In silico exploration of the fructose-6-phosphate phosphorylation step in glycolysis: genomic evidence of the coexistence of an atypical ATP-dependent along with a PPi-dependent phosphofructokinase in Propionibacterium freudenreichii subsp. shermanii

We performed a detailed bioinformatic study of the catalytic step of fructose-6-phosphate phosphorylation in glycolysis based on the raw genomic draft of Propionibacterium freudenreichii subsp. shermanii (P. shermanii) ATCC9614 [Meurice et al., 2004]. Our results provide the first in silico evidence of the coexistence of genes coding for an ATP-dependent phosphofructokinase (ATP-PFK) and a PPi-dependent phosphofructokinase (PPi-PFK), whereas the fructose-1,6-bisphosphatase (FBP) and ADP-dependent phosphofructokinase (ADP-PFK) are absent. The deduced amino acid sequence corresponding to the PPi-PFK (AJ508922) shares 100% similarity with the already characterised propionibacterial protein (P29495; Ladror et al., 1991]. The unexpected ATP-PFK gene (AJ509827) encodes a protein of 373 aa which is highly similar (50% positive residues) along at least 95% of its sequence length to different well-characterised ATP-PFKs. The characteristic PROSITE pattern important for the enzyme function of ATP-PFKs (PS00433) was conserved in the putative ATP-PFK sequence: 8 out of 9 amino acid residues. According to the recent evolutionary study of PFK proteins with different phosphate donors [Bapteste et al., 2003], the propionibacterial ATP-PFK harbours a G104-K124 residue combination, which strongly suggested that this enzyme belongs to the group of atypical ATP-PFKs. According to our phylogenetic analyses the amino acid sequence of the ATP-PFK is clustered with the atypical ATP-PFKs from group III of the Siebers classification [Siebers et al., 1998], whereas the expected PPi-PFK protein is closer to the PPi-PFKs from clade P [Müller et al., 2001]. The possible significance of the co-existence of these two PFKs and their importance for the regulation of glycolytic pathway flux in P. shermanii is discussed.     

Quantification of random mutations in the mitochondrial genome

Mitochondrial DNA (mtDNA) mutations contribute to the pathology of a number of age-related disorders, including Parkinson disease [A. Bender et al., Nat. Genet. 38 (2006) 515,Y. Kraytsberg et al., Nat. Genet. 38 (2006) 518], muscle-wasting [J. Wanagat, Z. Cao, P. Pathare, J.M. Aiken, FASEB J. 15 (2001) 322], and the metastatic potential of cancers [K. Ishikawa et al., Science 320 (2008) 661]. The impact of mitochondrial DNA mutations on a wide variety of human diseases has made it increasingly important to understand the mechanisms that drive mitochondrial mutagenesis. In order to provide new insight into the etiology and natural history of mtDNA mutations, we have developed an assay that can detect mitochondrial mutations in a variety of tissues and experimental settings [M. Vermulst et al., Nat. Genet. 40 (2008) 4, M. Vermulst et al., Nat. Genet. 39 (2007) 540]. This methodology, termed the Random Mutation Capture assay, relies on single-molecule amplification to detect rare mutations among millions of wild-type bases [J.H. Bielas, L.A. Loeb, Nat. Methods 2 (2005) 285], and can be used to analyze mitochondrial mutagenesis to a single base pair level in mammals.     

Do deposed adult male Sichuan snub-nosed monkeys Rhinopithecus roxellana roam as solitary bachelors or continue to interact with former band members?

Dispersal patterns exhibited by group-living animals play an important role in individual reproductive success and survival,as well as population and social dynamics(Greenwood,1980;Isbell and van Vuren,1996;Kappeler and van Schaik,2002).Dispersing individuals may emigrate voluntarily,or they may be forcibly evicted by other individuals(Pusey and Packer,1987;Clobert et al.,2001).One cause of individual dispersal is when an extra-group male compels another male to leave a group of females.This phenomenon has ...     

