ALBERT

Description: Environmental risk assessment of chemicals is essential but often relies on ethically controversial and expensive methods. We show that tests using cell cultures, combined with modeling of toxicological effects, can replace tests with juvenile fish. Hundreds of thousands of fish at this developmental stage are annually used to assess the influence of chemicals on growth. Juveniles are more sensitive than adult fish, and their growth can affect their chances to survive and reproduce. Thus, to reduce the number of fish used for such tests, we propose a method that can quantitatively predict chemical impact on fish growth based on in vitro data. Our model predicts reduced fish growth in two fish species in excellent agreement with measured in vivo data of two pesticides. This promising step toward alternatives to fish toxicity testing is simple, inexpensive, and fast and only requires in vitro data for model calibration.

Description: Helicobacter pylori is a leading cause of peptic ulceration and gastric cancer worldwide. To achieve colonization of the stomach, this Gram-negative bacterium adheres to Lewis b (Le b ) antigens in the gastric mucosa using its outer membrane protein BabA. Structural information for BabA has been elusive, and thus, its molecular mechanism for recognizing Le b antigens remains unknown. We present the crystal structure of the extracellular domain of BabA, from H. pylori strain J99, in the absence and presence of Le b at 2.0- and 2.1-Å resolutions, respectively. BabA is a predominantly α-helical molecule with a markedly kinked tertiary structure containing a single, shallow Le b binding site at its tip within a β-strand motif. No conformational change occurs in BabA upon binding of Le b , which is characterized by low affinity under acidic [ K D (dissociation constant) of ~227 μM] and neutral ( K D of ~252 μM) conditions. Binding is mediated by a network of hydrogen bonds between Le b Fuc1, GlcNAc3, Fuc4, and Gal5 residues and a total of eight BabA amino acids (C189, G191, N194, N206, D233, S234, S244, and T246) through both carbonyl backbone and side-chain interactions. The structural model was validated through the generation of two BabA variants containing N206A and combined D233A/S244A substitutions, which result in a reduction and complete loss of binding affinity to Le b , respectively. Knowledge of the molecular basis of Le b recognition by BabA provides a platform for the development of therapeutics targeted at inhibiting H. pylori adherence to the gastric mucosa.

Description: In the absence of sensory stimulation or motor output, the brain exhibits complex spatiotemporal patterns of intrinsically generated neural activity. Analysis of ongoing brain dynamics has identified the prevailing modes of cortico-cortical interaction; however, little is known about how such patterns of intrinsically generated activity are correlated between cortical and subcortical brain areas. We investigate the correlation structure of ongoing cortical and superior colliculus (SC) activity across multiple spatial and temporal scales. Ongoing cortico-tectal interaction was characterized by correlated fluctuations in the amplitude of delta, spindle, low gamma, and high-frequency oscillations (〉100 Hz). Of these identified coupling modes, topographical patterns of high-frequency coupling were the most consistent with patterns of anatomical connectivity, reflecting synchronized spiking within cortico-tectal networks. Cortico-tectal coupling at high frequencies was temporally parcellated by the phase of slow cortical oscillations and was strongest for SC-cortex channel pairs that displayed overlapping visual spatial receptive fields. Despite displaying a high degree of spatial specificity, cortico-tectal coupling in lower-frequency bands did not match patterns of cortex-to-SC anatomical connectivity. Collectively, our findings demonstrate that neural activity is spontaneously coupled between cortex and SC, with high- and low-frequency modes of coupling reflecting direct and indirect cortico-tectal interactions, respectively.

Description: There is a striking correlation between terrestrial species’ pupil shape and ecological niche (that is, foraging mode and time of day they are active). Species with vertically elongated pupils are very likely to be ambush predators and active day and night. Species with horizontally elongated pupils are very likely to be prey and to have laterally placed eyes. Vertically elongated pupils create astigmatic depth of field such that images of vertical contours nearer or farther than the distance to which the eye is focused are sharp, whereas images of horizontal contours at different distances are blurred. This is advantageous for ambush predators to use stereopsis to estimate distances of vertical contours and defocus blur to estimate distances of horizontal contours. Horizontally elongated pupils create sharp images of horizontal contours ahead and behind, creating a horizontally panoramic view that facilitates detection of predators from various directions and forward locomotion across uneven terrain.

Description: Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase Pc Cel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium . Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton’s cradle"–like proton relay pathway of the catalytic cycle. Amide–imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.

