1H, 13C and 15N NMR assignments of the C1A and C1B subdomains of PKC-delta

The Protein Kinase C family of enzymes is a group of serine/threonine kinases that play central roles in cell-cycle regulation, development and cancer. A key step in the activation of PKC is translocation to membranes and binding of membrane-associated activators including diacylglycerol (DAG). Interaction of novel and conventional isotypes of PKC with DAG and phorbol esters occurs through the two C1 regulatory domains (C1A and C1B), which exhibit distinct ligand binding selectivity that likely controls enzyme activation by different co-activators. PKC has also been implicated in physiological responses to alcohol consumption and it has been proposed that PKCα (Slater et al. J Biol Chem 272(10):6167–6173, 1997; Slater et al. Biochemistry 43(23):7601–7609, 2004), PKCε (Das et al. Biochem J 421(3):405–413, 2009) and PKCδ (Das et al. J Biol Chem 279(36):37964–37972, 2004; Das et al. Protein Sci 15(9):2107–2119, 2006) contain specific alcohol-binding sites in their C1 domains. We are interested in understanding how ethanol affects signal transduction processes through its affects on the structure and function of the C1 domains of PKC. Here we present the ¹H, ¹⁵N and ¹³C NMR chemical shift assignments for the Rattus norvegicus PKCδ C1A and C1B proteins.     

Spatial clustering property and its self-similarity in membrane potentials of hippocampal CA1 pyramidal neurons for a spatio-temporal input sequence

To clarify how the information of spatiotemporal sequence of the hippocampal CA3 affects the postsynaptic membrane potentials of single pyramidal cells in the hippocampal CA1, the spatio-temporal stimuli was delivered to Schaffer collaterals of the CA3 through a pair of electrodes and the post-synaptic membrane potentials were recorded using the patch-clamp recording method. The input–output relations were sequentially analyzed by applying two measures; “spatial clustering” and its “self-similarity” index. The membrane potentials were hierarchically clustered in a self-similar manner to the input sequences. The property was significantly observed at two and three time-history steps. In addition, the properties were maintained under two different stimulus conditions, weak and strong current stimulation. The experimental results are discussed in relation to theoretical results of Cantor coding, reported by Tsuda (Behav Brain Sci 24(5):793–847, 2001) and Tsuda and Kuroda (Jpn J Indust Appl Math 18:249–258, 2001; Cortical dynamics, pp 129–139, Springer-Verlag, 2004).     

Trials and tribulations of immunotherapy as a treatment option for patients with squamous cell carcinoma of the head and neck

Head and neck squamous cell carcinoma (HNSCC) is an aggressive epithelial malignancy that is the sixth most common neoplasm in the world. Despite numerous advances in treatments involving surgery, radiation, and chemotherapy, the 5-year survival has remained at less than 50% for the last 30 years primarily due to local recurrences [66]. Consequently, the possibility of developing immunotherapeutic approaches as a treatment for HNSCC has gained interest. The present review has 3 objectives pertaining to immunotherapeutic means to treat HNSCC patients: (1) to summarize the feasibility of such approaches, (2) to provide an overview of the obstacles to attaining protective immune reactivity, and (3) to consider how these obstacles can be overcome to stimulate immune reactivity to HNSCC. These objectives will also be considered in the context of what lessons have been learned from immunotherapeutic trials for other solid malignancies and the applicability of this information to HNSCC.     

On the use of hybrid reinforcement learning for autonomic resource allocation

Reinforcement Learning (RL) provides a promising new approach to systems performance management that differs radically from standard queuing-theoretic approaches making use of explicit system performance models. In principle, RL can automatically learn high-quality management policies without an explicit performance model or traffic model, and with little or no built-in system specific knowledge. In our original work (Das, R., Tesauro, G., Walsh, W.E.: IBM Research, Tech. Rep. RC23802 (2005), Tesauro, G.: In: Proc. of AAAI-05, pp. 886–891 (2005), Tesauro, G., Das, R., Walsh, W.E., Kephart, J.O.: In: Proc. of ICAC-05, pp. 342–343 (2005)) we showed the feasibility of using online RL to learn resource valuation estimates (in lookup table form) which can be used to make high-quality server allocation decisions in a multi-application prototype Data Center scenario. The present work shows how to combine the strengths of both RL and queuing models in a hybrid approach, in which RL trains offline on data collected while a queuing model policy controls the system. By training offline we avoid suffering potentially poor performance in live online training. We also now use RL to train nonlinear function approximators (e.g. multi-layer perceptrons) instead of lookup tables; this enables scaling to substantially larger state spaces. Our results now show that, in both open-loop and closed-loop traffic, hybrid RL training can achieve significant performance improvements over a variety of initial model-based policies. We also find that, as expected, RL can deal effectively with both transients and switching delays, which lie outside the scope of traditional steady-state queuing theory.

