Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda).

The infraorder Anomura is a species-rich clade of decapod crustaceans recognized by its remarkable disparity in terms of morphology, anatomy, ecology, physiology, and behavior. This study assembled and characterized the complete mitochondrial genomes of two anomuran species, the hermit crab Coenobita clypeatus and the mole crab Emerita talpoida. The AT-rich mitochondrial genomes of C. clypeatus and E. talpoida are 16,469 bp and 15,810 bp long, respectively, and are composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 1,390 bp and 553 bp long intergenic space is assumed to be the D-loop in C. clypeatus and E. talpoida, respectively. Mitochondrial synteny in C. clypeatus is identical to that reported in other congeneric hermit crabs while synteny in E. talpoida is identical to that described for the confamilial mole crab Stemonopa insignis. No major differences occur between the studied species and their respective congeneric / cofamilial species in terms of nucleotide composition and codon usage profiles of PCGs. Selective pressure analysis in PCGs, rarely conducted in anomuran crabs, indicate that all these mitochondrial PCGs experience purifying selection and that this purifying selection is stronger in some (i.e., cox family genes and cob) compared to other PCGs (e.g., atp8). Most of the tRNA genes exhibited a typical 'cloverleaf' secondary structure with few exceptions in the two studied species. In C. clypeatus, tRNA-Ser1 lacks the thymine pseudouracil cytosine (TΨC) loop while tRNA-Phe and tRNA-Tyr each exhibit a deletion of the dihydroxyuridine (DHU) loop but not the arm. In turn, in E. talpoida, tRNA-Phe and tRNA-Arg exhibit a deletion of the DHU loop but not the arm while tRNA-Ser1 lacks the TΨC arm. A phylogenomic analysis based on translated PCGs confirms the monophyly of the infraorder Anomura and retrieves most/all relationships at the superfamily and family level previously reported for anomurans. The analysis supports the monophyletic status of the families Albuneidae, Lithodidae, Coenobitidae, and Porcellanidae. In turn, the superfamily Paguroidea, and the families Paguridae and Diogenidae are polyphyletic.

Methylation in the CHH Context Allows to Predict Recombination in Rice.

DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics.

Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA.

The early DNA damage induced by ionizing radiation depends on how ionizing particles transfer energy to this molecule and the surrounding medium, mostly water. In preliminary studies, we found that the energy transferred by a 4 keV proton to a cytosine-guanine base pair in a classical simulation collision using the ReaxFF potential is much smaller than that obtained by a quantum calculation using time-dependent density functional theory (TDDFT). We observed that there are two main reasons for that: no accurate force-field for this situation and problems while dealing with the proton charge during the collision. Here, we only focus on the interaction potential. We calibrated the van der Waals energy term of the ReaxFF potential using TDDFT calculations and a genetic algorithm, specifically for the interaction of a proton with the DNA constituent atoms (carbon, hydrogen, phosphorus, nitrogen, and oxygen). We obtained a significant improvement in the interaction potential and, consequently, in the scattering angle of the proton colliding with the target atoms in question. However, we conclude that despite the improvement for the force-field and scattering angle, the classical charge equilibration method should also be improved to properly describe the proton-DNA collision process.

Solvent effects on the NMR shieldings of stacked DNA base pairs.

Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).

Cytosine base editing enables quadruple-edited allogeneic CART cells for T-ALL.

Allogeneic chimeric antigen receptor T-cell (CART) therapies require multiple gene edits to be clinically tractable. Most allogeneic CARTs have been created using gene editing techniques that induce DNA double-stranded breaks (DSBs), resulting in unintended on-target editing outcomes with potentially unforeseen consequences. Cytosine base editors (CBEs) install C•G to T•A point mutations in T cells, with between 90% and 99% efficiency to silence gene expression without creating DSBs, greatly reducing or eliminating undesired editing outcomes following multiplexed editing as compared with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). Using CBE, we developed 7CAR8, a CD7-directed allogeneic CART created using 4 simultaneous base edits. We show that CBE, unlike CRISPR-Cas9, does not impact T-cell proliferation, lead to aberrant DNA damage response pathway activation, or result in karyotypic abnormalities following multiplexed editing. We demonstrate 7CAR8 to be highly efficacious against T-cell acute lymphoblastic leukemia (T-ALL) using multiple in vitro and in vivo models. Thus, CBE is a promising technology for applications requiring multiplexed gene editing and can be used to manufacture quadruple-edited 7CAR8 cells, with high potential for clinical translation for relapsed and refractory T-ALL.

