Question: What are some possible ways bacteria can spread between cells?
About the article "Bacteria", section "DNA transfer".

Candidate passages:
The T3SS in many bacteria has been manipulated by researchers.
Observing the influence of individual manipulations can be used to draw insights into the role of each component of the system.
Examples of manipulations are:  Deletion of one or more T3SS genes (gene knockout).
Overexpression of one or more T3SS genes (in other words: production "in vivo" of a T3SS protein in quantities larger than usual).
Point or regional changes in T3SS genes or proteins.
This is done in order to define the function of specific amino acids or regions in a protein.
The introduction of a gene or a protein from one species of bacteria into another (cross-complementation assay).
This is done in order to check for differences and similarities between two T3SSs.
Manipulation of T3SS components can have influence on several aspects of bacterial function and pathogenicity.
Examples of possible influences:  The ability of the bacteria to invade host cells, in the case of intracellular pathogens.
This can be measured using an invasion assay (gentamicin protection assay).
The ability of intracellular bacteria to migrate between host cells.
The ability of the bacteria to kill host cells.
This can be measured by several methods, for instance by the LDH-release assay, in which the enzyme LDH, which leaks from dead cells, is identified by measuring its enzymatic activity.
The ability of a T3SS to secrete a specific protein or to secrete at all.
In order to assay this, secretion is induced in bacteria growing in liquid medium.
The bacteria and medium are then separated by centrifugation, and the medium fraction (the supernatant) is then assayed for the presence of secreted proteins.
In order to prevent a normally secreted protein from being secreted, a large molecule can be artificially attached to it.
If the then non-secreted protein stays "stuck" at the bottom of the needle complex, the secretion is effectively blocked.
The ability of the bacteria to assemble an intact needle complex.
NCs can be isolated from manipulated bacteria and examined microscopically.
Minor changes, however cannot always be detected by microscopy.
The ability of bacteria to infect live animals or plants.
Even if manipulated bacteria are shown "in vitro" to be able to infect host cells, their ability to sustain an infection in a live organism cannot be taken for granted.
The expression levels of other genes.
This can be assayed in several ways, notably northern blot and RT-PCR.
The expression levels of the entire genome can be assayed by microarray.
Many type III transcription factors and regulatory networks were discovered using these methods.
The growth and fitness of bacteria.  
"Nucleus" is a puzzle-based shooting game with a dual stick control system similar to .
Players are tasked with ridding a host body of a virus infestation, moving through the body's three main biological systems, the digestive system, the circulatory system, and finally the nervous system, culminating in a final battle in the brain.
The basic game consists of shooting bacteria or progressively larger and larger viruses, which break down into smaller viruses when shot, or if left alone combine themselves into ever larger viruses.
Each level also has a number of cells which clump together and interact in a physical manner, the players can move them around and manipulate them with a traction beam to construct barriers to hide behind or to block of parts of the dynamically changing levels.
The main resource available to the player is protein, these are released each time an enemy or a cell is destroyed.
By clumping cells together the player can harvest more bacteria, creating a trade off between using the cells available to protect their ship and shooting them to release enough bacteria to be able to fire the more powerful protein bomb weapon.
Interspersed along the game progression are encounters with super enemies (the Nucleus of the game title).
These boss-type enemies fire spores at cells to turn them into bacteria, and can only be damaged by protein bombs.
The player has to attempt to maintain a cell barrier between itself and the possibly multiple, possibly mobile Nucleus enemies, while harvesting as much protein as possible in order to fight them back.
As the Nucleus enemies get damaged they become more and more violent, producing more spore and eventually attacking the player directly.
The game entities are all physically dynamic, each imparting a force on other nearby enities.
Cells exert an attractive force on each other, clumping into a tesselating mass and reacting to the various forces in the game as a flexing and spongy whole.
Exploding protein bombs or angry Nucleus enemies exert a large force over a wide area, which can break the various arrangements of cells the player may have constructed to fend off bacteria or virus.
There's a sense of zombie pressure as the amount of enemies build up and the player tries to keep their defences intact while harvesting protein fast enough.
Other styles of level are also offered—some levels require the player to move cells from one section of the level to another to complete them, some are straight shootouts with no Nucleus enemies, or collect'em-ups in a dynamic environment.
There are survival levels where the player is given a source of cells and have to keep back a more and more quickly expanding herd of bacteria and virus by arranging the cells in a free-form way.
