New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia.

A recent field-intensive program in Shark Bay, Western Australia provides new multi-scale perspectives on the world's most extensive modern stromatolite system. Mapping revealed a unique geographic distribution of morphologically distinct stromatolite structures, many of them previously undocumented. These distinctive structures combined with characteristic shelf physiography define eight 'Stromatolite Provinces'. Morphological and molecular studies of microbial mat composition resulted in a revised growth model where coccoid cyanobacteria predominate in mat communities forming lithified discrete stromatolite buildups. This contradicts traditional views that stromatolites with the best lamination in Hamelin Pool are formed by filamentous cyanobacterial mats. Finally, analysis of internal fabrics of stromatolites revealed pervasive precipitation of microcrystalline carbonate (i.e. micrite) in microbial mats forming framework and cement that may be analogous to the micritic microstructures typical of Precambrian stromatolites. These discoveries represent fundamental advances in our knowledge of the Shark Bay microbial system, laying a foundation for detailed studies of stromatolite morphogenesis that will advance our understanding of benthic ecosystems on the early Earth.

DNA-based and geometric morphometric analysis to validate species designation: a case study of the subterranean rodent Ctenomys bicolor.

The genus Ctenomys (Rodentia: Ctenomyidae) shows several taxonomic inconsistencies. In this study, we used an integrative approach including DNA sequences, karyotypes, and geometric morphometrics to evaluate the taxonomic validity of a nominal species, Ctenomys bicolor, which was described based on only one specimen in 1912 by Miranda Ribeiro, and since then neglected. We sampled near the type locality assigned to this species and collected 10 specimens. A total of 820 base pairs of the cytochrome b gene were sequenced and analyzed together with nine other species and four morphotypes obtained from GenBank. Bayesian analyses showed that C. bicolor is monophyletic and related to the Bolivian-Matogrossense group, a clade that originated about 3 mya. We compared the cranial shape through morphometric geometrics of C. bicolor, including the specimen originally sampled in 1912, with other species representative of the same phylogenetic group (C. boliviensis and C. steinbachi). C. bicolor shows unique skull traits that distinguish it from all other currently known taxa. Our findings confirm that the specimen collected by Miranda Ribeiro is a valid species, and improve the knowledge about Ctenomys in the Amazon region.

Microbial mat controls on infaunal abundance and diversity in modern marine microbialites.

Microbialites are the most abundant macrofossils of the Precambrian. Decline in microbialite abundance and diversity during the terminal Proterozoic and early Phanerozoic has historically been attributed to the concurrent radiation of complex metazoans. Similarly, the apparent resurgence of microbialites in the wake of Paleozoic and Mesozoic mass extinctions is frequently linked to drastic declines in metazoan diversity and abundance. However, it has become increasing clear that microbialites are relatively common in certain modern shallow, normal marine carbonate environments-foremost the Bahamas. For the first time, we present data, collected from the Exuma Cays, the Bahamas, systematically characterizing the relationship between framework-building cyanobacteria, microbialite fabrics, and microbialite-associated metazoan abundance and diversity. We document the coexistence of diverse microbialite and infaunal metazoan communities and demonstrate that the predominant control upon both microbialite fabric and metazoan community structure is microbial mat type. These findings necessitate that we rethink prevalent interpretations of microbialite-metazoan interactions and imply that microbialites are not passive recipients of metazoan-mediated alteration. Additionally, this work provides support for the theory that certain Precambrian microbialites may have been havens of early complex metazoan life, rather than bereft of metazoans, as has been traditionally envisaged.

Importance of miR-20a expression in prostate cancer tissue.

