The mechanisms of microtubule catastrophe and rescue: implications from analysis of a dimer-scale computational model

Microtubule (MT) dynamic instability is fundamental to many cell functions, but its mechanism remains poorly understood, in part because it is difficult to gain information about the dimer-scale events at the MT tip. To address this issue, we used a dimer-scale computational model of MT assembly that is consistent with tubulin structure and biochemistry, displays dynamic instability, and covers experimentally relevant spans of time. It allows us to correlate macroscopic behaviors (dynamic instability parameters) with microscopic structures (tip conformations) and examine protofilament structure as the tip spontaneously progresses through both catastrophe and rescue. The model's behavior suggests that several commonly held assumptions about MT dynamics should be reconsidered. Moreover, it predicts that short, interprotofilament "cracks" (laterally unbonded regions between protofilaments) exist even at the tips of growing MTs and that rapid fluctuations in the depths of these cracks influence both catastrophe and rescue. We conclude that experimentally observed microtubule behavior can best be explained by a "stochastic cap" model in which tubulin subunits hydrolyze GTP according to a first-order reaction after they are incorporated into the lattice; catastrophe and rescue result from stochastic fluctuations in the size, shape, and extent of lateral bonding of the cap.     

Evolution of the tetraploid Anemone multifida (2n = 32) and hexaploid A. baldensis (2n = 48) (Ranunculaceae) was accompanied by rDNA loci loss and intergenomic translocation: evidence for their common genome origin

Background and Aims

In the genus Anemone two small groups of taxa occur with the highest ploidy levels 2n = 6x = 48, belonging to the closely related clades: the montane/alpine Baldensis clade and the more temperate Multifida clade. To understand the formation of polyploids within these groups, the evolution of allohexaploid A. baldensis (AABBDD, 2n = 6x = 48) from Europe and allotetraploid Anemone multifida (BBDD, 2n = 4x = 32) from America was analysed.

Methods

Internal transcribed spacer and non-transcribed spacer sequences were used as molecular markers for phylogenetic analyses. Cytogenetic studies, including genomic in situ hybridization with genomic DNA of potential parental species as probe, fluorescence in situ hybridization with 5S and 18S rDNA as probes and 18S rDNA restriction analyses, were used to identify the parental origin of chromosomes and to study genomic changes following polyploidization.

Key Results

This study shows that A. multifida (BBDD, 2n= 4x = 32) and A. baldensis (AABBDD, 2n = 6x = 48) are allopolyploids originating from the crosses of diploid members of the Multifida (donor of the A and B subgenomes) and Baldensis groups (donor of the D subgenome). The A and B subgenomes are closely related to the genomes of A. sylvestris, A. virginiana and A. cylindrica, indicating that these species or their progeny might be the ancestral donors of the B subgenome of A. multifida and A and B subgenomes of A. baldensis. Both polyploids have undergone genomic changes such as interchromosomal translocation affecting B and D subgenomes and changes at rDNA sites. Anemone multifida has lost the 35S rDNA loci characteristic of the maternal donor (B subgenome) and maintained only the rDNA loci of the paternal donor (D subgenome).

Conclusions

It is proposed that A. multifida and A. baldensis probably had a common ancestor and their evolution was facilitated by vegetation changes during the Quaternary, resulting in their present disjunctive distribution.     

Microbial Ecology and Association of Bacillus thuringiensis in Chicken Feces Originating from Feed

To explain the association of Bacillus thuringiensis (Bt) with animal feces, an ecological analysis in chickens was conducted by introducing a cry ^? strain marked by production of green fluorescent protein (GFP). After feeding with the tagged Bt strains, the feces of the tested chickens were collected at different times, isolated, and the morphology of Bt was observed. It was shown that Bt strain HD-73GFP in spore form could be isolated from feces of chickens for a period of 13 d, and then it disappeared thereafter. Bt could be detected only up to day 4 (but not thereafter), when chickens were fed with vegetative cells of HD-73GFP. To confirm the source of newly isolated strains, the gfp gene was examined by polymerase chain reaction (PCR), which showed that all the isolated strains harbored the marker gene. Recent data from isolation and PCR had suggested that fecal Bt strains had originated from food. Chicken tissues were thus dissected to isolate Bt strains and to investigate whether Bt could be located in vivo. Bt was located within the duodenum in spore form. Compared to the morphology of the isolated strains at different growth times, the growth rates of all the tested Bt had little changes when passing through the digestive system to the feces. Dissection of the chickens confirmed that Bt was safe for the tested animal.     

Neural ensemble coding of satiety states

The motivation to start or terminate a meal involves the continual updating of information on current body status by central gustatory and reward systems. Previous electrophysiological and neuroimaging investigations revealed region-specific decreases in activity as the subject's state transitions from hunger to satiety. By implanting bundles of microelectrodes in the lateral hypothalamus, orbitofrontal cortex, insular cortex, and amygdala of hungry rats that voluntarily eat to satiety, we have measured the behavior of neuronal populations through the different phases of a complete feeding cycle (hunger-satiety-hunger). Our data show that while most satiety-sensitive units preferentially responded to a unique hunger phase within a cycle, neuronal populations integrated single-unit information in order to reflect the animal's motivational state across the entire cycle, with higher activity levels during the hunger phases. This distributed population code might constitute a neural mechanism underlying meal initiation under different metabolic states.     

