Hidden Markov Models

In this chapter theory of Hidden Markov Models is described. Specially the gradient based ML and MMI training is treated mathematically in detail. Finally it is shown how the idea of HMM can be used in isolated and continuous recognition.

• Introduction
• Definition of Hidden Markov Model
• Assumptions in the theory of HMMs
• There basic problems of HMMs

1. The Evaluation Problems and the Forward Algorithm
2. The Decoding Problem nd the Viterbi Algoritma
3. The Learning Problem

• Maximum Lielihood (ML) eriterion
• Baum-Weleh Algorithm
• Gradien based method
• Maximum Mutual Information (MMI) criterion
• Gradien wrt transition probabilities
• Gradient wrt observation probabilities
• Use of HMMs in isolated recognition
  

1. Training
   
2. Recognition

Use of HMMs in continuous recognition

• Statistical Language models
• training of a HMM based continuous recognizer

1. ML training
2. MMI training

• recognition using a HMM continuous recognizer
• Viterbi based recognition
• Level Building
• N-best search
• Calculatin of the recognizer performance

Introduction

As mentioned earlier, ASR problem can be attacked from two sides; namely

1. From the side of speech generation
2. From the side of speech perception

The Hidden Markov MOdel (HMM) is a result of the attempt to model the speech generation statistically, and thus belongs to the first category above. During the pas several years it has become the most successful speeh model used in ASR. The main reason for this success is it's wonderful ability to characterize te speech signal in a mathemathically tractable way.

In a typical HMM based ASR system, the HMM stage ids proceeded by the preprocessing (parameter extraction) stages. Thus the input to the HMM is a discrete time sequence of parameter vectors, such as those described in the previous chapter. The parameter vectors can be supplied to the HMM, either in vektor quantized form or in raw continuous form. It can be desiganed HMM is to handle any of the cases, but importand point is how

