RNAget: an API to securely retrieve RNA quantifications.

SUMMARY: Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in matrix form. RNAget provides for slicing matrices to extract desired subsets of data and is applicable to all expression matrix-format data, including RNA sequencing and microarrays. Further, it generalizes to quantification matrices of other sequence-based genomics such as ATAC-seq and ChIP-seq. AVAILABILITY AND IMPLEMENTATION: https://ga4gh-rnaseq.github.io/schema/docs/index.html.

NF1+/ex42del miniswine model the cellular disruptions and behavioral presentations of NF1-associated cognitive and motor impairment.

Cognitive or motor impairment is common among individuals with neurofibromatosis type 1 (NF1), an autosomal dominant tumor-predisposition disorder. As many as 70% of children with NF1 report difficulties with spatial/working memory, attention, executive function, and fine motor movements. In contrast to the utilization of various Nf1 mouse models, here we employ an NF1+/ex42del miniswine model to evaluate the mechanisms and characteristics of these presentations, taking advantage of a large animal species more like human anatomy and physiology. The prefrontal lobe, anterior cingulate, and hippocampus from NF1+/ex42del and wild-type miniswine were examined longitudinally, revealing abnormalities in mature oligodendrocytes and astrocytes, and microglial activation over time. Imbalances in GABA: Glutamate ratios and GAD67 expression were observed in the hippocampus and motor cortex, supporting the role of disruption in inhibitory neurotransmission in NF1 cognitive impairment and motor dysfunction. Moreover, NF1+/ex42del miniswine demonstrated slower and shorter steps, indicative of a balance-preserving response commonly observed in NF1 patients, and progressive memory and learning impairments. Collectively, our findings affirm the effectiveness of NF1+/ex42del miniswine as a valuable resource for assessing cognitive and motor impairments associated with NF1, investigating the involvement of specific neural circuits and glia in these processes, and evaluating potential therapeutic interventions.

Aluminum intake in the neonatal phase disrupts endochondral ossification in rodents.

OBJECTIVE: This study evaluated the effects of aluminum (Al) intake on endochondral ossification during the neonatal phase. METHOD: Twelve male newborn Gerbils (Meriones unguiculatus) were randomly divided into control (C) and aluminum (Al) groups (n = 6 animals/group). From the 1st to 15th day of life, gerbils received an AlCl3 solution (10 mg/kg/day) via gavage. The control group received only the saline solution. On the 16th day, their tibias were processed for paraffin embedding and were submitted to histomorphometric, histochemical, and immunohistochemical analyses. RESULTS: In the epiphyseal cartilage Al did not affect the proteoglycan content or cell proliferation; however, it increased matrix metalloprotease-2 (MMP-2) immunostaining and the hypertrophic layer thickness. In bone, Al decreased trabeculae number, trabecular width, cortical bone width, and proliferation. Furthermore, the relative frequency of bone matrix and fibrillar collagen decreased 3.9% and 16.2%, respectively. The number of osteoclasts and osteocalcin digital optical density (D.O.D) remained the same. CONCLUSION: The results suggest that Al intake during the neonatal period impairs endochondral ossification by affecting epiphyseal cartilage and bone architecture.

Human adipose-derived stromal vascular fraction: characterization, safety and therapeutic potential in an experimental mouse model of articular injury.

Due to their capacity to self-renew, proliferate and generate multi-lineage cells, adult-derived stem cells offer great potential in regenerative therapies to treat maladies such as diabetes, cardiac disease, neurological disorders and orthopedic injuries. Commonly derived from adipose tissue, the stromal vascular fraction (SVF), a heterogeneous cell population enriched with mesenchymal stem cells (MSCs), has garnered interest as a cellular therapy due to ease of accessibility as an autologous, point-of-care application. However, the heterogeneous cell population within SVF is not historically taken into consideration when injecting into patients. Here, we characterized SVF, determined its safety and verify its therapeutic effects in a NOD/scid mouse model of articular injury. SVF were isolated from lipoaspirates utilizing a commercially available system (InGeneron Inc.), while MSCs were isolated from SVF via cell culture. Flow cytometry showed that neither age nor BMI affects the frequency of progenitor cells-like (CD31+CD34+), immune cells-like (CD4+) T cells, (CD14+) monocytes and total number of cells obtained. However, there was a negative correlation between donor BMI and MSC frequency within the SVF. ELISAs showed that following LPS activation in SVF, there were low levels of TNF-α and high levels of IL-10 secreted. However, T cell activation with anti-CD3 or anti-CD3+ anti-CD28, while leading to expected high levels of IFN-γ, did not lead to significant levels of TGF-ß. PCR analysis showed no significant numbers of cells outside the joint 1-hour post injection, moreover, no engraftment or abnormal growth in other organs 60-days post injection. Finally, both cell populations were able to ameliorate disease progression, as confirmed by the increase in movement of treated groups compared to injured groups. Noteworthy, the histological analysis indicated that there was no cartilage growth, suggesting an alternative therapeutic mechanism to cartilage regeneration.

