PlasCAT: Plasmid Cloud Assembly Tool.

SUMMARY: PlasCAT (Plasmid Cloud Assembly Tool) is an easy-to-use cloud-based bioinformatics tool that enables de novo plasmid sequence assembly from raw sequencing data. Nontechnical users can now assemble sequences from long reads and short reads without ever touching a line of code. PlasCAT uses high-performance computing servers to reduce run times on assemblies and deliver results faster. AVAILABILITY AND IMPLEMENTATION: PlasCAT is freely available on the web at https://sequencing.genofab.com. The assembly pipeline source code and server code are available for download at https://bitbucket.org/genofabinc/workspace/projects/PLASCAT. Click the Cancel button to access the source code without authenticating. Web servers implemented in React.js and Python, with all major browsers supported.

Sequencing Strategy to Ensure Accurate Plasmid Assembly.

Despite the wide use of plasmids in research and clinical production, verifying plasmid sequences is a bottleneck often underestimated in the manufacturing process. While sequencing platforms continue to improve, the chosen method and assembly pipeline still significantly influence the final plasmid assembly sequence. Furthermore, few dedicated tools exist for plasmid assembly, particularly for de novo assembly. Here, we evaluated short-read, long-read, and hybrid (both short and long reads) de novo assembly pipelines across three replicates of a 24-plasmid library. Consistent with previous characterizations of each sequencing technology, short-read assemblies faced challenges in resolving GC-rich regions, and long-read assemblies commonly exhibited small insertions and deletions, especially in repetitive regions. The hybrid approach facilitated the most accurate and consistent assembly generation, identifying mutations relative to the reference sequence. While Sanger sequencing can verify specific regions, some GC-rich and repetitive regions were challenging to resolve using any method, indicating that easily sequenced genetic parts should be prioritized in designing new genetic constructs.

Reliability Generalization of the Triarchic Psychopathy Measure.

The extent to which psychopathy can be reliably assessed via self-report has been debated. One step in informing this debate is examining the internal consistency of self-report psychopathy measures, such as the Triarchic Psychopathy Measure (TriPM; Patrick, 2010). Reliability generalization (RG) studies apply a meta-analytic approach to examine the internal consistency of an instrument in a more robust manner by aggregating internal consistency statistics reported across the published literature. This study conducted an RG analysis to yield the average Cronbach's alpha among published studies (k = 219) that administered the TriPM. Meta-analytic alphas were high for TriPM Total (α = .88) Boldness (α = .81), Meanness (α = .87), and Disinhibition (α = .85). Moderator analyses indicated internal consistency differed minimally as a function of study characteristics, like gender, age, or the nature of the sample (i.e., forensic or community). Subsequent RG analyses were performed for McDonald's omega (k = 40), which yielded comparable internal consistency estimates. The results of this study provide strong evidence that the TriPM measures coherent, internally consistent constructs and thus could be a viable, cost-effective mechanism for measuring psychopathy across a broad range of samples.

Loss of Preproinsulin Interaction with Signal Recognition Particle Activates Protein Quality Control, Decreasing mRNA Stability.

Many insulin gene variants alter the protein sequence and result in monogenic diabetes due to insulin insufficiency. However, the molecular mechanisms of various disease-causing mutations are unknown. Insulin is synthesized as preproinsulin containing a signal peptide (SP). SPs of secreted proteins are recognized by the signal recognition particle (SRP) or by another factor in a SRP-independent pathway. If preproinsulin uses SRP-dependent or independent pathways is still debatable. We demonstrate by the use of site-specific photocrosslinking that the SRP subunit, SRP54, interacts with the preproinsulin SP. Moreover, SRP54 depletion leads to the decrease of insulin mRNA and protein expression, supporting the involvement of the RAPP protein quality control in insulin biogenesis. RAPP regulates the quality of secretory proteins through degradation of their mRNA. We tested five disease-causing mutations in the preproinsulin SP on recognition by SRP and on their effects on mRNA and protein levels. We demonstrate that the effects of mutations are associated with their position in the SP and their severity. The data support diverse molecular mechanisms involved in the pathogenesis of these mutations. We show for the first time the involvement of the RAPP protein quality control pathway in insulin biogenesis that is implicated in the development of neonatal diabetes caused by the Leu13Arg mutation.