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

Several pilot experiments have indicated that improvements in older NMR structures can be expected by applying modern software and new protocols (Nabuurs et al. in Proteins 55:483–186, 2004; Nederveen et al. in Proteins 59:662–672, 2005; Saccenti and Rosato in J Biomol NMR 40:251–261, 2008). A recent large scale X-ray study also has shown that modern software can significantly improve the quality of X-ray structures that were deposited more than a few years ago (Joosten et al. in J. Appl Crystallogr 42:376–384, 2009; Sanderson in Nature 459:1038–1039, 2009). Recalculation of three-dimensional coordinates requires that the original experimental data are available and complete, and are semantically and syntactically correct, or are at least correct enough to be reconstructed. For multiple reasons, including a lack of standards, the heterogeneity of the experimental data and the many NMR experiment types, it has not been practical to parse a large proportion of the originally deposited NMR experimental data files related to protein NMR structures. This has made impractical the automatic recalculation, and thus improvement, of the three dimensional coordinates of these structures. We here describe a large-scale international collaborative effort to make all deposited experimental NMR data semantically and syntactically homogeneous, and thus useful for further research. A total of 4,014 out of 5,266 entries were ‘cleaned’ in this process. For 1,387 entries, human intervention was needed. Continuous efforts in automating the parsing of both old, and newly deposited files is steadily decreasing this fraction. The cleaned data files are available from the NMR restraints grid at .     

Electrophysiological recording from parasitic nematode muscle

Infection of man and animals with parasitic nematodes is recognized as a significant global problem (McLeod in Int J Parasitol 25(11):1363–1367, 1994; Hotez et al. in N Engl J Med 357(10):1018–1027, 2007). At present control of these infections relies primarily on chemotherapy. There are a limited number of classes of anthelmintic compounds and the majority of these act on ion-channels of the parasite (Martin et al. in Parasitology 113:S137–S156, 1996). In this report, we describe electrophysiological recording techniques as applied to parasitic nematodes. The aim of this report is: (1) to promote the study of ion channels in nematodes to help further the understanding of antinematodal drug action; (2) to describe our recording equipment and experimental protocols; and (3) provide some examples of the information to be gleaned from this approach and how it can increase our understanding of these important pathogens.     

A general linear framework for the comparison and evaluation of models of sensorimotor synchronization

Sensorimotor synchronization (SMS), the temporal coordination of a rhythmic movement with an external rhythm, has been studied most often in tasks that require tapping along with a metronome. Models of SMS use information about the timing of preceding stimuli and responses to predict when the next response will be made. This article compares the theoretical structure and empirical predictions of four two-parameter models proposed in the literature: Michon (Timing in temporal tracking, Van Gorcum, Assen, 1967), Hary and Moore (Br J Math Stat Psychol 40:109–124, 1987b), Mates (Biol Cybern 70:463–473, 1994a; Biol Cybern 70:475–484, 1994b), and Schulze et al. (Mus Percept 22:461–467, 2005). By embedding these models within a general linear framework, the mathematical equivalence of the Michon, Hary and Moore, and Schulze et al. models is demonstrated. The Mates model, which differs from the other three, is then tested empirically with new data from a tapping experiment in which the metronome alternated between two tempi. The Mates model predictions are found to be invalid for about one-third of the trials, suggesting that at least one of the model’s underlying assumptions is incorrect. The other models cannot be refuted as easily, but they do not predict some features of the data very accurately. Comparison of the models’ predictions in a training/test procedure did not yield any significant differences. The general linear framework introduced here may help in the formulation of new models that make better predictions.     

