eChapters

The cornea is the anterior transparent part of the fibrous tunic of the globe which has both mechanical and optical function. It functions to support the intraocular contents and transmit and refract light. Histologically, the cornea is composed of an outer stratified squamous corneal epithelium and its basement membrane, an underlying collagenous stroma, a thin acellular membrane, and an inner monolayer of cells, the corneal endothelium. In dogs, the central cornea is thinner than the peripheral cornea, whereas regional differences in thickness may not exist in cats. The active pumping mechanism of corneal endothelium and the barrier function of anterior epithelium keep the cornea in a state of relative dehydration. Compromise of either of these mechanisms will allow corneal edema to develop, with a concomitant increase in corneal thickness. Corneal ulceration is one of the most common ophthalmic disorders in veterinary medicine. Corneal ulcers are classified based on depth and ease of healing. There are several phases during the corneal epithelial wound healing process, including a lag phase where cells alter their metabolic status; a migration phase to cover the bare surface; a proliferation phase and a differentiation phase, where cells stratify and re-establish multiple layers of distinct cells. Methods of surgical treatment for canine corneal ulcers include temporary tarsorrhaphy, third eyelid flap, conjunctival pedicle graft, tissue adhesive, corneo-scleral graft and transplantation of natural or synthetic material.

The liver is an organ that plays a central role in maintaining metabolic homeostasis, in its functions of metabolism, synthesis and storage of nutrients. The cells in the liver are parenchyma cells and non- parenchyma cells. The former include hepatocytes (80% of the cell population) and the later includes endothelial cells, Kupffer cells, lymphocytes and stellate cells. Liver dysfunction or failures are having different etiologies. Liver cancer has the fifth highest cancer incidence in the world, and is the third highest cause of cancer related deaths, with resection of the liver remaining the only curative option.

Following liver injury, the repair process involves two distinct phases: a regenerative phase, in which injured liver cells are replaced with regenerated hepatocytes; and a phase known as fibroplasia or fibrosis, in which connective tissue replace normal parenchyma tissue. The process even though initially beneficial becomes pathogenic when it is not controlled appropriately. Extensive accumulation of extra-cellular matrix (ECM) components ultimately leads to cirrhosis and liver failure. Thus, the ideal strategy to treat liver injury is to generate new hepatocytes replacing damaged cells without causing excessive ECM deposition.

Epididymal Total Sperm Count

The epididymal sperm is obtained as described above, incubated at 35°C, which is the optimum temperature of rat epididymal sperm. The epididymal f luid is then diluted to a volume of 5 mL of pre-warmed (32°C) the spermatozoa are counted by hemocytometer using the Improved Neubaur (Deep 1/10mm. LABART, Germany) chamber as described by Pant and Srivastava (2003).

Total viable cell/ml = (Average number of sperm per chamber) x 103 x (Dilution Factor)

Liveability and abnormal sperm

Per cent live spermatozoa is estimated by differential staining technique using Eosin-Nigrosin stain (NE) (Campbell et al., 1953). These slides are also used for estimating the per cent abnormal sperm morphologically on the basis of observable abnormalities of head, neck, mid-piece and trail region of the spermatozoa.

The percent live spermatozoa are determined adopting the differential staining technique using Eosin-Nigrosin stain.

• A drop of epididymal semen is taken on a clean, grease free pre warmed glass slide.

• 4-5 drops of Eosin-Nigrosine stain (1% Eosin and 5% Nigrosine in 3% sodium citrate dehydrate solution) is placed near the semen drop.

• Epididymal semen and stain are mixed gently using a blunt fine glass rod.

• After 30 seconds to 1 minute a thin smear is made on a clean, grease free glass slide.

• The smear is examined under oil immersion objective.

