Review of the large catfish fisheries in the upper Amazon and the stock depletion of <Emphasis Type="Italic">piraíba</Emphasis> (<Emphasis Type="Italic">Brachyplatystoma filamentosum</Emphasis>Lichtenstein)

In this paper we describe the present status of the large migratory catfish fisheries in the Upper Amazon. We present biological information about the main species and we give strong evidence that the stock of piraíba (Brachyplatystoma filamentosum),the largest catfish in the Amazon Basin is probably over-exploited. In conclusion, we raise some hypotheses about the causes and prospects for the future.     

Functional organization of calcium stores in polarized secretory cells and transcellular calcium transport

In this short review, we will first discuss localized cytoplasmic calcium signals in pancreatic acinar cells. In the second part of the review, we will describe recently discovered polarized calcium efflux and calcium propagation through the lumen of the endoplasmic reticulum — ER (a phenomenon we have termed “calcium tunnelling”). Finally, we will present a hypothesis concerning the roles that these mechanisms could play in transcellular calcium flux.     

<Emphasis Type="Italic">In vitro</Emphasis> and <Emphasis Type="Italic">in vivo</Emphasis> assays for osteoclast apoptosis

Mature osteoclasts, multinucleated giant cells responsible for bone resorption, are terminally differentiated cells with a short life span. Recently, we have demonstrated that osteoclast apoptosis is regulated by ERK activity and Bcl-2 family member Bim. In this paper, we summarize the methods we used to study osteoclast apoptosis in vitro and in vivo. Using adenovirus and retrovirus vectors, we were able to introduce foreign genes into osteoclasts and examine their effects on osteoclast survival in vitro. In addition, we established the modified methods for in situ hybridization and BrdU labeling of bone sections from mice to study osteoclast survival in vivo. The detailed methods described here could be useful for studying the biological process in bone.     

Experimental study of the function of the excreted/secreted <Emphasis Type="Italic">Leishmania</Emphasis>LmSIR2 protein by heterologous expression in eukaryotic cell line

Background  

In yeast and Caenorhabditis elegans, Silent Information Regulator (SIR2) proteins have been shown to be involved in ageing regulation. In Leishmania, the LmSIR2rp was originally isolated from the excreted/secreted material of the Leishmania parasites. Among the function(s) of this protein in Leishmania biology, we have documented its implication in parasite survival, and in particular in Leishmania amastigotes. In this paper we question the role of the excreted/secreted form of the protein. In particular we wonder if the Leishmania Sir2 homologue is involved in some aspect of its biological function(s), in various components and pathways, which could promote the host cell survival. To test this hypothesis we have mimicked an intracellular release of the protein through constitutive expression in mouse L929 fibrosarcoma cells.     

Pathogenic synergy: mixed intra-abdominal infections

In this article we review our researches into the pathogenesis of mixed infections. These may conveniently be divided into in vitro and in vivo studies. In vitro we confirmed that interference with the killing of aerobes by polymorphonuclear leucocytes (PMN’s) is a property of theBacteroides strains tested and appears to depend on competition for opsonins i.e. complement factors. Further studies are in progress to define which complement factors and which bacterial structures are involved. The influence ofB. fragilis on chemotaxis has also been studied. Our preliminary data suggest thatB. fragilis is itself poorly chemotactic and reduces the chemoattractivity ofProteus mirabilis. This observation is surprising when we consider that abscess formation is the hall-mark ofB. fragilis infections and needs clarification. In vivo we have developed a skin infection model in mice which is economical and gives reproducible and quantitative results. In this model we have demonstrated pathogenic synergy betweenEscherichia coli andB. fragilis. Further studies are planned to assess the role of complement and bacterial factors in this in vivo synergy.     