Modeling the heating and cooling of a chromophore after photoexcitation.

The heating of a chromophore due to internal conversion and its cooling down due to energy dissipation to the solvent are crucial phenomena to characterize molecular photoprocesses. In this work, we simulated the ab initio nonadiabatic dynamics of cytosine, a prototypical chromophore undergoing ultrafast internal conversion, in three solvents-argon matrix, benzene, and water-spanning an extensive range of interactions. We implemented an analytical energy-transfer model to analyze these data and extract heating and cooling times. The model accounts for nonadiabatic effects, and excited- and ground-state energy transfer, and can analyze data from any dataset containing kinetic energy as a function of time. Cytosine heats up in the subpicosecond scale and cools down within 25, 4, and 1.3 ps in argon, benzene, and water, respectively. The time constants reveal that a significant fraction of the benzene and water heating occurs while cytosine is still electronically excited.

Methyl-CpG binding proteins (MBD) family evolution and conservation in plants.

DNA methylation is an epigenetic mechanism that acts on cytosine residues. The methyl-CpG-binding domain proteins (MBD) are involved in the recognition of methyl-cytosines by activating a signaling cascade that induces the formation of heterochromatin or euchromatin, thereby regulating gene expression. In this study, we analyzed the evolution and conservation of MBD proteins in plants. First, we performed a genome-wide identification and analysis of the MBD family in common bean and soybean, since they have experienced one and two whole-genome duplication events, respectively. We found one pair of MBD paralogs in soybean (GmMBD2) has subfunctionalized after their recent divergence, which was corroborated with their expression profile. Phylogenetic analysis revealed that classes of MBD proteins clustered with human MBD. Interestingly, the MBD9 may have emerged after the hexaploidization event in eudicots. We found that plants and humans share a great similarity in MBDs' binding affinity in the mCpG context. MBD2 and MBD4 from different plant species have the conserved four amino acid residues -Arg (R), Asp (D), Tyr (Y) and Arg (R)- reported to be responsible for MBD-binding in the mCpG. However, MBD8, MBD9, MBD10, and MBD11 underwent substitutions in these residues, suggesting the non-interaction in the mCpG context, but a heterochromatin association as MBD5 and MBD6 from human. This study represents the first genome-wide analysis of the MBD gene family in eurosids I - soybean and common bean. The data presented here contribute towards understanding the evolution of MBDs proteins in plants and their specific binding affinity on mCpG site.

Inter- and Intramolecular Proton Transfer in an Isolated (Cytosine-Guanine)H+ Pair: Direct Evidence from IRMPD Spectroscopy.

The collision-induced dissociation of the protonated cytosine-guanine pair was studied using tandem mass spectrometry (MS3) coupled to infrared multiple photon dissociation spectroscopy with the free electron laser at Orsay (CLIO) to determine the structure of the CH+ and GH+ ionic fragments. The results were rationalized with the help of electronic structure calculations at the density functional theory level with the B3LYP/6-311++G(3df,2p) method. Several tautomers of each fragment were identified for the first time, some of which were previously predicted by other authors. In addition, two unexpected and minor tautomers were also found: cytosine keto-imino [CKI(1,2,3,4)H+] and guanine keto-amino [GKA(1,3,7)H+]. These results highlight the importance of the DNA base tautomerization assisted by inter- and intramolecular proton or hydrogen transfer within the protonated pairs.

CRISPR-mediated base editing in mice using cytosine deaminase base editor 4

BACKGROUND: Many human genetic diseases arise from point mutations. These genetic diseases can theoretically be corrected through gene therapy. However, gene therapy in clinical application is still far from mature. Nearly half of the pathogenic single-nucleotide polymorphisms (SNPs) are caused by G:C>A:T or T:A>C:G base changes and the ideal approaches to correct these mutations are base editing. These CRISPR-Cas9-mediated base editing does not leave any footprint in genome and does not require donor DNA sequences for homologous recombination. These base editing methods have been successfully applied to cultured mammalian cells with high precision and efficiency, but BE4 has not been confirmed in mice. Animal models are important for dissecting pathogenic mechanism of human genetic diseases and testing of base correction efficacy in vivo. Cytidine base editor BE4 is a newly developed version of cytidine base editing system that converts cytidine (C) to uridine (U). RESULTS: In this study, BE4 system was tested in cells to inactivate GFP gene and in mice to introduce single-base substitution that would lead to a stop codon in tyrosinase gene. High percentage albino coat-colored mice were obtained from black coat-colored donor zygotes after pronuclei microinjection. Sequencing results showed that expected base changes were obtained with high precision and efficiency (56.25%). There are no off-targeting events identified in predicted potential off-target sites. CONCLUSIONS: Results confirm BE4 system can work in vivo with high precision and efficacy, and has great potentials in clinic to repair human genetic mutations.

