Evolutionary relationships among hares from North Africa (Lepus sp. or Lepus spp.), cape hares (L. capensis) from South Africa, and brown hares (L. europaeus), as inferred from mtDNA PCR-RFLP and allozyme data

Systematics and taxonomy of hares of the genus Lepus (Lagomorpha) are under contentious debate, and phylogenetic relationships among many taxa are not well understood. Here we study genetic differentiation and evolutionary relationships among North African hares, currently considered subspecies of Lepus capensis , cape hares ( L. capensis ) from the Cape province in South Africa, and brown hares ( L. europeaus ) from Europe and Anatolia, using maternally (mtDNA) and biparentally (allozymes) inherited markers. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of a c. 1.8 kb long segment of the mitochondrial control region using eight hexanucleotide-recognizing restriction endonucleases yielded 28 haplotypes, and horizontal starch gel electrophoresis of proteins encoded by 25 structural gene loci revealed 52 alleles at 18 polymorphic loci. Diverse phylogenetic analyses (neighbor joining dendrogram, median joining network, multidimensional scaling of pairwise distances, AMOVA, F -statistics, hierarchical F -statistics) of genetic variants revealed marked substructuring of mtDNA into three phylogeographic groups, namely an African, a central European, and an Anatolian, but a somewhat less pronounced overall differentiation of the nuclear genome, despite a relatively high number of population-specific (private) alleles. However, all our results are not incongruent with Petter's (1959: Mammalia 23 , 41; 1961: Z. f. Säugetierkunde 26 , 30; 1972 : Société Des Sciences Naturelles et Physiques du Maroc 52 , 122) hypothesis that North African hares generally belong to L. capensis and that brown hares should be included in this species as well.     

Distribution and breeding biology of offshore cichlids in Lake Malawi/ Niassa

Synopsis Lake Malawi/Niassa is the second largest rift valley lake in Africa, with an area of 28 800 km², and an average and maximum depth of 292 m and>700 m, respectively. The lake is well known for the great diversity of fish occurring in the inshore zone. However, the offshore fish community is poorly documented. To rectify this, regular sampling was undertaken over two years, using trawl and gillnets at six offshore locations. This paper reports on the species composition, spatial distribution and breeding biology of the dominant cichlids species from the offshore pelagic zone. Cichlids formed approximately 88% of the offshore fish biomass. Most abundant were two species of zooplanktivores in the genus Diplotaxodon that made up 71% of the offshore fish biomass. An undescribed species, given the cheironym D. bigeye, was mainly found at a depth of 220 m during the day, but moved into near surface waters at night when the moon was full. This species was absent from the shallow regions of the lake. The most abundant offshore species was D. limnothrissa, which was distributed evenly throughout the lake to depths of 220 m. A less common offshore zooplanktivore was Copadichromis quadrimaculatus that formed 5% of the biomass and was confined to the upper 100 m of the water column. The main piscivores were in the genus Rhamphochromis and formed approximately 10% of the offshore fish biomass. The two dominant taxa were R. longiceps and the large Rhamphochromis group, and both were more common in the southern half of the lake. The former occurred mainly in the upper 100 m of the water column and the latter mainly at depths of 100–150 m. The length at maturity and fecundity for the dominant offshore species were estimated and seasonal breeding cycles determined from gonad activity and gonado-somatic indices.     

Analyzing Craniofacial Morphogenesis in Zebrafish Using 4D Confocal Microscopy

Time-lapse imaging is a technique that allows for the direct observation of the process of morphogenesis, or the generation of shape. Due to their optical clarity and amenability to genetic manipulation, the zebrafish embryo has become a popular model organism with which to perform time-lapse analysis of morphogenesis in living embryos. Confocal imaging of a live zebrafish embryo requires that a tissue of interest is persistently labeled with a fluorescent marker, such as a transgene or injected dye. The process demands that the embryo is anesthetized and held in place in such a way that healthy development proceeds normally. Parameters for imaging must be set to account for three-dimensional growth and to balance the demands of resolving individual cells while getting quick snapshots of development. Our results demonstrate the ability to perform long-term in vivo imaging of fluorescence-labeled zebrafish embryos and to detect varied tissue behaviors in the cranial neural crest that cause craniofacial abnormalities. Developmental delays caused by anesthesia and mounting are minimal, and embryos are unharmed by the process. Time-lapse imaged embryos can be returned to liquid medium and subsequently imaged or fixed at later points in development. With an increasing abundance of transgenic zebrafish lines and well-characterized fate mapping and transplantation techniques, imaging any desired tissue is possible. As such, time-lapse in vivo imaging combines powerfully with zebrafish genetic methods, including analyses of mutant and microinjected embryos.     

