1. Introduction 2

2. Structure of the bacterial PSU 5

2.1 Organization of the bacterial PSU 5

2.2 The crystal structure of the RC 9

2.3 The crystal structures of LH-II 11

2.4 Bacteriochlorophyll pairs in LH-II and the RC 13

2.5 Models of LH-I and the LH-I-RC complex 15

2.6 Model for the PSU 17

3. Excitation transfer in the PSU 18

3.1 Electronic excitations of BChls 22

3.1.1 Individual BChls 22

3.1.2 Rings of BChls 22

3.1.2.1 Exciton states 22

3.1.3 Effective Hamiltonian 24

3.1.4 Optical properties 25

3.1.5 The effect of disorder 26

3.2 Theory of excitation transfer 29

3.2.1 General theory 29

3.2.2 Mechanisms of excitation transfer 32

3.2.3 Approximation for long-range transfer 34

3.2.4 Transfer to exciton states 35

3.3 Rates for transfer processes in the PSU 37

3.3.1 Car→BChl transfer 37

3.3.1.1 Mechanism of Car→BChl transfer 39

3.3.1.2 Pathways of Car→BChl transfer 40

3.3.2 Efficiency of Car→BChl transfer 40

3.3.3 B800-B850 transfer 44

3.3.4 LH-II→LH-II transfer 44

3.3.5 LH-II→LH-I transfer 45

3.3.6 LH-I→RC transfer 45

3.3.7 Excitation migration in the PSU 46

3.3.8 Genetic basis of PSU assembly 49

4. Concluding remarks 53

5. Acknowledgments 55

6. References 55

Life as we know it today exists largely because of photosynthesis, the process through which light energy is converted into chemical energy by plants, algae, and photosynthetic bacteria (Priestley, 1772; Barnes, 1893; Wurmser, 1925; Van Niel, 1941; Clayton & Sistrom, 1978; Blankenship et al. 1995; Ort & Yocum, 1996). Historically, photosynthetic organisms are grouped into two classes. When photosynthesis is carried out in the presence of air it is called oxygenic photosynthesis (Ort & Yocum, 1996). Otherwise, it is anoxygenic (Blankenship et al. 1995). Higher plants, algae and cyanobacteria perform oxygenic photosynthesis, which involves reduction of carbon dioxide to carbohydrate and oxidation of water to produce molecular oxygen. Some photosynthetic bacteria, such as purple bacteria, carry out anoxygenic photosynthesis that involves oxidation of molecules other than water. In spite of these differences, the general principles of energy transduction are the same in anoxygenic and oxygenic photosynthesis (Van Niel, 1931, 1941; Stanier, 1961; Wraight, 1982; Gest, 1993). The primary processes of photosynthesis involve absorption of photons by light-harvesting complexes (LHs), transfer of excitation energy from LHs to the photosynthetic reaction centers (RCs), and the primary charge separation across the photosynthetic membrane (Sauer, 1975; Knox, 1977; Fleming & van Grondelle, 1994; van Grondelle et al. 1994). In this article, we will focus on the anoxygenic photosynthetic process in purple bacteria, since its photosynthetic system is the most studied and best characterized during the past 50 years.

