Toxicity test of flavonoid compounds from the leaves of Dendrophthoe pentandra (L.) Miq. using in vitro culture cell models.

Background and Aim: The flavonoids from mistletoe are thought to have antimicrobial action. This encouraging finding supports the benefits of medicinal plants as a substitute for synthetic antimicrobials, thus promoting healthy lifestyles. In contrast, it is known that the use of topical drug formulations made from flavonoids of mistletoe (Dendrophthoe pentandra (L.) Miq. Loranthaceae) with Indonesian name, Benalu duku (BD) is required in skin cell irritation. This study aimed to assess the toxic effects of the flavonoid substances of BD, as an initial screening. Materials and Methods: A myeloma cell line was cultured in Roswell Park Memorial Institute medium, and the Baby Hamster Kidney clone 12 (BHK21) cell line was cultured in Dulbecco's Modified Eagle's Medium from stock (±9 × 107 cells/mL), and 1.2 mL of culture were distributed into each well of a microtiter plate. Subsequently, 0.2 mL of serially diluted flavonoid compounds (0.5-3 µg/mL) were added to 12 wells for each concentration, as trial groups (including control groups), followed by a 2-day incubation. Observations were performed based on the cytopathic effect (CPE) using an inverted microscope at a magnification of 100×. Results: Cytopathic effect was detected on the microtiter plate wells for the groups of myeloma and BHK21 cells at a flavonoid concentration of 0.5 µg/mL-3 µg/mL. Conclusion: Flavonoid compounds from BD were safely used for topical treatment of cancer cells at a concentration <2.491 µg/mL, whereas for non-cancerous cells, a concentration <2.582 µg/mL was sufficient (p < 0.05).

Diagnosis and potential treatments for acute hepatopancreatic necrosis disease (AHPND): a review.

Acute hepatopancreatic necrosis disease (AHPND) or formerly known as early mortality syndrome (EMS) is an emerging disease that has caused significant economic losses to the aquaculture industry. The primary causative agent of AHPND is Vibrio parahaemolyticus, a Gram-negative rod-shaped bacterium that has gained plasmids encoding the fatal binary toxins Pir A/Pir B that cause rapid death of the infected shrimp. In this review, the current research studies and information about AHPND in shrimps have been presented. Molecular diagnostic tools and potential treatments regarding AHPND were also included. This review also includes relevant findings which may serve as guidelines that can help for further investigation and studies on AHPND or other shrimp diseases.

PON-1 carbamylation is enhanced in HDL of uremia patients.

High-density lipoprotein (HDL) carbamylation has been known in uremia patients. Paraoxonase-1 (PON-1) is an important HDL protein responsible for HDL anti-oxidant, arylesterase and lactonase activities. PON-1 carbamylation in uremic HDL has never been explored. We isolated HDL from uremia patients and control healthy subjects for study. Sandwich ELISA was used to estimate carbamylated PON-1 protein expression in HDL, and nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) was applied to identify the amino acid in PON-1 carbamylated. PON-1 enzyme activities were estimated by substrates conversion method. HDL anti-oxidant activity was gauged by fluorescence changes of indicator dye in the presence of H2O2. Our study results proved that the degree of PON-1 carbamylation was higher in uremic HDL than in control HDL. Sandwich ELISA study showed that carbamylated PON-1 concentration in uremic HDL was 1.49 ± 0.08 fold higher than that in HDL from controls (p < 0.05). The nanoLC-MS/MS showed that the carbamylation of lysine 290 (K290) of PON-1, a residue adjacent to PON-1 activity determining site, was detected in uremic HDL but not detected in control HDL. K290 carbamylation leads to local conformation changes that reduce accessible solvent accessibility. The HDL paraoxonase, arylesterase, and lactonase activities were all significantly lower in uremia patients than in control subjects. Additionally, HDL anti-antioxidant ability was also lower in uremia patients. Carbamylation of PON-1 in uremia patients could be one of the factors in impairing PON-1 enzyme activities and HDL anti-oxidation function.

Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids.

The conservation level of a residue is a useful measure about the importance of that residue in protein structure and function. Much information about sequence conservation comes from aligning homologous sequences. Profiles showing the variation of the conservation level along the sequence are usually interpreted in evolutionary terms and dictated by site similarities of a proper set of homologous sequences. Here, we report that, of the viral icosahedral capsids, the sequence conservation profile can be determined by variations in the distances between residues and the centroid of the capsid - with a direct inverse proportionality between the conservation level and the centroid distance - as well as by the spatial variations in local packing density. Examining both the centroid and the packing density models against a dataset of 51 crystal structures of nonhomologous icosahedral capsids, we found that many global patterns and minor features derived from the viral structures are consistent with those present in the sequence conservation profiles. The quantitative link between the level of conservation and structural features like centroid-distance or packing density allows us to look at residue conservation from a structural viewpoint as well as from an evolutionary viewpoint.

