Distribution of silicoflagellates in plankton and core top samples from the Gulf of California

Plankton and surface sediment samples from the Gulf of California were examined to determine the present geographic distribution of silicoflagellate species in this area. Variations in the species composition of the silicoflagellate assemblage were found to be related to water mass distributions. Eight species were identified in these samples. Octactis pulchra is associated with high levels of primary productivity in the surface waters and is found in greatest abundance in the central Gulf of California. Dictyocha messanensis dominates the silicoflagellate assemblage in stations outside the Gulf of California and increases in relative abundance with decreasing amounts of Octactis pulchra. Dictyocha calida, Dictyocha sp. A, and Dictyocha sp. B are associated with equatorial waters and have the highest relative abundance near the mouth of the Gulf. Dictyocha epiodon and Distephanus speculum are associated with cold California Current Water, and Dictyocha epiodon is present in minor abundance in Gulf samples. Dictyocha sp. 2 has a patchy distribution with low relative abundance.     

Flume tank experiments to estimate the volume filtered by highspeed plankton samplers and to assess the effect of net clogging

Two types of flowmeter were used to measure the velocity ofwater passing into Lowestoft high-speed tow nets and hence toestimate the volume filtered. Miniature (Streamflo) flowmeterswere used to estimate the average velocity through the circularopening plane by measuring the velocity at several points alongthe radius of the opening and taking a weighted average of these.The velocity varies along the radius of the opening and becausethe Braystoke internal flowmeters, which are used routinelyin field deployments, only measure the velocity in the centralpart of the opening, they do not give an accurate estimate ofthe average velocity through the opening plane. This will resultin biassed estimates of volume filtered unless a correctionis applied. Linear models are used to show that the correctiondepends on the type of gear and the degree of clogging of thenet, but is independent of water velocity. Clogging was simulatedin the experiments using impervious patches of material, andcan be estimated in the field from the ratio of internal:externalflowmeter readings. Corrections for bias and estimates of filtrationefficiency are given for three gear configurations under a rangeof clogging states. Further experiments are needed to resolveremaining uncertainty over estimates of filtration efficiency.     

Temporal and spatial variation of plankton abundance in the Gulf of Carpentaria, Australia 1975-1977

The Gulf of Carpentaria is a large (ca. 3.7 x 10⁵ km²) shallow(<70 m) embayment in tropical northern Australia lying between11 and 17.5°S latitude. Although it contains a multi-speciespenaeid prawn fishery which is Australia's largest and mostvaluable fishery its hydrology and planktology are largely unknown.As a background to a study of the larval ecology of penaeidstocks, ten Gulf-wide survey cruises, sampling the planktonand hydrography, were undertaken over a twenty month periodfrom August 1975 to May 1977. Though comparisons with otherstudies are difficult because of variations in sampling techniquesand biomass estimation methods, the plankton biomass in theGulf of Carpentaria appears to be high by comparison with otherareas around Australia. The mean estimate over all stationsand all cruises of 77 mg/m³ dry weight (1880 mg/m²) compareswith the very high abundances found only in seasonal upwellingareas south of Java and off the northwest shelf of Australia.Further, the Gulf of Carpentaria standing stocks of planktoncompare with other coastal areas supporting important fisheriesoff the west coast of North America, the eastern North AtlanticOcean and some European waters. Because of its depth, relativelyhigh temperature and primary production rates, secondary productionrates are assumed to be high as well but as yet are unmeasured. ^*Microfiche of station list available upon request. CSIRO MarineLaboratories Reprint No. 1280     

A comparison of the length distributions of larval capelin (Mallotus villosus) taken by Gulf III, MIK and MOCNESS samplers

Abundance of Barents Sea capelin larvae (6–25 mm) is estimated every summer using samples from a Gulf III sampler. It has been suggested that a MIK net would be more efficient in sampling larvae exceeding 18–20 mm in length. On this basis the length distributions of larval capelin captured by Gulf III, MIK, and MOCNESS in six consecutive hauls were compared. The catches taken by Gulf III and MIK nets had similar length distributions whereas the MOCNESS captured smaller larvae than the other samplers. There would thus be no gain in replacing the Gulf III with the MIK for estimating abundance of larval capelin smaller than 25 mm.     

Construction and characterization of a copy number-inducible fosmid library of Xanthomonas oryzae pathovar oryzae MAFF311018

A fosmid library of Xanthomonas oryzae pathovar oryzae MAFF311018 (T7174), the causative agent of bacterial blight on rice, was constructed and characterized. The average fosmid library insert size was > 34 kb, and 967 clones were uniquely positioned on its sequenced genome. The entire Xoo MAFF311018 genome was covered by end-sequenced clones with at least 5 kb of overlap. The fosmid vector contains both the single-copy Escherichia coli fertility factor origin, which enhances fosmid stability, and the multi-copy IncPα origin, allowing amplification of copy number upon induction with l-arabinose. Real-time quantitative PCR on 12 randomly picked fosmid library clones determined that fosmid copy number increased 8- to 58-fold after 5 hour induction. This library provides a new resource for complementation experiments and systematic functional studies in Xoo and related species.     