A fuzzy-neural system for identification of species-specific alarm calls of Gunnison's prairie dogs

In this study we describe the design and application of an automated classification system that utilizes artificial intelligence to corroborate the finding that Gunnison's prairie dogs have different alarm calls for different species of predators. This corroboration is strong because it utilizes an entirely different analysis technique than that used in the original research by Slobodchikoff et al. [Slobodchikoff, C.N., Fischer, C., Shapiro, J., 1986. Predator-specific alarm calls of prairie dogs. Am. Zool. 26, 557] or in subsequent study done by Slobodchikoff et al. [Slobodchikoff, C.N., Kiriazis, J., Fischer, C., Creef, E., 1991. Semantic information distinguishing individual predators in the alarm calls of Gunnison's prairie dogs. Anim. Behav. 42, 713-719]. The study described here also is more completely automated than earlier study in this area. This automation allowed a large volume of field data to be processed where all measurements of relevant parameters were performed through software control. Previous study processed a smaller data set and utilized manual measurement techniques. The new classification system, which combines fuzzy logic and an artificial neural network, classified alarm calls correctly according to the eliciting predator species, achieving accuracy levels ranging from 78.6 to 96.3% on raw field data digitized with low quality audio equipment.     

Referential calls signal predator behavior in a group-living bird species

Predation is a powerful agent of natural selection, driving the evolution of antipredator calls [1]. These calls have been shown to communicate predator category [2-4] and/or predator distance to conspecifics [5-7]. However, the risk posed by predators depends also on predator behavior [8], and the ability of prey to communicate predator behavior to conspecifics would be a selective advantage reducing their predation risk. I tested this idea in Siberian jays (Perisoreus infaustus), a group-living bird species. Predation by hawks, and to a lesser extent by owls, is substantial and the sole cause of mortality in adult jays [9]. By using field data and predator-exposure experiments, I show here that jays used antipredator calls for hawks depending on predator behavior. A playback experiment demonstrated that these prey-to-prey calls were specific to hawk behavior (perch, prey search, attack) and elicited distinct, situation-specific escape responses. This is the first study to demonstrate that prey signals convey information about predator behavior to conspecifics. Given that antipredator calls in jays aim at protecting kin group members [10, 11], consequently lowering their mortality [9], kin-selected benefits could be an important factor for the evolution of predator-behavior-specific antipredator calls in such systems.     

Semi-parametric differential expression analysis via partial mixture estimation

We develop an approach for microarray differential expression analysis, i.e. identifying genes whose expression levels differ between two or more groups. Current approaches to inference rely either on full parametric assumptions or on permutation-based techniques for sampling under the null distribution. In some situations, however, a full parametric model cannot be justified, or the sample size per group is too small for permutation methods to be valid. We propose a semi-parametric framework based on partial mixture estimation which only requires a parametric assumption for the null (equally expressed) distribution and can handle small sample sizes where permutation methods break down. We develop two novel improvements of Scott's minimum integrated square error criterion for partial mixture estimation [Scott, 2004a,b]. As a side benefit, we obtain interpretable and closed-form estimates for the proportion of EE genes. Pseudo-Bayesian and frequentist procedures for controlling the false discovery rate are given. Results from simulations and real datasets indicate that our approach can provide substantial advantages for small sample sizes over the SAM method of Tusher et al. [2001], the empirical Bayes procedure of Efron and Tibshirani [2002], the mixture of normals of Pan et al. [2003] and a t-test with p-value adjustment [Dudoit et al., 2003] to control the FDR [Benjamini and Hochberg, 1995].     

Sequence similarities among monkey ori-enriched (ors) fragments

Nucleotide sequences have been determined for eight ors (ori-enriched sequence) fragments isolated from monkey DNA by a method that was designed to enrich for origins of DNA replication [Kaufmann et al., Mol. Cell. Biol. 5 (1985) 721-727]. Evidence has been presented that some or possibly all of these sequences can serve, albeit inefficiently, as oris in vivo [Frappier and Zannis-Hadjopoulos, Proc. Natl. Acad. Sci. USA 84 (1987) 6668-6672]. Two of the fragments were found to contain the long terminal repeat-like elements of the 'O-family' of moderately repetitive sequences that are present in human DNA as a transposon-like element [Paulson et al., Nature 315 (1985) 359-361]. Extensive pair-wise comparisons of the sequences failed to detect any statistically significant common sequences, except for long asymmetrically distributed A + T-rich stretches. Nonetheless, when the ors fragments were examined for the presence of published consensus sequences, seven of eight were found to contain the control sequence described by Dierks et al. [Cell 32 (1983) 695-706], and the same seven of eight were found to contain both the scaffold attachment region T consensus [Gasser and Laemmli, Cell 46 (1986) 521-530] and the minimal Saccharomyces cerevisiae autonomously replicating sequence consensus [e.g., Palzkill and Newlon, Cell 53 (1988) 441-450].     

