Quantifying Förster Resonance Energy Transfer from Single Perovskite Quantum Dots to Organic Dyes

Colloidal quantum dots (QDs) are promising regenerable photoredox catalysts offering broadly tunable redox potentials along with high absorption coefficients. QDs have thus far been examined for various organic transformations, water splitting, and CO2 reduction. Vast opportunities emerge from coupling QDs with other homogeneous catalysts, such as transition metal complexes or organic dyes, into hybrid nanoassemblies exploiting energy transfer (ET), leveraging a large absorption cross-section of QDs and long-lived triplet states of cocatalysts. However, a thorough understanding and further engineering of the complex operational mechanisms of hybrid nanoassemblies require simultaneously controlling the surface chemistry of the QDs and probing dynamics at sufficient spatiotemporal resolution. Here, we probe the ET from single lead halide perovskite QDs, capped by alkylphospholipid ligands, to organic dye molecules employing single-particle photoluminescence spectroscopy with single-photon resolution. We identify a Förster-type ET by spatial, temporal, and photon-photon correlations in the QD and dye emission. Discrete quenching steps in the acceptor emission reveal stochastic photobleaching events of individual organic dyes, allowing a precise quantification of the transfer efficiency, which is >70% for QD-dye complexes with strong donor-acceptor spectral overlap. Our work explores the processes occurring at the QD/molecule interface and demonstrates the feasibility of sensitizing organic photocatalysts with QDs.

NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing

Many biochemical processes use the Watson-Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson-Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson-Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T-/U-) Watson-Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU- formed with a ten-fold higher propensity relative to dT-·rG and dG·dT- and this could be attributed to the lower pKa (ΔpKa ∼0.4-0.9) of U versus T. Our findings suggest plausible roles for Watson-Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson-Crick-like G·U- could play a significant role evading Watson-Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.

Phosphorylation of PP2Ac by PKC is a key regulatory step in the PP2A-switch-dependent AKT dephosphorylation that leads to apoptosis

BACKGROUND

Although GqPCR activation often leads to cell survival by activating the PI3K/AKT pathway, it was previously shown that in several cell types AKT activity is reduced and leads to JNK activation and apoptosis. The mechanism of AKT inactivation in these cells involves an IGBP1-coupled PP2Ac switch that induces the dephosphorylation and inactivation of both PI3K and AKT. However, the machinery involved in the initiation of PP2A switch is not known.

METHODS

We used phospho-mass spectrometry to identify the phosphorylation site of PP2Ac, and raised specific antibodies to follow the regulation of this phosphorylation. Other phosphorylations were monitored by commercial antibodies. In addition, we used coimmunoprecipitation and proximity ligation assays to follow protein-protein interactions. Apoptosis was detected by a TUNEL assay as well as PARP1 cleavage using SDS-PAGE and Western blotting.

RESULTS

We identified Ser24 as a phosphorylation site in PP2Ac. The phosphorylation is mediated mainly by classical PKCs (PKCα and PKCβ) but not by novel PKCs (PKCδ and PKCε). By replacing the phosphorylated residue with either unphosphorylatable or phosphomimetic residues (S24A and S24E), we found that this phosphorylation event is necessary and sufficient to mediate the PP2A switch, which ultimately induces AKT inactivation, and a robust JNK-dependent apoptosis.

CONCLUSION

Our results show that the PP2A switch is induced by PKC-mediated phosphorylation of Ser24-PP2Ac and that this phosphorylation leads to apoptosis upon GqPCR induction of various cells. We propose that this mechanism may provide an unexpected way to treat some cancer types or problems in the endocrine machinery.

Local Environment of Sc and Y Dopant Ions in Aluminum Nitride Thin Films

The local environments of Sc and Y in predominantly ⟨002⟩ textured, Al1-xDoxN (Do = Sc, x = 0.25, 0.30 or Y, x = 0.25) sputtered thin films with wurtzite symmetry were investigated using X-ray absorption (XAS) and photoelectron (XPS) spectroscopies. We present evidence from the X-ray absorption fine structure (XAFS) spectra that, when x = 0.25, both Sc3+ and Y3+ ions are able to substitute for Al3+, thereby acquiring four tetrahedrally coordinated nitrogen ligands, i.e., coordination number (CN) of 4. On this basis, the crystal radius of the dopant species in the wurtzite lattice, not available heretofore, could be calculated. By modeling the scandium local environment, extended XAFS (EXAFS) analysis suggests that when x increases from 0.25 to 0.30, CN for a fraction of the Sc ions increases from 4 to 6, signaling octahedral coordination. This change occurs at a dopant concentration significantly lower than the reported maximum concentration of Sc (42 mol % Sc) in wurtzite (Al, Sc)N. XPS spectra provide support for our observation that the local environment of Sc in (Al, Sc)N may include more than one type of coordination.

Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids

BACKGROUND

N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability is driven by changes in genetic sequences ('cis') or cellular environments ('trans') and via which mechanisms.

RESULTS

Here we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis. We find that m6A evolution and variability is driven primarily in 'cis', via two mechanisms: (1) variations altering m6A consensus motifs, and (2) variation impacting mRNA secondary structure. We establish that mutations impacting RNA structure - even when distant from an m6A consensus motif - causally dictate methylation propensity. Finally, we demonstrate that allele-specific differences in m6A levels lead to allele-specific changes in gene expression.

CONCLUSIONS

Our findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.

Microbial Biomineralization of Alkaline Earth Metal Carbonates on 3D-Printed Surfaces

The biomineralizing bacterium Sporosarcina pasteurii has attracted considerable interest in the area of geotechnical engineering due to its ability to induce extracellular mineralization. The presented study investigated S. pasteurii's potential to induce the mineralization of alkali-earth metal carbonate coatings on different polymeric 3D-printed flat surfaces fabricated by different additive manufacturing methods. The use of calcium, barium, strontium, or magnesium ions as the source resulted in the formation of vaterite (CaCO3), witherite (BaCO3), strontianite (SrCO3), and nesquehonite MgCO3·3H2O, respectively. These mineral coatings generally exhibit a compact, yet variable, thickness and are composed of agglomerated microparticles similar to those formed in solution. However, the mechanism behind this clustering remains unclear. The thermal properties of these biologically induced mineral coatings differ from their inorganic counterpart, highlighting the unique characteristics imparted by the biomineralization process. This work seeks to capitalize on the bacterium S. pasteurii's ability to form an alkali-earth metal carbonate coating to expand beyond its traditional use in geoengineering applications. It lays the ground for a novel integration of biologically induced mineralization of single or multilayered and multifunctional coating materials, for example, aerospace applications.

