Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars

To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F2 populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F2 combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study

Parallel Real-Time PCR on a Chip for Genetic Tug-of-War (gTOW) Method

A microchip-based real-time polymerase chain reaction (PCR) device has been developed for the genetic tug-of-war (gTOW) method that provides quantitative data for research on biorobustness and systems biology. The device was constructed of a silicon glass chip, a temperature controlling Peltier element, and a microscope. A parallel real-time amplification process of target genes on the plasmids and the housekeeping genes in a model eukaryote Saccharomyces cerevisiae were detected simultaneously, and the copy number of the target genes were estimated. The device provides unique quantitative data that can be used to augment understanding of the system-level properties of living cells

NR4a1/2 deletion promotes accumulation of TCF1+ stem-like precursors of exhausted CD8+ T cells in the tumor microenvironment

Summary: T cell exhaustion impairs tumor immunity and contributes to resistance against immune checkpoint inhibitors. The nuclear receptor subfamily 4 group A (NR4a) family of nuclear receptors plays a crucial role in driving T cell exhaustion. In this study, we observe that NR4a1 and NR4a2 deficiency in CD8+ tumor-infiltrating lymphocytes (TILs) results in potent tumor eradication and exhibits not only reduced exhaustion characteristics but also an increase in the precursors/progenitors of exhausted T (Pre-Tex) cell fraction. Serial transfers of NR4a1−/−NR4a2−/−CD8+ TILs into tumor-bearing mice result in the expansion of TCF1+ (Tcf7+) stem-like Pre-Tex cells, whereas wild-type TILs are depleted upon secondary transfer. NR4a1/2-deficient CD8+ T cells express higher levels of stemness/memory-related genes and illustrate potent mitochondrial oxidative phosphorylation. Collectively, these findings suggest that inhibiting NR4a in tumors represents a potent immuno-oncotherapy strategy by increasing stem-like Pre-Tex cells and reducing exhaustion of CD8+ T cells

Monolithic CMOS sensors for sub-nanosecond timing

In the ATTRACT project FASTPIX we investigate monolithic pixel sensors with small collection electrodes in CMOS technologies for fast signal collection and precise timing in the sub-nanosecond range. Deep submicron CMOS technologies allow tiny, sub-femtofarad collection electrodes, and large signal-to-noise ratios, essential for very precise timing. However, complex in-pixel circuits require some area, and one ofthe key limitations for precise timing is the longer drift time of signal charge generated near the pixel borders.Laying out the collection electrodes on a hexagonal grid and reducing the pixel pitch minimize the maximumdistance from the pixel border to the collection electrode. The electric field optimized with TCAD simulationspulls the signal charge away from the pixel border towards the collection electrode as fast as possible. Thisalso reduces charge sharing and maximizes the seed pixel signal hence reducing time-walk effects. Here thehexagonal geometry also contributes by limiting charge sharing at the pixel corners to only three pixels insteadof four. We reach pixel pitches down to about 8.7 μmbetween collection electrodes in this 180 nm technologyby placing only a minimum amount of circuitry in the pixel and the rest at the matrix periphery. Consumingseveral tens of micro-ampere per pixel from a 1.8 V supply offers a time jitter of only a few tens of picoseconds.This allows detailed characterization of the sensor timing performance in a prototype chip with several minimatrices of 64 pixels each with amplifier, comparator and digital readout and 4 additional pixels with analogbuffers. The aim is to prove sensor concepts before moving to a much finer line width technology and fullyintegrate the readout within the pixel at lower power consumption