4.3.4 Wetlands

Wetlands can be used in a similar way to buffer strips as a pollution control mechanism. They often present a relatively cost-effective and practical option for treatment, particularly in environmentally sensitive areas where large waste-water treatment plants are not acceptable. For example, Lake Manzala in Egypt has been suffering from severe pollution problems for several years. This lake is located on the northeastern edge of the Nile Delta, between Damietta and Port Said. Land reclamatio
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4.4.1 Diversion of effluent

In some circumstances it may be possible to divert sewage effluent away from a water body in order to reduce nutrient loads. This was achieved at Lake Washington, near Seattle, USA, which is close to the sea. Lake Washington is surrounded by Seattle and its suburbs, and in 1955 a cyanobacterium, Oscitilloria rubescens, became dominant in the lake. The lake was receiving sewage effluent from about 70 000 people; this input represented about 56% of the total phosphorus load to the lake.
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3.3 Mechanisms of eutrophication

Direct effects of eutrophication occur when growth of organisms (usually the primary producers) is released from nutrient limitation. The resulting increased NPP becomes available for consumers, either as living biomass for herbivores or as detritus for detritivores. Associated indirect effects occur as eutrophication alters the food supply for other consumers. Changes in the amount, relative abundance, size or nutritional content of the food supply influence competitive relationships between
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3.2.5 Sediments

Sediments have a variable but complex role in nutrient cycling in most aquatic systems, and are a potential ‘internal’ source of pollutants. Release of phosphorus from lake sediment is a complex function of physical, biological and chemical processes and is not easy to predict for different systems. Nitrogen is not stored and released from sediments in the same way, so its turnover time within aquatic systems is quite rapid. Nitrogen concentrations tend to fall off relatively quickly foll
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3.1 Agents of eutrophication

Light availability, water availability, temperature and the supply of plant nutrients are the four most important factors determining NPP. Altered availability of nutrients affects the rate of primary production in all ecosystems, which in turn changes the biomass and the species composition of communities.

SAQ 15
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2.4.1 Estuarine species

Nutrient runoff from the land is a major source of nutrients in estuarine habitats. Shallow-water estuaries are some of the most nutrient-rich ecosystems on Earth, due to coastal development and the effects of urbanization on nutrient runoff. Figure 2.19 shows some typical nitrogen pathways. Nitrogen loadings in rainfall are typically assimilated by plants or denitrified, but septic tanks tend to add nitrogen below the reach of plant roots, and if situated near the coast or rivers can lead to
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2.1.1 Loss of submerged plant communities

One of the symptoms of extreme eutrophication in shallow waters is often a substantial or complete loss of submerged plant communities and their replacement by dense phytoplankton communities (algal blooms). This results not only in the loss of characteristic plant species (macrophytes) but also in reduced habitat structure within the water body. Submerged plants provide refuges for invertebrate species against predation by fish. Some of these invertebrate species are phytoplankton-grazers an
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1.4 Human-induced eutrophication

While eutrophication does occur independently of human activity, increasingly it is caused, or amplified, by human inputs. Human activities are causing pollution of water bodies and soils to occur to an unprecedented degree, resulting in an array of symptomatic changes in water quality and in species and communities of associated organisms. In 1848 W. Gardiner produced a flora of Forfarshire, in which he described the plants growing in Balgavies Loch. He talked of ‘potamogetons [pondweeds]
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1.2 Resource availability and species diversity

A wide range of ecosystems has been studied in terms of their species diversity and the availability of resources. Each produces an individual relationship between these two variables, but a common pattern emerges from most of them, especially when plant diversity is being considered. This pattern has been named the humped-back relationship and suggests diversity is greatest at intermediate levels of productivity in many systems (Figure 1.5).