Fatty alcohols, a minor component of the tree tobacco surface wax, are associated with defence against caterpillar herbivory

Despite decades of research resulting in a comprehensive understanding of epicuticular wax metabolism, the function of these almost ubiquitous metabolites in plant-herbivore interactions remains unresolved. In this study, we examined the effects of CRISPR-induced knockout mutations in four Nicotiana glauca (tree tobacco) wax metabolism genes. These mutations cause a wide range of changes in epicuticular wax composition, leading to altered interactions with insects and snails. Three interaction classes were examined: chewing herbivory by seven caterpillars and one snail species, phloem feeding by Myzus persicae (green peach aphid) and oviposition by Bemisia tabaci (whitefly). Although total wax load and alkane abundance did not affect caterpillar growth, a correlation across species, showed that fatty alcohols, a minor component of N. glauca surface waxes, negatively affected the growth of both a generalist caterpillar (Spodoptera littoralis) and a tobacco-feeding specialist (Manduca sexta). This negative correlation was overshadowed by the stronger effect of anabasine, a nicotine isomer, and was apparent when fatty alcohols were added to an artificial lepidopteran diet. By contrast, snails fed more on waxy leaves. Aphid reproduction and feeding activity were unaffected by wax composition but were potentially affected by altered cutin composition. Wax crystal morphology could explain the preference of B. tabaci to lay eggs on waxy wild-type plants relative to both alkane and fatty alcohol-deficient mutants. Together, our results suggest that the varied responses among herbivore classes and species are likely to be a consequence of the co-evolution that shaped the specific effects of different surface wax components in plant-herbivore interactions.

PRDM16 co-operates with LHX2 to shape the human brain

PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a de novo nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.

Impact of airborne algicidal bacteria on marine phytoplankton blooms

Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.

Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C

In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins (INPs) of common environmental bacteria like Pseudomonas syringae and Pseudomonas borealis. However, individually, these 100 kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an INP gene into Escherichia coli led to efficient ice nucleation. Here, we demonstrate that a positively charged subdomain at the C-terminal end of the central β-solenoid of the INP is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the INP multimers form fibres that are ~5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.

High-sensitivity deuterium metabolic MRI differentiates acute pancreatitis from pancreatic cancers in murine models

Deuterium metabolic imaging (DMI) is a promising tool for investigating a tumor's biology, and eventually contribute in cancer diagnosis and prognosis. In DMI, [6,6'-2H2]-glucose is taken up and metabolized by different tissues, resulting in the formation of HDO but also in an enhanced formation of [3,3'-2H2]-lactate at the tumor site as a result of the Warburg effect. Recent studies have shown DMI's suitability to highlight pancreatic cancer in murine models by [3,3'-2H2]-lactate formation; an important question is whether DMI can also differentiate between these tumors and pancreatitis. This differentiation is critical, as these two diseases are hard to distinguish today radiologically, but have very different prognoses requiring distinctive treatments. Recent studies have shown the limitations that hyperpolarized MRI faces when trying to distinguish these pancreatic diseases by monitoring the [1-13C1]-pyruvate→[1-13C1]-lactate conversion. In this work, we explore DMI's capability to achieve such differentiation. Initial tests used a multi-echo (ME) SSFP sequence, to identify any metabolic differences between tumor and acute pancreatitis models that had been previously elicited very similar [1-13C1]-pyruvate→[1-13C1]-lactate conversion rates. Although ME-SSFP provides approximately 5 times greater signal-to-noise ratio (SNR) than the standard chemical shift imaging (CSI) experiment used in DMI, no lactate signal was observed in the pancreatitis model. To enhance lactate sensitivity further, we developed a new, weighted-average, CSI-SSFP approach for DMI. Weighted-average CSI-SSFP improved DMI's SNR by another factor of 4 over ME-SSFP-a sensitivity enhancement that sufficed to evidence natural abundance 2H fat in abdominal images, something that had escaped the previous approaches even at ultrahigh (15.2 T) MRI fields. Despite these efforts to enhance DMI's sensitivity, no lactate signal could be detected in acute pancreatitis models (n = 10; [3,3'-2H2]-lactate limit of detection < 100 µM; 15.2 T). This leads to the conclusion that pancreatic tumors and acute pancreatitis may be clearly distinguished by DMI, based on their different abilities to generate deuterated lactate.

Near-Temperature-Independent Electron Transport Well beyond Expected Quantum Tunneling Range via Bacteriorhodopsin Multilayers

A key conundrum of biomolecular electronics is efficient electron transport (ETp) through solid-state junctions up to 10 nm, often without temperature activation. Such behavior challenges known charge transport mechanisms, especially via nonconjugated molecules such as proteins. Single-step, coherent quantum-mechanical tunneling proposed for ETp across small protein, 2-3 nm wide junctions, but it is problematic for larger proteins. Here we exploit the ability of bacteriorhodopsin (bR), a well-studied, 4-5 nm long membrane protein, to assemble into well-defined single and multiple bilayers, from ∼9 to 60 nm thick, to investigate ETp limits as a function of junction width. To ensure sufficient signal/noise, we use large area (∼10-3 cm2) Au-protein-Si junctions. Photoemission spectra indicate a wide energy separation between electrode Fermi and the nearest protein-energy levels, as expected for a polymer of mostly saturated components. Junction currents decreased exponentially with increasing junction width, with uniquely low length-decay constants (0.05-0.5 nm-1). Remarkably, even for the widest junctions, currents are nearly temperature-independent, completely so below 160 K. While, among other things, the lack of temperature-dependence excludes, hopping as a plausible mechanism, coherent quantum-mechanical tunneling over 60 nm is physically implausible. The results may be understood if ETp is limited by injection into one of the contacts, followed by more efficient charge propagation across the protein. Still, the electrostatics of the protein films further limit the number of charge carriers injected into the protein film. How electron transport across dozens of nanometers of protein layers is more efficient than injection defines a riddle, requiring further study.