Identification of a Region within the Placental Alkaline Phosphatase mRNA That Mediates p180-dependent Targeting to the Endoplasmic Reticulum

In both eukaryotic and prokaryotic cells, it has been recently established that mRNAs encoding secreted and membrane proteins can be localized to the surface of membranes via both translation-dependent and RNA element-mediated mechanisms. Previously, we showed that the placental alkaline phosphatase (ALPP) mRNA can be localized to the ER membrane independently of translation, and this localization is mediated by p180, an mRNA receptor present in the ER. In this article, we aimed to identify the cis-acting RNA element in ALPP. Using chimera constructs containing fragments of the ALPP mRNA, we demonstrate that the ER-localizing RNA element is present within the 3′ end of the open reading frame and codes for a transmembrane domain. In addition, we show that this region requires p180 for efficient ER anchoring. Taken together, we provide the first insight into the nature of cis-acting ER-localizing RNA elements responsible for localizing mRNAs on the ER in mammalian cells.     

Synthesis and biological evaluation of 4,5-dihydro-1H-pyrazole derivatives as potential nNOS/iNOS selective inhibitors. Part 2: Influence of diverse substituents in both the phenyl moiety and the acyl group

In a preliminary article, we reported a series of 4,5-dihydro-1H-pyrazole derivatives as neuronal nitric oxide synthase (nNOS) inhibitors. Here we present the data about the inhibition of inducible nitric oxide synthase (iNOS) of these compounds. In general, we can confirm that these pyrazoles are nNOS selective inhibitors. In addition, taking these compounds as a reference, we have designed and synthesized a series of new derivatives by modification of the heterocycle in 1-position, and by introduction of electron-donating or electron-withdrawing substituents in the aromatic ring. These derivatives have been evaluated as nNOS and iNOS inhibitors in order to identify new compounds with improved activity and selectivity. Compound 3r, with three methoxy electron-donating groups in the phenyl moiety, is the most potent nNOS inhibitor, showing good selectivity nNOS/iNOS.     

The we Gene is a Modifier of the walGene in Mice

Interaction of gene wellhaarig (we) with genes waved alopecia(wal) and hairless (hr) was studied in mice. The mutant gene weis responsible for the development of a specific waved coat in homozygotes. Homozygous mice carrying mutant gene walalso have a wavy coat, though a partial alopecia develops with time in these animals. In homozygotes for thehr gene, hair loss is observed beginning from the age of ten days. A series of crosses we/weand wal/wal yielded animals with we/+wal/wal and we/we wal/wal genotypes. In micewe/+wal/wal carrying gene we at a single dose, alopecia is accelerated significantly as compared to the single-dose homozygotes +/+wal/wal. In we/we wal/wal mice, alopecia starts earlier than in we/+wal/wal mice; by the age of one month, the double homozygotes are almost hairless except for small body areas covered with a sparse coat. In addition, curliness of the first-generation hair in mice we/we wal/wal is much more expressed than in +/+wal/wal and we/we+/+ mice. The obtained evidence suggests that the wegene is a modifier of the wal gene because the former enhances the effects of the walgene, which is confirmed by the earlier onset of alopecia and progression of the latter in mice having the we/+wal/wal genotype and especially in we/we wal/wal animals. The we/we hr/+ mice do not differ in coat from we/we+/+ mice; in both cases, the coat is wavy. The coat of double homozygotes we/we hr/hr, is similar to that of we/we+/+ mice until ten days of age, when the signs of alopecia appear. By the age of 21 days, mice we/we hr/hr have lost their coat completely like mice +/+ hr/hr. Hence, the we gene is a modifier of the walgene though it does not interact with hrgene during the coat formation.     

Irreducibility in RNA Structures

In this paper, we study irreducibility in RNA structures. By RNA structure, we mean RNA secondary as well as RNA pseudoknot structures as abstract contact structures. We give an analysis contrasting random and minimum free energy (mfe) configurations and secondary versus pseudoknots structures. In the process, we compute various distributions: the numbers of irreducible substructures and their locations and sizes, parameterized in terms of the maximal number of mutually crossing arcs, k−1, and the minimal size of stacks σ. In particular, we analyze the size of the largest irreducible substructure for random and mfe structures, which is the key factor for the folding time of mfe configurations. We show that the largest irreducible substructure is typically unique and contains almost all nucleotides.     

