Paleo-climatic control on recharge and fresh-salt groundwater distribution in the Red River delta plain, Vietnam.

Paleo-climatic induced sedimentation controls present-day recharge and the fresh-salt groundwater distribution in Quaternary delta systems. During sea-level highstands, marine clays with saline pore water were deposited and are interbedded with aquifers of coarse-grained sandy fluvial and shallow marine deposits, laid down during lowstands. The low-permeable marine layers may inhibit recent recharge to deeper aquifers, and thereby limit sustainable use of these freshwater resources. This phenomenon has been investigated in the Red River delta plain, using geophysical borehole logging, transient electromagnetic soundings, groundwater chemistry, stable isotope analysis and 3H and 14C dating of groundwater. Results reveal that marine saline pore water is still present in the Holocene marine clays, implying that fresh water has not entered the clays since their deposition. Therefore, recharge within the delta plain is not occurring and the deeper aquifers are hydraulically disconnected from the upper sandy layers. Today, recharge only occurs from the hinterland. Recharge during the last glacial period has flushed saline pore water from Pleistocene marine clays, but these clays were again affected by saline water during the Holocene transgression. The use of the groundwater resources in the delta plain must be adjusted to the present recharge to be sustainable.

A Novel Confocal Scanning Protein-Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin.

Protein-protein interactions (PPIs) are some of the most challenging target classes in drug discovery. Highly sensitive detection techniques are required for the identification of chemical modulators of PPIs. Here, we introduce PPI confocal nanoscanning (PPI-CONA), a miniaturized, microbead based high-resolution fluorescence imaging assay. We demonstrate the capabilities of PPI-CONA by detecting low affinity ternary complex formation between the human CDC34A ubiquitin-conjugating (E2) enzyme, ubiquitin, and CC0651, a small molecule enhancer of the CDC34A-ubiquitin interaction. We further exemplify PPI-CONA with an E2 enzyme binding study on CC0651 and a CDC34A binding specificity study of a series of CC0651 analogues. Our results indicate that CC0651 is highly selective toward CDC34A. We further demonstrate how PPI-CONA can be applied to screening very low affinity interactions. PPI-CONA holds potential for high-throughput screening for modulators of PPI targets and characterization of their affinity, specificity, and selectivity.

Multicenter comparison using two AI stroke CT perfusion software packages for determining thrombectomy eligibility.

BACKGROUND: Stroke AI platforms assess infarcted core and potentially salvageable tissue (penumbra) to identify patients suitable for mechanical thrombectomy. Few studies have compared outputs of these platforms, and none have been multicenter or considered NIHSS or scanner/protocol differences. Our objective was to compare volume estimates and thrombectomy eligibility from two widely used CT perfusion (CTP) packages, Viz.ai and RAPID.AI, in a large multicenter cohort. METHODS: We analyzed CTP data of acute stroke patients with large vessel occlusion (LVO) from four institutions. Core and penumbra volumes were estimated by each software and DEFUSE-3 thrombectomy eligibility assessed. Results between software packages were compared and categorized by NIHSS score, scanner manufacturer/model, and institution. RESULTS: Primary analysis of 362 cases found statistically significant differences in both software's volume estimations, with subgroup analysis showing these differences were driven by results from a single scanner model, the Canon Aquilion One. Viz.ai provided larger estimates with mean differences of 8cc and 18cc for core and penumbra, respectively (p<0.001). NIHSS subgroup analysis also showed systematically larger Viz.ai volumes (p<0.001). Despite volume differences, a significant difference in thrombectomy eligibility was not found. Additional subgroup analysis showed significant differences in penumbra volume for the Phillips Ingenuity scanner, and thrombectomy eligibility for the Canon Aquilion One scanner at one center (7 % increased eligibility with Viz.ai, p=0.03). CONCLUSIONS: Despite systematic differences in core and penumbra volume estimates between Viz.ai and RAPID.AI, DEFUSE-3 eligibility was not statistically different in primary or NIHSS subgroup analysis. A DEFUSE-3 eligibility difference, however, was seen on one scanner at one institution, suggesting scanner model and local CTP protocols can influence performance and cause discrepancies in thrombectomy eligibility. We thus recommend centers discuss optimal scanning protocols with software vendors and scanner manufacturers to maximize CTP accuracy.

