Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted Co-delivery of Tumor Antigen and α-Galactosylceramide to CD141+ Dendritic Cells Induces a Potent Tumor Antigen-Specific Human CD8+ T Cell Response in Human Immune System Mice

Active co-delivery of tumor antigens (Ag) and α-galactosylceramide (α-GalCer), a potent agonist for invariant Natural Killer T (iNKT) cells, to cross-priming CD8α+ dendritic cells (DCs) was previously shown to promote strong anti-tumor responses in mice. Here, we designed a nanoparticle-based vaccine able to target human CD141+ (BDCA3+) DCs - the equivalent of murine CD8α+ DCs – and deliver both tumor Ag (Melan A) and α-GalCer. This nanovaccine was inoculated into humanized mice that mimic the human immune system (HIS) and possess functional iNKT cells and CD8+ T cells, called HIS-CD8/NKT mice. We found that multiple immunizations of HIS-CD8/NKT mice with the nanovaccine resulted in the activation and/or expansion of human CD141+ DCs and iNKT cells and ultimately elicited a potent Melan-A-specific CD8+ T cell response, as determined by tetramer staining and ELISpot assay. Single-cell proteomics further detailed the highly polyfunctional CD8+ T cells induced by the nanovaccine and revealed their predictive potential for vaccine potency. This finding demonstrates for the first time the unique ability of human iNKT cells to license cross-priming DCs in vivo and adds a new dimension to the current strategy of cancer vaccine development.
Insight From Animals Resistant to Prion Diseases: Deciphering the Genotype – Morphotype – Phenotype Code for the Prion Protein

Prion diseases are a group of neurodegenerative diseases endemic in humans and several ruminants caused by the misfolding of native prion protein (PrP) into pathological conformations. Experimental work and the mad-cow epidemic of the 1980s exposed a wide spectrum of animal susceptibility to prion diseases, including a few highly resistant animals: horses, rabbits, pigs, and dogs/canids. The variable susceptibility to disease offers a unique opportunity to uncover the mechanisms governing PrP misfolding, neurotoxicity, and transmission. Previous work indicates that PrP-intrinsic differences (sequence) are the main contributors to disease susceptibility. Several residues have been cited as critical for encoding PrP conformational stability in prion-resistant animals, including D/E159 in dog, S167 in horse, and S174 in rabbit and pig PrP (all according to human numbering). These amino acids alter PrP properties in a variety of assays, but we still do not clearly understand the structural correlates of PrP toxicity. Additional insight can be extracted from comparative structural studies, followed by molecular dynamics simulations of selected mutations, and testing in manipulable animal models. Our working hypothesis is that protective amino acids generate more compact and stable structures in a C-terminal subdomain of the PrP globular domain. We will explore this idea in this review and identify subdomains within the globular domain that may hold the key to unravel how conformational stability and disease susceptibility are encoded in PrP.
Protein Domain Guided Screen for Sequence Specific and Phosphorothioate-Dependent Restriction Endonucleases

Modification dependent restriction endonucleases (MDREs) restrict modified DNA, typically with limited sequence specificity (∼2–4 bp). Here, we focus on MDREs that have an SRA and/or SBD (sulfur binding domain) fused to an HNH endonuclease domain, cleaving cytosine modified or phosphorothioated (PT) DNA. We independently characterized the SBD-SRA-HNH endonuclease ScoMcrA, which preferentially cleaves 5hmC modified DNA. We report five SBD-HNH endonucleases, all recognizing GpsAAC/GpsTTC sequence and cleaving outside with a single nucleotide 3′ stagger: EcoWI (N7/N6), Ksp11411I (N5/N4), Bsp305I (N6/N4-5), Mae9806I [N(8-10)/N(8-9)], and Sau43800I [N(8-9)/N(7-8)]. EcoWI and Bsp305I are more specific for PT modified DNA in Mg2+ buffer, and promiscuous with Mn2+. Ksp11411I is more PT specific with Ni2+. EcoWI and Ksp11411I cleave fully- and hemi-PT modified oligos, while Bsp305I cleaves only fully modified ones. EcoWI forms a dimer in solution and cleaves more efficiently in the presence of two modified sites. In addition, we demonstrate that EcoWI PT-dependent activity has biological function: EcoWI expressing cells restrict dnd+ GpsAAC modified plasmid strongly, and GpsGCC DNA weakly. This work establishes a framework for biotechnology applications of PT-dependent restriction endonucleases (PTDRs).
Persistent and Emerging Organic Pollutants in the Marine Coastal Environment of the Gulf of Milazzo (Southern Italy): Human Health Risk Assessment

