Centrosymmetry-Breaking Morphotropic Phase Boundary: A Pathway to Highly Sensitive and Strong Pressure-Responsive Nonlinear Optical Switches.

The quest for high-performance piezoelectric materials has been synonymous with the pursuit of the morphotropic phase boundary (MPB), yet the full potential of MPBs remains largely untapped outside of the realm of ferroelectrics. In this study, we reveal a new class of MPB by creating continuous molecular-based solid solutions between centro- and noncentrosymmetric compounds, exemplified by (tert-butylammonium)1-x(tert-amylammonium)xFeCl4 (0 ≤ x ≤ 1), where the MPB is formed due to disorder of molecular cations. Near the MPB, we discovered an exceptionally sensitive nonlinear optical material in the centrosymmetric phase, capable of activation at pressures as low as 0.12-0.27 GPa, and producing tunable second-harmonic generation (SHG) signals from zero to 18.8 times that of KH2PO4 (KDP). Meanwhile, synchrotron diffraction experiments have unveiled a third competing phase (P212121) appearing at low pressure, forming a triple-phase point near the MPB, thereby providing insight into the mechanism underpinning the nonlinear optical (NLO) switch behavior. These findings highlight the opportunity to harness exceptional physical properties in symmetry-breaking solid solution systems by strategically designing novel MPBs.

Two-Dimensional Pb Square Nets from Bulk (RO)nPb (R = Rare Earth Metals, n = 1,2).

All two-dimensional (2D) materials of group IV elements from Si to Pb are stabilized by carrier doping and interface bonding from substrates except graphene which can be free-standing. The involvement of strong hybrid of bonds, adsorption of exotic atomic species, and the high concentration of crystalline defects are often unavoidable, complicating the measurement of the intrinsic properties. In this work, we report the discovery of seven kinds of hitherto unreported bulk compounds (RO)nPb (R = rare earth metals, n = 1,2), which consist of quasi-2D Pb square nets that are spatially and electronically detached from the [RO]δ+ blocking layers. The band structures of these compounds near Fermi levels are relatively clean and dominantly contributed by Pb, resembling the electron-doped free-standing Pb monolayer. The R2O2Pb compounds are metallic at ambient pressure and become superconductors under high pressures with much enhanced critical fields. In particular, Gd2O2Pb (9.1 µB/Gd) exhibits an interesting bulk response of lattice distortion in conjunction with the emergence of superconductivity and magnetic anomalies at a critical pressure of 10 GPa. Our findings reveal the unexpected facets of 2D Pb sheets that are considerably different from their bulk counterparts and provide an alternative route for exploring 2D properties in bulk materials.

Supersolidus liquid phase sintering of water-atomized low-alloy steel in binder jetting additive manufacturing.

This work investigates the feasibility of net shape manufacturing of parts using water-atomized (WA) low-alloy steel with comparable densities to conventional powder metallurgy parts via binder jetting additive manufacturing (BJAM) and supersolidus liquid phase sintering (SLPS). In this study, a modified water-atomized powder grade with similar composition as MPIF FL-4405 was printed and pressure-less sintered under a 95% N2-5% H2 atmosphere. Combinations of two different sintering schedules (direct-sintering and step-sintering) and three different heating rates (1, 3, and 5 °C/min) were applied to study the densification, shrinkage, and microstructural evolution of BJAM parts. This study demonstrated that, although the green density of the BJAM samples was ∼42% of the theoretical density, the sintered parts experienced large linear shrinkage up to ∼25% and reached ∼97% density without compromising shape fidelity. This was ascribed to a more homogeneous pore distribution throughout the part before ramping up to the SLPS region. The synergistic effects of carbon residue, the slow heating rate, and the additional isothermal holding stage at the solid-phase sintering region were determined to be the key factors for sintering BJAM WA low-alloy steel powders with resulting minimal entrapped porosity and good shape fidelity.

The conserved domain database in 2023.