Description: A unique functional electrode made of hierarchal Ni-Mo-S nanosheets with abundant exposed edges anchored on conductive and flexible carbon fiber cloth, referred to as Ni-Mo-S/C, has been developed through a facile biomolecule-assisted hydrothermal method. The incorporation of Ni atoms in Mo-S plays a crucial role in tuning its intrinsic catalytic property by creating substantial defect sites as well as modifying the morphology of Ni-Mo-S network at atomic scale, resulting in an impressive enhancement in the catalytic activity. The Ni-Mo-S/C electrode exhibits a large cathodic current and a low onset potential for hydrogen evolution reaction in neutral electrolyte (pH ~7), for example, current density of 10 mA/cm 2 at a very small overpotential of 200 mV. Furthermore, the Ni-Mo-S/C electrode has excellent electrocatalytic stability over an extended period, much better than those of MoS 2 /C and Pt plate electrodes. Scanning and transmission electron microscopy, Raman spectroscopy, x-ray diffraction, x-ray photoelectron spectroscopy, and x-ray absorption spectroscopy were used to understand the formation process and electrocatalytic properties of Ni-Mo-S/C. The intuitive comparison test was designed to reveal the superior gas-evolving profile of Ni-Mo-S/C over that of MoS 2 /C, and a laboratory-scale hydrogen generator was further assembled to demonstrate its potential application in practical appliances.

Description: The implementation of nanomedicine in cellular, preclinical, and clinical studies has led to exciting advances ranging from fundamental to translational, particularly in the field of cancer. Many of the current barriers in cancer treatment are being successfully addressed using nanotechnology-modified compounds. These barriers include drug resistance leading to suboptimal intratumoral retention, poor circulation times resulting in decreased efficacy, and off-target toxicity, among others. The first clinical nanomedicine advances to overcome these issues were based on monotherapy, where small-molecule and nucleic acid delivery demonstrated substantial improvements over unmodified drug administration. Recent preclinical studies have shown that combination nanotherapies, composed of either multiple classes of nanomaterials or a single nanoplatform functionalized with several therapeutic agents, can image and treat tumors with improved efficacy over single-compound delivery. Among the many promising nanomaterials that are being developed, nanodiamonds have received increasing attention because of the unique chemical-mechanical properties on their faceted surfaces. More recently, nanodiamond-based drug delivery has been included in the rational and systematic design of optimal therapeutic combinations using an implicitly de-risked drug development platform technology, termed Phenotypic Personalized Medicine–Drug Development (PPM-DD). The application of PPM-DD to rapidly identify globally optimized drug combinations successfully addressed a pervasive challenge confronting all aspects of drug development, both nano and non-nano. This review will examine various nanomaterials and the use of PPM-DD to optimize the efficacy and safety of current and future cancer treatment. How this platform can accelerate combinatorial nanomedicine and the broader pharmaceutical industry toward unprecedented clinical impact will also be discussed.

Description: Alkali-doped fullerides A 3 C 60 ( A = K, Rb, Cs) are surprising materials where conventional phonon-mediated superconductivity and unconventional Mott physics meet, leading to a remarkable phase diagram as a function of volume per C 60 molecule. We address these materials with a state-of-the-art calculation, where we construct a realistic low-energy model from first principles without using a priori information other than the crystal structure and solve it with an accurate many-body theory. Remarkably, our scheme comprehensively reproduces the experimental phase diagram including the low-spin Mott-insulating phase next to the superconducting phase. More remarkably, the critical temperatures T c ’s calculated from first principles quantitatively reproduce the experimental values. The driving force behind the surprising phase diagram of A 3 C 60 is a subtle competition between Hund’s coupling and Jahn-Teller phonons, which leads to an effectively inverted Hund’s coupling. Our results establish that the fullerides are the first members of a novel class of molecular superconductors in which the multiorbital electronic correlations and phonons cooperate to reach high T c s -wave superconductivity.

Description: Nitrogen oxides, released from fossil fuel use and other combustion processes, affect air quality and climate. From the mid-1990s onward, nitrogen dioxide (NO 2 ) has been monitored from space, and since 2004 with relatively high spatial resolution by the Ozone Monitoring Instrument. Strong upward NO 2 trends have been observed over South and East Asia and the Middle East, in particular over major cities. We show, however, that a combination of air quality control and political factors, including economical crisis and armed conflict, has drastically altered the emission landscape of nitrogen oxides in the Middle East. Large changes, including trend reversals, have occurred since about 2010 that could not have been predicted and therefore are at odds with emission scenarios used in projections of air pollution and climate change in the early 21st century.

Description: Cluster analysis is one of the most popular data analysis tools in a wide range of applied disciplines. We propose and justify a computationally efficient and straightforward-to-implement way of imposing the available information from networks/graphs (a priori available in many application areas) on a broad family of clustering methods. The introduced approach is illustrated on the problem of a noninvasive unsupervised brain signal classification. This task is faced with several challenging difficulties such as nonstationary noisy signals and a small sample size, combined with a high-dimensional feature space and huge noise-to-signal ratios. Applying this approach results in an exact unsupervised classification of very short signals, opening new possibilities for clustering methods in the area of a noninvasive brain-computer interface.