Heat-killed Mycobacterium tuberculosis induces trained immunity in vitro and in vivo administered systemically or intranasally.

Trained immunity (TI) represents a memory-like process of innate immune cells. TI can be initiated with various compounds such as fungal ß-glucan or the tuberculosis vaccine, Bacillus Calmette-Guérin. Nevertheless, considering the clinical applications of harnessing TI against infections and cancer, there is a growing need for new, simple, and easy-to-use TI inducers. Here, we demonstrate that heat-killed Mycobacterium tuberculosis (HKMtb) induces TI both in vitro and in vivo. In human monocytes, this effect represents a truly trained process, as HKMtb confers boosted inflammatory responses against various heterologous challenges, such as lipopolysaccharide (Toll-like receptor [TLR] 4 ligand) and R848 (TLR7/8 ligand). Mechanistically, HKMtb-induced TI relies on epigenetic mechanisms in a Syk/HIF-1α-dependent manner. In vivo, HKMtb induced TI when administered both systemically and intranasally, with the latter generating a more robust TI response. Summarizing, our research has demonstrated that HKMtb has the potential to act as a mucosal immunotherapy that can successfully induce trained responses.

LUD, a new protein domain associated with lactate utilization.

BACKGROUND: A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family. RESULTS: JCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome. CONCLUSIONS: We propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states.

An X-ray crystal structure of CYP2B4 in complex with the drug paroxetine [(3S,4R)-3-[(2H-1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine] was solved at 2.14 Å resolution. The structure revealed a conformation intermediate to that of the recently solved complex with amlodipine and that of the more compact complex with 4-(4-chlorophenyl)imidazole in terms of the placement of the F-G cassette. Moreover, comparison of the new structure with 15 previously solved structures of CYP2B4 revealed some new insights into the determinants of active-site size and shape. The 2B4-paroxetine structure is nearly superimposable on a previously solved closed structure in a ligand-free state. Despite the overall conformational similarity among multiple closed structures, the active-site cavity volume of the paroxetine complex is enlarged. Further analysis of the accessible space and binding pocket near the heme reveals a new subchamber that resulted from the movement of secondary structural elements and rearrangements of active-site side chains. Overall, the results from the comparison of all 16 structures of CYP2B4 demonstrate a cluster of protein conformations that were observed in the presence or absence of various ligands.

Impacts of Organic Emerging Contaminants (Erythromycin, Ibuprofen, and Diclofenac) on the Performance of a Membrane Bioreactor Treating Urban Wastewater: A Heterotrophic Kinetic Investigation.

The occurrence of emerging organic contaminants, such as pharmaceuticals, is a growing global concern. In this research, for a membrane bioreactor (MBR) laboratory plant operating at a hydraulic retention time (HRT) of 24 h, fed with real urban wastewater, the heterotrophic biomass behaviour was analysed for two concentrations of erythromycin, ibuprofen, and diclofenac. The concentrations studied for the first phase were erythromycin 0.576 mg L-1, ibuprofen 0.056 mg L-1, and diclofenac 0.948 mg L-1. For Phase 2, the concentrations were increased to erythromycin 1.440 mg L-1, ibuprofen 0.140 mg L-1, and diclofenac 2.370 mg L-1. Heterotrophic biomass was affected and inhibited by the presence of pharmaceutical compounds in both phases. The system response to low concentrations of pharmaceutical compounds occurred in the initial phase of plant doping. Under these operating conditions, there was a gradual decrease in the concentration of mixed liquor suspended solids and the removal of chemical oxygen demand of the system, as it was not able to absorb the effect produced by the pharmaceutical compounds added in both phases.

Conformational adaptation of human cytochrome P450 2B6 and rabbit cytochrome P450 2B4 revealed upon binding multiple amlodipine molecules.

