The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase

Aminoacyl-tRNA synthetases catalyze ATP-dependent covalent coupling of cognate amino acids and tRNAs for ribosomal protein synthesis. Escherichia coli isoleucyl-tRNA synthetase (IleRS) exploits both the tRNA-dependent pre- and post-transfer editing pathways to minimize errors in translation. However, the molecular mechanisms by which tRNA^Ile organizes the synthetic site to enhance pre-transfer editing, an idiosyncratic feature of IleRS, remains elusive. Here we show that tRNA^Ile affects both the synthetic and editing reactions localized within the IleRS synthetic site. In a complex with cognate tRNA, IleRS exhibits a 10-fold faster aminoacyl-AMP hydrolysis and a 10-fold drop in amino acid affinity relative to the free enzyme. Remarkably, the specificity against non-cognate valine was not improved by the presence of tRNA in either of these processes. Instead, amino acid specificity is determined by the protein component per se, whereas the tRNA promotes catalytic performance of the synthetic site, bringing about less error-prone and kinetically optimized isoleucyl-tRNA^Ile synthesis under cellular conditions. Finally, the extent to which tRNA^Ile modulates activation and pre-transfer editing is independent of the intactness of its 3′-end. This finding decouples aminoacylation and pre-transfer editing within the IleRS synthetic site and further demonstrates that the A76 hydroxyl groups participate in post-transfer editing only. The data are consistent with a model whereby the 3′-end of the tRNA remains free to sample different positions within the IleRS·tRNA complex, whereas the fine-tuning of the synthetic site is attained via conformational rearrangement of the enzyme through the interactions with the remaining parts of the tRNA body.     

The usefulness of semi‐solid medium in the isolation of highly virulent Leptospira strains from wild rats in an urban area of Fukuoka,Japan

Leptospirosis is a worldwide zoonosis. The importance of urban leptospirosis is recognized in Japan: urban rats carry pathogenic leptospires and people acquire these pathogens through contact with surface water or soil contaminated by the urine of the infected animals. To determine the current Leptospira carriage rate in urban rats, 29 wild rats were trapped in the central area of Fukuoka and strains isolated from their kidneys and urine analyzed. When semi‐solid Korthof's medium containing 0.1% agar was used for isolation, 72.2% and 30.8% of the kidney and urine cultures, respectively, were found to be Leptospira‐positive. The isolates belonged to Leptospira interrogans, and were classified into two groups (serogroups Pomona and Icterohaemorrhagiae) based on the results of gyrB sequence analysis and microscopic agglutination testing (MAT). Strains belonging to serogroup Icterohemorrhagiae grew well in liquid medium. On the other hand, serogroup Pomona isolates multiplied very little in liquid medium, but did grow in a semi‐solid medium. Although strains belonging to serogroup Pomona have not been recognized as native to Japan, this strain may be widely distributed in urban rats. Representative strains from each group were found to be highly pathogenic to hamsters. Our findings should serve as a warning that it is still possible to become infected with leptospires from wild rats living in inner cities of Japan. Furthermore, the use of semi‐solid medium for culture will improve the isolation rate of leptospires from the kidneys of wild rats.     

QSAR,DFT and quantum chemical studies on the inhibition potentials of some carbozones for the corrosion of mild steel in HCl

Experimental aspects of the inhibition of the corrosion of mild steel in HCl solutions by some carbozones were studied using gravimetric, thermometric and gasometric methods, while a theoretical study was carried out using density functional theory, a quantitative structure–activity relation, and quantum chemical principles. The results obtained indicated that the studied carbozones are good adsorption inhibitors for the corrosion of mild steel in HCl. The inhibition efficiencies of the studied carbozones were found to increase with increasing concentration of the respective inhibitor. A strong correlation was found between the average inhibition efficiency and some quantum chemical parameters, and also between the experimental and theoretical inhibition efficiencies (obtained from the quantitative structure–activity relation).     