BACKGROUND: MicroRNAs (miRNAs), which are endogenously expressed regulatory noncoding RNAs, have an altered expression in tumor tissues. MiRNAs regulate cancer-related processes such as cell growth and tissue differentiation, and therefore, might function as oncogenes or tumor-suppressor genes. The aim of our study was to assess the expression of mir-20a, let-7a, miR-15a and miR-16 in prostate cancer (PCa) and benign prostatic hyperplasia (BPH) tissue and to investigate the relation between the expression of miRNAs and the clinicopathological features of PCa. PATIENTS AND METHODS: The study group comprised 138 patients: 85 patients with BPH and 53 patients with PCa. The total RNA was isolated from the tissue specimen core and miRNA expressions were quantified using a real-time RT-PCR method (TaqMan MicroRNA Assays). U6snRNA was used for the normalization of the miRNA expression. RESULTS: miR-20a expression was significantly higher in the group of patients with a Gleason score of 7-10 in comparison with the group of patients with a Gleason score of 0-6 (p=0.0082). We found no statistical differences in the miRNA expressions (mir-20a, let-7a, miR-15a and miR-16) in the PCa tissue samples in comparison with the BPH tissue samples. CONCLUSION: Our result shows that the more dedifferentiated PCa cells have a higher expression of miR-20a and this supports the oncogenic role of miR-20a in PCa carcinogenesis. The evaluation of miRNA expression could yield new information about PCa pathogenesis.

Differential display code 3 (DD3/PCA3) in prostate cancer diagnosis.

BACKGROUND: Early diagnosis of prostate cancer (PCa) in an organ-confined stage following radical treatment is the only potential curative approach in PCa. Prostatic-specific antigen (PSA) is very helpful in early diagnosis, but the main disadvantage is that it has a low positive predictive value in the range of the grey zone of 2.5-10 ng/mL, which results in a high number of needless biopsies. For this reason, new tests with better parameters are needed. One promising test is that for differential display code 3 (DD3(PCA3)), which is a prostate-specific non-coding mRNA that is highly overexpressed in prostate tumor cells. The aim of the present study was to evaluate the potential of DD3(PCA3) for mRNA in PCa diagnosis. PATIENTS AND METHODS: A total of 186 patients were examined. In a group of patients with suspected PCa, one tissue specimen core was collected for testing DD3(PCA3) expression. According to the histological verification there were 100 patients with benign prostatic hyperplasia, 12 patients with prostatic intraepithelial neoplasia and 74 patients with PCa. The total RNA was isolated and DD3(PCA3) and PSA expressions were quantified using quantitative RT real-time PCR method. The DD3(PCA3)/PSA mRNA ratio was determined for all groups. RESULTS: It was found that the levels of the mRNA expression of DD3(PCA3) were significantly higher (p<0.045) in patients with PCa than in patients with benign prostatic hyperplasia. No statistically significant differences in levels of mRNA expression of DD3(PCA3) between patients with organ-confined and those with advanced or metastatic disease, nor according to Gleason score, were found. CONCLUSION: DD3(PCA3) appears to be a promising marker for early detection of PCa and also for differential diagnosis between patients with benign prostate hyperplasia and those with PCa.

Enrichment and isolation of Bacillus beveridgei sp. nov., a facultative anaerobic haloalkaliphile from Mono Lake, California, that respires oxyanions of tellurium, selenium, and arsenic.

Mono Lake sediment slurries incubated with lactate and tellurite [Te(IV)] turned progressively black with time because of the precipitation of elemental tellurium [Te(0)]. An enrichment culture was established from these slurries that demonstrated Te(IV)-dependent growth. The enrichment was purified by picking isolated black colonies from lactate/Te(IV) agar plates, followed by repeated streaking and picking. The isolate, strain MLTeJB, grew in aqueous Te(IV)-medium if provided with a small amount of sterile solid phase material (e.g., agar plug; glass beads). Strain MLTeJB grew at high concentrations of Te(IV) (~8 mM) by oxidizing lactate to acetate plus formate, while reducing Te(IV) to Te(0). Other electron acceptors that were found to sustain growth were tellurate, selenate, selenite, arsenate, nitrate, nitrite, fumarate and oxygen. Notably, growth on arsenate, nitrate, nitrite and fumarate did not result in the accumulation of formate, implying that in these cases lactate was oxidized to acetate plus CO(2). Strain MLTeJB is a low G + C Gram positive motile rod with pH, sodium, and temperature growth optima at 8.5-9.0, 0.5-1.5 M, and 40 degrees C, respectively. The epithet Bacillus beveridgei strain MLTeJB(T) is proposed.

[Mid-term outcomes and survival rates in patients with radical retropubic prostatectomy (RRP) under current Czech healthcare system]. / Strednedobé výsledky a prezití nemocných po radikální retropubické prostatektomii (RRP) v soucasných podmínkách ceského zdravotnictví.