Ten simple rules for managing laboratory information.

Information is the cornerstone of research, from experimental (meta)data and computational processes to complex inventories of reagents and equipment. These 10 simple rules discuss best practices for leveraging laboratory information management systems to transform this large information load into useful scientific findings.

An Exploration of Green Burial in the Natural Death Care Movement.

An exploration of the Natural Death Care Movement's economic and eco-friendly mediums of green burial and how the movement is revolutionizing an ecological, sociocultural, and spiritual connection in our inevitable passage toward organic death and decay.

Single-nuclei transcriptome analysis of Huntington disease iPSC and mouse astrocytes implicates maturation and functional deficits.

Huntington disease (HD) is a neurodegenerative disorder caused by expanded CAG repeats in the huntingtin gene that alters cellular homeostasis, particularly in the striatum and cortex. Astrocyte signaling that establishes and maintains neuronal functions are often altered under pathological conditions. We performed single-nuclei RNA-sequencing on human HD patient-induced pluripotent stem cell (iPSC)-derived astrocytes and on striatal and cortical tissue from R6/2 HD mice to investigate high-resolution HD astrocyte cell state transitions. We observed altered maturation and glutamate signaling in HD human and mouse astrocytes. Human HD astrocytes also showed upregulated actin-mediated signaling, suggesting that some states may be cell-autonomous and human specific. In both species, astrogliogenesis transcription factors may drive HD astrocyte maturation deficits, which are supported by rescued climbing deficits in HD drosophila with NFIA knockdown. Thus, dysregulated HD astrocyte states may induce dysfunctional astrocytic properties, in part due to maturation deficits influenced by astrogliogenesis transcription factor dysregulation.

SARS-CoV-2 genotyping and sequencing following a simple and economical RNA extraction and storage protocol.

Since the beginning of the SARS-CoV-2 pandemic, supply chain shortages have caused major disruptions in sourcing the materials needed for laboratory-based molecular assays. With increasing demand for molecular testing, these disruptions have limited testing capacity and hindered efforts to mitigate spread of the virus and new variants. Here we evaluate an economical and reliable protocol for the extraction and short-term ambient temperature storage of SARS-CoV-2 RNA. Additional objectives of the study were to evaluate RNA from this protocol for 1) detection of single nucleotide polymorphisms (SNPs) in the spike gene and 2) whole genome sequencing of SARS-CoV-2. The RNAES protocol was evaluated with residual nasopharyngeal (NP) samples collected from Emory Healthcare and Emory Student Health services. All RNAES extractions were performed in duplicate and once with a commercial extraction robot for comparison. Following extraction, eluates were immediately tested by rRT-PCR. SARS-CoV-2 RNA was successfully detected in 56/60 (93.3%) RNAES replicates, and Ct values corresponded with comparator results. Upon testing in spike SNP assays, three genotypes were identified, and all variant calls were consistent with those previously obtained after commercial extraction. Additionally, the SARS-RNAES protocol yield eluate pure enough for downstream whole genome sequencing, and results were consistent with SARS-CoV-2 whole genome sequencing of eluates matched for Ct value. With reproducible results across a range of virus concentrations, the SARS-RNAES protocol could help increase SARS-CoV-2 diagnostic testing and monitoring for emerging variants in resource-constrained communities.

An altered extracellular matrix-integrin interface contributes to Huntington's disease-associated CNS dysfunction in glial and vascular cells.