The functioning of the Swedish food system from a consumer perspective

1
The functioning of the Swedish food system from a consumer
perspective
By Solveig Wikström & Maria Frostling-Henningsson, Stockholm University,
School of business.
It is well documented that what consumers express as important regarding food
is far from coherent with their actual choice of food (Grunert & Kristensen, 1992;
Bjerke, 1992; Connors et al. 2001; AC Nielsen, 2006). This gap between consumers’
expressed intentions (goals), on one hand, and their actual choice, on the other hand,
signals problems for the consumers. This gap causes difficulties also for food
retailers and food producers because they can’t trust the market signals from the
consumers. This state indicates a deficient functioning of the food market. Moreover,
it is a well documented fact that peoples’ food intake is responsible for many of
today’s serious illnesses (WHO 2003). There are many possible explanations for the
mismatch between consumer intentions and actual choice concerning food
consumption. Some explanations are imbedded in the consumers’ own domain, such
as scarcity of time and limited knowledge relevant for choosing the right products.
Other explanations are imbedded in the food retailers’ and producers’ domains. For
instance, food producers and retailers are often criticized for poor product quality,
misleading or unclear information and aggressive marketing, which complicate
consumers’ choice of food and indirectly impede the quality of their food
consumption. It is a paradox that this mismatch occurs in societies with highly
educated and generally well informed consumers, and with food supply that is more
abundant with varieties than ever before. There is today no good explanation of this
apparent paradox.
Naturally, food production and food consumption have been extensively
researched by a multitude of disciplines and from a variety of perspectives: technical,
health, medical, nutrition, safety, culinary, economy, as well as from ethical,
religious, social and identity perspectives (see e. g. European Commission). However,
each research project deals with limited aspects of the food area. Food consumption,
for instance, may focus on eating ceremonies (Wallendorf and Arnould 1991), or the
eating habits among elderly consumers (Brembeck et al, 2005; Brembeck et al. 2006)
or among children (Johansson, 2006). Other research projects address eating-habits in
the Nordic countries (Grunow et al., 1998), and food provisioning in the public sector
in England (Edwards, Engström and Gustafsson, 2007; Edwards, Hartwell, Reeve and
Schafheitle, 2007; Hartwell, Edwards and Beavis, 2007). Likewise, there is an
abundance of research dealing with food production, marketing and information
provision of food (Grunert and Willis 2007), structural changes, competition and
market power (Reed and Clark 2000).
Aim of the study
In reality, all these aspects have bearings on an understanding of the food
system. However, to comprehend how different elements of the complex food system
influence food consumption, it is important to examine the working of the system as a
whole. This study will try to do that starting with exploring certain characteristics of
the main actors –food producers, retailers/wholesalers and consumers – and with the
issue how their organizational routines and activities influence food consumption.
2
Theories on actor networks and consumer value creation will guide this research. To
get relevant empirical data, we collect information from several representatives of the
food system – including a large retail chain, its suppliers (represented by four food
producers) and consumers represented by a panel of 35 households from the retailer’s
customer base.
Theory framework
We will apply a network perspective to conceptualize the relations between
consumers, retailers and producers. The characteristic features of a “network
approach” are the focus on the “actors” and the relationships between them
(Gummesson 2002; Håkansson et. al. 2004). A market network can be defined as a
group of actors (firms and/or consumers) which interact (cooperate) in an activity
promoting value creation. The cooperation may concern quite different activities. In
the case of the food system the cooperation may, for instance, deal with buying, sale,
product development, production processes, information acquisition, or lobbying.
Such a network approach highlights the interdependence of actors. In the network
approach, market exchange is combined with direct interaction between cooperating
actors. This means that the distinct boundaries characteristic for market transactions
are blurred by network relations as a result of alliances, joint ventures, etc.
Consequently, the actors are influenced by and influence each other directly in a long
term perspective, not only through market transactions, but also via non-market
relations.
Another important characteristic of a network relates to how value is created.
While value creation and innovation has traditionally been considered the supplier’s
responsibility, value is increasingly perceived as originating from interaction and cooperation
between the actors in the network (Wikström and Normann 1996; Normann
and Ramirez, 1998; Wikström 1996a; Gummesson 2002; Håkansson et al. 2004). In a
similar vein, Porters’ (1985) value chain has increasingly been substituted by the
concept of value creating network or “value stars” (Wikström and Normann 1996;
Normann and Ramirez, 1998). Distributors and other intermediaries are highly
involved in innovation and value creation (Håkansson et al. 2004). Moreover, endusers
do not just consume, they also directly influence the nature of the offering and
take an active part in the value creation – an aspect extensively brought to the fore in
modern marketing literature (Dabholcar, 1990; Kelley et al., 1990; Gummesson 1995;
Lengnick-Hall, 1996; Wikström 1996b; Grönroos, 2000; Prahalad and Ramswany,
2004; Vargo and Lusch, 2004). An additional observation is that the offerings are not
just tangible products that can be inspected and evaluated. Other aspects such as
reputation, service and interactions also matter.
We will also keep other network characteristics in mind in our analyses of the
organizing and performance of the food system (see e.g. Latour 1990, 2005; Callon
1998; Law 2001; Kjellberg 2001; Charniawska and Hernes 2005; Feldman and
Pentland 2005). Actors have projects, and goals/interests – things they want to
accomplish. For instance, consumers are interested in finding the “right” products
when they shop for food, i.e. products that contribute to the goals concerning their
food consumption. Retailers are supposed to supply products and services that offer
maximum value for the consumers. Producers are engaged in developing products
and services that are supposed to fit both consumes’ and retailers value creation.
3
Moreover, actors pursue their goals by a bundle of activities aggregated in
organizational routines. Those routines are manifest in recognizable patterns of
interdependent actions carried out by several actors (Feldman and Pentland 2005).
The organizational patterns typically appear in the shape of value creating
constellations (Normann and Ramirez 1998). Further, organizational routines can be
viewed as having two parts: a “manifest part” and a “performative part”. The manifest
part is about a formulated policy exhibited in a story/narrative for how the activities
should be pursued. For instance, in the case of a consumer, the manifest part may
imply that the consumer is a “green shopper”, largely going for vegetables. In the
case of a firm, the manifest part may imply that the firm should be consumer oriented.
The other part, the “performative” part consists of specific activities by which the
manifest policy is performed. For instance, the consumer may try hard to actually get
vegetables for the meals, and the firm may work hard to test its new products on a
consumer panel before the products are launched in the market. The coherence of the
manifest and performative aspects of the actors’ policies and routines can be taken as
one of the criteria for a well functioning network. Lack of correspondence signals
deficiencies in the network. Following this network perspective implies that we
should explore how consumers, retailers and food producers, describe (manifest) both
their policies and routines and the way they perform their expressed routines in real
action
Empirical methodology
We use a case-study methodology to generate data concerning the complex
food system. The case consists basically of three groups of actors: (i) a large retail
grocery chain (Axfood), (ii) a set of customers of the retail firm representing different
categories of consumers, and (iii) four producer firms serving as suppliers to the retail
firm (Lantmännen Axa, Atria, Findus and Santa Maria kryddor), chosen to represent
different product areas.
The consumer study, guided by theories on social psychology and sociology of
culture (Levi-Strauss, 1978; Fürst, 1988; Corrigan, 1997; Östberg, 2004)), explores how
consumers’ intensions and visions are materialized in the actual execution of actions, and
how they perceive the eventual gap between goals and actual behavior – and how they deal
with this gap. In-depth interviews with a panel of 35 households, representing different
demographic categories, provide the data. Additional data are collected from shopping
receipts and from a so-called shop-along approach, a process according to which the
researchers follow the consumers in the store while shopping. Data collection and analyses
follow established procedures for qualitative research (Thompson et al. 1989; Strauss and
Corbin, 1990; Spiggle, 1994; Frostling-Henningsson, 2003; Wikström, 2005), using an
interpretive approach. The data analysis is supposed to identify both manifest patterns of
consumers’ ambitions (expressed goals) and patterns of actual choice of food (performative
choice).
Data on retailers’ and producers’ organizational routines (manifest and performative)
as well as actions are also collected with a broad approach. A central issue in data
acquisitions is how the interaction with the other actors in the food network affects their
organizational routines in the case of product development and marketing. First, what are
the retailers’ and producers’ policies for interacting with the consumers, and how are the
activities accomplished? Second, how do retailers and food producers interact with each
4
other, i.e. what are their expressed policies for this interaction and how are the policies
manifested in actions?
The analysis of firms’ interaction with the consumers will be based on data on
consumers collected by firms such as sales statistics, market research, observations, and/or
trend reports. We will also take notes on the conclusions that firms actually draw from the
data about the consumers’ goals, as well as how the consumers’ goals are met. Data about
organizational routines and their materialization will be collected in different ways. Policies
and organizational routines will be discussed at the recurrent workshops, where field notes
from the discussion are taken. Further, individual interviews with employees responsible for
the different activity areas will be held. Some of the interviews will be held as open