The mid-term results (5 yr) after radical retropubic prostatectomy (RRP) are outlined and compared with pre- and postoperative parameters of patients. While 5 years survival could be expected in as many as 92.4%, relatively higher age (majority over 65) brings a higher risk of complications with it, though fully comparable with international standards. No perioperative mortality was recorded (0%), obstructive symptoms post-operatively developed in 13.4% patients, who were subsequently managed successfully endoscopically. Continence with maximum one pad per 24 hours was recorded in 77.2%, the severe incontinence was only in 3.3%. Spontaneous erection was reported in 4.3%, but except for higher age, the other objective factors were involved.

Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California.

Phylogenetic analysis indicates that microbial arsenic metabolism is ancient and probably extends back to the primordial Earth. In microbial biofilms growing on the rock surfaces of anoxic brine pools fed by hot springs containing arsenite and sulfide at high concentrations, we discovered light-dependent oxidation of arsenite [As(III)] to arsenate [As(V)] occurring under anoxic conditions. The communities were composed primarily of Ectothiorhodospira-like purple bacteria or Oscillatoria-like cyanobacteria. A pure culture of a photosynthetic bacterium grew as a photoautotroph when As(III) was used as the sole photosynthetic electron donor. The strain contained genes encoding a putative As(V) reductase but no detectable homologs of the As(III) oxidase genes of aerobic chemolithotrophs, suggesting a reverse functionality for the reductase. Production of As(V) by anoxygenic photosynthesis probably opened niches for primordial Earth's first As(V)-respiring prokaryotes.

[Detection of prostate cancer by ultrasonographically-guided transrectal prostate biopsies at the Department of Urology of the First Faculty of Medicine, Charles University and General Teaching Hospital in Prague, analysis of 1464 cases]. / Detekce karcinomu prostaty transrektální ultrasonograficky cílenou biopsií na urologické klinice 1. LF UK a VFN v Praze: analýza 1464 pozorování.

BACKGROUND: Early diagnostics of prostate cancer is still the most important factor in tumor-specific survival of patients harbouring this malignant disease. Without better understanding of the etiology and without relevant markers of the disease progression, only the early diagnostics of organ-confined disease can save the patient's life. METHODS AND RESULTS: Throughout 7 consecutive years, 1464 transrectal prostate biopsies in 1302 patients were performed. In all cases, the age, DRE (positive or negative), prostatic volume (ccm), total PSA in peripheral blood (ng/ml) were assigned, as well as free/total PSA ratio (%) in most of them. Apart from previously used linear regression, we applied logistic regression, since only age grows linear and DRE is determined only as positive or negative. The surrogate endpoint was ROC, which determines the area applying to the relations of sensitivity and specificity of any marker. Multifactorial logistic regression then reached best results at values over 0.8 in all tested age categories with maximal deviation of 8%, which had not been achieved before. CONCLUSIONS: Despite hundreds of papers published on this topic, the question of when and how the patient is indicated to the biopsy of the prostate has not been solved. A computer driven model based on 1464 documented examinations on the relatively homogeneous population is presented. On the basis of the combination of biological and statistical methods, the model can give correct predictions in 9 out of 10 cases.

[Analysis of results of percutaneous nephrolithotomies]. / Analýza výsledku perkutánních extrakcí konkrementu.

BACKGROUND: Percutaneous nephrolithotomy is an effective less invasive method for the treatment of nephrolithiasis. Authors retrospectively analysed results of this procedure performed in a single centre (Department of Urology, General University Hospital, Prague) from January 2005 till June 2007. METHODS AND RESULTS: Patients were acquired by an analysis of operating reports performed over a period January 2005 till June 2007 and subsequently a retrospective analysis of electronic and paper patient's records was carried out. Percutaneous nephrolithotomy was performed in 150 patients. Of those, 117 (78%) patients underwent primary and 33 (21.3%) secondary procedure. Analysed group consisted of 85 (56.7%) men and 65 (43.3%) women. Right-sided procedure was performed in 46% (69 times) and left-sided in 54% (81 times) of cases. Mean patient's age was 52.9 years (SD +/- 16.3). Mean stone size was 18.3 (SD +/- 9.5) mm. Staghorn calculi were present in 19 (12.7%) patients and 77 (51.3%) patients had more than 1 stone. Intracorporeal lithotripsy was necessary in 82 (54.7%) cases. Seventy eight (52.9%) patients were stone free after the procedure. There were 24 (16%) patients with an anatomic abnormality of upper urinary tract. The most common (in 64.3%) component in analysed stones was a calcium oxalate. CONCLUSIONS: The amount of stone free patients is rather lower compared to the literature results. However, definitive results are always affected by auxiliary procedures (mainly extracorporeal shock wave lithotripsy), which are not included in the analysis.