Astrocytes and brain endothelial cells are components of the neurovascular unit that comprises the blood-brain barrier (BBB) and their dysfunction contributes to pathogenesis in Huntington's disease (HD). Defining the contribution of these cells to disease can inform cell-type-specific effects and uncover new disease-modifying therapeutic targets. These cells express integrin (ITG) adhesion receptors that anchor the cells to the extracellular matrix (ECM) to maintain the integrity of the BBB. We used HD patient-derived induced pluripotent stem cell (iPSC) modeling to study the ECM-ITG interface in astrocytes and brain microvascular endothelial cells and found ECM-ITG dysregulation in human iPSC-derived cells that may contribute to the dysfunction of the BBB in HD. This disruption has functional consequences since reducing ITG expression in glia in an HD Drosophila model suppressed disease-associated CNS dysfunction. Since ITGs can be targeted therapeutically and manipulating ITG signaling prevents neurodegeneration in other diseases, defining the role of ITGs in HD may provide a novel strategy of intervention to slow CNS pathophysiology to treat HD.

Simple and Economical Extraction of Viral RNA and Storage at Ambient Temperature.

RNA extraction is essential for the molecular detection of common viral pathogens. However, available extraction methods and the need for ultra-cold storage limit molecular testing in resource-constrained settings. Herein, we describe the development of an economical RNAExtraction and Storage (RNAES) protocol that eliminates requirements for instrumentation, expensive materials, and preserved cold chain. Through an iterative process, we optimized viral lysis and RNA binding to and elution from glass fiber membranes included in simple RNAES packets. Efficient viral lysis was achieved with a nontoxic buffer containing sucrose, KCl, proteinase K, and carrier RNA. Viral RNA binding to glass fiber membranes was concentration dependent across seven orders of magnitude (4.0-10.0 log10 copies/µL) and significantly increased with an acidic arginine binding buffer. For the clinical evaluation, 36 dengue virus (DENV)-positive serum samples were extracted in duplicate with the optimized RNAES protocol and once in an EMAG instrument (bioMérieux). DENV RNA was successfully extracted from 71/72 replicates (98.6%) in the RNAES protocol, and real-time RT-PCR cycle threshold (CT) values correlated between extraction methods. DENV RNA, extracted from clinical samples, was stable when stored on dried RNAES membranes at ambient temperature for up to 35 days, with median eluate RNA concentration decreasing by 0.18 and 0.29 log10 copies/µL between day 0 and days 7 and 35, respectively. At a cost of $0.08/sample, RNAES packets address key limitations to available protocols and may increase capacity for molecular detection of RNA viruses. IMPORTANCE RNA extraction methods and ultra-cold storage requirements limit molecular testing for common viruses. We developed a simple, flexible, and economical method that simultaneously addresses these limitations. At $0.08/sample, the new RNAExtraction and Storage (RNAES) protocol successfully extracted viral RNA from acute-phase sera and provided stable, ambient-temperature RNA storage for 35 days. Using this approach, we expect to improve RNA virus detection and outbreak response in resource-constrained settings.

E6/E7 from Beta-2-HPVs 122, 38b, and 107 possess transforming properties in a fibroblast model in vitro.

Beta-2 Human papillomaviruses 38b, 107, and 122 have been frequently found in cervical cancer samples in western Mexico. Because their E6/E7 genes functions are not fully elucidated, we deepen into their transformation capabilities. To achieve this goal, primary human fibroblasts (FB) were transduced with E6/E7 genotype-specific viral particles. Additionally, E6/E7 from HPVs 16 and 18 were included as controls. All E6/E7-cell models increased their lifespan; however, it is important to highlight that FB-E6/E7-122 showed growth as accelerated as FB-E6/E7-16 and 18. Furthermore, both FB-E6/E7-38b and 122 exhibited abilities to migrate, and FB-E6/E7-122 presented high invasive capacity. On the other hand, ΔNp73 expression was found in all cell models, except for FB-pLVX (empty-vector). Finally, RNAseq found differentially expressed genes enriched in signaling pathways related to cell cycle, epithelial-mesenchymal transition, and cancer, among others. This study shows for the first time, the great transformative potential that genotypes of the Beta-2 also possess, especially HPV122. These Beta-2 HPVs can modulate some of the genes that are well known to be regulated by Alpha-HPVs, however, they also possess alternative strategies to modulate diverse signaling pathways. These data support the idea that Beta-2 HPVs should play an important role in co-infections with Alpha-HPV during carcinogenesis.

