Cancer: a single disease with a multitude of manifestions?

The relationships of critical nutrients such as plant phenolics, vitamins, minerals and lipids are considered with respect to the incidence of a variety of cancers, and analyzed in terms of how these nutrient deficiencies alter immune function, DNA integrity and cell proliferation. With a significant correlation found between cancer and these nutrient deficiencies, the hypothesis is presented here that nutrition could provide a unifying perception of cancer and recast it as a single disease. This further suggests that a coordinated administration of specific, critical nutrients to cancer patients could lead to the reversal of the disease. It is also proposed that the concurrent presence of a variety of nutritional deficiencies in cancer patients requires a multilevel, systemic approach to this disease as opposed to the single active therapeutic agent approach that is the cornerstone of contemporary research and pharmacology.     

Analysis of a competitive prey–predator system with a prey refuge

Gauss's competitive exclusive principle states that two competing species having analogous environment cannot usually occupy the same space at a time but in order to exploit their common environment in a different manner, they can co-exist only when they are active in different times. On the other hand, several studies on predators in various natural and laboratory situations have shown that competitive coexistence can result from predation in a way by resisting any one prey species from becoming sufficiently abundant to outcompete other species such that the predator makes the coexistence possible. It has also been shown that the use of refuges by a fraction of the prey population exerts a stabilizing effect in the interacting population dynamics. Further, the field surveys in the Sundarban mangrove ecosystem reveal that two detritivorous fishes, viz. Liza parsia and Liza tade (prey population) coexist in nature with the presence of the predator fish population, viz. Lates calcarifer by using refuges.     

Interaction of β-sheet folds with a gold surface

The adsorption of proteins on inorganic surfaces is of fundamental biological importance. Further, biomedical and nanotechnological applications increasingly use interfaces between inorganic material and polypeptides. Yet, the underlying adsorption mechanism of polypeptides on surfaces is not well understood and experimentally difficult to analyze. Therefore, we investigate here the interactions of polypeptides with a gold(111) surface using computational molecular dynamics (MD) simulations with a polarizable gold model in explicit water. Our focus in this paper is the investigation of the interaction of polypeptides with β-sheet folds. First, we concentrate on a β-sheet forming model peptide. Second, we investigate the interactions of two domains with high β-sheet content of the biologically important extracellular matrix protein fibronectin (FN). We find that adsorption occurs in a stepwise mechanism both for the model peptide and the protein. The positively charged amino acid Arg facilitates the initial contact formation between protein and gold surface. Our results suggest that an effective gold-binding surface patch is overall uncharged, but contains Arg for contact initiation. The polypeptides do not unfold on the gold surface within the simulation time. However, for the two FN domains, the relative domain-domain orientation changes. The observation of a very fast and strong adsorption indicates that in a biological matrix, no bare gold surfaces will be present. Hence, the bioactivity of gold surfaces (like bare gold nanoparticles) will critically depend on the history of particle administration and the proteins present during initial contact between gold and biological material. Further, gold particles may act as seeds for protein aggregation. Structural re-organization and protein aggregation are potentially of immunological importance.     

Functionalization of a protein surface with per-O-methylated β-cyclodextrin

Per-O-methylated β-cyclodextrin (CD) bearing an iodoacetamide group at the 6-position was synthesized to functionalize protein surfaces. Bovine serum albumin (BSA) was quantitatively modified with the CD derivative by the S(N) 2 reaction of iodoacetamide with a cysteine residue (Cys34) on the BSA surface. The resultant CD-functionalized BSA (BSA-CD) spontaneously dimerized upon addition of an anionic tetraarylporphyrin (TPPS) through the supramolecular 1:2 complexation between TPPS and CD on the protein surface. The BSA-CD/TPPS complex further complexed with ferric protoporphyrin IX (hemin) in the hydrophobic pockets of albumin to form a hemin/BSA-CD/TPPS ternary complex in which static fluorescence quenching occurred owing to intramolecular electron transfer from the photoexcited TPPS to hemin.     