A common evolutionary origin of two elementary enzyme folds

The (beta alpha)(8)-barrel is the most frequent and most versatile fold among enzymes [H?cker et al., Curr. Opin. Biotechnol. 12 (2001) 376-381; Wierenga, FEBS Lett. 492 (2001) 193-198]. Structural and functional evidence suggests that (beta alpha)(8)-barrels evolved from an ancestral half-barrel, which consisted of four (beta alpha) units stabilized by dimerization [Lang et al., Science 289 (2000) 1546-550; H?cker et al., Nat. Struct. Biol. 8 (2001) 32-36; Gerlt and Babbitt, Nat. Struct. Biol. 8 (2001) 5-7]. Here, by performing a comprehensive database search, we detect a striking and unexpected structural and amino acid sequence similarity between (beta alpha)(4) half-barrels and members of the (beta alpha)(5) flavodoxin-like fold. These findings provoke the hypothesis that a large fraction of the modern-day enzymes evolved from a basic structural building block, which can be identified by a combination of sequence and structural analyses.     

Contributions of Myc to tumorigenesis

Despite intensive research, the mechanisms by which deregulation of myc gene expression contributes to tumorigenesis are still not fully resolved and many aspects are still enigmatic. Several recent reviews, including one published in this series a few months ago, have summarized recent progress in our understanding of the biochemistry of Myc proteins [Eisenmann, Genes Dev. (2001) in press; Amati et al., Biochim. Biophys. Acta 1471 (2001) 135-145]. Also, the evidence documenting a central role of Myc proteins in human tumorigenesis has been extensively reviewed [Henriksson and Lüscher, Cancer Res. 68 (1996) 109-182]. In this article, we will argue that current progress allows us to present testable hypotheses on how Myc affects specific properties of transformed cells.     

Pathological and molecular mechanisms of prostate carcinogenesis: implications for diagnosis, detection, prevention, and treatment

Prostate cancer is an increasing threat throughout the world. As a result of a demographic shift in population, the number of men at risk for developing prostate cancer is growing rapidly. For 2002, an estimated 189,000 prostate cancer cases were diagnosed in the U.S., accompanied by an estimated 30,200 prostate cancer deaths [Jemal et al., 2002]. Most prostate cancer is now diagnosed in men who were biopsied as a result of an elevated serum PSA (>4 ng/ml) level detected following routine screening. Autopsy studies [Breslow et al., 1977; Yatani et al., 1982; Sakr et al., 1993], and the recent results of the Prostate Cancer Prevention Trial (PCPT) [Thompson et al., 2003], a large scale clinical trial where all men entered the trial without an elevated PSA (<3 ng/ml) were subsequently biopsied, indicate the prevalence of histologic prostate cancer is much higher than anticipated by PSA screening. Environmental factors, such as diet and lifestyle, have long been recognized contributors to the development of prostate cancer. Recent studies of the molecular alterations in prostate cancer cells have begun to provide clues as to how prostate cancer may arise and progress. For example, while inflammation in the prostate has been suggested previously as a contributor to prostate cancer development [Gardner and Bennett, 1992; Platz, 1998; De Marzo et al., 1999; Nelson et al., 2003], research regarding the genetic and pathological aspects of prostate inflammation has only recently begun to receive attention. Here, we review the subject of inflammation and prostate cancer as part of a "chronic epithelial injury" hypothesis of prostate carcinogenesis, and the somatic genome and phenotypic changes characteristic of prostate cancer cells. We also present the implications of these changes for prostate cancer diagnosis, detection, prevention, and treatment.     

Detecting and estimating rectification of gap junction conductance based on simulations of dual-cell recordings from a pair and a network of coupled cells

Gap junctions can exhibit rectification of conductance. Some reports use inequality of coupling coefficients as the first sign of the possible existence of rectification ( [Devor and Yarom, 2002], [Fan et al., 2005], [31], [Mann-Metzer and Yarom, 1999], [Nolan et al., 1999] and [Szabadics et al., 2001]). However, mathematical modeling and simulations of electrotonic coupling between an isolated pair of neurons showed conditions where the coupling coefficients were unreliable indicators of rectification. On the other hand, the transfer resistances were found to be reliable indicators of junctional rectification. The existing mathematical model of cell coupling ( [Bennett, 1966], [Devor and Yarom, 2002] and [Verselis and Veenstra, 2000]) was extended in order to measure rectification of the junctional conductances directly between dual-recorded neurons whether isolated or surrounded by a simulated 3-dimensional network of heterogeneous cells whose gap junctions offered parallel paths for current flow between the recorded neurons. The results showed that the transfer resistances could still detect rectification of the gap junction linking the dual-recorded neurons when embedded in a coupled cell network and that a mathematical model could estimate the conductances in both directions through this gap junction using only data that would be available from real dual-intracellular penetrations which allow electrophysiological recordings and intracellular staining. Rectification of gap junctions in unrecorded cells of a biologically realistic coupled cell network had negligible effects on the voltage responses of the dual-recorded neurons because of minimal current passing through these surrounding cells.     