Simulation of biological evolution under attack,but not really: a response to Meester

The leading Intelligent Design theorist William Dembski (Rowman & Littlefield, Lanham MD, 2002) argued that the first No Free Lunch theorem, first formulated by Wolpert and Macready (IEEE Trans Evol Comput 1: 67–82, 1997), renders Darwinian evolution impossible. In response, Dembski’s critics pointed out that the theorem is irrelevant to biological evolution. Meester (Biol Phil 24: 461–472, 2009) agrees with this conclusion, but still thinks that the theorem does apply to simulations of evolutionary processes. According to Meester, the theorem shows that simulations of Darwinian evolution, as these are typically set in advance by the programmer, are teleological and therefore non-Darwinian. Therefore, Meester argues, they are useless in showing how complex adaptations arise in the universe. Meester uses the term “teleological” inconsistently, however, and we argue that, no matter how we interpret the term, a Darwinian algorithm does not become non-Darwinian by simulation. We show that the NFL theorem is entirely irrelevant to this argument, and conclude that it does not pose a threat to the relevance of simulations of biological evolution.     

Evolution of dispersal distance

The problem of how often to disperse in a randomly fluctuating environment has long been investigated, primarily using patch models with uniform dispersal. Here, we consider the problem of choice of seed size for plants in a stable environment when there is a trade off between survivability and dispersal range. Ezoe (J Theor Biol 190:287–293, 1998) and Levin and Muller-Landau (Evol Ecol Res 2:409–435, 2000) approached this problem using models that were essentially deterministic, and used calculus to find optimal dispersal parameters. Here we follow Hiebeler (Theor Pop Biol 66:205–218, 2004) and use a stochastic spatial model to study the competition of different dispersal strategies. Most work on such systems is done by simulation or nonrigorous methods such as pair approximation. Here, we use machinery developed by Cox et al. (Voter model perturbations and reaction diffusion equations 2011) to rigorously and explicitly compute evolutionarily stable strategies.     

A Closer Look at Amphetamine-Induced Reverse Transport and Trafficking of the Dopamine and Norepinephrine Transporters

Amphetamine (AMPH) and its derivatives are regularly used in the treatment of a wide array of disorders such as attention-deficit hyperactivity disorder (ADHD), obesity, traumatic brain injury, and narcolepsy (Prog Neurobiol 75:406–433, 2005; J Am Med Assoc 105:2051–2054, 1935; J Am Acad Child Adolesc Psychiatry 41:514–521, 2002; Neuron 43:261–269, 2004; Annu Rev Pharmacol Toxicol 47:681–698, 2007; Drugs Aging 21:67–79, 2004). Despite the important medicinal role for AMPH, it is more widely known for its psychostimulant and addictive properties as a drug of abuse. The primary molecular targets of AMPH are both the vesicular monoamine transporters (VMATs) and plasma membrane monoamine—dopamine (DA), norepinephrine (NE), and serotonin (5-HT)—transporters. The rewarding and addicting properties of AMPH rely on its ability to act as a substrate for these transporters and ultimately increase extracellular levels of monoamines. AMPH achieves this elevation in extracellular levels of neurotransmitter by inducing synaptic vesicle depletion, which increases intracellular monoamine levels, and also by promoting reverse transport (efflux) through plasma membrane monoamine transporters (J Biol Chem 237:2311–2317, 1962; Med Exp Int J Exp Med 6:47–53, 1962; Neuron 19:1271–1283, 1997; J Physiol 144:314–336, 1958; J Neurosci 18:1979–1986, 1998; Science 237:1219–1223, 1987; J Neurosc 15:4102–4108, 1995). This review will focus on two important aspects of AMPH-induced regulation of the plasma membrane monoamine transporters—transporter mediated monoamine efflux and transporter trafficking.     

