A comparison of line transect versus linear percentage sampling for evaluating stony coral (Scleractinia andMilleporina) community similarity and area coverage on reefs of the central Bahamas

Three methods of evaluating stony coral communities were used on selected reefs in the Exuma Cays Land and Sea Park (24°22N, 77°30W) in the central Bahamas. Shallow reefs (< 4 meters depth) were selected from aerial surveys based on size, location, and physical setting, and grouped into three community types: (1) channel patch reefs, (2) soft-coral-sponge patch reefs and (3) fringing reefs. Three survey techniques used to evaluate the stony coral communities were a) species presence and absence lists, b) linear percentage and c) line transects using 1 mx1 m grids. Data collected from these survey methods was used to calculate coral colony density, species area coverage, and species diversity based on colony number and based on linear (cm) coral cover. The linear percentage sampling was considered too convervative in determining distribution patterns of a reef community; this technique takes into account the massive reef framework species such asM. annularis. The line transect technique can account for both colony number and area coverage, thus is a better method for characterizing reef communities. Sample size considerations are discussed for future applications of survey techniques for ground-truthing digital images of small, shallow reef communities.     

Recent changes in coral assemblages of a South African coral reef, with recommendations for long-term monitoring

Two-mile reef, Sodwana, South Africa is an unusual coral reef, being situated on a submerged fossilized sand dune and being very southerly (27°54). It is a popular Scuba diving venue receiving about 100000 dives year^–1. The line-intercept transect method, as recommended by the global coral reef monitoring network (GCRMN), was used to determine soft coral, hard coral and other benthos percentage cover. Physical coral damage, disease and bleaching were also recorded. Results were compared with those of B. Riegl (1993 – unpublished PhD thesis) 5 to 7 years earlier. The reef appears to be ecologically and highly dynamic. In the interim, there has been an increase in living benthos cover of 22.3% but also an increase in coral bleaching from 0% in 1993 to 1% in 1998. Physical damage, despite the large number of dives on the reef was minimal (1.52%), although it appears as if coral diseases may be increasing. The 20-m transects recommended by GCRMN are too long for this highly rugose reef with its distinct ridges and gullies. It is recommended that benthos cover, coral damage, bleaching and disease should be monitored annually using 40 5-m transects on the reef ridges and 40 5-m transects on the reef slopes.     

Observation of a distinct transition in the mode of interconversion of ring pucker conformers in non-crystalline d-ribose-2'-d from 2H NMR spin-alignment

Internal motions of d-ribose selectively ²H-labeled at the 2 position were measured using solid state ²H NMR experiments. A sample of d-ribose-2 -d was prepared in a hydrated, non-crystalline state to eliminate effects of crystal-packing. Between temperatures of –74 and –60°C the C2–H2 bond was observed to undergo two kinds of motions which were similar to those of C2–H2/H2 found previously in crystalline deoxythymidine (Hiyama et al. (1989) J. Am. Chem. Soc., 111, 8609–8613): (1) Nanosecond motion of small angular displacement with an apparent activation energy of 3.6 ± 0.7 kcal mol^–1, and (2) millisecond to microsecond motion of large amplitude with an apparent activation energy 4 kcal mol^–1. At –74°C, the slow, large-amplitude motion was best characterized as a two-site jump with a correlation time on the millisecond time scale, whereas at –60°C it was diffusive on the microsecond time scale. The slow, large-amplitude motions of the C2–H2 bond are most likely from interconversions between C2-endo and C3-endo by way of the O4-endo conformation, whereas the fast, small-amplitude motions are probably librations of the C2–H2 bond within the C2-endo and C3-endo potential energy minima.     