The Gulf of Milazzo (north-eastern Sicily) has been recognized as Italian Site of National Interest (SNI; areas characterized by high level of contamination with potential effects on human health) in 2005 because of its high level of pollution. In this study we measured the concentration of polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs), and polyBrominated diphenyl ether (PBDE) in seawater and sediments sampled from the Gulf of Milazzo in order to assess (i) the environmental status of contamination, and (ii) cancer and non-cancer human health risk potentially due to dermal absorption from contaminated seawater and/or ingestion of contaminated fish. Particularly, POPs content in pelagic and demersal fish of different size classes (small, medium, and large) were estimated, starting from the measured seawater and sediments concentrations, using the KABAM model. In particular, Monte Carlo simulation techniques were applied to address uncertainty in assessment of the risk and to provide quantitative estimates of probability of exposition. Ingestion of contaminated pelagic and demersal fish was the dominant pathway of exposition with high probability of significant cancer risk (Ingestion Cancer Risk >10–4) and significant non-cancer risk (Hazard Index >1). No human health risks emerged to be associated to dermal adsorption from contaminated seawater. Benzo(a)pyrene show the highest Ingestion Cancer Risk with respect to the other PAHs, while the highest Hazard Index for non-cancerogenic molecules was estimated for the PBDE47 congener.
The Current State-of-the Art of LRRK2-Based Biomarker Assay Development in Parkinson’s Disease

Evidence is mounting that LRRK2 function, particularly its kinase activity, is elevated in multiple forms of Parkinson’s disease, both idiopathic as well as familial forms linked to mutations in the LRRK2 gene. However, sensitive quantitative markers of LRRK2 activation in clinical samples remain at the early stages of development. There are several measures of LRRK2 activity that could potentially be used in longitudinal studies of disease progression, as inclusion/exclusion criteria for clinical trials, to predict response to therapy, or as markers of target engagement. Among these are levels of LRRK2, phosphorylation of LRRK2 itself, either by other kinases or via auto-phosphorylation, its in vitro kinase activity, or phosphorylation of downstream substrates. This is advantageous on many levels, in that multiple indices of elevated kinase activity clearly strengthen the rationale for targeting this kinase with novel therapeutic candidates, and provide alternate markers of activation in certain tissues or biofluids for which specific measures are not detectable. However, this can also complicate interpretation of findings from different studies using disparate measures. In this review we discuss the current state of LRRK2-focused biomarkers, the advantages and disadvantages of the current pallet of outcome measures, the gaps that need to be addressed, and the priorities that the field has defined.
Creating Neuroscientific Knowledge Organization System Based on Word Representation and Agglomerative Clustering Algorithm

The literature on neuroscience has grown rapidly in recent years with the emergence of new domains of research. In the context of this progress, creating a knowledge organization system (KOS) that can quickly incorporate terms of a given domain is an important aim in the area. In this article, we develop a systematic method based on word representation and the agglomerative clustering algorithm to semi-automatically build a hierarchical KOS. We collected 35,832 research keywords and 11,497 research methods from PubMed Central database, and organized them in a hierarchical structure according to semantic distance. We show that the proposed KOS can help find terms related to the given topics, analyze articles related to specific domains of research, and characterize the features of article clusters. The proposed method can significantly reduce the manual work required by experts to organize the KOS.
Novel Fig-Associated Viroid-Like RNAs Containing Hammerhead Ribozymes in Both Polarity Strands Identified by High-Throughput Sequencing

