Biochemistry

Conformal stabilty molecular docking

by Sigge Hermann

Never published before.

This is a paper of my own invented chemical structure based Approach to molecular docking. This is a paper of my own invented chemical structure based Approach to molecular docking.

Peptidic coating for gold nanospheres multifunctionalizable with photostable and photolabile moieties

by Valerio Voliani

Journal of Materials Chemistry 2012 (RSC), doi: 10.1039/C2JM31782F

A single-step method to coat and trifunctionalize water-dispersed gold nanospheres (AuNss) with
carboxylic acids,... more A single-step method to coat and trifunctionalize water-dispersed gold nanospheres (AuNss) with
carboxylic acids, amines, and alkynes is reported. The coating is based on a mix of two hexa-peptides,
differing only in the C-terminal amino acid. The process yields AuNss that are non-cytotoxic, stable in
physiological environments, and which present three reactive surface groups allowing rapid, selective,
10 and modular conjugation (click- and peptide-reactions) to virtually any chosen biomolecule or
fluorophore. Conjugated nanostructures were analyzed in vitro and in living cells. Confocal imaging and
colocalization analyses demonstrate the presence and reactivity of three different types of covalent bonds
with payloads: two of these are photostable while one bond is photolabile and can be cleaved by *Wpower
irradiation with a 561-nm cw laser.

Consistent temperature dependence of respiration across ecosystems contrasting in thermal history

by Dan Perkins

Ecosystem respiration is a primary component of the carbon cycle and understanding the mechanisms that determine its... more Ecosystem respiration is a primary component of the carbon cycle and understanding the mechanisms that determine its temperature dependence will be important for predicting how rates of carbon efflux might respond to global warming. We used a rare model system, comprising a network of geothermally heated streams ranging in temperature from 5 °C to 25 °C, to explore the nature of the relationship between respiration and temperature. Using this ‘natural experiment’, we tested whether the natal thermal regime of stream communities influenced the temperature dependence of respiration in the absence of other potentially confounding variables. An empirical survey of 13 streams across the thermal gradient revealed that the temperature dependence of whole-stream respiration was equivalent to the average activation energy of the respiratory complex (0.6–0.7 eV). This observation was also consistent for in-situ benthic respiration. Laboratory experiments, incubating biofilms from four streams across the thermal gradient at a range of temperatures, revealed that the activation energy and Q10 of respiration were remarkably consistent across streams, despite marked differences in their thermal history and significant turnover in species composition. Furthermore, absolute rates of respiration at standardised temperature were also unrelated to ambient stream temperature, but strongly reflected differences in biofilm biomass. Together, our results suggest that the core biochemistry,which drives the kinetics of oxidative respiratory metabolism, may be well conserved among diverse taxa and environments, and that the intrinsic sensitivity of respiration to temperature is not influenced by ambient environmental temperature.

pH-dependence of the specific binding of Cu(II) and Zn(II) ions to the amyloid-beta peptide

by sebastian wärmländer

N‐terminal engineering of amyloid‐β‐binding Affibody molecules yields improved chemical synthesis and higher binding affinity

by sebastian wärmländer

Beyond the Barrier: A Hypothetical Model for Cause and Progression of Morgellons Disease

by Joseph Keleher

The author proposes the symptoms set often referred to as Morgellons Disease is the result of increasing inorganic more The author proposes the symptoms set often referred to as Morgellons Disease is the result of increasing inorganic
mercury levels beyond the blood/brain barrier (hereafter referred to as the Barrier Theory). While inorganic
mercury does not easily pass beyond the barrier, organic mercury does and may return to an inorganic
state beyond the barrier. If proven valid, our present understanding of mercury will need reevaluation.

Crystal Structure of ChrR - A Quinone Reductase with the Capacity to Reduce Chromate

by Sebastien Poulain

PLoS ONE, 2012
Eswaramoorthy S and Poulain S (equal contributors), Hienerwadel R, Brémond N, Sylvester MD, Zhang Y-B, Berthomieu C, Van Der Lelie D, Matin A.

The Escherichia coli ChrR enzyme is an obligatory two-electron quinone reductase that has many applications, such as... more The Escherichia coli ChrR enzyme is an obligatory two-electron quinone reductase that has many applications, such as in chromate bioremediation. Its crystal structure, solved at 2.2 Å resolution, shows that it belongs to the flavodoxin superfamily in which flavin mononucleotide (FMN) is firmly anchored to the protein. ChrR crystallized as a tetramer, and size exclusion chromatography showed that this is the oligomeric form that catalyzes chromate reduction. Within the tetramer, the dimers interact by a pair of two hydrogen bond networks, each involving Tyr128 and Glu146 of one dimer and Arg125 and Tyr85 of the other; the latter extends to one of the redox FMN cofactors. Changes in each of these amino acids enhanced chromate reductase activity of the enzyme, showing that this network is centrally involved in chromate reduction.

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

by Melanie Stefan

A Necessary Condition for Proof of Abiotic Semiosis

by Marc Champagne

To appear in Semiotica.

