Neural stem cells traffic functional mitochondria via extracellular vesicles.

Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs). EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids, and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs are yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics. Herein, we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells. Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs with conserved membrane potential and respiration. We found that the transfer of these mitochondria from EVs to mtDNA-deficient L929 Rho0 cells rescued mitochondrial function and increased Rho0 cell survival. Furthermore, the incorporation of mitochondria from EVs into inflammatory mononuclear phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits. Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases.

Andiroba oil (Carapa guianensis Aubl) shows cytotoxicity but no mutagenicity in the ACPP02 gastric cancer cell line.

Andiroba (Carapa guianensis Aubl) is an Amazonian plant whose oil has been widely used in traditional medicine for various purposes, including anti-inflammation. Research reports indicate that the oil can confer antitumor activity due to the presence of fatty acids, which can directly influence cell death mechanisms. Thus, andiroba oil (AO) has gained interest for its potential to be used in antineoplastic therapies. Here, we report an in vitro analysis of the cytotoxic and mutagenic potential of AO in the gastric cancer cell line, ACP02. Cell survival was assessed by the MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, differential staining with ethidium bromide and acridine orange assessed apoptosis-necrosis, and mutagenesis was assessed by the micronucleus test. The apolar oil was first diluted in 0.1% dimethyl sulfoxide (DMSO) and then further diluted to six concentrations (0.01, 0.1, 1, 10 and 100 µg/mL and 1 mg/mL) in RPMI medium. Controls included RPMI alone (negative control) and 0.1% DMSO diluted in medium (vehicle control). The MTT test showed that AO significantly reduced cell viability (P < .05) only when the highest tested concentration was applied for 48 hours. The apoptosis/necrosis test showed that the highest concentration of AO induced cell death by apoptosis at 24 and 48 hours. There was no statistically significant increase in the frequency of micronuclei. The ability of the AO to decrease the viability of ACP02 cells via apoptosis, without exerting mutagenic effects, suggests that the oil could be useful as an alternative therapeutic agent for primary tumors of stomach cancer.

Extracellular vesicles are independent metabolic units with asparaginase activity.

Extracellular vesicles (EVs) are membrane particles involved in the exchange of a broad range of bioactive molecules between cells and the microenvironment. Although it has been shown that cells can traffic metabolic enzymes via EVs, much remains to be elucidated with regard to their intrinsic metabolic activity. Accordingly, herein we assessed the ability of neural stem/progenitor cell (NSC)-derived EVs to consume and produce metabolites. Our metabolomics and functional analyses both revealed that EVs harbor L-asparaginase activity, catalyzed by the enzyme asparaginase-like protein 1 (Asrgl1). Critically, we show that Asrgl1 activity is selective for asparagine and is devoid of glutaminase activity. We found that mouse and human NSC EVs traffic Asrgl1. Our results demonstrate, for the first time, that NSC EVs function as independent metabolic units that are able to modify the concentrations of critical nutrients, with the potential to affect the physiology of their microenvironment.

The exceptional genomic word symmetry along DNA sequences.

BACKGROUND: The second Chargaff's parity rule and its extensions are recognized as universal phenomena in DNA sequences. However, parity of the frequencies of reverse complementary oligonucleotides could be a mere consequence of the single nucleotide parity rule, if nucleotide independence is assumed. Exceptional symmetry (symmetry beyond that expected under an independent nucleotide assumption) was proposed previously as a meaningful measure of the extension of the second parity rule to oligonucleotides. The global exceptional symmetry was detected in long and short genomes. RESULTS: To explore the exceptional genomic word symmetry along the genome sequences, we propose a sliding window method to extract the values of exceptional symmetry (for all words or by word groups). We compare the exceptional symmetry effect size distribution in all human chromosomes against control scenarios (positive and negative controls), testing the differences and performing a residual analysis. We explore local exceptional symmetry in equivalent composition word groups, and find that the behaviour of the local exceptional symmetry depends on the word group. CONCLUSIONS: We conclude that the exceptional symmetry is a local phenomenon in genome sequences, with distinct characteristics along the sequence of each chromosome. The local exceptional symmetry along the genomic sequences shows outlying segments, and those segments have high biological annotation density.

Analysis of single-strand exceptional word symmetry in the human genome: new measures.