Current status of inclusion of black participants in neuropsychological studies: A scoping review and call to action.

In recognition that insufficient diversity in research impedes the generalizability of findings and negatively impacts clinical outcomes, the 1993 National Institutes of Health (NIH) Revitalization Act required NIH-funded clinical trials to include and assess outcomes for women and minority participants. Since that time, the American Psychological Association (APA) and the American Academy of Clinical Neuropsychology (AACN) have also acknowledged the reporting of this information as an essential element of research, and they have established similar aspirational goals. Nevertheless, Black communities remain disproportionately underrepresented in neuropsychology research. The objective of this study was to investigate current levels of inclusion and reporting of Black research participation in neuropsychological studies.Publications from high impact neuropsychology journals between 2019-2020 were selected via established methodologies. Studies were analyzed to determine the rates of demographic inclusion and reporting of minority, particularly Black, participants.A total of 1,764 articles were reviewed across seven neuropsychology journals. Of the 653 studies not excluded for other reasons, 43% neglected to include sufficient information about participants' race/ethnicity. Of the subset of eligible studies that did include racial/ethnic demographic information (n = 349), only 61% included any Black participants at all. Only 34.1% of them included enough Black participants equal to or greater than the proportion of Black individuals within the United States.Setting a standard of routinely reporting and analytically reflecting on demographic information is necessary to make valid inferences regarding disease sequelae, treatment, and public health strategies. The authors offer specific recommendations to improve the inclusion and reporting of Black research participation, ensure compliance with established policies, and improve the quality of neuropsychological research.

Cooperation of cell adhesion and autophagy in the brain: Functional roles in development and neurodegenerative disease.

Cellular adhesive connections directed by the extracellular matrix (ECM) and maintenance of cellular homeostasis by autophagy are seemingly disparate functions that are molecularly intertwined, each regulating the other. This is an emerging field in the brain where the interplay between adhesion and autophagy functions at the intersection of neuroprotection and neurodegeneration. The ECM and adhesion proteins regulate autophagic responses to direct protein clearance and guide regenerative programs that go awry in brain disorders. Concomitantly, autophagic flux acts to regulate adhesion dynamics to mediate neurite outgrowth and synaptic plasticity with functional disruption contributed by neurodegenerative disease. This review highlights the cooperative exchange between cellular adhesion and autophagy in the brain during health and disease. As the mechanistic alliance between adhesion and autophagy has been leveraged therapeutically for metastatic disease, understanding overlapping molecular functions that direct the interplay between adhesion and autophagy might uncover therapeutic strategies to correct or compensate for neurodegeneration.

Unexpected Implication of SRP and AGO2 in Parkinson's Disease: Involvement in Alpha-Synuclein Biogenesis.

