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Based on 4.4 fb−1 of e+e− annihilation data collected at the center-of-mass energies between 4.60 and 4.70 GeV with the BESIII detector at the BEPCII collider, the pure \textit{W}-boson-exchange decay Λ+c→Ξ0K+ is studied with a full angular analysis. The corresponding decay asymmetry is measured for the first time to be αΞ0K+=0.01±0.16(stat.)±0.03(syst.). This result reflects the non-interference effect between the S- and P-wave amplitudes. The phase shift between S- and P-wave amplitudes has two solutions, which are δp−δs=−1.55±0.25(stat.)±0.05(syst.) rad or 1.59±0.25(stat.)±0.05(syst.) rad.
Based on 4.4 fb−1 of e+e− annihilation data collected at the center-of-mass energies between 4.60 and 4.70 GeV with the BESIII detector at the BEPCII collider, the pure W-exchange decay Λ+c→Ξ0K+ is studied with a full angular analysis. The corresponding decay asymmetry is measured for the first time to be αΞ0K+=0.01±0.16(stat.)±0.03(syst.). This result reflects the interference between the S- and P-wave amplitudes. The phase shift between S- and P-wave amplitudes is δp−δs=−1.55±0.25(stat.)±0.05(syst.) rad.
By analyzing e+e− annihilation da ta corresponding to an integrated luminosity of 2.93 fb−1 collected at a center-of-mass energy of 3.773 GeV with the \text{BESIII} detector, the first observation of the semileptonic decays D0→K0Sπ−π0e+νe and D+→K0Sπ+π−e+νe is reported. With a dominant hadronic contribution from K1(1270), the branching fractions are measured to be B(D0→K1(1270)−(→K0Sπ−π0)e+νe) = (1.69+0.53−0.46±0.15)×10−4 and B(D+→K¯1(1270)0(→K0Sπ+π−)e+νe) = (1.47+0.45−0.40±0.20)×10−4 with statistical significance of 5.4σ and 5.6σ, respectively. When combined with measurements of the K1(1270)→K+π−π decays, the absolute branching fractions are determined to be B(D0→K1(1270)−e+νe) = (1.05+0.33−0.28±0.12±0.12)×10−3 and B(D+→K¯1(1270)0e+νe) = (1.29+0.40−0.35±0.18±0.15)×10−3. The first and second uncertainties are statistical and systematic, respectively, and the third uncertainties originate from the assumed branching fractions of the K1(1270)→Kππ decays.
We report the measurement of the cross sections for e+e−→hadrons at center-of-mass (c.m.) energies from 3.645 to 3.871 GeV. We observe a new resonance R(3810) in the cross sections for the first time, and observe the R(3760) resonance with high significance in the cross sections. The R(3810) has a mass of (3804.5±0.9±0.9) ~MeV/c2, a total width of (5.4±3.5±3.2)~MeV, and an electronic partial width of (19.4±7.4±12.1)~eV. Its significance is 7.7σ. The R(3810) could be interpreted as a hadro-charmonium resonance predicted by Quantum Chromodynamics (QCD). In addition, we measure the mass (3751.9±3.8±2.8) ~MeV/c2, the total width (32.8±5.8±8.7)~MeV, and the electronic partial width (184±75±86)~eV with improved precision for the R(3760). Furthermore, for the R(3780) we measure the mass (3778.7±0.5±0.3) ~MeV/c2 and total width (20.3±0.8±1.7)~MeV with improved precision, and the electronic partial width (265±69±83)~eV. The R(3780) can be interpreted as the 13D1 state of charmonium. Its mass and total width differ significantly from the corresponding fitted values given by the Particle Data Group in 2022 by 7.1 and 3.2 times the uncertainties for ψ(3770), respectively. ψ(3770) has been interpreted as the 13D1 state for 45 years.
We measured the Born cross sections for the process e+e− → ωη′ at 22 center-of-mass energies from 2.000 to 3.080 GeV with the BESIII detector at the BEPCII collider. We observed a resonant structure with a statistical significance of 9.6σ. A Breit-Wigner fit determines its mass to be MR = (2153 ± 30 ± 31) MeV/c2 and its width to be ΓR = (167 ± 77 ± 7) MeV, where the first uncertainties are statistical and the second are systematic.