On visual pigment templates and the spectral shape of invertebrate rhodopsins and metarhodopsins

The absorbance spectra of visual pigments can be approximated with mathematical expressions using as single parameter the absorbance peak wavelength. A comparison of the formulae of Stavenga et al. in Vision Res 33:1011–1017 (1993) and Govardovskii et al. in Vis Neurosci 17:509–528 (2000) applied to a number of invertebrate rhodopsins reveals that both templates well describe the normalized α-band of rhodopsins with peak wavelength > 400 nm; the template spectra are virtually indistinguishable in an absorbance range of about three log units. The template formulae of Govardovskii et al. in Vis Neurosci 17:509–528 (2000) describe the rhodopsin spectra better for absorbances below 10⁻³. The template predicted spectra deviate in the ultraviolet wavelength range from each other as well as from measured spectra, preventing a definite conclusion about the spectral shape in the wavelength range <400 nm. The metarhodopsin spectra of blowfly and fruitfly R1-6 photoreceptors derived from measured data appear to be virtually identical. The established templates describe the spectral shape of fly metarhodopsin reasonably well. However, the best fitting template spectrum slightly deviates from the experimental spectra near the peak and in the long-wavelength tail. Improved formulae for fitting the fly metarhodopsin spectra are proposed.     

The synaptonemal complex and meiotic recombination in humans: new approaches to old questions

Meiotic prophase serves as an arena for the interplay of two important cellular activities, meiotic recombination and synapsis of homologous chromosomes. Synapsis is mediated by the synaptonemal complex (SC), originally characterized as a structure linked to pairing of meiotic chromosomes (Moses (1958) J Biophys Biochem Cytol 4:633–638). In 1975, the first electron micrographs of human pachytene stage SCs were presented (Moses et al. (1975) Science 187:363–365) and over the next 15 years the importance of the SC to normal meiotic progression in human males and females was established (Jhanwar and Chaganti (1980) Hum Genet 54:405–408; Pathak and Elder (1980) Hum Genet 54:171–175; Solari (1980) Chromosoma 81:315–337; Speed (1984) Hum Genet 66:176–180; Wallace and Hulten (1985) Ann Hum Genet 49(Pt 3):215–226). Further, these studies made it clear that abnormalities in the assembly or maintenance of the SC were an important contributor to human infertility (Chaganti et al. (1980) Am J Hum Genet 32:833–848; Vidal et al. (1982) Hum Genet 60:301–304; Bojko (1983) Carlsberg Res Commun 48:285–305; Bojko (1985) Carlsberg Res Commun 50:43–72; Templado et al. (1984) Hum Genet 67:162–165; Navarro et al. (1986) Hum Reprod 1:523–527; Garcia et al. (1989) Hum Genet 2:147–53). However, the utility of these early studies was limited by lack of information on the structural composition of the SC and the identity of other SC-associated proteins. Fortunately, studies of the past 15 years have gone a long way toward remedying this problem. In this minireview, we highlight the most important of these advances as they pertain to human meiosis, focusing on temporal aspects of SC assembly, the relationship between the SC and meiotic recombination, and the contribution of SC abnormalities to human infertility.The synaptonemal complex–50 years     

Genome-wide meta-analysis for rheumatoid arthritis

Meta-analysis is being increasingly used as a tool for integrating data from different studies of complex phenotypes, because the power of any one study to identify causal loci is limited. We applied a novel meta-analytical approach (Loesgen et al. in Genet Epidemiol 21(Suppl 1):S142–S147, 2001) in compiling results from four studies of rheumatoid arthritis in Caucasians including two studies from NARAC (Jawaheer et al. in Am J Hum Genet 68:927–936, 2001; Jawaheer et al. in Arthritis Rheum 48:906–916, 2003), one study from the UK (MacKay et al. in Arthritis Rheum 46:632–639, 2001) and one from France (Cornelis et al. in Proc Natl Acad Sci USA 95:10746–10750, 1998). For each study, we obtained NPL scores by performing interval mapping (2 cM intervals) using GeneHunter2 (Kruglyak et al. in Am J Hum Genet 58:1347–1363, 1996; Markianos et al. in Am J Hum Genet 68:963–977, 2001). The marker maps differed among the three consortium groups, therefore, the marker maps were aligned after the interval mapping was completed and the NPL scores that were within 1 cM of each other were combined using the method of Loesgen et al. (Genet Epidemiol 21(Suppl 1):S142–S147, 2001) by calculating the weighted average of the NPL score. This approach avoids some problems in analysis encountered by using GeneHunter2 when some markers in the sample are not genotyped. This procedure provided marginal evidence (P<0.05) of linkage on chromosome 1, 2, 5 and 18, strong evidence (P<0.01) on chromosomes 8 and 16, and overwhelming evidence in the HLA region of chromosome 6.     