Structures of human cytochrome P450 2B6 and rabbit cytochrome P450 2B4 in complex with two molecules of the calcium channel blocker amlodipine have been determined by X-ray crystallography. The presence of two drug molecules suggests clear substrate access channels in each P450. According to a previously established nomenclature, amlodipine molecules were trapped in access pathway 2f in P450 2B6 and in pathway 2a or 2f in P450 2B4. These pathways overlap for part of the length and then diverge as they extend toward the protein surface. A previously described solvent channel was also found in each enzyme. The results indicate that key residues located on the surface and at the entrance of the substrate access channels in each of these P450s may play a crucial role in guiding substrate entry. In addition, the region of P450 2B6 and 2B4 involving helices B', F, F', and G' and part of helix G is substantially more open in the amlodipine complexes than in the corresponding 4-(4-chlorophenyl)imidazole complexes. The increased active site volume observed results from the major retraction of helices F, F', and B' and the ß4 sheet region located close to the binding cavity to accommodate amlodipine. These structures demonstrate novel insight into distinct conformational states not observed with previous P450 2B structures and provide clear evidence of the substrate access channels in two drug-metabolizing P450s. In addition, the structures exhibit the versatility that can be exploited via in silico studies with other P450 2B6 ligands as large as raloxifene and itraconazole.

Microalgae bioreactor for nutrient removal and resource recovery from wastewater in the paradigm of circular economy.

Every day, large quantities of wastewater are discharged from various sources that could be reused. Wastewater contains nutrients such as nitrogen or phosphorus, which can be recovered. Microalgae-based technologies have attracted attention in this sector, as they are able to bioremediate wastewater, harnessing its nutrients and generating algal biomass useful for different downstream uses, as well as having other advantages. There are multiple species of microalgae capable of growing in wastewater, achieving nutrient removal efficiencies surpassing 70%. On the other hand, microalgae contain lipids that can be extracted for energy recovery in biodiesel. Currently, there are several methods of lipid extraction from microalgae. Other biofuels can also be obtained from microalgae biomass, such as bioethanol, biohydrogen or biogas. This review also provides information on bioenergy products and products in the agri-food industry as well as in the field of human health based on microalgae biomass within the concept of circular bioeconomy.

Nutrient Removal and Membrane Performance of an Algae Membrane Photobioreactor in Urban Wastewater Regeneration.

The increase in industry and population, together with the need for wastewater reuse, makes it necessary to implement new technologies in the circular economy framework. The aim of this research was to evaluate the quality of the effluent of an algae membrane photobioreactor for the treatment of the effluent of an urban wastewater treatment plant, to characterise the ultrafiltration membranes, to study the effectiveness of a proposed cleaning protocol, and to analyse the performance of the photobioreactor. The photobioreactor operated under two days of hydraulic retention times feed with the effluent from the Los Vados wastewater treatment plant (WWTP) (Granada, Spain). The microalgae community in the photobioreactor grew according to the pseudo-second-order model. The effluent obtained could be reused for different uses of diverse quality with the removal of total nitrogen and phosphorus of 56.3% and 64.27%, respectively. The fouling of the polyvinylidene difluoride ultrafiltration membrane after 80 days of operation was slight, increasing the total membrane resistance by approximately 22%. Moreover, the higher temperature of the medium was, the lower intrinsic resistance of the membrane. A total of 100% recovery of the membrane was obtained in the two-phase cleaning protocol, with 42% and 58%, respectively.

Factors associated with recruitment success in the phase 2a study of aztreonam-avibactam development programme: a descriptive qualitative analysis among sites in Spain.