discussions, others as structured interviews suitable for comparison between the firms.
Internal documents will provide complementary data.
Data collection and analysis in summary
Following the “actor network approach” we explore how the characteristics of the
food producers, retailers and consumers – and their organizational routines and activities –
influence food consumption. As emphasized above, the influence from the three actor
groups is direct as well as indirect as depicted in figure 1. Media and organizations related
to the food area are not included in the study besides when referred to by the main actors as
representing restrictions or support in their goal directed activities.
Figure 1. How consumers, retailers and food producers influence the food consumption.
Each actor group is directly dependent on the other actor groups when pursuing
its tasks. The organization of this interdependence, we hypothesize, is of paramount
interest. As recent literature indicates, when the interdependence, besides market
transaction, takes the form of interaction and co-operation, it may substantially
increase the consumer value of the food consumption. In the analyzes, it is important
to identify which activities and routines within different actor groups that support,
respectively mitigate, the generation of consumer value, as measured by the
consumers’ realizations of their goals and visions.
Food
consumption
Food producers’
routines for their
goal oriented
activities
Consumers’
routines for their
goal oriented
activities
Retailers’
routines for their
goal oriented
activities
5
Contributions
Previous research on food consumption, food quality, eating habits and its determinant
has mainly addressed special actors and/or specific issues of the food system. However,
each different piece – actors, activities and artifacts – are related and influence the outcome.
Hence, this study attempts to look at the food system as a whole using an actor network
framework. The focus will be on the interdependence, interaction and cooperation between
the three main actors of the food system.
Studies of production and marketing systems that encompass consumers as actors
within the system are scares. Thus, including the consumers in the study of the food system
should generate conceptual knowledge for developing the network theory. Another
contribution is methodological. Utilizing a case - study method and a network approach for
exploring the functioning of the food system is a fresh approach hopefully providing a
methodological contribution. The case-study method – based on close and long term
cooperation with a set of retail and food producer as well as a panel of consumers – ensures
access to deep data. Doing empirical research in areas sensitive to firms could otherwise
cause problems. Long term interaction with a consumer panel also generates new and
important data.
The study also contributes to the theory of consumer value creation in a network
context. Finally the study may have managerial implications. Firms and consumers as well
as different consumer representatives, should benefit from an improved understanding of
how the problems related to food consumption are created, what the roots of the problems
are, and how the problems may be mitigated/resolved.
Time schedule and financing
This study is an extension of the ongoing study of consumers’ choice of food as part
of their everyday life. As mentioned above, the consumer study focuses on the gap between
consumers’ expressed wants and their actual choice, and how this gap can be understood.
The ongoing consumer study is a two years project ending in late 2008. The consumer study
will be used as input in the study on the functioning of the food system. As a consequence,
the study of the food system is scheduled for only two years.
Different research councils and the firms included in the research are funding the
project on equal bases.
References
ACNielsen (2006), Health in Sweden (Hälsa i Sverige) and What Shoppers Really Want.
Bjerke, F (1992), Forbrugernes interesse for økologiske produkter [Consumer interest in
organic products], Istitut for Samfundsøkonomi og Planlaegning, Roskilde
University
Brembeck, H, Karlsson, M, Ossiansson, E, Shanahan, H, Jonsson and Bergström, K (2005)
The multidimensional food consumer. Values and behavior of consumers 55+, Report
2005:04, Center for Consumer Studies at School of Business, Economics and Law at
Göteborg University.
6
Brembeck, H, Karlsson, M, Ossiansson, E, Shanahan, H, Jonsson, L, Bergström, K and
Engelbrektsson P (2006) Food and the new country, Report 2006:05, Center for
Consumer Studies at School of Business, Economics and Law at
Callon, M. (1998), Introduction: The embeddedness of economic markets in economics. In
Callon, M.(ed)The laws of the markets. Oxford, Blackwell, 1-57.
Charniawska, B and Hernes, T. (2005) Actor-network Theory and Organizing, Sweden,
Liber & Copenhagen business Press.
Connors, M, Bisogni, C.A, Sobal, J, Devine, C.M (2001) “Managing Values in Personal
Food Systems”, Appetite, Vol. 36, pp 189-200
Corrigan, P (1997) The Sociology of Consumption, London: Sage Publications.
Dabholcar, P (1990), “How to improve Perceived Service Quality by Improving Customer
Participation”. In: Dunlap, B. J., ed., Developments in Marketing Science, Cullowhee, NC:
Academy of Marketing Science, pp. 483-87.
Edwards, J, Engström, K and Gustafsson, I-B, (2007, forthcoming) “Body Mass Index
(BMI), perceptions of portion size and knowledge of energy intake and expenditure,”
Journal of Culinary Science & Technology, Vol. 5, No. 2, pp 39-57
Edwards, J, Hartwell, H J Reeve W G and Schafheitle, J (2007, forthcoming) “The diet of
prisoners in England”, British Food Journal, Vol. 109, No. 3, pp 216-232
Feldman, M and Pentland, B (2005) “Organizational Routines and the Macro-Actor.” In
Czarniawska, B and Hernes, T (Eds.) Actor-Network theory and organizing.
Stockholm: Liber and CBS Press. (p. 91-111)
Frostling-Henningsson, M. (2003) “Internet Grocery Shopping. A necessity, A Pleasurable
Adventure, Or An Act of Love?” Doctoral Theses, Stockholm University School of
Business Research report No. 2003:8, Intellecta
Fürst, E (1988) “The cultural significance of food,” in Otnes, P (ed.) The Sociology of
Consumption, Oslo, Norway: Solum Forlag A/S, pp. 89-100
Grunert, S. C. & Kristensen, K (1992), Den danske forbrugger or økologiske fødevarer
[The Danish consumer and organic food products], Aarhus: Institut for
Informationsbehandling, The Aarhus School of Business
Grunert, K. and Willis, J. (2007), “A review of European research on consumer response to
nutrition information on food labels”, Journal of Public Health, Vol. 15, No. 5, pp
384-399
Grunow, J., Mäkelä, J., Kjaernes, U., Ekström, M.P., Holm, L., Björkum, E (1998) ”A
Comperative Study of Nordic Meal Patterns” In: Culinary Arts and Science: Global
and National Perspektive, pp 377-382
7
Grönroos, C. (2000), “Relationship Marketing: The Nordic School Perspective”. In: Shet, J. and
Parvatuyar, A., eds. Handbook of Relationship Marketing,. Thousand Oaks, Ca, Sage.
Gummesson, E. (1995), “Relationship Marketing: Its Role in Service economy”. In: Glynn, W. J.
and Barnes, G. J. eds., Understanding Service Management, Dublin/London; Wiley, pp.
244 –268.
Gummesson (2002) “Relationship Marketing in the New Economy”, Journal of
Relationship Marketing, vol.1, pp 37-57.
Hartwell, H J, Edwards, J and Beavis, J (2007, forthcoming), “Plate versus Bulk trolley
food service in a hospital: Comparison of patients’ satisfaction,” Nutrition, Vol. 23,
No. 3, pp 211-218
Håkansson, H., Henjesand, IJ and Waluszewaki, X.Y (2004), Introduction: Rethinking
marketing. In Håkansson, H., Harrisson, D. and Waluszewski, XY(eds.) Rethinking
marketing, Chichester, John Wiley, pp 1-13.
Johansson, B (2006) Nordic childrens’ images of food and eating, Report 2006:04, Center
for Consumer Studies at School of Business, Economics and Law at Gothenburg
University.
Kelley, S.J., Donnelly, J.W. and Skinner, S.J. (1990), “Customer Participation in Service
Production and Delivery”, Journal of Retailing, Vol.66, No. 3, pp 315 - 35
Kjellberg, H. (2001), Organising Distribution, Stockholm, Stockholm School of Economics.
Latour, B. (1990) Drawing things together. In: Lynch,M. and Woolgar, S. (eds.)
Representation in scientific practice, Cambridge University Press, Cambridge, 19-68.
Latour, B. (2005) Reassembling the Social, An introduction to Actor-Network-theory,
Oxford University Press.
Law, J. (2001), Notes on the Theory of the Actor Network: Ordering, Strategy and
Heterogeneity, Center for Science Studies, Lancaster University
Lengnick-Hall, C.A. (1996), “Customer Contribution to Quality: A different View of the
Customer-Oriented Firm,” The Academy of Management Review, Vol. 21, No. 3, pp
76-87
Lévi-Strauss, C (1978) “The origin of table manners,” in Introduction to a Science of
Mythology, vol. 3, London: Cape
Normann, R. and Ramirez, R. (1998) Designing Interactive Strategy. From value chain to
value constellation, Chichester, John Wiley.
Porter, M.E (1985) Competitive Advantage – Creating and Sustaining Superior
Performance, Simon & Schuster, New York
8
Prahalad, C. K. and Ramaswamy, V. (2004), The Future of Competition. Co-Creating Unique
Value with Customers, Boston, Ma., Harvard Business School Press.
Reed, A.J. and Clark, J.S. (2000), “Structural Changes and Competition in Seven U.S. Food
Markets”, Food and Rural Economics Division, Economic research Service, U.S.
Department of Agriculture, Technical Bulletin No. 1881
Spiggle, S (1994) “Analysis and interpretation of qualitative data in consumer research,”
Journal of Consumer Research, Vol. 21, No. 3 December, pp. 491-503.
Strauss, A, and Corbin, J (1990) Basic Qualitative Research: Grounded theory, Procedures
and Techniques. Sage Publications, Beverly Hills, Ca.
Thompson, CJ, Locander, WB and Pollo, HR (1989) “Putting Consumer Experience Back
into Consumer Research: The Philosophy and Method of Existential-
Phenomenology,” Journal of Consumer Research, Vol. 16, pp. 133-146.
Vargo, S. and Lusch, R. (2004), “Evolving to a New Dominant Logic for Marketing”, Journal of
Marketing, Vol. 68, No.1 January, pp. 1-17.
Wallendorf, M and Arnould, E.J (1991) “We Gather Together – Consumption Rituals of
Thanksgiving Day”, Journal of Consumer Research, Vol. 18, No. 1, pp 13-31
WHO (2003), Diet, Nutrition and the Prevention of Chronic Diseases. Report of the
WHO/FAO Joint Expert Consultation. WHO Tech Rep Ser 916
Wikström, S. and Normann, R. (1996), Knowledge and Value. A new perspective of corporate
transformation, London, Routledge.
Wikström, S. (1996a) “Extending the knowledge Base through Customer – Firm Interaction”,
Cems Business Review, Vol.1, pp. 1-14.
Wikström, S. (1996b) “Value Creation by Company – Consumer Interaction”, Journal of
Marketing Management, Vol. 12, No. 5 pp. 357-374.
Wikström, S (1997) the Changing Consumer in Sweden, International Journal of Research
in Marketing, Vol. 14, pp. 261-274.
Wikström, S (2005) “From E-Channel to Channel Mix and Channel Integration”, Journal
of Marketing Management, Vol. 21, No. 7 pp. 725-75.
Östberg, J (2004) what’s eating the Eater? Perspectives on the Everyday Anxiety of Food
Consumption in Late Modernity, Doctoral thesis, Lund: Institute of Economic
Research, Lund Business Press, Lund studies in Economics and Management 75.

