Thiophenacetamide as a potential modulator to NF-κB: structure and dynamics study using in silico and molecular biology assays

Abstract

Nuclear factor kappa B (NF-κB) plays critical roles in the regulation of many pathophysiological processes, including inflammation and immune responses, cell growth and apoptosis. This DNA-binding protein receptor is considered an important molecular target to treat many diseases through host-directed therapy. In this line, several drugs containing thiophene cores have been extensively evaluated due to their ability to interfere on NF-κB translocation to the nucleus. In this work, assays using drug affinity responsive target stability (DARTS) revealed that the parent compound N-(Aryl)-2-thiophen-2-ylacetamide referred to as thiophenacetamide (TAA) specifically binds to the p65 subunit of the NF-κB. Since no experimental binding mode of TAA with p65 is available, we explored TAA within putative sites in silico to gain insights into its possible binding mode and behavior. The binding mode of TAA found in Site 1 formed hydrogen bonds with Lys37 and Asp125 on p65, important residues near DNA-binding region. Molecular dynamics simulations showed the stability of this mode of binding in contrast to the other also tested modes. Our results suggest that TAA binding could occur in regions close to residues responsible for DNA binding, increasing NF-κB protein rigidity and affecting the association between DNA and NF-κB.

Communicated by Ramaswamy H. Sarma     

Global trends of habitat destruction and consequences for parrot conservation

Human advance on natural habitats is a major cause of biodiversity loss. This transformation process represents a profound change in wooded environments, disrupting original communities of flora and fauna. Many species are highly dependent on forests, especially parrots (Psittaciformes) with almost a third of their species threatened by extinction. Most parrot species occur in tropical and subtropical forests, and given the forest dependence of most species, this is the main reason why habitat loss has been highlighted as the main threat for the group. Such habitat loss acts in synergy with other important threats (e.g., logging and poaching), which become especially problematic in certain developing countries along tropical latitudes. In this study, we used available information on parrot distributions, species traits, IUCN assessment, habitat loss and timber extraction for different periods, and distribution of protected areas, to determine conservation hotspots for the group, and analyze potential changes in the conservation status of these species. We detected four conservation hotspots for parrots: two in the Neotropics and two in Oceania, all of them facing different degrees of threat in regard of current habitat loss and agricultural trends. Our results suggest that the future of the group is subject to policymaking in specific regions, especially in the northeastern Andes and the Atlantic Forest. In addition, we predicted that agricultural expansion will have a further negative effect on the conservation status of parrots, pushing many parrot species to the edge of extinction in the near future. Our results have conservation implications by recommending protected areas in specific parrot conservation hotspots. Our recommendations to mitigate conservation risks to this group of umbrella species would also benefit many other coexisting species as well.     

Discovery and Validation of a Prostate Cancer Genomic Classifier that Predicts Early Metastasis Following Radical Prostatectomy

Purpose

Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis.

Methods

A nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry who underwent radical prostatectomy between 1987 and 2001. A genomic classifier (GC) was developed by modeling differential RNA expression using 1.4 million feature high-density expression arrays of men enriched for rising PSA after prostatectomy, including 213 who experienced early clinical metastasis after biochemical recurrence. A training set was used to develop a random forest classifier of 22 markers to predict for cases - men with early clinical metastasis after rising PSA. Performance of GC was compared to prognostic factors such as Gleason score and previous gene expression signatures in a withheld validation set.

Results

Expression profiles were generated from 545 unique patient samples, with median follow-up of 16.9 years. GC achieved an area under the receiver operating characteristic curve of 0.75 (0.67–0.83) in validation, outperforming clinical variables and gene signatures. GC was the only significant prognostic factor in multivariable analyses. Within Gleason score groups, cases with high GC scores experienced earlier death from prostate cancer and reduced overall survival. The markers in the classifier were found to be associated with a number of key biological processes in prostate cancer metastatic disease progression.

Conclusion

A genomic classifier was developed and validated in a large patient cohort enriched with prostate cancer metastasis patients and a rising PSA that went on to experience metastatic disease. This early metastasis prediction model based on genomic expression in the primary tumor may be useful for identification of aggressive prostate cancer.     

Biochemical responses and photosynthetic performance of Gracilaria sp. (Rhodophyta) from Cádiz,Spain, cultured under different inorganic carbon and nitrogen levels

Photosynthetic acclimation and the interactions between carbon (C) and nitrogen (N) metabolism have been studied in the red macroalga Gracilaria sp. from Cádiz, Spain, cultured under different inorganic C and N levels. The use of chemostats and buffered medium allowed continuous restoration of the alkaline reserve and constancy of pH during the experiments. The N:C ratios and phycobiliprotein, chlorophyll a and soluble protein contents decreased when Gracilaria sp. was grown at low N levels. Algae grown in a high inorganic C concentration (5% CO₂) displayed a higher soluble carbohydrate concentration and maximum photosynthesis rates but a lower photosynthesic affinity for inorganic C, and lower phycobiliprotein and Rubisco contents, than those cultured at low inorganic C levels (air CO₂). The inorganic C enrichment also affected the N uptake and assimilation in Gracilaria sp., causing a decrease in the N uptake rate even under conditions of N sufficiency. These results reflect the significant influence of the inorganic C growth regime on N assimilation in Gracilaria sp.     