Descriptions of the lower limb skeleton of Homo floresiensis

Bones of the lower extremity have been recovered for up to nine different individuals of Homo floresiensis - LB1, LB4, LB6, LB8, LB9, LB10, LB11, LB13, and LB14. LB1 is represented by a bony pelvis (damaged but now repaired), femora, tibiae, fibulae, patellae, and numerous foot bones. LB4/2 is an immature right tibia lacking epiphyses. LB6 includes a fragmentary metatarsal and two pedal phalanges. LB8 is a nearly complete right tibia (shorter than that of LB1). LB9 is a fragment of a hominin femoral diaphysis. LB10 is a proximal hallucal phalanx. LB11 includes pelvic fragments and a fragmentary metatarsal. LB13 is a patellar fragment, and LB14 is a fragment of an acetabulum. All skeletal remains recovered from Liang Bua were extremely fragile, and some were badly damaged when they were removed temporarily from Jakarta. At present, virtually all fossil materials have been returned, stabilized, and hardened. These skeletal remains are described and illustrated photographically. The lower limb skeleton exhibits a uniquely mosaic pattern, with many primitive-like morphologies; we have been unable to find this combination of ancient and derived (more human-like) features in either healthy or pathological modern humans, regardless of body size. Bilateral asymmetries are slight in the postcranium, and muscle markings are clearly delineated on all bones. The long bones are robust, and the thickness of their cortices is well within the ranges seen in healthy modern humans. LB1 is most probably a female based on the shape of her greater sciatic notch, and the marked degree of lateral iliac flaring recalls that seen in australopithecines such as “Lucy” (AL 288-1). The metatarsus has a human-like robusticity formula, but the proximal pedal phalanges are relatively long and robust (and slightly curved). The hallux is fully adducted, but we suspect that a medial longitudinal arch was absent.     

Descriptions of the upper limb skeleton of Homo floresiensis

Several bones of the upper extremity were recovered during excavations of Late Pleistocene deposits at Liang Bua, Flores, and these have been attributed to Homo floresiensis. At present, these upper limb remains have been assigned to six different individuals - LB1, LB2, LB3, LB4, LB5, and LB6. Several of these bones are complete or nearly so, but some are quite fragmentary. All skeletal remains recovered from Liang Bua were extremely fragile, but have now been stabilized and hardened in the laboratory in Jakarta. They are now curated in museum-quality containers at the National Research and Development Centre for Archaeology in Jakarta, Indonesia. These skeletal remains are described and illustrated photographically. The upper limb presents a unique mosaic of derived (human-like) and primitive morphologies, the combination of which is never found in either healthy or pathological modern humans.     

Interspersion of the VHQ52 and VH7183 gene families in the NFS/N mouse

Deletion mapping analysis has shown that members of the VH7183 and VHQ52 gene families are interspersed in the NFS/N mouse. To obtain direct evidence that members of these gene families are physically linked, an NFS/N liver library was constructed and genomic clones were analyzed for hybridization to both VHQ52 and VH7183 gene probes. Four clones were identified which contained both VHQ52 and VH7183 hybridizable restriction fragments. Two clones containing rearranged VHQ52 genes were also found to hybridize with the VH7183 gene probe. Sequence analysis of three of the VH7183-containing restriction fragments indicate that all are pseudogenes which contain interruptions at either the 5' and/or 3' ends of the VH coding region. Given the D-proximal location of at least a portion of the VHQ52 gene family relative to VH7183 in NFS/N mice, and the known correlation between D proximity and the frequency of VH gene utilization, 22 NFS/N-derived pre-B cell lines were analyzed for VHQ52 gene utilization. More than 40% of the identified H chain (VHDJH) rearrangements in this survey used members of this gene family. Furthermore, analysis of poly(A)+ RNA from NFS/N fetal liver and adult spleen also indicates preferential utilization of VHQ52 family in fetal liver. Kinetic studies show, however, that there are no changes in relative utilization throughout fetal ontogeny. The implications of these findings for the expression and randomization of the VH repertoire are discussed.     

