Desorption electrospray ionization and matrix-assisted laser desorption/ionization as imaging approaches for biological samples analysis.

The imaging of biological tissues can offer valuable information about the sample composition, which improves the understanding of analyte distribution in such complex samples. Different approaches using mass spectrometry imaging (MSI), also known as imaging mass spectrometry (IMS), enabled the visualization of the distribution of numerous metabolites, drugs, lipids, and glycans in biological samples. The high sensitivity and multiple analyte evaluation/visualization in a single sample provided by MSI methods lead to various advantages and overcome drawbacks of classical microscopy techniques. In this context, the application of MSI methods, such as desorption electrospray ionization-MSI (DESI-MSI) and matrix-assisted laser desorption/ionization-MSI (MALDI-MSI), has significantly contributed to this field. This review discusses the evaluation of exogenous and endogenous molecules in biological samples using DESI and MALDI imaging. It offers rare technical insights not commonly found in the literature (scanning speed and geometric parameters), making it a comprehensive guide for applying these techniques step-by-step. Furthermore, we provide an in-depth discussion of recent research findings on using these methods to study biological tissues.

Genomic analyses of ciprofloxacin-resistant Neisseria gonorrhoeae isolates recovered from the largest South American metropolitan area.

We sequenced 13 Neisseria gonorrhoeae isolates exhibiting distinct susceptibility profiles and which were recovered over 12 years in the metropolitan region of São Paulo, Brazil. Whole Genome Sequencing (WGS) was performed on an Illumina MiSeq™ 2 × 300 bp paired-end reads. Bioinformatics analyses were carried out using CGE, PATRIC, and BLAST databases for manual curation of obtained genomes. Multilocus sequence typing (MLST) analysis identified seven STs, namely ST1580, ST1590, ST1901, ST1902, ST8161, ST9363, and ST15640. Moreover, a diversity of mutations was observed in MtrR/G45D-A39T, PIB/G120K-A121S, and PBP1/L421P. Mutations associated with sulfonamides (DHPS/R228S) and rifampicin (RNAP/H552N) were also detected, as well as tetracycline resistance determinants, namely rpsJ/V57M and tet(M). The results presented herein can contribute to the knowledge of N. gonorrhoeae strains circulating in Sao Paulo, Brazil.

Detection of Failures in Metal Oxide Surge Arresters Using Frequency Response Analysis.

This work presents an innovative application of Frequency Response Analysis (FRA) in order to detect early degradation of Metal Oxide Surge Arresters (MOSAs). This technique has been widely used in power transformers, but has never been applied to MOSAs. It consists in comparisons of spectra, measured at different instants of the lifetime of the arrester. Differences between these spectra are an indicator that some electrical properties of the arrester have changed. An incremental deterioration test has been performed on arrester samples (with controlled circulation of leakage current, which increases the energy dissipation over the device), and the FRA spectra correctly identified the progression of damage. Although preliminary, the FRA results seemed promising, and it is expected that this technology could be used as another diagnostic tool for arresters.

Influence of Restorative Material on the Distribution of Loads to the Bone in Hybrid Abutment Crowns-In Vitro Study.

Background: The objective of this study was to evaluate the load transmitted to the peri-implant bone by seven different restorative materials in single-unit rehabilitations with morse taper implants using a strain gauge. Materials: In a polyurethane block that simulated type III bone, a morse taper platform implant was installed (3.5 × 11 mm) in the center and 1 mm below the test base surface, and four strain gauges were installed around the implant, simulating the mesial, distal, buccal and lingual positions. Seven similar hybrid abutment crowns were crafted to simulate a lower premolar using different materials: 1-PMMA; 2-glass ceramic over resin matrix; 3-PEEK + lithium disilicate; 4-metal-ceramic; 5-lithium disilicate; 6-zirconia + feldspathic; 7-monolithic zirconia. All groups underwent axial and oblique loads (45 degrees) of 150 N from a universal testing machine. Five measurements (n = 5) were performed with each material and for each load type; the microdeformation data underwent statistical analysis. The data were obtained in microdeformation (µÎµ), and the significance level was set at p ≤ 0.05. Results: There was no statistically significant difference in the evaluation among the materials under either the axial load or the oblique load at 45 degrees. In turn, in the comparison between axial load and oblique load, there was a difference in load for all materials. Conclusion: The restorative material did not influence the load transmitted to the bone. Furthermore, the load transmitted to the bone was greater when it occurred obliquely at 45° regardless of the material used. In conclusion, it appeared that the different elastic modulus of each material did not influence the load transmission to the peri-implant bone.