The Born cross section of the process e+e−→ηJ/ψ at a center-of-mass energy s√=3.773 GeV is measured to be (8.89±0.88±0.42) pb, using a data sample collected with the BESIII detector operating at the BEPCII storage ring. The decay ψ(3770)→ηJ/ψ is observed for the first time with a statistical significance of 7.4σ. From a fit to the dressed cross-section line-shape of e+e−→ηJ/ψ from s√=3.773 to 4.600 GeV we obtain the branching fraction of the decay ψ(3770)→ηJ/ψ to be (11.6±6.1±1.0)×10−4 when the ψ(3770) decay amplitude is added coherently to the other contributions, and (7.9±1.0±0.7)×10−4 when it is added incoherently. Here the first uncertainties are statistical and the second are systematic.
Using a data sample collected with the BESIII detector operating at the BEPCII storage ring, the Born cross section of the process 𝑒+𝑒−→𝜂𝐽/𝜓 at a center-of-mass energy √𝑠=3.773 GeV is measured to be (8.88±0.87±0.42) pb. We fit the cross section line shape before correcting for the initial state radiation from √𝑠=3.773 to 4.600 GeV to obtain the branching fraction ℬ(𝜓(3770)→𝜂𝐽/𝜓). We obtain ℬ(𝜓(3770)→𝜂𝐽/𝜓)=(11.3±5.9±1.1)×10−4 when the 𝜓(3770) decay amplitude is added coherently to the other contributions, and (8.7±1.0±0.8)×10−4 when it is added incoherently. Here the quoted uncertainties are statistical and systematic, respectively. In both cases, the statistical significance of 𝜓(3770) resonance is above 7𝜎. This is the first time the decay 𝜓(3770)→𝜂𝐽/𝜓 is observed with a statistical significance greater than 5𝜎.
The Born cross sections of the e+e− → D*+D*− and e+e− → D*+D− processes are measured using e+e− collision data collected with the BESIII experiment at center-of-mass energies from 4.085 to 4.600 GeV, corresponding to an integrated luminosity of 15.7 fb−1. The results are consistent with and more precise than the previous measurements by the Belle, Babar and CLEO collaborations. The measurements are essential for understanding the nature of vector charmonium and charmonium-like states.
Using 448 million ψ(2S) events, the spin-singlet P-wave charmonium state hc(11P1) is studied via the ψ(2S)→π0hc decay followed by the hc→γηc transition. The branching fractions are measured to be BInc(ψ(2S)→π0hc)×BTag(hc→γηc)=(4.22+0.27−0.26±0.19)×10−4 , BInc(ψ(2S)→π0hc)=(7.32±0.34±0.41)×10−4, and BTag(hc→γηc)=(57.66+3.62−3.50±0.58)%, where the uncertainties are statistical and systematic, respectively. The hc(11P1) mass and width are determined to be M=(3525.32±0.06±0.15) MeV/c2 and Γ=(0.78+0.27−0.24±0.12) MeV. Using the center of gravity mass of the three χcJ(13PJ) mesons (M(c.o.g.)), the 1P hyperfine mass splitting is estimated to be Δhyp=M(hc)−M(c.o.g.)=(0.03±0.06±0.15) MeV/c2, which is consistent with the expectation that the 1P hyperfine splitting is zero at the lowest-order.
We search for the semi-leptonic decays Λ + c → Λπ+π−e+νe and Λ + c → pK0 Sπ−e+νe in a sample of 4.5 fb−1 of e+e− annihilation data collected in the center-of-mass energy region between 4.600 GeV and 4.699 GeV by the BESIII detector at the BEPCII. No significant signals are observed, and the upper limits on the decay branching fractions are set to be B(Λ+c → Λπ+π−e+νe ) < 3.9 × 10−4 and B(Λ + c → pK0Sπ−e+νe ) < 3.3 × 10−4 at the 90% confidence level, respectively.
We search for an axion-like particle (ALP) a through the process ψ(3686)→π+π−J/ψ, J/ψ→γa, a→γγ in a data sample of (2.71±0.01)×109 ψ(3686) events collected by the BESIII detector. No significant ALP signal is observed over the expected background, and the upper limits on the branching fraction of the decay J/ψ→γa and the ALP-photon coupling constant gaγγ are set at 95% confidence level in the mass range of 0.165≤ma≤2.84GeV/c2. The limits on B(J/ψ→γa) range from 8.3×10−8 to 1.8×10−6 over the search region, and the constraints on the ALP-photon coupling are the most stringent to date for 0.165≤ma≤1.468GeV/c2.