The peril of the plankton

The pelagic environment is characterized by unevenly distributed resources and risks. Such unpredictability presents adaptive challenges to diverse planktonic organisms including the larvae of benthic marine invertebrates. Estimates of mortality during planktonic development are highly variable, ranging from 0% to 100% per day. Predation is considered a significant source of this mortality, but what explains the variability in estimates of the mortality of marine invertebrate larvae? While differential exposure of larval prey to predators may explain these widely variable estimates, adaptations that reduce vulnerability of marine larvae to predators may also be important. Although there are excellent reviews of predation upon larvae and of larval mortality and defenses, nearly 15 years have elapsed since these topics were formally reviewed. Here, we highlight recent advances in understanding the behavioral, chemical, and morphological defenses that larvae possess and assess their effectiveness in reducing the risk of predation. While recent work confirms that larval mortality is generally high, it also demonstrates that larvae can reduce their risk of predation in several ways, including: (1) temporarily escaping the benthos during vulnerable early stages, (2) producing chemical compounds that reduce palatability, (3) possessing morphological defenses such as spines and shells, and (4) exhibiting induced defensive responses whereby larvae can alter their behavior, morphology, and life histories in the presence of predators. Taken together, these studies indicate that marine invertebrate larvae possess a sophisticated suite of defensive phenotypes that have allowed them to persist in the life cycle of benthic invertebrates for eons.     

Mesoscale vortices and the paradox of the plankton

Coexistence of competitive species is severely limited by the availability of resources and the characteristics of the environment. In particular, the so-called 'competitive exclusion principle' states that, at equilibrium, the number of coexisting species cannot be larger than the number of resources for which they compete. However, many in situ observations have revealed prolonged coexistence of a large number of competitive plankton species, a phenomenon known as 'the paradox of the plankton'. Here we investigate this problem and show that ocean mesoscale vortices generate transport barriers and incomplete horizontal mixing, allowing for a prolonged survival of the less-fit species, even for fully homogeneous resource distributions. In such a situation, the temporarily less-fit plankton species are protected from competition by the action of the vortices.     

The principles of aerosol samplers and sampling

The principles of aerosol sampling involve both a) the scientific factors which govern the way in which particles are transported from the air outside the sampler to a filter or sensing region inside it, and b) recognition of particle size-selective criteria which relate the act of sampling to the reason it is being carried out (e.g., assessment of health risk associated with inhalation). This paper reviews the state-of-the-art in both these areas, and goes on to mention some recent technical developments concerning practical sampling instruments.     

Eleven MRL-lpr/lpr anti-DNA autoantibodies are encoded by genes from four VH gene families: a potentially biased usage of VH genes

The genes encoding 11 independently derived anti-DNA autoantibodies from the lupus-prone mouse strain, MRL-lpr/lpr, were examined with VH, D, and JH gene probes. These autoantibodies do not define new VH gene families, since all of the autoantibodies were encoded by VH genes from four of the nine known gene families. A minimum of nine different VH genes encoded this panel of 11 anti-DNA autoantibodies. These results are consistent with the stochastic use of the VH gene repertoire and the expression of multiple VH genes. However, the data is also consistent with a biased usage of the VH gene repertoire. First, two pairs of autoantibodies, one from the J558 family and one from the 7183 family, appear to express identical or closely related VH genes as determined by the position of two restriction enzyme sites 5' of the expressed VH genes. In addition, three autoantibodies that appear to be sister clones might define a third VH gene that is used repeatedly. Secondly, about 45% of the panel is encoded by the Q52 and 7183 families, which are the 3' most families. These families have been shown to be preferentially rearranged early in B cell ontogeny. This suggests that some anti-DNA autoantibodies might originate from a population of B cells that predominate early in ontogeny. An alternative hypothesis is that the potential bias in VH gene and gene family usage could be due to antigen selection. All four JH genes are expressed, although the JH1 gene appears to be underutilized in both expressed and unexpressed rearrangements. Two members of the panel that bind double-stranded DNA were encoded by two different VH gene families, the S107 family and the J558 family.     

VH gene segments in the mouse and human genomes

We have examined the mouse genome sequence to determine its VH gene segment repertoire. In all, 141 segments are mapped to a 3 Mb region of chromosome 12. There is evidence that 92 of these are functional in the mouse strain used for the genome sequence, C57BL/6J; 12 are functional in other mouse strains, and 37 are pseudogenes. The mouse VH gene segment repertoire is therefore twice the size of that in humans. The mouse and human loci bear no large-scale similarity to each other. The 104 functional segments belong to one of the 15 known sequence subgroups, which have been further clustered into eight sets here. Seven of these sets, comprising 101 sequences, are related to five of the human VH families and have the same canonical structures in their hypervariable regions. Duplication of members of one set in the distal half of the locus is mainly responsible for the larger size of the mouse repertoire. Phylogenetic analysis of the VH segments indicates that most of the sequences in the human and mouse VH loci have arisen subsequent to the divergence of the two organisms from their common ancestor.     