Tumour antigen-targeted immunotherapy for chronic myeloid leukaemia: is it still viable?

In haematological cancers, malignant cells circulate in the blood and lymphatic system. This may make leukaemic cells easier to target by immunotherapy than in other types of cancer. Various immunotherapy strategies have been trialled in several leukaemias including chronic myeloid leukaemia (CML) and in general, these have been aimed at targeting tumour-associated antigens (TAA). There are numerous TAA expressed by CML patients including WT1, proteinase 3, BCR-ABL and HAGE amongst others. The immunogenicity of the CML-specific tumour antigen, BCR-ABL, has been the subject of much debate and its role in the development of the disease and its unique sequence spanning the breakpoint region make it an ideal target for immunotherapy. However, there are a limited number of immunogenic epitopes across the junctional region, which are restricted to only a few HLA types, namely A2, A3 and B7 (Clark et al. in Blood 98:2887–2893, 2001). The second CML-associated antigen is the helicase antigen HAGE, a cancer-testis antigen found to be over-expressed in more than 50% of myeloid leukaemias (Adams et al. in Leukaemia 16:2238–2242, 2002). Very little is known about the function of this antigen and its significance to CML. However, its membership of the DEAD-box family of ATP-dependent RNA helicases and the involvement of other members of this family in tumour cell proliferation (Eberle et al. in Br J Cancer 86:1957–1962, 2002; Yang et al. in Cell Signal 17:1495–504, 2005) suggest a crucial role in the RNA metabolism of tumour cells. For these reasons, HAGE also seems to be a good target for immunotherapy as it would be applicable for the majority of patients with CML. This review aims to discuss the potential of immunotherapy for the treatment of leukaemia, in particular CML, and the prospect of targeting three CML associated antigens: BCR, ABL and HAGE. During his career, Prof. Tony Dodi made a significant contribution in this area of leukaemia research, confirming the identity of immunogenic HLA-A3 and B7-restricted peptides as targets for CTL. Published, as a highlighted paper in Clark et al. (Blood 98:2887–2893, 2001), this study demonstrated the expression of MHC-peptide complexes on the surface of CML cells and the presence of tetramer-positive CTL activity in CML patients positive for these two HLA alleles. His drive and dedication for research excellence will be remembered by all who knew and worked with him. C. L. Riley and M. G. Mathieu are joint first authors and have contributed equally to this paper. This paper is a Focussed Research Review from the meeting which took place 28–29 May 2008 in Nottingham, UK, celebrating the contribution of Prof. I. A. “Tony” Dodi (+29.1.2008) to the EU project “Network for the identification and validation of antigens and biomarkers in cancer and their application in clinical tumour immunology (ENACT)”. This review is dedicated to Prof. Tony Dodi (who passed away suddenly on 29 January 2008) and is written by colleagues who worked with him on research collaborations for more than 10 years. The paper deals with an area of research that Tony dedicated his working life to, that of leukaemia and immunotherapy. His contribution to this research was immense and he will be remembered for his drive, enthusiasm and passion for research excellence, which was infectious. Catherine Riley was Tony’s graduate student who successfully completed her doctorate degree, owing much to his wise direction and advice.     

