rajpurkar/squad huggingface dataset:
Title: Bacteria

Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide. Heterotrophic bacteria include parasitic types. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many chemolithotrophic species, such as nitrifying or sulfur-oxidising bacteria. Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or based on chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration).

Question: How does heterotrophic carbon metabolism occur?
Answer: organic carbon compounds are used as carbon sources

Question: When carbon metabolism is called autotrophic?
Answer: cellular carbon is obtained by fixing carbon dioxide

Question: What category do parasitic bacteria fall into?
Answer: Heterotrophic bacteria

Question: Green sulfur-bacteria is typical representative of what type of bacteria?
Answer: autotrophic bacteria

Question: What is chemotrophy ?
Answer: the use of chemical substances for energy
Title: Bacteria

Bacteria are further divided into lithotrophs that use inorganic electron donors and organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g., carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the reduced substrate and transferring them to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to synthesise ATP and drive metabolism. In aerobic organisms, oxygen is used as the electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively.

Question: What do lithotrophs use ?
Answer: inorganic electron donors

Question: What type of electron donors organotrophs use?
Answer: organic compounds

Question: In what organisms is oxygen used as eelectron acceptor?
Answer: anaerobic organisms

Question: What do respiratory organisms use as electron donors?
Answer: chemical compounds
Title: Bacteria

These processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment. Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves.

Question: What is sulfate-reducing bacteria accountable for?
Answer: the production of the highly toxic forms of mercury

Question: What is the by-product of non-repiratory anaerobes?
Answer: ethanol

Question: How can anaerobes adjust to the surrounding environment?
Answer: can switch between fermentation and different terminal electron acceptors
Title: Bacteria

Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron and other reduced metal ions, and several reduced sulfur compounds. In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism. In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, whereas under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic.

Question: What are hydrogen and carbon monoxide for Lithotrophic bacteria?
Answer: Common inorganic electron donors

Question: How can gas methane be used in exceptional set of conditions by methanotrophic bacteria?
Answer: both a source of electrons and a substrate for carbon anabolism

Question: What is the main element for aerobic photorophy?
Answer: oxygen
Title: Bacteria

Regardless of the type of metabolic process they employ, the majority of bacteria are able to take in raw materials only in the form of relatively small molecules, which enter the cell by diffusion or through molecular channels in cell membranes. The Planctomycetes are the exception (as they are in possessing membranes around their nuclear material). It has recently been shown that Gemmata obscuriglobus is able to take in large molecules via a process that in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external items.

Question: What chemical process  helps bacteria to absorb raw materials?
Answer: diffusion

Question: How can bacteria obtain raw materials from the environment?
Answer: in the form of relatively small molecules

Question: What process is used by eukaryotic cells to absorb external items?
Answer: endocytosis

Question: What part of bacteria cell is used during diffusion?
Answer: molecular channels in cell membranes
Title: Bacteria

Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

Question: How size and reproduction are linked in bacteria?
Answer: Bacteria grow to a fixed size and then reproduce

Question: How does bacteria reproduce?
Answer: through binary fission

Question: If the conditions are right how long does it take for bacteria to reproduce?
Answer: divide extremely rapidly

Question: What are produced in cell division?
Answer: two identical clone daughter cells
Title: Bacteria

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.

Question: In what environment are bacteria being cultivated in labs?
Answer: solid or liquid media

Question: What is typical solid setting?
Answer: agar plates

Question: What can help to indentify specific bacteria?
Answer: The use of selective media

Question: Which environment is better to isolate a single example of bacteria strain?
Answer: agar plates

Question: Which media is preffered to grow larger volumes of bacteria?
Answer: liquid growth media
Title: Bacteria

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

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

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

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

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

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

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

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

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

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

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

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