Cell lineage-guided mass spectrometry reveals increased energy metabolism and reactive oxygen species in the vertebrate organizer.

Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been mostly limited to transcripts and a few proteins, the latter due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog (X. laevis), a popular model of development, has long been known to be the origin of signals that pattern the mesoderm and central nervous system. Molecular screens of the SMO have identified several genes responsible for the ability of the SMO to establish the body axis. Nonetheless, a comprehensive study of proteins and metabolites produced specifically in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the remainder of the embryo using high-resolution mass spectrometry (HRMS). Quantification of ~4,600 proteins and a panel of targeted metabolites documented differential expression for 460 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the SMO. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO. Chemical perturbation of the redox gradient perturbed mesoderm involution during early gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.

Cell Lineage-Guided Microanalytical Mass Spectrometry Reveals Increased Energy Metabolism and Reactive Oxygen Species in the Vertebrate Organizer.

Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been limited to transcripts and some proteins due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog ( X. laevis ), a popular model of development, has long been discovered to induce the patterning of the central nervous system. Molecular screens on the tissue have identified several genes, such as goosecoid, chordin, and noggin, with independent ability to establish a body axis. A comprehensive study of proteins and metabolites produced in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the rest of the embryo using liquid chromatography high-resolution mass spectrometry (HRMS). Quantification of ∼4,600 proteins and a panel of metabolites documented differential expression for ∼450 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation (OXPHOS) and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the Organizer. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO tissue. Chemical perturbation of the redox gradient affected mesoderm involution during early tissue movements of gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.

Temporal considerations in the 2021 COVID-19 lockdown of Ho Chi Minh City

The success of Vietnam in controlling the spread of COVID-19 hinges on a timely implementation of its coherent strategy of containment and rapid tracing and testing efforts. The Vietnamese living in Mekong Delta are currently being besieged by the SARS-Cov-2 Delta variant as they undergo several and extended levels of lockdown. In this work we examine the temporal aspects of the lockdown in Ho Chi Minh City and predict the progress of the outbreak in terms of the total number of confirmed cases. A compartmental model with containment is fit to data to estimate the rate of transmission in Ho Chi Minh City. The severity of the lockdown is estimated from publicly-available data on mobility and coupled to the rate of infection. Various scenarios on when to begin a lockdown and its duration are assessed. This report, dated 27 July 2021, supports a lockdown of at least 3 weeks and predicts that there could be half as many cases had the inevitable lockdown started a week earlier.

Activity pulses induce spontaneous flow reversals in viscoelastic environments.

Complex interactions between cellular systems and their surrounding extracellular matrices are emerging as important mechanical regulators of cell functions, such as proliferation, motility and cell death, and such cellular systems are often characterized by pulsating actomyosin activities. Here, using an active gel model, we numerically explore spontaneous flow generation by activity pulses in the presence of a viscoelastic medium. The results show that cross-talk between the activity-induced deformations of the viscoelastic surroundings and the time-dependent response of the active medium to these deformations can lead to the reversal of spontaneously generated active flows. We explain the mechanism behind this phenomenon based on the interaction between the active flow and the viscoelastic medium. We show the importance of relaxation time scales of both the polymers and the active particles and provide a phase space over which such spontaneous flow reversals can be observed. Our results suggest new experiments investigating the role of controlled pulses of activity in living systems ensnared in complex mircoenvironments.

Anthocyanin Colorimetric Strip for Volatile Amine Determination.

Food freshness is one of the main concerns of consumers. Food spoilage is mainly caused by contamination and microbial growth in which the latter produces volatile amines in the process. Several methods have been used to determine volatile amines to indicate food freshness, and indicator films are deemed as the most time-efficient and economical. In this study, anthocyanin was extracted from mangosteen rind as a natural dye indicator and was incorporated in a chitosan/PVA polymer matrix. The film with different concentrations of anthocyanin extract (5%, 15%, and 25%) was prepared and tested for their sensitivity to 136 ppm ammonia vapor followed by colorimetric analysis using ImageJ software. The film with 25% anthocyanin yielded the most visible color change upon exposure to ammonia vapor. The color changed from pink to yellowish-brown within 14 minutes of exposure. The RGB-converted images of the film with 25% anthocyanin extract showed gradual loss of red coloration being replaced by cyan spots. FTIR spectra showed incorporation of anthocyanin to the chitosan/PVA matrix with the decrease in the intensity of the C-N stretching peak. Thermogravimetric analysis showed that the film has high thermal stability with onset temperature of 310.43°C. Thus, the film developed is an excellent candidate for optimization and production of a thermally stable amine detector for food products.

