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Immunology, Serology and Parasitology – II
1. Explain the structure and replication of viriods
Taguchi's use of loss functions
Taguchi knew statistical theory mainly from the followers of Ronald A. Fisher, who also avoided loss
functions. Reacting to Fisher's methods in the design of experiments, Taguchi interpreted Fisher's
methods as being adapted for seeking to improve the mean outcome of a process. Indeed, Fisher's work
had been largely motivated by programmes to compare agricultural yields under different treatments and
blocks, and such experiments were done as part of a long-term programme to improve harvests.
However, Taguchi realised that in much industrial production, there is a need to produce an outcome on
target, for example, to machine a hole to a specified diameter, or to manufacture a cell to produce a
given voltage. He also realised, as had Walter A. Shewhart and others before him, that excessive
variation lay at the root of poor manufactured quality and that reacting to individual items inside and
outside specification was counterproductive.
He therefore argued that quality engineering should start with an understanding of quality costs in various
situations. In much conventional industrial engineering, the quality costs are simply represented by the
number of items outside specification multiplied by the cost of rework or scrap. However, Taguchi insisted
that manufacturers broaden their horizons to consider cost to society. Though the short-term costs may
simply be those of non-conformance, any item manufactured away from nominal would result in some
loss to the customer or the wider community through early wear-out; difficulties in interfacing with other
parts, themselves probably wide of nominal; or the need to build in safety margins. These losses
are externalities and are usually ignored by manufacturers, which are more interested in their private
costs than social costs. Such externalities prevent markets from operating efficiently, according to
analyses of public economics. Taguchi argued that such losses would inevitably find their way back to the
originating corporation (in an effect similar to the tragedy of the commons), and that by working to
minimise them, manufacturers would enhance brand reputation, win markets and generate profits.
Such losses are, of course, very small when an item is near to negligible. Donald J.
Wheeler characterised the region within specification limits as where we deny that losses exist. As we
diverge from nominal, losses grow until the point where losses are too great to deny and the specification
limit is drawn. All these losses are, as W. Edwards Deming would describe them, unknown and
unknowable, but Taguchi wanted to find a useful way of representing them statistically. Taguchi specified
three situations:
1. Larger the better (for example, agricultural yield);
2. Smaller the better (for example, carbon dioxide emissions); and
3. On-target, minimum-variation (for example, a mating part in an assembly).
The first two cases are represented by simple monotonic loss functions. In the third case, Taguchi
adopted a squared-error loss function for several reasons:

It is the first "symmetric" term in the Taylor series expansion of real analytic loss-functions.

Total loss is measured by the variance. For uncorrelated random variables, as variance is additive
the total loss is an additive measurement of cost.

The squared-error loss function is widely used in statistics, following Gauss's use of the squared-error
loss function in justifying the method of least squares.
2. Describe the mechanism of lysogeny.
Lysogeny broth (LB), a nutritionally rich medium, is primarily used for the growth of bacteria. The
acronym has been incorrectly interpreted as Luria broth,Lennox broth, or Luria-Bertani medium;
according to its creator Giuseppe Bertani, the abbreviation LB was actually intended to stand
for lysogeny broth.[1]The formula of the LB medium was published in 1951 in the first paper of Bertani
on lysogeny. In this article he described the modified single-burst experimentand the isolation of the
phages P1, P2, and P3. He had developed the LB medium to optimize Shigella growth and plaque
formation.[1][2]
LB media formulations have been an industry standard for the cultivation of Escherichia coli as far back
as the 1950s.[3][4][5][6][7] These media have been widely used in molecular microbiology applications for the
preparation of plasmid DNA and recombinant proteins. It continues to be one of the most common media
used for maintaining and cultivating laboratory recombinant strains of Escherichia coli.[8] For physiological
studies however, the use of LB medium is to be discouraged.[9]
There are several common formulations of LB. Although they are different, they generally share a
somewhat similar composition of ingredients used to promote growth, including the following:

Peptides and casein peptones

Vitamins (including B vitamins)

Trace elements (e.g. nitrogen, sulfur, magnesium)