OBJECTIVE: Successful clinical trials are subject to recruitment. Recently, the REJUVENATE trial, a prospective phase 2a open-label, single-arm interventional clinical trial conducted within the Innovative Medicines Initiative-supported Combatting Bacterial Resistance in Europe-Carbapenem Resistance project, was published, with 85% of the recruitment performed in Spain. We analysed the recruitment success in this trial by establishing a model of recruitment practice. METHODS: A descriptive qualitative study was performed from May 2016 to October 2017 at 10 participating Spanish centres. Data were extracted from: (1) feasibility questionnaires to assess the centre's potential for patient enrolment; (2) delegation of responsibility records; (3) pre-screening records including an anonymised list of potentially eligible and (4) screening and enrolment records. A descriptive analysis of the features was performed by the participating centre. Pearson's and Spearman's correlation coefficients were calculated to determine factors of recruitment success. RESULTS: The highest recruitment rate was observed in Hospitals 3 and 6 (58.8 and 47.0 patients per month, respectively). All the study teams were multidisciplinary with a median of 15 members (range: 7-22). Only Hospitals 3, 5 and 6 had dedicated nursing staff appointed exclusively to this study. Moreover, in those three hospitals and in Hospital 9, the study coordinator performed exclusive functions as a research planner, and did not assume these functions for the other hospitals. The univariate analysis showed a significant association between recruitment success and months of recruitment (p=0.024), number of staff (p<0.001), higher number of pharmacists (p=0.005), infectious disease specialists (p<0.001), the presence of microbiologist in the research team (p=0.018) and specifically dedicated nursing staff (p=0.036). CONCLUSIONS: The existence of broad multidisciplinary teams with staff dedicated exclusively to the study as well as the implementation of a well-designed local patient assessment strategy were the essential optimisation factors for recruitment success in Spain. TRIAL REGISTRATION NUMBER: NCT02655419; EudraCT 2015-002726-39; analysis of pre-screened patients.

Structures of cytochrome P450 2B6 bound to 4-benzylpyridine and 4-(4-nitrobenzyl)pyridine: insight into inhibitor binding and rearrangement of active site side chains.

The biochemical, biophysical, and structural analysis of the cytochrome P450 2B subfamily of enzymes has provided a wealth of information regarding conformational plasticity and substrate recognition. The recent X-ray crystal structure of the drug-metabolizing P450 2B6 in complex with 4-(4-chlorophenyl)imidazole (4-CPI) yielded the first atomic view of this human enzyme. However, knowledge of the structural basis of P450 2B6 specificity and inhibition has remained limited. In this study, structures of P450 2B6 were determined in complex with the potent inhibitors 4-benzylpyridine (4-BP) and 4-(4-nitrobenzyl)pyridine (4-NBP). Comparison of the present structures with the previous P450 2B6-4-CPI complex showed that reorientation of side chains of the active site residue Phe206 on the F-helix and Phe297 on the I-helix was necessary to accommodate the inhibitors. However, P450 2B6 does not require any major side chain rearrangement to bind 4-NBP compared with 4-BP, and the enzyme provides no hydrogen-bonding partners for the polar nitro group of 4-NBP within the hydrophobic active site. In addition, on the basis of these new structures, substitution of residue 172 with histidine as observed in the single nucleotide polymorphism Q172H and in P450 2B4 may contribute to a hydrogen bonding network connecting the E- and I-helices, thereby stabilizing active site residues on the I-helix. These results provide insight into the role of active site side chains upon inhibitor binding and indicate that the recognition of the benzylpyridines in the closed conformation structure of P450 2B6 is based solely on hydrophobicity, size, and shape.

Anoikis effector Bit1 negatively regulates Erk activity.

Bcl-2 inhibitor of transcription (Bit1) is a mitochondrial protein that functions as a peptidyl-tRNA hydrolase, but, when released into the cytoplasm, it elicits apoptosis. The proapoptotic function is uniquely counteracted by integrin-mediated cell attachment. We generated a conditional KO mouse of the Bit1 gene by using the Cre-LoxP recombination system. Bit1-null mice were born alive but with some developmental abnormalities. They developed a runting syndrome after birth and died within the first 2 weeks. Cultured fibroblasts from the Bit1-null embryos [mouse embryo fibroblasts (MEFs)] were more resistant to cell death induced by loss of attachment to extracellular matrix (anoikis) than cells from the wild-type or heterozygous littermates. MEFs and tissues from Bit1 KO mice displayed a marked increase in Erk phosphorylation. Knocking down Bit1 expression in cultured cells resulted in increased Erk activation, and partially knocking down Erk reversed the increased anoikis resistance of Bit1 knockdown. The enhanced Erk activation was associated with decreased Erk phosphatase activity. These studies establish the physiological significance of Bit1 activity and begin to delineate a Bit1 signaling pathway that acts through Erk regulation.

Resultados de lesión del nervio laríngeo recurrente en cirugía de tiroides con el uso del neuroestimulador.