Abstract

The data for the present investigation were obtained from the performance records of 1081 crossbred cattle progeny of 65 sires maintained at Instructional Dairy Farm Nagla of G.B. Pant University of Agriculture & Technology Pantnagar, distributed over a period of 40 years from 1966-2005. A total of 65 sires were evaluated on the basis of single and multi traits of their progeny. For single trait sire evaluation, FLMY was considered as principal trait under univariate models viz- simple daughter’s average () method, least squares method (LSM), DFREML-I method and BLUP-I method. However, for evaluation of sires by multi traits FLMY+AFC, FLMY+FLP and FLMY+AFC+FLP, the multivariate models viz. DFREML-II, DFREML-III, DFREML-IV, BLUP-II, BLUP-III and BLUP-IV method were used. The lowest average breeding value (2616.25) for the trait was obtained by () method and the highest average breeding value (2660.42 kg) was obtained by the rest nine methods. The accuracy, efficiency and stability of different sire indices were compared to judge their effectiveness. The evaluation method that gave the lowest error variance was considered to be most efficient.

Origin of Species

A biological species is a group of reproductively isolated individuals

Speciation usually occurs via a branching process called cladogenesis

Divergent evolution can be allopatric, parapatric, or sympatric

Müntzing was able to re-create an allotetraploid species

Evolution can proceed gradually or be punctuated by periods of rapid change

12.1 Assays for molecular diagnosis of Acute Myeloid Leukaemia (AML)

Acute Myeloid Leukaemia (AML), also known as Acute Myelogenous Leukaemia or Acute Myeloblastic Leukaemia or Acute Granulocytic Leukaemia or Acute non Lymphocytic Leukaemia is an aggressive type of cancer which affects blood and bone marrow. AML is a heterogeneous disorder if one considers its clinical status, therapeutic responses and overall prognosis.¹ This disease called acute because it progresses very fast and myeloid as it originates from myeloid cell line in the bone marrow.

In bone marrow blood cells are made in a controlled way. When AML occurs excess numbers of immature leukaemia cells are produced. Overproduction of leukaemia cells in bone marrow disables bone marrow to make mature white blood cells. These accumulated immature cells are unable to function properly (Inability to fight infection).

Diagnosis: Correct diagnosis is important for a successive treatment for AML. There are several tests available to diagnose AML but not all tests will be used for each person. The following tests may be used to diagnose AML.

When Gene Expression Appears to Alter Mendelian Ratios Lethal Allele Combinations

Us recessive lethal alleles eliminaters a progeny class. Multiple Alleles

A gene can have more than two alleles, but a diploid individual only has one or two of them.

Different allele combinations can produce different phenotypes and different severities of symptoms.

Different Dominance Relationships

Incomplete dominance of an allele produces a phenotype in the heterozygote that is intermediate between that of either homozygote.

Codominant alleles are both expressed in a heterozygote. Epistasis-When One Gene Affects Expression of Another

In epistasis, one gene masks the effect of another. An example of epistasis in humans is the Bombay phenotype.

The Bombay phenotype results in O type blood for individuals homozygous recessive for the recessive “h” allele.

here are many methods for extracting DNA from gel apart from using commercial kits, some methods however yield cleaner DNA than others.

1. Freeze squeeze

Excise band and place pieces of it in a home-made spin-column (a piece of filter placed in a PCR 0.5ml eppendorf, pierced the bottom of the PCR tube with a needle). Place the PCR tube at -20 °C for 15-20 mins or freeze in liquid N2. Then place the PCR tube into the 1.5 ml eppendorf and spin at top speed in a microfuge for 15 mins, collect DNA solution which can be EtOH ppt or use directly.

2. Powdered silica

Melt excised bands at 70°C cool and add equal volume of TE-buffered phenol and mix. Spin for 5 min, remove aqueous phase, repeat and EtOh ppt. the DNA.

3. Electroelution

12.1 Introduction

The name was coined by George W. Snedecor, in honour of Sir Ronald A. Fisher. The object of the F-test is to find out whether the two independent estimates of population variance differ significantly or whether the two samples may be regarded as drawn from the normal populations having the same variance.

The F-test for the equality of two variances

Rationale

The two-sample t-test and the analysis of variance make the assumption of homoscedasticity, i.e. of equal variances in groups of data. The F-test, often called the variance ratio test, may be used to investigate the homoscedasticity of two data sets.

We have to make a decision whether or not the population variances are likely to be different. This means that we need a cut-off for the variance ratio; if the variance ratio exceeds this cut-off value, we will conclude that the variances are unequal.