Territoriality and Survivorship of the Sierra Madre Sparrow in La Cima,México

We studied the life-history of the Sierra Madre sparrow (Xenospiza baileyi) in a subalpine grassland-agriculture mosaic south of Mexico City. From March to early September 1999 we captured and color-banded 53 adults with mist-nets and mapped the breeding territories of 21 males. We again mapped territories in the same spot in April and May 2000. The number of breeding territories was found to be the same in the two consecutive years and interannual survivorship was found to be relatively high. Breeding territories were restricted to the bunchgrass-covered areas. We used the density of territories and the amount of remaining habitat to estimate a total population size of 5,380–6,150 adults for this species. Using this and other recent data, we recommend raising the Sierra Madre sparrow to the status of critically endangered using BirdLife International criteria.     

Morphological Variation in Wild Marmosets (Callithrix penicillata and C. geoffroyi) and Their Hybrids

Evolutionary theory and observation predict wider phenotypic variation in hybrids than parental species. Emergent phenotypic novelty in hybrids may in turn drive new adaptations or speciation by breaking parental phenotypic constraints. Primate hybridization is often documented through genetic evidence, but knowledge about the primate hybrid phenotype remains limited due to a small number of available studies on hybrid primate morphology. Here, we examine pelage and morphometric variation in two Brazilian marmoset species (Callithrix penicillata and C. geoffroyi) and their hybrids. Hybrids were sampled in an anthropogenic hybrid zone in the municipality of Viçosa, Minas Gerais state, Brazil. We analyzed hybrid facial and body pelage color variation, and compared 13 morphometric measures between hybrids and parental species. Five different hybrid facial morphotypes were observed, varying from intermediate to parental-like. Hybrid facial morphotypes were biased towards C. penicillata, suggesting that the pelage of this species may be dominant to that of C. geoffroyi in this context, and indicating that mate preference, and therefore gene flow/introgression, may be biased towards C. penicillata within the hybrid zone. Hybrid morphometric features were on average intermediate to parental species traits, but transgressive hybrids were also observed, suggesting that morphometric variation for the studied traits is consistent with Rieseberg’s complementary allele model. Finally, we observed a decoupling of facial patterning and size/shape in hybrids, relative to parent phenotypes, suggesting that an important factor driving phenotypic novelty within the Viçosa marmoset hybrid zone might be the loosening of evolutionary constraints on phenotypic trait integration.     

Distribution of human papillomavirus types in different histological subtypes of cervical adenocarcinoma

Little information is available regarding distribution of HPV types in different histological subtypes of adenocarcinoma (AC). Thus, in this study we examined the frequency of high-risk (hr) HPV types in AC, adenocarcinoma in situ (AIS) and adenosquamous carcinoma (ADSQ). A total of 102 cases of primary cervical adenocarcinoma (26 AIS and 76 invasive AC) obtained from pathology files from 1995-2006 were histologically subtyped. Our results demonstrated that endocervical type occupied the major subtype of AC (22/66) followed by ADSQ (17/66) where as in the group of AIS endocervical type (12/23) was followed by intestinal type of AIS (7/23). Successful DNA extraction was obtained in 89 samples; 81 out of 89 (91.0%) tested positive for HPV DNA. The prevalence of HPV DNA in AIS, AC and ADSQ was 91.3% (21/23), 90.9% (60/66) and 94.1% (16/17), respectively. We found HPV 18 type to be the most predominant type in AIS (11/21) and AC (17/60) followed by HPVof undeternmined type in AIS (3/21) and HPV 16 in AC (9/60) as the sole viral type. HPV 18 was most frequently detected type in all histological subtypes of AIS and AC. We have detected HPV DNA in all 5 samples of clear cell carcinoma (CCC), although other studies have reported a highly variable prevalence of HPVDNA in CCC. The most prevalent HPV type in ADSQ was HPV-16 followed by HPV 33 as single type. The observed overall predominance of HPV 18 in AIS (chi(2) = 6.109, p< or = 0.025) and AC (chi(2) = 8.927, p< or =0.01) as well as of HPV 16 in ADSQ (chi(2) = 10.164, p < or = 0.01) was statistically significant. Our data revealed statistically significant predominance of single hrHPV infections in AIS (16/21; chi(2) = 11.523, p < 0.001) and AC (37/60; X2 = 6.533, p < 0.025) whereas multiple hrHPV infections were more abundant in AC comparing to AIS (23/81and 5/81, respectively; chi(2) = 13.989, p< or =0.001).     