Based on high-throughput sequencing (HTS) data, the existence of viroid-like RNAs (Vd-LRNAs) associated with fig trees grown in the Hawaiian Islands has been predicted. One of these RNAs has been characterized as a circular RNA ranging in size from 357 to 360 nucleotides. Structural and biochemical features of this RNA, tentatively named fig hammerhead viroid-like RNA (FHVd-LR), markedly resemble those previously reported for several viroids and viroid-like satellite RNAs (Vd-LsatRNAs), which are non-protein-coding RNAs infecting their hosts autonomously and in combination with a helper virus, respectively. The full-length sequence of FHVd-LR variants was determined by RT-PCR, cloning, and sequencing. Despite a low global sequence identity with known viroids and Vd-LsatRNAs, FHVd-LR contains a hammerhead ribozyme (HRz) in each polarity strand. Northern blot hybridization assays identified the circular and linear forms of both polarity strands of FHVd-LR and showed that one strand, assigned the (+) polarity, accumulates at higher levels than the (−) polarity strand in vivo. The (+) polarity RNA assumes a rod-like secondary structure of minimal free energy with the conserved domains of the HRzs located in opposition to each other, a feature typical of several viroids and Vd-LRNAs. The HRzs of both FHVd-LR polarity strands were shown to be active in vitro during transcription, self-cleaving the RNAs at the predicted sites. These data, together with the sequence variability observed in the cloned and sequenced full-length variants, indicate that FHVd-LR is a novel viroid or Vd-LsatRNA. According to HTS data, the coexistence of FHVd-LR of different sizes in the same host cannot be excluded. The relationships of FHVd-LR with previously reported viroids and Vd-LsatRNAs, and the need to perform bioassays to conclusively clarify the biological nature of this circular RNA, are discussed.
Serum Metabolomics Associating With Circulating MicroRNA Profiles Reveal the Role of miR-383-5p in Rat Hippocampus Under Simulated Microgravity

Microgravity impacts various aspects of human health. Yet the mechanisms of spaceflight-induced health problems are not elucidated. Here, we mapped the fusion systemic analysis of the serum metabolome and the circulating microRNAome in a hindlimb unloading rat model to simulate microgravity. The response of serum metabolites and microRNAs to simulated microgravity was striking. Integrated pathway analysis of altered serum metabolites and target genes of the significantly altered circulating miRNAs with Integrated Molecular Pathway-Level Analysis (IMPaLA) software was mainly suggestive of modulation of neurofunctional signaling pathways. Particularly, we revealed significantly increased miR-383-5p and decreased aquaporin 4 (AQP4) in the hippocampus. Using rabies virus glycoprotein–modified exosomes, delivery of miR-383-5p inhibited the expression of AQP4 not only in rat C6 glioma cells in vitro but also in the hippocampus in vivo. Using bioinformatics to map the crosstalk between the circulating metabolome and miRNAome could offer opportunities to understand complex biological systems under microgravity. Our present results suggested that the change of miR-383-5p level and its regulation of target gene AQP4 was one of the potential molecular mechanisms of microgravity-induced cognitive impairment in the hippocampus.
Texture Analysis Based on Sagittal Fat-Suppression and Transverse T2-Weighted Magnetic Resonance Imaging for Determining Local Invasion of Rectal Cancer

Background: Accurate evaluation of local invasion (T-stage) of rectal cancer is essential for treatment planning. A search of PubMed database indicated that the correlation between texture features from T2-weighted magnetic resonance imaging (T2WI) (MRI) and T-stage has not been explored extensively. Purpose: To evaluate the performance of texture analysis using sagittal fat-suppression combined with transverse T2WI for determining T-stage of rectal cancer. Methods: One hundred and seventy-four rectal cancer cases who underwent preoperative MRI were retrospectively selected and divided into high (T3/4) and low (T1/2) T-stage groups. Texture features were, respectively, extracted from sagittal fat-suppression and transverse T2WI images. Univariate and multivariate analyses were conducted to determine T-stage. Discrimination performance was assessed by receiver operating characteristic (ROC) analysis. Results: For univariate analysis, the best performance in differentiating T1/2 from T3/4 tumors was achieved from transverse T2WI, and the area under the ROC curve (AUC) was 0.740. For multivariate analysis, the logical regression model incorporating the independent predictors achieved an AUC of 0.789. Conclusions: Texture features from sagittal fat-suppression combined with transverse T2WI presented moderate association with T-stage of rectal cancer. These findings may be valuable in selecting optimum treatment strategy.
The 5-HT6 Receptors in the Ventrolateral Orbital Cortex Attenuate Allodynia in a Rodent Model of Neuropathic Pain