Minerals
Peptides and peptones are provided by tryptone. Vitamins and certain trace elements are provided by
yeast extract. Sodium ions for transport and osmotic balance are provided by sodium chloride. Bactotryptone is used to provide essential amino acids to the growing bacteria, while the bacto-yeast extract is
used to provide a plethora of organic compounds helpful for bacterial growth.
In his original 1951 paper, Bertani used 10 grams of NaCl and 1 gram of glucose per 1 L of solution; Luria
in his "L broth" of 1957 copied Bertani's original recipe exactly. [6] Recipes published later have typically
left out the glucose.
3. Write a note on numerical taxonomy .
Numerical taxonomy is a classification system in biological systematics which deals with the grouping
by numerical methods of taxonomic units based on their character states.[1]. It aims to create
a taxonomy using numeric algorithms like cluster analysis rather than using subjective evaluation of their
properties. The concept was first developed by Robert R. Sokal & Peter H. A. Sneath in 1963[2]and later
elaborated by the same authors[3]. They divided the field into phenetics in which classifications are formed
based on the patterns of overall similarities and cladistics in which classifications based on the branching
patterns of the estimated evolutionary history of the taxa. Note: in recent years many authors treat
numerical taxonomy and phenetics as synonyms despite the distinctions made by those authors.
Although intended as an objective classification method, in practice the choice and implicit weighing of
characteristics is, of course, influenced by available data and research interests of the investigator. What
was made objective was the introduction of explicit steps to be used to create phenograms and
cladograms using numerical methods rather than subjective synthesis of data.
Taxonomy is the science dealing with description, identification, nomenclature, and
classification of living things.
A dichotomous key is a tool that allows users to identify items or organisms in a systematic and
reproducible fashion. Dichotomous keys may be used in a variety of situations, such as for
identifying rocks and minerals as well as for identifying unknown organisms to some taxonomic
level (e.g., species, genus, family, etc.). What makes these keys distinctive is that they are
ordered in such a way that a series of choices is made that leads the user to the correct identity
of the item they are looking at. "Dichotomous" means, "divided into two parts." Therefore,
dichotomous keys always offer two choices for each step, each of which describes key
characteristics of a particular organism or group of organisms.
4. Write an account on media used for microbial assay.
biological assay bioassay.
CH50 assay a test of total complement activity as the capacity of serum to lyse a standard preparation of
sheep red blood cells coated with antisheep erythrocyte antibody. The reciprocal of the dilution of serum
that lyses 50 per cent of the erythrocytes is the whole complement titer in CH50 units per milliliter of
serum.
enzyme-linked immunosorbent assay see ELISA.
microbiological assay assay by the use of microorganisms.
microcytotoxicity assay one using the pattern of lysis of peripheral blood lymphocytes in the presence
of complement and typing sera to type serologically defined HLA antigens (HLA-A, -B, and -C antigens).
radioimmunoprecipitation assay (RIPA) immunoprecipitation conducted with radiolabeled antibody or
antigen.
radioligand assay any assay procedure that uses radioisotopic labeling and biologically specific binding
of reagents.
stem cell assay a measurement of the potency of antineoplastic drugs, based on their ability to retard
the growth of cultures of human tumor cells.
5. Describe thallus organization in fungi.
The discipline of biology devoted to the study of fungi is known as mycology, which is often regarded as
a branch of botany, even though genetic studies have shown that fungi are more closely related to
animals than to plants.
Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and
their cryptic lifestyles in soil, on dead matter, and as symbionts of plants, animals, or other fungi. They
may become noticeable when fruiting, either as mushrooms or molds. Fungi perform an essential role in
the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange. They
have long been used as a direct source of food, such as mushrooms and truffles, as a leavening agent for
bread, and in fermentation of various food products, such as wine,beer, and soy sauce. Since the 1940s,
fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by
fungi are used industrially and in detergents. Fungi are also used as biological pesticides to control
weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins,
such as alkaloids and polyketides, that are toxic to animals including humans. The fruiting structures of a
few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual
ceremonies. Fungi can break down manufactured materials and buildings, and become
significant pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g. rice
blast disease) or food spoilage can have a large impact on human food supplies and local economies.
The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life
cycle strategies, and morphologies ranging from single-celled aquatic chytrids to large mushrooms.
However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at around
1.5 million species, with about 5% of these having been formally classified.[citation needed] Ever since the
