Sound production by the Shi drum Umbrina cirrosa and comparison with the brown meagre Sciaena umbra: a passive acoustic monitoring perspective

Sounds produced by the Shi drum Umbrina cirrosa were short trains of pulses with an average pulse period of 180 ms, pulse duration of c. 40 ms and an average peak frequency of 400 Hz; average values of acoustical properties differed from those recorded from the brown meagre Sciaena umbra in previous studies. The present study provides a preliminary tool for discriminating between these two species while conducting passive acoustic monitoring. The potential effects of ontogeny on sound production in both species are discussed and recommendations are made for further research.     

Bacterial communities involved in sulfur transformations in wastewater treatment plants

The main sulfate-reducing (SRB) and sulfur-oxidizing bacteria (SOB) in six wastewater treatment plants (WWTPs) located at southern Brazil were described based on high-throughput sequencing of the 16S rDNA. Specific taxa of SRB and SOB were correlated with some abiotic factors, such as the source of the wastewater, oxygen content, sample type, and physical chemical attributes of these WWTPs. When the 22 families of SRB and SOB were clustered together, the samples presented a striking distribution, demonstrating grouping patterns according to the sample type. For SOB, the most abundant families were Spirochaetaceae, Chromatiaceae, Helicobacteriaceae, Rhodospirillaceae, and Neisseriaceae, whereas, for SRB, were Syntrophaceae, Desulfobacteraceae, Nitrospiraceae, and Desulfovibriaceae. The structure and composition of the major families related to the sulfur cycle were also influenced by six chemical attributes (sulfur, potassium, zinc, manganese, phosphorus, and nitrogen). Sulfur was the chemical attribute that most influenced the variation of bacterial communities in the WWTPs (λ = 0.14, p = 0.008). The OTUs affiliated to Syntrophus showed the highest response to the increase of total sulfur. All these findings can contribute to improve the understanding in relation to the sulfur-oxidizing and sulfate-reducing communities in WWTPs aiming to reduce H₂S emissions.     

An NcoI restriction fragment length polymorphism at the human steroid sulphatase gene locus

Summary The DNA diagnosis of X-linked recessive ichthyosis vulgaris (incidence: approx. 1 in 5000 males) can be complicated by the absence of restriction fragment length polymorphisms (RFLPs) in the STS (steroid sulphatase) gene. An RFLP sequence in NcoI-digested genomic DNA is reported, which it is hoped may prove helpful in diagnosis.     

Energetic limitation of avian parental effort: Field experiments in the kestrel (Falco tinnunculus)

We studied the limiting factors for brood size in the kestrel, Falco tinnunculus, by measuring parental effort in natural broods of different size and parental response to manipulation of food satiation of the brood. Parental effort was quantified as total daily time spent in flight, and total daily energy expenditure, from all-day observations. During nestling care males with different natural brood sizes (4 to 7 chicks), spent an average of 4.75 h · d^?1 in flight independent of brood size, and expended an average total daily energy of 382 kJ · d^?1. Due to a higher flight-hunting yield (mammal-prey caught per hour hunting), males with larger natural broods were able to provision their broods with the same amount of food (mainly Microtus arvalis) per chick (62.6 g · d^?1), with the same effort as males with smaller broods. This provisioning rate was close to the mean feeding rate of hand-raised chicks in the laboratory, that were fed ad libitum, (66.8 g · d^?1 · chick^?1). Our food deprivation experiments revealed that male kestrels strongly respond to food shortage in the nest. In the older nestling phase males on average increased their daily rate of food delivery to the nest as a response to experimental food deprivation by almost three times to 646.4 g · d^?1, by increasing their flight activity level from 4.46 to 8.41 h · d^?1. This increased energy expenditure was sustained, for as long as eleven days, by increasing the metabolizable energy intake up to what is presumed to be the maximum rate. Even under considerable experimental food stress (chicks not being satiated due to continuous removal of delivered food by the observers) about half of the available daylight time remained unused for foraging. We conclude 1) that the mean daily energy expenditure of males during nestling care — to which clutch size is apparently initially adjusted — is well below the maximum they are able to sustain and 2) that the energy expenditure they can sustain under extremely high nestling demand is not set by the available time for foraging or the available energy in the environment. Thus the birds normally operate well below their presumed maximum, and only during food shortage, e.g., as caused by our experiments, do they increase activity up to this maximum. Therefore we conclude that the kestrels have costs other than energy expenditure, such as parental survival, that are involved in the increased “cost” of parental effort. We discuss possible generalisations about existing energetic limitations during parental care in altricial birds. From published estimates of daily energy expenditure during parental care (DEE_par) in 30 different bird species we derived the equation: DEE_par = 14.26 kg^0.65 Watt. This relationship differs significantly in slope (T = 2.49; p > 0.02) from the allometric equation for the maximum rate of energy assimilation (DME_max) as provided by Kirkwood (1983): DME_max = 19.82 kg^0.72 Watt. In smaller species (ca. 25 g) DEE_par about equals DME_max, while in the larger species (ca. 10 kg) DEE_par represents only about 60% of the predicted DME_max. This suggests that limitations in parental effort are more frequently set by the maximum sustainable energy intake in the smaller species than in larger species. Our allometric equations for DEE_par suggests that the relation between BMR, estimated using the equations of Aschoff and Pohl (1970), and the observed parental energy expenditure, is such that on average bird parents work at a daily level somewhere between 3 and 4 times BMR.     