Lihatlah Mereka Tersenyum

Suatu pagi, menjelang berangkat sekolah banyak anak-anak sekolah dasar yang sibuk menyiapkan diri. Ada yang meminta sarapan, mandi dengan air hangat, minta didandanin, pakai baju seragam yang rapi dn kesibukan lainnya. Kadang yang dibuat super repot adalah orangtua, ibu dan ayah. Betapa dimanjanya mereka, ingin mandi dimandikan, tidak bisa membetulkan baju, bajunya dikanjingkan oleh ayah atau ibu, ingin makan dibuatkan nasi goreng, telur mata sapi, dibuatkan susu dan disuapin. Itu adalah gambaran kebanyakan anak yang diasuh dengan kasih sayang yang lebih dari cukup.

Lain halnya dengan Intan, yang harus bangun sebelum subuh, menyalakan tungku, memasak air dan menanak nasi, kemudian menyambi mencuci berkakas, mencucu baju setembor, isi pakaian orang satu rumah, menyapu, memberi makan ternak, dan banyak sekali. Kalau lapar ingin sarapan, ya harus masak dulu, ingin mandi mandi sendiri, ingin baju yang bersih ya mencuci sendiri, dan itu baru berumur 8 tahun, baru kelas 2 SD. Betapa kakek dan neneknya mengajar keras pada dirinya sejak dini, dengan harapan suatu saat bisa bertarung keras berkompetisi melawan dingin dan kerasnya dunia luar.

Ketika akan berangkat sekolah Intan harus berjalan kaki, jangankan diantar pake sepeda motor, atau barang digandeng tangannya oleh ibu, ia harus berani berjalan sendiri menghadapi tantangan di jalan, seperti banyak kendaraan yang lewat, ada anjing tetangga yang siap menggonggong dan menggigit, ada banyak hewan ternak di jalanan, yang siap mengeluarkan kotoran, dan melewati pesawahan yang licin setelah digujur hujan. Tapi ia beranikan berangat dengan semangat menuntut ilmu. Jangankan Diberi saku dan antarpun tidak. begitu kerasnya ia harus belajar.
Namun, satu hal yang membuat dirinya merasa tenang, walaupun jarang diberi uang saku, karena kalau ingin jajan ia diharuska bekerja terlebih dahulu di lahan, ia tetap diwajibkan sarapan pagi, walaupun hanya dengan ikan asin atau sambal bawang mentah. Jadi perutnya merasa tenang, dan bisa menahan keinginan untuk jajan.

Banyak teman-temanya yang dengan enaknya membeli roti-roti manis, kembang gula, dan jajanan enak lainnya, namun Intan hanya menahan segala keinginan itu, karena memang ia tak punya uang untuk membelinya. Ia yang sejak kecil sudah tak punya ayah, bahkan semenjak ia dalam kandungan ibunya, ia tidak pernah merasakan sentuhan lembut ayahnya, usapan halus di kepala atau bahkan hanya memandang wajahnya. Jadi sejak bayi pun Intan sudah diajarkan untuk hidup tanpa ayah, untuk menjadi seorang gadis yang kuat, yang pemperani, yang berani bertarung berkompetisi dalam kejamnya hidup.
Oleh karena kesibukannya untuk bekerja dan belajar, ia jarang merasakan indahnya bermain dengan teman-temanya, ia banyak bekerja dan mengerjakan pekerjaan rumah. Bahkan untuk sekedar menonton televisi pun jarang ia lakukan. Anak yang barus berusia 8 tahun itu, harus bekerja di sawah membantu kakek neneknya menanam padi, memetik sayur untuk dijual, yang uangnya bisa ia gunakan untuk membeli buku. Bahkan bila ia ingin mendapatkan uang jajan yang lebih, ia harus berani bertempur dengan lumpur yang gatal untuk sekedar mencari sayur genjer, bila ia mendapatkan lebih dari satu ember, maka ia dapat menjual lebih banyak dan uangnya dapat ia belikan sedikit roti atuu es crim keliling kesukaannya. Begitulah kakek dan neneknya mengajarkannya. Hingga ia dapat terus melanjutkan pendidikan di SMP.

Ketika di SMP perjoengannya lebih keras lagi, dibandigkan di SD. Karena kakek dan neneknya tak dapat membiayainya, maka ia harus tinggal d rumah bibi dan pamanya unuk bisa terus sekolah. Di sana Ia harus membantu di sawah, mulai dari pagi sebelum berangakat sekolah, dan sesudah pulang sekolah hingga menjelang magrib tiba. Setelah itu ia harus mencari air di kali untuk mandi pamanya dan memenuhi gentong-gentong tampungan yang tidak sedikit jumlahnya. Baru setelah itu ia memasak untuk makan malam, lalu belanja untuk masak esok pagi sambil sekedar membelkkan cerutu untuk pamanya. Ketika menjelang malam baru ia bisa bergelut dengan buku-bukunya untuk sekedar mendapatkan beasiswa. Ia terus berjoeang untuk terus melanjutkan sekolahnya. Hingga suatu ketika ia mendapatkan beasisswa Full hingga ia lulus SMP, rasanya Perjueangannya selama ini tak sia-sia. Kerja kerasnya, belajarnya sambil menahan kantuk dan lelah, membuahkan hasil.

Waktu terus bergulir, hingga ia ia duduk di bangku SMA, dan kemudian ia bisa melanjutka ke perguruan tinggi.

Ingin tahu kelanjutannya . . . . .

Hari Ini Lebih Baik Dari Hari Kemarin

Waktu terus bergulir, detik-demi detik terus berlalu, jam demi jam hari demi hari, minggu, bulan, dan tahun, hingga tak terasa umur kita sudah mulai bertambah. Sadarkah kita, bahwa aktivitas yang acap kali kita lakukan, baik untuk belajar, bekerja, bermain, atau sekedar mengobrol, atau bahkan menulis dan membaca tulisan ini terus berlalu tanpa mau istirahat barang sejenak. Apakah kita sadar, bahwa yang namanya waktu ini gkj mau kompromi, gak mau bersahabat dengan siap saja. Ia terus secara continue, pelan, dan pasti bergulir menjangkau ruang. Nah .... apakah dengan berlalunya waktu yang gak mau barang sebentr kompromi dengan kita, kita kan menganggap ia bersahabat? Kukira tidak . . . bahkan ia mengajarkan kita untuk terus bergulir bersamanya tanpa mau berhenti. Nah ketika kita bergulir bersamanya, dimana kita menjlanan aktivitas hingga menghabiskan banyak waktu, pernahkan berpikir bahwa semuannya itu bermanfaat untuk kita? atau bermanfaat, ada yang dihasilkan atau paling tidak kita sudah mengalami perubahan dengan tanda kutip, perubahan yang lebih baik? Atau justru sebaliknya, kita mengikuti waktu yang tidak bersahabat itu dengan bersantai-santai, tanpa ada tujuan yang jelas, bahkan sering kali

Pendidikan merupakan hal yang terpenting untuk mencapai kehidupan yang lebih baik. Dengan pendidikan, maka akan merupakan media pembelajaran dasar untuk untuk dapt di jadikan jembatan dalam mengarungi perjongan hidup yang sesungguhnya. pendidikan pula yang mengahjarkan anak manusia untuk dapat menyelesaikan problem-problemnya di masa yang akan datang. Memang untuk mencapai pendidikan yang tinggi tidaklah mudah. Apalagi di era globalisasi seperti ini, dimana naik turunya perekonomian akan berdampak pada financial yang menjadi alat dalam mencapai pendidikan yang tinggi. Tinggi di sini adalah pendidikan yang mencapai pada pendalaman suatu bidang, dimana seseoang dikatakan menempuh pendidikan tinggi bila kemampuan seseorang dalam mendalami suatu ilmu pengetahuan. Dan hal ini bukan artikan bahwa pendidikan tinggi dapat dicapai dengan gelar kesarjanaan, walaupun faktanya memang seperti itu, namun pendidikan di sini adalah pembelajaran secara continue yang tidak terpatok pada sekolah maupun media belajar formal.