Carbon dioxide regulates cholesterol levels through SREBP2

In mammals, O2 and CO2 levels are tightly regulated and are altered under various pathological conditions. While the molecular mechanisms that participate in O2 sensing are well characterized, little is known regarding the signaling pathways that participate in CO2 signaling and adaptation. Here, we show that CO2 levels control a distinct cellular transcriptional response that differs from mere pH changes. Unexpectedly, we discovered that CO2 regulates the expression of cholesterogenic genes in a SREBP2-dependent manner and modulates cellular cholesterol accumulation. Molecular dissection of the underlying mechanism suggests that CO2 triggers SREBP2 activation through changes in endoplasmic reticulum (ER) membrane cholesterol levels. Collectively, we propose that SREBP2 participates in CO2 signaling and that cellular cholesterol levels can be modulated by CO2 through SREBP2.

Deuterium imaging of the Warburg effect at sub-millimolar concentrations by joint processing of the kinetic and spectral dimensions

Deuterium metabolic imaging (DMI) is a promising molecular MRI approach, which follows the administration of deuterated substrates and their metabolization. [6,6'-2 H2 ]-glucose for instance is preferentially converted in tumors to [3,3'-2 H2 ]-lactate as a result of the Warburg effect, providing a distinct resonance whose mapping using time-resolved spectroscopic imaging can diagnose cancer. The MR detection of low-concentration metabolites such as lactate, however, is challenging. It has been recently shown that multi-echo balanced steady-state free precession (ME-bSSFP) increases the signal-to-noise ratio (SNR) of these experiments approximately threefold over regular chemical shift imaging; the present study examines how DMI's sensitivity can be increased further by advanced processing methods. Some of these, such as compressed sensing multiplicative denoising and block-matching/3D filtering, can be applied to any spectroscopic/imaging methods. Sensitivity-enhancing approaches were also specifically tailored to ME-bSSFP DMI, by relying on priors related to the resonances' positions and to features of the metabolic kinetics. Two new methods are thus proposed that use these constraints for enhancing the sensitivity of both the spectral images and the metabolic kinetics. The ability of these methods to improve DMI is evidenced in pancreatic cancer studies carried at 15.2 T, where suitable implementations of the proposals imparted eightfold or more SNR improvement over the original ME-bSSFP data, at no informational cost. Comparisons with other propositions in the literature are briefly discussed.

Correlation Consistent Basis Sets for Explicitly Correlated Theory: The Transition Metals

We present correlation consistent basis sets for explicitly correlated (F12) calculations, denoted VnZ(-PP)-F12-wis (n = D,T), for the d-block elements. The cc-pVDZ-F12-wis basis set is contracted to [8s7p5d2f] for the 3d-block, while its ECP counterpart for the 4d and 5d-blocks, cc-pVDZ-PP-F12-wis, is contracted to [6s6p5d2f]. The corresponding contracted sizes for cc-pVTZ(-PP)-F12-wis are [9s8p6d3f2g] for the 3d-block elements and [7s7p6d3f2g] for the 4d and 5d-block elements. Our VnZ(-PP)-F12-wis basis sets are evaluated on challenging test sets for metal-organic barrier heights (MOBH35) and group-11 metal clusters (CUAGAU-2). In F12 calculations, they are found to be about as close to the complete basis set limit as the combination of standard cc-pVnZ-F12 on main-group elements with the standard aug-cc-pV(n+1)Z(-PP) basis sets on the transition metal(s). While our basis sets are somewhat more compact than aug-cc-pV(n+1)Z(-PP), the CPU time benefit is negligible for catalytic complexes that contain only one or two transition metals among dozens of main-group elements; however, it is somewhat more significant for metal clusters.

Electro-Freezing of Supercooled Water Is Induced by Hydrated Al3+ and Mg2+ Ions: Experimental and Theoretical Studies

This work reports that the octahedral hydrated Al3+ and Mg2+ ions operate within electrolytic cells as kosmotropic (long-range order-making) "ice makers" of supercooled water (SCW). 10-5 M solutions of hydrated Al3+ and Mg2+ ions each trigger, near the cathode (-20 ± 5 V), electro-freezing of SCW at -4 °C. The hydrated Al3+ ions do so with 100% efficiency, whereas the Mg2+ ions induce icing with 40% efficiency. In contrast, hydrated Na+ ions, under the same experimental conditions, do not induce icing differently than pure water. As such, our study shows that the role played by Al3+ and Mg2+ ions in water electro-freezing is impacted by two synchronous effects: (1) a geometric effect due to the octahedral packing of the coordinated water molecules around the metallic ions, and (2) the degree of polarization which these two ions induce and thereby acidify the coordinated water molecules, which in turn imparts them with an ice-like structure. Long-duration molecular dynamics (MD) simulations of the Al3+ and Mg2+ indeed reveal the formation of "ice-like" hexagons in the vicinity of these ions. Furthermore, the MD shows that these hexagons and the electric fields of the coordinate water molecules give rise to ultimate icing. As such, the MD simulations provide a rational explanation for the order-making properties of these ions during electro-freezing.