A role for anions in ATP synthesis and its molecular mechanistic interpretation

ATP, the ‘universal biological energy currency’, is synthesized by utilizing energy either from oxidation of fuels or from light, via the process of oxidative and photo-phosphorylation respectively. The process is mediated by the enzyme F₁F₀-ATP synthase, using the free energy of ion gradients in the final energy catalyzing step, i.e., the synthesis of ATP from ADP and inorganic phosphate (P_i). The details of the molecular mechanism of ATP synthesis are among the most important fundamental issues in biology and hence need to be properly understood. In this work, a role for anions in making ATP has been found. New experimental data has been reported on the inhibition of ATP synthesis at nanomolar concentrations by the potent, specific anion channel blockers 4,4′-diisothiocyanostilbene-2, 2′-disulphonic acid (DIDS) and tributyltin chloride (TBTCl). Based on these inhibition studies, attention has been drawn to anion translocation (in addition to proton translocation) as a requirement for ATP synthesis. The type of inhibition has been quantified and an overall kinetic scheme for mixed inhibition that explains the data has been evolved. The experimental data and the type of inhibition found have been interpreted in the light of the torsional mechanism of energy transduction and ATP synthesis (Nath J Bioenerg Biomembr 42:293–300, 2010a; J Bioenerg Biomembr 42:301–309, 2010b). This detailed and unified mechanism resolves long-standing problems and inconsistencies in the first theories (Slater Nature 172:975–978, 1953; Williams J Theor Biol 1:1–17, 1961; Mitchell Nature 191:144–148, 1961; Mitchell Biol Rev 41:445–502, 1966), makes several novel predictions that are experimentally verifiable (Nath Biophys J 90:8–21, 2006a; Process Biochem 41:2218–2235, 2006b), and provides us with a new and fruitful paradigm in bioenergetics. The interpretation presented here provides intelligent answers to the unexplained existing results in the literature. It is shown that mechanistic interpretation of the experimental data requires substantial addition to available conceptual foundations such that present concepts, theories, and mechanisms must be revised.     

A translational study “case report” on the small molecule “energy blocker” 3-bromopyruvate (3BP) as a potent anticancer agent: from bench side to bedside

The small alkylating molecule, 3-bromopyruvate (3BP), is a potent and specific anticancer agent. 3BP is different in its action from most currently available chemo-drugs. Thus, 3BP targets cancer cells’ energy metabolism, both its high glycolysis (“Warburg Effect”) and mitochondrial oxidative phosphorylation. This inhibits/ blocks total energy production leading to a depletion of energy reserves. Moreover, 3BP as an “Energy Blocker”, is very rapid in killing such cells. This is in sharp contrast to most commonly used anticancer agents that usually take longer to show a noticeable effect. In addition, 3BP at its effective concentrations that kill cancer cells has little or no effect on normal cells. Therefore, 3BP can be considered a member, perhaps one of the first, of a new class of anticancer agents. Following 3BP’s discovery as a novel anticancer agent in vitro in the Year 2000 (Published in Ko et al. Can Lett 173:83–91, 2001), and also as a highly effective and rapid anticancer agent in vivo shortly thereafter (Ko et al. Biochem Biophys Res Commun 324:269–275, 2004), its efficacy as a potent anticancer agent in humans was demonstrated. Here, based on translational research, we report results of a case study in a young adult cancer patient with fibrolamellar hepatocellular carcinoma. Thus, a bench side discovery in the Department of Biological Chemistry at Johns Hopkins University, School of Medicine was taken effectively to bedside treatment at Johann Wolfgang Goethe University Frankfurt/Main Hospital, Germany. The results obtained hold promise for 3BP as a future cancer therapeutic without apparent cyto-toxicity when formulated properly.     

Bone tissue,lyophilized and stored at room temperature for 15 days or more,is not capable of transmitting HIV,HCV or HBV

Over the past 57 years, 17 recipients of frozen bone have been infected with: HIV (Centers for Disease Control and Prevention in Morb Mortal Wkly Rep MMWR 37(39):597–599, 1988; Li et al. in J Formos Med Assoc 100(5):350–351, 2001; Simonds et al. in NEJM 326(11):726–732, 1992; Schratt et al. in Unfallchirurg 99(9):679–684, 1996); HCV (Eggen and Nordbo in NEJM 326(6):411, 1992; Conrad et al. in J Bone Joint Surg Am 77:214–224, 1995; Trotter in J Bone Joint Surg Am 851(11):2215–2217, 2003; Tugwell et al. in Ann of Internal Med 143(9):648–654, 2005); or HBV (Shutkin in J Bone Joint Surg Am 36:160–162, 1954). However, bone, lyophilized and stored at room temperature, has never transmitted these viral diseases. A literature review was undertaken to determine whether there is any evidence that lyophilized bone is capable of transmitting HIV, HCV and HBV.