Expression of cell cycle and apoptosis regulatory proteins and telomerase in melanocitic lesions

To gain insight into the role and association of cell cycle and apoptosis regulatory proteins and telomerase activity in the course of progression of melanocitic lesions we have examined immunohistochemicaly, expression and the distribution of p53, bcl-2, Ki-67 and telomerase in 25 samples of common and dysplastic nevi, and 45 samples of primary invasive melanomas. Protein p53 expression was significantly increased in dysplastic as compared with common nevi and melanomas (p < 0.001). Bcl-2 protein expression was significantly increased in melanomas as compared with common aquired and dysplastic nevi (p = 0.001). Nevi and melanomas exhibited clear-cut differences in terms of Ki-67 expression. Telomerase expression was significantly increased in melanomas as compared with common acquired (p = 0.014) and dysplastic nevi (p < 0.001). Enhanced telomerase activity in association with increased bcl-2 expression in the course of melanoma progression could contribute to development and progression of melanoma.     

Morphometry of nucleoli and expression of nucleolin analyzed by laser scanning cytometry in mitogenically stimulated lymphocytes.

BACKGROUND: Various attributes of nucleoli, including abundance of the nucleolar product (rRNA), correlate with cell-proliferative status and are useful markers for tumor diagnosis and prognosis. However, there is a paucity of methods that can quantitatively probe nucleolus. The aim of the present study was to utilize the morphometric capacity of the laser scanning cytometer (LSC) to analyze nucleoli and measure expression of the nucleolar protein nucleolin (NCL) in individual cells and correlate it with their state of proliferation. MATERIALS AND METHODS: Human lymphocytes were mitogenically stimulated, and at different time points their nucleoli were detected immunocytochemically using NCL Ab. The frequency of nucleoli per nucleus, their area, and the level of expression of NCL, separately in the nuclear and nucleolar compartments, were estimated in relation to the G(0) to G(1) transition and the cell cycle progression. RESULTS: During the first 24 h of stimulation, when the cells underwent G(0) to G(1) transition, their RNA content was increased nearly 8-fold, the level of NCL per nucleus also increased 8-fold, the NCL per nucleolus increased 12-fold, nucleolear area increased 3-fold, and NCL/nucleolar area increased nearly 4-fold. During the subsequent 24-48 h of stimulation, when cells were progressing through S, G(2), and M and reentering the next cycle, the number of nucleoli per nucleus was increased and a massive translocation of NCL from nucleoli to nucleoplasm was observed; its overall level per nucleus, however, still remained high, at 6-fold above of that of G(0) cells. CONCLUSIONS: While high expression of NCL in the nucleolar compartment correlates with the rate of rRNA accumulation in the cell and is a sensitive marker of the G(0) to G(1) transition, the cells progressing through the remainder of the cycle are better distinguished from G(0) cells by high overall level of NCL within the nucleus. Such an analysis, when applied to tumors, may be helpful in obtaining the quantitative parameters related to the kinetic status of the tumor-cell population and tumor prognosis. The capability of LSC to measure the protein translocation between nucleolus and nucleoplasm can be used to study the function and regulatory mechanisms of other proteins that reside in these compartments.     

Evidence for the Predator Attraction Hypothesis in an amphibian predator–prey system

Many species possess damage-released chemical alarm cues that function in alerting nearby individuals to a predator attack. One hypothesis for the evolution and/or maintenance of such cues is the Predator Attraction Hypothesis, where predators, rather than prey, are the “intended” recipients of these cues. If a predator attack attracts additional predators, these secondary predators might interfere with the predation event, providing the prey with a better chance to escape. In this study, we conducted two experiments to explore this hypothesis in an amphibian predator/prey system. In Experiment 1, we found that tiger salamanders (Ambystoma mavortium) showed a foraging attraction to chemical cues from wood frog (Lithobates sylvaticus) tadpoles. Salamanders that were experienced with tadpole prey, in particular, were strongly attracted to tadpole alarm cues. In Experiment 2, we observed experimental encounters between a tadpole and either one or two salamanders. The presence of the second predator caused salamanders to increase attack speed at the cost of decreased attack accuracy (i.e., increasing the probability that the tadpole would escape attacks). We also found that the mere presence of visual and chemical cues from a second predator did not affect this speed/accuracy trade-off but did cause enough of a distraction to increase tadpole survival. Thus, our findings are consistent with the Predator Attraction Hypothesis for the evolution and/or maintenance of alarm cues.