Dr. Autar Krishen Mattoo (1943-2024): an outstanding plant biologist with a focus on photosynthesis.

We provide here the academic life of Dr. Autar Krishen Mattoo (1943-2024), including his role as a research leader at the United States Department of Agriculture and his outstanding contributions in photosynthesis, plant physiology and molecular biology with a focus to enhance nutrients. His work included ways to regulate Photosystem II (PSII) reaction center proteins, as well as to exploit, for our benefit, the role of polyamines in the plant world.

A Structure-Based Computational Pipeline for Broad-Spectrum Antiviral Discovery.

The rapid emergence of viruses with pandemic potential continues to pose a threat to public health worldwide. With the typical drug discovery pipeline taking an average of 5-10 years to reach clinical readiness, there is an urgent need for strategies to develop broad-spectrum antivirals that can target multiple viral family members and variants of concern. We present a structure-based computational pipeline designed to identify and evaluate broad-spectrum inhibitors across viral family members for a given target in order to support spectrum breadth assessment and prioritization in lead optimization programs.

Unraveling the Decomposition Pathways of LaS-TaS Misfit-Layered Compound Nanostructures under Extreme Electrical Currents by In Situ TEM.

Nanostructures of the misfit-layered compound (MLC) LaS-TaS are brought to breakdown by application of high electrical currents within a transmission electron microscope. Imaging, diffraction, and spectroscopy techniques are employed to study their decomposition process and the resulting structures. The main decomposition route is the breakdown of the TaS layers, which induces the formation of metallic Ta on the surface of the nanostructures when the critical current density is surpassed.

Evolution of nervous systems: Molecular divergence in a conserved body plan.

Comparative inter-species single-cell atlases of Caenorhabditis whole embryos and larval nervous systems reveal deep conservation of cell type identities alongside extensive divergence in signaling pathways. These findings illustrate how stable cellular architectures support evolving molecular logic across development and behavior.

Intersegment Transfer and the Dynamical Architecture of Fis Protein-DNA Multimer Complexes.

Gene regulation often entails a cooperative dynamic interplay among several protein molecules and several distinct DNA segments. Intersegment transfer of the Fis protein stimulates DNA inversion during DNA recombination. Individual DNA segments have been found to facilitate the dissociation of Fis proteins already bound to DNA and also allow for the transfer of the Fis between segments.

Calcium signaling in postsynaptic mitochondria: mechanisms, dynamics, and role in ATP production.

While the overall ATP level in neurons remains relatively stable, local fluctuations in synaptic compartments - driven by synaptic potentials - necessitate rapid ATP adjustments. The energy supply for synaptic activity in neurons must be under precise homeostatic control: increased ATP consumption in active synapses requires continuous replenishment, whereas in periods of inactivity, excess ATP production may occur. Overproduction of ATP in thousands of individual synapses is metabolically wasteful, while underproduction threatens to disrupt molecular cascades associated with ongoing synaptic bursts, ion homeostasis, protein synthesis, and neural plasticity.

Quantum Interfaces with Multilayered Superwavelength Atomic Arrays.

We consider quantum light-matter interfaces comprised of multiple layers of two-dimensional tweezer atomic arrays, wherein the lattice spacings exceed the wavelength of light. While the coupling of light to a single layer of such a "superwavelength" lattice is considerably reduced due to scattering losses to high diffraction orders, we show that the addition of layers can suppress these losses through destructive interference between the layers. Mapping the problem to a 1D model of a quantum interface wherein the coupling efficiency is characterized by a reflectivity, we analyze the latter by developing a geometrical optics formulation, accounting for realistic finite-size arrays.

Electrical XPS meets biology: chemo-electrical sensing and activation of organic materials.

X-ray photoelectron spectroscopy (XPS) is a popular analytical technique in materials sciences owing to its versatile coverage of broad energy ranges and the reliability of its quantitative compositional analysis. Hence, tailoring XPS capabilities to the research frontiers of biological systems and nature-inspired materials can potentially be of great value. However, the application of XPS in bio/organic systems encounters critical inherent challenges, specifically amplified by the rich nuances that are at the heart of biological functions.

Metal-induced conformational changes in the Sabiá virus spike complex.

