premature termination. Hence, attenuators can function in either transcription-attenuation or translation-attenuation.

Transcription-attenuation is characterized by the presence of 5&prime-cis acting regulatory regions that fold into alternative RNA structures which can terminate transcription. These RNA structures dictate whether transcription will proceed successfully or be terminated early, specifically, by causing transcription-attenuation. The result is a misfolded RNA structure where the Rho-independent terminator disrupts transcription and produced a non-functional RNA product. This characterizes the mechanisms of transcription-attenuation. The other RNA structure produced will be an anti-terminator that allows transcription to proceed.

Translation-attenuation is characterized by the sequestration of the Shine-Dalgarno sequence, which is a bacterial specific sequence that indicates the site for ribosomal binding to allow for proper translation to occur. However, in translation-attenuation, the attenuation mechanism results in the Shine-Dalgarno sequence forming as a hairpin-loop structure. The formation of this hairpin-loop structure results in the inability of the ribosomal complexes to form and proceed with proper translation. Hence, this specific process is referred to as translation-attenuation.


Authority on Microbiological Definitions - Biology

Definition and Examples

Logarithms are encountered throughout the biological sciences. Some examples include calculating the pH of a solution or the change in free energy associated with a biochemical reactions. To understand how to solve these equations, we must first consider the definition of a logarithm.

Definition- The formal definition of a logarithm is as follows:

The base a logarithm of a positive number x is the exponent you get when you write x as a power of a where a > 0 and a &ne 1. That is,

loga x = k if and only if a k = x.

The key to taking the logarithm of x > 0 is to rewrite x using base a. For example,

Who invented such a thing?

John Napier, a Scottish mathematician is credited with the invention of logarithms. His book, A Description of the Wonderful Law of Logarithms, was published in 1614. Napier devised a method to facilitate calculations by using addition and subtraction rather than multiplication and division. Today, we ususally use logarithms to the base 10, common logs, or logarithms to the base e, or natural logs. In Napier's publication, he describes logs to the base 2.

Some examples of logarithms

Logarithms, just like exponents, can have different bases. In the biological sciences, you are likely to encounter the base 10 logarithm, known as the common logarithm and denoted simply as log and the base e logarithm, known as the natural log and denoted as ln. Most calculators will easily compute these widely used logarithms.

B ase 10 logarithm The common logarithm of a positive number x , is the exponent you get when you write x as a power of 10. That is,

log x = k if and only if 10 k = x

Computing the common logarithm of x > 0 by hand can only be done under special circumstances, and we will examine these first. Let&rsquos begin with computing the value of,

log 10.

According to our definition of the common logarithm, we need to rewrite x = 10 using base 10. This is easy to do because 10 = 10 1 . So the exponent, k, we get when rewriting 10 using base 10 is, k = 1. Thus, we conclude,

log 10 = log 10 1 = 1.

While this example is rather simple, it is good practice to follow this method of solution. Now try the following exercises.

As you worked through these exercies, did you notice the outputs of logarithms increase linearly as the inputs increase exponentially?

Natural logarithms

The natural logarithm of a positive number x , is the exponent you get when you write x as a power of e. Recall that

loge x = ln x

therefore

ln x = k if and only if e k = x .

Logarithmic calculations you cannot do by hand.

Now, suppose you were asked to compute the value of log 20. What would you do (or try to do) to get an answer? Do you notice anything different about this problem?

As you most likely noticed, there is no integer k, such that 10 k = 20. So, in this case, you will need to rely on your calculator for help. Using your calculator you will find,

log 20 &asymp 1.30.

Remember that this is true because,

10 1.30 &asymp 20.

After completing these exercises you will notice that your answers (outputs) are small relative to your large inputs. Remember that logarithms transform exponentially increasing inputs into linearly increasing outputs. This is quite convenient for biologists who work over many orders of magnitude and on many different scales.

Since exponential and logarithmic functions are inverses, the domain of logarithms is the range of exponentials (i.e. positive real numbers), and the range of logarithms is the domain of exponentials (i.e. all real numbers). This is true of all logarithms, regardless of base.

Recall that an exponential function with base a is written as f (x) = a x . The inverse of this function is a base a logarithmic function written as,

f &minus1 (x) = g (x) = loga x.