An Increase in Mucin2 Expression Is Required for Colon Cancer Progression Mediated by L1

An induction in the expression of the cell adhesion receptor L1, a Wnt target gene, is a characteristic feature of Wnt/β-catenin activation in colon cancer cells at later stages of the disease. We investigated the proteins secreted following L1 expression in colon cancer cells and identified Mucin2 among the most abundant secreted proteins. We found that suppressing Mucin2 expression in L1-expressing colon cancer cells inhibits cell proliferation, motility, tumorigenesis, and liver metastasis. We detected several signaling pathways involved in Mucin2 induction in L1-expressing cells. In human colon cancer tissue, Mucin2 expression was significantly reduced or lost in the adenocarcinoma tissue, while in the mucinous subtype of colon cancer tissue, Mucin2 expression was increased. An increased signature of L1/Mucin2 expression reduced the survival rate of human colon cancer patients. Thus, induction of Mucin2 expression by L1 is required during mucinous colon cancer progression and can serve as a marker for diagnosis and a target for therapy.

Functional MRI of murine olfactory bulbs at 15.2T reveals characteristic activation patters when stimulated by different odors

Thanks to its increased sensitivity, single-shot ultrahigh field functional MRI (UHF fMRI) could lead to valuable insight about subtle brain functions such as olfaction. However, UHF fMRI experiments targeting small organs next to air voids, such as the olfactory bulb, are severely affected by field inhomogeneity problems. Spatiotemporal Encoding (SPEN) is an emerging single-shot MRI technique that could provide a route for bypassing these complications. This is here explored with single-shot fMRI studies on the olfactory bulbs of male and female mice performed at 15.2T. SPEN images collected on these organs at a 108 µm in-plane resolution yielded remarkably large and well-defined responses to olfactory cues. Under suitable T2* weightings these activation-driven changes exceeded 5% of the overall signal intensity, becoming clearly visible in the images without statistical treatment. The nature of the SPEN signal intensity changes in such experiments was unambiguously linked to olfaction, via single-nostril experiments. These experiments highlighted specific activation regions in the external plexiform region and in glomeruli in the lateral part of the bulb, when stimulated by aversive or appetitive odors, respectively. These strong signal activations were non-linear with concentration, and shed light on how chemosensory signals reaching the olfactory epithelium react in response to different cues. Second-level analyses highlighted clear differences among the appetitive, aversive and neutral odor maps; no such differences were evident upon comparing male against female olfactory activation regions.

Spindle Position Checkpoint Kinase Kin4 Regulates Organelle Transport in Saccharomyces cerevisiae

Membrane-bound organelles play important, frequently essential, roles in cellular metabolism in eukaryotes. Hence, cells have evolved molecular mechanisms to closely monitor organelle dynamics and maintenance. The actin cytoskeleton plays a vital role in organelle transport and positioning across all eukaryotes. Studies in the budding yeast Saccharomyces cerevisiae (S. cerevisiae) revealed that a block in actomyosin-dependent transport affects organelle inheritance to daughter cells. Indeed, class V Myosins, Myo2, and Myo4, and many of their organelle receptors, have been identified as key factors in organelle inheritance. However, the spatiotemporal regulation of yeast organelle transport remains poorly understood. Using peroxisome inheritance as a proxy to study actomyosin-based organelle transport, we performed an automated genome-wide genetic screen in S. cerevisiae. We report that the spindle position checkpoint (SPOC) kinase Kin4 and, to a lesser extent, its paralog Frk1, regulates peroxisome transport, independent of their role in the SPOC. We show that Kin4 requires its kinase activity to function and that both Kin4 and Frk1 protect Inp2, the peroxisomal Myo2 receptor, from degradation in mother cells. In addition, vacuole inheritance is also affected in kin4/frk1-deficient cells, suggesting a common regulatory mechanism for actin-based transport for these two organelles in yeast. More broadly our findings have implications for understanding actomyosin-based transport in cells.

Improved isolation of extracellular vesicles by removal of both free proteins and lipoproteins

Extracellular vesicles (EVs) are released by all cells into biofluids such as plasma. The separation of EVs from highly abundant free proteins and similarly sized lipoproteins remains technically challenging. We developed a digital ELISA assay based on Single Molecule Array (Simoa) technology for ApoB-100, the protein component of several lipoproteins. Combining this ApoB-100 assay with previously developed Simoa assays for albumin and three tetraspanin proteins found on EVs (Ter-Ovanesyan, Norman et al., 2021), we were able to measure the separation of EVs from both lipoproteins and free proteins. We used these five assays to compare EV separation from lipoproteins using size exclusion chromatography with resins containing different pore sizes. We also developed improved methods for EV isolation based on combining several types of chromatography resins in the same column. We present a simple approach to quantitatively measure the main impurities of EV isolation in plasma and apply this approach to develop novel methods for enriching EVs from human plasma. These methods will enable applications where high-purity EVs are required to both understand EV biology and profile EVs for biomarker discovery.

Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling

Increasing evidence suggests that ribosome composition and modifications contribute to translation control. Whether direct mRNA binding by ribosomal proteins regulates the translation of specific mRNA and contributes to ribosome specialization has been poorly investigated. Here, we used CRISPR-Cas9 to mutate the RPS26 C-terminus (RPS26dC) predicted to bind AUG upstream nucleotides at the exit channel. RPS26 binding to positions -10 to -16 of short 5' untranslated region (5'UTR) mRNAs exerts positive and negative effects on translation directed by Kozak and Translation Initiator of Short 5'UTR (TISU), respectively. Consistent with that, shortening the 5'UTR from 16 to 10 nt diminished Kozak and enhanced TISU-driven translation. As TISU is resistant and Kozak is sensitive to energy stress, we examined stress responses and found that the RPS26dC mutation confers resistance to glucose starvation and mTOR inhibition. Furthermore, the basal mTOR activity is reduced while AMP-activated protein kinase is activated in RPS26dC cells, mirroring energy-deprived wild-type (WT) cells. Likewise, the translatome of RPS26dC cells is correlated to glucose-starved WT cells. Our findings uncover the central roles of RPS26 C-terminal RNA binding in energy metabolism, in the translation of mRNAs bearing specific features and in the translation tolerance of TISU genes to energy stress.

