Photomorphogenesis: Light receptor kinases in plants!

AbstractPlants must adapt to a capricious light environment, but the mechanism by which light signals are transmitted to cause changes in development has long eluded us. The search might be over, however, as two photoreceptors, phytochrome and NPH1, have been shown to autophosphorylate in a light-dependent fashion

Light-induced degradation of phyA is promoted by transfer of the photoreceptor into the nucleus

Higher plants possess multiple members of the phytochrome family of red, far-red light sensors to modulate plant growth and development according to competition from neighbors. The phytochrome family is composed of the light-labile phyA and several light-stable members (phyB-phyE in Arabidopsis). phyA accumulates to high levels in etiolated seedlings and is essential for young seedling establishment under a dense canopy. In photosynthetically active seedlings high levels of phyA counteract the shade avoidance response. phyA levels are maintained low in light-grown plants by a combination of light-dependent repression of PHYA transcription and light-induced proteasome-mediated degradation of the activated photoreceptor. Light-activated phyA is transported from the cytoplasm where it resides in darkness to the nucleus where it is needed for most phytochrome-induced responses. Here we show that phyA is degraded by a proteasome-dependent mechanism both in the cytoplasm and the nucleus. However, phyA degradation is significantly slower in the cytoplasm than in the nucleus. In the nucleus phyA is degraded in a proteasome-dependent mechanism even in its inactive Pr (red light absorbing) form, preventing the accumulation of high levels of nuclear phyA in darkness. Thus, light-induced degradation of phyA is in part controlled by a light-regulated import into the nucleus where the turnover is faster. Although most phyA responses require nuclear phyA it might be useful to maintain phyA in the cytoplasm in its inactive form to allow accumulation of high levels of the light sensor in etiolated seedling

Patents as Early Indicators of Technology and Investment Trends: Analyzing the Microbiome Space as a Case Study

The human microbiome is the collective of microbes living in symbiosis on and within humans. Modulating its composition and function has become an attractive means for the prevention and treatment of a variety of diseases including cancer. Since the initiation of the human microbiome project in 2007, the number of academic publications and active patent families around the microbiome has grown exponentially. Screening patent databases can be useful for the early detection and the tracking of new technology trends. However, it is not sufficient to assess portfolio sizes because emerging players with small but high-quality patent portfolios will be missed within the noise of large but low-quality portfolio owners. Here we used the consolidated database and software tool PatentSight to benchmark patent portfolios, and to analyze key patent owners and innovators in the microbiome space. Our study shows how in-depth patent analyses combining qualitative and quantitative parameters can identify actionable early indicators of technology and investment trends from large patent datasets

A Primer on the Differential Calculus of 3D Orientations

The proper handling of 3D orientations is a central element in many optimization problems in engineering. Unfortunately many researchers and engineers struggle with the formulation of such problems and often fall back to suboptimal solutions. The existence of many different conventions further complicates this issue, especially when interfacing multiple differing implementations. This document discusses an alternative approach which makes use of a more abstract notion of 3D orientations. The relative orientation between two coordinate systems is primarily identified by the coordinate mapping it induces. This is combined with the standard exponential map in order to introduce representation-independent and minimal differentials, which are very convenient in optimization based methods

Is conservative management safe in patients with acute ureterolithiasis and perirenal stranding?

In patients presenting with ureterolithiasis, perirenal stranding is frequently observed in non-contrast computed tomography. Because perirenal stranding may be caused by tears in the collecting system, previous studies have described an increased risk of infectious complications and suggested broad empiric antibiotic therapy and immediate decompressing of the upper urinary tract. We hypothesized that these patients can also be managed conservatively. Therefore, we retrospectively identified patients with ureterolithiasis and perirenal stranding and compared diagnostic and treatment characteristics as well as treatment outcomes between patients undergoing conservative versus interventional management by ureteral stenting, percutaneous drainage or primary ureteroscopic stone removal. We classified perirenal stranding as mild, moderate or severe based on its radiological extent. Of 211 patients, 98 were managed conservatively. Patients in the interventional group had larger ureteral stones, more proximal ureteral stone location, more severe perirenal stranding, higher systemic and urinary infectious parameters, higher creatinine levels, and received more frequent antibiotic therapy. The conservatively managed group experienced a spontaneous stone passage rate of 77%, while 23% required delayed intervention. In the interventional and conservative groups, 4% and 2% of patients, respectively, developed sepsis. None of the patients in either group developed a perirenal abscess. Comparison of perirenal stranding grade between mild, moderate and severe in the conservatively treated group showed no difference in the spontaneous stone passage and infectious complications. In conclusion, conservative management without prophylactic antibiotics for ureterolithiasis and perirenal stranding is a valid treatment option as long as no clinical or laboratory signs of renal failure or infections are observed

The evolutionary conserved BER1 gene is involved in microtubule stability in yeast