Division and retention of floating plastic at river bifurcations.

The transport of floating macroplastics (>2.5 cm) can be impacted by variations in hydrometeorological forcing. Several studies have demonstrated that river discharge, wind, and tides can either accelerate or impede the downstream travel path of plastic. However, there remains a substantial gap in our understanding of the impact of river geomorphological complexity on this process. In this context, the role that river bifurcations play in driving plastic dynamics under different hydrometeorological conditions is largely unexplored. Here, we show that specific plastic item categories react differently to the transport drivers, and bifurcation areas can function both as a retention and release site of plastic litter. We found that hard polyolefin appears to be the most responsive plastic to changes in flow discharge (ρ≈0.40, p≈0.01). Absolute wind velocity magnitude does not correlate to plastic transport. We explored correlations of the various plastic items types with wind vector components in all directions. Multilayer plastics correlated highest to the wind vector component that is most effective in driving plastics from an urban area to the river (ρ≈0.57, p≈0.0001). On a monthly scale, the bifurcation area retained up to 50% of the incoming upstream plastic flux. At other times, an additional 30% was released in the same area. Our results demonstrate how bifurcations distribute different plastic items types downstream under varied hydrometeorological conditions. These yields underscore the importance of assessing floating plastic transport in specific plastic item categories and taking river geomorphological complexity into account.

Short-chain fatty acids and insulin sensitivity: a systematic review and meta-analysis.

CONTEXT: There is substantial evidence that reduced short-chain fatty acids (SCFAs) in the gut are associated with obesity and type 2 diabetes, although findings from clinical interventions that can increase SCFAs are inconsistent. OBJECTIVE: This systematic review and meta-analysis aimed to assess the effect of SCFA interventions on fasting glucose, fasting insulin, and homeostatic model assessment of insulin resistance (HOMA-IR). DATA SOURCES: Relevant articles published up to July 28, 2022, were extracted from PubMed and Embase using the MeSH (Medical Subject Headings) terms of the defined keywords [(short-chain fatty acids) AND (obesity OR diabetes OR insulin sensitivity)] and their synonyms. Data analyses were performed independently by two researchers who used the Cochrane meta-analysis checklist and the PRISMA guidelines. DATA EXTRACTION: Clinical studies and trials that measured SCFAs and reported glucose homeostasis parameters were included in the analysis. Standardized mean differences (SMDs) with 95%CIs were calculated using a random-effects model in the data extraction tool Review Manager version 5.4 (RevMan 5.4). The risk-of-bias assessment was performed following the Cochrane checklist for randomized and crossover studies. DATA ANALYSIS: In total, 6040 nonduplicate studies were identified, 23 of which met the defined criteria, reported fasting insulin, fasting glucose, or HOMA-IR values, and reported change in SCFA concentrations post intervention. Meta-analyses of these studies indicated that fasting insulin concentrations were significantly reduced (overall effect: SMD = -0.15; 95%CI = -0.29 to -0.01, P = 0.04) in treatment groups, relative to placebo groups, at the end of the intervention. Studies with a confirmed increase in SCFAs at the end of intervention also had a significant effect on lowering fasting insulin (P = 0.008). Elevated levels of SCFAs, compared with baseline levels, were associated with beneficial effects on HOMA-IR (P < 0.00001). There was no significant change in fasting glucose concentrations. CONCLUSION: Increased postintervention levels of SCFAs are associated with lower fasting insulin concentrations, offering a beneficial effect on insulin sensitivity. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration number CRD42021257248.

Prevalence of stress and related factors among healthcare students: a cross - sectional study in Can Tho City, Vietnam.