BACKGROUND: Intermittent intraoperative neuromonitoring of the recurrent laryngeal nerve is the ideal complement in thyroid surgeries, decreasing thyroid injuries. OBJECTIVE: To analyze the prevalence of recurrent laryngeal nerve injuries with the use and without the use of neuromonitoring in thyroid surgery. METHOD: Observational, descriptive and retrospective study, in which a total of 571 patients were included between the years 2012-2018. Of which 180 neuromonitoring was used and 391 were not used. RESULTS: Of the 180 patients who underwent total thyroidectomy with the use of neuromonitoring, we had a total of 8 (4.4%) transient paralysis and 2 (1.1%) definitive. Without the use of neuromonitoring we obtain 12 (3%) transient paralysis and 7 (1.85%) definitive. CONCLUSIONS: We believe that the use of neuromonitoring complementary to surgery should be used routinely to the usual technique. And we also obtain significant results regarding the reduction of recurrent laryngeal nerve injuries with the use of intraoperative neuromonitoring.

ANTECEDENTES: La neuromonitorización intraoperatoria intermitente del nervio laríngeo recurrente es el complemento ideal en las cirugías tiroideas, ya que disminuye las lesiones. OBJETIVO: Analizar la prevalencia de lesiones del nervio laríngeo recurrente con y sin el uso de neuromonitorización en cirugía de tiroides. MÉTODO: Estudio observacional, descriptivo y retrospectivo, en el que se incluyeron 571 pacientes entre los años 2012 y 2018. De ellos, en 180 se utilizó neuromonitorización y en 391 no. RESULTADOS: De los 180 pacientes que se sometieron a tiroidectomía total con neuromonitorización hubo 8 (4.4%) parálisis transitorias y 2 (1.1%) parálisis definitivas. Sin el uso de neuromonitorización hubo 12 (3%) parálisis transitorias y 7 (1.85%) definitivas. CONCLUSIONES: Creemos que la neuromonitorización debe usarse sistemáticamente con la técnica habitual. Obtenemos resultados significativos con respecto a la reducción de las lesiones del nervio laríngeo recurrente con el uso de neuromonitorización intraoperatoria.

Contributions of fluorescence to endocrine surgery. / Aportaciones de la fluorescencia a la cirugía endocrina.

The use of fluorescence in surgery has expanded and become widespread in recent years, which has led to a real technological phenomenon with the emergence of devices adapted for use in laparoscopic and robotic approaches. Fluorescence-guided surgery in the field of endocrine surgery is also on the rise. More and more articles describe its use in surgery of the thyroid, parathyroid and adrenal glands, although the series are still modest in size and protocols have not been standardized. There are currently several developing areas for the application of fluorescence in endocrine surgery, including the use of fluorescence with indocyanine green in adrenal gland surgery, the identification and prediction of parathyroid perfusion with indocyanine green, and autofluorescence of the parathyroid glands. The objective of this article is to review the current applications of fluorescence in endocrine surgery.

Preliminary structural studies on the leucine-zipper homology region of the human protein Bap31.

B-cell receptor-associated protein 31 (Bap31) is an integral membrane protein located in the endoplasmic reticulum (ER) that participates in the transport and quality control of membrane proteins and plays a role in determining cell sensitivity to ER stress and apoptosis. Its cytoplasmic region contains two target sites for caspase cleavage in certain apoptotic pathways. Here, the subcloning, expression, purification and crystallization of the Homo sapiens Bap31 leucine-zipper C-terminal fragment, which spans residues Gly160-Glu246, are reported. An N-terminally His-tagged protein was overexpressed in Escherichia coli and purified by chromatographic methods. X-ray diffraction data were collected in-house to 2.5 A resolution. Crystals belong to space group P6(1)22/P6(5)22, with unit-cell parameters a = b = 70.7, c = 80.6 A. Data analysis indicates the presence of one molecule per asymmetric unit.