(PS)2: protein structure prediction server version 3.0.

Protein complexes are involved in many biological processes. Examining coupling between subunits of a complex would be useful to understand the molecular basis of protein function. Here, our updated (PS)(2) web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)(2) server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)(2) is freely available at http://ps2v3.life.nctu.edu.tw/.

The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein.

The conservation profile of a protein is a curve of the conservation levels of amino acids along the sequence. Biologists are usually more interested in individual points on the curve (namely, the conserved amino acids) than the overall shape of the curve. Here, we show that the conservation curves of proteins bear the imprints of molecules that are evolutionarily coupled to the proteins. Our method is based on recent studies that a sequence conservation profile is quantitatively linked to its structural packing profile. We find that the conservation profiles of nucleic acid (NA) binding proteins are better correlated with the packing profiles of the protein-NA complexes than those of the proteins alone. This indicates that a nucleic acid binding protein evolves to accommodate the nucleic acid in such a way that the residues involved in binding have their conservation levels closely coupled with the specific nucleotides.

Protein thermal stability enhancement by designing salt bridges: a combined computational and experimental study.

Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, a novel method for salt-bridge design was proposed based on the statistical analysis of 10,556 surface salt bridges on 6,493 X-ray protein structures. These salt bridges were first categorized based on pairing residues, secondary structure locations, and Cα-Cα distances. Pairing preferences generalized from statistical analysis were used to construct a salt-bridge pair index and utilized in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges. The model was also coupled with B-factor, weighted contact number, relative solvent accessibility, and conservation prescreening to determine the residues appropriate for the thermal adaptive design of salt bridges. According to our method, eight putative salt-bridges were designed on a mesophilic ß-glucosidase and 24 variants were constructed to verify the predictions. Six putative salt-bridges leaded to the increase of the enzyme thermal stability. A significant increase in melting temperature of 8.8, 4.8, 3.7, 1.3, 1.2, and 0.7°C of the putative salt-bridges N437K-D49, E96R-D28, E96K-D28, S440K-E70, T231K-D388, and Q277E-D282 was detected, respectively. Reversing the polarity of T231K-D388 to T231D-D388K resulted in a further increase in melting temperatures by 3.6°C, which may be caused by the transformation of an intra-subunit electrostatic interaction into an inter-subunit one depending on the local environment. The combination of the thermostable variants (N437K, E96R, T231D and D388K) generated a melting temperature increase of 15.7°C. Thus, this study demonstrated a novel method for the thermal adaptive design of salt bridges through inference of suitable positions and substitutions.

Post-injury regeneration in rat sciatic nerve facilitated by neurotrophic factors secreted by amniotic fluid mesenchymal stem cells.

Amniotic fluid mesenchymal stem cells have the ability to secrete neurotrophic factors that are able to promote neuron survival in vitro. The purpose of this study was to evaluate the effects of neurotrophic factors secreted by rat amniotic fluid mesenchymal stem cells on regeneration of sciatic nerve after crush injury. Fifty Sprague-Dawley rats weighing 250-300 g were used. The left sciatic nerve was crushed with a vessel clamp. Rat amniotic fluid mesenchymal stem cells embedded in fibrin glue were delivered to the injured nerve. Enzyme-linked immunosorbent assay (ELISA) and immunocytochemistry were used to detect neurotrophic factors secreted by the amniotic fluid mesenchymal stem cells. Nerve regeneration was assessed by motor function, electrophysiology, histology, and immunocytochemistry studies. Positive CD29/44, and negative CD11b/45, as well as high levels of expression of brain-derived neurotrophic factor, glia cell line-derived neurotrophic factor, ciliary neurotrophic factor (CNTF), nerve growth factor, and neurotrophin-3 (NT-3) were demonstrated in amniotic fluid mesenchymal stem cells. Motor function recovery, the compound muscle action potential, and nerve conduction latency showed significant improvement in rats treated with amniotic fluid mesenchymal stem cells. ELISA measurement in retrieved nerves displayed statistically significant elevation of CNTF and NT-3. The immunocytochemical studies demonstrated positive staining for NT-3 and CNTF in transplanted cells. The histology and immunocytochemistry studies revealed less fibrosis and a high level of expression of S-100 and glial fibrillary acid protein at the crush site. Rat amniotic fluid mesenchymal stem cells may facilitate regeneration in the sciatic nerve after crush injury. The increased nerve regeneration found in this study may be due to the neurotrophic factors secreted by amniotic fluid mesenchymal stem cells.