Some previous studies suggest the extension of Chargaff's second rule (the phenomenon of symmetry in a single DNA strand) to long DNA words. However, in random sequences generated under an independent symbol model where complementary nucleotides have equal occurrence probabilities, we expect the phenomenon of symmetry to hold for any word length. In this work, we develop new statistical methods to measure the exceptional symmetry. Exceptional symmetry is a refinement of Chargaff's second parity rule that highlights the words whose frequency of occurrence is similar to that of its reversed complement but dissimilar to the frequencies of occurrence of other words which contain the same number of nucleotides A or T. We analyze words of lengths up to 12 in the complete human genome and in each chromosome separately. We assess exceptional symmetry globally, by word group, and by word. We conclude that the global symmetry present in the human genome is clearly exceptional and significant. The chromosomes present distinct exceptional symmetry profiles. There are several exceptional word groups and exceptional words with a strong exceptional symmetry.

The breakdown of the word symmetry in the human genome.

Previous studies have suggested that Chargaff's second rule may hold for relatively long words (above 10nucleotides), but this has not been conclusively shown. In particular, the following questions remain open: Is the phenomenon of symmetry statistically significant? If so, what is the word length above which significance is lost? Can deviations in symmetry due to the finite size of the data be identified? This work addresses these questions by studying word symmetries in the human genome, chromosomes and transcriptome. To rule out finite-length effects, the results are compared with those obtained from random control sequences built to satisfy Chargaff's second parity rule. We use several techniques to evaluate the phenomenon of symmetry, including Pearson's correlation coefficient, total variational distance, a novel word symmetry distance, as well as traditional and equivalence statistical tests. We conclude that word symmetries are statistical significant in the human genome for word lengths up to 6nucleotides. For longer words, we present evidence that the phenomenon may not be as prevalent as previously thought.

Concentration of inverted repeats along human DNA.

This work aims to describe the observed enrichment of inverted repeats in the human genome; and to identify and describe, with detailed length profiles, the regions with significant and relevant enriched occurrence of inverted repeats. The enrichment is assessed and tested with a recently proposed measure (z-scores based measure). We simulate a genome using an order 7 Markov model trained with the data from the real genome. The simulated genome is used to establish the critical values which are used as decision thresholds to identify the regions with significant enriched concentrations. Several human genome regions are highly enriched in the occurrence of inverted repeats. This is observed in all the human chromosomes. The distribution of inverted repeat lengths varies along the genome. The majority of the regions with severely exaggerated enrichment contain mainly short length inverted repeats. There are also regions with regular peaks along the inverted repeats lengths distribution (periodic regularities) and other regions with exaggerated enrichment for long lengths (less frequent). However, adjacent regions tend to have similar distributions.

Small Extracellular Vesicles Secreted by Nigrostriatal Astrocytes Rescue Cell Death and Preserve Mitochondrial Function in Parkinson's Disease.

Extracellular vesicles (EVs) are emerging as powerful players in cell-to-cell communication both in healthy and diseased brain. In Parkinson's disease (PD)-characterized by selective dopaminergic neuron death in ventral midbrain (VMB) and degeneration of their terminals in striatum (STR)-astrocytes exert dual harmful/protective functions, with mechanisms not fully elucidated. Here, this study shows that astrocytes from the VMB-, STR-, and VMB/STR-depleted brains release a population of small EVs  in a region-specific manner. Interestingly, VMB-astrocytes secreted the highest rate of EVs, which is further exclusively increased in response to CCL3, a chemokine that promotes robust dopaminergic neuroprotection in different PD models. The neuroprotective potential of nigrostriatal astrocyte-EVs is investigated in differentiated versus undifferentiated SH-SY5Y cells exposed to oxidative stress and mitochondrial toxicity. EVs from both VMB- and STR-astrocytes counteract H2 O2 -induced caspase-3 activation specifically in differentiated cells, with EVs from CCL3-treated astrocytes showing a higher protective effect. High resolution respirometry further reveals that nigrostriatal astrocyte-EVs rescue neuronal mitochondrial complex I function impaired by the neurotoxin MPP+ . Notably, only EVs from VMB-astrocyte fully restore ATP production, again specifically in differentiated SH-SY5Y. These results highlight a regional diversity in the nigrostriatal system for the secretion and activities of astrocyte-EVs, with neuroprotective implications for PD.

Karyotypes of Manatees: New Insights into Hybrid Formation (Trichechus inunguis × Trichechus m. manatus) in the Amazon Estuary.

Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics and genomic organization in Trichechus. We analyzed the karyotype of TMM, TIN, and two hybrid specimens ("Poque" and "Vitor") by classical and molecular cytogenetics. G-band analysis revealed that TMM (2n = 48) and TIN (2n = 56) diverge by at least six Robertsonian translocations and a pericentric inversion. Hybrids had 2n = 50, however, with Autosomal Fundamental Number (FNA) = 88 in "Poque" and FNA = 74 in "Vitor", and chromosomal distinct pairs in heterozygous; additionally, "Vitor" exhibited heteromorphisms and chromosomes whose pairs could not be determined. The U2 snDNA and Histone H3 multi genes are distributed in small clusters along TIN and TMM chromosomes and have transposable Keno and Helitron elements (TEs) in their sequences. The different karyotypes observed among manatee hybrids may indicate that they represent different generations formed by crossing between fertile hybrids and TIN. On the other hand, it is also possible that all hybrids recorded represent F1 and the observed karyotype differences must result from mechanisms of elimination.

Genome analysis with distance to the nearest dissimilar nucleotide.

DNA may be represented by sequences of four symbols, but it is often useful to convert those symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but most of them seem to be unrelated to any intrinsic characteristic of DNA. The objective of this work was to study a mapping scheme that is directly related to DNA characteristics, and that could be useful in discriminating between different species. Recently, we have proposed a methodology based on the inter-nucleotide distance, which proved to contribute to the discrimination among species. In this paper, we introduce a new distance, the distance to the nearest dissimilar nucleotide, which is the distance of a nucleotide to first occurrence of a different nucleotide. This distance is related to the repetition structure of single nucleotides. Using the information resulting from the concatenation of the distance to the nearest dissimilar and the inter-nucleotide distance, we found that this new distance brings additional discriminative capabilities. This suggests that the distance to the nearest dissimilar nucleotide might contribute with useful information about the evolution of the species.

Acute Urinary Retention After Kidney Transplant: Effect on Graft Function, Predictive Factors, and Treatment.

BACKGROUND: Benign prostatic hyperplasia (BPH) is common in older adults. Although BPH may be asymptomatic in patients with chronic kidney disease (CKD) with low diuresis, the condition may become troublesome when diuresis resumes after transplantation. This study evaluated the effect that developing acute urinary retention (AUR) in first 4 months after kidney transplantation (KT) can have on graft function at 6 months. The study identified predictive factors and analyzed treatment of AUR in these patients. METHODS: This study retrospectively included 303 men who received KT. Independent samples Student t test was used to compare glomerular filtration rates (GFRs) at 6 months. Logistic regression was applied to identify predictors of AUR. RESULTS: The study found that 14 patients developed AUR within the first 4 months after KT. This group had lower GFR at 6 months post-KT. Nine patients required transurethral resection of the prostate, and 2 of these patients developed acute graft pyelonephritis following resection. Residual diuresis and recipient age were predictive factors. Recipient age >55 years was a risk factor. Medical therapy of BPH before transplantation was a protective factor. CONCLUSIONS: Developing AUR in the first 4 months after KT was associated with lower graft GFR at 6 months, and transurethral resection of the prostate was required in 64% of these patients, with good results. Medical therapy for BPH before the transplant was associated with a lower risk of AUR. Older patients and patients with pretransplant low urine output had a higher risk of AUR. These patients should be closely monitored in the posttransplant period for the presence of obstructive uropathy.

Early morning kidney transplantation: Perioperative complications.

INTRODUCTION: To reduce cold ischemia time (CIT), many kidney transplants are performed in the early morning. Conducting complex surgeries in the early morning may influence the surgeon's technical capacity and rate of surgical complications (SC). AIM: Evaluate the influence of surgery start hour (SSH) regarding duration of surgery (DS), immediate diuresis (ID), SC and acute rejection (AR); evaluate the influence of CIT regarding SC, ID, and AR. METHODS: 2855 cadaveric transplants performed between June 1980 and March 2018 were retrospectively evaluated. Regarding SSH, two groups were created: Group M (00: 00h-05.59h, n = 253) and Group D (06: 00h - 23: 59h, n = 2602). Analyzing the impact of SSH on DS, ID, SC and AR. Evaluate the relationship between CIT (< 18h, 18-30h and > 30h) on ID, SC and AR utilizing univariate and multivariate statistical analysis with SPSS. RESULTS AND CONCLUSION: Groups M and D were comparable in all evaluated demographic variables (p > 0.05), except cold ischemia time (Group M with higher CIT, p < 0.001). Regarding univariate analysis, Surgery start hour did not influence DS (p = 0.344), and SC (p = 0.264), but related with higher ID (p = 0.028) and AR (p = 0.018). CIT related with immediate diuresis (p = 0.020) and acute rejection (p < 0.001) but did not relate with complications (p = 0.734). Regarding multivariate analysis, SSH only influenced immediate diuresis (p = 0.026) and did not influenced acute rejection (p = 0.055). CIT influenced immediate diuresis (p = 0.019) and acute rejection (p < 0.001). Surgery start hour influences Immediate diuresis. With this study, we conclude that the priority must be a short cold ischemia time.

