Rapid detection of peptide markers for authentication purposes in raw and cooked meat using ambient liquid extraction surface analysis mass spectrometry

In this paper, our previously developed ambient LESA-MS methodology is implemented to analyze five types of thermally treated meat species, namely beef, pork, horse, chicken, and turkey meat, in order to select and identify heat-stable and species-specific peptide markers. In-solution tryptic digests of cooked meats were deposited onto a polymer surface, followed by LESA-MS analysis and evaluation using multivariate data analysis and tandem electrospray MS. The five types of cooked meat were clearly discriminated using principal component analysis and orthogonal partial least squares discriminant analysis. A number of 23 heat stable peptide markers unique to species and muscle protein were identified following data-dependent tandem LESA-MS analysis. Surface extraction and direct ambient MS analysis of mixtures of cooked meat species was performed for the first time and enabled detection of 10% (w/w) of pork, horse, and turkey meat, and 5% (w/w) of chicken meat in beef, using the developed LESA-MS/MS analysis. The study shows, for the first time, that ambient LESA-MS methodology displays specificity sufficient to be implemented effectively for the analysis of processed and complex peptide digests. The proposed approach is much faster and simpler than other measurement tools for meat speciation; it has potential for application in other areas of meat science or food production

To automate or not to automate: this is the question

New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected

Phosphorylation Regulates SIRT1 Function

BACKGROUND: SIR2 is an NAD(+)-dependent deacetylase [1]-[3] implicated in the regulation of lifespan in species as diverse as yeast [4], worms [5], and flies [6]. We previously reported that the level of SIRT1, the mammalian homologue of SIR2 [7], [8], is coupled to the level of mitotic activity in cells both in vitro and in vivo[9]. Cells from long-lived mice maintained SIRT1 levels of young mice in tissues that undergo continuous cell replacement by proliferating stem cells. Changes in SIRT1 protein level were not associated with changes in mRNA level, suggesting that SIRT1 could be regulated post-transcriptionally. However, other than a recent report on sumoylation [10] and identification of SIRT1 as a nuclear phospho-protein by mass spectrometry [11], post-translational modifications of this important protein have not been reported. METHODOLOGY/PRINCIPAL FINDINGS: We identified 13 residues in SIRT1 that are phosphorylated in vivo using mass spectrometry. Dephosphorylation by phosphatases in vitro resulted in decreased NAD(+)-dependent deacetylase activity. We identified cyclinB/Cdk1 as a cell cycle-dependent kinase that forms a complex with and phosphorylates SIRT1. Mutation of two residues phosphorylated by Cyclin B/Cdk1 (threonine 530 and serine 540) disturbs normal cell cycle progression and fails to rescue proliferation defects in SIRT1-deficient cells [12], [13]. CONCLUSIONS/SIGNIFICANCE: Pharmacological manipulation of SIRT1 activity is currently being tested as a means of extending lifespan in mammals. Treatment of obese mice with resveratrol, a pharmacological activator of SIRT1, modestly but significantly improved longevity and, perhaps more importantly, offered some protection against the development of type 2 diabetes mellitus and metabolic syndrome [14]-[16]. Understanding the endogenous mechanisms that regulate the level and activity of SIRT1, therefore, has obvious relevance to human health and disease. Our results identify phosphorylation by cell cycle dependent kinases as a major mechanism controlling the level and function of this sirtuin and complement recent reports of factors that inhibit [17], [18] and activate [19] SIRT1 by protein-protein interactions

A new approach to assess and predict the functional roles of proteins across all known structures