Polymer Gel with Tunable Conductive Properties: A Material for Thermal Energy Harvesting

The spontaneous gelation of poly(4-vinyl pyridine)/pyridine solution produces materials with conductive properties that are suitable for various energy conversion technologies. The gel is a thermoelectric material with a conductivity of 2.2-5.0 × 10^-6 S m^-1 and dielectric constant ε = 11.3. On the molecular scale, the gel contains various types of hydrogen bonding, which are formed via self-protonation of the pyridine side chains. Our measurements and calculations revealed that the gelation process produces bias-dependent polymer complexes: quasi-symmetric, strongly hydrogen-bonded species, and weakly bound protonated structures. Under an applied DC bias, the gelled complexes differ in their capacitance/conductive characteristics. In this work, we exploited the bias-responsive characteristics of poly(4-vinyl pyridine) gelled complexes to develop a prototype of a thermal energy harvesting device. The measured device efficiency is S = ΔV/ΔT = 0.18 mV/K within the temperature range of 296-360 K. Investigation of the mechanism underlying the conversion of thermal energy into electric charge showed that the heat-controlled proton diffusion (the Soret effect) produces thermogalvanic redox reactions of hydrogen ions on the anode. The charge can be stored in an external capacitor for heat energy harvesting. These results advance our understanding of the molecular mechanisms underlying thermal energy conversion in the poly(4-vinyl pyridine)/pyridine gel. A device prototype, enabling thermal energy harvesting, successfully demonstrates a simple path toward the development of inexpensive, low-energy thermoelectric generators.

Intrinsic Magnetic (EuIn)As Nanowire Shells with a Unique Crystal Structure

In the pursuit of magneto-electronic systems nonstoichiometric magnetic elements commonly introduce disorder and enhance magnetic scattering. We demonstrate the growth of (EuIn)As shells, with a unique crystal structure comprised of a dense net of Eu inversion planes, over InAs and InAs_1-xSb_x core nanowires. This is imaged with atomic and elemental resolution which reveal a prismatic configuration of the Eu planes. The results are supported by molecular dynamics simulations. Local magnetic and susceptibility mappings show magnetic response in all nanowires, while a subset bearing a DC signal points to ferromagnetic order. These provide a mechanism for enhancing Zeeman responses, operational at zero applied magnetic field. Such properties suggest that the obtained structures can serve as a preferred platform for time-reversal symmetry broken one-dimensional states including intrinsic topological superconductivity.

Immune Profiling and Multiplexed Label-Free Detection of 2D MXenes by Mass Cytometry and High-Dimensional Imaging

There is a critical unmet need to detect and image 2D materials within single cells and tissues while surveying a high degree of information from single cells. Here, a versatile multiplexed label-free single-cell detection strategy is proposed based on single-cell mass cytometry by time-of-flight (CyTOF) and ion-beam imaging by time-of-flight (MIBI-TOF). This strategy, "Label-free sINgle-cell tracKing of 2D matErials by mass cytometry and MIBI-TOF Design" (LINKED), enables nanomaterial detection and simultaneous measurement of multiple cell and tissue features. As a proof of concept, a set of 2D materials, transition metal carbides, nitrides, and carbonitrides (MXenes), is selected to ensure mass detection within the cytometry range while avoiding overlap with more than 70 currently available tags, each able to survey multiple biological parameters. First, their detection and quantification in 15 primary human immune cell subpopulations are demonstrated. Together with the detection, mass cytometry is used to capture several biological aspects of MXenes, such as their biocompatibility and cytokine production after their uptake. Through enzymatic labeling, MXenes' mediation of cell-cell interactions is simultaneously evaluated. In vivo biodistribution experiments using a mixture of MXenes in mice confirm the versatility of the detection strategy and reveal MXene accumulation in the liver, blood, spleen, lungs, and relative immune cell subtypes. Finally, MIBI-TOF is applied to detect MXenes in different organs revealing their spatial distribution. The label-free detection of 2D materials by mass cytometry at the single-cell level, on multiple cell subpopulations and in multiple organs simultaneously, will enable exciting new opportunities in biomedicine.

Anharmonic Lattice Dynamics in Sodium Ion Conductors

We employ terahertz-range temperature-dependent Raman spectroscopy and first-principles lattice dynamical calculations to show that the undoped sodium ion conductors Na₃PS₄ and isostructural Na₃PSe₄ both exhibit anharmonic lattice dynamics. The anharmonic effects in the compounds involve coupled host lattice-Na⁺ ion dynamics that drive the tetragonal-to-cubic phase transition in both cases, but with a qualitative difference in the anharmonic character of the transition. Na₃PSe₄ shows an almost purely displacive character with the soft modes disappearing in the cubic phase as the change in symmetry shifts these modes to the Raman-inactive Brillouin zone boundary. Na₃PS₄ instead shows an order-disorder character in the cubic phase, with the soft modes persisting through the phase transition and remaining Raman active in the cubic phase, violating Raman selection rules for that phase. Our findings highlight the important role of coupled host lattice-mobile ion dynamics in vibrational instabilities that are coincident with the exceptional conductivity of these Na⁺ ion conductors.

Quadrupolar Isotope-Correlation Spectroscopy in Solid-State NMR

Quadrupolar solid-state NMR carries a wealth of structural information, including insights about chemical environments arising through the determination of local coupling parameters. Current methods can successfully resolve these parameters for individual sites using sample-spinning methods techniques applicable to quadrupolar I ≥ 1 nuclei, provided second-order central transition broadenings do not exceed by much the spinning rate. For large quadrupolar coupling (C _Q) values, however, static acquisitions are often preferable, leading to challenges in extracting local structural information. This study explores the use of two-dimensional QUadrupolar Isotope Correlation SpectroscopY (QUICSY) experiments as a means to increase the NMR spectral resolution and enrich the characterization of quadrupolar NMR patterns under static conditions. QUICSY seeks to correlate the solid-state NMR powder line shapes for two quadrupolar isotopes belonging to the same element via a 2D experiment. In general, two isotopes of the same element will have different nuclear quadrupole moments, gyromagnetic ratios, and spin numbers but essentially identical chemical environments. The possibility then arises of obtaining sharp "ridges" in these 2D correlations, even in static samples showing large quadrupolar effects, which lead to second-order line shapes that are several kilohertz wide. Moreover, pairs of quadrupolar isotopes are recurrent in the periodic table and include important elements such as ^35,37Cl, ^69,71Ga, ^79,81Br, and ^85,87Rb. The potential of this approach is explored theoretically and experimentally on two rubidium-containing salts: RbClO₄ and Rb₂SO₄. We find that each compound gives rise to distinctive 2D QUICSY line shapes, depending on the quadrupolar and chemical shift anisotropy (CSA) parameters of its sites. These experimental line shapes show good agreement with analytically derived 2D spectra relying on literature values of the quadrupolar and CSA tensors of these compounds. The approach underlined here paves the way toward better characterization of wideline NMR spectra of quadrupolar nuclei possessing different nuclear isotopes.

