Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW-DNA extraction protocols

Marine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However, extracting high molecular weight DNA from marine organisms and subsequent DNA library preparation for whole genome sequencing is challenging. The challenges can be explained by excessive metabolites secretion that co-precipitates with DNA and barricades their sequencing. In this work, we sought to resolve this issue by describing an optimized isolation method and comparing its performance with the most commonly reported protocols or commercial kits: SDS/phenol–chloroform method, Qiagen Genomic Tips kit, Qiagen DNeasy Plant mini kit, a modified protocol of Qiagen DNeasy Plant kit, Qiagen DNeasy Blood and Tissue kit, and Qiagen Qiamp DNA Stool mini kit. Our method proved to work significantly better for different marine species regardless of their shape, consistency, and sample preservation, improving Oxford Nanopore Technologies sequencing yield by 39 folds for Spirobranchus sp. and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples

210Po Log-normal distribution in human urines: Survey from Central Italy people

The death in London of the former secret service agent Alexander Livtinenko on 23 November 2006 generally attracted the attention of the public to the rather unknown radionuclide 210Po. This paper presents the results of a monitoring programme of 210Po background levels in the urines of noncontaminated people living in Central Italy (near the Republic of S. Marino). The relationship between age, sex, years of smoking, number of cigarettes per day, and 210Po concentration was also studied. The results indicated that the urinary 210Po concentration follows a surprisingly perfect Log-normal distribution. Log 210Po concentrations were positively correlated to age (p < 0.0001), number of daily smoked cigarettes (p = 0.006), and years of smoking (p = 0.021), and associated to sex (p = 0.019). Consequently, this study provides upper reference limits for each sub-group identified by significantly predictive variables

Molecular investigation of waterborne protozoan contamination using marine Demospongiae

Sponges play important role within aquatic ecosystems due to their diverse abilities including filter-based feeding mechanisms. Hence, this study evaluated the potential use of sponges as ecological biomonitors for water safety surveillance, especially in the presence of Waterborne protozoan pathogens WBPP. Sponge specimens were collected from different Qatari marine ecosystems and subjected to gDNA extraction and real-time PCR using specific primer sets for the most common WBPP. Two sponges from the coastal marine ecosystems were found to be positive for Blastocystis sp., and one sponge was positive for Dientamoeba fragilis within offshore site. No Cryptosporidium spp., Giardia duodenalis, nor Toxoplasma gondii were detected. Further genotyping analysis revealed that the Blastocystis sp. positive samples were subtype ST3 (allele 34), which matched local clinical isolates and D. fragilis specimen was unambiguously clustering with Genotype 2. In conclusion, this study demonstrates the role of marine sponges as ecological biomonitors for WBPP screening and provide insights into these pathogens widespread and their potential transmission to marine and terrestrial organisms including human

Socket Shield Technique to Improve the Outcomes of Immediate Implant: A Systematic Review and Meta-Analysis

Background: The socket shield technique (SST) could address the challenges in immediate implant placement by minimizing post-extraction bone resorption while maintaining soft tissue levels. This study aimed to summarize the available evidence and systematically assess the effectiveness of SST immediate implant placement regarding all outcomes (bone loss, esthetics, implant stability, probing depth, complications, and survival rate). Methods: We searched seven electronic databases through April 2023 to identify randomized clinical trials that assessed the effect of immediate implant placed with SST (test group) versus other implant placement protocols without SST. The risk of bias was assessed using Cochrane’s randomized trial quality assessment Tool (RoB 2.0). Random-effects meta-analysis was conducted, with mean difference and 95% confidence intervals (MD, 95% CI) as effect estimates. We used the GRADE approach to assess the certainty of evidence. Results: Twelve RCTs, involving 414 immediate implants, placed in 398 patients, were included. Meta-analyses revealed that the immediate implants placed with SST had a statistically significant decrease in horizontal (MD = −0.28, 95% CI [−0.37, −0.19], p < 0.0001), vertical (MD = −0.85, 95% CI [−1.12, −0.58], p < 0.0001), and crestal (MD = −0.35, 95% CI [−0.56, −0.13], p = 0.002) bone loss, as well as probing depth (MD = −0.64, 95% CI [−0.99, −0.29], p = 0.0003). Additionally, SST had a significant increase in implant stability (MD = 3.46, 95 % CI [1.22, 5.69], p = 0.002) and pink esthetic score (MD = 1.60, 95% CI [0.90, 2.30], p < 0.0001). Only two studies reported shield exposure incidences in the SST group; however, all studies revealed no implant failure and a 100% survival rate. The evidence certainty was assessed as very low. Conclusions: Based on limited evidence, SST was more effective in minimizing bone resorption and improving implant stability and esthetic outcomes than conventional immediate implant placement. Still, SST could not be recommended as a routine clinical protocol due to the lack of a standardized surgical approach; thus, further high-quality RCTs are required to support this conclusion.Scopu

A putative relay circuit providing low-threshold mechanoreceptive input to lamina I projection neurons via vertical cells in lamina II of the rat dorsal horn