Mechanical allodynia, characterized by a painful sensation induced by innocuous stimuli, is thought to be caused by disruption in pain-related regions. Identification and reversal of this pathologic neuroadaptation are therefore beneficial for clinical treatment. Previous evidence suggests that 5-HT6 receptors in the ventrolateral orbital cortex (VLO) are involved in neuropathic pain, but their function is poorly understood. The aim of the present study is to unveil the role of 5-HT6 receptors in the VLO and the underlying mechanisms in pain modulation. Here, by using the spared nerve injury (SNI) pain model, first, we report that 5-HT6 receptor protein decreased in the contralateral VLO compared with the ipsilateral VLO in rats with allodynia. Second, microinjection of the selective 5-HT6 receptor agonists EMD-386088 and WAY-208466 into the contralateral VLO consistently and significantly depressed allodynia. Third, microinjection of the selective antagonist SB-258585 blocked the agonist-induced anti-allodynic effect, while the antagonist applied alone to the VLO had no effect. Furthermore, the anti-nociceptive effect of EMD-386088 on neuropathic pain was prevented by the adenylate cyclase (AC) inhibitor SQ-22536, and protein kinase A (PKA) inhibitor H89, suggesting that AC/PKA signaling might underlie the antinociception of agonists. Finally, the 5-HT6 receptors were found to be colocalized with a glutamate transporter (EAAC1) by immunofluorescent staining, and the glutamate receptor antagonist kynurenic acid was found to completely block antinociception. These findings indicated that the antinociceptive effect of 5-HT6 receptor agonists might occur via interaction with the glutamatergic system. Altogether, the agonists activated 5-HT6 receptors present in the glutamatergic neurons in the VLO to facilitate the AC/PKA cascade, which subsequently might evoke glutamate release, thus depressing allodynia. These findings suggest a potential therapeutic role of 5-HT6 receptor agonists in treating neuropathic pain.
Analysis of the telomere length of subpopulations of primary human hematopoietic cells

Telomeres are structures at the ends of eukaryotic chromosomes; they protect the ends from degradation and end-to-end fusions. Mammalian telomeres consist of a tandem array of G-rich repeats, with a length of two to 12 kb in human somatic cells. Somatic cell telomere length shortens with each cell division, leading to senescence or apoptosis. Critically short telomeres can lead to genomic instability, thus in cells that divide continually, such as germ cells, telomere length is maintained by telomerase. In a rare autosomal dominant form of dyskeratosis congenita, patients carry a mutation in the RNA template of telomerase, resulting in half maximal telomerase activity. Patients with this genotype die of aplastic anemia, indicating that maintenance of telomere length is likely critical, and may be particularly important in hematopoietic stem cells. Telomere length can be measured by a quantitative fluorescence in situ hybridisation and flow cytometry based method (FlowFISH). In the present study, this technique was used to measure telomere length in lymphocytes and in "candidate" stem cell populations isolated from eight cadaveric marrow samples from normal adults (aged 14 to 48 years). Telomere length analysis of B and T cells two populations that undergo activation-induced telomerase up-regulation revealed that CD20 + B cells in the bone marrow had longer telomeres than CD3T cells (p<0.002). The CD34+CD38populations from each of the eight donors also had longer telomeres than the T cell subsets. The telomerase activity in T lymphocyte populations thus appears insufficient to prevent telomere shortening during differentiation from the pluripotent stem cell. To compare telomere length in different subsets of primitive hematopoietic ceils, we analysed FACS-purified CD34+CD38and CD34 4CD38 + populations. The CD34+CD38cells had significantly longer telomeres than the CD34 4CD38 + cells (p<0.02, n=8). The Side Population (SP) cells identified by FACS as Hoechst 33342'° cells did not have significantly longer telomeres than the CD34+CD38population. In two donor samples, additional populations were sorted, and the data is consistent with the proposed hierarchical pattern of these cell populations, with CD34+CD38thought to have the greatest proliferative potential and the longest telomeres. This data supports the hypothesis that hematopoietic cells with the greatest proliferative potential will have the longest telomere length. It is still unclear if a hematopoietic cell population exists within the SP with "germ-line" or "fetal" length telomeres. While we cannot exclude that a small subset of more primitive cells capable of maintaining long telomere length exists within the sorted SP cells that were analysed, we conclude that telomere length declines in the majority of the primitive hematopoietic cells examined here. Table of
Reducing Ruminal Ammonia Production With Improvement in Feed Utilization Efficiency and Performance of Murrah Buffalo (Bubalus bubalis) Through Dietary Supplementation of Plant-Based Feed Additive Blend