Neuroprotective effect of N-acetyl-aspartyl-glutamate in combination with mild hypothermia in the endothelin-1 rat model of focal cerebral ischaemia

Previously we showed that treatment with mild hypothermia (34 degrees C for 2 h) after a focal cerebral infarct was neuroprotective by reducing apoptosis in the penumbra (cortex), but not in the core (striatum) of the infarct. In this study we examined whether administration of N-acetyl-aspartyl-glutamate (NAAG) in combination with mild hypothermia could improve striatal neuroprotection in the endothelin-1 rat model. NAAG (10 mg/kg i.p.) was injected under normothermic (37 degrees C) or mild hypothermic conditions, either 40 min before or 20 min after the insult. NAAG reduced caspase 3 immunoreactivity in the striatum, irrespective of the time of administration and brain temperature. This neuroprotective effect could be explained, at least partially, by decreased nitric oxide synthase activity in the striatum and was blocked by the group II metabotropic glutamate receptor antagonist, LY341495. Hypothermia applied together with NAAG reduced both cortical and striatal caspase 3 immunoreactivity, as well as the overall ischaemic damage in these areas. However, no pronounced improvement was seen in total damaged brain volume. Extracellular glutamate levels did not correlate with the observed protection, whatever treatment protocol was applied. We conclude that treatment with NAAG causes the same degree of neuroprotection as treatment with hypothermia. Combination of the two treatments, although reducing apoptosis, does not considerably improve ischaemic damage.     

Isolation and partial characterization of a lectin from ground elder (Aegopodium podagraria) rhizomes

A lectin has been isolated from rhizomes of ground elder (Aegopodium podagraria) using a combination of affinity chromatography on erythrocyte membrane proteins immobilized on cross-linked agarose and hydroxyapatite, and ion-exchange chromatography. The molecular structure of the lectin was determined by gelfiltration, sucrose density-gradient centrifugation and gel electrophoresis under denaturing conditions. It has an unusually high M_r (about 480000) and is most probably an octamer composed of two distinct types of subunits with slightly different M_r (about 60000). Hapten inhibition assays indicated that the Aegopodium lectin is preferentially inhibited by N-acetylgalactosamine. Nevertheless, it does not agglutinate preferentially blood-group-A erythrocytes. The ground-elder lectin is a typical non-seed lectin, which occurs virtually exclusively in the underground rhizomes. In this organ it is an abundant protein as it represents up to 5% of the total protein content. The lectin content of the rhizome tissue varies strongly according to its particular location along the organ. In addition, the lectin content changes dramatically as a function of the seasons. The ground-elder lectin differs from all other plant lectins by its unusually high molecular weight. In addition, it is the first lectin to be isolated from a species of the family Apiaceae.Abbreviations APA Aegopodium podagraria agglutinin - PBS phosphate-buffered saline - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis     

Characterization of lactobacilli isolated from caper berry fermentations

AIMS: To determine the metabolic and functional properties of lactobacilli isolated from caper fermentation. METHODS AND RESULTS: A collection of 58 lactobacilli from fermentation of caper berries (including species of Lactobacillus plantarum, Lactobacillus paraplantarum, Lactobacillus pentosus, Lactobacillus brevis and Lactobacillus fermentum) was studied. Strains were classified in different clusters according to sugar fermentation patterns. Most strains of L. plantarum (the predominant species in the fermentation) clustered in a single group. Analysis of enzymatic activities revealed a high incidence of leucine aminopeptidase, acid phosphatase, beta-galactosidase and beta-glucosidase among the different strains of lactobacilli. A high number of strains were able to degrade raffinose and stachyose. Phytase activity and bile salt hydrolase activity were only detected in certain strains of L. plantarum. CONCLUSIONS: Lactobacilli from caper fermentation are metabolically diverse, and some strains display functional properties of interest. SIGNIFICANCE AND IMPACT OF THE STUDY: Strains of lactobacilli with selected functional properties could be good candidates for future development of commercial starters for industrial caper fermentation.     

On the effect of glucono-δ-lactone on the yeast Pichia polymorpha

Investigation has been made into the action of glucono--lactone on living cells of Pichia polymorpha in relation to the uptake of D-(U-¹⁴C) glucose, and the incorporation of (2-¹⁴C) uracil and L-(U-¹⁴C)-threonine into RNA and protein respectively. Other factors such as the action of glucono--lactone on cell morphology and on enzymic synthesis have also been studied. The action of this compound on -glucanase has been found to take place in the hydrolytic power and not in the synthesis.     

The contribution of naturally occurring polymorphisms in altering the biochemical and structural characteristics of HIV-1 subtype C protease

Fourteen subtype B and C protease variants have been engineered in an effort to study whether the preexistent baseline polymorphisms, by themselves or in combination with drug resistance mutations, differentially alter the biochemical and structural features of the subtype C protease when compared with those of subtype B protease. The kinetic studies performed in this work showed that the preexistent polymorphisms in subtype C protease, by themselves, do not provide for a greater level of resistance. Inhibition analysis with eight clinically used protease inhibitors revealed that the natural polymorphisms found in subtype C protease, in combination with drug resistance mutations, can influence enzymatic catalytic efficiency and inhibitor resistance. Structural analyses of the subtype C protease bound to nelfinavir and indinavir showed that these inhibitors form similar interactions with the residues in the active site of subtype B and C proteases. It also revealed that the naturally occurring polymorphisms could alter the position of the outer loops of the subtype C protease, especially the 60's loop.     

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.