Search

Objective: To evaluate whether changes in central venous pressure during fluid expansion and baseline cyclic respiratory variation in the central venous pressure amplitude (RespCVP) curve could be used to discriminate between fluid responders and nonresponders., Methods: This prospective observational study included critically ill adult patients who underwent fluid expansion in the form of a fluid bolus or fluid challenge with crystalloids. All patients were under mechanical ventilation and adequately sedated. We determined the central venous pressure at baseline (CVPT0) and the changes at 5 (ΔCVPT5), 10 (ΔCVPT10) and 15 (ΔCVPT15) minutes during fluid infusion. We also measured the RespCVP at baseline. Fluid responsiveness was defined as a cardiac index increase of ≥ 15%., Results: The study included 30 patients (11 responders and 19 nonresponders). The CVPT0 and the changes after a fluid challenge at all three time points did not adequately predict fluid responsiveness, as determined by their area under the curve values (CVPT0: 0.70, (95%CI: 0.49 - 0.90; ΔCVPT5: 0.78, (95%CI: 0.57 - 0.99; ΔCVPT10: 0.63, (95%CI: 0.39 - 0.88; ΔCVPT15: 0.68, ((95%CI: 0.45 - 0.92). The RespCVP at baseline also had a poor performance (area under the curve: 0.70; 95%CI: 0.50 - 0.91)., Conclusion: Changes in central venous pressure have limited value in predicting fluid responsiveness.

Deep learning methods, trained on the increasing set of available protein 3D structures and sequences, have substantially impacted the protein modeling and design field. These advancements have facilitated the creation of novel proteins, or the optimization of existing ones designed for specific functions, such as binding a target protein. Despite the demonstrated potential of such approaches in designing general protein binders, their application in designing immunotherapeutics remains relatively underexplored. A relevant application is the design of T cell receptors (TCRs). Given the crucial role of T cells in mediating immune responses, redirecting these cells to tumor or infected target cells through the engineering of TCRs has shown promising results in treating diseases, especially cancer. However, the computational design of TCR interactions presents challenges for current physics-based methods, particularly due to the unique natural characteristics of these interfaces, such as low affinity and cross-reactivity. For this reason, in this study, we explored the potential of two structure-based deep learning protein design methods, ProteinMPNN and ESM-IF1, in designing fixed-backbone TCRs for binding target antigenic peptides presented by the MHC through different design scenarios. To evaluate TCR designs, we employed a comprehensive set of sequence- and structure-based metrics, highlighting the benefits of these methods in comparison to classical physics-based design methods and identifying deficiencies for improvement., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Ribeiro-Filho et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Inguinal lymph node dissection plays an important role in the management of melanoma, penile and vulval cancer. Inguinal lymph node dissection is associated with various intraoperative and postoperative complications with significant heterogeneity in classification and reporting. This lack of standardization challenges efforts to study and report inguinal lymph node dissection outcomes. The aim of this study was to devise a system to standardize the classification and reporting of inguinal lymph node dissection perioperative complications by creating a worldwide collaborative, the complications and adverse events in lymphadenectomy of the inguinal area (CALI) group., Methods: A modified 3-round Delphi consensus approach surveyed a worldwide group of experts in inguinal lymph node dissection for melanoma, penile and vulval cancer. The group of experts included general surgeons, urologists and oncologists (gynaecological and surgical). The survey assessed expert agreement on inguinal lymph node dissection perioperative complications. Panel interrater agreement and consistency were assessed as the overall percentage agreement and Cronbach's α., Results: Forty-seven experienced consultants were enrolled: 26 (55.3%) urologists, 11 (23.4%) surgical oncologists, 6 (12.8%) general surgeons and 4 (8.5%) gynaecology oncologists. Based on their expertise, 31 (66%), 10 (21.3%) and 22 (46.8%) of the participants treat penile cancer, vulval cancer and melanoma using inguinal lymph node dissection respectively; 89.4% (42 of 47) agreed with the definitions and inclusion as part of the inguinal lymph node dissection intraoperative complication group, while 93.6% (44 of 47) agreed that postoperative complications should be subclassified into five macrocategories. Unanimous agreement (100%, 37 of 37) was achieved with the final standardized classification system for reporting inguinal lymph node dissection complications in melanoma, vulval cancer and penile cancer., Conclusion: The complications and adverse events in lymphadenectomy of the inguinal area classification system has been developed as a tool to standardize the assessment and reporting of complications during inguinal lymph node dissection for the treatment of melanoma, vulval and penile cancer., (© The Author(s) 2024. Published by Oxford University Press on behalf of BJS Foundation Ltd.)

Diverse proteomics-based strategies have been applied to saliva to quantitatively identify diagnostic and prognostic targets for oral cancer. Considering that these targets may be regulated by events that do not imply variation in protein abundance levels, we hypothesized that changes in protein conformation can be associated with diagnosis and prognosis, revealing biological processes and novel targets of clinical relevance. For this, we employed limited proteolysis-mass spectrometry in saliva samples to explore structural alterations, comparing the proteome of healthy control and oral squamous cell carcinoma (OSCC) patients with and without lymph node metastasis. Thirty-six proteins with potential structural rearrangements were associated with clinical patient features including transketolase and its interacting partners. Moreover, N -glycosylated peptides contribute to structural rearrangements of potential diagnostic and prognostic markers. Altogether, this approach utilizes saliva proteins to search for targets for diagnosing and prognosing oral cancer and can guide the discovery of potential regulated sites beyond protein-level abundance.