Randomized Clinical Trial Comparing Insertion Torque and Implant Stability of Two Different Implant Macrogeometries in the Initial Periods of Osseointegration.

Objectives: The present study compared two implants with different macrogeometries placed in healed alveolar sites, evaluating the insertion torque (ITV) and implant stability quotient (ISQ) values at three different periods. Methods: Seventy patients with a total of 100 dental implants were allocated into two groups (n = 50 per group): DuoCone implants (DC group) that included 28 implants in the maxilla and 22 in the mandible, and Maestro implants (MAE group) that included 26 in the maxilla and 24 in the mandible. The ITV was measured during the implant placement, and the ISQ values were measured immediately at implant placement (baseline) and after 30 and 45 days. Results: The mean and standard deviations of the ITV were statistically significant (p < 0.0001), 56.4 ± 6.41 Ncm for the DC group and 29.3 ± 9.65 Ncm for the MAE group. In the DC group, the ISQs ranged between 61.1 ± 3.78 and 69.8 ± 3.86, while the MAE group presented similar values compared with the other group, ranging between 61.9 ± 3.92 and 72.1 ± 2.37. Conclusions: The value of implant insertion torque did not influence the ISQ values measured immediately after implant placement. However, the ITV influenced the ISQ values measured in the two initial periods of osseointegration, with implants installed with lower torques presenting higher ISQ values.

Plasmodium falciparum sexual parasites develop in human erythroblasts and affect erythropoiesis.

Plasmodium falciparum gametocytes, the sexual stage responsible for malaria parasite transmission from humans to mosquitoes, are key targets for malaria elimination. Immature gametocytes develop in the human bone marrow parenchyma, where they accumulate around erythroblastic islands. Notably though, the interactions between gametocytes and this hematopoietic niche have not been investigated. Here, we identify late erythroblasts as a new host cell for P falciparum sexual stages and show that gametocytes can fully develop inside these nucleated cells in vitro and in vivo, leading to infectious mature gametocytes within reticulocytes. Strikingly, we found that infection of erythroblasts by gametocytes and parasite-derived extracellular vesicles delay erythroid differentiation, thereby allowing gametocyte maturation to coincide with the release of their host cell from the bone marrow. Taken together, our findings highlight new mechanisms that are pivotal for the maintenance of immature gametocytes in the bone marrow and provide further insights on how Plasmodium parasites interfere with erythropoiesis and contribute to anemia in malaria patients.

PfGBP2 is a novel G-quadruplex binding protein in Plasmodium falciparum.

Guanine-quadruplexes (G4s) are non-canonical DNA structures that can regulate key biological processes such as transcription, replication and telomere maintenance in several organisms including eukaryotes, prokaryotes and viruses. Recent reports have identified the presence of G4s within the AT-rich genome of Plasmodium falciparum, the protozoan parasite causing malaria. In Plasmodium, potential G4-forming sequences (G4FS) are enriched in the telomeric and sub-telomeric regions of the genome where they are associated with telomere maintenance and recombination events within virulence genes. However, there is a little understanding about the biological role of G4s and G4-binding proteins. Here, we provide the first snapshot of G4-interactome in P. falciparum using DNA pull-down assay followed by LC-MS/MS. Interestingly, we identified ~24 potential G4-binding proteins (G4-BP) that bind to a stable G4FS (AP2_G4). Furthermore, we characterised the role of G-strand binding protein 2 (PfGBP2), a putative telomere-binding protein in P. falciparum. We validated the interaction of PfGBP2 with G4 in vitro as well as in vivo. PfGBP2 is expressed throughout the intra-erythrocytic developmental cycle and is essential for the parasites in the presence of G4-stabilising ligand, pyridostatin. Gene knockout studies showed the role of PfGBP2 in the expression of var genes. Taken together, this study suggests that PfGBP2 is a bona fide G4-binding protein, which is likely to be involved in the regulation of G4-related functions in these malarial parasites. In addition, this study sheds light on this understudied G4 biology in P. falciparum.

Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.

Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We present here a computational approach named DExTER (Domain Exploration To Explain gene Regulation) dedicated to the identification of candidate LREs (cLREs) and apply it to the analysis of the genomes of P. falciparum and other eukaryotes. Our analyses show that all tested genomes contain several cLREs that are somewhat conserved along evolution, and that gene expression can be predicted with surprising accuracy on the basis of these long regions only. Regulation by cLREs exhibits very different behaviours depending on species and conditions. In P. falciparum and other Apicomplexan organisms as well as in Dictyostelium discoideum, the process appears highly dynamic, with different cLREs involved at different phases of the life cycle. For multicellular organisms, the same cLREs are involved in all tissues, but a dynamic behavior is observed along embryonic development stages. In P. falciparum, whose genome is known to be strongly depleted of transcription factors, cLREs are predictive of expression with an accuracy above 70%, and our analyses show that they are associated with both transcriptional and post-transcriptional regulation signals. Moreover, we assessed the biological relevance of one LRE discovered by DExTER in P. falciparum using an in vivo reporter assay. The source code (python) of DExTER is available at https://gite.lirmm.fr/menichelli/DExTER.

Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum.

Post-translational modifications of histone H3 N-terminal tails are key epigenetic regulators of virulence gene expression and sexual commitment in the human malaria parasite Plasmodium falciparum Here, we identify proteolytic clipping of the N-terminal tail of nucleosome-associated histone H3 at amino acid position 21 as a new chromatin modification. A cathepsin C-like proteolytic clipping activity is observed in nuclear parasite extracts. Notably, an ectopically expressed version of clipped histone H3, PfH3p-HA, is targeted to the nucleus and integrates into mononucleosomes. Furthermore, chromatin immunoprecipitation and next-generation sequencing analysis identified PfH3p-HA as being highly enriched in the upstream region of six genes that play a key role in DNA replication and repair: In these genes, PfH3p-HA demarcates a specific 1.5 kb chromatin island adjacent to the open reading frame. Our results indicate that, in P. falciparum, the process of histone clipping may precede chromatin integration hinting at preferential targeting of pre-assembled PfH3p-containing nucleosomes to specific genomic regions. The discovery of a protease-directed mode of chromatin organization in P. falciparum opens up new avenues to develop new anti-malarials.

Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria.

Antigenic variation of the Plasmodium falciparum multicopy var gene family enables parasite evasion of immune destruction by host antibodies. Expression of a particular var subgroup, termed upsA, is linked to the obstruction of blood vessels in the brain and to the pathogenesis of human cerebral malaria. The mechanism determining upsA activation remains unknown. Here we show that an entirely new type of gene silencing mechanism involving an exonuclease-mediated degradation of nascent RNA controls the silencing of genes linked to severe malaria. We identify a novel chromatin-associated exoribonuclease, termed PfRNase II, that controls the silencing of upsA var genes by marking their transcription start site and intron-promoter regions leading to short-lived cryptic RNA. Parasites carrying a deficient PfRNase II gene produce full-length upsA var transcripts and intron-derived antisense long non-coding RNA. The presence of stable upsA var transcripts overcomes monoallelic expression, resulting in the simultaneous expression of both upsA and upsC type PfEMP1 proteins on the surface of individual infected red blood cells. In addition, we observe an inverse relationship between transcript levels of PfRNase II and upsA-type var genes in parasites from severe malaria patients, implying a crucial role of PfRNase II in severe malaria. Our results uncover a previously unknown type of post-transcriptional gene silencing mechanism in malaria parasites with repercussions for other organisms. Additionally, the identification of RNase II as a parasite protein controlling the expression of virulence genes involved in pathogenesis in patients with severe malaria may provide new strategies for reducing malaria mortality.