Hard-coral distribution and cold-water disturbances in South Florida: variation with depth and location

Line transects were used to sample the structure and diversity of the hermatypic coral community (Scleractinia) on four shallow shelf-edge reefs in South Florida (25° 22N to 25° 29N). Low diversities, cover and abundance indicated that this area was a suboptimum habitat for reef-building corals. The lack of acroporids on the shallow fore-reef, the increase in total coral cover with depth and the greater abundance of Montastrea annularis in the deepest zones suggests that cooling of surface water during severe winter cold fronts is a major environmental control on the distribution of hermatypic corals with depth. Such disturbances, occurring more frequently than hurricanes, may preclude the hard-coral community from attaining higher levels of cover and abundance. The shallow zones on the reefs nearest to tidal passes, through which cooled by water enters the reef tract, had the least developed community. In the deeper reef-zones, species richness and abundance increased from north to south over a distance of 13 km.     

The influence of habitat on the size distribution of groupers in the upper Florida Keys

Synopsis The influence of habitat on the size distribution of groupers was examined at sites in the middle and upper Florida Keys. Transects were used to quantify the size distribution of groupers at study sites. There were significant differences in the size distribution of groupers within and among reef community types related to differences in species composition and patch reef size. Groupers with a giant life-history style (Sullivan & de Garine 1994) were more abundant, but smaller, on inshore patch reefs than offshore reef community types. However, grouper species with a dwarf life-history style (Sullivan & de Garine 1994) showed an opposite pattern with a lower abundance, but larger size, inshore than offshore. The length category of groupers constituting the majority of individuals observed on patch reefs was inversely related to reef size. Graysby Epinephelus cruentatus were shown to recruit to deeper (15–20 m), low-relief habitats offshore. Several factors influenced the size distribution of groupers in the study sites including habitat type, spear-fishing, competition, predation, and recruitment.     

Purification and characterization of the 5′ → 3′ exonuclease domain-deleted Thermus filiformis DNA polymerase expressed in Escherichia coli

The gene encoding 5 3 exonuclease domain-deleted Tfi DNA polymerase, named 5 3 Exo^– Tfi fragment, from Thermus filiformis was expressed in Escherichia coli under the control of the tac promoter on a high-copy plasmid, pJR. The expressed enzyme was purified 27-fold with a 19% yield and a specific activity of 2621 U mg^–1 protein. The 5 3 exonuclease domain of Tfi DNA polymerase was removed without significant effect on enzyme activity and stability. PCR conditions for the 5 3 Exo^– Tfi fragment were more tolerant to the buffer composition as compared to the full-length enzyme.     

Oligomerization of deoxynucleoside-bisphosphate dimers: Template and linkage specificity

Evidence is presented that a poly(U) template selectively favors the oligomerization of the activated, 3–5 pyrophosphate-linked dimer pdAppdAp, in comparison with the 3–3 and 5–5 linked dimers. In the absence of poly(U), the 5–5linked dimer is the most reactive, and chains are formed which are more than 60 monomer units in length.Nucleic Acid-Like Structures V. For the previous paper in this series see Visscher and Schwartz (1988).     

Identification of the site of translational frameshifting required for production of the transposase encoded by insertion sequence IS 1.

Summary Previous genetic analyses indicated that translational frameshifting in the –1 direction occurs within the run of six adenines in the sequence 5-TTAAAAAACTC-3 at nucleotide positions 305–315 in IS 1, where the two out-of-phase reading frames insA and B-insB overlap, to produce transposase with a polypeptide segment Leu-Lys-Lys-Leu at residues 84–87. IS 1 mutants with a 1 by insertion, which encode mutant transposases with an amino acid substitution within the polypeptide segment at residues 84–87, did not efficiently mediate cointegration, except for an IS 1 mutant which encodes a mutant transposase with a Leu-Arg-Lys-Leu segment instead of Leu-LysLys-Leu. An IS 1 mutant with the DNA segment 5-CTTAAAAACTC-3 at positions 305–315 carrying the termination codon TAA in the B-insB reading frame could still mediate cointegration, indicating that codon AAA for Lys corresponding to second, third and fourth positions in the run of adenines is the site of frameshifting. The -galactosidase activity specified by several IS 1- lacZ fusion plasmids, in which B-insB is in-frame with lacZ, showed that the region 292–377 is sufficient for frameshifting. The protein produced by frameshifting from the IS 1-lacZ plasmid in fact contained the polypeptide segment Leu - Lys - Lys - Leu encoded by the DNA segment 5-TTAAAAAACTC-3, indicating that –1 frameshifting does occur within the run of adenines.     

