romikgosai/squad_modified_2 huggingface dataset:
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.

Q1: What makes bacteria an asexual organism?
A1: inherit identical copies of their parent's genes
Q2: What can cause mutation in bacteria?
A2: changes to their genetic material DNA
Q3: What are two ways changes to DNA of bacteria can occur?
A3: random mutation during replication or "stress-directed mutation"
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.

Q1: What is the aftermath of infrequent errors during intracellular assembly of virus particles?
A1: Transduction of bacterial genes
Q2: What is the result of bacterial adaptation of E.coli bacteria host and plasmid of another bacteria?
A2: Conjugation
Q3: How does conjugation take place?
A3: conjugative plasmid integrates into the host bacterial chromosome
Q4: Is conjugation a common bacterial adaptation?
A4: It is seldom
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.

Q1: What does transformation of bacteria depends on?
A1: numerous bacterial gene products
Q2: How simple is the process of transformation?
A2: this complex process
Q3: What is the first requirement in order for bacteria to bind and recombine with other bacteria's DNA
A3: enter a special physiological state termed competence
Q4: How big can be the transformation level?
A4: between a third of a chromosome up to the whole chromosome
Q5: How rare is the transformation among bacteria organisms?
A5: common
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.

Q1: Between what species do usually transduction, conjugation and transformation take place?
A1: the same species
Q2: What are the consequences of transfer between different species of bacteria?
A2: transfer of antibiotic resistance
Q3: What is horizontal gene transfer?
A3: gene acquisition from other bacteria or the environment
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.

Q1: What are Bacteriophages?
A1: viruses that infect bacteria
Q2: What can viruses do to bacteria?
A2: infect and lyse their host bacteria
Q3: What can happen if Bacteriophage contain genes of host's phenotype?
A3: lethal pathogen
Q4: How can bacteria resist virus DNA?
A4: CRISPR system provides bacteria with acquired immunity
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.

Q1: What is monotrichous?
A1: single flagellum
Q2: How many proteins is typical flagellum consist os?
A2: 20 proteins
Q3: When flagellum is distributed throughout the surface of the cell?
A3: peritrichous
Q4: If bacteria has flagellum at each end what is the name of the species?
A4: amphitrichous
Q5: How does flagellum function within the cell?
A5: uses the electrochemical gradient across the membrane
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.

Q1: How can we classify the vast variety of bacterial species?
A1: grouping organisms based on similarities
Q2: Can classification be helpful in determining differences between distinct species?
A2: unclear
Q3: What supports the uncertainty in classification between the same kind of bacteria?
A3: lack of distinctive structures in most bacteria,
Q4: What can lateral gene transfer create in bacteria?
A4: different morphologies and metabolisms
Q5: What is the way modern classification tries to determine species?
A5: emphasizes molecular systematics
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.

Q1: What would original term "bacteria" determine?
A1: all microscopic, single-cell prokaryotes
Q2: What are two main groups of prokaryotic organisms are divided into?
A2: Eubacteria and Archaebacteria
Q3: What groups of organisms are closely related to each other?
A3: archaea and eukaryotes
Q4: What domain system is commonly used nowdays to classify microorganisms?
A4: three-domain system
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.

Q1: What was developed by Hans Christian  Gram?
A1: The Gram stain
Q2: What year was the Grahm stain was developed?
A2: 1884
Q3: What color do Gram positive bacteria cell walls turn to after being stained?
A3: purple
Q4: What color is typical for Gram-negative bacteria after staining?
A4: pink
Q5: What stain shows better test results on Norcadia bacteria?
A5: Ziehl–Neelsen
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.

Q1: What technique has becoming more popular in classification of bacteria?
A1: molecular methods
Q2: What tool does DNA based diagnostics use?
A2: polymerase chain reaction
Q3: What else can molecular methods of classification reveal?
A3: identification of "viable but nonculturable" cells
Q4: Can new methods determine a total number of bacteria species?
A4: cannot even be estimated with any certainty
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.