Background: Hansen's disease is a chronic, infectious and transmissible disease that is considered a public health problem in Brazil. Hansen's disease is marked by stigma and prejudice, because it carries with it a strong negative social image, reinforced by policies of social isolation in the community., Methods: A qualitative study was conducted in Ribeirão Preto, an inland city of the state of São Paulo, Brazil. Eleven patients under treatment for the disease were interviewed. The interviews were audio recorded and transcribed in full, then were analyzed through the stages of transcription, transposition and reconstitution, as informed by concepts proposed by Goffman., Results: The results showed that the marks of stigma are still present in the twenty-first century and were presented in two axes: 'Stigma and work for the person affected by Hansen's disease' and 'The experience of stigma in the family'. The participants refer to fears of losing their jobs and of being ridiculed, which stops them talking about the disease. Regarding their families, the participants reported episodes of discrimination, the creation of family secrets and fear of relatives' reactions., Conclusions: All these aspects interfere in the follow-up and treatment of patients and need to be considered and welcomed by health professionals. It is recommended that these aspects are addressed in the initial training and continuing education of health professionals., Contexte: La maladie de Hansen est une maladie chronique, infectieuse et transmissible, considérée comme un problème de santé publique au Brésil. La maladie de Hansen est marquée par la stigmatisation et les préjugés, car elle véhicule une image sociale fortement négative, renforcée par des politiques d'isolement social au sein de la communauté., Méthodes: Étude qualitative menée à Ribeirão Preto, une ville intérieure de l'État de São Paulo, au Brésil. Onze patients traités pour la maladie ont été interrogés. Les entretiens ont été enregistrés et transcrits intégralement, et ont été analysés en suivant les étapes de transcription, de transposition et de reconstitution, selon les concepts proposés par Goffman., Résultats: Les résultats montrent que les marques de la stigmatisation sont toujours présentes au 21ème siècle et ont été présentées selon deux axes : 'La stigmatisation et le travail pour la personne affectée par la maladie de Hansen' et 'L'expérience de la stigmatisation dans la famille'. Les participants évoquent la peur de perdre leur emploi, la peur d'être ridiculisés, ce qui les pousse à ne pas parler de la maladie. En ce qui concerne les familles, les participants ont rapporté des épisodes de discrimination, la création de secrets de famille et la peur des réactions des proches., Conclusions: Tous ces aspects interfèrent dans le suivi et le traitement des patients et doivent être pris en compte et accueillis par les professionnels de la santé. Il est recommandé que ces aspects soient abordés dans la formation initiale et la formation continue des professionnels de la santé., Antecedentes: La enfermedad de Hansen es una enfermedad crónica, infecciosa y transmisible, considerada un problema de salud pública en Brasil. La enfermedad de Hansen está marcada por el estigma y el prejuicio, ya que conlleva una fuerte imagen social negativa, reforzada por políticas de aislamiento social en la comunidad., Métodos: Estudio cualitativo realizado en Ribeirão Preto, una ciudad del interior del estado de São Paulo, Brasil. Se entrevistaron a once pacientes en tratamiento para la enfermedad. Las entrevistas fueron grabadas en audio, transcritas en su totalidad y analizadas a través de etapas de transcripción, transposición y reconstitución, según los conceptos propuestos por Goffman., Resultados: Los resultados muestran que las marcas del estigma siguen presentes en el siglo XXI y se presentaron en dos ejes: 'Estigma y trabajo para la persona afectada por la enfermedad de Hansen' y 'La experiencia del estigma en la familia'. Los participantes mencionan el miedo a perder sus trabajos, el temor a ser ridiculizados, lo que les impide comentar sobre la enfermedad. En cuanto a las familias, los participantes reportaron episodios de discriminación, la creación de secretos familiares y el miedo a las reacciones de los familiares., Conclusiones: Todos estos aspectos interfieren en el seguimiento y tratamiento de los pacientes y deben ser considerados y acogidos por los profesionales sanitarios. Se recomienda abordar estos aspectos en la formación inicial y la educación continua de los profesionales sanitarios., (© The Author(s) 2024. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.)

Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: a RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.

Urethral reconstruction is an important area of expertise for urologists. The buccal mucosa is considered the best option when urethral grafting is necessary, although in some cases, it is inappropriate or needs to be optimized to repair a given stricture. Therefore, developing innovative procedures and evaluating their putative success in experimental models is crucial to fit the clinical need. With this goal, this study describes a protocol in which urethral stricture was induced by electrocautery in Wistar rats. Urethral reconstruction was performed 1 week later with a buccal mucosa graft, harvested from the lower lip, and placed in a ventral onlay fashion. A retrograde urethrogram showed a significant improvement in urethral diameter after urethroplasty compared to the respective value after stricture induction. Additionally, the graft placement was assessed by blood perfusion analysis using laser Doppler. As expected, a dark blue area corresponded to the non-vascularized buccal mucosa graft. This procedure can successfully simulate the normal pathophysiological process of urethral injury and tissue modulation, as well as urethral reconstruction using a buccal mucosa graft in a reproducible manner, and serve as the basis for future research based on tissue engineering or urethral grafts.

The Hippo pathway plays central roles in relaying mechanical signals during development and tumorigenesis, but how the proteostasis of the Hippo kinase MST2 is regulated remains unknown. Here, we found that chemical inhibition of proteasomal proteolysis resulted in increased levels of MST2 in human breast epithelial cells. MST2 binds SCF βTrCP E3 ubiquitin ligase and silencing βTrCP resulted in MST2 accumulation. Site-directed mutagenesis combined with computational molecular dynamics studies revealed that βTrCP binds MST2 via a non-canonical degradation motif. Additionally, stiffer extracellular matrix, as well as hyperactivation of integrins resulted in enhanced MST2 degradation mediated by integrin-linked kinase (ILK) and actomyosin stress fibers. Our study uncovers the underlying biochemical mechanisms controlling MST2 degradation and underscores how alterations in the microenvironment rigidity regulate the proteostasis of a central Hippo pathway component., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Michele Pagano reports a relationship with Coho Therapeutics that includes: equity or stocks. Michele Pagano reports a relationship with CullGen that includes: board membership. Michele Pagano reports a relationship with Kymera Therapeutics that includes: board membership. Michele Pagano reports a relationship with SEED Therapeutics that includes: board membership. Michele Pagano reports a relationship with Santi Therapeutics that includes: consulting or advisory. M.P. is a consultant for and has financial interests in Coho Therapeutics, CullGen, Kymera Therapeutics, and SEED Therapeutics. M.P. is a cofounder of Coho Therapeutics, is on the SAB of CullGen and Kymera Therapeutics, and is a consultant for Santi Therapeutics. The other authors declare no competing interests., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, 1 H-STD and 15 N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target., (© 2022. The Author(s).)

