praj-17/QA-MCQ-Open-ended huggingface dataset:
Title: Bacteria
Context: Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer. Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms. In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).

question: What is the simple way of producing large volume of bacteria cells? 

answer: high levels of nutrients

question: What caused the evolution of different growth strategies in bacteria? 

answer: nutrients are limited

question: What can create a subsequent increase of nutrients in natural environment? 

answer: biofilms

question: What do algal bacteria if nutrients are available? 

answer: grow extremely rapidly
Title: Bacteria
Context: Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. The second phase of growth is the log phase, also known as the logarithmic or exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport. The final phase is the death phase where the bacteria run out of nutrients and die.

question: What is the first stage of bacteria adaptation? 

answer: lag phase

question: What is the second phase of bacteria growth known for? 

answer: rapid exponential growth

question: The absence of what causes the last stage of bacteria growth? 

answer: nutrients

question: What is called the third statge of growth of bacteria? 

answer: stationary phase

question: How many phase are in the growth of bacteria? 

answer: four phases
Title: Bacteria
Context: Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii, to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum. Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome. The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.

question: What shape is chromosome of bacteria? 

answer: circular chromosome

question: What bacteria is an exception to single circular chromosome rule? 

answer: Spirochaetes of the genus Borrelia

question: What bacteria is responsible for Lyme disease? 

answer: Borrelia burgdorferi

question: How does chromosome of Borrelia burgdoferi look like? 

answer: single linear chromosome
Title: Bacteria
Context: Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clonal). However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.

question: What makes bacteria an asexual organism? 

answer: inherit identical copies of their parent's genes

question: What can cause mutation in bacteria? 

answer: changes to their genetic material DNA

question: What are two ways changes to DNA of bacteria can occur? 

answer: random mutation during replication or "stress-directed mutation"
Title: Bacteria
Context: Transduction of bacterial genes by bacteriophage appears to be a consequence of infrequent errors during intracellular assembly of virus particles, rather than a bacterial adaptation. Conjugation, in the much-studied E. coli system is determined by plasmid genes, and is an adaptation for transferring copies of the plasmid from one bacterial host to another. It is seldom that a conjugative plasmid integrates into the host bacterial chromosome, and subsequently transfers part of the host bacterial DNA to another bacterium. Plasmid-mediated transfer of host bacterial DNA also appears to be an accidental process rather than a bacterial adaptation.

question: What is the aftermath of infrequent errors during intracellular assembly of virus particles? 

answer: Transduction of bacterial genes

question: What is the result of bacterial adaptation of E.coli bacteria host and plasmid of another bacteria? 

answer: Conjugation

question: How does conjugation take place? 

answer: conjugative plasmid integrates into the host bacterial chromosome

question: Is conjugation a common bacterial adaptation? 

answer: It is seldom
Title: Bacteria
Context: Transformation, unlike transduction or conjugation, depends on numerous bacterial gene products that specifically interact to perform this complex process, and thus transformation is clearly a bacterial adaptation for DNA transfer. In order for a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state termed competence (see Natural competence). In Bacillus subtilis, about 40 genes are required for the development of competence. The length of DNA transferred during B. subtilis transformation can be between a third of a chromosome up to the whole chromosome. Transformation appears to be common among bacterial species, and thus far at least 60 species are known to have the natural ability to become competent for transformation. The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells.

question: What does transformation of bacteria depends on? 

answer: numerous bacterial gene products

question: How simple is the process of transformation? 

answer: this complex process

question: What is the first requirement in order for bacteria to bind and recombine with other bacteria's DNA 

answer: enter a special physiological state termed competence

question: How big can be the transformation level? 

answer: between a third of a chromosome up to the whole chromosome

question: How rare is the transformation among bacteria organisms? 

answer: common
Title: Bacteria
Context: In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance. In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions. Gene transfer is particularly important in antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.

question: Between what species do usually transduction, conjugation and transformation take place? 

answer: the same species

question: What are the consequences of transfer between different species of bacteria? 

answer: transfer of antibiotic resistance

question: What is horizontal gene transfer? 

answer: gene acquisition from other bacteria or the environment
Title: Bacteria
Context: Bacteriophages are viruses that infect bacteria. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. A bacteriophage can contain genes that contribute to its host's phenotype: for example, in the evolution of Escherichia coli O157:H7 and Clostridium botulinum, the toxin genes in an integrated phage converted a harmless ancestral bacterium into a lethal pathogen. Bacteria resist phage infection through restriction modification systems that degrade foreign DNA, and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference. This CRISPR system provides bacteria with acquired immunity to infection.

question: What are Bacteriophages? 

answer: viruses that infect bacteria

question: What can viruses do to bacteria? 