Rejoinder: race scholarship and the future

ABSTRACT

In this Rejoinder we seek to address the key issues raised by the four commentaries on our edited book. We focus on the question of the shifting boundaries of the field of race and ethnic studies, the absences and gaps in what is covered, the limits of the post-racial, and the whitening of sociology. In conclusion, we suggest some alternative ways in which we would seek to address them.     

Courtship song, male agonistic encounters, and female mate choice in the house cricket,Acheta domesticus (Orthoptera: Gryllidae)

Whether female crickets choose among males based on characteristics of the courtship song is uncertain, but in many species, males not producing courtship song do not mate. In the house cricket,Acheta domesticus, we examined whether a female chose or rejected a male based on his size, latency to chirp, latency to produce courtship song, or rate of the high-frequency pulse of courtship song (“court rate”). We confirmed that females mated only with males that produced courtship song, but we found no evidence that the other factors we measured affected a female’s decision to mate. In addition, we investigated whether the outcome of male agonistic encounters affected the subsequent production of courtship song. In one experiment, we observed courtship and mating behavior when a single female was placed with a pair of males following a 10-min interaction period between the two males. Winners of male agonistic encounters had higher mating success. However, winners and losers of agonistic encounters were not different in their likelihood or latency to produce courtship song or in the number of times they were disrupted by the other male in the pair. In a second experiment, we allowed two males to interact for a 10-min period, but following this interaction period, we placed a female with each male separately and observed courtship and mating behavior. The mating success of winners and losers was not different under these circumstances, and we found no differences between winners and losers in any subsequent courtship or mating behavior examined. We conclude that winning agonistic encounters influences a male’s mating success in ways other than his production of courtship song and this effect is lost when winning and losing males are separated and each is given an opportunity to mate.     

Notes in Case-Control Studies with Matched Pairs under Inverse Sampling

In case-control studies with matched pairs, the traditional point estimator of odds ratio (OR) is well-known to be biased with no exact finite variance under binomial sampling. In this paper, we consider use of inverse sampling in which we continue to sample subjects to form matched pairs until we obtain a pre-determined number (>0) of index pairs with the case unexposed but the control exposed. In contrast to use of binomial sampling, we show that the uniformly minimum variance unbiased estimator (UMVUE) of OR does exist under inverse sampling. We further derive an exact confidence interval of OR in closed form. Finally, we develop an exact test and an asymptotic test for testing the null hypothesis H₀: OR = 1, as well as discuss sample size determination on the minimum required number of index pairs for a desired power at α-level.     

Expression of S100B during embryonic development of the mouse cerebellum

Background  

In the cerebellum of newborn S100B-EGFP mice, we had previously noted the presence of a large population of S100B-expressing cells, which we assumed to be immature Bergmann glial cells. In the present study, we have drawn on this observation to establish the precise spatio-temporal pattern of S100B gene expression in the embryonic cerebellum.     

Testing the level of ant activity associated with quorum sensing: an empirical approach leading to the establishment and test of a null-model (response to the comment of Richardson et al.)

In a paper in this journal (Nouvellet et al., 2010), we presented results from experiments on the behaviour of the Pharaoh's ant, Monomorium pharaonis, along with a substantial statistical and theoretical analysis of the results. In a minor part of our paper, we compared our results with the related work of Richardson et al. (2010a). These authors have subsequently commented on our interpretation of their work (Richardson et al., 2011). In this Letter we respond to the comments of Richardson et al. (2011), and give detailed arguments why we stand by our original conclusions.     