1. Introduction 63

1.1 Outline 63

1.2 Universals versus realizations in the study of learning and memory 64

2. Large random cortical networks developing ex vivo 65

2.1 Preparation 65

2.2 Measuring electrical activity 67

3. Spontaneous development 69

3.1 Activity 69

3.2 Connectivity 70

4. Consequences of spontaneous activity: pharmacological manipulations 72

4.1 Structural consequences 72

4.2 Functional consequences 73

5. Effects of stimulation 74

5.1 Response to focal stimulation 74

5.2 Stimulation-induced changes in connectivity 74

6. Embedding functionality in real neural networks 77

6.1 Facing the physiological definition of ‘reward’: two classes of theories 78

6.2 Closing the loop 79

7. Concluding remarks 84

8. Acknowledgments 85

9. References 85

The phenomena of learning and memory are inherent to neural systems that differ from each other markedly. The differences, at the molecular, cellular and anatomical levels, reflect the wealth of possible instantiations of two neural learning and memory universals: (i) an extensive functional connectivity that enables a large repertoire of possible responses to stimuli; and (ii) sensitivity of the functional connectivity to activity, allowing for selection of adaptive responses. These universals can now be fully realized in ex-vivo developing neuronal networks due to advances in multi-electrode recording techniques and desktop computing. Applied to the study of ex-vivo networks of neurons, these approaches provide a unique view into learning and memory in networks, over a wide range of spatio-temporal scales. In this review, we summarize experimental data obtained from large random developing ex-vivo cortical networks. We describe how these networks are prepared, their structure, stages of functional development, and the forms of spontaneous activity they exhibit (Sections 2–4). In Section 5 we describe studies that seek to characterize the rules of activity-dependent changes in neural ensembles and their relation to monosynaptic rules. In Section 6, we demonstrate that it is possible to embed functionality into ex-vivo networks, that is, to teach them to perform desired firing patterns in both time and space. This requires ‘closing a loop’ between the network and the environment. Section 7 emphasizes the potential of ex-vivo developing cortical networks in the study of neural learning and memory universals. This may be achieved by combining closed loop experiments and ensemble-defined rules of activity-dependent change.

1. Triple-helical nucleic acids 89

1.1 History 89

1.2 Use of oligomers in triplex formation 90

2. Modes of triplex formation 90

2.1 Intermolecular triplexes 90

2.2 Intramolecular triplexes (H-DNA) 92

2.3 R-DNA (recombination DNA) 92

2.4 PNA (peptide nucleic acids) 93

3. Triplex structural models 93

3.1 YR-Y triplexes 94

3.2 GT-A base triplets 94

3.3 TC-G base triplets 94

3.4 TA-T and C+G-C base triplets 94

3.5 RR-Y triplexes 94

4. Modifications of TFOs 95

4.1 Backbone modification of oligonucleotides 95

4.2 Modification of the ribose in oligonucleotides 96

4.3 Base modification of oligonucleotides 97

5. Gene targeting and modification via triplex technology 98

5.1 Transcription and replication inhibition 99

5.2 TFO-directed mutagenesis 99

5.3 TFO-induced recombination 100

5.4 Future challenges in triplex-directed genome modification 100

6. References 101

The first description of triple-helical nucleic acids was by Felsenfeld and Rich in 1957 (Felsenfeld et al. 1957). While studying the binding characteristics of polyribonucleotides by fiber diffraction studies, they determined that polyuridylic acid [poly(U)] and polyadenylic acid [poly(A)] strands were capable of forming a stable complex of poly(U) and poly(A) in a 2:1 ratio. It was therefore concluded that the nucleic acids must be capable of forming a helical three-stranded structure. The formation of the three-stranded complex was preferred over duplex formation in the presence of divalent cations (e.g. 10 mm MgCl2). The reaction was quite specific, since the (U-A) molecule did not react with polycytidylic acid [(poly(C)], polyadenylic acid or polyinosinic acid [(poly(I)] (Felsenfeld et al. 1957). It was later found that poly(dT-dC) and poly(dG-dA) also have the capacity to form triple-stranded structures (Howard & Miles, 1964; Michelson & Monny, 1967). Other triple helical combinations of polynucleotide strands were identified from X-ray fiber-diffraction studies including, (A)n.2(I)n and (A)n.2(T)n (Arnott & Selsing, 1974). X-ray diffraction patterns of triple-stranded fibers of poly(A).2poly(U) and poly(dA).2poly(dT) showed an A-form conformation of the Watson–Crick strands. The third strand was bound in a parallel orientation to the purine strand by Hoogsteen hydrogen bonds (Hoogsteen, 1959; Arnott & Selsing, 1974). In 1968, the first potential biological role of these structures was identified by Morgan & Wells (1968). Using an in vitro assay, they found that transcription by E. coli RNA polymerase was inhibited by an RNA third strand. Thus, the recent developments identifying the potential of triplex formation for gene regulation and genome modification came more than 20 years after this first study of transcription inhibition by triplex formation.