Prenatal Lead (Pb) Exposure and Peripheral Blood DNA Methylation (5mC) and Hydroxymethylation (5hmC) in Mexican Adolescents from the ELEMENT Birth Cohort.

BACKGROUND: Gestational lead (Pb) exposure can adversely affect offspring health through multiple mechanisms, including epigenomic alterations via DNA methylation (5mC) and hydroxymethylation (5hmC), an intermediate in oxidative demethylation. Most current methods do not distinguish between 5mC and 5hmC, limiting insights into their individual roles. OBJECTIVE: Our study sought to identify the association of trimester-specific (T1, T2, T3) prenatal Pb exposure with 5mC and 5hmC levels at multiple cytosine-phosphate-guanine sites within gene regions previously associated with prenatal Pb (HCN2, NINJ2, RAB5A, TPPP) in whole blood leukocytes of children ages 11-18 years of age. METHODS: Participants from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) birth cohorts were selected (n=144) for pyrosequencing analysis following oxidative or standard sodium bisulfite treatment. This workflow directly quantifies total methylation (5mC+5hmC) and 5mC only; 5hmC is estimated by subtraction. RESULTS: Participants were 51% male, and mean maternal blood lead levels (BLL) were 6.43±5.16µg/dL in Trimester 1 (T1), 5.66±5.21µg/dL in Trimester 2 (T2), and 5.86±4.34µg/dL in Trimester 3 (T3). In addition, 5hmC levels were calculated for HCN2 (mean±standard deviation(SD), 2.08±4.18%), NINJ2 (G/C: 2.01±5.95; GG: 0.90±3.97), RAB5A (0.66±0.80%), and TPPP (1.11±6.67%). Furthermore, 5mC levels were measured in HCN2 (81.3±9.63%), NINJ2 (heterozygotes: 38.6±7.39%; GG homozygotes: 67.3±9.83%), RAB5A (1.41±1.21%), and TPPP (92.5±8.03%). Several significant associations between BLLs and 5mC/5hmC were identified: T1 BLLs with 5mC in HCN2 (ß=-0.37, p=0.03) and 5hmC in NINJ2 (ß=0.49, p=0.003); T2 BLLs with 5mC in HCN2 (ß=0.37, p=0.03) and 5hmC in NINJ2 (ß=0.27, p=0.008); and T3 BLLs with 5mC in HCN2 (ß=0.50, p=0.01) and NINJ2 (ß=-0.35, p=0.004) and 5hmC in NINJ2 (ß=0.45, p<0.001). NINJ2 5mC was negatively correlated with gene expression (Pearson r=-0.5, p-value=0.005), whereas 5hmC was positively correlated (r=0.4, p-value=0.04). DISCUSSION: These findings suggest there is variable 5hmC in human whole blood and that prenatal Pb exposure is associated with gene-specific 5mC and 5hmC levels at adolescence, providing evidence to consider 5hmC as a regulatory mechanism that is responsive to environmental exposures. https://doi.org/10.1289/EHP8507.

A New Approach to Identify the Methylation Sites in the Control Region of Mitochondrial DNA.

Mitochondrial DNA (mtDNA) methylation has the potential to be used as a biomarker of human development or disease. However, mtDNA methylation procedures are costly and time-consuming. Therefore, we developed a new approach based on an RT-PCR assay for the base site identification of methylated cytosine in the control region of mtDNA through a simple, fast, specific, and low-cost strategy. Total DNA was purified, and methylation was determined by RT-PCR bisulfite sequencing. This procedure included the DNA purification, bisulfite treatment and RT-PCR amplification of the control region divided into three subregions with specific primers. Sequences obtained with and without the bisulfite treatment were compared to identify the methylated cytosine dinucleotides. Furthermore, the efficiency of C to U conversion of cytosines was assessed by including a negative control. Interestingly, mtDNA methylation was observed mainly within non-Cphosphate- G (non-CpG) dinucleotides and mostly in the regions containing regulatory elements, such as OH or CSBI, CSBII, and CSBIII. This new approach will promote the generation of new information regarding mtDNA methylation patterns in samples from patients with different pathologies or that are exposed to a toxic environment in diverse human populations.