Effects of temperature and gibberellin on the activity of endogenous cytokinin-like substances in leaves of Begonia x cheimantha

Changes in activity of endogenous cytokinin-like substances were examined in intact plants and excised leaves of Begonia x chemantha Everett cv. Prinsesse Astrid (Christimas Begonia) by means of the tobacco callus bioassay. Cytokinin activity in the leaves of intact plants was higher in plants grown at 18°C than in those grown at 21° or 24°C. In excised leaves, an increase in cytokinin activity was observed during the first 4 days following leaf detachment. However, after the seventh day cylokinin activity decreased again. This decrease was more profound in leaves exposed to 24°C than in those exposed to 18°C.
Treatment of detached leaves with gibberellic acid (2.8 m M ) caused an increase in measurable cytokinin activity. This increase was more profound in the zones of activity which correspond with zeatin glucosides on paper and Sephadex LH-20 chromatography. Additional zones of activity appeared after Sephadex chromatography. These were of a more slow moving nature with elution volumes corresponding to N^b-(Δ²-isopentenyl)adenine and its derivaties. Water-treated control leaves had higher activity in the regions corresponding to zeatin and zeatin riboside.     

Ribosomal Protein Mutations Induce Autophagy through S6 Kinase Inhibition of the Insulin Pathway

Mutations affecting the ribosome lead to several diseases known as ribosomopathies, with phenotypes that include growth defects, cytopenia, and bone marrow failure. Diamond-Blackfan anemia (DBA), for example, is a pure red cell aplasia linked to the mutation of ribosomal protein (RP) genes. Here we show the knock-down of the DBA-linked RPS19 gene induces the cellular self-digestion process of autophagy, a pathway critical for proper hematopoiesis. We also observe an increase of autophagy in cells derived from DBA patients, in CD34⁺ erythrocyte progenitor cells with RPS19 knock down, in the red blood cells of zebrafish embryos with RP-deficiency, and in cells from patients with Shwachman-Diamond syndrome (SDS). The loss of RPs in all these models results in a marked increase in S6 kinase phosphorylation that we find is triggered by an increase in reactive oxygen species (ROS). We show that this increase in S6 kinase phosphorylation inhibits the insulin pathway and AKT phosphorylation activity through a mechanism reminiscent of insulin resistance. While stimulating RP-deficient cells with insulin reduces autophagy, antioxidant treatment reduces S6 kinase phosphorylation, autophagy, and stabilization of the p53 tumor suppressor. Our data suggest that RP loss promotes the aberrant activation of both S6 kinase and p53 by increasing intracellular ROS levels. The deregulation of these signaling pathways is likely playing a major role in the pathophysiology of ribosomopathies.     