Background: Stress is a major public health issue that can impact both physical and mental well-being. It is prevalent in many areas of modern life, including education. Healthcare students are at a high risk of experiencing stress due to the unique demands of their fields of study. Study design and methods: An online survey was conducted on 2,515 undergraduate students pursuing degrees in medicine, preventive medicine, pharmacy, and nursing at Can Tho University of Medicine and Pharmacy in Can Tho City, Vietnam. Results: Using the Perceived Stress Scale-10 (PSS-10), it was found that 35.2% of students reported mild stress, 62.7% had moderate stress, and only 2.1% experienced severe stress. Multivariable logistic regression analysis revealed nine significant factors associated with students' stress levels (p ≤ 0.05). Particularly, medicine students exhibited a significantly higher level of moderate and severe stress (95% CI = 1.22-2.01), 1.57 times higher than preventive medicine students. Sixth-year students had a stress level 1.58 times higher (95% CI = 1.11-2.26) than first-year students. Students achieving excellent and very good academic performances in the last semester had a stress level 1.60 times higher (95% CI = 1.16-2.22) than students with average and lower academic performance. Students living at home had a stress level 1.73 times higher (95% CI = 1.05-2.84) than students living in their relatives' houses. Students who rarely or never had a part-time job during academic years had a stress level 1.70 times higher (95% CI = 1.31-2.20) than those who often or sometimes had a part-time job. Students with a family history of smoking addiction had a stress level 1.69 times higher (95% CI = 1.28-2.22) than students without such a family history. Students who rarely or never received concern and sharing from family had a stress level 7.41 times higher (95% CI = 5.07-10.84) than students who often or sometimes received concern and sharing from family. Students who were often or sometimes cursed by family had a stress level 2.04 times higher (95% CI = 1.09-3.81) than students who were rarely or never cursed by family. Students without close friends had a stress level 1.46 times higher (95% CI = 1.11-1.91) than students with close friends. Conclusions: The rates of mild and moderate stress levels were significantly higher than severe stress level among healthcare students. Research has provided scientific findings as the basis for determining risk factors and imposing solutions that aim to reduce the rate of stress in students. Therefore, it helps students overcome difficulties and enhance their physical and mental health.

Nanoscaled Discovery of a Shunt Rifamycin from Salinispora arenicola Using a Three-Color GFP-Tagged Staphylococcus aureus Macrophage Infection Assay.

Antimicrobial resistance has emerged as a global public health threat, and development of novel therapeutics for treating infections caused by multi-drug resistant bacteria is urgent. Staphylococcus aureus is a major human and animal pathogen, responsible for high levels of morbidity and mortality worldwide. The intracellular survival of S. aureus in macrophages contributes to immune evasion, dissemination, and resilience to antibiotic treatment. Here, we present a confocal fluorescence imaging assay for monitoring macrophage infection by green fluorescent protein (GFP)-tagged S. aureus as a front-line tool to identify antibiotic leads. The assay was employed in combination with nanoscaled chemical analyses to facilitate the discovery of a new, active rifamycin analogue. Our findings indicate a promising new approach for the identification of antimicrobial compounds with macrophage intracellular activity. The antibiotic identified here may represent a useful addition to our armory in tackling the silent pandemic of antimicrobial resistance.

Reduction in Nuclear Size by DHRS7 in Prostate Cancer Cells and by Estradiol Propionate in DHRS7-Depleted Cells.

Increased nuclear size correlates with lower survival rates and higher grades for prostate cancer. The short-chain dehydrogenase/reductase (SDR) family member DHRS7 was suggested as a biomarker for use in prostate cancer grading because it is largely lost in higher-grade tumors. Here, we found that reduction in DHRS7 from the LNCaP prostate cancer cell line with normally high levels of DHRS7 increases nuclear size, potentially explaining the nuclear size increase observed in higher-grade prostate tumors where it is lost. An exogenous expression of DHRS7 in the PC3 prostate cancer cell line with normally low DHRS7 levels correspondingly decreases nuclear size. We separately tested 80 compounds from the Microsource Spectrum library for their ability to restore normal smaller nuclear size to PC3 cells, finding that estradiol propionate had the same effect as the re-expression of DHRS7 in PC3 cells. However, the drug had no effect on LNCaP cells or PC3 cells re-expressing DHRS7. We speculate that separately reported beneficial effects of estrogens in androgen-independent prostate cancer may only occur with the loss of DHRS7/ increased nuclear size, and thus propose DHRS7 levels and nuclear size as potential biomarkers for the likely effectiveness of estrogen-based treatments.

Groundwater arsenic content in quaternary aquifers of the Red River delta, Vietnam, controlled by the hydrogeological processes.