Solution structure of a novel α-conotoxin with a distinctive loop spacing pattern

α-Pharmacological conotoxins are among the most selective ligands of nicotinic acetylcholine receptors with typical cysteine frameworks. They are characterized by the intercysteine loop and classified into various subfamilies, such as α3/5 and α4/7 conotoxins. A novel α-conotoxin, Pu14a (DCPPHPVPGMHKCVCLKTC), with a distinct loop spacing pattern between cysteines was reported recently. Pu14a belongs to the Cys framework 14 (-C-C-C-C) family containing four proline residues in the loop 1 region. Similar to another framework 14 conotoxin Lt14a (MCPPLCKPSCTNC-NH2), Pu14a has C1-C3/C2-C4 disulfide linkage, and can inhibit some subtypes of nicotinic acetylcholine receptors. In this study, the solution structure of Pu14a was investigated using 1H nuclear magnetic resonance spectroscopy to understand the structure-activity relationship of this conotoxin. 20 converged structures of this conopeptide, with RMSD value of 0.77 ?, were obtained based on distance constraints, dihedral angles and disulfide bond constraints. The three-dimensional structure of Pu14a showed remarkable difference from typical α-conotoxins because of a large intercysteine loop between C2 and C13, as well as a 3(10)-helix near the C-terminal. Furthermore, four proline residues in Pu14a adopted the trans conformation that may correlate with the large loop configuration and the biological activity of this conopeptide. The distinct structural characteristics of Pu14a will be very useful for studying the structure-activity relationship of α-conotoxins.     

Selective recognition of alkanoates by a β-cyclodextrin flexibly capped with a chromophore

The association between 6-deoxy-6-(p-hydroxy-m-nitrophenacylthio)-β-cyclodextrin 1 and sodium n-alkanoate, sodium 2,2-dimethylpropionate, or sodium 3,3-dimethylbutyrate was investigated. Host-guest association was measured by means of electronic spectroscopy and circular dichroism spectroscopy and ascertained to be 1:1. The inclusion of 2,2-dimethylpropionate or butanoate marginally affected the circular dichroism spectrum of 1. The inclusion of 3,3-dimethylbutyrate, hexanoate, octanoate, decanoate, or dodecanoate, however, dramatically affected the spectrum of 1. The plots of molecular ellipticities of the inclusion complexes against the carbon number of the n-alkanoates were sigmoid. From these observations, the effective size of the guest molecule to push the chromophore in the cavity to the capping position was estimated. From the similarity of the spectrum of the octanoate-1 complex to that of 1-adamantanecarboxylate-1 complex, the carbon chain of octanoate appears to be folded in the cavity of the cyclodextrin.     

Recovery of the motor function of the arm with the aid of a hand exoskeleton controlled by a brain–computer interface in a patient with an extensive brain lesion

The dynamics of motor function recovery in a patient with an extensive brain lesion has been investigated during a course of neurorehabilitation assisted by a hand exoskeleton controlled by a brain–computer interface. Biomechanical analysis of the movements of the paretic arm recorded during the rehabilitation course was used for an unbiased assessment of motor function. Fifteen procedures involving hand exoskeleton control (one procedure per week) yielded the following results: (a) the velocity profile for targeted movements of the paretic hand became nearly bell-shaped; (b) the patient began to extend and abduct the hand, which was flexed and adducted at the beginning of the course; and (c) the patient started supinating the forearm, which was pronated at the beginning of the rehabilitation course. The first result is interpreted as improvement of the general level of control over the paretic hand, and the two other results are interpreted as a decrease in spasticity of the paretic hand.     

Fecal metabolite of a gnotobiotic mouse transplanted with gut microbiota from a patient with Alzheimer’s disease

ABSTRACT

Studies of Alzheimer’s disease are based on model mice that have been altered by transgenesis and other techniques to elicit pathogenesis. However, changes in the gut microbiota were recently suggested to diminish cognitive function in patients, as well as in model mice. Accordingly, we have created model mice of the human gut microbiota by transplanting germ-free C57BL/6N mice with fecal samples from a healthy volunteer and from an affected patient. These humanized mice were stably colonized and reproduced the bacterial diversity in donors. Remarkably, performance on Object Location Test and Object Recognition Test was significantly reduced in the latter than in the former at 55 weeks of age, suggesting that gut microbiota transplanted from an affected patient affects mouse behavior. In addition, metabolites related to the nervous system, including γ-aminobutyrate, taurine, and valine, were significantly less abundant in the feces of mice transplanted with microbiota from the affected patient.     

