eChapters

7.1 Introduction

There are numerous wavelength dependent phenomena that may be used to modulate the wavelength of incident light source. These are wavelength dependent absorption, luminescence, dispersion, interference and scattering. Wavelength modulated sensors use a broadband source, a wavelength modulator or measurand (i.e. analyte), a form of spectrometer (using prisms, gratings or interference filters), a detector (single photodiode or array) and signal processing unit. Silicon photodiode is cheap and can be used for detection but it limits the detection wavelengths to the region 400 to 1050 nm. The sensitivity or the resolution of the wavelength modulated sensor depends on the characteristics of the detector, the inherent resolution of the spectrometer, mechanical stability of the modulation unit and the spectrometer, and the capability of the signal processing unit. However, wavelength modulated sensors do not require any form of referencing like intensity modulated sensors. In intensity modulated sensors, loss in intensity occurs due to connectors and splices, microbending, mechanical creep and misalignment of light sources and detectors due to environmental effect. Further the fluctuations in light source can affect the performance of the sensor. Thus, for intensity modulated sensors one needs referencing to cancel out these losses. In some intensity modulated sensors two wavelengths are used. One wavelength is used to cancel out all of the losses while the second is used to sense the measurand.

Wavelength detection is relatively easy if the spectral changes result from changes in chemical indicator dyes, fluorescence, phosphorescence, or black-body radiation. In these cases the incident and emitted wavelengths are far apart and therefore detection is easy. If the spectral change occurs due to mechanical movement, then the wavelength filtering mechanisms must have sufficient resolvable spectral points. The reasons for using fluorescence in the fiber optic sensors are well known. Fluorescence is intrinsically more sensitive than absorbance and is more flexible in that a great variety of analytes and physical parameters are known to change the emission of particular fluorophores. The fluorescence based sensors utilize the change in the intensity, lifetime or colour of fluorescence as the affected parameter by the measurand. That means, any interpretable observation of fluorescence can be made the basis of a sensor. In this chapter we shall first describe luminescence phenomenon and then various physical and chemical fiber optic sensors based on wavelength modulation and fluorescence phenomenon.

6.1 Introduction

There are a variety of intrinsic and extrinsic fiber-optic sensors which use absorption spectroscopy indirectly for the detection of various chemical species. These include pH, metal ions, oxygen in water etc. In such sensors a suitable reagent is immobilized on a solid support. The support can be the core of the fiber or some optical material attached at the end of the fiber. Further it is optically transparent to allow transmission of the light signal from the interface and should remain inert to the chemical reaction being analyzed. The analyte (or the chemical species) when comes in contact of the reagent affects the absorption properties of the reagent. In other words, in these sensors, the reagent acts as a chemical transducer for analytes that are not directly measurable by optical techniques. Following conditions for the use of reagents in sensors must be met:

5.1 Introduction

Evanescent field absorption spectroscopy is a powerful well-established laboratory technique for chemical analysis. The technique utilizes the evanescent wave penetration at the boundary between two dielectric media in conditions of attenuated total reflection (ATR). One of the media, a thin slab-shaped non-absorbing crystal, is called a waveguide, while the other medium of lower refractive index is the absorbing sample being studied. At each reflection at the boundary of the crystal and the sample, the penetration of the evanescent wave of the guided ray into the absorbing sample gives rise to a reduction of the power propagating in the crystal. The degree of absorption depends on the amplitude of the evanescent field in the sample medium and the number of reflections within the waveguide. The former increases dramatically for incident angles approaching the crystal-sample critical angle while the latter increases with the decrease in the thickness of the waveguide. The number of reflections can also be increased by increasing the length of the waveguide. Thus, to achieve maximum absorption, an unclad optical fiber is well suited for evanescent wave absorption spectroscopy. This is because, unlike the crystal waveguide, the narrow core diameter of the fiber provides a large number of reflections per unit length. Further, the use of an optical fiber to transmit light to a section of its core in contact with an absorbing sample offers the possibility of remote sensing or in-line analysis. These advantages, together with the benefits of simplicity, reliability, flexibility and relatively low cost have motivated a number of research groups all over the world to investigate evanescent wave spectroscopy at the surface of an unclad optical fiber. This chapter will be devoted to the fiber optic sensors utilizing evanescent field absorption spectroscopy.