Background: Lamina I projection neurons respond to painful stimuli, and some are also activated by touch or hair movement. Neuropathic pain resulting from peripheral nerve damage is often associated with tactile allodynia (touch-evoked pain), and this may result from increased responsiveness of lamina I projection neurons to non-noxious mechanical stimuli. It is thought that polysynaptic pathways involving excitatory interneurons can transmit tactile inputs to lamina I projection neurons, but that these are normally suppressed by inhibitory interneurons. Vertical cells in lamina II provide a potential route through which tactile stimuli can activate lamina I projection neurons, since their dendrites extend into the region where tactile afferents terminate, while their axons can innervate the projection cells. The aim of this study was to determine whether vertical cell dendrites were contacted by the central terminals of low-threshold mechanoreceptive primary afferents. Results: We initially demonstrated contacts between dendritic spines of vertical cells that had been recorded in spinal cord slices and axonal boutons containing the vesicular glutamate transporter 1 (VGLUT1), which is expressed by myelinated low-threshold mechanoreceptive afferents. To confirm that the VGLUT1 boutons included primary afferents, we then examined vertical cells recorded in rats that had received injections of cholera toxin B subunit (CTb) into the sciatic nerve. We found that over half of the VGLUT1 boutons contacting the vertical cells were CTb-immunoreactive, indicating that they were of primary afferent origin. Conclusions: These results show that vertical cell dendritic spines are frequently contacted by the central terminals of myelinated low-threshold mechanoreceptive afferents. Since dendritic spines are associated with excitatory synapses, it is likely that most of these contacts were synaptic. Vertical cells in lamina II are therefore a potential route through which tactile afferents can activate lamina I projection neurons, and this pathway could play a role in tactile allodynia

Neuronal circuitry for pain processing in the dorsal horn

Neurons in the spinal dorsal horn process sensory information, which is then transmitted to several brain regions, including those responsible for pain perception. The dorsal horn provides numerous potential targets for the development of novel analgesics and is thought to undergo changes that contribute to the exaggerated pain felt after nerve injury and inflammation. Despite its obvious importance, we still know little about the neuronal circuits that process sensory information, mainly because of the heterogeneity of the various neuronal components that make up these circuits. Recent studies have begun to shed light on the neuronal organization and circuitry of this complex region

Phytic acid attenuates acetaminophen-induced hepatotoxicity via modulating iron-mediated oxidative stress and SIRT-1 expression in mice

Introduction: Administration of high doses of acetaminophen (APAP) results in liver injury. Oxidative stress and iron overload play roles in the pathogenesis of APAP-induced hepatotoxicity. The present study assessed the potential hepatoprotective effects of phytic acid (PA), a natural antioxidant and iron chelator, on APAP-induced hepatotoxicity and the possible underlying mechanism through its effects on CYP2E1 gene expression, iron homeostasis, oxidative stress, and SIRT-1 expression levels.Methods: Twenty-four adult male albino mice were used in this study. Mice were divided into four groups (six mice in each group): control, APAP-treated, PA-treated and APAP + PA-treated groups. Liver function tests, serum and liver tissue iron load were evaluated in all the study groups. Hepatic tissue homogenates were used to detect oxidative stress markers, including malondialdehyde (MDA) and reduced glutathione (GSH). Histological hepatic evaluation and immunohistochemistry of SIRT-1 were performed. Quantitative real-time PCR was used for the assessment of CYP2E1 and SIRT-1 gene expressions. APAP-induced biochemical and structural hepatic changes were reported.Results: PA administration showed beneficial effects on APAP-induced hepatotoxicity through improvements in liver functions, decreased CYP2E1 gene expression, decreased serum and liver iron load, decreased MDA, increased GSH, increased SIRT-1 expression level and improvement in hepatic architecture.Conclusion: Conclusively, PA can be considered a potential compound that can attenuate acetaminophen-induced hepatotoxicity through its role as an iron chelator and antioxidant, as well as the up-regulation of SIRT-1 and down-regulation of CYP2E1

Predicting the environmental suitability for onchocerciasis in Africa as an aid to elimination planning

Recent evidence suggests that, in some foci, elimination of onchocerciasis from Africa may be feasible with mass drug administration (MDA) of ivermectin. To achieve continental elimination of transmission, mapping surveys will need to be conducted across all implementation units (IUs) for which endemicity status is currently unknown. Using boosted regression tree models with optimised hyperparameter selection, we estimated environmental suitability for onchocerciasis at the 5 × 5-km resolution across Africa. In order to classify IUs that include locations that are environmentally suitable, we used receiver operating characteristic (ROC) analysis to identify an optimal threshold for suitability concordant with locations where onchocerciasis has been previously detected. This threshold value was then used to classify IUs (more suitable or less suitable) based on the location within the IU with the largest mean prediction. Mean estimates of environmental suitability suggest large areas across West and Central Africa, as well as focal areas of East Africa, are suitable for onchocerciasis transmission, consistent with the presence of current control and elimination of transmission efforts. The ROC analysis identified a mean environmental suitability index of 0.71 as a threshold to classify based on the location with the largest mean prediction within the IU. Of the IUs considered for mapping surveys, 50.2% exceed this threshold for suitability in at least one 5×5-km location. The formidable scale of data collection required to map onchocerciasis endemicity across the African continent presents an opportunity to use spatial data to identify areas likely to be suitable for onchocerciasis transmission. National onchocerciasis elimination programmes may wish to consider prioritising these IUs for mapping surveys as human resources, laboratory capacity, and programmatic schedules may constrain survey implementation, and possibly delaying MDA initiation in areas that would ultimately qualify