Identification of a Survival-independent Metastasis-enhancing Role of Hypoxia-inducible Factor-1α with a Hypoxia-tolerant Tumor Cell Line

During tumor progression, malignant cells must repeatedly survive microenvironmental stress. Hypoxia-inducible factor-1 (HIF-1) signaling has emerged as one major pathway allowing cellular adaptation to stress. Recent findings led to the hypothesis that HIF-1α may enhance the metastatic potential of tumor cells by a survival-independent mechanism. So far it has not been shown that HIF-1α also directly regulates invasive processes during metastasis in addition to conferring a survival advantage to metastasizing tumor cells. In a hypoxia-tolerant tumor cell line (L-CI.5s), which did not rely on HIF-1 signaling for viability in vitro and in vivo, knockdown of Hif-1α reduced invasiveness of the tumor cells in vitro as well as extravasation and secondary infiltration in vivo. Liver metastases associated induction of proinvasive receptor tyrosine kinase Met phosphorylation as well as gelatinolytic activity were Hif-1α-dependent. Indeed, promoter activity of the matrix metalloproteinase-9 (mmp-9) was shown to be Hif-1α-dependent. This study uncovers a new survival-independent biological function of HIF-1α contributing to the efficacy of metastases formation.     

Interaction of porphyrins with heme proteins – a brief review

In the past years, in our laboratory, several cell lines have been generated starting from a human liver (H7). Some of them have been used successfully in studies of the infection with and propagation of Hepatitis B and Hepatitis C viruses. Recently, several lines of evidence indicated that the origin of these cell lines was uncertain. Therefore, we now have determined the genetic characteristics of these cell lines in comparison to HepG2 cells received from ATCC and to HepG2 isolates grown at other laboratories. Quadruplex fluorescent short tandem repeat (STR) typing and karyotyping were performed. In addition, some biochemical characteristics of selected clones were studied. Genetically, all H7-derived cell lines were identical to HepG2 cells. However, some liver-specific functions varied between the different sub-cloned lines. The H7-derived cell lines that were generated proved to be sub-cloned lines of HepG2. The problem of cross-contamination during cloning of cell lines appears to be not uncommon. We found that two out of six HepG2 isolates obtained from other laboratories were not derived from the same individual as the original HepG2 cells. Therefore, STR typing should be applied as a rapid and sensitive technique to determine and monitor the origin of cell lines and to safeguard against contamination.     

The daily dietary intake of ochratoxin a — Results of a duplicate portion study with Bavarian schoolchildren

The daily dietary intakes of ochratoxin A (OTA) were estimated for 28 school-children at the age of seven and eight years using duplicate portions of the total diets collected on three successive days. For most children and collection days the dietary OTA intakes were below the PTDI-value of 5 ng/kg bw/day. The mean dietary intake was 1.52 ng/kg bw/day for all children. According to sex the mean intakes were 1.21 ng/kg bw/day for boys and 1.83 ng/kg bw/day for girls.     

Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases

Background

One of the main concerns of the modern medicine is the frightening spread of antimicrobial resistance caused mainly by the misuse of antibiotics. The researchers worldwide are actively involved in the search for new classes of antibiotics, and for the modification of known molecules in order to face this threatening problem. We have applied a computational approach to predict the interactions between a new cephalosporin derivative containing an additional β-lactam ring with different substituents, and several serine β-lactamases representative of the different classes of this family of enzymes.

Results

The results of the simulations, performed by using a covalent docking approach, has shown that this compound, although able to bind the selected β-lactamases, has a different predicted binding score for the two β-lactam rings, suggesting that one of them could be more resistant to the attack of these enzymes and stay available to perform its bactericidal activity.

Conclusions

The detailed analysis of the complexes obtained by these simulations suggests possible hints to modulate the affinity of this compound towards these enzymes, in order to develop new derivatives with improved features to escape to degradation.