Sistem pembelajaran secara kontinue atau belajar sepanjang hayat itu perlu diterapkan, bila dala diri seseorang maka tercipta suatu komunitas yang memimpikan sebuah kemajuan, bak kemajuan baik untuk dirinya sendiri maupun oranglain.

dewasa ini, masyarakat Indonesia, beranggapan bahwa untuk menempuh pendidikan tinggi diperlukan biaya yang tidak sedikit, apa lagi bagi para orangtua yang yang notabene golongan menengah ke bawah. Mereka akan memikirkan dua kali bahkan kelipatannya, bila akan menyekolahkan anaknya sampai jenjang yang lebih, untuk memnuhi kbutuhan sehari-hari saja mereka masih kesusahan.

Plant Organization

The main interest of many of those growing plants is the nature of the plant's external appearance, its form or morphology. This chapter begins by describing the external feature and discusses ways in which plants are used in garden and landscapes.

A intracellular organism such as the plant, which carries out growth and development, requires a complex organization to carry out its functions. To be efficient , the plant's structural unit must be subdivided so that a particular area in the plant, i.e. an organ, carries out each major function. The individual units of the plant, the Cells are grouped together into tissues of similar cell types, and each tissue contributes to the activities of the whole organ. These structures and the nature of plant growth are explored and explained in the context of the stem.

Soil as a Growing Medium

The plant takes up water and nutrients from the growing medium through is roots, which also provide anchorage (see root structure). The root also requires a supply of oxygen and produces carbon dioxide, which is harmful if it build up in the root zone (see respiration).

In order to secure water throughout the season the roots penetrate deep into the soil. The plant nutrients are extracted from a very dilute soil solution and so the roots are normally very extensive and with a shape that bring the maximum absorptive surface into contact with soil particle surface around which is the water and nutrients. Within one growing season a single plant growing in open ground develops some 700 km of root, which has a surface area includes the root hairs.

Liana, Lahir di Wonosobo, 22 Pebruari 1989. Menyelesaikan pendidikan dasar dan menengah di SD Negeri 1 Bumitirta dan SMP Negeri 2 Kalikajar. Menamatkan SMA di SMA Negeri 1 Kertek Wonosobo, Jawa Tengah pada tahun 2007. Sekarang sedang menempuh pendidikan S1 di Universitas Muhammadiyah Yogyakarta, Fakultas Pertanian, jurusan Agroteknologi. Saat ini sedang sibuk membuat karya, seperti mengajukan berbagai macam proposal penelitian, nulis di berbagai media termasuk Blogger mania.
Mulai akhir-akhir ini sedang melahirkan ratusan karya seperti paper, artikel yang akan diterbitkan lewat internet. Selama kuliah bahkan sejak SD saya sudah dilatih untuk mandiri. Hingga sekarang ketika duduk di bangku perkuliahan, saya mencoba mandiri dengan bekerja part time Job atau Arubaito.
Pernah mendapatkan kesempatan dalam event competisi LPIR ( lomba karya tulis ilmiah remaja) tingkat Jawa Tengah dan DIY, Alhamdullilah mendapat two Winner( Juara II), lomba penelitian tingkat Nasional, Dan Alhamdullilah lagi masuk 10 besar, predikat siswa teladan waktu SMA pernah menghiasiku hingga beberapa tahun. Mendapatkan beasiswa penuh selama tiga tahun dari menteri pendidikan Indonesia sewaktu SMP dan SMA.
Selain tema di atas juga memiliki minat dan aktif menulis dalam tema yang berhubungan dengan Agriculture, Botany, Biology, Education, self improvement, motivation. Aktifis organisasi pada masa SMA dan kuliah, pernah menjadi ketua kelompok ilmiah remaja semasa SMA.

Horticulture in Context

The many faces f hortculture have much in common, each being concerned the growing of plants. Despite the wide range of the industry, embracing as it does activities from the preparation of a cricket square to the production of uniformly sized cucumbers, there are common principles which quide the succesful management of the palants involved. This chapter put the industry, the plant, the plant communities and ecology into perspective, and considers the aspects of conservation and organic growing and looks forward to the more detailed explanations of horticulturel practice in te following chapters.

Horticulture may be described as the practice of growing plants in a relatively intensive manner. This contrasts with agriculture,which, in most western European countries, relies on a high level of machinery use voe an extensive area of land, consequently involving few people in the production process. However, the boundary between the two is far from clear, especially when considering large-scale vegetable production. Horticulture often involves the manipulation of plant material by propagation, by changing the above ground environment. There is a fundamental difference between production horticulture, whether producing plants themselves or plant products, and service horticulture, the development and upkeep of gardens and land scape for their amenity, culture and recreational values. Increasingly, horticulture can be seen to be involved with social well-being and welfare through the impact of plants for human physical and mental health. It encompasses environmental protection and conservation through large and small scale landscape design and management. Where the tending of plants for leisure moves from being horticulture to countryside management is another moot point. In contrast, the change associated with replacing plants with alternative materials, as in the creation of artificial playing surfaces, tests what is means by horticulture in a quite difference way.

Plant Cell Structure

Like the fungi, another kingdom of eukaryotes, plant cells have retained the protective cell wall structure of their prokaryotic ancestors. The basic plant cell shares a similar construction motif with the typical eukaryote cell, but does not have centrioles, lysosomes, intermediate filaments, cilia, or flagella, as does the animal cell. Plant cells do, however, have a number of other specialized structures, including a rigid cell wall, central vacuole, plasmodesmata, and chloroplasts. Although plants (and their typical cells) are non-motile, some species produce gametes that do exhibit flagella and are, therefore, able to move about.

Plants can be broadly categorized into two basic types: vascular and nonvascular. Vascular plants are considered to be more advanced than nonvascular plants because they have evolved specialized tissues, namely xylem, which is involved in structural support and water conduction, and phloem, which functions in food conduction. Consequently, they also possess roots, stems, and leaves, representing a higher form of organization that is characteristically absent in plants lacking vascular tissues. The nonvascular plants, members of the division Bryophyta, are usually no more than an inch or two in height because they do not have adequate support, which is provided by vascular tissues to other plants, to grow bigger. They also are more dependent on the environment that surrounds them to maintain appropriate amounts of moisture and, therefore, tend to inhabit damp, shady areas.