Haemorrhagic fever viruses from the Arenaviridae are a source of concern owing to their potential to cause lethal outbreaks and the lack of effective therapeutics. While structures of spike proteins from 'Old World' arenaviruses are available, the differences and similarities to 'New World' arenaviruses, such as the Sabiá virus, remain unclear owing to the lack of New World spike structures. Here we present the structure of the isolated spike complex from the Sabiá virus, which mediates viral attachment and entry to the host cells, using single-particle cryo-electron microscopy.

Coastal aquifers key contributors to ocean chemistry through solute fluxes.

Understanding the ocean's chemical composition is key to assessing the carbon cycle and its climate impact, especially through its control on calcium carbonate saturation and preservation. While rivers and hydrothermal systems are recognized contributors to ocean chemistry, the role of coastal aquifers has been underestimated. This study shows that long-term submarine groundwater discharge (SGD) is a major source of solute fluxes to the ocean, especially of calcium and alkalinity, while removing sodium and potassium.

Molecular processes as quantum information resources.

In this contribution to Abraham Nitzan's Festschrift, we present a perspective of theoretical research over the years that has pointed to the potential of molecular processes to act as quantum information resources. Under appropriate control, homonuclear dimer (diatom) dissociation (half-collision) and the inverse process of atom-pair collisions are shown to reveal translational (EPR-like) entanglement that enables molecular wave packet teleportation. When such processes involve electronic-state excitation of the diatom, the fluorescence following dissociation can serve as an entanglement witness that unravels the molecular-state characteristics and evolution.

Selective Choice of the Efficient Carotenoid Antenna by a Xanthorhodopsin: Controlling Factors for Binding and Excitation Energy Transfer.

Despite extensive research on carotenoids and microbial rhodopsins in aquatic environments, a fundamental understanding of the binding requirements of carotenoids that serve as auxiliary light-harvesting antennas for rhodopsins is still lacking. Our recent discovery of 3-hydroxylated xanthophyll-binding proteorhodopsins and xanthorhodopsins prompted us to investigate the role of keto and hydroxy functional groups in carotenoid binding to rhodopsins and their influence on energy transfer to the retinal chromophore. In this study, we examined the binding of 12 carotenoids to rhodopsin Kin4B8 (a protein of the xanthorhodopsin family, GenBank: OP056329) and assessed the energy transfer between the carotenoid and the retinal chromophore.

Multimodal AI correlates of glucose spikes in people with normal glucose regulation, pre-diabetes and type 2 diabetes.

Type 2 diabetes (T2D) is a multifaceted disease associated with several factors, including diet, genetics, exercise, sleep and gut microbiome. Current diagnostic and monitoring methods based on episodic assays like glycated hemoglobin (HbA1c) fail to capture its full complexity. Here, in a prospective cohort of 1,137 participants in the United States, we analyzed multimodal data from 347 deeply phenotyped individuals (174 normoglycemic, 79 prediabetic and 94 T2D).

PNKP targeting engages the autophagic machinery through STING and STAT3 to potentiate ferroptosis and chemotherapy in TNBC.

The polynucleotide kinase/phosphatase (PNKP) is a DNA repair enzyme possessing bifunctional DNA 3'-phosphatase and DNA 5'-kinase activities. It plays an important role in the rejoining of single- and double-strand DNA breaks and is considered as a potential therapeutic target for different cancer types. Here we show that PNKP is highly expressed in triple negative breast cancer (TNBC) and associated with poor prognosis and chemoresistance.

Internal Entropy of Non-Abelian Anyons from Heat Current through a Tunneling Barrier.

We demonstrate that the effective internal entropy of quasiparticles within the non-Abelian fractional quantum Hall effect manifests in the heat current through a tunneling barrier. We derive the electric current and heat current resulting from voltage and heat biases of the junction, taking into account the quasiparticles' internal entropy. We find that when the tunneling processes are dominated by quasiparticle tunneling of one type of charge, the effective internal entropy can be inferred from the measurement of the heat current and the charge current.

Topological Nature of Edge States for One-Dimensional Systems without Symmetry Protection.

We numerically verify and analytically prove a winding number invariant that correctly predicts the number of edge states in one-dimensional, nearest-neighbor (between unit cells), two-band models with any complex couplings and open boundaries. Our winding number uses analytical continuation of the wave-vector into the complex plane and involves two special points on the full Riemann surface band structure that correspond to bulk eigenvector degeneracies. Our winding number is invariant under unitary or similarity transforms.

Multiple Mechanisms for Emerging Conductance Plateaus in Fractional Quantum Hall States.