     

Reconstitution of Photosystem Ⅱ Reaction Center with Cu-ChlorophyⅡ a

An Isolated photosystem （PS） II reaction center （RC） with altered pigment content was obtained by chemical exchange of native chlorophyll a （Chl） with externally added Cu-Chl a （Cu-Chl）. Pigment composition and spectroscopic properties of the RC exchanged with Cu-Chl were compared with native RC and RC treated with Chl In the same way. High-performance liquid chromatography analysis showed approximately 0.5 Cu-Chl per two pheophytln in the Cu-Chl-reconstltuted RC preparation. Insertion of Cu-Chl resulted in a decrease In absorption at 670 nm and an Increase at 660 nm, suggesting that the peripheral Chl may have been displaced. Fluorescence emission spectra of the Cu-Chl-reconstituted RC displayed a marked decrease In fluorescence yield and a blue shift of the band maximum, accompanied by the appearance of a broad peak at a shorter wavelength, Indicating that energy transfer In the modified RC was disturbed by Cu-Chl, a quencher of the excited state. However, there were few differences in the circular dichrolsm （CD） spectra, suggesting that the arrangement of pigments and proteins responsible for the CD signal was not significantly affected. In addition, no obvious change In peptlde components was found after the exchange procedure.     

Three dimensional structure of a bacterial α-l-fucosidase with a 5-membered iminocyclitol inhibitor

Fucosidases, enzymes that cleave fucose from the non-reducing end of a glycan, represent promising medicinal targets reflecting their roles in cancer metastasis, inflammation, host-parasite interactions and the lysosomal storage disorder fucosidosis. The X-ray crystal structures of Bacteroides thetaiotaomicron GH29 α-l-fucosidase (BtFuc2970) in a new crystal form (at a resolution of 1.59 Å) and liganded with a 5-membered iminocyclitol inhibitor (1.73 Å) are reported herein. The 5-membered iminocyclitol binds in a ³E conformation, mimicking the proposed ³H₄ half chair transition-state of the enzyme catalysed reaction, and its K_i for BtFuc2970 was determined as 2 μM. Structural analysis of fucosidase inhibition through 5-membered iminocyclitols will aid in the rational design of more potent fucosidase inhibitors for treatment of a range of medical conditions.     

ABRF-ESRG’03: Analysis of a PVDF-Bound Known Protein with a Homogeneous Amino-Terminus

The Association of Biomolecular Resource Facilities 2003 Edman Sequencing Research Group (ABRF-ESRG’03) sample is the 15th in a series of studies designed to allow participating members to evaluate their abilities to analyze the N-terminus of a protein or peptide using automated Edman degradation chemistry. It is a follow-up study to the ESRG’02 sample, which was a single protein with a heterogeneous N-terminus. Both the 2002 and 2003 samples were obtained from the same protein complex and were resolved by SDS-PAGE followed by electrophoretic transfer to PVDF membrane. The ABRF-ESRG’03 sample had an apparent molecular weight of 49 kDa and a single N-terminus, with initial yields of approximately 2 pmol. Participants were asked to sequence 25 residues and return their results to the ESRG for analysis along with two completed surveys and an area/pmol table for repetitive and initial yield calculations. Data for 46 responses are presented which include initial yields, repetitive yields, sequencer performance, and ability to identify the protein.     

Enhanced cytotoxicity of a polymer–drug conjugate with triple payload of paclitaxel

The development of targeting approaches to selectively release chemotherapeutic drugs into malignant tissue is a major challenge in anticancer therapy. We have synthesized an N-(2-hydroxypropyl)-methacrylamide (HPMA) copolymer–drug conjugate with an AB₃ self-immolative dendritic linker. HPMA copolymers are known to accumulate selectively in tumors. The water-soluble polymer–drug conjugate was designed to release a triple payload of the hydrophobic drug paclitaxel as a result of cleavage by the endogenous enzyme cathepsin B. The polymer–drug conjugate exhibited enhanced cytotoxicity on murine prostate adenocarcinoma (TRAMP C2) cells in comparison to a classic monomeric drug–polymer conjugate.