The game can be played in a 2-player co-operative mode offering more ways to build and manipulate cell structures or to distract and defeat the Nucleus enemies.
Ultimately the game is a high-score attack.
Each level is tuned so that certain advanced techniques have to be used in order to achieve the higher scores, with correspondingly higher grades given to mark progress.
These techniques are all discoverable to begin with, but they aren't explained in the initial instruction set.
Later levels force you to learn these techniques, hints for failed attempts point the way, and by going back to earlier levels you can more easily achieve the higher level grades.
"Nucleus" doesn't come with trophies, as a PSN release title it was before the introduction of the system.
A patch has been released which offers a new mode of play, Nucleus+, which speeds up the gameplay, tweaks most of the existing levels (of which there are over 40), and introduces some new ones. 
Antimicrobials destroy bacteria, viruses, fungi, algae, and other microbes.
The cells of bacteria (prokaryotes), such as salmonella, differ from those of higher-level organisms (eukaryotes), such as fish.
Antibiotics are chemicals designed to either kill or inhibit the growth of pathogenic bacteria while exploiting the differences between prokaryotes and eukaryotes in order to make them relatively harmless in higher-level organisms.
Antibiotics are constructed to act in one of three ways: by disrupting cell membranes of bacteria (rendering them unable to regulate themselves), by impeding DNA or protein synthesis, or by hampering the activity of certain enzymes unique to bacteria.
Antibiotics are used in aquaculture to treat diseases caused by bacteria.
Sometimes the antibiotics are used to treat diseases, but more commonly antibiotics are used to prevent diseases by treating the water or fish before disease occurs.
While this prophylactic method of preventing disease is profitable because it prevents loss and allows fish to grow more quickly, there are several downsides.
The overuse of antibiotics can create antibiotic-resistant bacteria.
Antibiotic-resistant bacteria can spontaneously arise when selective pressure to survive results in changes to the DNA sequence of a bacteria allowing that bacteria to survive antibiotic treatments.
Because some of the same antibiotics are used to treat fish that are used to treat human disease, pathogenic bacteria causing human disease can also become resistant to antibiotics as a result of treatment of fish with antibiotics.
For this reason, the overuse of antibiotics in treatment of fish aquaculture (among other agricultural uses) could create public health issues. 
Bacterial mycophagy was a term coined in 2005, to describe the ability of some bacteria to "grow at the expense of living fungal hyphae".
In a 2007 review in the "New Phytologist" this definition was adapted to only include bacteria which play an active role in gaining nutrition from fungi, excluding those that feed off passive secretions by fungi, or off dead or damaged hyphae.
The majority of our knowledge in this area relates to interactions between bacteria and fungi in the soil and in or around plants, little is known about interactions in marine and freshwater habitats, or those occurring on or inside animals.
It is not known what affects bacterial mycophagy has on the fungal communities in nature.
There are three mechanisms by which bacteria feed on fungi; they either kill fungal cells, cause them to secrete more material out of their cells or enter into the cells to feed internally and they are categorised according to these habits.
Those that kill fungal cells are called nectrotrophs, the molecular mechanisms of this feeding are thought to overlap considerably with bacteria that feed on fungi after they have died naturally.
Necrotrophs may kill the fungi through digesting their cell wall or by producing toxins which kill fungi, such as tolaasin produced by "Pseudomonas tolaasii".
Both of these mechanisms may be required since fungal cell walls are highly complex, so require many different enzymes to degarde them, and because experiments demonstrate that bacteria that produce toxins cannot always infect fungi.
It is likely that these two systems act synergistically, with the toxins killing or inhibiting the fungi and exoenzymes degrading the cell wall and digesting the fungus.
Examples of necrotrophs include "Staphylococcus aureus" which feed on "Cryptococcus neoformans", "Aeromonas caviae" which feed on "Rhizoctonia solani", "Sclerotium rolfsii" and "Fusarium oxysporum", and some myxobacteria which feed on "Cochliobolus miyabeanus" and "Rhizoctonia solani".
Bacteria which manipulate fungi to produce more secretions which they in turn feed off are called extracellular biotrophs; many bacteria feed on fungal secretions, but do not interact directly with the fungi and these are called saprotrophs, rather than biotrophs.
Extracellular biotrophs could alter fungal physiology in three ways; they alter their development, the permeability of their membranes (including the efflux of nutrients) and their metabolism.