CAG Repeat Size Influences the Progression Rate of Spinocerebellar Ataxia Type 3.

OBJECTIVE: In spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD), the expanded cytosine adenine guanine (CAG) repeat in ATXN3 is the causal mutation, and its length is the main factor in determining the age at onset (AO) of clinical symptoms. However, the contribution of the expanded CAG repeat length to the rate of disease progression after onset has remained a matter of debate, even though an understanding of this factor is crucial for experimental data on disease modifiers and their translation to clinical trials and their design. METHODS: Eighty-two Dutch patients with SCA3/MJD were evaluated annually for 15 years using the International Cooperative Ataxia Rating Scale (ICARS). Using linear growth curve models, ICARS progression rates were calculated and tested for their relation to the length of the CAG repeat expansion and to the residual age at onset (RAO): The difference between the observed AO and the AO predicted on the basis of the CAG repeat length. RESULTS: On average, ICARS scores increased 2.57 points/year of disease. The length of the CAG repeat was positively correlated with a more rapid ICARS progression, explaining 30% of the differences between patients. Combining both the length of the CAG repeat and RAO as comodifiers explained up to 47% of the interpatient variation in ICARS progression. INTERPRETATION: Our data imply that the length of the expanded CAG repeat in ATXN3 is a major determinant of clinical decline, which suggests that CAG-dependent molecular mechanisms similar to those responsible for disease onset also contribute to the rate of disease progression in SCA3/MJD. ANN NEUROL 2021;89:66-73.

Does Oral Hygiene Influence Salivary pH, Lactate, and IL-1β of Basketball Players During Intense Exercise? / La Higiene Oral Influye en el pH Salival, el Lactato y la IL-1β de los Jugadores de Baloncesto Durante el Ejercicio Intenso?

ABSTRACT: This study examined the salivary pH, salivary lactate, and salivary IL-1 β responses from a high-intensity intermittent running test, and the influence of hygiene oral status on these biomarkers in elite adolescent basketball players. Forty-six adolescent players participated. Saliva sampling was taken before and 3 min after a high-intensity exercise (Yo-Yo Intermittent Recovery Test Level 1; Yo-Yo IR1). In order to quantify and classify the oral hygiene level, the athletes were submitted to a dental examination, and an adapted Simplified Oral Hygiene Index was applied. After the dental examination, the whole group was divided into good oral hygiene group (GHG) and poor oral hygiene group (PHG). The results of a two- way analysis of variance showed a significant interaction effect (P = 0.0003), group effect (P < 0.0001), and time effect (pre to post Yo-yo IR1; P < 0.0001) for salivary pH and for salivary lactate (interaction effect, P = 0.008; group effect, P < 0.000 1; time effect, P < 0.0001) with a lower salivary pH and a higher salivary lactate at pre and post-Yo-Yo IR1 for PHG, but no difference was observed for IL-1β. The data demonstrated that the high-intensity exercise led to a significant change in salivary pH and salivary lactate concentration of the basketball players, and that the oral hygiene status influenced these responses, with a greater change for those players showing a poor oral hygiene.

RESUMEN: Este estudio examinó las respuestas de pH salival, lactato salival e IL-1β salival de una prueba de carrera intermitente de alta intensidad, y la influencia del estado de higiene oral en los biomarcadores en jugadores adolescentes de baloncesto de élite. En el análisis participaron 46 jugadores adolescentes. Se tomó una muestra de saliva antes y 3 minutos después de un ejercicio de alta intensidad (Prueba de recuperación intermitente Yo-Yo Nivel 1; Yo-Yo IR1). Para cuantificar y clasificar el nivel de higiene oral, los atletas fueron sometidos a un examen dental y se aplicó un índice adaptado de higiene oral simplificado. Después del examen dental, el grupo se dividió en un grupo de buena higiene oral (GHG) y un grupo de mala higiene oral (PHG). Los resultados de un análisis de varianza mostraron un efecto de interacción significativo (P = 0.0003), efecto de grupo (P<0.0001) y efecto de tiempo (antes y después de Yo-yo IR1; P <0.0001) para el pH salival y para lactato salival (efecto de interacción, P = 0.008; efecto de grupo, P <0.0001; efecto de tiempo, P <0.0001) con pH salival más bajo y lactato salival más alto en IR1 pre y post YoY para PHG, pero no se observó una diferencia para IL-1β. Los datos demostraron que el ejercicio de alta intensidad genera un cambio significativo en el pH salival y el lactato de los jugadores de baloncesto, y que el estado de higiene oral influyó en estas respuestas, con un cambio mayor para aquellos jugadores que mostraron una mala higiene oral.