The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we show that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein., Competing Interests: The authors have declared that no competing interests exist.

Coronavirus disease 2019 (Covid-19) is an emerging novel respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that rapidly spread worldwide. In addition to lung injury, Covid-19 patients may develop extrapulmonary symptoms, including cardiac, liver, kidney, digestive tract, and neurological injuries. Angiotensin converting enzyme 2 is the major receptor for the entry of SARS-CoV-2 into host cells. The specific mechanisms that lead to cell death in different tissues during infection by SARS-CoV-2 remains unknown. Based on data of the previous human coronavirus SARS-CoV together with information about SARS-CoV-2, this review provides a summary of the mechanisms involved in cell death, including apoptosis, autophagy, and necrosis, provoked by severe acute respiratory syndrome coronavirus., (© 2021 John Wiley & Sons Ltd.)

The aim of the present investigation was to evaluate the efficacy of an antibacterial coating of implant-abutment prosthetic junctions by real time measurement of Volatile Organic Compounds (VOCs). A total of 20 patients and 40 internal prosthetic junction implants were evaluated in the present investigation: 20 fixtures with antibacterial internal coating (Test) and 20 without treatment (Control). The VOCs measurements were evaluated at the baseline (T 0 ) after the cover unit unscrewing, after 7 days (T 1 ) and at 14 days (T 2 ). No significant difference were detected at T0 (baseline), as Test and Control groups showed a VOCs max peak mean respectively of 2.15 ± 0.71 and 2.21 ± 0.69 ( p > 0.05). At T 1 and T 2 as significant difference between the Test and Control Groups was detected ( p < 0.01). At T2 the Test max peak was 2.29 ± 0.73 and the Control was 3.65 ± 0.91 ( p < 0.01). The antibacterial internal coating demonstrated the capacity to prevent microbial VOCS activity at the level of the implant internal chamber and could be useful for long-term peri-implant tissue health., (© 2021 The Author(s). Published by BRI.)

Background: Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and computational methods. In this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated data structures. To fulfill this need, we developed pyKVFinder, a Python package to detect and characterize cavities in biomolecular structures for data science and automated pipelines., Results: pyKVFinder efficiently detects cavities in biomolecular structures and computes their volume, area, depth and hydropathy, storing these cavity properties in NumPy arrays. Benefited from Python ecosystem interoperability and data structures, pyKVFinder can be integrated with third-party scientific packages and libraries for mathematical calculations, machine learning and 3D visualization in automated workflows. As proof of pyKVFinder's capabilities, we successfully identified and compared ADRP substrate-binding site of SARS-CoV-2 and a set of homologous proteins with pyKVFinder, showing its integrability with data science packages such as matplotlib, NGL Viewer, SciPy and Jupyter notebook., Conclusions: We introduce an efficient, highly versatile and easily integrable software for detecting and characterizing biomolecular cavities in data science applications and automated protocols. pyKVFinder facilitates biostructural data analysis with scripting routines in the Python ecosystem and can be building blocks for data science and drug design applications., (© 2021. The Author(s).)

Erectile dysfunction (ED) impacts a significant portion of the aging male population. Standard treatments such as oral medications, intracavernosal injections, intraurethral suppositories, vacuum erection aids, and penile prosthesis placement have stood the test of time. Recently, there has been a growing interest in the concept of regenerative medicine with the goal of restoring or renewing functional tissue. Low intensity shock wave therapy (LiSWT) is one example of a regenerative therapy. A strong body of basic science data suggests that shockwaves, when applied to local tissue, will encourage blood vessel and nerve regeneration. Clinical evidence supports the use of LiSWT to treat conditions ranging from ischemic heart disease, musculoskeletal injuries, and even chronic non-healing wounds. LiSWT is also being used to treat male sexual dysfunction conditions such as Peyronie's Disease and ED. The first studied application of LiSWT for ED was published in 2010. Since then multiple randomized, sham-controlled trials have sought to evaluate outcomes for this novel therapy in men with vasculogenic ED. Additionally, several meta-analyses are available with pooled data suggesting that LiSWT results in a significantly greater improvement in erectile function relative to sham-control. Despite these promising findings, the current body of literature is marred by significant heterogeneity relating to treatment protocols, patient populations, and follow-up duration. Further work is necessary to determine optimal device technologies, patient characteristics, and treatment duration prior to considering LiSWT as standard of care for men with ED., Competing Interests: Conflicts of Interest: The authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/tau-20-1286). The series “Controversies and Considerations of Penile Surgery” was commissioned by the editorial office without any funding or sponsorship. The authors have no other conflicts of interest to declare., (2021 Translational Andrology and Urology. All rights reserved.)

Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular "handshake" between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity.

Lateral cylinder extrusion is a potential complication of penile prosthesis implantation. Several methods have been proposed for repairing this complication. We present a case where a cylinder re-routing technique, first described by Dr. John Mulcahy, was used and a revision of the literature.