We determine this cut-off value formally, under the null hypothesis that the two population variances are equal, by referring the ratio to the table of the F-distribution. The degrees of freedom are (n1 – 1) in the numerator (the larger variance) and (n2 – 1) in the denominator (the smaller variance), where n1 and n2 represent the two sample sizes.

For the required significance level in a two-tailed test, therefore, we must halve this tail area. So, for a two-tailed test at the 5% level of significance, we have to relate the test statistic to P = 0.025. For convenience, we give the upper percentage points corresponding to P = 0.025 and P = 0.005 (relating to two tailed P-values of 0.05 and 0.01, respectively) in separate tables.

A treatment is the combination of N & P

If levels of N & P are 5 & 10 respectively, so number of treatments are 5x10=50.

Animal husbandry is an integral component of Indian agriculture supporting livelihood of more than two-third of the rural population. The livestock sector plays a significant role in supplementing family incomes and generating gainful employment in the rural sector, besides providing cheap nutritional food to millions of people. Livestock provides milk, egg, meat as nutritious food, draught power for agriculture, wool, fibre, manure and domestic fuel, hides & skin. In 2010-11, this sector contributed 121.84 million tonnes of milk, 63.02 billion eggs, 42.99 million kg wool, and 4.83 million tonnes of meat. Milk is the main output of livestock sector accounting around two third (67%) of the total output by livestock sector. Meat and egg share 17.5% and 3.6% of the value of livestock output. Livestock contributed 4% to the total GDP and 26% to the agricultural GDP in 2010-11. Livestock are the best insurance against the vagaries of nature like drought, famine and other natural calamities.

Start with a 1:2 molar ratio of vector: insert DNA when cloning a fragment into a plasmid vector. This ratio will vary with other types of vectors, for example, cDNA and genomic cloning vectors. The following example illustrates the conversion of molar ratios to mass ratios for a 3.0kb plasmid and a 0.5kb insert DNA fragment.

Abstract

FASTA, which stands for “Fast All”, is a sequence alignment tool developed by William R. Pearson and David J. Lipman in 1985. It is commonly used to identify similarities between DNA and protein sequences. FASTA employs a “hashing” strategy to locate matches for short stretches of identical residues with a length of k, referred to as k-tuples or k-tups. This method enables FASTA to quickly search large databases for sequence similarities, making it a popular tool for identifying homologous sequences, predicting gene functions, and analyzing evolutionary relationships. This chapter elaborates some basics of FASTA.

Introduction
Fertilization is sequence of events that begins with contact between a sperm and an oocyte, resulting in fusion of two gametes and formation of a zygote (unicellular embryo). Site of fertilization is distal end of ampulla of fallopian tube (ampulla-isthmus junction) in mammals and in birds, is infundibulum. Only 1% of sperms deposited in vagina enter cervix. Movement of sperm from cervix to uterine tube occurs by muscular contractions of uterus & uterine tube and by their own propulsion. Immediately after ovulation, ovum is caught by the fimbriae of the infundibular part of oviduct and is brought to the ampulla.Cilia along epithelium of oviduct moves OCc. In farm animals (except swine) corona radiata cells drop off in ampulla. In swine, they persist and help in attachment of ova to each other in forming egg-clumps. The optimum fertilizable life of egg in most mammals is 12-24 hours after ovulation, but in dog it may extend up to 4 days.
Site of ejaculation is
Cow, primates, sheep, goat: Anterior vagina
Horse, pig: Body of uterus
Capacitation
Spermatozoa are not able to fertilize the oocyte immediately after arrival in female genital tract. To acquire fertility, they must reside there for a certain period of time. The changes that occur during this period constitute capacitation. Ejaculated spermatozoa must be exposed to secretions of female reproductive tract for a variable period of time before they attain capacity to fertilize oocyte. The secretions of uterus & oviduct participate in capacitation. Important processes during capacitation are: 1. Surface of spermatozoa in region of epididymis acquires certain molecules (proteins & carbohydrates in nature) and in seminal plasma, these molecules are masked by surface proteins. In female reproductive tract, these molecules along with surface proteins are removed. Removal of cholesterol and GAGs sperm cell surface.