Parkinson's disease (PD) is a neurodegenerative disorder classified by the loss of dopaminergic neurons in the substantia nigra pars compacta, the region of the brain that is responsible for motor control. Surviving neurons in this region contain aggregated protein alpha-Synuclein (αSyn) in the form of cytoplasmic inclusions, referred to as Lewy bodies. Changes in αSyn expression are also associated with PD and its progression. Previously, we demonstrated that signal recognition particle (SRP) and Argonaute 2 (AGO2) proteins are involved in protein quality control at the ribosome during translation. We also demonstrated that SRP has an mRNA protection function in addition to a protein targeting function, thus controlling mRNA and protein expression. In this study, we tested involvement of these factors in αSyn biogenesis. We hypothesize that loss of these factors may interfere with αSyn expression, and subsequently, be associated with PD. Using depletion assays in human cell culture and analysis of these proteins in the brains of deceased PD patients, we demonstrate that SRP and AGO2 are involved in the control of αSyn expression and AGO2 has reduced expression in PD. We show for the first time that SRP is involved in mRNA protection of αSyn, a protein that does not have a signal sequence or transmembrane span. Our findings suggest that SRP may interact with a hydrophobic domain in the middle of αSyn during translation. Understanding the molecular mechanisms controlling αSyn biogenesis in cells is vital to developing preventative therapies against PD.

Alternative RNA extraction-free techniques for the real-time RT-PCR detection of SARS-CoV-2 in nasopharyngeal swab and sputum samples.

Standard diagnoses of SARS-CoV-2 infections are done by RNA extraction and real-time RT-PCR (rRT-PCR). However, the need for RNA extraction complicates testing due to increased processing time, high cost, and limited availability of commercial kits. Therefore, alternative methods for rRT-PCR detection of SARS-CoV-2 without RNA extraction were investigated. Nasopharyngeal and sputum samples were used to compare the sensitivity of three techniques: Trizol RNA extraction, thermal shock, and the direct use of samples with an RNase inhibitor. Direct, extraction-free use of primary samples plus the RNase inhibitor produced diagnostic values of 100 % sensitivity and specificity compared to standard protocols, and these findings were validated in a second, independent laboratory.

Inpatient early intervention for serious mental illnesses and post-discharge criminal involvement in a high-volume psychiatric hospital setting.

Individuals with serious mental illness (SMI) are at increased risk for arrest and incarceration relative to the same-community population without SMI. Publicly-funded inpatient psychiatric hospitals usually feature short lengths of stay and limited opportunities for extended services that might impact criminal justice involvement after discharge. This study examined the influence of an early intervention program for SMI at a high-volume public psychiatric hospital on involvement in the criminal justice system post-discharge. The Early Onset Treatment Program (EOTP) is an extended service intervention program for uninsured patients who are within 5 years of SMI onset. Criminal justice records (number of arrests with conviction, days of incarceration) were obtained for EOTP participants (n = 164) and comparison patients (n = 164) matched on demographics, diagnosis, and discharge date via propensity score matching. Data were zero-inflated and analyzed using hurdle models, controlling for prior arrests. The EOTP group was less likely to be convicted of at least one crime post-discharge (0 arrests vs. > 0, p < .001), and spent fewer days incarcerated (if incarcerated ≥1 day, p < .03). Participation in the EOTP service was linked to reduced likelihood of post-discharge arrest and days incarcerated. Several alternative variables may contribute to this preliminary observation, including length of stay, medication adherence, longer environmental stability, and individual patient characteristics.

Anti-Inflammatory and Immunomodulatory Effects of the Grifola frondosa Natural Compound o-Orsellinaldehyde on LPS-Challenged Murine Primary Glial Cells. Roles of NF-κß and MAPK.

In response to foreign or endogenous stimuli, both microglia and astrocytes adopt an activated phenotype that promotes the release of pro-inflammatory mediators. This inflammatory mechanism, known as neuroinflammation, is essential in the defense against foreign invasion and in normal tissue repair; nevertheless, when constantly activated, this process can become detrimental through the release of neurotoxic factors that amplify underlying disease. In consequence, this study presents the anti-inflammatory and immunomodulatory properties of o-orsellinaldehyde, a natural compound found by an in silico approach in the Grifola frondosa mushroom, in astrocytes and microglia cells. For this purpose, primary microglia and astrocytes were isolated from mice brain and cultured in vitro. Subsequently, cells were exposed to LPS in the absence or presence of increasing concentrations of this natural compound. Specifically, the results shown that o-orsellinaldehyde strongly inhibits the LPS-induced inflammatory response in astrocytes and microglia by decreasing nitrite formation and downregulating iNOS and HO-1 expression. Furthermore, in microglia cells o-orsellinaldehyde inhibits NF-κB activation; and potently counteracts LPS-mediated p38 kinase and JNK phosphorylation (MAPK). In this regard, o-orsellinaldehyde treatment also induces a significant cell immunomodulation by repolarizing microglia toward the M2 anti-inflammatory phenotype. Altogether, these results could partially explain the reported beneficial effects of G. frondosa extracts on inflammatory conditions.