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8.3 Chromosome distribution within the nucleus

DNA from any one particular chromosome is a single chain, many millions of bases long, and this chain is attached to a scaffold structure. It is not surprising then, that if we examine the interphase nucleus, each chromosome is seen to fill a localised area. This localised distribution of individual chromosomes is illustrated in Figure 42 with an examination of human chromosomes within the interphase nucleus. In these examples, special DNA probes have been used to detect the location of the e
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8.2 Chromosome scaffolds

Most of the chromosomal DNA chains within the interphase nucleus are believed to be held on a scaffold or backbone structure made from various proteins, with loops of between 20 and 200 kb extruding from attachment sites. This chromosome structure is shown schematically in Figure 40. The scaffold, as well as permitting further compaction, serves to bring the DNA together in organised regions. There are many different protein components of these scaffolds, amongst them DNA topoisomerases.


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8.1 Introduction

The average human cell has around two metres of DNA within its nucleus. In the interphase nucleus, in which transcription and replication are going on, this DNA is packaged into nucleosomes that are variably compacted, through association with H1, into larger 30nm fibres. In fact, the average nucleus most likely contains DNA with a continuum of chromatin configurations, ranging from highly open 10 nm fibres, through to 30 nm fibres and fibres that are even more tightly packed together, call
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Core histone tail modification regulates DNA compaction

SAQ 34

What effect would neutralising the positive charges on the octamer N-terminal tails have upon the compaction of DNA by H1?

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The histone fold and formation of the nucleosome

We have seen how in the eubacterial chromosome, bending DNA serves to facilitate its compaction. A similar process occurs in eukaryotic cells in that DNA is bent and wrapped around a protein unit. In this case, the core unit is a protein–DNA complex termed a nucleosome. The nucleosome comprises the core histone proteins H2A, H2B, H3 and H4 arranged in a structure known as the core histone octamer, with an associated length of DNA. In order to understand how the nucleosome is a
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The histone proteins

The genes for the histone proteins are very highly conserved across eukaryotes, reflecting their importance in DNA packaging. The histone family consists of five groups of proteins, histones H1, H2A, H2B, H3 and H4. An examination of their amino acid content gives us clues as to how the histones fulfil their role in DNA packaging. Rather like the polyamines in bacteria, these proteins are highly positively charged, with up to 20% of their amino acids being lysine or arginine, the charged side
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The DPS protein compacts the eubacterial chromosome during stress

When an E. coli cell enters into stationary phase, transcription and cell division cease completely. In such cells, the normal chromatin components, such as those described above, are replaced by a negatively charged protein called DPS. The interaction between DPS and DNA appears to be a specialised bacterial adaptation to survive starvation. In normal conditions of growth, the DNA within the bacterial cell is distributed evenly throughout the entire cytoplasm. In stationary cells, how
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7.2 The eubacterial chromosome

Some of the diverse roles of chromatin components can be illustrated by examining the E. coli chromosome. Like most prokaryotes, E. coli has a single chromosome consisting of a single double-stranded circular DNA molecule. There is no nucleus present, but the E. coli DNA is within a discrete entity in the cytoplasm called the nucleoid. The nucleoid contains a multitude of proteins and is in close proximity to the ribosomes, where translation occurs. In addition to
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7.1 Introduction

Until now, we have discussed DNA primarily as a double helix, but in its natural state within the cell it is found packaged as a complex mixture with many different proteins and other components. You have already seen examples of proteins with specific roles to play, such as topoisomerases and the proteins with various DNA binding domains, but in this section we will turn our attention to the proteins that serve to pack and organise the DNA into what we call chromatin.

The packaging of
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Alkylating agents

There are many different chemicals that directly chemically modify DNA. The methyl group (—CH3) can be added to DNA at various sites, two of which we will discuss further. There are several alkylation-sensitive sites in guanosine (identified in Table 3e). For example, methylation at the 7-position of the guanine base (
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Reactive oxygen species

The metabolism that occurs in every cell and is associated with the basic requirements of physiology inevitably leads to the production of reactive intermediates, many of which are capable of reacting with DNA or free dNTPs, which could subsequently be incorporated during synthesis. One particular group of such molecules are called reactive oxygen species (ROS). The essential feature of ROS is the presence of an unpaired electron on an oxygen atom in the molecule, which enables the ROS to rea
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