Genome analysis with inter-nucleotide distances.

MOTIVATION: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but they seem unrelated to any intrinsic characteristic of DNA. The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description. RESULTS: We developed a methodology to process DNA sequences based on inter-nucleotide distances. Our main contribution is a method to obtain genomic signatures for complete genomes, based on the inter-nucleotide distances, that are able to discriminate between different species. Using these signatures and hierarchical clustering, it is possible to build phylogenetic trees. Phylogenetic trees lead to genome differentiation and allow the inference of phylogenetic relations. The phylogenetic trees generated in this work display related species close to each other, suggesting that the inter-nucleotide distances are able to capture essential information about the genomes. To create the genomic signature, we construct a vector which describes the inter-nucleotide distance distribution of a complete genome and compare it with the reference distance distribution, which is the distribution of a sequence where the nucleotides are placed randomly and independently. It is the residual or relative error between the data and the reference distribution that is used to compare the DNA sequences of different organisms.

Making urinary extracellular vesicles a clinically tractable source of biomarkers for inherited tubulopathies using a small volume precipitation method: proof of concept.

Biomarkers of inherited tubulopathies would be useful for clarifying diagnoses in patients where genetic screening is not readily available or where disease-attributable mutations are not found. Urinary extracellular vesicles (uEVs) obtained by ultracentrifugation can be used as a source of biomarkers for inherited tubulopathies such as Gitelman Syndrome (GS), however, ultracentrifugation requires costly equipment and is thus not usually accessible. In contrast, precipitation methods can extract uEVs using standard laboratory centrifuges, thus making uEVs extracted by this method clinically tractable as a source of biomarkers for GS and other inherited tubulopathies. Here we optimise a precipitation method for extracting urinary extracellular vesicles (uEVs) and provide proof of concept that these uEVs are a source of biomarkers using GS an exemplar tubulopathy. For method optimisation, uEVs were precipitated from fresh and frozen (for up to 6 years), small volume (1-2 mL) urine samples from healthy volunteers and GS patients. Nanoparticle tracking analysis was used to calculate the concentration of uEVs. Thiazide sensitive sodium-chloride cotransporter (NCC) content was determined by densitometry of Western blots. NCC content of uEVs was lower in GS patients (n = 11) than healthy volunteers (n = 12; P = 0.001). Three of four patients clinically suspected for GS, in whom only a single SLC12A3 mutation was identified, had lower uEV NCC content than all healthy volunteers tested. In the clinical setting, sufficient uEVs can be extracted from frozen, small volume urine samples using precipitation methods to distinguish patients with GS from healthy volunteers, and thus this source of uEVs could be utilised as an additional diagnostic test for GS and similar disorders.

Correction to: Making urinary extracellular vesicles a clinically tractable source of biomarkers for inherited tubulopathies using a small volume precipitation method: proof of concept.

The original published article the section Acknowledgements is missing. The section is given below.

Robust rapid-setting antibacterial liquid bandages.

Bandaging is a steadfast but time-consuming component of wound care with limited technical advancements to date. Bandages must be changed and infection risk managed. Rapid-set liquid bandages are efficient alternatives but lack durability or inherent infection control. We show here that antibacterial zinc (Zn) and copper (Cu) species greatly enhance the barrier properties of the natural, waterproof, bio-adhesive polymer, shellac. The material demonstrated marked antibacterial contact properties and, in ex-vivo studies, effectively locked-in pre-applied therapeutics. When challenged in vivo with the polybacterial bovine wound infection 'digital dermatitis', Zn/Cu-shellac adhered rapidly and robustly over pre-applied antibiotic. The bandage self-degraded, appropriately, over 7 days despite extreme conditions (faecal slurry). Treatment was well-tolerated and clinical improvement was observed in animal mobility. This new class of bandage has promise for challenging topical situations in humans and other animals, especially away from controlled, sterile clinical settings where wounds urgently require protection from environmental and bacterial contamination.

Molecular cytogenetics characterization of Rhinoclemmys punctularia (Testudines, Geoemydidae) and description of a Gypsy-H3 association in its genome.

