The Mechanical Genome in Regulation and Infection

Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in the process of viral DNA ejection, which mediates information transfer and exchange and has prominent implications in evolution. As in the case of Kepler's laws of planetary motion leading to Newton's gravitational theory, and the allometric scaling laws in biology revealing the organizing principles of complex networks [4], experimental data collapse in these biological phenomena has guided much of our studies and urged us to find the underlying physical principles.

The Permanent Okavango River Basin Water Commission annual report 2009

First published annual report of OKACOM, covering first period of Sida-funded three year workplan from 2007 until 2009, during which the Secretariat was established. (PDF contains 32 pages)

The Okavango River Basin Transboundary Diagnostic Analysis: reimagining the river

OKACOM's Transboundary Diagnostic Analysis study used integrated flows analysis to develop scenarios for possible developments in the Okavango River Basin. (PDF contains 2 pages)

The Regulation of Sleep and Circadian Rhythms: The Role of Melatonin and Adenosine in Zebrafish

Sleep is a highly conserved behavioral state whose regulation is still unclear. In this thesis I initially briefly introduce the known sleep circuitry and regulation in vertebrates, and why zebrafish is seen as a good model to study sleep-regulation. I describe the existing two-process model of sleep regulation, which posits that the two processes C (circadian) and S (homeostatic) control timing of sleep-wake behavior. I then study the role melatonin plays in the circadian regulation of sleep using zebrafish. Firstly, we find that the absence of melatonin results in a reduction of sleep at night, establishing that endogenous melatonin is required for sleep at night. Secondly, melatonin mutants show a reduction in sleep in animals with no functional behavioral rhythms suggesting that melatonin does not require intact circadian rhythms for its effect on sleep. Thirdly, melatonin mutants do not exhibit any changes in circadian rhythms, suggesting that the circadian clock does not require melatonin for its function. Fourthly, we find that in the absence of melatonin, there is no rhythmic expression of sleep, suggesting that melatonin is the output molecule of process C. Lastly, we describe a connection between adenosine signaling (output molecules of process S), and melatonin. Following this we proceed to study the role adenosine signaling plays in sleep-wake behavior. We find that firstly, adenosine receptor A1 and A2 are involved in sleep- wake behavior in zebrafish, based on agonist/antagonist behavioral results. Secondly, we find that several brain regions such as PACAP cells in the rostral midbrain, GABAergic cells in the forebrain and hindbrain, Dopamine and serotonin cells in the caudal hypothalamus and sox2 cells lining the hindbrain ventricle are activated in response to the A1 antagonist and VMAT positive cells are activated in response to the A2A agonist, suggesting these areas are involved in adenosine signaling in zebrafish. Thirdly, we find that knocking out the zebrafish adenosine receptors has no effect on sleep architecture. Lastly, we find that while the A1 agonist phenotype requires the zfAdora1a receptor, the antagonist and the A2A agonist behavioral phenotypes are not mediated by the zfAdora1a, zfAdora1b and zfAdoraA2Aa, zfAdora2Ab receptors respectively.

Changes in Fish Communities in the Upper Patuxent River from 1966 to 1977

Ten year comparison of fish survey's with respect to diversity evenness and composition of fish communities. The upper Patuxent River was divided into Piedmont Plateau and Coastal Plain regions, not only for geographical purposes, but also because of the clustering of sewage treatment plants in the Coastal Plain region. In the Piedmont Plateau region, the fish species diversity changed very little from 1966 to 1977 ( Little Patuxent -- 2.82 to 2.66; Middle Patuxent -- 2.86 to 2.83; and main stem -- 2.46 to 2.63), except in a section of Little Patuxent River at and below the City of Columbia where the species diversity index showed a significant reduction from 2.97 to 1.99, and in a section of the main stem Patuxent River immediately downstream from the Brighton Dam of the Triadelphia Reservoir where the index increased significantly from 1.66 to 3.20. In the Coastal Plain region, a significant reduction in the fish species diversity index occurred between 1966 and 1977 below the two sewage treatment plant outfalls : Savage -- 2.69 to 0 and Patuxent-Crofton -- 3.06 to 1.33. Also, the substantial reduction in the species diversity index which had already occurred in 1966 below the six other plant: outfalls of Fort Meade No. I, Fort Meade No. 2, Maryland House of Correction, Maryland City , Parkway and Bowie, remained depressed in 1977. On the other hand, below the Horsepen Sewage Treatment Plant (a tertiary plant practicing dechlorination) the species diversity index increased from 1.91 to 2.8. (PDF contains 48 pages)

The Colorado River; a source of water and power for Los Angeles

The rapid growth and development of Los Angeles City and County has been one of the phenomena of the present age. The growth of a city from 50,600 to 576,000, an increase of over 1000% in thirty years is an unprecedented occurrence. It has given rise to a variety of problems of increasing magnitude.