Aportaciones de la fluorescencia a la cirugía endocrina / Contributions of fluorescence to endocrine surgery

El uso de la fluorescencia en cirugía se ha ampliado y difundido en los últimos años, lo que ha constituido un auténtico fenómeno tecnológico ligado a la aparición de dispositivos adaptados a su utilización en los abordajes laparoscópicos y robóticos. La cirugía guiada por fluorescencia en el campo de la cirugía endocrina está igualmente en auge. Cada vez son más los artículos que describen su uso en la cirugía de las glándulas tiroides, paratiroides y suprarrenal, aunque con series aun modestas y con protocolos diversos no estandarizados. Existen actualmente diversas áreas de desarrollo de la aplicación de la fluorescencia en cirugía endocrina. Cabe destacar el uso de la fluorescencia con verde de indocianina en cirugía suprarrenal, la identificación y predicción de la perfusión paratiroidea con verde de indocianina, y la autofluorescencia de las glándulas paratiroides. El objetivo de este artículo es revisar las actuales aplicaciones de la fluorescencia en cirugía endocrina

The use of fluorescence in surgery has expanded and become widespread in recent years, which has led to a real technological phenomenon with the emergence of devices adapted for use in laparoscopic and robotic approaches. Fluorescence-guided surgery in the field of endocrine surgery is also on the rise. More and more articles describe its use in surgery of the thyroid, parathyroid and adrenal glands, although the series are still modest in size and protocols have not been standardized. There are currently several developing areas for the application of fluorescence in endocrine surgery, including the use of fluorescence with indocyanine green in adrenal gland surgery, the identification and prediction of parathyroid perfusion with indocyanine green, and autofluorescence of the parathyroid glands. The objective of this article is to review the current applications of fluorescence in endocrine surgery

Comparative analysis of the bacterial diversity in a lab-scale moving bed biofilm reactor (MBBR) applied to treat urban wastewater under different operational conditions.

Different types of carriers were tested as support material in a lab-scale moving bed biofilm reactor (MBBR) used to treat urban wastewater under three different conditions of hydraulic retention time (HRT) and carrier filling ratios (FR). The bacterial diversity developed on the biofilms responsible of the treatment was studied using a cultivation-independent approach based on the polymerase chain reaction-temperature gradient gel electrophoresis technique (PCR-TGGE). Cluster analysis of TGGE fingerprints showed significant differences of community structure dependent upon the different operational conditions applied. Redundancy analysis (RDA) was used to determine the relationship between the operational conditions (type of carrier, HRT, FR) and bacterial biofilm diversity, demonstrating a significant effect of FR=50%. Phylogenetic analysis of PCR-reamplified and sequenced TGGE bands revealed that the prevalent Bacteria populations in the biofilm were related to Betaproteobacteria (46%), Firmicutes (34%),Alphaproteobacteria (14%) and Gammaproteobacteria (9%).

The crystal structure of a TIR domain from Arabidopsis thaliana reveals a conserved helical region unique to plants.

Plants use a highly evolved immune system to exhibit defense response against microbial infections. The plant TIR domain, together with the nucleotide-binding (NB) domain and/or a LRR region, forms a type of molecule, named resistance (R) proteins, that interact with microbial effector proteins and elicit hypersensitive responses against infection. Here, we report the first crystal structure of a plant TIR domain from Arabidopsis thaliana (AtTIR) solved at a resolution of 2.0 A. The structure consists of five beta-strands forming a parallel beta-sheet at the core of the protein. The beta-strands are connected by a series of alpha-helices and the overall fold mimics closely that of other mammalian and bacterial TIR domains. However, the region of the alphaD-helix reveals significant differences when compared with other TIR structures, especially the alphaD3-helix that corresponds to an insertion only present in plant TIR domains. Available mutagenesis data suggest that several conserved and exposed residues in this region are involved in the plant TIR signaling function.

Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain.