Childbearing vs. clinical trial participation: is it one or the other?

Recent advances have shed light on the importance of early therapeutic intervention for neurodegenerative diseases. Primary prevention trials present a potential disease-modifying strategy for pre-symptomatic patients of autosomal dominant neurodegenerative diseases (ADND), such as early onset familial Alzheimer's disease (AD) and Huntington's disease (HD). As trials target earlier disease stages, however, prospective participants face new ethical and logistical challenges, namely childbearing and reproductive health decisions. Since pregnancy is an exclusion criteria for such trials, participants of reproductive age must choose between participating in research and having a family. Such decisions carry significant burdens for ADND patients that if left unaddressed could impact patient well-being and the field as whole. We use our perspective as scientists, advocates, and ADND family members to highlight current shortcomings in the field regarding trial participation and family planning issues for ADND patients and call for the establishment of a normative standard to address these concerns.

Induction of Short-Term Sensitization by an Aversive Chemical Stimulus in Zebrafish Larvae.

Larval zebrafish possess a number of molecular and genetic advantages for rigorous biological analyses of learning and memory. These advantages have motivated the search for novel forms of memory in these animals that can be exploited for understanding the cellular and molecular bases of vertebrate memory formation and consolidation. Here, we report a new form of behavioral sensitization in zebrafish larvae that is elicited by an aversive chemical stimulus [allyl isothiocyanate (AITC)] and that persists for ≥30 min. This form of sensitization is expressed as enhanced locomotion and thigmotaxis, as well as elevated heart rate. To characterize the neural basis of this nonassociative memory, we used transgenic zebrafish expressing the fluorescent calcium indicator GCaMP6 (Chen et al., 2013); because of the transparency of larval zebrafish, we could optically monitor neural activity in the brain of intact transgenic zebrafish before and after the induction of sensitization. We found a distinct brain area, previously linked to locomotion, that exhibited persistently enhanced neural activity following washout of AITC; this enhanced neural activity correlated with the behavioral sensitization. These results establish a novel form of memory in larval zebrafish and begin to unravel the neural basis of this memory.

Hydration of α-UO3 following storage under controlled conditions of temperature and relative humidity.

Changes in chemical speciation of uranium oxides following storage under varied conditions of temperature and relative humidity are valuable for characterizing material provenance. In this study, subsamples of high purity α-UO3 were stored under four sets of controlled conditions of temperature and relative humidity over several years, and then measured periodically for chemical speciation. Powder X-ray diffraction (XRD) analysis and extended X-ray absorption fine structure spectroscopy confirm hydration of α-UO3 to a schoepite-like end product following storage under each of the varied storage conditions, but the species formed during exposure to the lower relative humidity and lower temperature condition follows different trends from those formed under the other three storage conditions (high relative humidity with high or low temperatures, and low relative humidity with a high temperature). Thermogravimetry coupled with XRD analysis was carried out to distinguish desorption pathways of water from the hydrated end products. Density functional theory calculations discern changes in the structure of α-UO3 following incorporation of 1, 2 or 3 H2O molecules or 1, 2 or 3 OH groups into the orthorhombic lattice, revealing differences in lattice constants, U-O bond lengths, and U-U distances. The collective results from this analysis are in contrast to analogous studies that report that U3O8 is oxidized and hydrated in air during storage under high relative humidity conditions.