[Expression of PAX2 and PAX8 genes in conventional type of renal carcinoma and their role in the tumor prognosis]. / Exprese genu PAX2 a PAX8 v konvencním typu renálního karcinomu a jejich role v prognostice tohoto onemocnení.

BACKGROUND: Sporadic renal cell carcinoma is one of the most common kidney malignancies in adults (85%). According to the IARC (The International Agency of Research on Cancer) Czech Republic has the first world position in the incidence and mortality for RCC. The prognosis of RCC is very poor because of high mortality around 70 to 50% and unpredictable progression after tumor removal. More precise molecular prognostic markers are required. Genes PAX2 and PAX8 control cell division during embryonic development and plays crucial role in tumor development because of stimulation of cell proliferation and/or inhibition of apoptotic program. METHODS AND RESULTS: Our RCC sample collection contains 64 tumor samples and 10 "normal" renal samples extracted from the affected kidney. mRNA was isolated from all samples and converted into cDNA. Expression of PAX genes was analyzed by using relative quantification real-time PCR with TaqMan labelled probe and GAPDH gene as an endogenous control. CONCLUSIONS: Expression of PAX2 gene was found in 97% and expression of PAX8 gene was found in 89% of analyzed tumor samples. The expression of both target genes was found in all "normal" renal samples. The level of expression of both PAX genes was very variable with the range from hundred times lower to forty times higher in comparison with the expression of chosen endogenous control. There were found no correlations between the expression of target genes and clinical-histological markers. These results do not have prognostic value yet because of short duration of patient observation. Follow-up clinical data are essential for completion of this research.

[Reconstruction surgical procedures for iatrogenic injuries to the ureter. Examples of uncommon, however successful approaches to their management]. / Rekonstrukcní operace po iatrogenním poskození mocovodu--príklady méne obvyklých avsak uspesných resení.

The authors present several less usual reconstructions of ureters after the primary iatrogenic lesions. The appropriate ureteric capacity to drain the urine after previous injury is quite demanding and hence before the definitive decision is made the wholesome health status of the patient is to be considered and all possible solutions should be weighted. The efficient primary urinary diversion above the lesion is unavoidable. The genuine reconstruction could be deferred by several weeks or months in the view that in some cases the least invasive (endourologic) methods can completely avoid the need of open surgery in difficult adhesions after previous major surgery.

[Benefits and risks of urologic laparoscopic surgery in adult patients]. / Výhody a rizika laparoskopických operací u dospelých pacientu v urologii.

The paper describes the advantages and disadvantages of the laparoscopic operations, the number of which steadily rises in urology. The laparoscopic surgery is considered to be a benefit regarding the short postoperative hospital stay, painless postoperative course, and virtually non-existing postoperative paralytic ileus. As disadvantage are deemed the long learning curve for the operating personal, and high economical costs, which could be cut down only if short off-work period in productive population is included. In the paper, the pathophysiological guidelines are outlined and emphasized during the laparoscopic operation, which the surgical and anesthesiological teams have to have in mind. On the own cohort of patients, the numbers and types of operations are described, which have been done at our department.

Microbial transformation of elements: the case of arsenic and selenium.

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.

[Adjuvant therapy of renal carcinoma]. / Adjuvantní lécba karcinomu ledviny.