Background/aims: Sacral neuromodulation (SNM) is a well-established treatment in several urinary and bowel dysfunctions, nevertheless its role on sexual dysfunction remains unclear. We evaluate the impact of SNM on sexual function and its association with age at SNM, functional diagnosis and post-void residual urine (PVR) before SNM., Methods: Patients who had SNM were retrospectively analyzed. Sexual function was assessed before and after treatment with the International Index of Erectile Function (IIEF-5) for men and the Female Sexual Function Index (FSFI) for women. IIEF-5 and FSFI were also associated with age at SNM, functional diagnosis, and PVR., Results: Fifteen females and 9 males, with a median age of 41 years (26-72 years), median follow-up 20.7 months (2-53 months) were enrolled. IIEF-5 improved in 4 patients (p = 0.06), and FSFI total score in 5 (p = 0.2). There was significant association between functional diagnosis and FSFI total score (p = 0.05), and FSFI specific domains of arousal (p = 0.03), lubrication (p = 0.04), and satisfaction (p = 0.03), with significant improvement showed in patients with detrusor overactivity with impaired contractility., Conclusion: Although gains observed in IIEF-5 and FSFI were modest, our preliminary results show that SNM may have favorable impact on sexual function., (Copyright © 2019 by S. Karger AG, Basel.)

Objective: Low-intensity shock-wave treatment (LiSWT) is a therapy for erectile dysfunction (ED) with good results reported in the literature. The aim of this study was to evaluate the results of LiSWT on patients treated for ED and the influence of ED duration in treatment outcomes., Material and Methods: We performed an open-label single-arm prospective study of patients treated with LiSWT for ED. Patients were assessed with the IIEF-5 at baseline and at six weeks and three months after LiSWT, and with penile dynamic Doppler ultrasound before treatment and six weeks after. Patients were divided into two groups accordingly to ED evolution time: ≤ 24 months and > 24 months., Results: Twenty-five patients were enrolled, 13 had ED ≤ 24 months and 12 > 24 months. Median baseline IIEF-5 was 14, at 6 weeks post LiSWT was 16 (p < 0.001) and at 3 months post LiSWT was 18 (p < 0.001). Mean baseline peak systolic velocity (PSV) was 29.3 ± 13.0 cm/s, after LiSWT was 35.9 ± 15.2 cm/s (p 0.001). Mean baseline end-diastolic velocity (EDV) was 2.6 ± 4.8 cm/s and after LiSWT was 1.3 ± 4.3 cm/s (p 0.015). No statistical significative difference was identified between the two groups., Conclusions: LiSWT is a safe, harmless and repeatable treatment tool for ED with good outcomes reported. Our results suggest that length of disease duration doesn´t negatively influences treatment results.

Firefly luciferases produce yellow-green light under physiological and alkaline conditions, however at acidic pH, higher temperatures or in the presence of heavy metals the color changes to red, a property called pH-sensitivity. Despite many decades of studies, the proton and metal binding sites responsible for pH-sensitivity remain enigmatic. Previously we suggested that the salt bridge E311/R337 keeps a closed conformation of the luciferin phenolate binding site. Here we further investigated the effect of this salt bridge and mutations of the neighbor residues H310 and E/N354, on metal and pH-sensitivity of firefly luciferases emitting distinct bioluminescence colors (Cratomorphus distinctus: 548 nm; Macrolampis sp2: 569 nm). The substitutions of H310 and E/N354 modulate metal sensitivity, whereas the carboxylate of E311 may work as the catalytic base essential for green bioluminescence and pH-sensitivity. Modeling studies showed that H310, E311 and E354 side-chains coordinate Zinc, constituting the metal binding site and the pH-sensor. Electrostatic potential and pKa calculations suggest that the external couple H310/E354 is affected by pH, whereas E311/R337 make a stabilized internal pair which retains excited oxyluciferin ejected proton near its phenolate group into a high energy state, promoting yellow-green bioluminescence. Protonation or metal binding weaken these electrostatic gates and their ability to retain the excited oxyluciferin released proton near its phenolate, promoting red light emission.

Background: The aim of this randomized controlled clinical trial was to compare the efficacy of two different techniques for maxillary sinus augmentation using a lateral window approach: Heterologous cortical lamina without any grafting material versus 100% collagenated granular collagen porcine bone., Methods: Twenty-three healthy patients with not relevant past medical history (14 women and 9 men, non-smokers, mean age 52 years, range 48⁻65 years) were included. In Group I, the sinus was filled with collagen porcine bone (Geno-os, OsteoBiol, Turin, Italy) and a collagen membrane (Evolution, OsteoBiol, Turin, Italy) was used to close the lateral window of the sinus. In Group II, the sinus was treated with heterologous cortical lamina only (Lamina, OsteoBiol, Turin, Italy)., Results: There was a statistically significant difference in the surgical time required to complete the augmentation procedures: 18.3 ± 2.1 min for lamina treated sites versus 12.5 ± 3.1 min for porcine bone treated sites. In Group I, the mean volume of the graft was 3101 ± 321 mm³ in the immediate postoperative examination (5⁻7 days), while after a six-month healing period it was 2716.7 ± 432 mm³., Conclusion: This study demonstrates that the use of heterologous cortical lamina is a valid technique for the mechanical support of sinus membranes resulting in only bone tissue formation and not mixed with the graft. The graft material was biocompatible and not completely resorbed after six months, although the remains were integrated into the bone.