We report a search for a dark photon using 14.9~fb−1 of e+e− annihilation data taken at center-of-mass energies from 4.13 to 4.60~GeV with the BESIII detector operated at the BEPCII storage ring. The dark photon is assumed to be produced in the radiative annihilation process of e+e− and to predominantly decay into light dark matter particles, which escape from the detector undetected. The mass range from 1.5 to 2.9~GeV is scanned for the dark photon candidate, and no significant signal is observed. The mass dependent upper limits at the 90% confidence level on the coupling strength parameter ϵ for a dark photon coupling with an ordinary photon vary between 1.6×10−3 and 5.7×10−3.
Global investment in biomedical research has grown significantly over the last decades, reaching approximately a quarter of a trillion US dollars in 2010. However, not all of this investment is distributed evenly by gender. It follows, arguably, that scarce research resources may not be optimally invested (by either not supporting the best science or by failing to investigate topics that benefit women and men equitably). Women across the world tend to be significantly underrepresented in research both as researchers and research participants, receive less research funding, and appear less frequently than men as authors on research publications. There is also some evidence that women are relatively disadvantaged as the beneficiaries of research, in terms of its health, societal and economic impacts. Historical gender biases may have created a path dependency that means that the research system and the impacts of research are biased towards male researchers and male beneficiaries, making it inherently difficult (though not impossible) to eliminate gender bias. In this commentary, we – a group of scholars and practitioners from Africa, America, Asia and Europe – argue that gender-sensitive research impact assessment could become a force for good in moving science policy and practice towards gender equity. Research impact assessment is the multidisciplinary field of scientific inquiry that examines the research process to maximise scientific, societal and economic returns on investment in research. It encompasses many theoretical and methodological approaches that can be used to investigate gender bias and recommend actions for change to maximise research impact. We offer a set of recommendations to research funders, research institutions and research evaluators who conduct impact assessment on how to include and strengthen analysis of gender equity in research impact assessment and issue a global call for action.
Men and women differ substantially regarding height, weight, and body fat. Interestingly, previous work detecting genetic effects for waist-to-hip ratio, to assess body fat distribution, has found that many of these showed sex-differences. However, systematic searches for sex-differences in genetic effects have not yet been conducted. Therefore, we undertook a genome-wide search for sexually dimorphic genetic effects for anthropometric traits including 133,723 individuals in a large meta-analysis and followed promising variants in further 137,052 individuals, including a total of 94 studies. We identified seven loci with significant sex-difference including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were significant in women, but not in men. Of interest is that sex-difference was only observed for waist phenotypes, but not for height or body-mass-index. We found no evidence for sex-differences with opposite effect direction for men and women. The PPARG locus is of specific interest due to its link to diabetes genetics and therapy. Our findings demonstrate the importance of investigating sex differences, which may lead to a better understanding of disease mechanisms with a potential relevance to treatment options.
In non-hadronic axion models, which have a tree-level axion-electron interaction, the Sun produces a strong axion flux by bremsstrahlung, Compton scattering, and axiorecombination, the "BCA processes." Based on a new calculation of this flux, including for the first time axio-recombination, we derive limits on the axion-electron Yukawa coupling gae and axion-photon interaction strength ga using the CAST phase-I data (vacuum phase). For ma <~ 10 meV/c2 we find ga gae < 8.1 × 10−23 GeV−1 at 95% CL. We stress that a next-generation axion helioscope such as the proposed IAXO could push this sensitivity into a range beyond stellar energy-loss limits and test the hypothesis that white-dwarf cooling is dominated by axion emission.
Knowledge about the biogeographic affinities of the world’s tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world’s tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests.
The transition from local to global patterns governs the differentiation of mouse blastocysts
(2020)
During mammalian blastocyst development, inner cell mass (ICM) cells differentiate into epiblast (Epi) or primitive endoderm (PrE). These two fates are characterized by the expression of the transcription factors NANOG and GATA6, respectively. Here, we investigate the spatio-temporal distribution of NANOG and GATA6 expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single cell-based neighbourhood analyses. We define the cell neighbourhood by local features, which include the expression levels of both fate markers expressed in each cell and its neighbours, and the number of neighbouring cells. We further include the position of a cell relative to the centre of the ICM as a global positional feature. Our analyses reveal a local three-dimensional pattern that is already present in early blastocysts: 1) Cells expressing the highest NANOG levels are surrounded by approximately nine neighbours, while 2) cells expressing GATA6 cluster according to their GATA6 levels. This local pattern evolves into a global pattern in the ICM that starts to emerge in mid blastocysts. We show that FGF/MAPK signalling is involved in the three-dimensional distribution of the cells and, using a mutant background, we further show that the GATA6 neighbourhood is regulated by NANOG. Our quantitative study suggests that the three-dimensional cell neighbourhood plays a role in Epi and PrE precursor specification. Our results highlight the importance of analysing the three-dimensional cell neighbourhood while investigating cell fate decisions during early mouse embryonic development.
Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid’s size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 105 to 1 × 106 cells/mm3. Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.
Background: Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset.
Results: We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91%) whereas the other methods each failed for at least one dataset (F-measure≤69%). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values.
Conclusion: We developed a novel and fully automated three-dimensional cell nuclei segmentation method incorporating LoS decomposition. LoS are easily accessible features that ensure correct splitting of apparently touching cell nuclei independent of their shape, size or intensity. Our method showed superior performance compared to state-of-the-art methods, performing accurately for a variety of test images. Hence, our LoS approach can be readily applied to quantitative evaluation in drug testing, developmental and cell biology.
The vast majority of European grasslands strongly depend on the regular removal of aboveground biomass by agricultural land use, mostly grazing or mowing or a combination of both. These specific management schemes have strong influence on plant diversity and vegetation composition, depending on their particular characteristics and their intensity. For example, the presence or absence of fertilization will favour some species over others, changing plant communities accordingly. Additionally, the farmer’s choice of a specific management scheme will also depend on the abiotic site conditions. This leads to a complex set of associated factors potentially affecting the structure and diversity of grasslands.
In this study, we compiled a unique dataset of 169 differently managed grasslands (in total 202 plots), which were sampled in five regions across Germany. For each plot, we documented management characteristics, measured plant diversity and functional group composition, recorded endangered species according to red lists, and calculated Ellenberg indicator values. We assessed patterns in vegetation composition and diversity in relation to the particular management scheme, which was categorized as meadow, meadow with autumn or winter grazing (with mowing as predominant management), mown pasture (where mowing and grazing are used at roughly equal intensity), seasonal pasture (with grazing as predominant management) and year-round pasture.
Our study showed that grasslands of different management schemes significantly differed in diversity, structure and functional composition. However, it also became obvious that vegetation composition was not strictly distinguished by management alone. Local and regional characteristics such as soil conditions, size of the grassland species pool or land-use history, often played a more prominent role than land use alone. Assumingly, the interplay of those local and regional characteristics with the proportion of grazing and mowing at a particular site inhibit clear differences among our predefined management schemes. Nevertheless, species richness was the lowest in year-round pastures, moderate in meadows and highest in seasonal pastures. In contrast, year-round pastures harboured the highest mean numbers of endangered species. The dependency of a certain management scheme on site-specific environmental factors such as soil fertility, further complicated the clear separation of management effects from those of the environmental background. In summary, modern grassland management strongly shaped grassland vegetation, but today’s combination of different management practices complicated the assessment of specific land-use effects on plant diversity. Thus, neither mowing nor grazing turned out to be “the one and only” management for nature conservation. Although our results challenge long-term prognoses for future vegetation development under modern grassland management, we clearly showed that low-intensity management and the absence of fertilization promoted plant diversity, with higher values in pastures compared to meadows and mown pastures.
Spheroids resemble features of tissues and serve as model systems to study cell–cell and cell–ECM interactions in non-adhesive three-dimensional environments. Although it is generally accepted that mature spheroids resemble tissue properties very well, no studies relate different phases in the spheroid formation processes that contribute to tissue integrity. Tissue integrity involves the cellular processes adhesion formation, adhesion reinforcement, rearrangement as well as proliferation. They maintain the structure and function of tissues and, upon dysregulation, contribute to malignancy. We investigated spheroid formation dynamics in cell lines of different metastatic potential. We dissected spheroid formation into phases of aggregation, compaction and growth to identify the respective contributions of E-cadherin, actin, microtubules and FAK. E-cadherin, actin and microtubules drive the first two phases. Microtubules and FAK are involved in the proliferation phase. FAK activity correlates with the metastatic potential of the cells. A robust computational model based on a very large number of experiments reveals the temporal resolution of cell adhesion. Our results provide novel hypotheses to unveil the general mechanisms that contribute to tissue integrity.
Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach
(2020)
During the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first decision, the trophectoderm and the inner cell mass are formed. Subsequently, the inner cell mass segregates into the epiblast and the primitive endoderm. Inner cell mass organoids represent an experimental model system, mimicking the second cell fate decision. It has been shown that cells of the same fate tend to cluster stronger than expected for random cell fate decisions. Three major processes are hypothesised to contribute to the cell fate arrangements: (1) chemical signalling; (2) cell sorting; and (3) cell proliferation. In order to quantify the influence of cell proliferation on the observed cell lineage type clustering, we developed an agent-based model accounting for mechanical cell–cell interaction, i.e. adhesion and repulsion, cell division, stochastic cell fate decision and cell fate heredity. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. Further, we show that the observed neighbourhood structures can emerge solely due to cell fate heredity during cell division.
Serumkomplement (C′), welches nach dem heutigen Stand der Forschung aus mindestens vier Komponenten besteht, ist an zahlreichen immunologischen und nicht-immunologischen Vorgängen beteiligt. Am besten erforscht ist die Sequenz der C′-Reaktionsstufen bei der Hämolyse sensibilisierter Hammelerythrocyten, jedoch ist noch ungeklärt, welcher Mechanismus letztlich die Zellveränderung, die zum Austritt von Hämoglobin führt, bewirkt.
In der vorliegenden Arbeit wird über das Endprodukt der C′-Reaktion — eine cytolytisch wirkende Substanz — berichtet. Es wird gezeigt, daß sowohl beim Altern von Komplement, wie auch bei C′ fixierenden Antigen/Antikörperreaktionen im Serum eine Substanz entsteht, die zellschädigend und auflösend wirkt.
Seren, in denen durch mehr oder weniger spezifische Vorbehandlung C′ oder einzelne seiner Komponenten ausgeschaltet wurden, sind nicht mehr zur Cytolysinbildung befähigt.
Das cytolytische Prinzip konnte gereinigt und papierchromatographisch als Lysolecithin charakterisiert werden.
The Kinase Chemogenomic Set (KCGS): an open science resource for kinase vulnerability identification
(2021)
We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS), current Version 1.0, is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.
Long non-coding RNAs (lncRNAs) contribute to cardiac (patho)physiology. Aging is the major risk factor for cardiovascular disease with cardiomyocyte apoptosis as one underlying cause. Here, we report the identification of the aging-regulated lncRNA Sarrah (ENSMUST00000140003) that is anti-apoptotic in cardiomyocytes. Importantly, loss of SARRAH (OXCT1-AS1) in human engineered heart tissue results in impaired contractile force development. SARRAH directly binds to the promoters of genes downregulated after SARRAH silencing via RNA-DNA triple helix formation and cardiomyocytes lacking the triple helix forming domain of Sarrah show an increase in apoptosis. One of the direct SARRAH targets is NRF2, and restoration of NRF2 levels after SARRAH silencing partially rescues the reduction in cell viability. Overexpression of Sarrah in mice shows better recovery of cardiac contractile function after AMI compared to control mice. In summary, we identified the anti-apoptotic evolutionary conserved lncRNA Sarrah, which is downregulated by aging, as a regulator of cardiomyocyte survival.
A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important lipid intermediate and signaling lipid at the branch point of these pathways and constantly monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. Here, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for the selective binding to membranes containing PA over phosphatidylserine (PS). The insertion of the AH into the hydrophobic core of the membrane renders Opi1 sensitive to the lipid acyl chain composition as an important factor contributing to the regulation of membrane biogenesis. Based on these findings, we rationally designed the membrane binding properties of Opi1 to control its responsiveness in the physiological context. Using extensive molecular dynamics (MD) simulations, we identified two PA-selective three-finger grips that tightly bind the phosphate headgroup, while interacting less intimately and more transiently with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.
The Kinase Chemogenomic Set (KCGS): An open science resource for kinase vulnerability identification
(2019)
We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS) is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.
A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS). The insertion of the AH into the membrane core renders Opi1 sensitive to the lipid acyl chain composition and provides a means to adjust membrane biogenesis. By rational design of the AH, we tune the membrane-binding properties of Opi1 and control its responsiveness in vivo. Using extensive molecular dynamics simulations, we identify two PA-selective three-finger grips that tightly bind the PA phosphate headgroup while interacting less intimately with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.