WO3 Nanowires Enhance Molecular Alignment and Optical Anisotropy in Electrospun Nanocomposite Fibers: Implications for Hybrid Light-Emitting Systems

The molecular orientation in polymer fibers is investigated for the purpose of enhancing their optical properties through nanoscale control by nanowires mixed in electrospun solutions. A prototypical system, consisting of a conjugated polymer blended with polyvinylpyrrolidone, mixed with WO₃ nanowires, is analyzed. A critical strain rate of the electrospinning jet is determined by theoretical modeling at which point the polymer network undergoes a stretch transition in the fiber direction, resulting in a high molecular orientation that is partially retained after solidification. Nearing a nanowire boundary, local adsorption of the polymer and hydrodynamic drag further enhance the molecular orientation. These theoretical predictions are supported by polarized scanning near-field optical microscopy experiments, where the dichroic ratio of the light transmitted by the fiber provides evidence of increased orientation nearby nanowires. The addition of nanowires to enhance molecular alignment in polymer fibers might consequently enhance properties such as photoluminescence quantum yield, polarized emission, and tailored energy migration, exploitable in light-emitting photonic and optoelectronic devices and for sensing applications.

Sustainable catalysis with fluxional acridine-based PNP pincer complexes

Because of the widespread use of fossil fuels and the resulting global warming, development of sustainable catalytic transformations is now more important than ever to obtain our desired fuels and building materials with the least carbon footprint and waste production. Many sustainable (de)hydrogenation reactions, including CO2 reduction, H2 carrier systems, and others, have been reported using molecular pincer complexes. A specific subset of pincer complexes containing a central acridine donor with flanking CH2PR2 ligands, known as acridine-based PNP pincer complexes, exhibit special reactivities that are not imitable by other PNP pincer complexes such as pyridine-based or (R2PCH2CH2)2NH type ligands. The goal of this article is to highlight the unique reactivities of acridine-based complexes and then investigate how these reactivities allow these complexes to catalyse many sustainable reactions that traditional pincer complexes cannot catalyse. To that end, we will initially go over the synthesis and structural features of acridine complexes, such as the labile coordination of the central N donor and the observed fac-mer fluxionality. Following that, distinct reactivity patterns of acridine-based complexes including their reactivity with acids and water will be discussed. Finally, we will discuss the reaction systems that have been developed with acridine complexes thus far, including the notable selective transformations of primary alcohols to primary amines using ammonia, N-heteroaromatic synthesis from alcohols and ammonia, oxidation reactions with water with H2 liberation, development of H2 carrier systems, and others, and conclude the article with future possible directions. We hope that the systemic study presented here will aid researchers in developing further sustainable reactions based on the unique acridine-based pincer complexes.

Dehydrogenative ester synthesis from enol ethers and water with a ruthenium complex catalyzing two reactions in synergy

We report the dehydrogenative synthesis of esters from enol ethers using water as the formal oxidant, catalyzed by a newly developed ruthenium acridine-based PNP(Ph)-type complex. Mechanistic experiments and density functional theory (DFT) studies suggest that an inner-sphere stepwise coupled reaction pathway is operational instead of a more intuitive outer-sphere tandem hydration-dehydrogenation pathway.

Catalytic Furfural/5-Hydroxymethyl Furfural Oxidation to Furoic Acid/Furan-2,5-dicarboxylic Acid with H2 Production Using Alkaline Water as the Formal Oxidant

Furfural and 5-hydroxymethyl furfural (HMF) are abundantly available biomass-derived renewable chemical feedstocks, and their oxidation to furoic acid and furan-2,5-dicarboxylic acid (FDCA), respectively, is a research area with huge prospective applications in food, cosmetics, optics, and renewable polymer industries. Water-based oxidation of furfural/HMF is a lucrative approach for simultaneous generation of H2 and furoic acid/FDCA. However, this process is currently limited to (photo)electrochemical methods that can be challenging to control, improve, and scale up. Herein, we report well-defined ruthenium pincer catalysts for direct homogeneous oxidation of furfural/HMF to furoic acid/FDCA, using alkaline water as the formal oxidant while producing pure H2 as the reaction byproduct. Mechanistic studies indicate that the ruthenium complex not only catalyzes the aqueous oxidation but also actively suppresses background decomposition by facilitating initial Tishchenko coupling of substrates, which is crucial for reaction selectivity. With further improvement, this process can be used in scaled-up facilities for a simultaneous renewable building block and fuel production.

Facile synthesis of amides via acceptorless dehydrogenative coupling of aryl epoxides and amines

The synthesis of amides is significant in a wide variety of academic and industrial fields. We report here a new reaction, namely acceptorless dehydrogenative coupling of epoxides and amines to form amides catalyzed by ruthenium pincer complexes. Various aryl epoxides and amines smoothly convert into the desired amides in high yields with the generation of H₂ gas as the only byproduct. Control experiments indicate that amides are generated kinetically faster than side products, possibly because of the facile activation of epoxides by metal–ligand cooperation, as supported by the observation of a ruthenium-enolate species. No alcohol or free aldehyde are involved. A mechanism is proposed involving a dual role of the catalyst, which is responsible for the high yield and selectivity of the new reaction.