Temporal evolution of antimicrobial resistance among Neisseria gonorrhoeae clinical isolates in the most populated South American Metropolitan Region.

A total of 124 Neisseria gonorrhoeae isolates recovered during a 12-year period (2003-2015) from outpatients assisted at Centro de Referência e Treinamento DST/AIDS-CRT of São Paulo city, Brazil, were analysed. The following resistance rates were observed: penicillin-59.6%, ciprofloxacin-15.3%, and azithromycin-6.7%. Although reduced susceptibility to these drugs was observed since 2003, no ceftriaxone-resistant isolates were detected. Ciprofloxacin- and azithromycin non-susceptible isolates were grouped in 11 clusters. Mutations were detected in GyrA and ParC of isolates 124 and 260, and a C2611T substitution on 23S rRNA alleles was also observed in isolate 260. Both isolates belonged to ST1901/ST6210 (MSLT/NG-MAST schemes).

First efficient CRISPR-Cas9-mediated genome editing in Leishmania parasites.

Protozoan pathogens that cause leishmaniasis in humans are relatively refractory to genetic manipulation. In this work, we implemented the CRISPR-Cas9 system in Leishmania parasites and demonstrated its efficient use for genome editing. The Cas9 endonuclease was expressed under the control of the Dihydrofolate Reductase-Thymidylate Synthase (DHFR-TS) promoter and the single guide RNA was produced under the control of the U6snRNA promoter and terminator. As a proof of concept, we chose to knockout a tandemly repeated gene family, the paraflagellar rod-2 locus. We were able to obtain null mutants in a single round of transfection. In addition, we confirmed the absence of off-target editions by whole genome sequencing of two independent clones. Our work demonstrates that CRISPR-Cas9-mediated gene knockout represents a major improvement in comparison with existing methods. Beyond gene knockout, this genome editing tool opens avenues for a multitude of functional studies to speed up research on leishmaniasis.

Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.

BACKGROUND: Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of organisms, where these transcripts have been shown to play important roles in the regulation of gene expression. Likewise, the existence of NATs has been observed in Plasmodium but our understanding towards their genome-wide distribution remains incomplete due to the limited depth and uncertainties in the level of strand specificity of previous datasets. RESULTS: To gain insights into the genome-wide distribution of NATs in P. falciparum, we performed RNA-ligation based strand-specific RNA sequencing at unprecedented depth. Our data indicate that 78.3% of the genome is transcribed during blood-stage development. Moreover, our analysis reveals significant levels of antisense transcription from at least 24% of protein-coding genes and that while expression levels of NATs change during the intraerythrocytic developmental cycle (IDC), they do not correlate with the corresponding mRNA levels. Interestingly, antisense transcription is not evenly distributed across coding regions (CDSs) but strongly clustered towards the 3'-end of CDSs. Furthermore, for a significant subset of NATs, transcript levels correlate with mRNA levels of neighboring genes.Finally, we were able to identify the polyadenylation sites (PASs) for a subset of NATs, demonstrating that at least some NATs are polyadenylated. We also mapped the PASs of 3443 coding genes, yielding an average 3' untranslated region length of 523 bp. CONCLUSIONS: Our strand-specific analysis of the P. falciparum transcriptome expands and strengthens the existing body of evidence that antisense transcription is a substantial phenomenon in P. falciparum. For a subset of neighboring genes we find that sense and antisense transcript levels are intricately linked while other NATs appear to be regulated independently of mRNA transcription. Our deep strand-specific dataset will provide a valuable resource for the precise determination of expression levels as it separates sense from antisense transcript levels, which we find to often significantly differ. In addition, the extensive novel data on 3' UTR length will allow others to perform searches for regulatory motifs in the UTRs and help understand post-translational regulation in P. falciparum.

Nuclear pores and perinuclear expression sites of var and ribosomal DNA genes correspond to physically distinct regions in Plasmodium falciparum.