Purpose: Post-operative pain and swelling are frequently observed after sinus lift procedures. The aim of the present study was the clinical evaluation of swelling and pain of two different sinus flap lift techniques using a visual analogue scale (VAS), verbal rating scale (VRS), and infrared thermal imaging (i.e., thermography). Materials Methods : A randomized controlled trial was conducted with 15 patients (30 sinuses in total) randomly allocated into two groups. For the sinuses of Group I a trapezoidal flap was used, while for Group II a modified triangular flap without anterior release was utilized. Postoperative pain was scored by means of a 100-mm VAS ranging from 0 (no pain) to 100 (worst pain imaginable), and was recorded at 2, 4, 6 and 14 days after surgery. Swelling was recorded by a verbal rating scale (VRS) and was classified into four categories: a score of 1 referred the absence of swelling, patients with intra-oral swelling in the surgical zone scored 2, any extra-oral swelling in the surgical zone scored 3, and intense swelling exhibited by extra-oral swelling extending beyond the surgical zone scored 4. The facial temperature was recorded before and after sinus augmentation, and at 2, 4, 6, and 14 days post-surgery to check the course of healing. Results : In Group I pain intensity was recorded at 2 days after surgery with a mean score of 38.67 ± 6.4 mm. Swelling was greater at 2 and 4 days, and was absent at day 6. The facial temperature difference before and after the procedure was 4.737 &deg;C ± 0.37. In Group II the pain score were lower than in Group I ( p < 0.05). The score for swelling was 2 on the first and second days, and was reduced on day 4. After the second day the difference in temperature was significantly reduced as compared to the day of surgery (0.77 &deg;C); at 2 and 4 days no difference was registered. Conclusions : The results of this clinical study show the significant effectiveness of the modified triangular flap in the sinus lift procedure for reducing pain and swelling.

Solidago chilensis Meyen (Asteraceae) is a medicinal important plant with few studies on nutrition and metabolism and none information on cadmium phytotoxicity. The objective of this study was to investigate Cd induced responses on the growth and metabolism in S. chilensis and on arbuscular mycorrhiza (AM). The experiment was carried out in a greenhouse, consisting of a 5 × 4 factorial with five doses of manure (0, 3.5, 7, 14 and 21gdm -3 ) and four doses of cadmium (0, 25, 50 and 75mgdm -3 ) applied to a Dystrophic Ultisol. After 250 days of plant cultivation, biomass, nutrient content, photosynthetic rate, guaiacol peroxidase activity, mycorrhizal colonization, glomalin content, anatomical and ultrastucture were evaluated. Plants were significantly affected by interaction of manure and Cd doses with anatomical, ultrastructural, physiological and nutritional modifications. Manure applied into Cd contaminated soil significantly improved mycorrhizal colonization and glomalin production. The highest organic manure dose (21gdm -3 ) alleviated toxicity symptoms of Cd on S. chilensis., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Objective: To present a case of a bilateral synchronous testicular seminoma in a young male clinical stage IIB., Material and Method: A 37 years old man presented a bilateral testicular mass with elevated tumoral markers. Histology of frozen section revealed bilateral seminoma and bilateral radical orchiectomy was performed., Result: Enhanced chest and abdominopelvic staging CT scan revealed a lymphadenopathy of 30 mm within the inter-aortocava nodal chain (stage IIB). Patient received three cycles of BEP. Three months later 18F-FDG PET showed no evidence of hypermetabolic activity and serum tumoral markers were normal., Conclusion: Bilateral testicular germ cell tumors are a rare disease. Management of this tumors is controversial. Bilateral radical orchiectomy is the standard of care, nevertheless, in order to preserve fertility and androgen production, an organsparing surgery can be attempted in selected cases. Although prognosis is good, with overall survival rates similar to patients with unilateral disease, life-long close follow-up may be advocated due to relapse risk.

Objective: To present a case of a Hutch bladder diverticulum containing the ureteral opening., Material and Methods: An 83-year-old man presented a giant bladder diverticulum causing obstructive azotemia due to bilateral ureteral compression. Endoscopy revealed an unusual and potentially harmful anatomical alteration: the left ureteral orifice was inside in the diverticulum. Despite bladder emptying, the diverticulum remained full, causing bilateral ureteral compression. The patient underwent diverticulectomy with ureteroneocystostomy., Result: Post-operative follow-up showed renal and voiding functions restoration., Conclusion: Although clinical watching is a valid option in patients with Hutch diverticulum, reconstructive surgical approach, especially when complications are present, should be the standard of care.

Purpose: The presence of a microgap between implant and abutment could produce a bacterial reservoir which could interfere with the long-term health of the periimplant tissues. The aim of this article was to evaluate, by x-ray 3-dimensional microtomography, implant-abutment contact surfaces and microgaps at the implant-abutment interface in different types of implant-abutment connections., Materials and Methods: A total of 40 implants were used in this in vitro study. Ten implants presented a screw-retained internal hexagon abutment (group I), 10 had a Morse Cone taper internal connection (group II), 10 another type of Morse Cone taper internal connection (group III), and 10 had a screwed trilobed connection (group IV)., Results: In both types of Morse Cone internal connections, there was no detectable separation at the implant-abutment in the area of the conical connection, and there was an absolute congruity without any microgaps between abutment and implant. No line was visible separating the implant and the abutment. On the contrary, in the screwed abutment implants, numerous gaps and voids were present., Conclusions: The results of this study support the hypothesis that different types of implant-abutment joints are responsible for the observed differences in bacterial penetration.

In contrast to the Mendelian inheritance model, parental alleles can contribute unequally to gene expression, which may result in phenotypic variance among individuals and bias in the predicted additive effect of molecular markers associated with production traits. Given the need to understand the effects of allelic variation and parent-of-origin effects on the expression of genes with a commercial interest in cattle, we analyzed the expression of KCNJ11 (potassium inwardly rectifying channel, subfamily J, member 11), which was previously described as a functional candidate gene for meat tenderness. Allele-specific and parent-of-origin-dependent expression of this gene were assessed in bovine muscle using the rs379610823 single nucleotide polymorphism as a reference. Biallelic expression was observed; however, the T allele was expressed at significantly higher levels than the C allele. Furthermore, increased expression of KCNJ11 was found in animals harboring the maternal T allele. This study is the first to describe the differential allelic expression of bovine KCNJ11. Our findings are important for understanding the mechanisms that underlie the pattern of KCNJ11 expression and its potential impact on the phenotypic variation of meat tenderness in Nelore beef cattle. This reinforces the need for further investigation of allelic- and parent-of-origin expression deviation in genetic markers eligible for the selection of target traits., Competing Interests: The authors declare no conflict of interest.