pioneering 18th and 19th centurytaxonomical works of Carl Linnaeus, Christian Hendrik Persoon,
and Elias Magnus Fries, fungi have been classified according to their morphology (e.g., characteristics
such as spore color or microscopic features) or physiology. Advances in molecular genetics have opened
the way for DNA analysis to be incorporated into taxonomy, which has sometimes challenged the
historical groupings based on morphology and other traits.Phylogenetic studies published in the last
decade have helped reshape the classification of Kingdom Fungi, which is divided into one subkingdom,
seven phyla, and ten subphyla.
6. Explain the structure and reproduction in rickettsia.
Bacteria in the genus Rickettsia are intracellular symbionts of disparate groups of
organisms. Some Rickettsia strains infect vertebrate animals and plants, where they
cause diseases, but most strains are vertically inherited symbionts of invertebrates. In
insects Rickettsia symbionts are known to have diverse effects on hosts ranging from
influencing host fitness to manipulating reproduction. Here we provide evidence that
a Rickettsia symbiont causes thelytokous parthenogenesis (in which mothers produce
only daughters from unfertilized eggs) in a parasitoid wasp, Pnigalio
soemius (Hymenoptera: Eulophidae). Feeding antibiotics to thelytokous female wasps
resulted in production of progeny that were almost all males. Cloning and sequencing of
a fragment of the 16S rRNA gene amplified with universal primers, diagnostic PCR
screening of symbiont lineages associated with manipulation of reproduction, and
fluorescence in situhybridization (FISH) revealed that Rickettsia is always associated with
thelytokousP. soemius and that no other bacteria that manipulate reproduction are
present. Molecular analyses and FISH showed that Rickettsia is distributed in the
reproductive tissues and is transovarially transmitted from mothers to offspring.
Comparison of antibiotic-treated females and untreated females showed that infection
had no cost. Phylogenetic analyses of 16S rRNA and gltA gene sequences placed the
symbiont of P. soemius in the bellii group and indicated that there have been two
separate origins of the parthenogenesis-inducing phenotype in the genus Rickettsia. A
possible route for evolution of induction of parthenogenesis in the two distantly
related Rickettsia lineages is discussed.
7. Describe the methods used for measuring microbial growth and discuss their significance.
Bacterial growth is the division of one bacterium into two daughter cells in a process called binary
fission. Providing no mutational event occurs the resulting daughter cells are genetically identical to the
original cell. Hence, "local doubling" of the bacterial population occurs. Both daughter cells from the
division do not necessarily survive. However, if the number surviving exceeds unity on average, the
bacterial population undergoes exponential growth. The measurement of an exponential bacterial growth
curve in batch culture was traditionally a part of the training of all microbiologists; the basic means
requires bacterial enumeration (cell counting) by direct and individual (microscopic, flow cytometry[1]),
direct and bulk (biomass), indirect and individual (colony counting), or indirect and bulk (most probable
number, turbidity, nutrient uptake) methods. Models reconcile theory with the measurements. [2] This basic
batch culture growth model draws out and emphasizes aspects of bacterial growth which may differ from
the growth of macrofauna. It emphasizes clonality, asexual binary division, the short development time
relative to replication itself, the seemingly low death rate, the need to move from a dormant state to a
reproductive state or to condition the media, and finally, the tendency of lab adapted strains to exhaust
their nutrients.
In reality, even in batch culture, the four phases are not well defined. The cells do not reproduce in
synchrony without explicit and continual prompting (as in experiments with stalked bacteria [5]) and their
exponential phase growth is often not ever a constant rate, but instead a slowly decaying rate, a constant
stochastic response to pressures both to reproduce and to go dormant in the face of declining nutrient
concentrations and increasing waste concentrations.
Batch culture is the most common laboratory growth method in which bacterial growth is studied, but it is
only one of many. It is ideally spatially unstructured and temporally structured. The bacterial culture is
incubated in a closed vessel with a single batch of medium. In some experimental regimes, some of the
bacterial culture is periodically removed and added to fresh sterile medium. In the extreme case, this
leads to the continual renewal of the nutrients. This is a chemostat, also known as continuous culture. It is
ideally spatially unstructured and temporally unstructured, in a steady state defined by the rates of
nutrient supply and bacterial growth. In comparison to batch culture, bacteria are maintained in
exponential growth phase, and the growth rate of the bacteria is known. Related devices
include turbidostats and auxostats.
Bacterial growth can be suppressed with bacteriostats, without necessarily killing the bacteria. In
a synecological, true-to-nature situation in which more than one bacterial species is present, the growth of
microbes is more dynamic and continual.
8. Describe in brief the classification of bacteria according to Bergy's manual of systematic
bacteriology.