Enhancement of mixing by rodlike polymers.

We study the mixing of a passive scalar field dispersed in a solution of rodlike polymers in two dimensions, by means of numerical simulations of a rheological model for the polymer solution. The flow is driven by a parallel sinusoidal force (Kolmogorov flow). Although the Reynolds number is lower than the critical value for inertial instabilities, the rotational dynamics of the polymers generates a chaotic flow similar to the so-called elastic-turbulence regime observed in extensible polymer solutions. The temporal decay of the variance of the scalar field and its gradients shows that this chaotic flow strongly enhances mixing.

Insights into arsenic retention dynamics of Pleistocene aquifer sediments by in situ sorption experiments.

The migration of arsenic (As) enriched groundwater into Pleistocene aquifers as a consequence of extensive groundwater abstraction represents an increasing threat to the precious water resources in Asian delta regions. Pleistocene aquifer sediments are typically rich in FeIII-(hydr)oxides and are capable to adsorb high amounts of As. This results in a pronounced accumulation of As in Pleistocene aquifers, where high As groundwater infiltrates from adjacent Holocene aquifers. However, As retention by Pleistocene aquifers over long-term time scales remains largely unknown. We studied As sorption in situ by placing natural Pleistocene sediments and pure mineral phases directly inside groundwater monitoring wells at a study site near Hanoi (Vietnam). This in situ exposure allows for constant flushing of the samples with unaltered groundwater and the establishment of undisturbed sorption equilibria similar to those in local aquifer sediments, which is not readily attainable in traditional laboratory sorption experiments. The groundwaters in our experimental wells were characterized by different As concentrations (0.01-6.63 µmol/L) and redox states, reaching from suboxic to anoxic conditions (Eh of +159 to -4 mV). Results show that adsorption is the dominant As retention mechanism, independent from the respective groundwater chemistry (i.e. concentrations of dissolved P, HCO3- and Si). Whilst most of the As sorbed within the first week, sorption further increased slowly but consistently by 6-189%, respectively, within six months. Hence, the As sorption behavior of Pleistocene aquifer sediments should be determined over longer periods to avoid an underestimation of the As sorption capacity. Accompanying desorption experiments revealed that about 51% of the sorbed As was remobilized within six months when exposed to low As groundwater. We therefore conclude that a considerable proportion of the As accumulated in the aquifer sediments is prone to remobilization once the As concentrations in migrating groundwater decline. Remobilization of As should be considered in local water management plans to avoid contamination of precious groundwater resources with this As legacy.

Biogeochemical phosphorus cycling in groundwater ecosystems - Insights from South and Southeast Asian floodplain and delta aquifers.

The biogeochemical cycling of phosphorus (P) in South and Southeast Asian floodplain and delta aquifers has received insufficient attention in research studies, even though dissolved orthophosphate (PO43-) in this region is closely linked with the widespread contamination of groundwater with toxic arsenic (As). The overarching aim of this study was to characterize the enrichment of P in anoxic groundwater and to provide insight into the biogeochemical mechanisms underlying its mobilization, subsurface transport, and microbial cycling. Detailed groundwater analyses and in situ experiments were conducted that focused on three representative field sites located in the Red River Delta (RRD) of Vietnam and the Bengal Delta Plain (BDP) in West Bengal, India. The results showed that the total concentrations of dissolved P (TDP) ranged from 0.03 to 1.50 mg L-1 in groundwater, with PO43- being the dominant P species. The highest concentrations occurred in anoxic sandy Holocene aquifers where PO43- was released into groundwater through the microbial degradation of organic carbon and the concomitant reductive dissolution of Fe(III)-(hydr)oxides. The mobilization of PO43- may still constitute an active process within shallow Holocene sediments. Furthermore, a sudden supply of organic carbon may rapidly decrease the redox potential, which causes an increase in TDP concentrations in groundwater, as demonstrated by a field experiment. Considering the subsurface transport of PO43-, Pleistocene aquifer sediments represented effective sinks; however, the enduring contact between oxic Pleistocene sediments and anoxic groundwater also changed the sediments PO43--sorption capacity over time. A stable isotope analysis of PO43--bound oxygen indicated the influences of intracellular microbial cycling as well as a specific PO43- source with a distinct isotopically heavy signal. Consequently, porous aquifers in Asian floodplain and delta regions proved to be ideal natural laboratories to study the biogeochemical cycling of P and its behavior in groundwater environments.