The three dimensional atomic structures of proteins provide information regarding their function; and codified relationships between structure and function enable the assessment of function from structure. In the current study, a new data mining tool was implemented that checks current gene ontology (GO) annotations and predicts new ones across all the protein structures available in the Protein Data Bank (PDB). The tool overcomes some of the challenges of utilizing large amounts of protein annotation and measurement information to form correspondences between protein structure and function. Protein attributes were extracted from the Structural Biology Knowledgebase and open source biological databases. Based on the presence or absence of a given set of attributes, a given protein’s functional annotations were inferred. The results show that attributes derived from the three dimensional structures of proteins enhanced predictions over that using attributes only derived from primary amino acid sequence. Some predictions reflected known but not completely documented GO annotations. For example, predictions for the GO term for copper ion binding reflected used information a copper ion was known to interact with the protein based on information in a ligand interaction database. Other predictions were novel and require further experimental validation. These include predictions for proteins labeled as unknown function in the PDB. Two examples are a role in the regulation of transcription for the protein AF1396 from Archaeoglobus fulgidus and a role in RNA metabolism for the protein psuG from Thermotoga maritima

Communally breeding bats use physiological and behavioural adjustments to optimise daily energy expenditure

Small endotherms must change roosting and thermoregulatory behaviour in response to changes in ambient conditions if they are to achieve positive energy balance. In social species, for example many bats, energy expenditure is influenced by environmental conditions, such as ambient temperature, and also by social thermoregulation. Direct measurements of daily fluctuations in metabolic rates in response to ambient and behavioural variables in the field have not been technologically feasible until recently. During different reproductive periods, we investigated the relationships between ambient temperature, group size and energy expenditure in wild maternity colonies of Bechstein’s bats (Myotis bechsteinii). Bats used behavioural and physiological adjustments to regulate energy expenditure. Whether bats maintained normothermia or used torpor, the number of bats in the roosts as well changed with reproductive status and ambient temperature. During pregnancy and lactation, bats remained mostly normothermic and daily group sizes were relatively large, presumably to participate in the energetic benefits of social thermoregulation. In contrast, smaller groups were formed on days when bats used torpor, which occurred mostly during the post-lactation period. Thus, we were able to demonstrate on wild animals under natural conditions the significance of behavioural and physiological flexibility for optimal thermoregulatory behaviour in small endotherms

Hydrogeochemical Aspects Associated with the Mixing of Formation Waters Injected Into the Hydrocarbon Reservoir

Wody złożowe wydobywane razem z ropą naftową i gazem ziemnym, ze względu na ich ilość oraz skład chemiczny, stanowią problem dla firm naftowych eksploatujących złoża węglowodorów. Przeciętnie na świecie wydobywa się 2 do 3 razy więcej wody niż ropy. Ilość wydobywanych wód wzrasta wraz z czasem eksploatacji złóż, w przypadku złóż na końcowym etapie sczerpania ilość eksploatowanej wody jest 5 do 8 razy większa niż ropy naftowej. Wody złożowe wydobywane z węglowodorami to najczęściej solanki o wysokiej mineralizacji. Duże ilości wysoko zmineralizowanych wód wydobywanych wraz z ropą i gazem są w różny sposób zagospodarowywane lub unieszkodliwiane. Najbardziej powszechny sposób unieszkodliwiania tych wód to zatłaczanie ich do warstw chłonnych. W wyniku zatłaczania wód złożowych do złóż węglowodorów dochodzi do oddziaływania wód z formacją do składowania. W formacji tej mogą następować rozliczne reakcje wody złożowej ze środowiskiem skalnym. Zatłaczanie wód złożowych będzie powodowało również mieszanie wód, które naruszy stany równowagi reakcji chemicznych i wpłynie na zmianę chemizmu mieszających się wód. Przeanalizowano metodą modelowania geochemicznego oddziaływania wód złożowych zatłaczanych do złoża gazu ziemnego Przemyśl. Przy wykorzystaniu programu PHREEQC przebadano reakcje chemiczne związane z mieszaniem wód złożowych różnych typów chemicznych. Stwierdzono możliwość wytrącania się odpowiednich minerałów jako efekt mieszania wód o zróżnicowanym składzie chemicznym.Formation waters extracted with crude oil and natural gas, due to their amount and chemical composition can be a problem for petroleum companies operating hydrocarbon deposits. On average, the world generates 2 to 3 times more water than oil. On average, the world generates 2 to 3 times more water than crude oil. The amount of extracted water increases with the time of exploitation of the deposit, in the case of deposits at the final stage of depletion, the amount of extracted water is 5 to 8 times bigger than petroleum. Formation waters from hydrocarbons deposits are usually the highly mineralized brines. Large quantities of highly mineralized waters extracted with crude oil and gas are disposed of in various ways or neutralized. The most common way of disposing of these waters is by injecting them into rock mass. As a result of injection of reservoir waters into hydrocarbon deposits, the waters interact with the storage formations. In these formations, there may be numerous reactions of mineral water with the rock environment. The injection of reservoir waters will also cause mixing of waters that can disturb the state of thermodynamic equilibrium and will alter the chemistry of these waters. It was analyzed by the geochemical modeling of the interaction of the reservoir waters of Przemyśl natural gas field. Using the PHREEQC program, the chemical reactions related to the mixing of reservoir waters of different chemical types have been studied. It has been found that is possible to precipitation appropriated minerals as a result of mixing water with different chemical composition

