A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division

Upstream events that trigger initiation of cell division, at a point called START in yeast, determine the overall rates of cell proliferation. The identity and complete sequence of those events remain unknown. Previous studies relied mainly on cell size changes to identify systematically genes required for the timely completion of START. Here, we evaluated panels of non-essential single gene deletion strains for altered DNA content by flow cytometry. This analysis revealed that most gene deletions that altered cell cycle progression did not change cell size. Our results highlight a strong requirement for ribosomal biogenesis and protein synthesis for initiation of cell division. We also identified numerous factors that have not been previously implicated in cell cycle control mechanisms. We found that CBS, which catalyzes the synthesis of cystathionine from serine and homocysteine, advances START in two ways: by promoting cell growth, which requires CBS's catalytic activity, and by a separate function, which does not require CBS's catalytic activity. CBS defects cause disease in humans, and in animals CBS has vital, non-catalytic, unknown roles. Hence, our results may be relevant for human biology. Taken together, these findings significantly expand the range of factors required for the timely initiation of cell division. The systematic identification of non-essential regulators of cell division we describe will be a valuable resource for analysis of cell cycle progression in yeast and other organisms.     

Isolation of Cronobacter spp. (formerly Enterobacter sakazakii) from infant food, herbs and environmental samples and the subsequent identification and confirmation of the isolates using biochemical, chromogenic assays, PCR and 16S rRNA sequencing

Background  

Cronobacter spp. (formerly Enterobacter sakazakii), are a group of Gram-negative pathogens that have been implicated as causative agents of meningitis and necrotizing enterocolitis in infants. The pathogens are linked to infant formula; however, they have also been isolated from a wide range of foods and environmental samples.     

Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs

Toward the goal of understanding how open basepairs in DNA interact with their heterogeneous environment, we have studied the steady-state intrinsic fluorescence properties of the purine and pyrimidine deoxynucleosides in organic solvents in the presence of small amounts of water. The organic solvents used in the present study were: n-butanol, acetonitrile, methanol, n-propanol, isopropanol, and isobutanol. For n-butanol and acetonitrile, which have a high degree of amphiphilicity and weak hydrogen bonding ability, respectively, the fluorescence spectral properties of the purines are found to depend on the sequence of steps in which the aqueous mixtures were formed. By contrast, no such dependence was observed in the mixtures with any of the other solvents used in the present study. Moreover, no such dependence was observed for the pyrimidines. These findings suggest that the final solvation network around the purines is dependent on the nature of the environment to which they were initially exposed. This would tend to present an impediment to the closing of AT or GC basepairs in DNA that become open as a result of structural fluctuations, DNA bending, or protein-DNA interactions.     

Hetero: a program to simulate the evolution of DNA on a four-taxon tree

We present a computer program to simulate the evolution of a nucleotide sequence on a phylogenetic tree with four tips. The program, Hetero, allows users to assign lineage-specific differences in the rate matrices used to describe the evolutionary process. It has a simple user interface and output, making it equally useful in the teaching and research of phylogenetics.     

Density-dependence and within-host competition in a semelparous parasite of leaf-cutting ants

Background  

Parasite heterogeneity and within-host competition are thought to be important factors influencing the dynamics of host-parasite relationships. Yet, while there have been many theoretical investigations of how these factors may act, empirical data is more limited. We investigated the effects of parasite density and heterogeneity on parasite virulence and fitness using four strains of the entomopathogenic fungus, Metarhizium anisopliae var. anisopliae, and its leaf-cutting ant host Acromyrmex echinatior as the model system.     

Did elevated atmospheric CO2 alter soil mineral weathering?: an analysis of 5‐year soil water chemistry data at Duke FACE study