Iron (Fe) is an essential mineral for metabolism and plays a central role in a range of biochemical processes. Therefore, this study aimed to identify differentially expressed (DE) genes and metabolic pathways in Longissimus dorsi (LD) muscle from cattle with divergent iron content, as well as to investigate the likely role of these DE genes in biological processes underlying beef quality parameters. Samples for RNA extraction for sequencing and iron, copper, manganese, and zinc determination were collected from LD muscles at slaughter. Eight Nelore steers, with extreme genomic estimated breeding values for iron content (Fe-GEBV), were selected from a reference population of 373 animals. From the 49 annotated DE genes (FDR<0.05) found between the two groups, 18 were up-regulated and 31 down-regulated for the animals in the low Fe-GEBV group. The functional enrichment analyses identified several biological processes, such as lipid transport and metabolism, and cell growth. Lipid metabolism was the main pathway observed in the analysis of metabolic and canonical signaling pathways for the genes identified as DE, including the genes FASN, FABP4, and THRSP, which are functional candidates for beef quality, suggesting reduced lipogenic activities with lower iron content. Our results indicate metabolic pathways that are partially influenced by iron, contributing to a better understanding of its participation in skeletal muscle physiology.

Sepsis, a leading cause of death worldwide, involves exacerbated proinflammatory responses and inefficient bacterial clearance. Phagocytic cells play a crucial part in the prevention of sepsis by clearing bacteria through host innate receptors. Here, we used a phage display library to identify two peptides in Escherichia coli that interact with host innate receptors. One of these peptides, encoded by the wzxE gene of E. coli K-12, was involved in the transbilayer movement of a trisaccharide-lipid intermediate in the assembly of enterobacterial common antigen. Peptide-receptor interactions induced CD16-mediated inhibitory immunoreceptor tyrosine-based activating motif signaling, blocking the production of ROS and bacterial killing. This CD16-mediated inhibitory signaling was abrogated in a WzxE(-/-) mutant of E. coli K-12, restoring the production of ROS and bacterial killing. Taken together, the two novel CD16 ligands identified negatively regulate bacterial killing and inflammation. Our findings may contribute toward the development of new immunotherapies for E. coli-mediated infectious diseases and inflammation., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Feed efficiency and carcass characteristics are late-measured traits. The detection of molecular markers associated with them can help breeding programs to select animals early in life, and to predict breeding values with high accuracy. The objective of this study was to identify polymorphisms in the functional and positional candidate gene NEUROD1 (neurogenic differentiation 1), and investigate their associations with production traits in reference families of Nelore cattle. A total of 585 steers were used, from 34 sires chosen to represent the variability of this breed. By sequencing 14 animals with extreme residual feed intake (RFI) values, seven single nucleotide polymorphisms (SNPs) in NEUROD1 were identified. The investigation of marker effects on the target traits RFI, backfat thickness (BFT), ribeye area (REA), average body weight (ABW), and metabolic body weight (MBW) was performed with a mixed model using the restricted maximum likelihood method. SNP1062, which changes cytosine for guanine, had no significant association with RFI or REA. However, we found an additive effect on ABW (P ≤ 0.05) and MBW (P ≤ 0.05), with an estimated allele substitution effect of -1.59 and -0.93 kg0.75, respectively. A dominant effect of this SNP for BFT was also found (P ≤ 0.010). Our results are the first that identify NEUROD1 as a candidate that affects BFT, ABW, and MBW. Once confirmed, the inclusion of this SNP in dense panels may improve the accuracy of genomic selection for these traits in Nelore beef cattle as this SNP is not currently represented on SNP chips.

Psychrophilic enzymes evolved from a plethora of structural scaffolds via multiple molecular pathways. Elucidating their adaptive strategies is instrumental to understand how life can thrive in cold ecosystems and to tailor enzymes for biotechnological applications at low temperatures. In this work, we used X-ray crystallography, in solution studies and molecular dynamics simulations to reveal the structural basis for cold adaptation of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. We discovered that the selective pressure of low temperatures favored mutations that redesigned the protein surface, reduced the number of salt bridges, exposed more hydrophobic regions to the solvent and gave rise to a tetrameric arrangement not found in mesophilic and thermophilic homologues. As a result, some solvent-exposed regions became more flexible in the cold-adapted tetramer, likely contributing to enhance enzymatic activity at cold environments. The tetramer stabilizes the native conformation of the enzyme, leading to a 10-fold higher activity compared to the disassembled monomers. According to phylogenetic analysis, diverse adaptive strategies to cold environments emerged in the GH1 family, being tetramerization an alternative, not a rule. These findings reveal a novel strategy for enzyme cold adaptation and provide a framework for the semi-rational engineering of β-glucosidases aiming at cold industrial processes.

Despite the efforts of pharmaceutical companies to develop specific kinase modulators, few drugs targeting kinases have been completely successful in the clinic. This is primarily due to the conserved nature of kinases, especially in the catalytic domains. Consequently, many currently available inhibitors lack sufficient selectivity for effective clinical application. Kinases phosphorylate their substrates to modulate their activity. One of the important steps in the catalytic reaction of protein phosphorylation is the correct positioning of the target residue within the catalytic site. This positioning is mediated by several regions in the substrate binding site, which is typically a shallow crevice that has critical subpockets that anchor and orient the substrate. The structural characterization of this protein-protein interaction can aid in the elucidation of the roles of distinct kinases in different cellular processes, the identification of substrates, and the development of specific inhibitors. Because the region of the substrate that is recognized by the kinase can be part of a linear consensus motif or a nonlinear motif, advances in technology beyond simple linear sequence scanning for consensus motifs were needed. Cost-effective bioinformatics tools are already frequently used to predict kinase-substrate interactions for linear consensus motifs, and new tools based on the structural data of these interactions improve the accuracy of these predictions and enable the identification of phosphorylation sites within nonlinear motifs. In this Review, we revisit kinase-substrate interactions and discuss the various approaches that can be used to identify them and analyze their binding structures for targeted drug development., (Copyright © 2016, American Association for the Advancement of Science.)