4.1 Introduction

Apart from an optical source, the optical detector is another important component of the optical fiber sensor. The optical detector converts the optical signal to an electrical one. The signal is then processed either to record or display. There are various kinds of optical detectors but the commonly used in sensors are semiconductor diodes. In some of the cases photomultiplier tube has been used. In this chapter we shall describe the basic principles of optical detectors and their operational characteristics.

3.1 Introduction

Optical sources are a key element in many fiber optic systems. This component converts the electrical signal into a corresponding light signal that can be injected into the fiber. Several factors such as wavelength, source output and spectral bandwidth are important when selecting light source to achieve the best performance of the sensor. The optical sources used for sensors range from hot filament lamps to semiconductor lasers. These sources can be placed into two groups - incoherent and coherent sources. The tungsten lamp and light-emitting diode (LED) are some of the incoherent sources while the lasers come in the category of coherent sources. The LED is normally preferred if the multimode fiber is used for the sensor. If the optical power requirement is high then the laser with multimode optical fiber is used. For the sensors based on interference phenomenon, coherent sources with single mode fibers are used. In the case of distributed sensing, short pulse high power lasers are used. In a laboratory demonstration experiment, a visible laser such as a simple He-Ne laser may be the preferred source while in commercial applications a compact and rugged source such as laser diode or an LED is preferred. Before using the source it is very essential to know its maximum power output, wavelength of emission, linewidth, radiation pattern and modulation bandwidth. The purpose of this chapter is to provide the physics of some of the light sources and their important operating characteristics that are used in sensors.

2.1 Introduction

In a fiber optic sensor the heart of the sensor is an optical fiber. An optical fiber in its simplest form is a cylindrical symmetric structure consisting of a central ‘core’ glass/plastic of uniform refractive index and of diameter 4-600 µm. It is surrounded by a ‘cladding’ glass/plastic of slightly lower refractive index. To provide the mechanical and environmental protection to the fiber, the cladding is covered with an external plastic coating (seeFig. 2.1). The light in the fiber propagates by bouncing back and forth from the core-cladding interface. The design of the fiber optic sensor depends critically on the choice of optical fiber. Telecommunication fibers are inexpensive but may not be the right choice for sensors. Some of the fiber optic sensors dictate the use of application-specific optical fibers. In this chapter we shall first describe ray analysis for the light propagation in the fiber. The modes propagation, numerical aperture of the fiber, fiber characteristics and different kinds of optical fibers used for sensing will be described later.

1.1 Introduction

Since 1990s optoelectronics and fiber optics technology underwent significant advances due to innovations in the telecommunications, semiconductor and consumer electronics sectors. The developments of compact disk (CD) players, laser printers and the high performance and reliable optical fiber communication are the result of these advances. The optical fiber sensor technology is a direct outgrowth of the revolutions taken place in optoelectronics and fiber optic communication industries. Many of the components associated with these industries are used for optical fiber sensor applications. In the beginning the main hurdle in the development of sensors was the cost of components such as optical sources and detectors. With the time, components prices are falling and the improvements in fiber, laser and photodetector technology have taken place. It is expected that as the time progresses the optical fiber sensors will replace the conventional devices for the measurements of various physical, chemical and biological parameters such as rotation, acceleration, electric and magnetic fields, temperature, pressure, acoustics, vibration, position, strain, humidity, viscosity, pH, glucose, heavy metals, gases, viral infection, pollutants etc.

Globally livestock sector is changing rapidly in response to globalization and increasing demand for quality foods of animal origin. Animal husbandry is the backbone of rural economy of our country. The value of output from livestock sector is about 29 percent of the total value of output (GDP) of the agriculture and allied sectors. The livestock sector has been contributing over 5% to total GDP. India ranks first in milk production which accounts for more than 15 percent of total world output and 40 percent of Asia’s total production. It continues to grow at about 4 percent per annum far exceeding the global average of 1-2 percent. Further, the manure from animals provides a good source of organic matter for improving soil fertility and crop yields. The gobar gas from the dung is used as fuel for domestic purposes. The surplus fodder and agricultural by-products are gainfully utilized for feeding the animals. Almost all draught power for farm operations and transportation is supplied by bullocks. Indian animal husbandry practices are based on minimal use of off-farm inputs and on management practices that restore, maintain and enhance ecological harmony. This principle also holds good for organic farming. The primary goal of organic agriculture is to optimize the health and productivity of interdependent communities of soil life, plants, animals and people (NOSB, 1995). Organic agriculture is an ecological production management system that promotes and enhances biodiversity, biological cycles and soil biological activity.