A principal driver of biogeochemical weathering of the Earth's crust is soil CO₂, produced mainly by plant roots and soil heterotrophs, a water‐soluble gas that forms carbonic acid which reacts with soil minerals via cation exchange and mineral dissolution. We examined effects of elevated atmospheric CO₂ (ambient + 200 ppmv) in a young pine forest on belowground carbonic acid chemistry of soil water. Soil water was collected every 2–3 weeks over a 5‐year period from O horizons and at 15, 70, and 200 cm in mineral soils at the Duke free air CO₂ enrichment facility located in a warm temperate climate in North Carolina, USA. Concentrations of major ions were volume‐weighted and statistically analyzed using linear mixed‐effects models. Experimental interest was placed on interactive effects of CO₂ treatment and time: to test effects of gradually increasing CO₂ in deep soil horizons where CO₂ is highest in concentration, and to protect against inherent plot‐to‐plot differences in soil water chemistry being interpreted as responses to CO₂ treatments. Although significant time‐dependent interactive effects were reported for soil CO₂, interactive effects were not significant for soil water constituents. These data, combined with limited pretreatment sampling of soil water chemistry and recently determined large heterogeneity in soil solid chemistry at this site, indicate that CO₂‐weathering response is smaller than the more‐than‐doubling of weathering reported previously and that increases in weathering are masked by in situ soil heterogeneity. Although the hypothesis that elevated CO₂ increases cation leaching and weathering dissolution is supported in laboratory experiments and field studies, quantifying the stimulation of chemical weathering by elevated atmospheric CO₂ remains to be tested rigorously in the field.     

External microstructure of the ambrosia beetle Platypus koryoensis (Coleoptera: Curculionidae: Platypodinae)

Platypus koryoensis is a minute ambrosia beetle found in forests. It can cause significant economic damage to oak trees. Recently in Korea, it has been reported as a major pest of oak trees, because it causes sooty mold of oak by introducing the pathogenic fungus Raffaelea sp. In this paper, we demonstrate the fine structural aspects of the external body of the ambrosia beetle using field emission scanning electron microscopy, as a part of basic research into this pest so that strategies for its control might be developed. This beetle has a sensory system well developed to respond to both visual and chemical stimuli. Both sexes have a pair of faceted compound eyes and a pair of knobbed antennae, but simple eyes are absent. The mouthparts on its distinct snouts are effective devices for penetration and for boring holes. The mouthparts consist of the labrum, a pair of mandibles, a pair of maxillae and the labium. Both the maxillary and the labial palpi have the function of directing the food to the mouth and holding it while the mandibles chew the food. The distal ends of these palpi are flattened and have shovel‐like setae. The thorax has a particularly hard exoskeleton and hard elytra, including powerful muscles that operate both the wings and the legs. The legs are multi‐segmented and have a strong femur and tibia, including one pair of claws on the end of each tarsal segment. Characteristically, both male and female beetles have mycangial cavities for storing spores and other microorganisms, but only females have three pairs of large depressions on their dorsal thorax.     

Phylogenetic relationships, taxonomy, character evolution and biogeography of the lacertid lizards of the genus Takydromus (Reptilia: Squamata): a molecular perspective

Historical relationships were inferred for the oriental lizards of the genus Takydromus Daudin 1802 (Lacertidae) on the basis of DNA sequences. Of the 17 species currently recognized for the genus, 13 species represented by 42 specimens from 29 localities were examined. Maximum-likelihood and maximum-parsimony analyses of data for 829 aligned sites from parts of the mitochondrial 12S and 16S rRNA genes yielded relationships that, while showing no substantial discrepancy with each other, were strikingly different from a currently prevailing phylogenetic hypothesis from a parsimony analysis of morphological characters. Based on the results of these molecular analyses, supplemented by results of the morphological analysis that offered robust evidence for positions of two additional species ( T. khasiensis and T. sylvaticus ), the following interrelationships were hypothesized as the most preferred phylogeny: ( kuehnei ( sexlineatus khasiensis ))( tachydromoides (( smaragdinus ( sauteri ( dorsalis sylvaticus ))) ( amurensis ((( formosanus wolteri ) hsuehshanensis )( toyamai ( septentrionalis stejnegeri )))))). These interrelationships indicate: (1) invalidity of Platyplacopus Boulenger 1917 , which was recently resurrected as a subgenus of Takydromus on the basis of the morphological analysis; (2) homoplasy in states of some morphological characters, such as green dorsal coloration, that were considered as synapomorphs of certain nodes in the morphological analysis; and (3) involvement of the genus in a series of vicariances in both the continental and insular parts of eastern Eurasia. Due to the paucity of available samples, phylogenetic status of T. intermedius and T. haughtonianus remain to be examined in future studies.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 76 , 493–509.     

Extensive genetic divergence in the East Asian natricine snake,Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations

We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I‐A, I‐B, and I‐C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 395–408.