Structural phase diagrams of animal communities in assessment of freshwater ecosystem conditions

A phase diagram method, using indices of biological diversity, was applied to describe the dynamics of zooplankton and fish community structure in natural and experimental conditions. The phase diagram is constructed in the coordinates H and dH × dt^–1, where H is the index of diversity of the community. The method reveals zones of steady state of a community and demonstrates community dynamics in undisturbed and disturbed conditions. Analysis of zooplankton dynamics in a fishless pond showed that in the absence of disturbances the community enters a zone of steady state (around dH × dt^–1=0) and stays in it for a long time. Under the action of disturbances (e.g. oxygen depletion for fish, influence of heavy metals for zooplankton) the community leaves the steady state zone. The greater the disturbance, the more the system deviates from steady state.     

The removal of a heated water discharge from a lake and the effect upon an epiphytic algal community

The effects of the removal of a heated water discharge from Lake Wabamun, Alberta (longitudes 114°26 and 114°44W; latitudes 53°30 and 53°35N) upon epiphytic algae has been documented. Due to the timing of the cessation of flow the first year without elevated temperatures was one of transition. Standing crops returned to normal lake levels the following year. Species composition changes occurred, and species such as Epithemia turgida, Amphipleura pellucida, Nitzschia fonticola, Rhopalodia gibba, Rivularia haematites, and Scytonema alatum, all of which were detrimentally affected by the elevated temperatures, returned to the previously affected area, while species such as Oedogonium sp., Spirogyra sp. and Cladophora glomerata, dominant at times in the heated area, diminished in importance. The ability of Cocconeis placentula to grow at low light intensities (15–110 µEinsteins m^–2 s^–1) was again demonstrated.     

Influence of the xyloadenosine analogue of 2′,5′-oligoriboadenylate on poly(A)-specific, 2′,5′-oligoriboadenylate degrading 2′,3′-exoribonuclease and further enzymes involved in poly(A)(+)mRNA metabolism

The homogeneous poly(A)-specific 2,3-exoribonuclease from calf thymus gland, which cleaves both 3,5-and 2,5-linked oligoriboadenylates, does not degrade (xyloA2'p)₂ xyloA, the xylofuranosyladenosine analogue of the 2-5A core. This oligonucleotide, which is supposed to enter intact cells rapidly, was found to possess an increased stability and an enhanced antiherpesvirus activity compared to the natural (A2'p)₂A (Eppstein, D. A., Barnett, J. W., Marsh, Y. V., Gosselin, G. and Imbach, J.-L. (1983) Nature 302, 723–724). The poly(A) anabolic enzyme, poly(A) polymerase (Mn²⁺-dependent), from the same source, which is initiated by (A3'p)₂A and its higher oligomers, does not accept 2–5A core and its xyloadenosine analogue as primer. Both oligonucleotides exert no influence on endoribonuclease IV and on the integrity of the poly(A)-ribonucleoprotein complex.Abbreviations 2-5A ppp(A2'p)_nA(n2). 5-triphospho-oligo [(2–5)adenylyl]adenosine - 2-5A core (A2'p)₂A, adenylyl(2–5) adenylyl(2–5)adenosine - xyto 2-tA core (xyloA2'p)₂ xyloA, xyloadenylyl(2–5)xyloadenylyl(2–5)xyloadenosine The other abbreviations are according to the recommendations of the Commission on Biochemical Nomenclature, see Europ. J. Biochem.15 (1970) 203–208.     