It is estimated that there are at least 260,000 species of plants in the world today. They range in size and complexity from small, nonvascular mosses to giant sequoia trees, the largest living organisms, growing as tall as 330 feet (100 meters). Only a tiny percentage of those species are directly used by people for food, shelter, fiber, and medicine. Nonetheless, plants are the basis for the Earth's ecosystem and food web, and without them complex animal life forms (such as humans) could never have evolved. Indeed, all living organisms are dependent either directly or indirectly on the energy produced by photosynthesis, and the byproduct of this process, oxygen, is essential to animals. Plants also reduce the amount of carbon dioxide present in the atmosphere, hinder soil erosion, and influence water levels and quality.

Plants exhibit life cycles that involve alternating generations of diploid forms, which contain paired chromosome sets in their cell nuclei, and haploid forms, which only possess a single set. Generally these two forms of a plant are very dissimilar in appearance. In higher plants, the diploid generation, the members of which are known as sporophytes due to their ability to produce spores, is usually dominant and more recognizable than the haploid gametophyte generation. In Bryophytes, however, the gametophyte form is dominant and physiologically necessary to the sporophyte form.

Animals are required to consume protein in order to obtain nitrogen, but plants are able to utilize inorganic forms of the element and, therefore, do not need an outside source of protein. Plants do, however, usually require significant amounts of water, which is needed for the photosynthetic process, to maintain cell structure and facilitate growth, and as a means of bringing nutrients to plant cells. The amount of nutrients needed by plant species varies significantly, but nine elements are generally considered to be necessary in relatively large amounts. Termed macroelements, these nutrients include calcium, carbon, hydrogen, magnesium, nitrogen, oxygen, phosphorus, potassium, and sulfur. Seven microelements, which are required by plants in smaller quantities, have also been identified: boron, chlorine, copper, iron, manganese, molybdenum, and zinc.

Thought to have evolved from the green algae, plants have been around since the early Paleozoic era, more than 500 million years ago. The earliest fossil evidence of land plants dates to the Ordovician Period (505 to 438 million years ago). By the Carboniferous Period, about 355 million years ago, most of the Earth was covered by forests of primitive vascular plants, such as lycopods (scale trees) and gymnosperms (pine trees, ginkgos). Angiosperms, the flowering plants, didn't develop until the end of the Cretaceous Period, about 65 million years ago—just as the dinosaurs became extinct.

• Cell Wall - Like their prokaryotic ancestors, plant cells have a rigid wall surrounding the plasma membrane. It is a far more complex structure, however, and serves a variety of functions, from protecting the cell to regulating the life cycle of the plant organism.

• Chloroplasts - The most important characteristic of plants is their ability to photosynthesize, in effect, to make their own food by converting light energy into chemical energy. This process is carried out in specialized organelles called chloroplasts.

• Endoplasmic Reticulum - The endoplasmic reticulum is a network of sacs that manufactures, processes, and transports chemical compounds for use inside and outside of the cell. It is connected to the double-layered nuclear envelope, providing a pipeline between the nucleus and the cytoplasm. In plants, the endoplasmic reticulum also connects between cells via the plasmodesmata.

• Golgi Apparatus - The Golgi apparatus is the distribution and shipping department for the cell's chemical products. It modifies proteins and fats built in the endoplasmic reticulum and prepares them for export as outside of the cell.

• Microfilaments - Microfilaments are solid rods made of globular proteins called actin. These filaments are primarily structural in function and are an important component of the cytoskeleton.

• Microtubules - These straight, hollow cylinders are found throughout the cytoplasm of all eukaryotic cells (prokaryotes don't have them) and carry out a variety of functions, ranging from transport to structural support.

• Mitochondria - Mitochondria are oblong shaped organelles found in the cytoplasm of all eukaryotic cells. In plant cells, they break down carbohydrate and sugar molecules to provide energy, particularly when light isn't available for the chloroplasts to produce energy.

• Nucleus - The nucleus is a highly specialized organelle that serves as the information processing and administrative center of the cell. This organelle has two major functions: it stores the cell's hereditary material, or DNA, and it coordinates the cell's activities, which include growth, intermediary metabolism, protein synthesis, and reproduction (cell division).

• Peroxisomes - Microbodies are a diverse group of organelles that are found in the cytoplasm, roughly spherical and bound by a single membrane. There are several types of microbodies but peroxisomes are the most common.

• Plasmodesmata - Plasmodesmata are small tubes that connect plant cells to each other, providing living bridges between cells.

• Plasma Membrane - All living cells have a plasma membrane that encloses their contents. In prokaryotes and plants, the membrane is the inner layer of protection surrounded by a rigid cell wall. These membranes also regulate the passage of molecules in and out of the cells.

• Ribosomes - All living cells contain ribosomes, tiny organelles composed of approximately 60 percent RNA and 40 percent protein. In eukaryotes, ribosomes are made of four strands of RNA. In prokaryotes, they consist of three strands of RNA.

• Vacuole - Each plant cell has a large, single vacuole that stores compounds, helps in plant growth, and plays an important structural role for the plant.

Leaf Tissue Organization - The plant body is divided into several organs: roots, stems, and leaves. The leaves are the primary photosynthetic organs of plants, serving as key sites where energy from light is converted into chemical energy. Similar to the other organs of a plant, a leaf is comprised of three basic tissue systems, including the dermal, vascular, and ground tissue systems. These three motifs are continuous throughout an entire plant, but their properties vary significantly based upon the organ type in which they are located. All three tissue systems are discussed in this section.

Imaging the passage of a single hydrocarbon chain through a nanopore

Our research group has succeeded for the first time in the world in direct TEM observation of shape changes and appearances in the space migration of a single molecule passing through a nanometer-size pore.

The processes by which molecules pass through pores in thin films and bio-membranes are basic phenomena for understanding various physical, chemical and biological phenomena. For instance, the fundamental behavior of molecules such as storage in porous solids (storage of hydrogen, methane, etc.), separation by membranes (separation of methane from methane hydrate, etc.) and transfer of molecules through cell membranes necessarily involves a process of molecules passing through pores. Previous research methods, however, were based on studying the statistical average of the behavior of plural molecules; there were no experimental approaches that examined the interaction of a single molecule with a pore. In other words, there was no research on the shape of a molecule going through a pore, and the interaction between molecules and pores. We reported last year that when boron-atom-labeled organic molecules were confined in carbon nanotubes and observed by a transmission electron microscope, conformation and movement to and fro of each molecule could be observed as moving images (Science, 2007, 316, 853).

We have now succeeded in observing a long chain of a fullerene-labeled hydrocarbon passing through a nanometer-size pore in the wall of a nanotube as if it were alive. We focused on a long and thin hydrocarbon chain, which was bonded to a soccer-ball-shaped molecule (C₆₀ fullerene) that was a little larger than its molecular size as a marker so that the chain part could move freely, and which was confined in a nanotube (Fig.1). Images of the molecule in various shapes in the space of the nanotube, and movement of the string-like molecule could then be filmed. By further close observation of each molecule, we also succeeded in observing the phenomenon of the string-like molecule passing through the pore in the wall of a nanotube (Fig.2).

A C₆₀ molecule having a hydrocarbon chain confined in a carbon nanotube of about 1.4-nanometer diameter was observed transforming into a straight configuration and passing through the pore in the carbon nanotube at room temperature. This is the first such observation of the moment when a molecule moves in a tube and its structure changes according to the environment.