The relation between arsenic groundwater concentrations and hydrogeological processes was investigated in the proximal part of the Red River delta, Vietnam, west of the depression cone formed by the exploitation of groundwater in Hanoi. Flow paths in the Quaternary aquifers were modeled based on previously interpreted geological structure and hydrogeological data gathered during field work in 2014-2017. Sedimentary structures and simulated flow patterns were compared with the spatial distribution of the groundwater arsenic concentration. The regression of the sea in the area started 4 ka BP in the Holocene. The low tectonic subsidence rate of the Red River delta led to intensive erosion and replacement of fine grained sediments of the sea level high stand by sandy channel belts, resulting in hydraulic connections between the Pleistocene and Holocene aquifers. The Pleistocene aquifer is recharged by both regional flow paths and naturally occurring vertical recharge through Holocene sand and clay layers. Young groundwater (<40 a) in the shallow Holocene aquifer generally discharges to surface water bodies. The shallow flow system is also seasonally recharged with surface water, as indicated by δ18O enrichment of groundwater and oscillating groundwater ages in wells in the vicinity of water channels. The deeper flow system discharges into the Red River and Day River or flows parallel to the rivers, toward the sea. The overall pattern of arsenic groundwater concentrations (decreasing with increasing sediment age) is modified by groundwater flow. The arsenic contamination of the Pleistocene aquifer of the Red River delta is not only caused by the intensive groundwater abstraction in Hanoi, as reported previously, but also by the natural flow of high arsenic groundwater from Holocene to Pleistocene aquifers in areas located outside of the depression cone. Groundwater with < 50 µg L-1 arsenic is found in the Pleistocene aquifer close to the recharge zone in the mountains bordering the Red River delta and in the Holocene and Pleistocene aquifers where clay deposits were eroded. Close to the recent Red River channel, recharge of older Holocene and Pleistocene sediments occurs partially by arsenic-contaminated groundwater from the youngest Holocene aquifers, and here arsenic concentrations exceed 50 µg L-1. A high arsenic concentration is also present in the early Holocene-Pleistocene aquifer, beneath thick clay layers, indicating a limited extent of flushing and the inflow of fresh organic matter.

CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens.

A simplistic assumption in setting up a competition assay is that a low affinity labeled ligand can be more easily displaced from a target protein than a high affinity ligand, which in turn produces a more sensitive assay. An often-cited paper correctly rallies against this assumption and recommends the use of the highest affinity ligand available for experiments aiming to determine competitive inhibitor affinities. However, we have noted this advice being applied incorrectly to competition-based primary screens where the goal is optimum assay sensitivity, enabling a clear yes/no binding determination for even low affinity interactions. The published advice only applies to secondary, confirmatory assays intended for accurate affinity determination of primary screening hits. We demonstrate that using very high affinity ligands in competition-based primary screening can lead to reduced assay sensitivity and, ultimately, the discarding of potentially valuable active compounds. We build on techniques developed in our PyBindingCurve software for a mechanistic understanding of complex biological interaction systems, developing the "CLAffinity tool" for simulating competition experiments using protein, ligand, and inhibitor concentrations common to drug screening campaigns. CLAffinity reveals optimum labeled ligand affinity ranges based on assay parameters, rather than general rules to optimize assay sensitivity. We provide the open source CLAffinity software toolset to carry out assay simulations and a video summarizing key findings to aid in understanding, along with a simple lookup table allowing identification of optimal dynamic ranges for competition-based primary screens. The application of our freely available software and lookup tables will lead to the consistent creation of more performant competition-based primary screens identifying valuable hit compounds, particularly for difficult targets.

Endocrine Regulation of Maturation and Sex Change in Groupers.

Groupers are widely distributed in tropical and subtropical areas worldwide, are key species to coastal ecosystems, and valuable fishery targets. To facilitate artificial seed production technology for grouper aquaculture, the mechanisms of reproduction and gonad development are being elucidated for these important species. In addition, since groupers are sexually dimorphic fish with female-first maturity (protogynous hermaphrodite fish), research is being conducted to clarify the ecological mechanism of sex change and their reproductive physiology, focusing on the endocrine system. In recent years, research on groupers has also been conducted to understand changes in the coastal environment caused by ocean warming and man-made chemicals. However, due to difficulties associated with conducting research using wild populations for breeding experiments, knowledge of the physiology and ecology of these fish is lacking, especially their reproductive physiology. In this review, we present information on the reproductive physiology and endocrinology of groupers obtained to date, together with the characteristics of their life history.

Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion.

Background: Lower survival rates for many cancer types correlate with changes in nuclear size/scaling in a tumor-type/tissue-specific manner. Hypothesizing that such changes might confer an advantage to tumor cells, we aimed at the identification of commercially available compounds to guide further mechanistic studies. We therefore screened for Food and Drug Administration (FDA)/European Medicines Agency (EMA)-approved compounds that reverse the direction of characteristic tumor nuclear size changes in PC3, HCT116, and H1299 cell lines reflecting, respectively, prostate adenocarcinoma, colonic adenocarcinoma, and small-cell squamous lung cancer. Results: We found distinct, largely nonoverlapping sets of compounds that rectify nuclear size changes for each tumor cell line. Several classes of compounds including, e.g., serotonin uptake inhibitors, cyclo-oxygenase inhibitors, ß-adrenergic receptor agonists, and Na+/K+ ATPase inhibitors, displayed coherent nuclear size phenotypes focused on a particular cell line or across cell lines and treatment conditions. Several compounds from classes far afield from current chemotherapy regimens were also identified. Seven nuclear size-rectifying compounds selected for further investigation all inhibited cell migration and/or invasion. Conclusions: Our study provides (a) proof of concept that nuclear size might be a valuable target to reduce cell migration/invasion in cancer treatment and (b) the most thorough collection of tool compounds to date reversing nuclear size changes specific to individual cancer-type cell lines. Although these compounds still need to be tested in primary cancer cells, the cell line-specific nuclear size and migration/invasion responses to particular drug classes suggest that cancer type-specific nuclear size rectifiers may help reduce metastatic spread.

The columbamine O-methyltransferase gene (CoOMT) is capable of increasing alkaloid content in transgenic tobacco plants.

BACKGROUND: In the alkaloid biosynthetic pathways of Stephania and Rannunculaceae, columbamine O-methyltransferase (CoOMT) is an important enzyme that catalyses the formation of the tetrahydropalmatin (rotundin) biosynthesis pathway. In this study, the transgenic construct pBI121-35S-CoOMT-cmyc-Kdel was designed successfully. METHODS AND RESULTS: The real-time RT-PCR results proved that the CoOMT transgene was successfully introduced into Nicotiana tabacum L. plants and produced mRNA. Its transcription levels in three transgenic tobacco lines, T0-7, T0-9, and T0-20, in the T0 generation were higher than those in wild-type tobacco plants. By analysing Western blots and ELISAs, three T0 generation transgenic tobacco lines also expressed recombinant CoOMT (rCoOMT) protein with a molecular weight of approximately 40 kDa, and its contents ranged from 0.048 µg mg-1 to 0.177 µg mg-1. These data illustrated that the CoOMT transgene was expressed; thus, the rCoOMT protein synthesis efficiency increased significantly in comparison with that of the wild-type tobacco plants. The total alkaloid contents ranged from 2.12 g 100 g-1 (of dry weight) to 3.88 g 100 g-1 (of dry weight). The T0-20 plant had the highest total alkaloid content (3.88 g 100 g-1 of dry weight), followed by the T0-7 line (2.75 g 100 g-1 of dry weight). The total alkaloid contents of the CoOMT transgenic tobacco lines increased by approximately 1.09-1.83-fold compared to the wild-type tobacco plants. CONCLUSIONS: This is the first study on the transformation and expression of the CoOMT gene in N. tabacum plants. Initial results of the analysis of transgenic plants proved that the transgenic structure pBI121- CoOMT-Cmyc-Kdel can be used for transformation into Stephania plants.

Groundwater arsenic content related to the sedimentology and stratigraphy of the Red River delta, Vietnam.