The precise signalling molecules that are used to achieve these changes are unknown, but it has been suggested that auxins (better known for their role as a plant hormone) and quorum sensing molecules may be involved.
Bacteria have been identified that manipulate fungi in these ways, for example mycorhizzal helper bacteria (MHBs) and "Pseudomonas putida", but it remains to be demonstrated whether the changes they make are cause are directly beneficial to the bacteria.
In the case of MHBs, which increase infection of plant roots by mycorrhizal fungi, they may benefit, because the fungi gain nutrition from the plant and in turn the fungi will secrete more sugars.
The third group, that enter into living fungal cells are called endocellular biotrophs.
Some of these are transmitted vertically whereas others are able to actively invade and subvert fungal cells.
The molecular interactions involved in these interactions are mostly unknown.
Many endocellular biotrophs, for example some "Burkholderia" species, belong to the β-proteobacteria which also contains species which live inside the cells of mammals and amoeba.
Some of them, for example "Candidatus" Glomeribacter gigasporarum, which colonises the spores of "Gigaspora margarita", have reduced genome sizes indicating that they have become entirely dependent on the metabolic functions of the fungal cells in which they live.
When all the endocellular bacteria inside "G. margarita" were removed, the fungus grew differently and was less fit, suggesting that some bacteria may also provide services to the fungi they live in. 
Lymphopoiesis can be viewed in a "mathematical" sense as a recursive process of cell division and also as a process of differentiation, measured by changes to the properties of cells.
Given that lymphocytes arise from specific types of limited stem cells - which we can call P (for Progenitor) cells - such cells can divide in several ways.
These are general principles of limited stem cells.
Considering the P as the ‘mother’ cell, but not a true stem cell, it may divide into two new cells, which are themselves identical, but differ to some degree from the mother.
Or the mother cell P may divide unequally into two new daughter cells both of which differ from each other and also from the mother.
Any daughter cell will usually have new specialized abilities and if it is able to divide it will form a new sub-lineage.
The difference of a daughter cell from the mother may be great, but it could also be much less, even subtle.
What the P mother cell does "not" do is divide into two new P mother cells or a mother and a daughter; this is a matter of observation as such limited progenitor cells are known to not self-renew.
There is a sort of exception when daughter cells at some level of the lineage may divide several times to form more seemingly identical cells, but then further differentiation and division will inevitably occur, until a final stage is reached in which no further division can occur and the cell type lineage is finally mature.
An example of maturity is a plasma cell, from the B cell lineage, which produces copious antibody, but cannot divide and eventually dies after a few days or weeks.
The progenitor CLP of the mouse or the progenitor MLP of the human differentiates into lymphocytes by first becoming a lymphoblast (Medical Immunology, p. 10).
It then divides several more times to become a prolymphocyte that has specific cell-surface markers unique to either a (1) T cell or (2) B cell.
The progenitor can also differentiate into (3) natural killer cells (NK) and (4) dendritic cells.
T Cells, B Cells and NK Cells (and all other Innate lymphoid cells) are unique to the lymphocyte family, but dendritic cells are not.
Dendritic cells of identical appearance but different markers are spread throughout the body, and come from either lymphoid and myeloid lineages, but these cells may have somewhat different tasks and may take up lodging preferentially in different locations.
(Revise in light of new research) This is now an open question; also, the different dendritic cell lineages may have different ‘tasks’ and stay in different ‘locations.’  T and B lymphocytes are indistinguishable histologically（that is, under a light microscope they cannot be told apart.）Indeed, the inactive B and T cells are so featureless with few cytoplasmic organelles and mostly inactive chromatin that until the 1960s textbooks could describe these cells, now the central focus of immunology, as having no known function!
!However T and B lymphocytes are very distinct cell lineages and they ‘grow up’ in different places in the body.
They perform quite different (although co-operative) functions in the body.
No evidence has ever been found that T and B cells can ever interconvert.
T and B cells are biochemically distinct and this is reflected in the differing markers and receptors they possess on their cell surfaces.
This seems to be true in all vertebrates, although there are many differences in the details between the species.
Regardless of whether the CLP (mouse) or MLP or a small closely related set of progenitor cells take credit for generating the profusion of lymphocytes, it remains an interesting observation that the same lymphoid progenitors can still opt to generate some cells that are clearly identifiably myeloid.