Chief among these are: supply of food, water and shelter development of industry and markets, prevention and removal of downtown congestion and protection of life and property. These, of course, are the problems that any city must face. But in the case of a community which doubles its population every ten years, radical and heroic measures must often be taken.

Ecological study of the River Lambourn. Report for the period October 1970 to March 1972

A small investigation of the ecology of the river Lambourn was carried out during 1967-70. During this period it became clear that detailed and reliable information could only be obtained by a much larger investigation. The present study was planned to meet the minimum requirements. No pumping is expected during this period and, since the pumping carried out during the pilot scheme was on a small scale, it is reasonable to assume that the river is still relatively unaffected by pumping.The present investigation has two main objectives both of which depend on obtaining a detailed picture of the ecology of the river at the present time. First, it will provide basic information on the state of the river prior to the development of the pumping scheme which will be available for comparison at any later date. Secondly, it may be possible to use some of the data to predict the ecological changes which may occur if the flow of the river is altered by the pumping scheme. This report is part of a series of fives studies on the River Lambourn which were undertaken between 1970 and 1979. [PDF contains 83 pages]

Ecological study of the River Lambourn. Report for the period October 1970 to September 1973

Few detailed studies have been made on the ecology of the chalk streams. A complex community of plants and animals is present and much more information is required to achieve an understanding of the requirements and interactions of all the species. It is important that the rivers affected by this scheme should be studied and kept under continued observation so that any effects produced by the scheme can be detected. This need has been recognised by the Thames Conservancy and the Water Resources Board who jointly sponsored this investigation on one of the chalk streams involved in the scheme. The present investigation has two main objectives both of which depend on obtaining a detailed picture of the ecology of the river at the present time. First, it will provide basic information on the state of the river prior to the development of the pumping scheme which will be available for comparison at any later date. Secondly, it may be possible to use some of the data to predict the ecological changes which may occur if the flow of the river is altered by the pumping scheme. The study covers suspended solids, invertebrates, fish.This report is part of a series of fives studies on the River Lambourn which were undertaken between 1970 and 1979. [PDF contains 24 pages]

Ecological study of the River Lambourn. Report for the period October 1973 to September 1977

The investigations described in this report were carried out to fulfill three distinct but interrelated objectives. In 1973 the Thames Conservancy were making plans for a second stage of their groundwater scheme which would take water from the chalk aquifers in the valley of the Kennet and they wanted basic information on the ecological state of this river and its upper tributaries. Little appeared to be known about limestone streams and a preliminary study of one of the streams in this area was desirable as a basis for planning more detailed studies if these were needed later. At a progress meeting held in March 1976 the problems and opportunities presented by the developing drought conditions were considered. It was concluded that the ecological effects of the exceptionally low natural flows should be studied and that it would be important to assess the ecological impact of the groundwater scheme if it was brought into operation that year. This could only be done on the Lambourn and the Winterbourne and it was decided that considerable effort should be diverted there for this purpose and that the field observations should be extended to cover any recovery period after the end of the drought. To make this possible it was agreed that the studies of invertebrates and detritus on the Kennet should be reduced considerably and that the proposed study of the limestone stream should be abandoned. The revised objectives were as follows: A detailed ecological study of several sites on the Kennet and its tributaries above Kintbury, extending over at least two years and involving observations on wate r weeds , invertebrates, fish, detritus and the trophic relationships within the river community. Quantitativ e and qualitative sampling of water weeds and invertebrates during one year at a number of sites on several chalk streams to determine whether the patterns and relationships found in the Lambourn are also found at the other sites. Observations on the Lambourn at Bagnor were to continue for most of the period to look for long-term fluctuations and to enable these sites to act as controls with which the other sites could be compared. Further detailed studies on the Lambourn and the Winterbourne to assess the impact of low flows, trial pumping and the operation of the groundwater scheme.