Macrophages detect pathogen infection via the activation of their plasma membrane-bound Toll-like receptor proteins (TLRs). The heterotypic interaction between the Toll/interleukin-1 receptor (TIR) domains of TLRs and adaptor proteins, like Myeloid differentiation primary response gene 88 (MyD88), is the first intracellular step in the signaling pathway of the mammalian innate immune response. The hetero-oligomerization of the TIRs of the receptor and adaptor brings about the activation of the transcription factor NF-kappaB, which regulates the synthesis of pro-inflammatory cytokines. Here, we report the first crystal structure of a bacterial TIR domain solved at 2.5 A resolution. The three-dimensional fold of Paracoccus denitrificans TIR is identical to that observed for the TIR of human TLRs and MyD88 proteins. The structure shows a unique dimerization interface involving the DD-loop and EE-loop residues, whereas leaving the BB-loop highly exposed. Peptide amide hydrogen-deuterium exchange mass spectrometry also reveals that the same region is used for dimerization in solution and in the context of the full-length protein. These results, together with a functional interaction between P. denitrificans TIR and MyD88 visualized in a co-immunoprecipitation assay, further substantiate the model that bacterial TIR proteins adopt structural mimicry of the host active receptor TIR domains to interfere with the signaling of TLRs and their adaptors to decrease the inflammatory response.

Human-murine transthyretin heterotetramers are kinetically stable and non-amyloidogenic. A lesson in the generation of transgenic models of diseases involving oligomeric proteins.

The transthyretin amyloidoses appear to be caused by rate-limiting tetramer dissociation and partial monomer unfolding of the human serum protein transthyretin, resulting in aggregation and extracellular deposition of amorphous aggregates and amyloid fibrils. Mice transgenic for few copies of amyloid-prone human transthyretin variants, including the aggressive L55P mutant, failed to develop deposits. Silencing the murine transthyretin gene in the presence of the L55P human gene resulted in enhanced tissue deposition. To test the hypothesis that the murine protein interacted with human transthyretin, preventing the dissociation and partial unfolding required for amyloidogenesis, we produced recombinant murine transthyretin and human/murine transthyretin heterotetramers and compared their structures and biophysical properties to recombinant human transthyretin. We found no significant differences between the crystal structures of murine and human homotetramers. Murine transthyretin is not amyloidogenic because the native homotetramer is kinetically stable under physiologic conditions and cannot dissociate into partially unfolded monomers, the misfolding and aggregation precursor. Heterotetramers composed of murine and human subunits are also kinetically stable. These observations explain the lack of transthyretin deposition in transgenics carrying a low copy number of human transthyretin genes. The incorporation of mouse subunits into tetramers otherwise composed of human amyloid-prone transthyretin subunits imposes kinetic stability, preventing dissociation and subsequent amyloidogenesis.

Canonical and alternative MAPK signaling.

The archetype of MAPK cascade activation is somewhat challenged by the most recent discovery of unexpected phosphorylation patterns, alternative activation mechanisms and sub-cellular localization, in various members of this protein kinase family. In particular, activation by autophosphorylation pathways has now been described for the three best understood MAPK subgroups: ERK1/2; JNK1/2 and p38 alpha/beta. Also, a form of dosage compensation between homologs has been shown to occur in the case of ERK1/2 and JNK1/2. In this paper we summarize the MAPK activation pathway, with an emphasis on non-canonical examples. We use this information to propose a model for MAPK signal transduction that considers a cross-talk between MAPKs with different activation loop sequence motifs and unique C-terminal extensions. We highlight the occurrence of non-canonical substrate specificity during MAPK auto-activation, in strong connection with MAPK homo- and hetero-dimerization events.

Characterization of a TIR-like protein from Paracoccus denitrificans.

Based on protein sequence homology searches, we found a conserved open reading frame within the genome of several human pathogenic bacteria showing a resemblance to the mammalian TIR domain. We cloned, expressed, and characterized the corresponding gene product from Paracoccus denitrificans using several biophysical techniques. The protein consists of two independently folded domains. As predicted from the amino acid sequence and experimentally confirmed here, the N-terminal domain consists of a alpha-helical coiled-coil. The NMR data indicates that the C-terminal TIR-like domain folds into a compact protein. Finally, using GST pull-down experiments, we show that the bacteria TIR-like domain binds to the mammalian receptor (TLR4) and adaptor (MyD88) TIR domains. We postulate that prokaryotic pathogens utilize the TIR-like proteins to interfere with the innate immune response of the mammalian host so that the bacterial infection can progress undetected.