The study evaluated the potential of blends of eucalyptus oil and aqueous extract of mulethi (root of Glycyrrhiza glabra) to reduce rate of ruminal ammonia production without affecting feed digestion to improve nitrogen utilization efficiency and performance of Murrah buffalo (Bubalus bubalis). Based on preliminary independent studies with graded doses of eucalyptus oil and mulethi root aqueous extract in modulating in vitro rumen fermentation, four blends of feed additive comprising graded doses (5, 10, 15, and 25 μL) of eucalyptus oil and a fixed quantity (15 μL) of aqueous extract of mulethi roots were prepared and examined for their effects on in vitro rumen fermentation and on methane and gas production in 100-mL calibrated glass syringes by standard IVGP protocol. Rumen liquor was collected from four rumen fistulated Murrah buffaloes fed a total mixed ration. Out of four blends, blend-1 comprising 5 μL of eucalyptus oil and 15 μL of aqueous extract (233.6 g/L DW) of mulethi per 40 mL of in vitro medium was found to reduce ammonia production significantly (p < 0.001) without affecting feed digestibility. An equivalent dose of blend-1 (10.5 mL of eucalyptus oil and 7.35 g of mulethi root powder/h/day) fed to four rumen fistulated buffaloes for 24 days resulted in 50% reduction (p < 0.05) in rumen ammonia level with no inhibition in feed fermentation or short-chain fatty acid production. The total bacterial population including Ruminococcus albus, Fibrobacter succinogenes, Butyrivibrio fibrisolvens, and Megasphaera elsdenii as well as anaerobic fungi and methanogenic archaea remained unaffected (p > 0.05). Twelve buffalo calves (avg. BW 137.5 ± 9.2 kg, 8–12 months old) divided into two groups of six each and fed a total mixed ration (concentrate: roughage; 60:40) with or without supplementation of blend-1 for about 3 months demonstrated 14% increase (p < 0.05) in average daily gain in BW with a trend (p < 0.10) in improvement of feed or protein utilization efficiency (1.4 vs. 1.1 g crude protein/g average daily gain; 21.4% increase). Thus, supplementation of eucalyptus oil–mulethi root blend could reduce ruminal ammonia production and improve feed utilization efficiency in ruminants.
Intracranial Large Artery Abnormalities and Association With Cerebral Small Vessel Disease in CADASIL

Background and objective: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited systemic arteriopathy, the classic feature of which is small vessel lesions. Studies on intracranial large arteries in CADASIL are not common. We aim to evaluate intracranial large arteries, describing the characteristics of large arteries in CADASIL and their association with cerebral small vessel associated lesions. Methods: Consecutive CADASIL patients from a single-center prospective cohort were analyzed. Brain magnetic resonance imaging and magnetic resonance angiography were performed to assess the intracranial large arteries and cerebral small vessels associated lesions' neuroimaging. Results: The study included 37 CADASIL patients. Of the patients, 28 of them (75.7%) had intracranial large artery abnormalities. Eighteen (48.6%) had congenital variations such as fenestration, vertebral artery (VA) hypoplasia and agenesis, or common trunk and fetus posterior cerebral artery. Seventeen (45.9%) had acquired anomalies such as arterial stenosis, prolongation, or tortuosity (seven of them had both congenital and acquired anomalies). CADASIL patients with anterior circulation middle cerebral artery (MCA) or internal cerebral artery (ICA) severe stenosis were more likely to have ipsilateral asymmetric white matter hyper-density (WMH) distribution. Patients with posterior circulation VA hypoplasia had a higher prevalence of posterior subcortical zone dominant WMH distribution. Conclusion: CADASIL patients can demonstrate various intracranial large artery abnormalities which might influence the development of microangiopathy. Assessment of great vessels seems essential in CADASIL.