Q1: Why are certain bacteria called predatory?
A1: bacteria kill and then consume other microorganisms
Q2: Which way do Vampirovibrio absorb nutrients of other microorganisms?
A2: attach to their prey in order to digest them
Q3: What technique do Daptobacter use in order to kill other microorganism?
A3: invade another cell and multiply inside the cytosol
Q4: Where do Daptobacter bacteria come from?
A4: saprophages
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.

Q1: What helps bacteria to survive?
A1: close spatial associations
Q2: What kind of bacteria can form interspecies hydrogen transfer?
A2: anaerobic bacteria
Q3: What do anaerobic bacteria consume?
A3: butyric acid or propionic acid
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.

Q1: Where do bacteria stay in soil?
A1: rhizosphere
Q2: What do bacteria do in soil?
A2: converting nitrogen gas to nitrogenous compounds
Q3: How does the conversion help the vegetation?
A3: provide an easily absorbable form of nitrogen
Q4: What is the amount of bacteria in human intestines?
A4: over 1,000 bacterial species
Q5: How does gut flora prevent growth of pathogenic bacteria?
A5: through competitive exclusion
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.

Q1: What are the pathogenes?
A1: bacteria form a parasitic association with other organisms
Q2: Can cause for most pathogenic diseases be found soon?
A2: may only be discovered many years after
Q3: What can pathogenes cause?
A3: human death and disease
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.

Q1: How pathogenes interact with it's human host?
A1: pathogen has a characteristic spectrum of interactions
Q2: Can all bacteria in human body  be harmful?
A2: exist on the skin or in the nose without causing any disease
Q3: Which bacteria cause Rocky Mountain spotted fever disiease?
A3: species of Rickettsia
Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome. Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations. Infections can be prevented by antiseptic measures such as sterilizing the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilized to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.

Q1: What type of antibiotics called bacterocidal?
A1: if they kill bacteria
Q2: What kind of antibiotics are used for prevention of bacterial growth
A2: bacteriostatic
Q3: What is the drawback of using antibiotics if agriculture?
A3: rapid development of antibiotic resistance in bacterial populations
Q4: Besides in treating human disease where else are antibiotics used?
A4: in intensive farming to promote animal growth
Q5: What is common prevention method of infections in medicine?
A5: sterilizing
The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Fertilizer was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes. In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.

Q1: What quality of bacteria is being widely used re-cyling?
A1: ability of bacteria to degrade a variety of organic compounds
Q2: What is being used in cleaning up oil spills?
A2: Bacteria
Q3: What other way is bacteria aiding to nature?
A3: used for the bioremediation
Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms. This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested. This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.

Q1: What sciences use bacteria?
A1: molecular biology, genetics and biochemistry
Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He then published his observations in a series of letters to the Royal Society of London. Bacteria were Leeuwenhoek's most remarkable microscopic discovery. They were just at the limit of what his simple lenses could make out and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century. Only then were his by-then-largely-forgotten observations of bacteria — as opposed to his famous "animalcules" (spermatozoa) — taken seriously.

Q1: When was the first time bacteria were observed?
A1: 1676
Q2: Who discovered bacteria?
A2: Dutch microscopist Antonie van Leeuwenhoek
Q3: How was he able to see bacteria?
A3: using a single-lens microscope of his own design
Q4: How long did it take for his discovery to be taken seriously?
A4: over a century
Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum — the spirochaete that causes syphilis — into compounds that selectively killed the pathogen. Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl–Neelsen stain.

Q1: When was the first antibiotic discovered?
A1: In 1910
Q2: Who was the creator of antibiotic?
A2: Paul Ehrlich
Q3: What bacteria did he treat first?
A3: Treponema pallidum
Q4: Who based their research on Enrlich's stains works?
A4: Gram stain and the Ziehl–Neelsen
Q5: How was his discovery aknowledged?
A5: had been awarded a 1908 Nobel Prize