Phase shifts in coral reef communities and their ecological significance

Many coral reefs around the world have degraded to a degree that their present intrinsic value and utility are greatly reduced: (mass coral mortality followed by algal invasions; local depletions of reef fisheries; deficit of reef accretion compared to physical and biological erosion). Though we can sometimes identify proximal causes (outbreaks of coral predators and eroders; over-fishing; habitat destruction), we do not have a good understanding of how population, community and ecosystem structure and function differ in degraded from un-degraded reefs. The deficiencies in our understanding limit our ability to interpret the long-term significance of reef degradation, and therefore to develop scientifically based plans for conservation and management of reefs.A particular course of action, or lack of action, based on uncritical acceptance of any of the various views of temporal variability can lead to further deterioration of specific reefs. None of these views — that reefs are either inherently robust, inherently fragile, or inherently resilient — is true over all time-space scales. This presentation reviews various models and case studies which suggest that reefs can be knocked precipitously or move slowly from one phase (coral-dominated) to another (coral-depleted and/or algal dominated). Transitions in the other direction (recovery) involve changes (e.g. succession) in populations and communities (of all reef-associated biota, not just sessile benthos), and in reef function (e.g. community metabolism, trophodynamics) which are of great intrinsic interest but only poorly understood.     

The role of herbivorous fishes and urchins in coral reef communities

Synopsis Herbivorous fishes and invertebrates are conspicious elements of coral reef communities where they predominate both in numbers and biomass. Herbivores and the coral reef algae on which they feed represent a co-evolved system of defense and counter-defense. Algal species have developed toxic, structural, spatial and temporal defense or escape mechanisms, while the herbivores employ strategies that involve anatomical, physiological and behavioral adaptations. Current research demonstrates that many reef fishes are highly selective in the algae they consume. Food selection in these fishes may be correlated with their morphological and digestive capabilities to rupture algal cell walls. Sea urchins select more in accordance with relative abundance, although certain algal species are clearly avoided.The determinants of community structure on coral reefs have yet to be established but evidence indicates a strong influence by herbivores. Reef herbivores may reduce the abundance of certain competitively superior algae, thus allowing corals and cementing coralline algae to survive. We discuss how the foraging activities of tropical marine herbivores affect the distribution and abundance of algae and how these activities contribute to the development of coral reef structure and the fish assemblages which are intimately associated with reef structure.This paper forms a part of the proceedings of a mini-symposium convened at Cornell University, Ithaca, N.Y., 18–19 May 1976, entitled Patterns of Community Structure in Fishes (G. S. Helfman, ed.).     

The life cycle of Laminaria abyssalis (Laminariales,Phaeophyta) in culture

Laminaria abyssalis occurs in deep water in tropical latitudes of the Brazilian coast (19° 23 S, 38° 28 W to 22° 54 S, 42° 13 09 W). Its life cycle has been completed in the laboratory in seven months using different conditions of light and temperature. The gametophytic stage required for growth the low photon flux density of 1.2 ± 0.3 µmol m^–2 s^–1 and 18 °C, while the juvenile and adult sporophytes needed 15 µmol m^–2 s^–1 and 18 °C. The sporophytes became fertile at 23 °C. Our results showed that light and temperature are the main factors regulating the growth and life history of this species under the culture conditions tested.     

Stand structure and woody species diversity in relation to stand stratification in a subtropical evergreen broadleaf forest, Okinawa Island

Stand structure and woody species diversity in a subtropical evergreen broadleaf forest grown in a silicate habitat, Okinawa Island, have been investigated on the basis of stand stratification. The forest stand consisted of four layers. The floristic composition of the top and the lower three layers was only slightly similar, although approximately one-third of the species were common to them. Mean tree weight decreased from the top toward the bottom layer whereas tree density increased from the top downward. This trend resembled the mean weight–density trajectory of self-thinning plant populations. The relationship between mean tree height and tree density for the upper two layers supported Yamakuras quasi –1/2 power law of tree height. The values of the Shannon–Wiener index, H, and the equitability index, J, tended to increase from the top layer downward except for the bottom layer. The values of H and J were, respectively, 4.83 bit and 0.82 for trees taller than 0.10 m. The lower layers contained many species of smaller height. High species diversity of the forest depended on small trees in the lower layers. Conservation of small trees in the lower layers, especially the bottom layer, is indispensable for sound maintenance of Okinawan evergreen broadleaf forests.     