The biotic component of earth is continuously and significantly affected by the abiotic components. Physical factors of the environment (temperature, humidity, rainfall, wind, solar radiation, light, atmospheric pressure, etc) surrounding the animal have influence on the production, reproduction and welfare of the animal. Livestock performance is best when environmental factors are optimum which is difficult to achieve due its variable nature. To this complex livestock-climate interaction, animal responds favorably by undergoing ‘adaptation’ or unfavorably by being under ‘stress’. Type and magnitude of stress due to physical environment depends on climatic factors of a particular area, animal adaptability, breed characteristics and managemental interventions by humans to minimize the losses. To understand the physical environment of livestock frequently used terms are mentioned below

Poultry sector in India has grown from a backyard activity into a major commercial activity in four and half decades. Poultry is one of the fastest growing subsectors of agricultural sector in India. Within the poultry sector, broiler production is growing faster than egg production and about 66.7% of the total output (in value term) comes from the poultry meat sector and only 33.3% from egg production (FAO, 2008). India ranks fifth in chicken and sixth in duck population. Presently, India is world’s third largest egg producer and the fifth major producer of chicken meat (FAO, 2010). Poultry is today the major source of meat in India. As per an estimate about 2 million people are employed, fully or partly, along the poultry value chain and that an increase in annual per caput availability of one egg or 50 gm or poultry meat generates about 20,000 to 25,000 full time jobs (Ciamarra & Otte, 2009). Distribution of chicken and duck population as well as poultry meat and egg production among different regions, countries of the world and among different Indian states has been already discussed in chapter one of this book.

Origin and Distribution of Camel

A camel is an even-toed ungulate within the genus Camelus of the family Camelidae bearing distinctive fatty deposits known as “humps” on its back. There are two species of camel, viz. Camelus dromedarius (single humped dromedary) having habitat in dry hot arid lands of Africa and Asia, and Camelus bacterianus (double humped or bactrian) habitat of cold arid lands of Central palaerctic (a zoogeographical region consisting of Europe, Africa north of the Sahara, and most of Asia north of the Himalayas) region. Family Camelidae also includes other species which are camel like mammals. Those are Lama (Lama glama), Alpaca (Lama pacos), Vicuna (Vicugna vicugna) and Guanaco (Lama guanicoe). These four species are termed as new-world Camelidae having habitat in South America. The Indian camel belongs to Camelus dromedarius. A very small numbers of double-humped camels are also available in Ladakh area of Jammu and Kashmir.

Camel is an important component of desert eco-system. It is capable of traveling long distance in hot, arid and sandy regions carrying men, material and providing energy to agricultural operations. They provide milk, meat, hair and used as work animals. It is believed that Camels were domesticated during the period from 3000 to 2500 BC. Average life expectancy of a camel is 40-50 years. The height at the shoulder and hump of a fully grown adult camel is 1.85 and 2.15 metres, respectively. Camel can run at a speed of up to 65km/h for a short distance and can sustain a speed of up to 40km/h for long distance.

Equines are herbivorous monogastric animals. Though, simple-stomached, they can digest considerable amount of fibrous feed in the caecum and are called as hindgut fermenters. Equine includes horse, donkey, zebra and mule which are used as work and pack animal. All three species of equine belongs to the family Equidae. The scientific name of Horse and Donkey is Equus caballus and Equus asinus, respectively. The horse was probably last farm animal domesticated by the man. Horses appear to have been domesticated first in central Asia or Persia, more than 3000 years ago.