Nanogap-based all-electronic DNA sequencing devices using MoS2 monolayers.

The realization of nanopores in atom-thick materials may pave the way towards electrical detection of single biomolecules in a stable and scalable manner. In this work, we theoretically study the potential of different phases of MoS2 nanogaps to act as all-electronic DNA sequencing devices. We carry out simulations based on density functional theory and the non-equilibrium Green's function formalism to investigate the electronic transport across the device. Our results suggest that the 1T'-MoS2 nanogap structure is energetically more favorable than its 2H counterpart. At zero bias, the changes in the conductance of the 1T'-MoS2 device can be well distinguished, making possible the selectivity of the DNA nucleobases. Although the conductance fluctuates around the resonances, the overall results suggest that it is possible to distinguish the four DNA bases for energies close to the Fermi level.

Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes.

Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.

Effect of the Electric Field on DNA Bases as Pigments for Nanodevices: A First-Principles Study.

In this work we used Density Functional Theory to simulate the molecular electronics behavior of the nitrogenous bases of human DNA under electric field effects. The results can describe some internal effects in the use of DNA-based as photoconductor or semiconductor nanodevices. For this investigation, calculations were performed to predict structural deformations, HOMO and LUMO orbitals, and thermodynamic properties of each one of the following nitrogenous bases: adenine, thymine, guanine and cytosine. All the quantities were calculated as functions of the electric field. This analysis allows us to verify the influence of the electric field in the molecular geometry of nitrogenous bases, enabling us to determine that adenine, thymine and guanine are those bases most susceptible to presenting substantial deformations when DNA is submitted to the action of an external electric field, while the molecular structure of cytosine is highly resistant to this effect.

Avaliação dos níveis solúveis de sTIM-3, s4-1BB e de citocinas inflamatórias em mulheres com câncer de mama triplo negativo localmente avançado submetidas a quimioterapia neoadjuvante / Evaluation of soluble levels of sTIM-3, s4-1BB and inflammatory cytokines in women with locally advanced triple negative breast cancer submitted to neoadjuvant chemotherapy