Testing compatibility between molecular and morphological techniques for arthropod systematics: a minimally destructive DNA extraction method that preserves morphological integrity, and the effect of lactic acid on DNA quality

Three practical aspects related to the preservation and destruction of DNA and/or morphological characters of spiders were examined: potential morphological damage during non-destructive DNA extraction was assessed by counting trichobothria, a fragile sensorial feature found on spider legs; the effect on yield of non-destructive DNA extraction; and whether possible DNA degradation is caused by residues of lactic acid, which is used as a temporary mounting medium for the study of morphological structures in spiders and insects. Destructive extractions yielded higher amounts of DNA than non-destructive methods. However, non-destructive methods yielded usable amounts of DNA while leaving delicate trichobothria intact. Of the non-destructive extractions, a longer digestion period (36 h vs. 12) yielded higher amounts of DNA and did not damage trichobothria. Lactic acid did not induce short-term DNA degradation or inhibit PCR reactions, even at high concentrations. These results show compatibility between molecular and morphological requirements without compromising DNA quality or specimen integrity.     

Gene Expression-Based Classification of Non-Small Cell Lung Carcinomas and Survival Prediction

Background

Current clinical therapy of non-small cell lung cancer depends on histo-pathological classification. This approach poorly predicts clinical outcome for individual patients. Gene expression profiling holds promise to improve clinical stratification, thus paving the way for individualized therapy.

Methodology and Principal Findings

A genome-wide gene expression analysis was performed on a cohort of 91 patients. We used 91 tumor- and 65 adjacent normal lung tissue samples. We defined sets of predictor genes (probe sets) with the expression profiles. The power of predictor genes was evaluated using an independent cohort of 96 non-small cell lung cancer- and 6 normal lung samples. We identified a tumor signature of 5 genes that aggregates the 156 tumor and normal samples into the expected groups. We also identified a histology signature of 75 genes, which classifies the samples in the major histological subtypes of non-small cell lung cancer. Correlation analysis identified 17 genes which showed the best association with post-surgery survival time. This signature was used for stratification of all patients in two risk groups. Kaplan-Meier survival curves show that the two groups display a significant difference in post-surgery survival time (p = 5.6E-6). The performance of the signatures was validated using a patient cohort of similar size (Duke University, n = 96). Compared to previously published prognostic signatures for NSCLC, the 17 gene signature performed well on these two cohorts.

Conclusions

The gene signatures identified are promising tools for histo-pathological classification of non-small cell lung cancer, and may improve the prediction of clinical outcome.     

Short-term metabolome dynamics and carbon, electron, and ATP balances in chemostat-grown Saccharomyces cerevisiae CEN.PK 113-7D following a glucose pulse

The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O(2) uptake and CO(2) evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO(2) evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.     

13C-labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum

In this study we developed a new method for accurately determining the pentose phosphate pathway (PPP) split ratio, an important metabolic parameter in the primary metabolism of a cell. This method is based on simultaneous feeding of unlabeled glucose and trace amounts of [U-13C]gluconate, followed by measurement of the mass isotopomers of the intracellular metabolites surrounding the 6-phosphogluconate node. The gluconate tracer method was used with a penicillin G-producing chemostat culture of the filamentous fungus Penicillium chrysogenum. For comparison, a 13C-labeling-based metabolic flux analysis (MFA) was performed for glycolysis and the PPP of P. chrysogenum. For the first time mass isotopomer measurements of 13C-labeled primary metabolites are reported for P. chrysogenum and used for a 13C-based MFA. Estimation of the PPP split ratio of P. chrysogenum at a growth rate of 0.02 h(-1) yielded comparable values for the gluconate tracer method and the 13C-based MFA method, 51.8% and 51.1%, respectively. A sensitivity analysis of the estimated PPP split ratios showed that the 95% confidence interval was almost threefold smaller for the gluconate tracer method than for the 13C-based MFA method (40.0 to 63.5% and 46.0 to 56.5%, respectively). From these results we concluded that the gluconate tracer method permits accurate determination of the PPP split ratio but provides no information about the remaining cellular metabolism, while the 13C-based MFA method permits estimation of multiple fluxes but provides a less accurate estimate of the PPP split ratio.