The group of animals constantly used in laboratories for general research in all discipline of science is called as laboratory animals. Commonly, it includes rats, mice, rabbits and guinea pigs. However, under certain circumstances, additional animal species like hamsters, non-human primates, amphibians, fowl, sheep and pigs can also be included. This term incorporates traditional laboratory animals, farm animals, wildlife and aquatic animals. Nontraditional animals, inclusive of invertebrate species are also included where they are relevant to the unit’s mission. Generally, these animals come under vertebrate but broadly laboratory animals may be classified in two major groups i.e. laboratory mammals and non-mammalian laboratory animals. The laboratory mammals include mouse, rat, guinea pig, rabbit, cat, dog, ferret, gerbil, bats, hamster, mink and monkey (Rhesus). Beside these mammalians the large domestic animals/livestock are also used as laboratory animals (horse, cow, sheep, goat etc) for fulfilling the demands of various laboratories. Poultry is also used as non-mammalian laboratory animals and Specific Pathogen Free (SPF) chicks are at utmost demand for production and testing of biologicals. The other non-mammalian laboratory animals includes reptiles (tortoise, lizzards and snakes), insects (cockroach, drosophila, house fly, house cricket, locusts, tsetse fly, stablefly etc) pisces (fishes and snails) and amphibians (toad and frog). Laboratory animals have been used extensively for basic research in drug and bacteria screening, toxicology, antibiotic sensitivity testing, animal models of diseases and production/testing of biologicals. Laboratory mammals are also valuable for diagnosis of infectious diseases in man and domestic animals. In this chapter the most commonly used laboratory animals i.e. mice, rats, guinea pigs and rabbits will be discussed.

Origin and Domestication of Pigs

Pigs are nonruminant, even-toed ungulates and belong to suborder Suina which includes hippopotamuses, peccaries and pigs. All true pigs are members of the family Suidae which includes five living genera namely Sus, Babirousa (babyrusa), Hylochoerus (giant forest hog), Phacochoerus (warthog), and Potamochoerus (bushpig and red river hog) that can be called as pigs. European breeds are believed to be descendants of the European wild pig Sus scrofa and Asiatic or oriental breeds originated from the Eastern Asiatic banded pig, Sus vittatus a successor of Sus crystatus.

Origin and Domestication of Sheep

The domesticated sheep belongs to phylum-Chordata, class-Mammalia, order- Artiodactyla, family - Bovidae, sub-family - Caprinae, genus - Ovis and species- aries. They are hollow horned, cloven-hoofed ruminants of relatively smaller size. Sheep plays an important role in Indian agrarian economy as it is having multi facet utilities like meat, wool, skin, manure and to some extent milk and transport also. Marginal and sub-marginal lands of arid and semi-arid tropics are well adapted by sheep. Among the different wild species, Asiatic (Ovis orientalis) species of mouflon is considered to be the ancestor of present day sheep. Sheep were domesticated by man at around 9000 BC. The reference of role of sheep in the economy of mankind is found in the history of civilization of Mesopotamia, Mohen-jo-Daro and Harappa in Northern India.

Origin and Domestication of Goat

Goat is a cloven-hoofed, hollow-horned ruminant which is comparatively smaller in size and belongs to class Mammalia, order Artiodactyla, family Bovidae and genus either Capra (2N=60) or Hemitragus/tahrs (2N=48). The distinction between these two genera was previously based on horn structure but the distinction has been confirmed genetically. The domestic goat (Capra hircus/Capra aegagrus hircus) belongs to the genus Capra and has possibly developed from five wild ancestors. On the basis of available information, it is most likely that bezoar is the main ancestor of most domestic goats. However, there is slight likelihood that Markhor has been involved in the parentage of some of the Indian goat breeds.

Evolutionary biology indicates that domestication of goats started during Neolithic age and it was perhaps the first ruminant and first animal after dog to be domesticated by the man around 9000-7000 BC. Domestication was associated with three of the oldest civilizations namely- (i) the Nile in northeast Africa, (ii) the Tigris-Euphrates in west Asia, and (iii) the Indus in the Indian subcontinent. Archaeologists indicate that the goat was first domesticated in the “Fertile Crescent” (landmass which extends between the Black and Caspian seas along the coast of Palestine and forms arc like a quarter moon towards the Persian Gulf) of the eastern Mediterranean. Since their domestication, goats remained associated with variety of functions in various aspects of human life including food, employment, economics, folklore and religion.