Introdução: O câncer de mama triplo negativo (CMTN) corresponde de 10 a 20% dos carcinomas invasivos de mama, é altamente agressivo e na maioria das vezes tem apenas a quimioterapia padrão como tratamento. As citocinas inflamatórias são um grupo heterogêneo de proteínas solúveis produzidas por diferentes tipos de células, que medeiam e regulam o sistema imune. A resposta imune celular é regulada por proteínas acessórias denominadas receptores co-estimuladores e co-inibidores, como 4-1BB e TIM-3, respectivamente. A procura por biomarcadores que possam predizer resposta à quimioterapia neoadjuvante (QT neo) ainda é um desafio na medicina. Objetivo: Avaliar os níveis solúveis de sTIM-3 e s4-1BB, e de citocinas inflamatórias no sangue de mulheres com câncer de mama triplo negativo localmente avançado e associá-los à sobrevida livre de doença e com o tipo de resposta patológica à QT neo. Métodos: O estudo foi realizado entre os anos de 2015 e 2017 no Hospital de Câncer de Pernambuco (HCP) e Laboratório de Pesquisa Translacional do Instituto de Medicina Integral Prof. Fernando Figueira (IMIP). Foram incluídas 29 mulheres, entre 18 e 60 anos de idade, com diagnóstico de CMTN localmente avançado e submetidas à QT neo, e um grupo de 30 mulheres saudáveis. Coletas de sangue periférico foram realizadas antes e após a QT neo. A dosagem dos níveis solúveis de s4-1BB e sTIM-3 foi realizada por enzyme linked immunonoSorbent assay (ELISA). As dosagens de IL-1ß, IL-6, IL-8, TNF-α e IL-10 foram realizadas pela técnica de Cytometric Bead Array por citometria de fluxo. O nível de significância estatística foi de p<0,05. Resultados: Níveis mais elevados de IL-6 e de IL-10 foram observados no grupo de pacientes com tumor T4 com relação as grupo T2-T3 (p<0.05). Níveis elevados de IL-6, IL-8, IL-10 e TNF-α no grupo CMTN com status linfonodal N2 versus N0 e N1 (p<0,05). Os níveis de IL-1ß, IL-6, IL-10 e TNF-α foram elevados no grupo com resposta patológica parcial (RP) quando comparado aos grupos com resposta patológica completa (RC) e controles (p<0,05). Com relação aos níveis de IL-8, os grupos de pacientes RC e RP apresentaram níveis elevados quando comparados aos controles (p<0,05). Não foi observada diferença significativa de IL-8 entre os grupos RC e RP. Não foram observadas diferenças significativas em níveis de s4-1BB E sTIM-3 de acordo com o tumor primário e status linfonodal. Elevados níveis de s4-1BB foram observados no grupo RC comparado aos grupos RP e de controles (p<0,0004 e p<0,0001, respectivamente). Da mesma forma, os níveis de sTIM-3 foram mais elevados nas pacientes com RC e RP em relação aos controles (p<0,0001 e p<0,0003, respectivamente). Para análise da sobrevida livre de doença (SLD) em 24 meses de seguimento, utilizamos como ponto de corte o valor da mediana (< ou ≥ percentil 50) dos níveis solúveis de sTIM-3 e s4-1BB. Não houve diferenças significativas na SLD entre os grupos com níveis de s4-1BB ≥ 122 e < 122 pg/mL. A SLD foi de 93,33% no grupo com níveis de sTIM-3 < 2874 pg/mL e de 60% no grupo com níveis ≥ 2874 pg/mL (p=0,03). Conclusão: O s4-1BB foi um bom indicador preditivo de resposta à QT neo, enquanto elevação de sTIM-3 mostrou estar associado ao risco de recidiva loco-regional e metástases à distância. Ambos, TIM-3 e 4-1BB, parecem ser potenciais alvos terapêuticos no CMTN localmente avançado por estarem associadas ao desfecho clínico da doença

Introduction: Triple negative breast cancer (TNBC) corresponds to 10 to 20% of invasive breast carcinoma with high aggressiveness and in most cases has only standard chemotherapy as treatment. Inflammatory cytokines are heterogeneous group of soluble proteins produced by different types of cell, that mediate and regulate the immune system. The cellular immune response is regulated by accessory proteins called co-stimulatory and co-inhibitory receptors, such as 4-1BB and TIM-3, respectively. The search for biomarkers that can predict response to neoadjuvant chemotherapy (NAC) is still a challenge to medicine. Objective: To evaluate the soluble levels of sTIM-3 and s4-1BB, and inflammatory cytokines in the blood of women with locally advanced triple negative breast cancer, and to associate them with disease-free survival and the type of pathological response to NAC. Methods: The study was carried out between the years 2015 and 2017 at the Hospital de Cancer de Pernanbuco (HCP) and Translational Research Laboratory of the Instituto de Medicina Integral Prof. Fernando Figueira (IMIP). Twenty-nine women, between 18 and 60 years old, diagnosed with locally advanced TNBC, and submitted to NAC, and 30 healthy women were included. Peripheral blood samples were taken before and after neo QT. The determination of the soluble levels of s4-1BB and sTIM-3 was performed by enzyme linked immunonosorbent assay (ELISA). The measurements of IL-1ß, IL-6, IL-8, TNF-α and IL-10 were performed using the Cytometric Bead Array by flow cytometry. The level of statistical significance was p <0.05. Results: There were higher levels of IL-6 and IL-10 in the group of patients with tumor size T4 compared to groups T2-T3 (p <0.05). High levels of IL-6, IL8, IL-10 and TNF-α were found in the TNBC group with lymph node status in N2 in relation to N0 and N1 (p <0.05). High levels of IL1ß, IL-6, IL-10 and TNF-α were observed in the group with partial pathological response (PR) when compared to groups with complete pathologial response (RC) and controls (p <0.05). With regard to IL-8 levels, the groups of CR and RP patients showed high levels when compared to controls (p <0.05). There was no significant difference in IL-8 between the CR and PR groups. No significant differences were observed in the levels of s4-1BB and sTIM-3 in accordance with primary tumor and lymph node status. High levels of s4-1BB were observed in the RC group compared to the PR and control groups (p <0.0004 and p <0.0001, respectively). As well, the levels of sTIM-3 were higher in patients with CR and PR compared to controls (p <0.0001 and p <0.0003, respectively). In the analyses of disease-free survival (DFS) with 24 months of follow-up, we used as a cut-off point the median value (< or ≥ 50th percentile) of the soluble levels of sTIM-3 and s4-1BB. There were no significant differences in DFS at 24 months between groups with levels of s4-1BB ≥ 122 and <122 pg/mL. The DFS was 93.33% in the group with sTIM-3 levels <2874 pg/mL and 60% in the group with levels ≥ 2874 pg/mL (p = 0.03). Conclusion: s4-1BB was a good predictive indicator of response to NAC, while elevation of sTIM-3 levels was shown to be associated with the risk of locoregional recurrence and distant metastases. Both TIM-3 and 4-1BB appear to be potential therapeutic targets in locally advanced TNBC because they were associated with the clinical outcome of the disease