The human malaria parasite Plasmodium falciparum modifies the erythrocyte it infects by exporting variant proteins to the host cell surface. The var gene family that codes for a large, variant adhesive surface protein called P. falciparum erythrocyte membrane protein 1 (PfEMP1) plays a particular role in this process, which is linked to pathogenesis and immune evasion. A single member of this gene family is highly transcribed while the other 59 members remain silenced. Importantly, var gene transcription occurs at a spatially restricted, but yet undefined, perinuclear site that is distinct from repressed var gene clusters. To advance our understanding of monoallelic expression, we investigated whether nuclear pores associate with the var gene expression site. To this end, we studied the nuclear pore organization during the asexual blood stage using a specific antibody directed against a subunit of the nuclear pore, P. falciparum Nup116 (PfNup116). Ring and schizont stage parasites showed highly polarized nuclear pore foci, whereas in trophozoite stage nuclear pores redistributed over the entire nuclear surface. Colocalization studies of var transcripts and anti-PfNup116 antibodies showed clear dissociation between nuclear pores and the var gene expression site in ring stage. Similar results were obtained for another differentially transcribed perinuclear gene family, the ribosomal DNA units. Furthermore, we show that in the poised state, the var gene locus is not physically linked to nuclear pores. Our results indicate that P. falciparum does form compartments of high transcriptional activity at the nuclear periphery which are, unlike the case in yeast, devoid of nuclear pores.

Biochemical Markers for Liver Injury in Zebrafish Larvae.

Liver plays a crucial role in detoxification processes and metabolism of xenobiotics, and therefore, it is a target organ of toxicity of different classes of chemicals. In this context, some key enzymes present in liver are considered to be good biochemical markers of hepatic damage and can have their activities determined via spectrophotometry. Aspartate and alanine aminotransferases, alkaline phosphatase, lactate dehydrogenase, and glutathione peroxidase are enzymes that have activities often changed in response to hepatotoxic compounds and can be accessed through the larval period of zebrafish (Danio rerio). In this chapter, we described methodologies for analyses of these five biomarkers in pooled zebrafish larvae through spectrophotometry.

2,4-D Herbicide-Induced Hepatotoxicity: Unveiling Disrupted Liver Functions and Associated Biomarkers.

2,4-dichlorophenoxyacetic acid (2,4-D) is a widely used herbicide worldwide and is frequently found in water samples. This knowledge has prompted studies on its effects on non-target organisms, revealing significant alterations to liver structure and function. In this review, we evaluated the literature on the hepatotoxicity of 2,4-D, focusing on morphological damages, toxicity biomarkers and affected liver functions. Searches were conducted on PubMed, Web of Science and Scopus and 83 articles were selected after curation. Among these studies, 72% used in vivo models and 30% used in vitro models. Additionally, 48% used the active ingredient, and 35% used commercial formulations in exposure experiments. The most affected biomarkers were related to a decrease in antioxidant capacity through alterations in the activities of catalase, superoxide dismutase and the levels of malondialdehyde. Changes in energy metabolism, lipids, liver function, and xenobiotic metabolism were also identified. Furthermore, studies about the effects of 2,4-D in mixtures with other pesticides were found, as well as hepatoprotection trials. The reviewed data indicate the essential role of reduction in antioxidant capacity and oxidative stress in 2,4-D-induced hepatotoxicity. However, the mechanism of action of the herbicide is still not fully understood and further research in this area is necessary.

Disentangling doping and strain effects at defects of grown MoS2 monolayers with nano-optical spectroscopy.

The role of defects in two-dimensional semiconductors and how they affect the intrinsic properties of these materials have been a widely researched topic over the past few decades. Optical characterization techniques such as photoluminescence and Raman spectroscopies are important tools to probe the physical properties of semiconductors and the impact of defects. However, confocal optical techniques present a spatial resolution limitation lying in a µm-scale, which can be overcome by the use of near-field optical measurements. Here, we use tip-enhanced photoluminescence and Raman spectroscopies to unveil the nanoscale optical properties of grown MoS2 monolayers, revealing that the impact of doping and strain can be disentangled by the combination of both techniques. A noticeable enhancement of the exciton peak intensity corresponding to trion emission quenching is observed at narrow regions down to a width of 47 nm at grain boundaries related to doping effects. Besides, localized strain fields inside the sample lead to non-uniformities in the intensity and energy position of photoluminescence peaks. Finally, two distinct MoS2 samples present different nano-optical responses at their edges associated with opposite strains. The edge of the first sample shows a photoluminescence intensity enhancement and energy blueshift corresponding to a frequency blueshift for E2g and 2LA Raman modes. In contrast, the other sample displays a photoluminescence energy redshift and frequency red shifts for E2g and 2LA Raman modes at their edges. Our work highlights the potential of combining tip-enhanced photoluminescence and Raman spectroscopies to probe localized strain fields and doping effects related to defects in two-dimensional materials.