Arsenic (As) is highly toxic and over 100 million people living on the floodplains of Asia are exposed to excessive groundwater As. A very large spatial variability over small distances has been observed in the groundwater As concentrations. Advances in the prediction of the As distribution in aquifers would support drinking water management. The application of remote sensing of geomorphic paleo river features combined with geological, geophysical and archeological data and available groundwater As measurements may be used to predict groundwater As levels in rural areas, as shown by the example from the Red River delta, Vietnam. Groundwater in sediments deposited in the marine environment is low in As, probably due to the precipitation of As in sulfide minerals under anoxic conditions. Groundwater As levels in freshwater alluvial deposits in undisturbed floodplain areas are slightly increased and the highest As concentrations are associated with meander belts. The meander belts remain clearly visible in remote sensing and may well reflect the youngest preserved alluvial sediments. High As levels in the meander belt aquifers are probably related to the availability of highly reactive organic matter and consequent reduction of iron oxyhydroxides and As release. Furthermore, given similar hydrogeological conditions, the extent of flushing of As from the youngest alluvial sands is limited compared to the older Pleistocene sands. Even within abandoned meander belts a high spatial variability of As concentrations was observed. The younger channel belts (<1 ka BP) and old Holocene aquifers below undisturbed floodplain environments deposited during a period with high sea level host groundwater enriched in As. Low As groundwater is found in sandy channel belts deposited during the regression of the sea and in Pleistocene islands preserved within the floodplain. The decisive influence of the depositional environment of the aquifer sediments on groundwater As content is revealed.

GmDREB6, a soybean transcription factor, notably affects the transcription of the NtP5CS and NtCLC genes in transgenic tobacco under salt stress conditions.

Soil is contaminated with salinity, which inhibits plant growth and development and reduces crop yields. The DREB (dehydration responsive element binding protein) gene responds to salt stresses through enhanced transcriptional expression and activation of genes involved in plant salinity resistance. In this study, we present the results of the analysis of the expression of the GmDREB6 transgene, a gene that encodes the soybean DREB6 transcription factor, regulating the transcription of the NtP5CS and NtCLC genes in transgenic tobacco under salt stress conditions. The transcription of GmDREB6, NtP5CS, and NtCLC in transgenic tobacco lines was confirmed by qRT-PCR. Under salt stress conditions, the GmDREB6 gene transcription levels in the transgenic tobacco lines L1 and L9 had increased from 2.40- to 3.22- fold compared with the condition without salinity treatment. Two transgenic lines, L1 and L9, had transcription levels of the P5CS gene that had increased from 1.24- to 3.60- fold compared with WT plants. For the NtCLC gene, under salt stress conditions, the transgenic lines had transcription levels that had increased by 3.65-4.54 (fold) compared with WT plants (P < 0.05). The L1-transgenic tobacco line showed simultaneous expression of both the GmDREB6 transgene and two intrinsic genes, the NtP5CS and NtCLC genes. This study demonstrated that expression of the GmDREB6 gene from soybean increases the transcription levels of the NtP5CS and NtCLC genes in transgenic tobacco plants under salt stress conditions. The analysis results have suggested that the GmDREB6 gene is a potential candidate for improving the salt tolerance of plants, opening up research and development opportunities for salt stress-tolerant crops to respond to climate change and the rise in sea levels.

A two-step resin based approach to reveal survivin-selective fluorescent probes.

The identification of modulators for proteins without assayable biochemical activity remains a challenge in chemical biology. The presented approach adapts a high-throughput fluorescence binding assay and functional chromatography, two protein-resin technologies, enabling the discovery and isolation of fluorescent natural product probes that target proteins independently of biochemical function. The resulting probes also suggest targetable pockets for lead discovery. Using human survivin as a model, we demonstrate this method with the discovery of members of the prodiginine family as fluorescent probes to the cancer target survivin.

RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels.

RNA-protein interactions are central to all gene expression processes and contribute to a variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as 'incurable'. Here, we developed a fluorescent on-bead screening platform, RNA Pull-Down COnfocal NAnoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7's primary target is an mRNA of α-synuclein, which contributes to the aetiology of Parkinson's disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of α-synuclein. This opens up new therapeutic avenues towards treatment of Parkinson's disease as well as provides a novel methodology to search for modulators of RNA-protein interaction.

PyBindingCurve, Simulation, and Curve Fitting to Complex Binding Systems at Equilibrium.