Although observation of molecules at room temperature has been considered very difficult since they move very rapidly with thermal energy (on a time scale of a trillionth of a second or less), the movement of molecules observed by a microscope at room temperature was found to be far slower than expected. Further, it was clarified that (1) the energy source of molecular movement is the energy of the electron beam used for observation since the velocity of molecular movement is not so different even at extremely low temperature, and (2) the velocity of movement and the life of observed molecules are not greatly different, whether they are inside or outside of the carbon nanotube.

The latter conclusion coincides with our recently reported result that biomolecules having peptide bonding bonded to the outside of carbon nanotubes can be stably observed (Nakamura et al.，Journal of American Chemical Society , 2008, 130, 7808). The fact that changes of conformation of molecules placed outside of tubes can be researched, as reported in that paper and the present paper, will solve the fundamental problem of the former report of confinement inside nanotubes, namely that the size and form of the observation target are restricted. We expect that it will soon be possible to freely observe, molecule and molecule, the movements of various molecules such as proteins and DNAs fixed outside of nanotubes.

The dynamic structural analysis of organic molecules utilizing the spaces inside and outside of carbon nanotubes is expected to develop as a new method in academic research on the chemical reactions and interactions of biomolecules. The results are also expected to be applied in key nanotechnology fields of Japanese industry and medical fields such as the development of new medicines.

Information about publication

This study was performed in research collaboration between the Department of Chemistry, The University of Tokyo, and the Exploratory Research for Advanced Technology (ERATO), Nakamura Functional Carbon Cluster Project, Japan Science and Technology Agency (JST).

A part of this study was supported by MEXT (KAKENHI, No. 18655012). Electron microscopy experiments were carried out in collaboration with the Nanotube Research Center, the National Institute of Advanced Industrial Science and Technology (AIST). This work has been published in Nature Nanotechnology:
http://www.nature.com/nnano/index.html
* This article was appeared on the front page of the Nature Nanotechnology as a highlight article.

Masanori Koshino, Niclas Solin, Takatsugu Tanaka, Hiroyuki Isobe, and Eiichi Nakamura,
“Imaging the passage of a single hydrocarbon chain through a nanopore”,
Nature Nanotechnology,

Arabidopsis thaliana

Arabidopsis thaliana (A-ra-bi-dóp-sis tha-li-á-na; thale cress, mouse-ear cress or Arabidopsis), is a small flowering plant native to Europe, Asia, and northwestern Africa.^[1] A spring annual with a relatively short life cycle, Arabidopsis is popular as a model organism in plant biology and genetics. Its genome is one of the smallest plant genomes and was the first plant genome to be sequenced. Arabidopsis is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing.

Habitat, morphology, and life cycle

Arabidopsis is native to Europe, Asia, and northwestern Africa. It is an annual (rarely biennial) plant usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, with a few leaves also on the flowering stem. The basal leaves are green to slightly purplish in colour, 1.5–5 cm long and 2–10 mm broad, with an entire to coarsely serrated margin; the stem leaves are smaller, unstalked, usually with an entire margin. Leaves are covered with small unicellular hairs (called trichomes). The flowers are 3 mm in diameter, arranged in a corymb; their structure is that of the typical Brassicacaea. The fruit is a siliqua 5–20 mm long, containing 20–30 seeds.^[2][3][4][5] Roots are simple in structure, with a single primary root that grows vertically downwards, later producing smaller lateral roots. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium.^[6]

Arabidopsis can complete its entire life cycle in six weeks. The central stem that produces flowers grows after about three weeks, and the flowers naturally self-pollinate. In the lab Arabidopsis may be grown in petri plates or pots, under fluorescent lights or in a greenhouse.^[7

Use as a model organism

Arabidopsis is widely used as one of the model organisms for studying plant sciences, including genetics and plant development.^[8][9] It plays the role for agricultural sciences that mice and fruit flies (Drosophila) play in animal biology. Although Arabidopsis thaliana has little direct significance for agriculture, it has several traits that make it a useful model for understanding the genetic, cellular, and molecular biology of flowering plants.

The small size of its genome make Arabidopsis thaliana useful for genetic mapping and sequencing — with about 157 million base pairs^[10] and five chromosomes, Arabidopsis has one of the smallest genomes among plants. It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative.^[11] Much work has been done to assign functions to its 27,000 genes and the 35,000 proteins they encode.^[12]

The plant's small size and rapid life cycle are also advantageous for research. Having specialized as a spring ephemeral, it has been used to found several laboratory strains that take about six weeks from germination to mature seed. The small size of the plant is convenient for cultivation in a small space and it produces many seeds. Further, the selfing nature of this plant assists genetic experiments. Also, as an individual plant can produce several thousand seeds, each of the above criteria leads to Arabidopsis thaliana being valued as a genetic model organism.

Plant transformation in Arabidopsis is routine, using Agrobacterium tumefaciens to transfer DNA to the plant genome. The current protocol, termed "floral-dip", involves simply dipping a flower into a solution containing Agrobacterium, the DNA of interest, and a detergent.^[13] This method avoids the need for tissue culture or plant regeneration.

Finally, the plant is well suited for light microscopy analysis. Seedlings up to several centimeters long are almost entirely transparent and all cells can be imaged in an intact living seedling using fluorescence microscopy, obviating the need for fixation and sectioning and allowing time-lapse measurements. Fluorescent protein constructs can be introduced through transformation. The developmental stage of each cell can be inferred from its location in the plant or by using fluorescent protein markers, allowing detailed developmental analysis.

History of Arabidopsis research

The first mutant in Arabidopsis was documented in 1873 by Alexander Braun, describing a double flower phenotype (the mutated gene was likely Agamous, cloned and characterized in 1990).^[14] However, it was not until 1943 that Friedrich Laibach (who had published the chromosome number in 1907) proposed Arabidopsis as a model organism.^[15] His student Erna Reinholz published her thesis on Arabidopsis in 1945, describing the first collection of Arabidopsis mutants that they generated using x-ray mutagenesis. Laibach continued his important contributions to Arabidopsis research by collecting a large number of ecotypes. With the help of Albert Kranz, these were organised into the current ecotype collection of 750 natural accessions of Arabidopsis thaliana from around the world.

In the 1950s and 1960s John Langridge and George Rédei played an important role in establishing arabidopsis as a useful organism for biological laboratory experiments. Rédei wrote several scholarly reviews instrumental in introducing the model to the scientific community. The start of the arabidopsis research community dates to a newsletter called Arabidopsis Information Service (AIS), established in 1964. The first International Arabidopsis Conference was held in 1965, in Göttingen, Germany.

In the 1980s Arabidopsis started to become widely used in plant research laboratories around the world. It was one of several candidates that included maize, petunia and tobacco.^[15] The latter two were attractive since they were easily transformable with the then current technologies, while maize was a well established genetic model for plant biology. The breakthrough year for Arabidopsis as the preferred model plant came in 1986 when T-DNA mediated transformation was first published and this coincided with the first gene to be cloned and published.^[16][17]

Research

Flower development

Arabidopsis has been extensively studied as a model for flower development. The developing flower has four basic organs: sepals, petals, stamens, and carpels (which go on to form pistils). These organs are arranged in a series of whorls: four sepals on the outer whorl, followed by six petals inside this, six stamens, and a central carpel region. Homeotic mutations in Arabidopsis result in the change of one organ to another — in the case of the Agamous mutation, for example, stamens become petals and carpels are replaced with a new flower, resulting in a recursively repeated sepal-petal-petal pattern.

