Improving the specificity of high-throughput ortholog prediction

Background  

Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function.     

The Capricorn Eddy: a prominent driver of the ecology and future of the southern Great Barrier Reef

This study focuses on a mesoscale eddy feature, the ‘Capricorn Eddy’, that typically forms within an indentation of the continental shelf in the southern GBR system. Satellite data at moderate resolution (1 km) are used to examine relevant mesoscale and sub-mesoscale sea surface dynamics. Available in situ measurements and model data are used to validate the satellite observations and to specify the nature of the processes occurring within the water column itself. The characteristic features are identified and physical theory employed to develop an understanding of associated processes. In particular, the effect of the eddy in raising cooler, nutrient-enriched oceanic subsurface water and transporting it to the reef zone, and eventually into the lagoon, is shown. This study demonstrates that the linkages between large-scale oceanography and the meso- and sub-mesoscale patterns are crucial to determining biologic responses on the scale of reef communities and may be key to understanding climate change impacts at the relevant spatial scales.     

Growth of dimorphic human pathogenicfungi on media containing cycloheximide and chloramphenicol

Summary Studies of 24 strains ofBlastomyces dermatitidis confirmed previously published results that the yeast-phase of this fungus is more sensitive than the mycelial-phase to cycloheximide and chloramphenicol.Studies of 5 strains each ofHistoplasma capsulatum, Paracoccidioides brasiliensis andSporotrichum schenckii show that that these species also have a similar yeast-phase mycelial -phase sensitivity differential in regard to these antibiotics.A cycloheximide resistant strain ofB. dermatitidis was developed from a sensitive strain.The experimental results support the general practice of using 0.5 mg/ml cycloheximide and 0.05 mg/ml chloramphenicol in media for the isolation of the four fungi at 25° C. The results indicate, however, that some strains would not be recovered at 37° C with similar concentrations of these antibiotics.It is recommended that a concentration of not more than 0.2 mg/ml chloramphenicol should be used to preserve sputum which is subsequently to be cultured forB. dermatitidis, Histoplasma capsulatum, Paracoccidioides brasiliensis orS. schenckii.     

The adverse metabolic effects of branched-chain amino acids are mediated by isoleucine and valine

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The hind limb step cycle of Iguana and primitive reptiles

The hind limb step cycle of Iguana is described and compared with other lizards. In generalized lizards with well developed limbs, the femur retracts through a large arc and rotates as it retracts, flexion of the crus on the metatarsus occurs during the initial part of the propulsive phase and extension of the knee and ankle during the final part, the crus rotates to face laterally, the metatarsus is laterally directed at the time of pedal plantarflexion, and pedal plantarflexion involves an initial rotation of the metatarsus around its long axis followed by an extension of the ankle joint. The evolutionary significance of the differences in the hind limb step cycle of lizards and salamanders is considered and it is shown that in many, but not all, features, primitive reptiles would have been like salamanders. The primitive step cycle differs from the mammalian pattern in the large amount of rotation of the limb segments, the large amount of femoral retraction, and the reduced amount of lateral movement of the hip relative to the knee that occurs during femoral retraction.     

In situ sampling of interstitial water from lake sediments

A sampler with a relatively high resolution has been developed, which allows interstitial water to be obtained from lake sediments at well defined depths, without serious disturbance of sediment structure. Oxidation effects are excluded. Sampling time is in the order of a day. Installation requires little additional equipment. The instrument has been developed for use in shallow lakes.