Understanding multicomponent binding interactions in protein-ligand, protein-protein, and competition systems is essential for fundamental biology and drug discovery. Hand-deriving equations quickly become unfeasible when the number of components is increased, and direct analytical solutions only exist to a certain complexity. To address this problem and allow easy access to simulation, plotting, and parameter fitting to complex systems at equilibrium, we present the Python package PyBindingCurve. We apply this software to explore homodimer and heterodimer formations culminating in the discovery that under certain conditions, homodimers are easier to break with an inhibitor than heterodimers and may also be more readily depleted. This is a potentially valuable and overlooked phenomenon of great importance to drug discovery. PyBindingCurve may be expanded to operate on any equilibrium binding system and allows definition of custom systems using a simple syntax. PyBindingCurve is available under the MIT license at https://github.com/stevenshave/pybindingcurve as the Python source code accompanied by examples and as an easily installable package within the Python Package Index.

Quantitative Microdialysis: Experimental Protocol and Software for Small Molecule Protein Affinity Determination and for Exclusion of Compounds with Poor Physicochemical Properties.

Quantitative microdialysis is a traditional biophysical affinity determination technique. In the development of the detailed experimental protocol presented, we used commercially available equipment, rapid equilibrium dialysis (RED) devices (ThermoFisher Scientific), which means that it is open to most laboratories. The target protein and test compound are incubated in a chamber partitioned to allow only small molecules to transition to a larger reservoir chamber, then reversed-phase high performance liquid chromatography (RP-HPLC) or liquid chromatography-mass spectrometry (LC-MS) is used to determine the abundance of compound in each chamber. A higher compound concentration measured in the chamber that contains the target protein indicates binding. As a novel, and differentiating contribution, we present a protocol for mathematical analysis of experimental data. We provide the equations and the software to yield dissociation constants for the test compound-target protein complex up to 0.5 mM KD, and we quantitatively discuss the limitations of affinities in relation to measured compound concentrations.

Overexpression of the GmDREB6 gene enhances proline accumulation and salt tolerance in genetically modified soybean plants.

Soybean plants are sensitive to the effects of abiotic stress and belong to the group of crops that are less drought and salt tolerant. The identification of genes involved in mechanisms targeted to cope with water shortage is an essential and indispensable task for improving the drought and salt tolerance of soybean. One of the approaches for obtaining lines with increased tolerance is genetic modification. The dehydration-responsive element binding proteins (DREBs), belonging to the AP2 family, are trans-active transcription factors that bind to the cis-sequences of the promoter for activating the expression of the target genes that mediate drought and salt tolerant responses. In this study, the GmDREB6 transgene was introduced into DT84 cultivar soybean plants, using Agrobacterium-mediated transformation. The efficacy of GmDREB6 overexpression in enhancing the transcriptional level of GmP5CS and proline accumulation in genetically modified (GM) soybean plants was also assayed. The results demonstrated that ten GM soybean plants (T0 generation) were successfully generated from the transformed explants after selecting with kanamycin. Among these plantlets, the presence of the GmDREB6 transgene was confirmed in nine plants by Polymerase Chain Reaction (PCR), and eight plants showed positive results in Southern blot. In the T1 generation, four GM lines, labelled T1-2, T1-4, T1-7, and T1-10, expressed the recombinant GmDREB6 protein. In the T2 generation, the transcriptional levels of the GmP5CS gene were higher in the GM lines than in the non-transgenic plants, under normal conditions and also under conditions of salt stress and drought, ranging from 1.36 to 2.01 folds and 1.58 to 3.16 folds that of the non-transgenic plants, respectively. The proline content was higher in the four GM soybean lines, T2-2, T2-4, T2-7, and T2-10 than in the non-transgenic plants, ranging from 0.82 µmol/g to 4.03 µmol/g. The proline content was the highest in the GM T2-7 line (7.77 µmol/g). In GM soybean lines, T2-2, T2-4, T2-7, and T2-10 proline content increased after plants were subjected to salt stress for seven days, in comparison to that under normal conditions, and ranged from 247.83% to 300%, while that of the non-GM plants was 238.22%. These results suggested that GmDREB6 could act as a potential candidate for genetic engineering for improving tolerance to salt stresses.