Psoriasis is a chronic and recurrent dermatitis, mediated by keratinocytes and T cells. Several proinflammatory cytokines contribute to formation and maintenance of psoriatic plaque. The Th1/Th17 pathways and some of IL-1 family members were involved in psoriasis pathogenesis and could contribute to disease activity. Therefore, we sought to analyse skin transcript levels of IL17A, IL22, RORC, IL8, IFNG, IL33, IL36A, FOXP3, and IL10 and correlate with clinic of patients with plaque-type psoriasis. In order to conduct that, we collected punch biopsies from lesional skin and obtained tissue RNA. After reverse transcription, qRT-PCR quantified the relative mRNA expression. The main results revealed increased transcripts levels of IL17A, IFNG, and FOXP3 in moderate-severe patients. Despite this, only IL17A can increase the chance to worsen disease severity. We also observed many significant positive correlations between each transcript. In conclusion, IL17A is elevated in lesional skin from psoriasis patients and plays crucial role in disease severity., Competing Interests: All authors declare no conflict of interests.

Hypoxia-inducible transcription factors (HIF) form heterodimeric complexes that mediate cell responses to hypoxia. The oxygen-dependent stability and activity of the HIF-α subunits is traditionally associated to post-translational modifications such as hydroxylation, acetylation, ubiquitination, and phosphorylation. Here we report novel evidence showing that unsaturated fatty acids are naturally occurring, non-covalent structural ligands of HIF-3α, thus providing the initial framework for exploring its exceptional role as a lipid sensor under hypoxia.

Chromatin is the major regulator of gene expression and genome maintenance. Proteins that bind the nucleosome, the repetitive unit of chromatin, and the histone H4 tail are critical to establishing chromatin architecture and phenotypic outcomes. Intriguingly, nucleosome-binding proteins (NBPs) and the H4 tail peptide compete for the same binding site at an acidic region on the nucleosome surface. Although the essential facts about the nucleosome were revealed 17 years ago, new insights into its atomic structure and molecular mechanisms are still emerging. Several complex nucleosome:NBP structures were recently revealed, characterizing the NBP-binding sites on the nucleosome surface. Here we discuss the potential of the nucleosome surface as a therapeutic target and the impact and development of exogenous nucleosome-binding molecules (eNBMs)., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Background: The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why exactly the canonical code was selected among this huge number of possible genetic codes. Many researchers argue that the organization of the canonical code is a product of natural selection and that the code's robustness against mutations would support this hypothesis. In order to investigate the natural selection hypothesis, some researches employ optimization algorithms to identify regions of the genetic code space where best codes, according to a given evaluation function, can be found (engineering approach). The optimization process uses only one objective to evaluate the codes, generally based on the robustness for an amino acid property. Only one objective is also employed in the statistical approach for the comparison of the canonical code with random codes. We propose a multiobjective approach where two or more objectives are considered simultaneously to evaluate the genetic codes., Results: In order to test our hypothesis that the multiobjective approach is useful for the analysis of the genetic code adaptability, we implemented a multiobjective optimization algorithm where two objectives are simultaneously optimized. Using as objectives the robustness against mutation with the amino acids properties polar requirement (objective 1) and robustness with respect to hydropathy index or molecular volume (objective 2), we found solutions closer to the canonical genetic code in terms of robustness, when compared with the results using only one objective reported by other authors., Conclusions: Using more objectives, more optimal solutions are obtained and, as a consequence, more information can be used to investigate the adaptability of the genetic code. The multiobjective approach is also more natural, because more than one objective was adapted during the evolutionary process of the canonical genetic code. Our results suggest that the evaluation function employed to compare genetic codes should consider simultaneously more than one objective, in contrast to what has been done in the literature.

Human Neks are a conserved protein kinase family related to cell cycle progression and cell division and are considered potential drug targets for the treatment of cancer and other pathologies. We screened the activation loop mutant kinases hNek1 and hNek2, wild-type hNek7, and five hNek6 variants in different activation/phosphorylation statesand compared them against 85 compounds using thermal shift denaturation. We identified three compounds with significant Tm shifts: JNK Inhibitor II for hNek1(Δ262-1258)-(T162A), Isogranulatimide for hNek6(S206A), andGSK-3 Inhibitor XIII for hNek7wt. Each one of these compounds was also validated by reducing the kinases activity by at least 25%. The binding sites for these compounds were identified by in silico docking at the ATP-binding site of the respective hNeks. Potential inhibitors were first screened by thermal shift assays, had their efficiency tested by a kinase assay, and were finally analyzed by molecular docking. Our findings corroborate the idea of ATP-competitive inhibition for hNek1 and hNek6 and suggest a novel non-competitive inhibition for hNek7 in regard to GSK-3 Inhibitor XIII. Our results demonstrate that our approach is useful for finding promising general and specific hNekscandidate inhibitors, which may also function as scaffolds to design more potent and selective inhibitors.

Psoriasis is a chronic inflammatory skin disease characterized by alterations in cytokines produced by both Th1 and Th17 pathways. The aim of this study was to evaluate serum levels of pivotal cytokines and correlate them with clinical parameters. Serum samples from 53 psoriasis patients and 35 healthy volunteers, matched by the proportion of sex and age ratios, were collected for ELISA cytokine detection. Psoriasis Area and Severity Index (PASI) was assessed at the time of sampling in psoriasis patients. Our findings demonstrate that IL-17A, IL-22, and IL-6 serum concentrations were significantly higher in psoriasis patients than in the control group. No statistical correlation could be found between cytokines concentrations, PASI score, and age in this study. Although our results do not show any correlation between serum levels of IL-17A, IL-22, and IL-6 and disease activity, the present study confirms that they were increased in Brazilian psoriasis patients in comparison to healthy volunteers.