Composition and bulk properties of Dorset river gravels

Considerable interest has been expressed in the composition of the stream gravels, the movement of bed materials and the relationship of sediment composition, packing and siltation of void space to invertebrate ecology. In the autumn of 1982, freeze-samples of gravel were obtained in Dorset streams. Data were required on the depth of salmonid egg pocke and were part of a broader investigation of regional variation in the independent variables of salmonid fish length, gravel size, current velocity and the resultant dependent variable ~egg burial depth. The Dorset river gravels examined are bimodal. The grain size distribution may be resolved into two near-normal frequency distributions interpreted as representing a primary framework or lattice of gravel particles into which a secondary matrix population of sand particles has penetrated.

The fish populations of the River Avon, Hampshire, downstream of Salisbury, in 1987

The objective of this study is to describe the present statu s of the coarse fish populations of the River Avon, Hampshire. The study arose from a widespread concern among anglers and riparian owners that fish numbers had decreased since the early 1970's, and from a scarcity of accurate information on population densities on which to assess this complaint. It was realised at the outset that, without such information from earlier years, the survey would not reveal the extent of any decline in the fisheries. The result s of the survey are compared with available data from other rivers , chiefly the nearby R. Frome and R. Stour. They may be used to assess any futur e changes in population densities and growth rates, and to indicate promising areas for future research. The data were collected from a quantitative survey of twelve river sections along the fifty kilometres of river between Salisbury and Sopley, and a qualitative survey of three weir pools within the same area from 14 September to 9 October, 1987.

Physiological aspects of the life cycle of the river lamprey, Lampetra fluviatilis L

The life cycle of the river lamprey, L. fluviatilis, is reviewed. The larval lamprey, or ammocoete, is a blind, filter-feeding animal, which normally lies concealed in the silt deposits of streams and rivers. After a period of 3-5 years in fresh water the ammocoete undergoes a metamorphosis in the summer months into a sexually immature, non-feeding stage known as the macrophthalia, which is active. This stage migrates downstream in late winter. It adopts a parasitic existence, in intertidal areas. After 18 months it returns to spawn in fresh water, after a final freshwater stage lasting up to 9 months. The river lamprey dies within a few days after the spawning period of 3-4 weeks, and none survive to spawn the following year.

The impact of Cow Green Reservoir on invertebrate populations in the River Tees

Cow Green is a new reservoir situated in Pennine moorland. It has an area of 312 ha, a capacity of 40 . 9 x 10 SUP-6 m SUP-3 and a maximum depth of 22 . 8 m. The function of the reservoir is to regulate flow in the River Tees to provide industrial Teesside with sufficient water during the dry spells. Invertebrate studies were carried out in the Tees to monitor changes resulting from the construction of the reservoir both in the flooded basin and below the dam. The overall effect of the reservoir on the Tees has been to increase the numbers and biomass of certain taxa, but generally not at the expense of previous fauna. Some of the positive effects, ie. increase in number and biomass, and maintenance of faunal diversity, may in part be attributable to the presence of the rapids and waterfall. Turbulence resulting from this rapid flow over heterogeneous bottom is sufficient to prevent clogging of interstitial spaces by silt and to maintain the variety of ecological niches necessary for a diverse fauna.

Effects of Cow Green Reservoir upon downstream fish populations

Post impoundment observations on the fish populations of the River Tees, downstream from the Cow Green Reservoir were made between 1971 and 1980. Both bullhead (Cottus gobio L.) and brown trout (Salmo trutta L.) population densities increased in the river after impoundment but changes in growth rate were small. Investigations into the stomach contents of the two species reflects the results of other work on increases of benthos in the river. Following regulation there was an increase in the quantity of Ephemerella ignita found in trout stomachs while in the bullhead, regulation caused an increase in the importance of Mollusca and a decrease in importance of Ephemeroptera and Plecoptera.

Impact of watercress cultivation on river water quality: progress report for the period, January - December 1987

The objective of this short project progress report is to investigate the possible water quality implications of modern watercress growing practices. Chalk receiving watercourses are usually of high supply, amenity, game fishing and fish farming value. Any headwater pollution load, therefore, needs characterising and quantifying. Two sites of watercress farming were studied in 1986-87 and nutrient levels examined. Different approaches of watercress farmers in Dorset and Hampshire are summarised.