This short essay seeks to identify and prevent a pitfall that attends less careful inquiries into “physiosemiosis.” It... more This short essay seeks to identify and prevent a pitfall that attends less careful inquiries into “physiosemiosis.” It is emphasized that, in order to truly establish the presence of sign-action in the non-living world, all the components of a triadic sign — including the interpretant — would have to be abiotic (that is, not dependent on a living organism). Failure to heed this necessary condition can lead one to hastily confuse a natural sign (like smoke coming from fire) for an instance of abiotic semiosis. A more rigorous and reserved approach to the topic is called for.

Filingeri, D., Matharoo, J., Jemni, M. (2011) Do football players need altitude training? A review. In: Jemni M, Bianco A, Palma A, Eds; Proceedings of the 1st International Conference in Science and Football. International Week of Football. 15-17 April 2011, Palermo, Italy. CONI publications ISBN 978 - 88 - 905268-2-4.

by Davide Filingeri

Paoli, A., Moro, T., Zonin, F., Filingeri, D., Bianco, A., Palma, A., Marcolin, G. (2011) Effects of high- intensity interval resistance training (HIRT) and pyramidal training (PYT) on some muscle and blood parameters . Journal of Sports Medicine and Physical Fitness. 51 (Suppl.1 to No. 3): 15.

by Davide Filingeri

Filingeri, D., Mancuso, E. P., Paoli, A., Bianco, A., Palma, A. (2011) Is hypoxia a training stimulus for endurance athletes’ performance? a brief review. Italian Journal of Sport Sciences and Law. 4 (4): 153-162.

by Davide Filingeri

Filingeri, D., Proia, P., Bianco, A., Schiera, G., Saladino, P., Pomara, F., Petrucci, M., Traina, M., Palma, A. (2011). Monitoring biomarkers during preseason preparation period in professional soccer players. Italian Journal Of Anatomy and Embryology. 116(2), 73.

by Davide Filingeri

The contribution of CK2 and spleen tyrosine kinase (SYK) to CFTR trafficking and PKA-induced activity

by Francisco Malta Romeiras

Simão Luz, Patthara Kongsuphol, Ana Mendes, Francisco Romeiras, Marisa Sousa, Rainer Schreiber, Paulo Matos, Peter Jordan, Anil Mehta, Margarida Amaral, Karl Kunzelmann, Carlos Farinha (2011) “The contribution of CK2 and spleen tyrosine kinase (SYK) to CFTR trafficking and PKA-induced activity” Mol Cell Biol [Epub ahead of print]

Metformin Treatment of Diabetes Mellitus Increases the Risk for Pancreatitis In Patients Bearing the CFTR-Mutation S573C

by Francisco Malta Romeiras

Patthara Kongsuphol, Diane Cassidy, Francisco Romeiras, Rainer Schreiber, Anil Mehta, Karl Kunzelmann (2010) “Metformin treatment of diabetes mellitus increases the risk for pancreatitis in patients bearing the CFTR-mutation S573C”. Cell Physiol Biochem. 25:389-396

Effect of Lead (Pb) Exposure on the Activity of Superoxide Dismutase and Catalase in Battery Manufacturing Workers (BMW) of Western Maharashtra (India) with Reference to Heme biosynthesis

by Vinod Bhagwat

Occupational lead exposure in battery manufacturing workers, silver jewelry workers, and spray painters in western Maharashtra (India): effect on liver and kidney function

by Vinod Bhagwat

Biochemical aspects of lead exposure in silver jewelry workers in western Maharashtra (India)

by Vinod Bhagwat

STUDYING ANCIENT CROP PROVENANCE: IMPLICATIONS FROM δ13C AND δ15N OF CHARRED BARLEY IN A MIDDLE BRONZE AGE SILO AT EBLA (NW SYRIA)

by Valentina Caracuta

Published in Rapid Communications in Mass Spectromentry 6, 327.
Co-authored with Girolamo Fiorentino, Grazia Casiello, Francesco Longobardi, Antonio Sacco,

The discovery of a storeroom full of barley and other cereals (L.9512) in the proto-historic site of Ebla has provided... more The discovery of a storeroom full of barley and other cereals (L.9512) in the proto-historic site of Ebla has provided a unique opportunity to study the early city-state’s centralized storage system from a different perspective. Epigraphic evidence available within the site reveals a complex system of taxation which included gathering grain tributes from satellite sites and redistributing semi-finished products such as flour. In this paper, we intend to explore the possibilities of a combined approach, based on estimated barley grain volumes and δ13C-δ15N analyses. This approach is used to distinguish between grain from different harvesting sites and to identify any grain cultivated using special agricultural practices (e.g. manuring or irrigation). The basic assumption for this kind of analysis is that the growth-site conditions, natural or anthropogenic, of harvested cereals are reflected in their grain size and δ13C-δ15N values. Since the remains found in the storeroom were charred, the first task was to evaluate the effect of carbonization on the δ13C-δ15N and the size of the grains. Thus, the effect of charring was tested on modern samples of Syrian barley landraces. Once ascertained that fresh grains reduced to charred remains retain their original biometric and isotopic traits, the ancient material was examined. 13 groups were identified, each characterized by a specific average volume and specific carbon and nitrogen values. The analysis revealed that what had first appeared to be a homogeneous concentration of grain was in fact an assemblage of barley harvested from different sites .

Auto-ethnography of my food habits

by Oleg Nekrassovski

draft only