We report the ruthenium pincer complex catalyzed acceptorless dehydrogenative coupling of epoxides and amines to form amides. The reaction offers a facile and atom economical two-step strategy for transforming alkenes into amides.

The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum

Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.

Sub-Band Spectrum Engineering via Structural Order in Tapered Nanowires

The cross-sectional dimensions of nanowires set the quantization conditions for the electronic subbands they host. These can be used as a platform to realize one-dimesional topological superconductivity. Here we develop a protocol that forces such nanowires to kink and change their growth direction. Consequently, a thin rectangular nanoplate is formed, which gradually converges into a very thin square tip. We characterize the resulting tapered nanowires structurally and spectroscopically by scanning and transmission electron microscopy and scanning tunneling microscopy and spectroscopy and model their growth. A unique structure composed of ordered rows of atoms on the (110) facet of the nanoflag is further revealed by atomically resolved topography and modeled by simulations. We discuss possible advantages tapered InAs nanowires offer for Majorana zero-mode realization and manipulation.

A Protein-Engineered, Enhanced Yeast Display Platform for Rapid Evolution of Challenging Targets

Here, we enhanced the popular yeast display method by multiple rounds of DNA and protein engineering. We introduced surface exposure-tailored reporters, eUnaG2 and DnbALFA, creating a new platform of C and N terminal fusion vectors. The optimization of eUnaG2 resulted in five times brighter fluorescence and 10 °C increased thermostability than UnaG. The optimized DnbALFA has 10-fold the level of expression of the starting protein. Following this, different plasmids were developed to create a complex platform allowing a broad range of protein expression organizations and labeling strategies. Our platform showed up to five times better separation between nonexpressing and expressing cells compared with traditional pCTcon2 and c-myc labeling, allowing for fewer rounds of selection and achieving higher binding affinities. Testing 16 different proteins, the enhanced system showed consistently stronger expression signals over c-myc labeling. In addition to gains in simplicity, speed, and cost-effectiveness, new applications were introduced to monitor protein surface exposure and protein retention in the secretion pathway that enabled successful protein engineering of hard-to-express proteins. As an example, we show how we optimized the WD40 domain of the ATG16L1 protein for yeast surface and soluble bacterial expression, starting from a nonexpressing protein. As a second example, we show how using the here-presented enhanced yeast display method we rapidly selected high-affinity binders toward two protein targets, demonstrating the simplicity of generating new protein-protein interactions. While the methodological changes are incremental, it results in a qualitative enhancement in the applicability of yeast display for many applications.

Consensus-based guidance for conducting and reporting multi-analyst studies

Any large dataset can be analyzed in a number of ways, and it is possible that the use of different analysis strategies will lead to different results and conclusions. One way to assess whether the results obtained depend on the analysis strategy chosen is to employ multiple analysts and leave each of them free to follow their own approach. Here, we present consensus-based guidance for conducting and reporting such multi-analyst studies, and we discuss how broader adoption of the multi-analyst approach has the potential to strengthen the robustness of results and conclusions obtained from analyses of datasets in basic and applied research.

Mechanistic dissection of dominant AIRE mutations in mouse models reveals AIRE autoregulation

The autoimmune regulator (AIRE) is essential for the establishment of central tolerance and prevention of autoimmunity. Interestingly, different AIRE mutations cause autoimmunity in either recessive or dominant-negative manners. Using engineered mouse models, we establish that some monoallelic mutants, including C311Y and C446G, cause breakdown of central tolerance. By using RNAseq, ATACseq, ChIPseq, and protein analyses, we dissect the underlying mechanisms for their dominancy. Specifically, we show that recessive mutations result in a lack of AIRE protein expression, while the dominant mutations in both PHD domains augment the expression of dysfunctional AIRE with altered capacity to bind chromatin and induce gene expression. Finally, we demonstrate that enhanced AIRE expression is partially due to increased chromatin accessibility of the AIRE proximal enhancer, which serves as a docking site for AIRE binding. Therefore, our data not only elucidate why some AIRE mutations are recessive while others dominant, but also identify an autoregulatory mechanism by which AIRE negatively modulates its own expression.

Heralded Spectroscopy Reveals Exciton-Exciton Correlations in Single Colloidal Quantum Dots

Multiply excited states in semiconductor quantum dots feature intriguing physics and play a crucial role in nanocrystal-based technologies. While photoluminescence provides a natural probe to investigate these states, room-temperature single-particle spectroscopy of their emission has proved elusive due to the temporal and spectral overlap with emission from the singly excited and charged states. Here, we introduce biexciton heralded spectroscopy enabled by a single-photon avalanche diode array based spectrometer. This allows us to directly observe biexciton-exciton emission cascades and measure the biexciton binding energy of single quantum dots at room temperature, even though it is well below the scale of thermal broadening and spectral diffusion. Furthermore, we uncover correlations hitherto masked in ensembles of the biexciton binding energy with both charge-carrier confinement and fluctuations of the local electrostatic potential. Heralded spectroscopy has the potential of greatly extending our understanding of charge-carrier dynamics in multielectron systems and of parallelization of quantum optics protocols.

Toxicity of Water- and Organic-Soluble Wood Tar Fractions from Biomass Burning in Lung Epithelial Cells

Widespread smoke from wildfires and biomass burning contributes to air pollution and the deterioration of air quality and human health. A common and major emission of biomass burning, often found in collected smoke particles, is spherical wood tar particles, also known as "tar balls". However, the toxicity of wood tar particles and the mechanisms that govern their health impacts and the impact of their complicated chemical matrix are not fully elucidated. To address these questions, we generated wood tar material from wood pyrolysis and isolated two main subfractions: water-soluble and organic-soluble fractions. The chemical characteristics as well as the cytotoxicity, oxidative damage, and DNA damage mechanisms were investigated after exposure of A549 and BEAS-2B lung epithelial cells to wood tar. Our results suggest that both wood tar subfractions reduce cell viability in exposed lung cells; however, these fractions have different modes of action that are related to their physicochemical properties. Exposure to the water-soluble wood tar fraction increased total reactive oxygen species production in the cells, decreased mitochondrial membrane potential (MMP), and induced oxidative damage and cell death, probably through apoptosis. Exposure to the organic-soluble fraction increased superoxide anion production, with a sharp decrease in MMP. DNA damage is a significant process that may explain the course of toxicity of the organic-soluble fraction. For both subfractions, exposure caused cell cycle alterations in the G2/M phase that were induced by upregulation of p21 and p16. Collectively, both subfractions of wood tar are toxic. The water-soluble fraction contains chemicals (such as phenolic compounds) that induce a strong oxidative stress response and penetrate living cells more easily. The organic-soluble fraction contained more polycyclic aromatic hydrocarbons (PAHs) and oxygenated PAHs and induced genotoxic processes, such as DNA damage.