Origin & Distribution of Cattle

All types of domestic cattle belongs to class Mammalia, subclass Ungulata, order Artiodactyla, suborder Ruminantia, family Bovidae, subfamily Bovinae, tribe Bovini, which includes genus Bos. The aurochs or urus (Bos primigenius) is the probable ancestor of most of the present day Bos taurus and Bos indicus cattle. The humped Bos primigenius namadicus were the forerunner of today’s zebu cattle while humpless Bos primigenius primigenius gave rise to modern European cattle. Both category of cattle possess the same number of chromosomes (2N=60). Other related animals in the Bovini tribe include the gaur cattle (Bos gaurus), banteng (Bos banteng), kouprey (Bos sauveli) of South and East Asia, bison (Bison bison) of North America, European bison (Bison bonasus) and the yak (Poephagus mutus) of central Asia. According to Payne & Hodges (1997), domestication of aurochs (Bos primigenius ) took place first probably on the lower mountain slopes in the region of western Asia known as the ‘fertile crescent’. They suggested that the first domestic cattle were humpless (Bos taurus) Hamitic Longhorn type and were domesticated around possibly 9000 BP (years before the present i.e. 1950). About 2000 years later the humpless (Bos taurus) shorthorn type evolved or was developed in the region and these two types of humpless cattle are believed to the ancestor of Bos taurus. Humped (Bos indicus) zebu cattle were domesticated in the northwest arid areas of the Fertile Crescent around c. 5000 BP.

Functions of Livestock Housing

The most important purpose of livestock production is to increase the conversion efficiency of feed energy into the livestock products like milk, eggs, meat, wool, hair, hides and skins, draught power and manure (fertilizer). Scientific housing of livestock is necessary in order to get higher productivity from them. A proper housing design/structure should alter/modify the micro-climate inside the house so that animals are least exposed to the extremes of climatic conditions. Moreover, it should also provide better control of diseases & parasites, desirable working conditions for farm staff & better living conditions for the animals, better integration of various routine farm practices, opportunity for higher labour efficiency at farm, protection from predators & thieves, opportunity to express species specific natural behavior patterns and it must not compromise the welfare of the animals. Some of these functions are discussed in subsequent sub-headings.

Livestock farming is an integral part of Indian agriculture system and vital source of livelihood particularly in the rural areas of the country. This sector has been the primary source of energy for agricultural operations (for land preparation, sowing, pulling bullock carts etc.) and major source of animal protein (mutton, chevon, chicken, pork, beef, eggs etc.) for majority of population. India has been habitate of major draught, milch and dual-purpose breeds of cattle as well as buffaloes. Besides their potential our indigenous as well as crossbred animals are unable to produce maximum output due to unavailability of adequate and nutritious feed and fodder throughout the year. The quantity and quality of forage production is directly proportional to the livestock health, production and productivity. There is colossal gap between demand and supply of good quality nutritious fodder. Besides, the availability of lesser area under cultivated fodder crops, the grazing lands also becoming smaller due to the degradation of the land, urbanization, industrial development and increased area under food production to fulfil the demand of increasing human population. To meet the nutritional requirement of such a huge population of indigenous, crossbreds as well as genetically upgraded animals, proper management and conservation of fodder and grasslands is necessary.

Animal Genetic Resources

Agricultural biodiversity is the product of thousand years of activity during which humans have sought to meet their needs in a wide range of climatic and ecological conditions. Well adapted livestock have been an essential element of agricultural production systems. For livestock keepers, animal genetic diversity is a resource to be drawn upon to select stocks and develop new breeds. More broadly, genetically diverse livestock populations provide society with a greater range of options to meet future demands, so the wise management of the world’s agricultural biodiversity is becoming an ever greater challenge for the international community. The livestock sector in particular is undergoing dramatic changes as large-scale production expands in response to surging demand for meat, milk and eggs (FAO, 2008).

Animal genetic resources (AnGR) include all animal species, breeds and strains that are of economic, scientific and cultural interest to humankind in terms of food and agricultural production for the present or the future. Domesticated animals are considered to be those species that are bred in captivity and modified from their wild ancestors to make them more useful to humans, who control their reproduction (breeding), care (shelter, protection against predators) and food supply (Diamond, 2002; Mignon-Grasteau, 2005). Only about 40 animal species have been domesticated since the Pleistocene. Common species include cattle, sheep, goat, chicken, duck, pig, horse, buffalo, rabbit, camel, donkey, elephants, various poultry species, reindeer, etc. All these AnGR are vital to the economic development of the majority of countries in the world playing an important role in the subsistence of many communities. Although only a subset of the diversity present in the ancestral species survived in the domestic counterparts, domestic livestock diversity has been continuously evolving.