13.1 Biosafety Research Trials: Scope and Implementation
Introduction
Biosafety research trials serve as a critical phase in the evaluation and regulation of genetically modified organisms (GMOs), particularly transgenic crops and microorganisms. These trials assess potential environmental and health impacts under confined and controlled conditions before the organism can be considered for commercial release. With the expansion of biotechnology applications, especially in agriculture, pharmaceuticals, and industrial processes, the need for scientifically rigorous and ethically sound biosafety research trials has become increasingly important.
13.1.1. Scope of Biosafety Research Trials
1.1. Definition and Objectives
Biosafety research trials are confined, stepwise, and monitored field or laboratory-based studies designed to evaluate the safety, stability, performance, and unintended effects of GMOs. The overarching objectives include:
• Assessment of potential risks to human health, non-target organisms, and the environment.
• Evaluation of gene stability, trait expression, and environmental adaptability.
• Monitoring of gene flow and potential invasiveness or weediness.
• Determination of agronomic efficacy under field conditions.
• Data generation for regulatory dossiers and risk assessment reports.

A TTO needs a planned budget of five years to sustain it in the long term. This involves budgeting the infrastructure, manpower, research, and outreach programs. The budgetary needs of a TTO will be based on the size and scope of the TTO and the maturity of the parent institution it caters to. The initial years will be focused on capacity development, the appointment of experts, and the establishment of processes of intellectual property management. The mature TTO will generate income through the returns of the licensing agreements and the collaborative efforts with the industry. Nevertheless, external funding through grants and government schemes plays a vital part, particularly in the initial years. The planned budget ensures long-term stability and development of the TTO.
9.1 Budgetary heads
9.1.1 Operational expenditure
Operational expenditure refers to the ongoing costs incurred by a TTO to maintain its day-to-day operations. This includes the cost of maintaining the office, including rent, power and utility bills, computer and network infrastructure, patent management cost, and administration charges. The filing and legal charges also fall within this category. The overheads will be a heavy burden if not planned with finances properly. A TTO has to be provided with a properly planned operational budget that covers the daily operational expenses. The operational expenses help the office perform effectively, sustain the employees, and effectively manage IP. The operational expenses that the budget normally covers include:

Functional Genomics

• Expressed genes can be identified in a cDNA library
• A microarray can identify genes that are transcribed
• The coordinate regulation of many genes is revealed by a DNA microarray analysis

Proteomics

The proteome is much larger than the genome

2D gel electrophoresis is used to separate a mixture of cellular proteins

Mass spectrometry is used to identify proteins

Protein microarrays can be used to study protein expression and function

Artificial intelligence offers practical solutions to agricultural problems associated with population growth, food demand, climate change and limited natural resources. This chapter introduces machine learning, deep learning, computer vision and natural language processing, together with enabling technologies such as IoT, remote sensing and cloud computing. It explains their applications in crop monitoring, disease recognition, yield forecasting, irrigation, soil assessment and livestock management. AI can improve decision-making, resource efficiency, automation and precision farming while reducing reliance on manual labour. The chapter also examines adoption barriers, including high costs, limited digital literacy, data-security concerns and weak rural infrastructure, and considers future developments in autonomous and climate-resilient farming.

7.1 Definitions and Classifications of Biohazards
7.1.1 Definition of Biohazards
Biohazards, or biological hazards, refer to biological substances that pose a threat to the health of living organisms, primarily humans, animals, and plants. These substances include a broad spectrum of infectious agents such as bacteria, viruses, fungi, protozoa, parasites, recombinant or synthetic nucleic acid molecules, genetically modified organisms (GMOs), and biological toxins. Biohazards can arise from research laboratories, agricultural practices, biotechnology industries, healthcare settings, or naturally occurring infectious diseases.
In biotechnology and molecular biology, biohazards are particularly significant due to the frequent use of genetically modified microbes, transgenic plants and animals, and gene-editing tools that may unintentionally cause ecological disturbances or health risks if not properly contained and managed.
7.1.2 Understanding Biosafety in the Context of Biohazards
Biosafety is the application of containment principles, facility design, practices, and procedures to prevent unintentional exposure to biohazards or their accidental release. It forms the foundational pillar in laboratories and institutions engaged in biotechnology, genetic engineering, and molecular biology.
The goal of biosafety is twofold
• To protect laboratory personnel, the community, and the environment from potential harm caused by biological agents.