The wide variation found in the size of eukaryotic genomes is largely related to the accumulation of repetitive sequences. Studies show that these sequences can go through an evolutionary process (molecular co-optation) and acquire new genomic functions. Cytogenetic studies reveal a wide karyotypic variation between chelonians (order Testudines) (2n = 26-68), attributed mainly to the number of microchromosomes. The study of repetitive DNAs has the potential to provide data on the dynamics of these sequences, and how they influence the organization of the genome. Here, we reveal the first in situ mapping data of 45S rDNA, histone H3 genes, and telomeric sequences, for a species of the genus Rhinoclemmys, R. punctularia. The karyotype described here for R. punctularia is different from previous reports for the diploid complement of this species, with differences probably attributable to centric fissions and pericentric inversions or centromere repositioning. The 45S rDNA are on a single chromosome pair (like in other turtles), telomeric sequences are in terminal position on all the chromosomes, and histone H3 is dispersed in low copy number, with clusters in pericentromeric regions of three chromosome pairs. We report on the presence of a Gypsy retrotransposon insert located within H3 histone of R. punctularia, and the H3 region sequenced contained the open reading frame of the histone sequence. Comparative modeling revealed a functional pattern for the protein, thus suggesting that the Gypsy element might have been recruited for new functions in the genome of this species.

Transplantectomy in the First 3 Months After Renal Transplantation: Experience of a Reference Center.

INTRODUCTION/OBJECTIVE: Transplantation is the treatment of choice in end-stage renal disease. However, there are complications that require transplantectomy. The objective of this study was to evaluate predictive factors for transplantectomy in the first 3 months after renal transplantation. MATERIAL AND METHODS: This retrospective study included 770 kidney transplants performed between June 2011 and June 2017. Logistic regression was applied to study the relationship between independent variables and the occurrence of transplantectomy. RESULTS: Analyzing variables of the recipients, it was verified that age over 65 years; body mass index; dialysis time; history of previous transplant and comorbidities such as obesity, overweight, hypertension, diabetes mellitus, dyslipidemia, peripheral arterial disease; or history of a thrombotic episode were not predictive factors. It was found that the use of expanded criteria donors, their age, or cause of death were not predictive factors. The use of a right renal graft or grafts with multiple arteries; the duration of surgery; the performance of surgery at dawn; the need for transfusion; the cold ischemia time; and hemodynamic parameters at reperfusion (central venous pressure, systolic or diastolic blood pressure) were not predictive factors. The recipient age at transplantation (p = .014; B=-0.059; Exp(B)=0.943 [0.899-0.988]) and reoperation in the first 10 days after transplantation (p < .001; B= -2.574; Exp(B)=0.076 [0.028-0.210]) were predictive factors. CONCLUSION: Reoperation in the first 10 days after transplantation decreased the risk of transplantectomy in the first 3 months. The lower the age of the recipient, the greater the risk of transplantectomy.

Aqueous ethanol extract of Libidibia ferrea (Mart. Ex Tul) L.P. Queiroz (juca) exhibits antioxidant and migration-inhibiting activity in human gastric adenocarcinoma (ACP02) cells.

Libidibia ferrea (juca) is a plant belonging to the Fabaceae (Leguminosae) family, whose antioxidant activity has been widely described in the literature. We evaluated this parameter of Aqueous ethanol extract (AE), ethyl acetate (ACO), chloroform (CLO) and hexane (HEX) extracts of L. ferrea. We then tested the most active extract for its toxicity and ability to inhibit migratory activity in the ACP02 gastric adenocarcinoma cell line in vitro. The AE and ACO extracts both had antioxidant activity, the AE extract showing greater potential. This may reflect that both extracts contained phenolic compounds. Although AE extract showed no cytotoxic, mutagenic or genotoxic effect, it altered cell morphology and migration activity. Analysis of apoptosis/necrosis indicated that this parameter does not appear to account for the apparent ability of AE to inhibit cancer cell migration. We speculate that the morphological changes in AE-treated cells could be due to cytoskeleton alterations related to the presence of myo-inositol in AE extract. Together, our results demonstrate this extract of L. ferrea can act as an exogenous antioxidant and might prove useful in efforts to fight secondary tumors.

Distribution of Distances Between Symmetric Words in the Human Genome: Analysis of Regular Peaks.

Finding DNA sites with high potential for the formation of hairpin/cruciform structures is an important task. Previous works studied the distances between adjacent reversed complement words (symmetric word pairs) and also for non-adjacent words. It was observed that for some words a few distances were favoured (peaks) and that in some distributions there was strong peak regularity. The present work extends previous studies, by improving the detection and characterization of peak regularities in the symmetric word pairs distance distributions of the human genome. This work also analyzes the location of the sequences that originate the observed strong peak periodicity in the distance distribution. The results obtained in this work may indicate genomic sites with potential for the formation of hairpin/cruciform structures.