answer: infect and lyse their host bacteria

question: What can happen if Bacteriophage contain genes of host's phenotype? 

answer: lethal pathogen

question: How can bacteria resist virus DNA? 

answer: CRISPR system provides bacteria with acquired immunity
Title: Bacteria
Context: Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The bacterial flagella is the best-understood motility structure in any organism and is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power. This motor drives the motion of the filament, which acts as a propeller.

question: What is monotrichous? 

answer: single flagellum

question: How many proteins is typical flagellum consist os? 

answer: 20 proteins

question: When flagellum is distributed throughout the surface of the cell? 

answer: peritrichous

question: If bacteria has flagellum at each end what is the name of the species? 

answer: amphitrichous

question: How does flagellum function within the cell? 

answer: uses the electrochemical gradient across the membrane
Title: Bacteria
Context: Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones. While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, and Bergey's Manual of Systematic Bacteriology. The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria.

question: How can we classify the vast variety of bacterial species? 

answer: grouping organisms based on similarities

question: Can classification be helpful in determining differences between distinct species? 

answer: unclear

question: What supports the uncertainty in classification between the same kind of bacteria? 

answer: lack of distinctive structures in most bacteria,

question: What can lateral gene transfer create in bacteria? 

answer: different morphologies and metabolisms

question: What is the way modern classification tries to determine species? 

answer: emphasizes molecular systematics
Title: Bacteria
Context: The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiolology. However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria.

question: What would original term "bacteria" determine? 

answer: all microscopic, single-cell prokaryotes

question: What are two main groups of prokaryotic organisms are divided into? 

answer: Eubacteria and Archaebacteria

question: What groups of organisms are closely related to each other? 

answer: archaea and eukaryotes

question: What domain system is commonly used nowdays to classify microorganisms? 

answer: three-domain system
Title: Bacteria
Context: The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains. Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.

question: What was developed by Hans Christian  Gram? 

answer: The Gram stain

question: What year was the Grahm stain was developed? 

answer: 1884

question: What color do Gram positive bacteria cell walls turn to after being stained? 

answer: purple

question: What color is typical for Gram-negative bacteria after staining? 

answer: pink

question: What stain shows better test results on Norcadia bacteria? 

answer: Ziehl–Neelsen
Title: Bacteria
Context: As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea; but attempts to estimate the true number of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude.

question: What technique has becoming more popular in classification of bacteria? 

answer: molecular methods

question: What tool does DNA based diagnostics use? 

answer: polymerase chain reaction

question: What else can molecular methods of classification reveal? 

answer: identification of "viable but nonculturable" cells

question: Can new methods determine a total number of bacteria species? 

answer: cannot even be estimated with any certainty
Title: Bacteria
Context: Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria. These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter. Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirovibrio chlorellavorus, or invade another cell and multiply inside the cytosol, such as Daptobacter. These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.

question: Why are certain bacteria called predatory? 

answer: bacteria kill and then consume other microorganisms

question: Which way do Vampirovibrio absorb nutrients of other microorganisms? 

answer: attach to their prey in order to digest them

question: What technique do Daptobacter use in order to kill other microorganism? 

answer: invade another cell and multiply inside the cytosol

question: Where do Daptobacter bacteria come from? 

answer: saprophages
Title: Bacteria
Context: Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic Archaea that consume hydrogen. The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.

question: What helps bacteria to survive? 

answer: close spatial associations

question: What kind of bacteria can form interspecies hydrogen transfer? 

answer: anaerobic bacteria

question: What do anaerobic bacteria consume? 

answer: butyric acid or propionic acid
Title: Bacteria
Context: In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds. This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates. The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.

question: Where do bacteria stay in soil? 

answer: rhizosphere

question: What do bacteria do in soil? 

answer: converting nitrogen gas to nitrogenous compounds

question: How does the conversion help the vegetation? 

answer: provide an easily absorbable form of nitrogen

question: What is the amount of bacteria in human intestines? 

answer: over 1,000 bacterial species

question: How does gut flora prevent growth of pathogenic bacteria? 

answer: through competitive exclusion
Title: Bacteria
Context: If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.

question: What are the pathogenes? 

answer: bacteria form a parasitic association with other organisms

question: Can cause for most pathogenic diseases be found soon? 

answer: may only be discovered many years after

question: What can pathogenes cause? 

answer: human death and disease
Title: Bacteria
Context: Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death. Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease. Finally, some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.

question: How pathogenes interact with it's human host? 

answer: pathogen has a characteristic spectrum of interactions

question: Can all bacteria in human body  be harmful? 

answer: exist on the skin or in the nose without causing any disease

question: Which bacteria cause Rocky Mountain spotted fever disiease? 

answer: species of Rickettsia