Biochemical and immunological responses of hairy cell leukemia patients to interferonβ

Summary Ten hairy-cell leukemia patients were treated with interferon (IFN-) at a dose rate of 2 × 10⁶ IU/m² × 5 days for 4 weeks (induction therapy) and, thereafter, at the same dose three times a week for 11 months (maintenance therapy). The effect of this treatment on serum neopterin, 2-microglobulin, (2–5)oligoadenylate [(2–5)A _n ] levels, intracellular (2–5)A _n values and human Mx protein synthesis was analysed. There were significant rises in serum neopterin and (2–5)A _n levels during both induction and maintenance, whereas 2-microglobulin levels rose only during induction. Rises in intracellular (2–5)A _n were documented mainly during induction, but they were not significantly higher than pretherapy values. IFN provoked an increase in human Mx protein synthesis over the entire induction — maintenance period, but was only significantly higher than baseline during induction. All markers proved useful for monitoring the effects of IFN dose schedules, but were not predictive of clinical outcome. Natural killer activity and IFN production, which were initially defective, followed a different trend from that of the other factors studied, in that increases were documented only late in the course of therapy when the disease was already in remission.     

Characteristics of βA chromosome haplotypes in Japanese

DNA polymorphism patterns linked to the ^A-globin gene were analyzed in healthy Japanese using four different restriction endonucleases. The chromosomes with the ^A-globin gene were mapped through an evaluation of the presence of seven different restriction sites (HincII 5 to ; HindIII in ^G and ^A; HincII in, and 3 to, ₁; AvaII in ; Bam-HI 3 to ). Among 36 chromosomes analyzed, 20 chromosomes had a haplotype of [+–––––+]. Among 55 individuals examined, 7 possessed a homozygous haplotye of [+–––––+]. All Japanese with the ^AT-globin gene had a subhaplotype of [–++–+] 5 to the -globin gene. Their major haplotypes were [–++–+–+] and [–++–++–]. It was expected that the presence of the ^AT-globin gene in Japanese may be deduced from subhaplotypes 5 to the -globin gene.     

Regioselective preparation of 2′, 3′-di-O-acylribonucleosides carrying lipophilic acyl groups through a lipase-catalysed alcoholysis

Candida antarctica B lipase-catalysed alcoholysis of 2, 3, 5-tri-O-hexanoyluridine (1a), 2, 3, 5-tri-O-dodecanoyluridine (1b), 2, 3, 5-tri-O-hexanoylinosine (1c) and 2, 3, 5-tri-O-dodecanoylinosine (1d) proceeded regioselectively to produce the corresponding 2, 3-di-O-acylribonucleosides 2a–d, providing a simple and efficient access to these new lipophilic compounds. Contrasting to the alcoholysis, enzymatic hydrolysis of 1a–d using different enzymes and experimental conditions did not proceed regioselectively.     

Template-directed oligomerization of 3-isoadenosine 5′-phosphate

Summary Template-directed oligomerization of an activated derivative of 3-isoadenosine 5-phosphate (piA) on polyuridylic acid [poly(U)] was studied. The reaction of ImpiA is more efficient than the corresponding reaction of ImpA, and produces 3–5-linked oligomers while the reaction of ImpA gives only 2–5-linked oligomers. The base pairing between piA and poly(U) in this system is probably of the Hoogsteen type (involving the 6-amino group and N7 of 3-isoadenosine) rather than of the Watson-Crick type.     

Free radicals from single crystals of deoxyguanosine 5′-monophosphate (Na Salt) irradiated at low temperatures

Summary In single crystals of the DNA nucleotide 2deoxyguanosine-5phosphate (5dGMP) X- or-irradiated at 4.2 K or 15 K, two primary radical species can be discriminated and assigned to the cation and anion of the guanine base,G(+) andG(–). Both species are unstable.G(–) partially transforms into a secondary radical at 4.2 K, the latter being the precursor to the dominant 300 K species formed by netH-addition to carbonC8. The secondary radical, together with another intermediate appearing at 77 K and perhaps connected with the anion decay could not be structurally identified. The guanine cationG(+) transforms upon annealing to temperatures above 77 K into a more stable species by deprotonation at positionN1.