When there is no explicit subscript a written, the logarithm is assumed to be common (i.e. base 10). There is one special exception to this notation for base e &asymp 2.718 , called the natural logarithm,

g (x) = loge x = ln x.

To compute the base a logarithm of x > 0 , rewrite x using base a (just as we did for base 10). For example, suppose a = 2 and we want to compute,

log2 8.

To find this value by hand, we convert the number 8 using base 2 as,

log2 8 = log2 2 3 = 3,

just as we did for base 10.

In the next section we will describe the properties of logarithms.


Canadian Public Health Laboratory Network

  • is a place for national public health lab professionals to share knowledge
  • supports rapid, organized nation-wide lab response to contagious diseases such as:

Read the network's Strategic Plan 2016-2020 to find out more.

Canadian Network for Public Health Intelligence

  • is a secure, web-based tool
  • allows public health professionals to gather and share knowledge in real-time
  • helps to coordinate public health responses better

To date, CNPHI has successfully piloted:

  • an alerting system for all of Canada
  • resource centres for local and global groups to collaborate
  • lab-based surveillance systems for human and animal health
  • a surveillance system to monitor infectious diseases

What is Molecular Biology?

Molecular biology is the study of biological activities at the molecular level. It mainly concerns various interactions between the different types of biological systems like DNA, RNA, proteins and their biosynthesis. Molecular biologists use specific techniques unique to molecular biology but often combine other techniques available in genetics and biochemistry. However, the field of bioinformatics and computational biology have helped to improve the interface between molecular biology and computer science.

Molecular biologists are able to characterize and manipulate molecular components of cells and organisms using various techniques. One of the most basic techniques of molecular biology is the molecular cloning, in which DNA coding for a particular protein is cloned into a plasmid in order to study the function of the protein. Polymerase chain reaction (PCR) is also an important technique used for copying DNA. Other techniques include gel electrophoresis, macromolecule bottling and probing, DNA microarray and allele-specific oligonucleotide.


Microbiological Research

Microbiological Research is devoted to publishing reports on prokaryotic and eukaryotic microorganisms such as yeasts, fungi, bacteria, archaea, and protozoa. Research on interactions between pathogenic microorganisms and their environment or hosts are also covered. The research should be original.

  • Reviews/Minireviews on all aspects
  • Microbiology and Genetics
  • Molecular and Cell Biology
  • Metabolism and Physiology
  • Signal transduction and Development
  • Biotechnology
  • Phytopathology
  • Environmental Microbiology and Ecology

Elsevier stands against racism and discrimination and fully supports the joint commitment for action in inclusion and diversity in publishing.

In partnership with the communities we serve we redouble our deep commitment to inclusion and diversity within our editorial, author and reviewer networks.

This journal has partnered with Heliyon Microbiology, a dedicated section of Heliyon, an open access journal from Cell Press that publishes scientifically accurate and valuable research in microbiology. Heliyon Microbiology aims to make it easier for authors to share their research with a global audience quickly and easily, while benefitting from the subject-area expertise of specialized section editors, who ensure your work is considered fairly and reaches the right audience. Authors can quickly and easily transfer their research from a Partner Journal to Heliyon without the need to edit, reformat, or resubmit.
Learn more


Microbes do more

Microbes are microscopic, single-celled organisms like bacteria and fungi. Although they are often associated with dirt and disease, most microbes are beneficial. For example, microbes keep nature clean by helping break down dead plants and animals into organic matter.

But there are many more natural benefits of microbes, including helping farmers increase yields and protect crops. They can also improve livestock health, growth and feed utilization.

Microbes also increase wastewater treatment efficiency and optimize healthy water quality in aquaculture.


Universal Buffers

Most buffers work over a relative narrow pH range. An exception is citric acid because it has three pKa values. When a compound has multiple pKa values, a larger pH range becomes available for a buffer. It's also possible to combine buffers, providing their pKa values are close (differing by 2 or less), and adjusting the pH with strong base or acid to reach the required range. For example, McIvaine's buffer is prepared by combining mixtures of Na2PO4 and citric acid. Depending on the ratio between the compounds, the buffer may be effective from pH 3.0 to 8.0. A mixture of citric acid, boric acid, monopotassium phosphate, and diethyl barbituic acid can cover the pH range from 2.6 to 12!


Watch the video: How can you test antimicrobial agents? (May 2022).