Comments on controversial tick (Acari: Ixodida) species names and species described or resurrected from 2003 to 2008

There are numerous discrepancies in recent published lists of the ticks of the world. Here we review the controversial names, presenting evidence for or against their validity and excluding some altogether. We also address spelling errors and present a list of 17 species described or resurrected during the years 2003–2008. We consider the following 35 tick species names to be invalid: Argas fischeri Audouin, 1826, Ornithodoros boliviensis Kohls and Clifford, 1964, Ornithodoros steini (Schulze, 1935), Amblyomma acutangulatum Neumann, 1899, Amblyomma arianae Keirans and Garris, 1986, Amblyomma bibroni (Gervais, 1842), Amblyomma colasbelcouri (Santos Dias, 1958), Amblyomma concolor Neumann, 1899, Amblyomma cooperi Nuttall and Warburton, 1908, Amblyomma curruca Schulze, 1936, Amblyomma cyprium Neumann, 1899, Amblyomma decorosum (Koch, 1867), Amblyomma nocens Robinson, 1912, Amblyomma perpunctatum (Packard, 1869), Amblyomma striatum Koch, 1844, Amblyomma superbum Santos Dias, 1953, Amblyomma testudinis (Conil, 1877), Amblyomma trinitatis Turk, 1948, Dermacentor confractus (Schulze 1933), Dermacentor daghestanicus Olenev, 1928, Haemaphysalis himalaya Hoogstraal, 1966, Haemaphysalis vietnamensis Hoogstraal and Wilson, 1966, Hyalomma detritum Schulze, 1919, Ixodes apteridis Maskell, 1897, Ixodes donarthuri Santos Dias, 1980, Ixodes kempi Nuttall, 1913, Ixodes neotomae Cooley, 1944, Ixodes rangtangensis Teng, 1973, Ixodes robertsi Camicas, Hervy, Adam and Morel, 1998, Ixodes serrafreirei Amorim, Gazetta, Bossi and Linhares, 2003, Ixodes tertiarius Scudder, 1885, Ixodes uruguayensis Kohls and Clifford, 1967, Ixodes zealandicus Dumbleton, 1961, Ixodes zumpti Arthur, 1960 and Rhipicephalus camelopardalis Walker and Wiley, 1959. We consider the following 40 names valid: Argas delicatus Neumann, 1910, Argas vulgaris Filippova, 1961, Ornithodoros aragaoi Fonseca, 1960, Ornithodoros dugesi Mazzoti, 1943, Ornithodoros knoxjonesi Jones and Clifford, 1972, Ornithodoros marocanus Velu, 1919, Ornithodoros nattereri Warburton, 1927, Amblyomma beaurepairei Vogelsang and Santos Dias, 1953, Amblyomma crassipes (Neumann, 1901), Amblyomma echidnae Roberts, 1953, Amblyomma fuscum Neumann, 1907, Amblyomma orlovi (Kolonin, 1995), Amblyomma parkeri Fonseca and Arag?o, 1952, Amblyomma pseudoconcolor Arag?o, 1908, Bothriocroton oudemansi (Neumann, 1910), Bothriocroton tachyglossi (Roberts, 1953), Dermacentor abaensis Teng, 1963, Dermacentor confragus (Schulze 1933), Dermacentor ushakovae Filippova and Panova, 1987, Haemaphysalis anomaloceraea Teng, 1984, Haemaphysalis filippovae Bolotin, 1979, Haemaphysalis pavlovskyi Pospelova-Shtrom, 1935, Hyalomma excavatum Koch, 1844, Hyalomma isaaci Sharif, 1928, Hyalomma rufipes Koch, 1844, Hyalomma turanicum Pomerantzev, 1946, Ixodes arabukiensis Arthur, 1959, Ixodes boliviensis Neumann, 1904, Ixodes columnae Takada and Fujita, 1992, Ixodes maslovi Emel′yanova and Kozlovskaya, 1967, Ixodes sachalinensis Filippova, 1971, Ixodes siamensis Kitaoka and Suzuki, 1983, Ixodes sigelos Keirans, Clifford and Corwin, 1976, Ixodes succineus Weidner, 1964, Rhipicephalus aurantiacus Neumann, 1907, Rhipicephalus cliffordi Morel, 1965, Rhipicephalus pilans Schulze, 1935, Rhipicephalus pseudolongus Santos Dias, 1953, Rhipicephalus serranoi Santos Dias, 1950 and Rhipicephalus tetracornus Kitaoka and Suzuki, 1983.     