The aim of this case report was to describe the surgical sequence of crown lengthening to apically reposition the dentogingival complex, in addition to an esthetic restorative procedure. Many different causes can be responsible for short clinical crown. In these cases, the correct execution of a restorative or prosthetic rehabilitation requires an increasing of the crown length. According to the 2003 American Academy of Periodontology (Practice Profile Survey), crown lengthening is the most habitual surgical periodontal treatment.

Xanthomonas pathogens attack a variety of economically relevant plants, and their xylan CUT system (carbohydrate utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, xynA and xynB, which influence biofilm formation and virulence by molecular mechanisms that are still elusive. Herein, we demonstrated that XynA is a rare reducing end xylose-releasing exo-oligoxylanase and not an endo-β-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the β7-α7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan, and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-β-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB proved to be a classical endo-β-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell wall barrier, providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses., (© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.)

Linear consensus motifs are short contiguous sequences of residues within a protein that can form recognition modules for protein interaction or catalytic modification. Protein kinase specificity and the matching of kinases to substrates have been mostly defined by phosphorylation sites that occur in linear consensus motifs. However, phosphorylation can also occur within sequences that do not match known linear consensus motifs recognized by kinases and within flexible loops. We report the identification of Thr(253) in α-tubulin as a site that is phosphorylated by protein kinase C βI (PKCβI). Thr(253) is not part of a linear PKC consensus motif. Instead, Thr(253) occurs within a region on the surface of α-tubulin that resembles a PKC phosphorylation site consensus motif formed by basic residues in different parts of the protein, which come together in the folded protein to form the recognition motif for PKCβI. Mutations of these basic residues decreased substrate phosphorylation, confirming the presence of this "structurally formed" consensus motif and its importance for the protein kinase-substrate interaction. Analysis of previously reported protein kinase A (PKA) and PKC substrates identified sites within structurally formed consensus motifs in many substrates of these two kinase families. Thus, the concept of consensus phosphorylation site motif needs to be expanded to include sites within these structurally formed consensus motifs., (Copyright © 2014, American Association for the Advancement of Science.)

Background: Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology., Results: Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7., Conclusions: Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.

Background: The characterization of protein binding sites is a major challenge in computational biology. Proteins interact with a wide variety of molecules and understanding of such complex interactions is essential to gain deeper knowledge of protein function. Shape complementarity is known to be important in determining protein-ligand interactions. Furthermore, these protein structural features have been shown to be useful in assisting medicinal chemists during lead discovery and optimization., Results: We developed KVFinder, a highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometry-based method that has an innovative customization of the search space. This feature provides the possibility of cavity segmentation, which alongside with the large set of customizable parameters, allows detailed cavity analyses. Although the main focus of KVFinder is the steered prospection of cavities, we tested it against a benchmark dataset of 198 known drug targets in order to validate our software and compare it with some of the largely accepted methods. Using the one click mode, we performed better than most of the other methods, staying behind only of hybrid prospection methods. When using just one of KVFinder's customizable features, we were able to outperform all other compared methods. KVFinder is also user friendly, as it is available as a PyMOL plugin, or command-line version., Conclusion: KVFinder presents novel usability features, granting full customizable and highly detailed cavity prospection on proteins, alongside with a friendly graphical interface. KVFinder is freely available on http://lnbio.cnpem.br/bioinformatics/main/software/.

The mechanism of alternative splicing in the transcriptome may increase the proteome diversity in eukaryotes. In proteomics, several studies aim to use protein sequence repositories to annotate MS experiments or to detect differentially expressed proteins. However, the available protein sequence repositories are not designed to fully detect protein isoforms derived from mRNA splice variants. To foster knowledge for the field, here we introduce SpliceProt, a new protein sequence repository of transcriptome experimental data used to investigate for putative splice variants in human proteomes. Current version of SpliceProt contains 159 719 non-redundant putative polypeptide sequences. The assessment of the potential of SpliceProt in detecting new protein isoforms resulting from alternative splicing was performed by using publicly available proteomics data. We detected 173 peptides hypothetically derived from splice variants, which 54 of them are not present in UniprotKB/TrEMBL sequence repository. In comparison to other protein sequence repositories, SpliceProt contains a greater number of unique peptides and is able to detect more splice variants. Therefore, SpliceProt provides a solution for the annotation of proteomics experiments regarding splice isofoms. The repository files containing the translated sequences of the predicted splice variants and a visualization tool are freely available at http://lbbc.inca.gov.br/spliceprot., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Cerato-platanins (CP) are small, cysteine-rich fungal-secreted proteins involved in the various stages of the host-fungus interaction process, acting as phytotoxins, elicitors, and allergens. We identified 12 CP genes (MpCP1 to MpCP12) in the genome of Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, and showed that they present distinct expression profiles throughout fungal development and infection. We determined the X-ray crystal structures of MpCP1, MpCP2, MpCP3, and MpCP5, representative of different branches of a phylogenetic tree and expressed at different stages of the disease. Structure-based biochemistry, in combination with nuclear magnetic resonance and mass spectrometry, allowed us to define specialized capabilities regarding self-assembling and the direct binding to chitin and N-acetylglucosamine (NAG) tetramers, a fungal cell wall building block, and to map a previously unknown binding region in MpCP5. Moreover, fibers of MpCP2 were shown to act as expansin and facilitate basidiospore germination whereas soluble MpCP5 blocked NAG6-induced defense response. The correlation between these roles, the fungus life cycle, and its tug-of-war interaction with cacao plants is discussed.

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.