A treatment approach in a group of 1498 patients with renal cell carcinoma (RCC) was studied. Out of these, 86 patients had the primarily generalised form. For the therapy of primary advanced metastasis, the treatment strategy was changed from conservative to an active approach. Such approach is based on the removal of 75% of the tumor mass, the patient should be in good conditions with no metastases in CNS, bone and liver, and the primary tumor should not be a sarcoma. The new treatment strategy of patients with advanced RCC combines surgery and chemoimmunotherapy. 47 patients from the studied group were treated with combined INF alpha + IL-2 + 5FU + isotretinoin using the Atzpodien scheme. The toxicity was minimal and only in six patients the treatment was interrupted because of the disease progression. Results of this treatment strategy are encouraging, however, further randomised trials are recommended.

Taking a bright view of negative priming in the light of dim stimuli: further evidence for memory confusion during episodic retrieval.

A same-different letter-matching task was used to examine the effects of stimulus intensity on negative priming, which is poorer performance when target letters have been presented as distractor letters on the immediately preceding trial. In Experiment 1, stimulus intensity was manipulated between-participants, whereas in Experiment 2, it varied randomly from trial-to-trial within-participants. In Experiment 1, negative priming was equivalent for both stimulus intensities. In Experiment 2, negative priming effects were larger for repeated intensity stimuli than for nonrepeated intensity stimuli, when stimulus intensity was dim. Furthermore, for repeated intensity stimuli, negative priming effects were enhanced when the overt response required to the stimulus was repeated from prime to probe trial. These results are consistent with the hypothesis that negative priming may be due to memory confusion, rather than to inhibition of the distractor stimuli.

Evidence for iron-dependent nitrate respiration in the dissimilatory iron-reducing bacterium Geobacter metallireducens.

The dissimilatory iron-reducing bacterium Geobacter metallireducens was found to require iron at a concentration in excess of 50 microM for continuous cultivation on nitrate. Growth yield (approximately 3-fold), cytochrome c content (approximately 7-fold), and nitrate (approximately 4.5-fold) and nitrite (approximately 70-fold) reductase activities were all increased significantly when the growth medium was amended with 500 microM iron.

Selenihalanaerobacter shriftii gen. nov., sp. nov., a halophilic anaerobe from Dead Sea sediments that respires selenate.

We isolated an obligately anaerobic halophilic bacterium from the Dead Sea that grew by respiration of selenate. The isolate, designated strain DSSe-1, was a gram-negative, non-motile rod. It oxidized glycerol or glucose to acetate + CO2 with concomitant reduction of selenate to selenite plus elemental selenium. Other electron acceptors that supported anaerobic growth on glycerol were nitrate and trimethylamine-N-oxide; nitrite, arsenate, fumarate, dimethylsulfoxide, thiosulfate, elemental sulfur, sulfite or sulfate could not serve as electron acceptors. Growth on glycerol in the presence of nitrate occurred over a salinity range from 100 to 240 g/l, with an optimum at 210 g/l. Analysis of the 16S rRNA gene sequence suggests that strain DSSe-1 belongs to the order Halanaerobiales, an order of halophilic anaerobes with a fermentative or homoacetogenic metabolism, in which anaerobic respiratory metabolism has never been documented. The highest 16S rRNA sequence similarity (90%) was found with Acetohalobium arabaticum (X89077). On the basis of physiological properties as well as the relatively low homology of 16S rRNA from strain DSSe-1 with known genera, classification in a new genus within the order Halanaerobiales, family Halobacteroidaceae is warranted. We propose the name Selenihalanaerobacter shriftii. Type strain is strain DSSe-1 (ATCC accession number BAA-73).

Disengaging attention: on the locus of the cue-duration effect in partial report.

Increasing cue duration impairs performance in bar-probe partial report when cues are presented peripherally, but not centrally (P. Dixon, R. Gordon, A. Leung, & V. Di Lollo, 1997). Three experiments examined whether this cue-duration effect reflects processes of exogenous attention. The effect of cue duration on partial report performance with peripheral, but not central, cues was replicated (Experiment 1). Further experiments manipulated the degree that exogenous versus endogenous modes of selection were favored and found that the cue-duration effect for peripheral cues was reduced (a) when blocks contained a high proportion of central cues (Experiment 2) and (b) when the color of the cue indicated the location of the target (Experiment 3). These findings challenge the view that the cue-duration effect is restricted to exogenous attention and are discussed in terms of the process of disengaging attention from the cue to reallocate attention to the target representation.