Assessment of nociception and related quality-of-life measures in a porcine model of neurofibromatosis type 1.

Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder resulting from germline mutations in the NF1 gene, which encodes neurofibromin. Patients experience a variety of symptoms, but pain in the context of NF1 remains largely underrecognized. Here, we characterize nociceptive signaling and pain behaviors in a miniswine harboring a disruptive NF1 mutation (exon 42 deletion). We present the first characterization of pain-related behaviors in a pig model of NF1, identifying unchanged agitation scores, lower tactile thresholds (allodynia), and decreased response latencies to thermal laser stimulation (hyperalgesia) in NF1 (females only) pigs. Male NF1 pigs with tumors showed reduced sleep quality and increased resting, 2 health-related quality-of-life symptoms found to be comorbid in people with NF1 pain. We explore these phenotypes in relationship to suppression of the increased activity of the N-type voltage-gated calcium (CaV2.2) channel by pharmacological antagonism of phosphorylation of a regulatory protein-the collapsin response mediator protein 2 (CRMP2), a known interactor of neurofibromin, and by targeting the interface between the α subunit of CaV2.2 and the accessory ß-subunits with small molecules. Our data support the use of NF1 pigs as a large animal model for studying NF1-associated pain and for understanding the pathophysiology of NF1. Our findings demonstrate the translational potential of 2 small molecules in reversing ion channel remodeling seen in NF1. Interfering with CaV2.2, a clinically validated target for pain management, might also be a promising therapeutic strategy for NF1-related pain management.

Efficiency of biomonitoring methods applying tropical bioindicator plants for assessing the phytoxicity of the air pollutants in SE, Brazil.

In the tropical region, the greatest challenge of the biomonitoring approach is to establish linear relationships between biomarkers measured in plants and pollutant concentrations, since the bioindicator responses can be intensified or restricted by climatic variations. In southeastern Brazil, there are two regions affected by air pollution, where the Atlantic Forest remains and should be preserved. Consequently, both areas have been monitored by biomonitoring procedures using standardized and tropical plants. The industrial complex settled in Cubatão is one of the world's most famous examples of environmental pollution and degradation, with consequent decline of the Atlantic Forest. An oil refinery is among the most polluting industries in the Cubatão region. The other region is located in the Metropolitan Region of Campinas (MRC). The MRC has been affected by high levels of air pollutants originated from road traffic and is responsible for over 80% of CO, NOx, and hydrocarbon emissions and develops industrial activities that emit about 70% of the particulate matter present in the region. Both regions are distinguished by the climate, despite the fact that they are only about 130 km far from each other. Several studies carried out by our group in these regions aimed to establish the best native tree species and respective potential biomarkers for future assessment of pollution effects on tropical Forests. We present a critical review about the efficiency of native species compared to standardized bioindicator plants considering antioxidant defense system, nutrient accumulation, and microscopic aspects when exposed to atmospheric pollutants and climate.

DO3SE model applicability and O3 flux performance compared to AOT40 for an O3-sensitive tropical tree species (Psidium guajava L. 'Paluma').

Phytotoxic ozone (O3) levels have been recorded in the Metropolitan Region of São Paulo (MRSP). Flux-based critical levels for O3 through stomata have been adopted for some northern hemisphere species, showing better accuracy than with accumulated ozone exposure above a threshold of 40 ppb (AOT40). In Brazil, critical levels for vegetation protection against O3 adverse effects do not exist. The study aimed to investigate the applicability of O3 deposition model (Deposition of Ozone for Stomatal Exchange (DO3SE)) to an O3-sensitive tropical tree species (Psidium guajava L. 'Paluma') under the MRSP environmental conditions, which are very unstable, and to assess the performance of O3 flux and AOT40 in relation to O3-induced leaf injuries. Stomatal conductance (g s) parameterization for 'Paluma' was carried out and used to calculate different rate thresholds (from 0 to 5 nmol O3 m(-2) projected leaf area (PLA) s(-1)) for the phytotoxic ozone dose (POD). The model performance was assessed through the relationship between the measured and modeled g sto. Leaf injuries were analyzed and associated with POD and AOT40. The model performance was satisfactory and significant (R (2) = 0.56; P < 0.0001; root-mean-square error (RMSE) = 116). As already expected, high AOT40 values did not result in high POD values. Although high POD values do not always account for more injuries, POD0 showed better performance than did AOT40 and other different rate thresholds for POD. Further investigation is necessary to improve our model and also to check if there is a critical level of ozone in which leaf injuries arise. The conclusion is that the DO3SE model for 'Paluma' is applicable in the MRSP as well as in temperate regions and may contribute to future directives.