Nucleotide sequence of the phosphinothricin N-acetyltransferase gene from Streptomyces viridochromogenes Tü494 and its expression in Nicotiana tabacum

The phosphinothricin (Pt) N-acetyltransferase gene (pat) of Streptomyces viridochromogenes Tü494 is located on a 0.8-kb BglII fragment [Strauch et al., Gene 63 (1988) 65-74]. By sequencing a 1.3-kb BglII-SstII fragment, an open reading frame representing the pat gene was found. It encodes a polypeptide of 183 amino acids with an Mr of 20,621. The base composition of the pat gene is typical for Streptomyces [70.1 mol% (G + C) in total and 93.5 mol% (G + C) in the third position]. Translation of pat is initiated by a GTG codon which was identified by frameshift mutations in Escherichia coli as well as in Streptomyces lividans. Significant homology of the pat gene was found to the bialaphos-resistance gene (bar) of Streptomyces hygroscopicus [Thompson et al., EMBO J. 9 (1987) 2519-2523]. However, variations were detected in the 5'-noncoding region of the two resistance genes which may reflect differences in regulation. Since Pt is a potent herbicide, the pat gene was modified and introduced into Nicotiana tabacum by Agrobacterium-mediated leaf-disc transformation. The GTG start codon of pat was replaced by ATG. Subsequently the modified pat-coding region was fused to the 35S promoter of the cauliflower mosaic virus. Transgenic plants could directly be selected on Pt-containing medium.     

Characterization of the mechanical properties of skin by inverse analysis combined with the indentation test

This study proposes a new method to determine the mechanical properties of human skin by the use of the indentation test [Pailler-Mattei, 2004. Caractérisation mécanique et tribologique de la peau humaine in vivo, Ph.D. Thesis, ECL-no. 2004-31; Pailler-Mattei, Zahouani, 2004. Journal of Adhesion Science and Technology 18, 1739-1758]. The principle of the measurements consists in applying an in vivo compressive stress [Zhang et al., 1994. Proceedings of the Institution of Mechanical Engineers 208, 217-222; Bosboom et al., 2001. Journal of Biomechanics 34, 1365-1368; Oomens et al., 1984. Selected Proceedings of Meetings of European Society of Biomechanics, pp. 227-232; Oomens et al., 1987. Journal of Biomechanics 20(9), 877-885] on the skin tissue of an individual's forearm. These measurements show an increase in the normal contact force as a function of the indentation depth. The interpretation of such results usually requires a long and tedious phenomenological study. We propose a new method to determine the mechanical parameters which control the response of skin tissue. This method is threefold: experimental, numerical, and comparative. It consists combining experimental results with a numerical finite elements model in order to find out the required parameters. This process uses a scheme of extended Kalman filters (EKF) [Gu et al., 2003. Materials Science and Engineering A345, 223-233; Nakamura et al., 2000. Acta Mater 48, 4293-4306; Leustean and Rosu, 2003. Certifying Kalman filters. RIACS Technical Report 03.02, 27pp. http://gureni.cs.uiuc.edu/~grosu/download/luta + leo.pdf; Welch and Bishop, An introduction to Kalman filter, University of North Carolina at Chapel Hill, 16p. http://www.cs.unc.edu/~welch/kalman/]. The first results presented in this study correspond to a simplified numerical modeling of the global system. The skin is assumed to be a semi-infinite layer with an isotropic linear elastic mechanical behavior [Zhang et al., 1994. Proceedings of the Institution of Mechanical Engineers 208, 217-222] This analysis will be extended to more realistic models in further works.     