In yeast, microtubules are dynamic filaments necessary for spindle and nucleus positioning, as well as for proper chromosome segregation. We identify a function for the yeast gene BER1 (Benomyl REsistant 1) in microtubule stability. BER1 belongs to an evolutionary conserved gene family whose founding member Sensitivity to Red light Reduced is involved in red-light perception and circadian rhythms in Arabidopsis. Here, we present data showing that the ber1Δ mutant is affected in microtubule stability, particularly in presence of microtubule-depolymerising drugs. The pattern of synthetic lethal interactions obtained with the ber1Δ mutant suggests that Ber1 may function in N-terminal protein acetylation. Our work thus suggests that microtubule stability might be regulated through this post-translational modification on yet-to-be determined protein

UV-B perceived by the UVR8 photoreceptor inhibits plant thermomorphogenesis

Small increases in ambient temperature can elicit striking effects on plant architecture, collectively termed thermomorphogenesis [1]. In Arabidopsis thaliana, these include marked stem elongation and leaf elevation, responses that have been predicted to enhance leaf cooling [ 2, 3, 4 and 5]. Thermomorphogenesis requires increased auxin biosynthesis, mediated by the bHLH transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) [ 6, 7 and 8], and enhanced stability of the auxin co-receptor TIR1, involving HEAT SHOCK PROTEIN 90 (HSP90) [9]. High-temperature-mediated hypocotyl elongation additionally involves localized changes in auxin metabolism, mediated by the indole-3-acetic acid (IAA)-amido synthetase Gretchen Hagen 3 (GH3).17 [10]. Here we show that ultraviolet-B light (UV-B) perceived by the photoreceptor UV RESISTANCE LOCUS 8 (UVR8) [11] strongly attenuates thermomorphogenesis via multiple mechanisms inhibiting PIF4 activity. Suppression of thermomorphogenesis involves UVR8 and CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1)-mediated repression of PIF4 transcript accumulation, reducing PIF4 abundance. UV-B also stabilizes the bHLH protein LONG HYPOCOTYL IN FAR RED (HFR1), which can bind to and inhibit PIF4 function. Collectively, our results demonstrate complex crosstalk between UV-B and high-temperature signaling. As plants grown in sunlight would most likely experience concomitant elevations in UV-B and ambient temperature, elucidating how these pathways are integrated is of key importance to the understanding of plant development in natural environments

Phosphorylation of phytochrome B inhibits light-induced signaling via accelerated dark reversion in Arabidopsis

The photoreceptor phytochrome B (phyB) interconverts between the biologically active Pfr (lmax = 730 nm) and inactive Pr (lmax = 660 nm) forms in a red/far-red–dependent fashion and regulates, as molecular switch, many aspects of lightdependent development in Arabidopsis thaliana. phyB signaling is launched by the biologically active Pfr conformer and mediated by specific protein–protein interactions between phyB Pfr and its downstream regulatory partners, whereas conversion of Pfr to Pr terminates signaling. Here, we provide evidence that phyB is phosphorylated in planta at Ser-86 located in the N-terminal domain of the photoreceptor. Analysis of phyB-9 transgenic plants expressing phospho-mimic and nonphosphorylatable phyB–yellow fluorescent protein (YFP) fusions demonstrated that phosphorylation of Ser-86 negatively regulates all physiological responses tested. The Ser86Asp and Ser86Ala substitutions do not affect stability, photoconversion, and spectral properties of the photoreceptor, but light-independent relaxation of the phyBSer86Asp Pfr into Pr, also termed dark reversion, is strongly enhanced both in vivo and in vitro. Faster dark reversion attenuates red light–induced nuclear import and interaction of phyBSer86Asp-YFP Pfr with the negative regulator PHYTOCHROME INTERACTING FACTOR3 compared with phyB–green fluorescent protein. These data suggest that accelerated inactivation of the photoreceptor phyB via phosphorylation of Ser-86 represents a new paradigm for modulating phytochrome-controlled signaling

No Survival Differences among Germ-Cell Cancer Patients from Urban and Rural Areas

INTRODUCTION Germ-cell cancer (GCC) is curable in the majority of men. However, previous reports have described inferior outcomes in men living in rural as compared to urban residential areas. METHODS We identified all GCC patients treated at two large university hospitals in Zürich and Bern, both in Switzerland, between 2010 and 2020 by retrospective chart review. In 400 patients from Zürich and 274 patients from Bern, details on presentation, diagnosis, treatment, and outcomes were abstracted from medical records. For follow-up, we contacted referring centers or private physicians. Residential region was allocated according to the Federal Statistical Office of Switzerland. RESULTS We found no differences in initial presentation (clinical stage I [CSI] versus de novo metastatic), relapse rate in CSI patients, response in metastatic patients (favorable vs. unfavorable), progression-free survival (PFS) or overall survival (OS) between patients from urban as compared to suburban or rural residential areas. PFS at 3 years for CSI patients was 78% (95% confidence interval 72-82%) and OS at 5 years was 98% (95% confidence interval 96-99%). PFS at 3 years for de novo metastatic patients was 74% (95% confidence interval 68-79%) and OS at 5 years was 86% (95% confidence interval 80-90%). CONCLUSION Treatment outcomes in GCC patients were excellent and comparable to international standards at both centers irrespective of the residential area of patients documenting equal access to high-level oncological care at both centers