Analytical characteristics and comparative evaluation of Aptima HCV quant Dx assay with the Abbott RealTime HCV assay and Roche COBAS AmpliPrep/COBAS TaqMan HCV quantitative test v2.0.

BACKGROUND: The Aptima HCV Quant Dx assay (Aptima assay) is a fully automated quantitative assay on the Panther® system. This assay is intended for confirmation of diagnosis and monitoring of HCV RNA in plasma and serum specimens. The purpose of the testing described in this paper was to evaluate the performance of the Aptima assay. METHODS: The analytical sensitivity, analytical specificity, precision, and linearity of the Aptima assay were assessed. The performance of the Aptima assay was compared to two commercially available HCV assays; the Abbott RealTime HCV assay (Abbott assay, Abbott Labs Illinois, USA) and the Roche COBAS Ampliprep/COBAS Taqman HCV Quantitative Test v2.0 (Roche Assay, Roche Molecular Systems, Pleasanton CA, USA). The 95% Lower Limit of Detection (LoD) of the assay was determined from dilutions of the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) and HCV positive clinical specimens in HCV negative human plasma and serum. Probit analysis was performed to generate the 95% predicted detection limits. The Lower Limit of Quantitation (LLoQ) was established for each genotype by diluting clinical specimens and the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) in HCV negative human plasma and serum. Specificity was determined using 200 fresh and 536 frozen HCV RNA negative clinical specimens including 370 plasma specimens and 366 serum specimens. Linearity for genotypes 1 to 6 was established by diluting armored RNA or HCV positive clinical specimens in HCV negative serum or plasma from 8.08 log IU/mL to below 1 log IU/mL. Precision was tested using a 10 member panel made by diluting HCV positive clinical specimens or spiking armored RNA into HCV negative plasma and serum. A method comparison was conducted against the Abbott assay using 1058 clinical specimens and against the Roche assay using 608 clinical specimens from HCV infected patients. In addition, agreement between the Roche assay and the Aptima assay using specimens with low HCV concentrations (

Emergence of chaos in a viscous solution of rods.

It is shown that the addition of small amounts of microscopic rods in a viscous fluid at low Reynolds number causes a significant increase of the flow resistance. Numerical simulations of the dynamics of the solution reveal that this phenomenon is associated to a transition from laminar to chaotic flow. Polymer stresses give rise to flow instabilities which, in turn, perturb the alignment of the rods. This coupled dynamics results in the activation of a wide range of scales, which enhances the mixing efficiency of viscous flows.

A new ultrasensitive assay for quantitation of HIV-1 RNA in plasma.

Nucleic acid-based diagnostic assays for the quantitation of plasma HIV-1 RNA levels are used to monitor disease progression and the response of patients to antiretroviral drug therapy. The LCx HIV RNA Quantitative Assay (Abbott Laboratories, North Chicago, IL) is an assay for the quantitation of HIV type 1 RNA in plasma that uses competitive reverse transcription PCR (RT-PCR) followed by Microparticle Enzyme Immunoassay, and includes an internal control for inhibition and RNA recovery, that is taken through the entire sample preparation procedure. The performance of the assay was assessed for 1 and 0.2 ml sample volumes. For a 1 ml sample volume, the lower limit of detection was found to be 50 copies/ml with a linear range from 50 to 1 million copies/ml. For a 0.2 ml sample volume, the lower limit of detection was found to be 178 copies/ml with a linear range from 178 to 5 million copies/ml. The assay is able to detect and quantitate HIV subtypes A-G and group O. LCx HIV RNA assay quantitation results are highly correlated to the standard and ultrasensitive Amplicor HIV-1 Monitor assay (Roche Molecular Systems) quantitation results. Assay performance is consistent with the use of this test for routine quantitation of HIV-1 RNA in plasma.