The Arabidopsis MATERNAL EFFECT EMBRYO ARREST45 protein modulates maternal auxin biosynthesis and controls seed size by inducingAINTEGUMENTA

Seed size is a major factor determining crop yields that is controlled through the coordinated development of maternal and zygotic tissues. Here, we identified Arabidopsis MATERNAL EFFECT EMBRYO ARREST45 (MEE45) as a B3 transcription factor that controls cell proliferation and maternally regulates seed size through its transcriptional activation of AINTEGUMENTA (ANT) and its downstream control of auxin biosynthesis in the ovule integument. After characterizing reduced seed and organ size phenotypes in mee45 mutants and finding that overexpression of MEE45 causes oversized seeds, we discovered that the MEE45 protein can bind to the promoter region of the ANT locus and positively regulate its transcription. ANT in-turn activates the expression of auxin biosynthetic genes (e.g. YUCCA4) in the ovule integument. Our results thus illustrate mechanisms underlying maternal tissue-mediated regulation of seed size and suggest that MEE45 and its downstream components can be harnessed to develop higher-yielding crop varieties.

How does the downstream boundary affect avulsion dynamics in a laboratory bifurcation?

Bifurcations play a major role in the evolution of landscapes by controlling how fluxes such as water and sediment are partitioned in distributary and multithread channel networks. In this paper, we present the first experimental investigation on the effect of the downstream boundary on bifurcations. Our experiments in a fixed-wall Y-shaped flume consist of three phases: progradation, transitional, and bypass; the first two phases are net depositional, whereas during the third the sediment flux exiting the downstream boundary matches the input on average. We find that deposition qualitatively changes bifurcation dynamics; we observe frequent switching in the discharge partitioning under net depositional conditions, whereas bypass results in long periods of time where one branch captures most of the flow. We compare our results with a previously developed model for the effect of deposition on bifurcation dynamics. The switching dynamics we observe are more irregular and complex than those predicted by the model. Furthermore, while we observe long periods of time where one branch dominates under bypass conditions, these are not permanent, unlike in the model. We propose that the range of switching timescales we observe arises from a complex interplay of downstream-controlled avulsion and the effect of bars in the upstream channel, including previously unrecognized long-term dynamics associated with a steady bar. Finally, we describe bifurcation experiments conducted with sand but no water. These experiments share the essential feedbacks of our fluvial bifurcation experiments, but do not include bars. In these experiments, we find that the sandpile grows symmetrically while it progrades, but bypass leads to one branch permanently capturing all avalanches. We conclude that the downstream control of deposition vs. bypass is likely a major influence on bifurcation dynamics across a range of physical systems, from river deltas to talus slopes.

Control of oblique-type breakdown in a supersonic boundary layer employing streaks

The effectiveness of streak modes in controlling the oblique-type breakdown in a supersonic boundary-layer at Mach 2.0 is investigated using direct numerical simulations. Investigations in the literature have shown the effectiveness of streak modes in delaying the onset of transition dominated by two-dimensional waves, but in oblique breakdown, three-dimensional waves and a strong streak mode dominate the transition process. Paredes et al. (J. Fluid Mech., vol. 831, 2017, pp. 524–553) discussed the possible stabilization of supersonic boundary layers by optimally growing streaks using parabolized stability equations. However, no study has as yet been reported regarding direct nonlinear control of oblique breakdown. This study deals with the effects of large-amplitude decaying streak modes generated by a blowing–suction strip at the wall to control full breakdown in a reference case. Modes with four to five times the fundamental wavenumber are found to be beneficial for controlling the transition. In the first region after the control-mode forcing, the beneficial mean-flow distortion (MFD), generated by inducing the control mode, is solely responsible for hampering the growth of the fundamental-mode. On the whole, the MFD and the three-dimensional part of the control contribute equally towards controlling the oblique breakdown. The results show significant suppression of transition, and substantial improvements have been observed in the levels of the skin-friction coefficient and wall-temperature in comparison to the uncontrolled case. Moreover, refreshing the control using an additional downstream control strip increases the gain. However, the forcing amplitude must be carefully chosen in order not to introduce a generalized inflection point in the spanwise averaged mean flow invoking enhanced disturbance growth.