Modifications in electrospray tandem mass spectrometry for a neonatal-screening pilot study in Japan

In a neonatal-screening pilot study for inherited disorders in organic acid and amino acid metabolism, we analyzed butyrated acylcarnitines and amino acids in blood spots of more than 20 000 newborns by electrospray tandem mass spectrometry. In order to screen urea cycle disorders, we performed multiple scanning functions with additional stable isotope-labelled internal standards, since such reported functions as neutral loss of m/z 102 or 109 for butyrated amino acids were not sufficient. Arginine levels were measured with arginine-¹³C₆. Hypocitrullinemia for the screening of some urea cycle disorders was detectable by measurement with synthesized citrulline-d₆, although we did not find any such disorders. In the acylcarnitine analysis, we found a patient with propionic acidemia, who has been treated effectively. The increasing false positive rate due to the use of pivalic acid-containing antibiotics in the diagnosis of isovaleric acidemia was a problem in Japan.     

L’Aurignacien archaïque de la grotte El Castillo (Espagne) : caractérisation technologique et typologique

In this paper, we present the techno-typological study of level 16 of El Castillo cave (Archaic Aurignacian). In this level, we can identify an important bladelet production from schémas opératoires of unipolar prismatic cores, carinated endscraper and carinated burins types. Besides, we find a specific production of Discoid conception. The retouched blanks, though scanty, are dominated by the Dufour bladelets. Level 16 is in relation with the Archaic Aurignacian at the Cantabrian Iberia, which is present in sites like Cueva Morín, Labeko Koba, Gatzarria, or Isturitz and it also is in relation with the Mediterranean Archaic Aurignacian. Finally, we analyse the different hypotheses about the Initial Upper Paleolithic origin in Europe. The mosaic hypothesis is acceptable for us.     

MRI-Based Intelligence Quotient (IQ) Estimation with Sparse Learning

In this paper, we propose a novel framework for IQ estimation using Magnetic Resonance Imaging (MRI) data. In particular, we devise a new feature selection method based on an extended dirty model for jointly considering both element-wise sparsity and group-wise sparsity. Meanwhile, due to the absence of large dataset with consistent scanning protocols for the IQ estimation, we integrate multiple datasets scanned from different sites with different scanning parameters and protocols. In this way, there is large variability in these different datasets. To address this issue, we design a two-step procedure for 1) first identifying the possible scanning site for each testing subject and 2) then estimating the testing subject’s IQ by using a specific estimator designed for that scanning site. We perform two experiments to test the performance of our method by using the MRI data collected from 164 typically developing children between 6 and 15 years old. In the first experiment, we use a multi-kernel Support Vector Regression (SVR) for estimating IQ values, and obtain an average correlation coefficient of 0.718 and also an average root mean square error of 8.695 between the true IQs and the estimated ones. In the second experiment, we use a single-kernel SVR for IQ estimation, and achieve an average correlation coefficient of 0.684 and an average root mean square error of 9.166. All these results show the effectiveness of using imaging data for IQ prediction, which is rarely done in the field according to our knowledge.     

A model-independent approach to the theory of experimental designs and a special discussion of bib. II. properties and construction of bib

In addition to the first part we prove independently of the model some theorems on properties of balanced block designs. Then we propose nine methods of construction of BIB and prove theorems in connection with these methods. In a table we give a survey on block designs with v$25 and possibilities of their construction with these methods. Further follow theorems with the number of nonisomorphic BIB for some fixed v and k.     

Network design meets in silico evolutionary biology

Cell fate is programmed through gene regulatory networks that perform several calculations to take the appropriate decision. In silico evolutionary optimization mimics the way Nature has designed such gene regulatory networks. In this review we discuss the basic principles of these evolutionary approaches and how they can be applied to engineer synthetic networks. We summarize the basic guidelines to implement an in silico evolutionary design method, the operators for mutation and selection that iteratively drive the network architecture towards a specified dynamical behavior. Interestingly, as it happens in natural evolution, we show the existence of patterns of punctuated evolution. In addition, we highlight several examples of models that have been designed using automated procedures, together with different objective functions to select for the proper behavior. Finally, we briefly discuss the modular designability of gene regulatory networks and its potential application in biotechnology.