Observations of homeotic mutations led to the formulation of the ABC model of flower development by E. Coen and E. Meyerowitz.^[18] According to this model floral organ identity genes are divided into three classes: class A genes (which affect sepals and petals), class B genes (which affect petals and stamens), and class C genes (which affect stamens and carpels). These genes code for transcription factors that combine to cause tissue specification in their respective regions during development. Although developed through study of Arabidopsis flowers, this model is generally applicable to other flowering plants.

Light sensing

The photoreceptors phytochrome A, B, C, D and E mediate red light based phototropic response. Understanding the function of these receptors has helped plant biologists understand the signalling cascades that regulate photoperiodism, germination, de-etiolation and shade avoidance in plants.

Arabidopsis was used extensively in the study of the genetic basis of phototropism, chloroplast alignment, and stomatal aperture and other blue light-influenced processes.^[19] These traits respond to blue light, which is perceived by the phototropin light receptors. Arabidopsis has also been important in understanding the functions of another blue light receptor, cryptochrome, which is especially important for light entrainment to control the plants circadian rhythms.^[20]

Light response was even found in roots, which were thought not to be particularly sensitive to light. While gravitropic response of Arabidopsis root organs is their predominant tropic response, specimens treated with mutagens and selected for the absence of gravitropic action showed negative phototropic response to blue or white light, and positive response to red light.^[21]

Non-Mendelian inheritance

In 2005, scientists at Purdue University proposed that Arabidopsis possessed an alternative to previously known mechanisms of DNA repair, which one scientist called a "parallel path of inheritance". It was observed in mutations of the HOTHEAD gene. Plants mutant in this gene exhibit organ fusion, and pollen can germinate on all plant surfaces, not just the stigma. After spending over a year eliminating simpler explanations, it was indicated that the plants "cached" versions of their ancestors' genes going back at least four generations, and used these records as templates to correct the HOTHEAD mutation and other single nucleotide polymorphisms. The initial hypothesis proposed that the record may be RNA-based^[22] Since then, alternative models have been proposed which would explain the phenotype without requiring a new model of inheritance^[23][24] More recently the whole phenomenon is being challenged as a being a simple artifact of pollen contamination.^[25] "When Jacobsen took great pains to isolate the plants, he couldn't reproduce the [reversion] phenomenon", notes Steven Henikoff.^[26] In response to the new finding, Lolle and Pruitt agree that Peng et al. did observe cross-pollination but note that some of their own data, such as double reversions of both mutant genes to the regular form, cannot be explained by cross pollination.^[27]

Multigen

This is an ongoing experiment on the International Space Station, it is being performed by the European Space Agency. The goals are to study the growth and reproduction of plants from seed to seed in microgravity.

Plant tissue culture

Plant Tissue Culture is a practice used to propagate plants under sterile conditions, often to produce clones of a plant. Different techniques in plant tissue culture may offer certain advantages over traditional methods of propagation, including:

• The production of exact copies of plants that produce particularly good flowers, fruits, or have other desirable traits.
• To quickly produce mature plants.
• The production of multiples of plants in the absence of seeds or necessary pollinators to produce seeds.
• The regeneration of whole plants from plant cells that have been genetically modified.
• The production of plants in sterile containers that allows them to be moved with greatly reduced chances of transmitting diseases, pests, and pathogens.
• The production of plants from seeds that otherwise have very low chances of germinating and growing, i.e.: orchids and nepenthes.
• To clean particular plant of viral and other infections and to quickly multiply these plants as 'cleaned stock' for horticulture and agriculture.

Plant tissue culture relies on the fact that many plant cells have the ability to regenerate a whole plant (totipotency). Single cells, plant cells without cell walls (protoplasts), pieces of leaves, or (less commonly) roots can often be used to generate a new plant on culture media given the required nutrients and plant hormones.

Techniques

Modern plant tissue culture is performed under aseptic conditions under filtered air. Living plant materials from the environment are naturally contaminated on their surfaces (and sometimes interiors) with microorganisms, so surface sterilization of starting materials (explants) in chemical solutions (usually alcohol or bleach) is required. Mercuric chloride is seldom used as a plant sterilant today, as it is dangerous to use, and is difficult to dispose of. Explants are then usually placed on the surface of a solid culture medium, but are sometimes placed directly into a liquid medium, particularly when cell suspension cultures are desired. Solid and liquid media are generally composed of inorganic salts plus a few organic nutrients, vitamins and plant hormones. Solid media are prepared from liquid media with the addition of a gelling agent, usually purified agar.

The composition of the medium, particularly the plant hormones and the nitrogen source (nitrate versus ammonium salts or amino acids) have profound effects on the morphology of the tissues that grow from the initial explant. For example, an excess of auxin will often result in a proliferation of roots, while an excess of cytokinin may yield shoots. A balance of both auxin and cytokinin will often produce an unorganised growth of cells, or callus, but the morphology of the outgrowth will depend on the plant species as well as the medium composition. As cultures grow, pieces are typically sliced off and transferred to new media (subcultured) to allow for growth or to alter the morphology of the culture. The skill and experience of the tissue culturist are important in judging which pieces to culture and which to discard.

As shoots emerge from a culture, they may be sliced off and rooted with auxin to produce plantlets which, when mature, can be transferred to potting soil for further growth in the greenhouse as normal plants.

Choice of explant

The tissue which is obtained from the plant to culture is called an explant. Based on work with certain model systems, particularly tobacco, it has often been claimed that a totipotent explant can be grown from any part of the plant. However, this concept has been vitiated in practice. In many species explants of various organs vary in their rates of growth and regeneration, while some do not grow at all. The choice of explant material also determines if the plantlets developed via tissue culture are haploid or diploid. Also the risk of microbial contamination is increased with inappropriate explants. Thus it is very important that an appropriate choice of explant be made prior to tissue culture.

The specific differences in the regeneration potential of different organs and explants have various explanations. The significant factors include differences in the stage of the cells in the cell cycle, the availability of or ability to transport endogenous growth regulators, and the metabolic capabilities of the cells. The most commonly used tissue explants are the meristematic ends of the plants like the stem tip, auxiliary bud tip and root tip. These tissues have high rates of cell division and either concentrate or produce required growth regulating substances including auxins and cytokinins.

Some explants, like the root tip, are hard to isolate and are contaminated with soil microflora that become problematic during the tissue culture process. Certain soil microflora can form tight associations with the root systems, or even grow within the root. Soil particles bound to roots are difficult to remove without injury to the roots that then allows microbial attack. These associated microflora will generally overgrow the tissue culture medium before there is significant growth of plant tissue.

Aerial (above soil) explants are also rich in undesirable microflora. However, they are more easily removed from the explant by gentle rinsing, and the remainder usually can be killed by surface sterilization. Most of the surface microflora do not form tight associations with the plant tissue. Such associations can usually be found by visual inspection as a mosaic, de-colorization or localized necrosis on the surface of the explant.

An alternative for obtaining uncontaminated explants is to take explants from seedlings which are aseptically grown from surface-sterilized seeds. The hard surface of the seed is less permeable to penetration of harsh surface sterilizing agents, such as hypochlorite, so the acceptable conditions of sterilization used for seeds can be much more stringent than for vegetative tissues.