Two-terminal conductance quantization in the context of quantum Hall (QH) physics is intimately related to the current carried by a discrete number of chiral edge modes. Upon pinching off a QH bar, one may engineer setups where some modes are fully transmitted (while the others are fully reflected), giving rise to the orthodox theory of quantized conductance plateaus. Here, we note that the observation of quantized plateaus does not uniquely indicate the underlying mechanism.

PEX39 facilitates the peroxisomal import of PTS2-containing proteins.

Peroxisomes are metabolic organelles essential for human health. Defects in peroxisomal biogenesis proteins (also known as peroxins (PEXs)) cause devastating disease. PEX7 binds proteins containing a type 2 peroxisomal targeting signal (PTS2) to enable their import from the cytosol into peroxisomes, although many aspects of this process remain enigmatic.

Black carbon emissions generally underestimated in the global south as revealed by globally distributed measurements.

Characterizing black carbon (BC) on a fine scale globally is essential for understanding its climate and health impacts. However, sparse BC mass measurements in different parts of the world and coarse model resolution have inhibited evaluation of global BC emission inventories. Here, we apply globally distributed BC mass measurements from the Surface Particulate Matter Network (SPARTAN) and complementary measurement networks to evaluate contemporary BC emission inventories.

Text-related functionality and dynamics of visual human pre-frontal activations revealed through neural network convergence.

Human prefrontal areas show enhanced activations when individuals are presented with images, under diverse task conditions. However, the functional role of these increased activations remains a deeply debated question. Here we addressed this question by comparing, dynamically, the relational structure of prefrontal activations and both visual and textual-trained deep neural networks (DNNs) during a visual memorization task.

Selective association of short tandem repeats with DNA-binding domains and intrinsically disordered regions of transcription factors.

Short tandem repeats (STRs) are enriched in regulatory regions and can bind transcription factors (TFs), as shown for selected examples in vitro. Here, we use a library-based assay to systematically measure TF binding to STRs of 2-5 bp units within budding yeast cells. We examined STR binding by four TFs, including Msn2, and further tested six Msn2 mutants, including two that contained only the DNA-binding domain (DBD) or only the 642-aa intrinsically disordered region (IDR).

DNA mutagenesis driven by transcription factor competition with mismatch repair.

Despite the remarkable fidelity of eukaryotic DNA replication, nucleotide misincorporation errors occur in every replication cycle, generating mutations that drive genetic diseases and genome evolution. Here, we show that transcription factor (TF) proteins, key players in gene regulation, can increase mutagenesis from replication errors by directly competing with the recognition of DNA mismatches by MutSα, the primary initiator of eukaryotic mismatch repair (MMR). We demonstrate this TF-induced mutagenesis mechanism using a yeast genetic assay that quantifies the accumulation of mutations in TF binding sites.

Manipulation of the nucleotide pool in human, bacterial and plant immunity.

The cell-autonomous innate immune system is responsible for sensing and mitigating viral infection at the level of individual cells. Many of the mechanisms used by the cell-autonomous innate immune system in eukaryotic cells are ancient and have evolutionary roots in bacterial systems that defend against phage infection. Studies from recent years have shown that modification of the free nucleotide pool is central to many of these conserved immune mechanisms.

Cross-Activity Analysis of CRISPR/Cas9 Editing in Gene Families of Detected by Long-Read Sequencing.

CRISPR/Cas9 genome editing holds promise for precise genetic modifications, yet off-target effects remain a concern-particularly in gene families with high sequence similarity. In this study, we present a computational framework for analyzing editing specificity and cross-reactivity in gene families using long-read sequencing data. The pipeline integrates multiplex PCR, NGS, and CRISPECTOR-based analysis to detect and quantify on- and off-target events with high sensitivity.

Synergistic Efficacy of WST11-VTP and P-Selectin-Targeted Nanotherapy in a Preclinical Prostate Cancer Model.

Radical therapies are associated with significant morbidity in patients with localized prostate cancer (PCa). While advances in nuclear magnetic resonance techniques have enabled the development of focal ablation procedures that can selectively destroy tumors, preserve the gland and surrounding structures, and minimize side effects, existing vascular-targeted photodynamic therapy (VTP) and nanodrug therapies often face limitations, such as recurrence and insufficient drug concentration at the tumor site. This study investigated a novel approach that combines VTP with systemic treatment using drug-loaded nanoparticles in a murine model, demonstrating substantial advancements beyond current monotherapies.