Antimicrobial resistance pattern of methicillin-resistant Staphylococcus aureus in the food industry

There is increasing concern about the impact on public health of methicillin-resistant Staphylococcus aureus (MRSA) associated with animal food products. MRSA remains a serious problem because of the high incidence and multidrug resistance of the strains, even for strains isolated from foods, food environments and food handlers. The objectives of this study are: (i) to evaluate the susceptibility of S. aureus strains isolated from food, food handlers and food-processing environments to 14 antibiotics currently used in veterinary and human therapy; (ii) to assess the presence of the mecA gene. A total of 1007 samples were collected from food, food handlers, and environments and were analyzed for the presence of S. aureus. S. aureus was present in 165 of the 1007 samples. A total of 157 isolates were methicillin-susceptible S. aureus (MSSA) and 8 isolates were MRSA. In particular, out of 8 MRSA strains detected, 4 strains harboured the mecA gene. All MRSA strains were resistant to at least one of the tested antibiotics and 6 strains demonstrated multi-resistance. Considering the high level of resistances in S. aureus and the isolation of MRSA strains, the surveillance of antimicrobial resistance and the spreading of this pathogen is of crucial importance in the food production chain. These data are useful in improving background data on antimicrobial resistance of S. aureus isolated from food, processing environments and food handlers, supporting the prudent use of antibiotics and the development of international control programs.     

The Na conductance in the sarcolemma and the transverse tubular system membranes of mammalian skeletal muscle fibers

Na (and Li) currents and fluorescence transients were recorded simultaneously under voltage-clamp conditions from mouse flexor digitorum brevis fibers stained with the potentiometric dye di-8-ANEPPS to investigate the distribution of Na channels between the surface and transverse tubular system (TTS) membranes. In fibers rendered electrically passive, voltage pulses resulted in step-like fluorescence changes that were used to calibrate the dye response. The effects of Na channel activation on the TTS voltage were investigated using Li, instead of Na, because di-8-ANEPPS transients show anomalies in the presence of the latter. Na and Li inward currents (I(Na), I(Li); using half of the physiological ion concentration) showed very steep voltage dependences, with no reversal for depolarizations beyond the calculated equilibrium potential, suggesting that most of the current originates from a noncontrolled membrane compartment. Maximum peak I(Li) was ～ 30% smaller than for I(Na), suggesting a Li-blocking effect. I(Li) activation resulted in the appearance of overshoots in otherwise step-like di-8-ANEPPS transients. Overshoots had comparable durations and voltage dependence as those of I(Li). Simultaneously measured maximal overshoot and peak I(Li) were 54 ± 5% and 773 ± 53 μA/cm(2), respectively. Radial cable model simulations predicted the properties of I(Li) and di-8-ANEPPS transients when TTS access resistances of 10-20 Ω cm(2), and TTS-to-surface Na permeability density ratios in the range of 40:60 to 70:30, were used. Formamide-based osmotic shock resulted in incomplete detubulation. However, results from a subpopulation of treated fibers (low capacitance) provide confirmatory evidence that a significant proportion of I(Li), and the overshoot in the optical signals, arises from the TTS in normal fibers. The quantitative evaluation of the distribution of Na channels between the sarcolemma and the TTS membranes, as provided here, is crucial for the understanding of the radial and longitudinal propagation of the action potential, which ultimately govern the mechanical activation of muscle in normal and diseased conditions.     

A marker-assisted backcross approach for developing submergence-tolerant rice cultivars

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC₂F₂ generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC₃F₂ double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3–3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Updated geographical distribution and ecoepidemiology of the triatomine fauna (Reduviidae: Triatominae) in Colombia

Information concerning triatomine records from provinces and municipalities was accumulated-including data indicating natural infections with trypanosomatides-that has been previously published or reported by Colombian provincial health services and research institutes. Altitude appeared to be the main factor responsible for the distribution of the insects. Illustrations summarize the information provided by the above records. A triatomine fauna classification is presented that corresponds to the eco-epidemiological conditions of the country, considering altitude as the factor determining the geographical distribution of these vectors. Rhodnius prolixus, Triatoma dimidiata, Triatoma maculata and Triatoma venosa are considered the major transmission risk species in Colombia, according to the frequency in which they are reported inside dwellings and peridomiciliary areas. Entomological surveillance providess a necessary tool to reinforce the control strategies for Chagas disease. This also allows the evaluation of transmission risk that the sylvatic triatomines represent in Colombia.     

The Protein-disulfide Isomerase ERp57 Regulates the Steady-state Levels of the Prion Protein

Although the accumulation of a misfolded and protease-resistant form of the prion protein (PrP) is a key event in prion pathogenesis, the cellular factors involved in its folding and quality control are poorly understood. PrP is a glycosylated and disulfide-bonded protein synthesized at the endoplasmic reticulum (ER). The ER foldase ERp57 (also known as Grp58) is highly expressed in the brain of sporadic and infectious forms of prion-related disorders. ERp57 is a disulfide isomerase involved in the folding of a subset of glycoproteins in the ER as part of the calnexin/calreticulin cycle. Here, we show that levels of ERp57 increase mainly in neurons of Creutzfeldt-Jacob patients. Using gain- and loss-of-function approaches in cell culture, we demonstrate that ERp57 expression controls the maturation and total levels of wild-type PrP and mutant forms associated with human disease. In addition, we found that PrP physically interacts with ERp57, and also with the closest family member PDIA1, but not ERp72. Furthermore, we generated a conditional knock-out mouse for ERp57 in the nervous system and detected a reduction in the steady-state levels of the mono- and nonglycosylated forms of PrP in the brain. In contrast, ERp57 transgenic mice showed increased levels of endogenous PrP. Unexpectedly, ERp57 expression did not affect the susceptibility of cells to ER stress in vitro and in vivo. This study identifies ERp57 as a new modulator of PrP levels and may help with understanding the consequences of ERp57 up-regulation observed in human disease.