Simultaneous recognition of cysteine and cytosine using thiophene-based organic nanoparticles decorated with Au NPs and bio-imaging of cells.

Biomolecules like cysteine and cytosine play a significant role in many physiological processes, and their unusual level in biological systems can lead to many diseases including cancer. Indeed, the need for selective detection of these moieties by a fluorescence probe is imperative. Thus, thiophene based Schiff N,N'-bis(thiophene-2-ylmethylene)thiophenemethane (BMTM) was synthesized and then characterized using several analytical techniques before converting it into organic nanoparticles (ONPs). Then, fluorescent organic inorganic nanohybrids (FONs) were obtained after decorating ONPs with AuNPs to yield BMTM-Au-ONPs (FONPs). The morphology of the particles, analyzed using a Transmission Electron Microscope (TEM), shows that AuNPs were embedded with low density organic matter (ONPs). FONPs were employed to recognize cysteine and cytosine simultaneously. No interference was observed from other moieties such as guanine, uracyl, NADH, NAD, ATP, and adenine during the detection. It means that the intensity of the fluorescence signal was significantly changed (enhanced for cytosine and quenched for cysteine). So, FONPs were used to detect cysteine and cytosine in real samples, like Saccharomyces cerevisiae cells. As expected, no considerable fluorescence signal for cysteine was observed, while for cytosine, strong fluorescence signals were detected in the cells. DFT was used to explain the interaction of FONPs with cysteine or cytosine.

The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.

Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, SmPNP2. Thermofluorescence screening of different ligands suggested cytidine and cytosine are potential ligands. The binding of cytosine and cytidine were confirmed by isothermal titration calorimetry, with a KD of 27 µM for cytosine, and a KM of 76.3 µM for cytidine. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystal structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capacity of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site thus permitting an alternative binding mode for nucleosides, with a 180° rotation from the canonical binding mode. The remarkable plasticity of this binding site enhances our understanding of the correlation between structure and nucleotide selectivity, thus suggesting new ways to analyse PNP activity.

Comparison of the phenolic contents and epigenetic and genetic variability of wild and cultivated watercress (Rorippa nasturtium var. aquaticum L.)

Background: Epigenetic modifications are key factors modulating the expression of genes involved in the synthesis of phytochemicals. The knowledge of plant epigenetic and genetic variations can contribute to enhance the production of bioactive compounds. These issues have been little explored thus far in Rorippa nasturtium var. aquaticum L. (watercress), an edible and medicinal plant. The aim of the current study was to determine and compare the phenolic composition and epigenetic and genetic variations between wild and cultivated watercress. Results: Significant differences were found in the quantitative phenolic composition between wild and cultivated watercress. The eight primer combinations used in the methylation-sensitive amplification polymorphism (MSAP) method revealed different epigenetic status for each watercress type, the cultivated one being the most epigenetically variable. The genetic variability revealed by the EcoRI/MspI amplification profile and also by eight inter-simple sequence repeat (ISSR) primers was different between the two types of watercress. The results of the Mantel test showed that the correlation between genetic and epigenetic variations has diminished in the cultivated type. Cluster analyses showed that the epigenetic and genetic characterizations clearly discriminated between wild and cultivated watercress. Conclusions: Relevant chemical, epigenetic, and genetic differences have emerged between wild and cultivated watercress. These differences can contribute to fingerprint and develop quality control tools for the integral and safety use and the commercialization of watercress. The richness of epialleles could support the development of tools to manipulate the watercress epigenome to develop high bioproduct­producing cultivars