Mesoscale phase separation of chromatin in the nucleus

Intact-organism imaging of Drosophila larvae reveals and quantifies chromatin-aqueous phase separation. The chromatin can be organized near the lamina layer of the nuclear envelope, conventionally fill the nucleus, be organized centrally, or as a wetting droplet. These transitions are controlled by changes in nuclear volume and the interaction of chromatin with the lamina (part of the nuclear envelope) at the nuclear periphery. Using a simple polymeric model that includes the key features of chromatin self-attraction and its binding to the lamina, we demonstrate theoretically that it is the competition of these two effects that determines the mode of chromatin distribution. The qualitative trends as well as the composition profiles obtained in our simulations compare well with the observed intact-organism imaging and quantification. Since the simulations contain only a small number of physical variables we can identify the generic mechanisms underlying the changes in the observed phase separations.

222 Rn emanation measurements for the XENON1T experiment

The selection of low-radioactive construction materials is of utmost importance for the success of low-energy rare event search experiments. Besides radioactive contaminants in the bulk, the emanation of radioactive radon atoms from material surfaces attains increasing relevance in the effort to further reduce the background of such experiments. In this work, we present the 222 Rn emanation measurements performed for the XENON1T dark matter experiment. Together with the bulk impurity screening campaign, the results enabled us to select the radio-purest construction materials, targeting a 222 Rn activity concentration of 10 μ Bq / kg in 3.2 t of xenon. The knowledge of the distribution of the 222 Rn sources allowed us to selectively eliminate problematic components in the course of the experiment. The predictions from the emanation measurements were compared to data of the 222 Rn activity concentration in XENON1T. The final 222 Rn activity concentration of ( 4.5 ± 0.1 ) μ Bq / kg in the target of XENON1T is the lowest ever achieved in a xenon dark matter experiment.

Optical analogues of black-hole horizons

Hawking radiation is unlikely to be measured from a real black hole, but can be tested in laboratory analogues. It was predicted as a consequence of quantum mechanics and general relativity, but turned out to be more universal. A refractive index perturbation produces an optical analogue of the black-hole horizon and Hawking radiation that is made of light. We discuss the central and recent experiments of the optical analogue, using hands-on physics. We stress the roles of classical fields, negative frequencies, 'regular optics' and dispersion. Opportunities and challenges ahead are briefly mentioned. This article is part of a discussion meeting issue 'The next generation of analogue gravity experiments'.

SARS-CoV-2 (COVID-19) by the numbers

The COVID-19 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this article we provide a one-stop, curated graphical source for the key numbers (based mostly on the peer-reviewed literature) about the SARS-CoV-2 virus that is responsible for the pandemic. The discussion is framed around two broad themes: i) the biology of the virus itself; ii) the characteristics of the infection of a single human host.

Synthesizing developmental trajectories

Dynamical processes in biology are studied using an ever-increasing number of techniques, each of which brings out unique features of the system. One of the current challenges is to develop systematic approaches for fusing heterogeneous datasets into an integrated view of multivariable dynamics. We demonstrate that heterogeneous data fusion can be successfully implemented within a semi-supervised learning framework that exploits the intrinsic geometry of high-dimensional datasets. We illustrate our approach using a dataset from studies of pattern formation in Drosophila. The result is a continuous trajectory that reveals the joint dynamics of gene expression, subcellular protein localization, protein phosphorylation, and tissue morphogenesis. Our approach can be readily adapted to other imaging modalities and forms a starting point for further steps of data analytics and modeling of biological dynamics.

A wide range of problems in biology require analysis of multivariable dynamics in space and time. As a rule, the multiscale nature and complexity of real systems precludes simultaneous monitoring of all the relevant variables, and multivariable dynamics must be synthesized from partial views provided by different experimental techniques. We present a formal framework for accomplishing this task in the context of imaging studies of pattern formation in developing tissues.

Tomato HAIRY MERISTEM genes are involved in meristem maintenance and compound leaf morphogenesis

The HAIRY MERISTEM (HAM) genes function in meristem maintenance but play minor roles in the morphogenesis of a simple leaf that is determinate. Here, we functionally analyzed HAM genes in tomato and uncovered their involvement in compound leaf morphogenesis. Tomato encodes three HAM homologs, of which SlHAM and SlHAM2 (SlHAMs) are guided for cleavage by microRNA171 and are abundant in the shoot and floral meristems as well as in the compound leaf primordia. We found that SlHAMs silencing led to overproliferation of cells in the periphery of the meristems where SlHAM is localized. As in meristems, leaf-specific silencing of SlHAMs provoked overproliferation of meristematic cells in the organogenic compound leaf rachis. We further demonstrate that the meristematic cell overproliferation in both meristems and leaves was in part due to the misexpression of the stem cell regulator WUSCHEL, previously shown to be induced by cytokinin. Strikingly, reduction of cytokinin levels in SlHAMs-silenced leaves completely suppressed the overproliferation phenotype, suggesting a regulatory link between SlHAMs and cytokinin, a key hormone found to promote indeterminacy in meristems and leaves. Taken together, our data provide evidence that in addition to their conserved function in meristem maintenance, SlHAMs are also required for the proper morphogenesis of the compound leaf.