Hydrogeochemical aspects associated with the mixing of formation waters injected into the hydrocarbon reservoir

Wody złożowe wydobywane razem z ropą naftową i gazem ziemnym, ze względu na ich ilość oraz skład chemiczny, stanowią problem dla firm naftowych eksploatujących złoża węglowodorów. Przeciętnie na świecie wydobywa się 2 do 3 razy więcej wody niż ropy. Ilość wydobywanych wód wzrasta wraz z czasem eksploatacji złóż, w przypadku złóż na końcowym etapie sczerpania ilość eksploatowanej wody jest 5 do 8 razy większa niż ropy naftowej. Wody złożowe wydobywane z węglowodorami to najczęściej solanki o wysokiej mineralizacji. Duże ilości wysoko zmineralizowanych wód wydobywanych wraz z ropą i gazem są w różny sposób zagospodarowywane lub unieszkodliwiane. Najbardziej powszechny sposób unieszkodliwiania tych wód to zatłaczanie ich do warstw chłonnych. W wyniku zatłaczania wód złożowych do złóż węglowodorów dochodzi do oddziaływania wód z formacją do składowania. W formacji tej mogą następować rozliczne reakcje wody złożowej ze środowiskiem skalnym. Zatłaczanie wód złożowych będzie powodowało również mieszanie wód, które naruszy stany równowagi reakcji chemicznych i wpłynie na zmianę chemizmu mieszających się wód. Przeanalizowano metodą modelowania geochemicznego oddziaływania wód złożowych zatłaczanych do złoża gazu ziemnego Przemyśl. Przy wykorzystaniu programu PHREEQC przebadano reakcje chemiczne związane z mieszaniem wód złożowych różnych typów chemicznych. Stwierdzono możliwość wytrącania się odpowiednich minerałów jako efekt mieszania wód o zróżnicowanym składzie chemicznym.Formation waters extracted with crude oil and natural gas, due to their amount and chemical composition can be a problem for petroleum companies operating hydrocarbon deposits. On average, the world generates 2 to 3 times more water than oil. On average, the world generates 2 to 3 times more water than crude oil. The amount of extracted water increases with the time of exploitation of the deposit, in the case of deposits at the final stage of depletion, the amount of extracted water is 5 to 8 times bigger than petroleum. Formation waters from hydrocarbons deposits are usually the highly mineralized brines. Large quantities of highly mineralized waters extracted with crude oil and gas are disposed of in various ways or neutralized. The most common way of disposing of these waters is by injecting them into rock mass. As a result of injection of reservoir waters into hydrocarbon deposits, the waters interact with the storage formations. In these formations, there may be numerous reactions of mineral water with the rock environment. The injection of reservoir waters will also cause mixing of waters that can disturb the state of thermodynamic equilibrium and will alter the chemistry of these waters. It was analyzed by the geochemical modeling of the interaction of the reservoir waters of Przemyśl natural gas field. Using the PHREEQC program, the chemical reactions related to the mixing of reservoir waters of different chemical types have been studied. It has been found that is possible to precipitation appropriated minerals as a result of mixing water with different chemical composition