Presence of a blastocyst and mast cell depletion of the mouse uterus

The mast cell population has been studied during early decidualization of the mouse uterus. The number increases in early pregnancy until the attachment phase when a sharp depletion is noticed. This fall has been correlated with stimuli of maternal origin, but at the same time the presence of a blastocyst at the presumptive implantation sites seems to exert a significant effect on the depletion of mast cells. A relationship between the number of mast cells in the uterus and the physiological state of the organ has definitely been established [Harvey, 1964; Likar and Likar, 1964; Gibbons and Chang, 1972; Brandon and Evans, 1983]. The number of mast cells in the pregnant uterus is known to decrease around the time of implantation in the rat [Shelesnyak, 1960; De Feo, 1967; Brandon and Bibby, 1979]. Several workers believe that the mast cell population and histamine content decrease as a result of a rise in circulating estrogen [Westin, 1955; Gibbons and Chang, 1972; Spaziani, 1975]. In the present communication the possibility of a relationship between the decrease in mast cell population and the presence of a blastocyst, whose estrogenic role has been reported [Dickmann and Dey, 1973; Dickmann et al., 1975; Sengupta et al., 1977], in the uterine horn has been discussed.     

Fatty acid synthase: A metabolic oncogene in prostate cancer?

In 1920, Warburg suggested that tumors consistently rely on anaerobic pathways to convert glucose to ATP even in the presence of abundant oxygen [Warberg, 1956] despite the fact that it is less efficient for energy supply than aerobic glycolysis. The reasons for this remain obscure to date. More often than not, the microenvironment of solid tumors contains regions of poor oxygenation and high acidity. In this context hypoxia can act in an epigenetic fashion, inducing changes in gene expression and in metabolism for survival. It is reasonable to assume that only the tumor cells capable of developing an unusual tolerance to limiting oxygen availability and to the acidosis resulting from excessive lactate production, can survive. In addition to the striking changes that occur in glucose metabolism, studies in human cancer patients suggest that there is often also an increase in free fatty acid turnover, oxidation and clearance [Legaspi et al., 1987; Hyltander et al., 1991]. For instance, a lipid mobilizing factor produced by tumor cells appears to be responsible for the increase in whole body fatty acid oxidation [Russell and Tisdale, 2002]. Fatty acids synthesis in tumor tissues also occurs at very high rates, as first demonstrated more than half a century ago [Medes et al., 1953]. Importantly, (14)C glucose studies have shown that in tumor cells almost all fatty acids derive from de novo synthesis despite adequate nutritional supply [Sabine and Abraham, 1967; Ookhtens et al., 1984; Weiss et al., 1986]. In addition, tumors overexpressing fatty acid synthase (FAS), the enzyme responsible for de novo synthesis of fatty acids, display aggressive biologic behavior compared to those tumors with normal FAS levels, suggesting that FAS overexpression confers a selective growth advantage. Here, we will review the roles that FAS plays in important cellular processes such as apoptosis and proliferation. In addition, speculations on the putative role of FAS in the altered metabolic pathways of prostate cancer cells will be explored. Because of the frequent overexpression of this enzyme prostate cancer, FAS constitutes a therapeutic target in this disease.     

Probable cloning artefacts previously interpreted as unusual leader sequences of rodent ornithine decarboxylase mRNAs--a cautionary tale

Messenger RNAs that have structurally unusual 5' leaders attract interest and provoke conjecture. Cloning and sequencing of two rodent ornithine decarboxylase (ODC) cDNAs, those for mouse [Kahana and Nathans, Proc. Natl. Acad. Sci. USA 82 (1985) 1673-1677] and, recently as published in this journal, for rat [Van Kranen et al., Gene 60 (1987) 145-155], have indicated the presence of such features. In both cases, the leader is unusually long and contains multiple AUG start codons preceding that which encodes the N terminus of the protein. In addition, the leader of the rat clone contains a 54-nt perfect inverted repeat. Because ODC expression appears to be regulated translationally, functional implications immediately suggest themselves. Certain unusual features of the mouse cDNA have proven artefactual [Brabant et al., Proc. Natl. Acad. Sci. USA 85 (1988) 2200-2204; Katz and Kahana, J. Biol. Chem. 263 (1988) 7604-7609]. It is likely that the putative leader sequence of rat ODC cDNA also resulted from a cloning artefact.     

Investigation of AC-DC magnetic field effects in planar phospholipid bilayers.

Observations recently reported by others indicate that a combination of a weak dc magnetic field and extremely-low-frequency ac magnetic field can produce resonant effects in biological systems. We report measurements of the effects of combined dc and ac magnetic fields on the dc current through channel-free planar phospholipid membranes. The combined dc-ac magnetic fields did affect the dc current through planar phospholipid membranes, but not in every membrane, and not consistently at the same values of magnetic flux density and frequency. None of our measurements showed resonant response akin to the cyclotron-like resonance reported in diatoms [Smith et al., 1987] and lymphocytes [Liboff et al., 1987].