Simple evanescent field sensor for NIR spectroscopy

Near-Infrared (NIR) spectroscopy is a powerful tool for chemical analysis in applications ranging from biomedicine to analysis of food products and textiles [1]. However, molar absorptivities in this spectral region are usually weak, so that high-sensitivity measurement devices are required. Optical waveguides provide for highly sensitive attenuated total reflection (ATR) spectroscopy in a robust mass-producible format, and allow for ultra-small sample volume, due to the 100 nm scale extent of the evanescent field, and the potential for lab-on-chip integration

T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation

A microflow cytometer for microsphere-based immunoassays using integrated optics and inertial particle focussing

We present work towards a microflow cytometer for performing multiplex immunoassays using commercially available fluorescently-labelled microspheres. The device consists of a silica chip with integrated GeO2:SiO2 channel waveguides which deliver excitation light orthogonally to an etched flow channel [1], [2]. The rectangular cross section, 2:1 aspect ratio flow channel and flow rate create an inertial focussing effect on the microspheres [3] which ensures they flow through the plane of maximum optical excitation, halfway up the height of the channel, with minimal positional variation. The optical waveguide core is fabricated by magnetron sputtering of GeO2:SiO2 films which are then etched to form channel waveguides by ICP etching. The silica cladding, up to 13.5 µm thick, is deposited by either flame hydrolysis deposition or a combination of magnetron sputtering followed by PECVD. Fluidic channels are etched with ICP etching. Channels with the dimensions of 14.1 µm x 27.5 µm and near vertical sidewalls (91°±4°) have been produced in silica as shown in the cross section in Figure 1A. Figure 1B shows a device with the fluidic channel etched through waveguides clad with PECVD silica. Design parameters were established with PDMS test channels 25.5 µm deep by 12.2 µm wide. Figures 2A and 2B show transmission fluorescence imaging of streaks from multiple 5.6µm diameter microspheres flowing at 0.49 m/s down the fluidic channel. The microspheres are shown to be focused into a tight stream at 15 mm from the channel entrance in Figure 2C, indicating the minimum channel length required for the final devices. Future work will include dual channel quantification of microsphere fluorescence and development of an assay for TNFalpha and later multiplex measurements. Collection of fluorescence with channel waveguides and also characterisation of transmission measurements from flowing microspheres will also be studied

Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.)

An indica pyramiding line, DK151, and its recurrent parent, IR64, were evaluated under drought stress and non-stress conditions for three consecutive seasons. DK151 showed significantly improved tolerance to drought. The DNA methylation changes in DK151 and IR64 under drought stress and subsequent recovery were assessed using methylation-sensitive amplified polymorphism analysis. Our results indicate that drought-induced genome-wide DNA methylation changes accounted for ∼12.1% of the total site-specific methylation differences in the rice genome. This drought-induced DNA methylation pattern showed three interesting properties. The most important one was its genotypic specificity reflected by large differences in the detected DNA methylation/demethylation sites between DK151 and IR64, which result from introgressed genomic fragments in DK151. Second, most drought-induced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of the sites at which drought-induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought-induced DNA demethylation/methylation changes remain even after recovery. Third, the drought-induced DNA methylation alteration showed a significant level of developmental and tissue specificity. Together, these properties are expected to have contributed greatly to rice response and adaptation to drought stress. Thus, induced epigenetic changes in rice genome can be considered as a very important regulatory mechanism for rice plants to adapt to drought and possibly other environmental stresses

A Holistic Perspective on the Dynamics of G035.39-00.33 : The Interplay between Gas and Magnetic Fields

Magnetic field plays a crucial role in shaping molecular clouds and regulating star formation, yet the complete information on the magnetic field is not well constrained owing to the limitations in observations. We study the magnetic field in the massive infrared dark cloud G035.39-00.33 from dust continuum polarization observations at 850 mu m with SCUBA-2/POL-2 at JCMT for the first time. The magnetic field tends to be perpendicular to the densest part of the main filament (F-M), whereas it has a less defined relative orientation in the rest of the structure, where it tends to be parallel to some diffuse regions. A mean plane-of-the-sky magnetic field strength of similar to 50 mu G for F-M is obtained using the Davis-Chandrasekhar-Fermi method. Based on (CO)-C-13 (1-0) line observations, we suggest a formation scenario of F-M due to large-scale (similar to 10 pc) cloud-cloud collision. Using additional NH3 line data, we estimate that F-M will be gravitationally unstable if it is only supported by thermal pressure and turbulence. The northern part of F-M, however, can be stabilized by a modest additional support from the local magnetic field. The middle and southern parts of F-M are likely unstable even if the magnetic field support is taken into account. We claim that the clumps in F-M may be supported by turbulence and magnetic fields against gravitational collapse. Finally, we identified for the first time a massive (similar to 200 M-circle dot, collapsing starless clump candidate, "c8," in G035.39-00.33. The magnetic field surrounding "c8" is likely pinched, hinting at an accretion flow along the filament.Peer reviewe

The TOP-SCOPE Survey of Planck Galactic Cold Clumps : Survey Overview and Results of an Exemplar Source, PGCC G26.53+0.17

The low dust temperatures (<14 K) of Planck Galactic cold clumps (PGCCs) make them ideal targets to probe the initial conditions and very early phase of star formation. "TOP-SCOPE" is a joint survey program targeting similar to 2000 PGCCs in J = 1-0 transitions of CO isotopologues and similar to 1000 PGCCs in 850 mu m continuum emission. The objective of the "TOP-SCOPE" survey and the joint surveys (SMT 10 m, KVN 21 m, and NRO 45 m) is to statistically study the initial conditions occurring during star formation and the evolution of molecular clouds, across a wide range of environments. The observations, data analysis, and example science cases for these surveys are introduced with an exemplar source, PGCC G26.53+0.17 (G26), which is a filamentary infrared dark cloud (IRDC). The total mass, length, and mean line mass (M/L) of the G26 filament are similar to 6200 M-circle dot, similar to 12 pc, and similar to 500 M-circle dot pc(-1), respectively. Ten massive clumps, including eight starless ones, are found along the filament. The most massive clump as a whole may still be in global collapse, while its denser part seems to be undergoing expansion owing to outflow feedback. The fragmentation in the G26 filament from cloud scale to clump scale is in agreement with gravitational fragmentation of an isothermal, nonmagnetized, and turbulent supported cylinder. A bimodal behavior in dust emissivity spectral index (beta) distribution is found in G26, suggesting grain growth along the filament. The G26 filament may be formed owing to large-scale compression flows evidenced by the temperature and velocity gradients across its natal cloud.Peer reviewe