Killing of Plasmodium Sporozoites by Basic Amphipathic α-Helical Fusion Peptides.

Membranolytic molecules constitute the first line of innate immune defense against pathogenic microorganisms. Plasmodium sporozoites are potentially exposed to these cytotoxic molecules in the hemolymph and salivary glands of mosquitoes, as well as in the skin, blood, and liver of the mammalian host. Here, we show that sporozoites are resistant to bacteriolytic concentration of cecropin B, a cationic amphipathic antimicrobial insect peptide. Intriguingly, anti-tumoral cell-penetrating peptides derived from the anti-apoptotic protein AAC11 killed P. berghei and P. falciparum sporozoites. Using dynamic imaging, we demonstrated that the most cytotoxic peptide, called RT39, did not significantly inhibit the sporozoite motility until the occurrence of a fast permeabilization of the parasite membrane by the peptide. Concomitantly, the cytosolic fluorescent protein constitutively expressed by sporozoites leaked from the treated parasite body while To-Pro 3 and FITC-labeled RT39 internalized, respectively, binding to the nucleic acids and membranes of sporozoites. This led to an increase in the parasite granularity as assessed by flow cytometry. Most permeabilization events started at the parasite's posterior end, resulting in the appearance of a fluorescent dot in the anterior part of sporozoites. Understanding and exploiting the susceptibility of sporozoites and other plasmodial stages to membranolytic molecules might foster strategies to eliminate the parasite and block its transmission.

Exposure to Smartphones and Tablets, Physical Activity and Sleep in Children From 5 to 10 Years Old: A Systematic Review and Meta-Analysis.

OBJECTIVE: To conduct a systematic review and meta-analysis to verify the association between smartphone/tablet exposure and physical activity and sleep in children from 5 to 10 years old. Data Source: This study followed the guidelines of PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) and included studies that met eligibility criteria based on the "PECO" strategy: participants (children from 5 to 10 years old), exposure (smartphone and tablet use), and outcome (physical activity and sleep). STUDY INCLUSION AND EXCLUSION CRITERIA: The inclusion criteria were observational studies published in indexed scientific journals and written in Portuguese, English, and Spanish that verified the association of exposure to smartphones/tablets with physical activity and sleep in children aged 5 to 10 years of both sexes. Studies were considered eligible only if they met the previous criteria. Data Extraction: The search was conducted in January 2023 on databases from electronic journals without the restriction of the period. To meta-analyze were extracted and grouped using models of fixed and random effects, the coefficients Odds Ratio (OR), Beta (ß), Standard Error (SE), and Confidence Intervals of 95% (95%CI). Data Synthesis: 2396 potentially relevant papers were identified, and 17 met the inclusion criteria. RESULTS: It can be verified that there was an inverse association between smartphones with physical activity and sleep. Studies indicate that for every additional hour of smartphone and tablet use, sleep can be expected to decrease by an average of 11 minutes (ß = - 0.11; 95%CI = -0.13; -0.09). Children using smartphones and tablets were 1.79 times (OR = 1.79; 95%CI = 1.72-1.86) more likely to have shorter sleep duration and 1.53 times (OR = 1.53; 95%CI = 1.41-1.65) more likely to have worse sleep quality. Children with shorter smartphone and tablet usage were 1.19 times more likely to be active (OR = 1.19; 95% CI = 1.03-1.37). CONCLUSION: Children of 5 to 10 years who are more often exposed to smartphones and tablets are prone to have worse quality and quantity of sleep, as well as less practice of physical activity. Health promotion actions can be encouraged based on the results, aiming to reduce the use time of these devices and improve children's health and quality of life.