Retrospective study of the prevalence of high-risk human papillomaviruses among Croatian women

The infection with Human papillomavirus (HPV) is the necessary cause for cervical cancer. There are at least 15 High-Risk (HR) HPV types that are significantly associated with progression of cervical intraepithelial neoplasia to cervical cancer. Since previous studies showed that the prevalence of HPV in cervical cancers varies among different geographic regions, we wanted to investigate the prevalence of HPV types in Croatia, especially low abundant HR HPV types. By means of consensus primers directed polymerase chain reaction (PCR), we analysed cervical DNA samples of 2,136 Croatian women, mostly with abnormal cervical smears, in order to detect the presence of HPV Type-specific primers were then used to determine Low-Risk (LR) HPV types 6/11 and HR HPV types 16, 18, 31, 33, 45, 52 and 58. Out of 2,136 specimens, 1,255 (58.8%) were positive for HPV More than half of positive samples were typed (64.5%) and 35.5% still remained untyped. Multiple HPV infections were found in 10.3% of the cases. The most prevalent type, including both single and multiple infections, was HPV16 with the prevalence of 15.9%, followed by HPV types 31, 6/11, 33, 18, 52, 45 and 58 with 8.7%, 7.1%, 4.5%, 3.8%, 2.3%, 1.2% and 1.1%, respectively. The significant increase of frequency from Low-grade Squamous Intraepithelial Lesions (LSIL) to High-grade Squamous Intraepithelial Lesions (HSIL) was observed for HR HPV types 16, 18, 31 and 33 but not 45, 52 and 58. The frequency of unknown HPV types was almost the same in cervical specimens of women with LSIL and those with HSIL, 19.8% and 21.1%, respectively. The prevalence of HPV infection rate decreased significantly with patient age from 68.5% (age group 12 to 24 years) to 38.8% (age group 45 to 54 years). But, in women aged 55 or older the overall prevalence increased to 56.6%. Our results indicate that prevalence of HR HPV types in Croatia is similar to other countries. We suggest that HPV positive women in Croatia should be closely monitored by typing for HR HPV types: 16, 18, 31, 33, 45, 52 and 58.     

The likely impact of elevated [CO2], nitrogen deposition, increased temperature and management on carbon sequestration in temperate and boreal forest ecosystems: a literature review

Temperate and boreal forest ecosystems contain a large part of the carbon stored on land, in the form of both biomass and soil organic matter. Increasing atmospheric [CO2], increasing temperature, elevated nitrogen deposition and intensified management will change this C store. Well documented single-factor responses of net primary production are: higher photosynthetic rate (the main [CO2] response); increasing length of growing season (the main temperature response); and higher leaf-area index (the main N deposition and partly [CO2] response). Soil organic matter will increase with increasing litter input, although priming may decrease the soil C stock initially, but litter quality effects should be minimal (response to [CO2], N deposition, and temperature); will decrease because of increasing temperature; and will increase because of retardation of decomposition with N deposition, although the rate of decomposition of high-quality litter can be increased and that of low-quality litter decreased. Single-factor responses can be misleading because of interactions between factors, in particular those between N and other factors, and indirect effects such as increased N availability from temperature-induced decomposition. In the long term the strength of feedbacks, for example the increasing demand for N from increased growth, will dominate over short-term responses to single factors. However, management has considerable potential for controlling the C store.     

Predicting enzyme class from protein structure using Bayesian classification

Predicting enzyme class from protein structure parameters is a challenging problem in protein analysis. We developed a method to predict enzyme class that combines the strengths of statistical and data-mining methods. This method has a strong mathematical foundation and is simple to implement, achieving an accuracy of 45%. A comparison with the methods found in the literature designed to predict enzyme class showed that our method outperforms the existing methods.     

Influence of Dry Season and Food Quality and Quantity on Behavior and Feeding Strategy of Propithecus verreauxi in Kirindy, Madagascar

According to optimal foraging theory, herbivores can base food choice mainly on the quality or the quantity of food, or both. Among herbivorous primates, folivorous lemurs living in the highly seasonal environment of Madagascar have to cope with the shortage of high-quality food during the dry season, at least in deciduous forests. We studied (Verreaux's sifaka) in Kirindy, western Madagascar, to understand the influence of dry season and food quality and quantity on behavioral patterns and feeding strategy (qualitative vs. quantitative dietary choice) of a folivorous lemur in a deciduous forest. We followed 7 groups (4 groups/period; 3 individuals/group/month) during 4 periods of the year (wet season: February–March; early/middle/late dry season: May–June; July–September; October–November). We collected samples of plants eaten and examined behavioral and feeding patterns, considering food quality (macronutrients, proteins/fibers ratio, and tannins) and abundance. We found 1) a significant reduction of home range, core area, and daily path length from the wet to the dry season, possibly related to dietary change and 2) a daily period of inactivity in the dry season for energy conservation. Regarding the feeding strategy, Kirindy sifakas showed 1) high variation and selection in choosing food items and 2) a dietary choice based mainly on quality: Kirindy sifakas fed on plant species/families independently from their abundance and tannins represented a feeding deterrent during the dry season. Overall, behavioral and dietary adaptations allow Kirindy sifakas to overcome the shortage of high-quality food in the lean period.