DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence.

Motivation: Due to the breakthrough in protein structure prediction by AlphaFold, the scientific community has access to 200 million predicted protein structures with near-atomic accuracy from the AlphaFold protein structure DataBase (AFDB), covering nearly the entire protein universe. Segmenting these models into domains and classifying them into an evolutionary hierarchy hold tremendous potential for unraveling essential insights into protein function.

Results: We introduce DPAM-AI, a Domain Parser for AlphaFold Models based on Artificial Intelligence.

Arsenic speciation in freshwater organisms from the river Danube in Hungary.

Total arsenic and arsenic species were determined in a range of freshwater samples (sediment, water, algae, plants, sponge, mussels, frog and fish species), collected in June 2004 from the river Danube in Hungary. Total arsenic concentrations were measured by ICPMS and arsenic species were measured in aqueous extracts of the samples by ion-exchange HPLC-ICPMS. In order to separately determine the efficiency of the extraction method and the column recovery, total arsenic concentrations in the extracts were obtained in three ways: (i) ICPMS determination after acid digestion; (ii) flow injection analysis performed directly on the extract; (iii) the sum of arsenic species eluting from the HPLC column.

Development of a liquid chromatography/electrospray selected reaction monitoring method for the determination of organoarsenic species in marine and freshwater samples.

Cation- and anion-exchange high-performance liquid chromatography/electrospray selected reaction monitoring (HPLC/ES-SRM) methods were developed for the determination of 15 organoarsenic compounds in marine and freshwater samples. The results demonstrate that the developed HPLC/ES-SRM methods are powerful approaches for the identification of organoarsenic species in crude sample extracts. The detection limits, linearity as well as reproducibility for most of the species are comparable or even better than those measured by the HPLC/inductively coupled plasma mass spectrometry (ICPMS) technique.

Cytosine arabinoside induces programmed endothelial cell death through the caspase-3 pathway.

The anti-cancer effects of cytosine arabinoside (ARA-C) are well known. However, effects on nonmalignant cells have not been elucidated and may be important to understanding treatment-related toxicity. The purpose of this study was to examine the effect of ARA-C on nondividing vascular endothelial cells.

In vitro age-related responses of endothelial cells to breast cancer cell addition.

Aim: The purpose of this study was to determine if the in vitro age of endothelial cells alters endothelial response(s) to breast cancer cells.

Method: After characterizing lower passage ("young"; passages 10-16) and higher passage ("old"; passages 30-36) bovine pulmonary artery endothelial cells (BPAECs), fluorescently labeled MCF-7 breast cancer cells were added to confluent monolayers of young and old BPAECs.

Results: Transient gaps that peaked in size by 12 h and closed by 48h occurred between the young BPAECs, while large persistent gaps formed between the old BPAECs.

Arsenic speciation in farmed Hungarian freshwater fish.

Arsenic speciation analysis was carried out on freshwater farmed fish collected from an area with elevated groundwater arsenic concentrations in Hungary as well as from outside of the area (control samples). The arsenic species were determined by high-performance liquid chromatography-inductively coupled plasma mass spectrometry on methanol extracts of the muscle tissue from the fish. Catfish (Claries gariepinus) were raised in geothermal water where the average total arsenic concentrations were 167 (contaminated sites) and 15.

Menadione causes endothelial barrier failure by a direct effect on intracellular thiols, independent of reactive oxidant production.

Menadione (MQ), a quinone used with cancer chemotherapeutic agents, causes cytotoxicity to endothelial cells (EC). Previous studies have suggested that MQ induces an oxidative stress and dysfunction in EC by either increasing hydrogen peroxide (H(2)O(2)) production or depleting intracellular glutathione (GSH), the main intracellular antioxidant. Since a primary function of EC is to form a barrier to fluid movement into tissues, protecting organs from edema formation and dysfunction, our aim was to see if MQ would cause a barrier dysfunction and to ascertain the mechanism.

Endothelial contraction and monolayer hyperpermeability are regulated by Src kinase.

Endothelial monolayer hyperpermeability is regulated by a myosin light chain phosphorylation (MLCP)-dependent contractile mechanism. In this study, we tested the role of Src-dependent tyrosine phosphorylation to modulate endothelial contraction and monolayer barrier function with the use of the myosin phosphatase inhibitor calyculin A (CalA) to directly elevate MLCP with the Src family tyrosine kinase inhibitor herbimycin A (HA) in bovine pulmonary artery endothelial cells (EC). CalA stimulated an increase in MLCP, Src kinase activity, an increase in the tyrosine phosphorylation of paxillin and focal adhesion (FA) kinase (p125(FAK)), and monolayer hyperpermeability.

The rat glomerular filtration barrier does not show negative charge selectivity.

Objective: To characterize the effects of size, shape, and negative charge on the transport of macromolecules across the glomerular capillary wall by using the sieving curves (fractional clearance vs. solute molecular radii) of fluorescent polydispersed polysaccharide tracers.

Methods: Glomerular fractional clearances (FC) were measured with fluorescent neutral [isoelectric point (pI) = 7.