Concerted evolution of the immunoglobulin VH gene family

With the aim of understanding the concerted evolution of the immunoglobulin VH multigene family, a phylogenetic tree for the DNA sequences of 16 mouse and five human germ line genes was constructed. This tree indicates that all genes in this family have undergone substantial evolutionary divergence. The most closely related genes so far identified in the mouse genome seem to have diverged about 6 million years (MY) ago, whereas the most distantly related genes diverged about 300 MY ago. This suggests that gene duplication caused by unequal crossing-over or gene conversion occurs very slowly in this gene family. The rate of occurrence of gene duplication in the VH gene family has been estimated to be 5 x 10(-7) per gene per year, which seems to be at least about 100 times lower than that for the rRNA gene family. This low rate of concerted evolution in the VH gene family helps retain intergenic genetic variability that in turn contributes to antibody diversity. Because of accumulation of destructive mutations, however, about one-third of the mouse and human VH genes seem to have become nonfunctional. Many of these pseudogenes have apparently originated recently, but some of them seem to have existed in the genome for more than 10 MY. The rate of nucleotide substitution for the complementarity-determining regions (CDRs) is as high as that of pseudogenes. This suggests that there is virtually no purifying selection operating in the CDRs and that germ line mutations are effectively used for generating antibody diversity.      

Content and organization of the human Ig VH locus: definition of three new VH families and linkage to the Ig CH locus.

We present a detailed analysis of the content and organization of the human immunoglobulin VH locus. Human VH genes representing five distinct families were isolated, including novel members belonging to two out of three of the known VH gene families (VH1 and VH3) as well as members of three new families (VH4, VH5, and VH6). We report the nucleotide sequence of 21 novel human VH genes, many of which belong to the three new VH gene families. In addition, we provide a preliminary analysis of the organization of these gene segments over the full extent of the locus. We find that the five multi-segment families (VH1-5) have members interspersed over nearly the full 1500-2000 kb of the VH locus, and estimate that the entire heavy chain locus covers 2500 kb or less. Finally, we provide the first report of the physical linkage of the variable and constant loci of a human Ig gene family by demonstrating that the most proximal known human VH segments lie within 100 kb of the constant region locus.     

A wind tunnel comparison of the rotorod and samplair pollen samplers

Summary The relative sampling efficiency of the Samplair (Allergenco Inc.) and Rotorod samplers (Sampling Technologies Inc.) were compared for different conifer pollen sizes and at different wind speeds. The wind tunnel experiments conducted with the two samplers are valid for the range of wind speeds and conifer pollen types which might be expected in seed orchards in Canada. A Quadratic relationship was established between the two samplers which revealed a decrease in relative efficiency on the part of the Samplair as compared to the Rotorod at wind speeds less than 5 m/s. An apparent increase in the efficiency of the samplair at higher wind speeds resulted from a decrease in the sampling ability of the rotorod.     

Interactions of detrital particulates and plankton

Detrital particulates, i.e. inorganic and non-living organic material of colloidal size and larger, span ten orders of magnitude in size and are ubiquitous in inland waters. Interactions between plankton and detrital particulates are reciprocal. Release of dissolved organics by living organisms enter the particulate size fraction by flocculation on bubbles or adsorption to inorganic particles. Bacteria benefit from attachment to particles and are agents in the aggregation of particulates. Nutrients released by decaying plankton can support phytoplankton growth. Potentially toxic compounds adsorb to particulates and then can enter pelagic food webs or sediment. Material egested by zooplankton contributes to the detrital pool which in turn is a food source for zooplankton.     

Structural repertoire of the human VH segments.

The VH gene segments produce the part of the VH domains of antibodies that contains the first two hypervariable regions. The sequences of 83 human VH segments with open reading frames, from several individuals, are currently known. It has been shown that these sequences are likely to form a high proportion of the total human repertoire and that an individual's gene repertoire produces about 50 VH segments with different protein sequences. In this paper we present a structural analysis of the amino acid sequences produced by the 83 segments. Particular residue patterns in the sequences of V domains imply particular main-chain conformations, canonical structures, for the hypervariable regions. We show that, in almost all cases, the residue patterns in the VH segments imply that the first hypervariable regions have one of three different canonical structures and that the second hypervariable regions have one of five different canonical structures. The different observed combinations of the canonical structures in the first and second regions means that almost all sequences have one of seven main-chain folds. We describe, in outline, structures of the antigen binding site loops produced by nearly all the VH segments. The exact specificity of the loops is produced by (1) sequence differences in their surface residues, particularly at sites near the centre of the combining site, and (2) sequence differences in the hypervariable and framework regions that modulate the relative positions of the loops.