How does the downstream boundary affect avulsion dynamics in a laboratory bifurcation?

Bifurcations play a major role in the evolution of landscapes by controlling how fluxes such as water and sediment are partitioned in distributary and multi-thread channel networks. In this paper, we present the first experimental investigation on the effect of the downstream boundary on bifurcations. Our experiments in a fixed-wall Y-shaped flume consist of three phases: progradation, transitional, and bypass; the first two phases are depositional, whereas during the third, the sediment flux exiting the downstream boundary matches the input on average. We find that deposition qualitatively changes bifurcation dynamics; we observe frequent switching in the discharge partitioning under depositional conditions, whereas bypass results in long periods of time where one branch captures most of the flow. We compare our results with a previously developed model for the effect of deposition on bifurcation dynamics. The switching dynamics we observe are more irregular and complex than those predicted by the model. Furthermore, while we observe long periods of time where one branch dominates under bypass conditions, these are not permanent, unlike in the model. We propose that the range of switching timescales we observe arises from a complex interplay of downstream-controlled avulsion, and the effect of bars in the upstream-channel, including previously unrecognized long-timescale bar dynamics. Finally, we describe bifurcation experiments conducted with sand but no water. These experiments share the essential feedbacks of our fluvial bifurcation experiments, but do not include bars. In these experiments, we find that the sandpile grows symmetrically while it progrades, but bypass leads to one branch permanently capturing all avalanches. We conclude that the downstream control of deposition vs. bypass is likely a major influence on bifurcation dynamics across a range of physical systems, from river deltas to talus slopes.

A novel tool for monitoring endogenous human MYC transcription and translation by EGFP tag insertion at the 3’ end using CRISPR-Cas9 genome editing

The MYC oncogene is overexpressed in over 70% of human cancers. Since its identification, the study of MYC has led to the discovery of the various ways through which oncogenes contribute to the ability of normal cells to become malignant. However, there are many aspects of MYC biology that remain unknown or controversial in terms of its regulation, targetability and downstream control of its targets. We developed two stable cell lines expressing MYC endogenously tagged with EGFP via CRISPR/Cas9-mediated genome editing. This system allows efficient detection of transcriptional activity of MYC as well the resulting fusion protein while maintaining the gene expression profiles, growth factors-associated MYC induction and growth kinetics of the parental cells. To our knowledge, this is the first report showing endogenous monitoring of MYC expression in colorectal adenocarcinoma through an EGFP tag, thus making it an efficient tool for high-throughput approaches such as genetic and drug screens.

Numerical simulation of flow over a square cylinder with upstream and downstream circular bar using lattice Boltzmann method

A numerical investigation is carried out to analyze the flow patterns, drag and lift coefficients, and vortex shedding around a square cylinder using a control circular bar upstream and downstream. Lattice Boltzmann method (LBM) was used to investigate flow over a square cylinder controlled by upstream and downstream circular bar, which is the main novelty of this study. Compared with those available results in the literature, the code for flow over a single square cylinder proves valid. The Reynolds number (Re) based on the width of the square cylinder ([Formula: see text]) and diameter of circular bar ([Formula: see text]) are 100 for square cylinder, 30 and 50 for different circular bars. Numerical simulations are performed in the ranges of [Formula: see text] and [Formula: see text], where [Formula: see text] and [Formula: see text] are the center-to-center distances between the bar and cylinder. Five distinct flow patterns are observed in the present study. It is found that the maximum percentage reduction in drag coefficient is 59.86% by upstream control bar, and the maximum percentage reduction in r.m.s. lift coefficient is 73.69% by downstream control bar. By varying the distance ratio for the downstream control bar, a critical value of distance ratio is found where there are two domain frequencies.