NLM's conserved domain database (CDD) is a collection of protein domain and protein family models constructed as multiple sequence alignments. Its main purpose is to provide annotation for protein and translated nucleotide sequences with the location of domain footprints and associated functional sites, and to define protein domain architecture as a basis for assigning gene product names and putative/predicted function. CDD has been available publicly for over 20 years and has grown substantially during that time. Maintaining an archive of pre-computed annotation continues to be a challenge and has slowed down the cadence of CDD releases. CDD curation staff builds hierarchical classifications of large protein domain families, adds models for novel domain families via surveillance of the protein 'dark matter' that currently lacks annotation, and now spends considerable effort on providing names and attribution for conserved domain architectures. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Superconductivity in an Orbital-Reoriented SnAs Square Lattice: A Case Study of Li0.6 Sn2 As2 and NaSnAs.

Searching for functional square lattices in layered superconductor systems offers an explicit clue to modify the electron behavior and find exotic properties. The trigonal SnAs3 structural units in SnAs-based systems are relatively conformable to distortion, which provides the possibility to achieve structurally topological transformation and higher superconducting transition temperatures. In the present work, the functional As square lattice was realized and activated in Li0.6 Sn2 As2 and NaSnAs through a topotactic structural transformation of trigonal SnAs3 to square SnAs4 under pressure, resulting in a record-high Tc among all synthesized SnAs-based compounds. Meanwhile, the conductive channel transfers from the out-of-plane pz orbital to the in-plane px +py orbitals, facilitating electron hopping within the square 2D lattice and boosting the superconductivity. The reorientation of p-orbital following a directed local structure transformation provides an effective strategy to modify layered superconducting systems.

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.

The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted in a substantial reduction in spurious annotation. The hierarchical collection of protein family models (PFMs) used by PGAP as evidence for structural and functional annotation was expanded to over 35 000 protein profile hidden Markov models (HMMs), 12 300 BlastRules and 36 000 curated CDD architectures. As a result, >122 million or 79% of RefSeq proteins are now named based on a match to a curated PFM. Gene symbols, Enzyme Commission numbers or supporting publication attributes are available on over 40% of the PFMs and are inherited by the proteins and features they name, facilitating multi-genome analyses and connections to the literature. In adherence with the principles of FAIR (findable, accessible, interoperable, reusable), the PFMs are available in the Protein Family Models Entrez database to any user. Finally, the reference and representative genome set, a taxonomically diverse subset of RefSeq prokaryotic genomes, is now recalculated regularly and available for download and homology searches with BLAST. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/.

NCBI's Conserved Domain Database and Tools for Protein Domain Analysis.

The Conserved Domain Database (CDD) is a freely available resource for the annotation of sequences with the locations of conserved protein domain footprints, as well as functional sites and motifs inferred from these footprints. It includes protein domain and protein family models curated in house by CDD staff, as well as imported from a variety of other sources. The latest CDD release (v3.17, April 2019) contains more than 57,000 domain models, of which almost 15,000 were curated by CDD staff. The CDD curation effort increases coverage and provides finer-grained classifications of common and widely distributed protein domain families, for which a wealth of functional and structural data have become available. The CDD maintains both live search capabilities and an archive of pre-computed domain annotations for a selected subset of sequences tracked by the NCBI's Entrez protein database. These can be retrieved or computed for a single sequence using CD-Search or in bulk using Batch CD-Search, or computed via standalone RPS-BLAST plus the rpsbproc software package. The CDD can be accessed via https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. The three protocols listed here describe how to perform a CD-Search (Basic Protocol 1), a Batch CD-Search (Basic Protocol 2), and a Standalone RPS-BLAST and rpsbproc (Basic Protocol 3). © 2019 The Authors. Basic Protocol 1: CD-search Basic Protocol 2: Batch CD-search Basic Protocol 3: Standalone RPS-BLAST and rpsbproc.

CDD/SPARCLE: the conserved domain database in 2020.

As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Crystal structures of MBOgg1 in complex with two abasic DNA ligands.

7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common oxidative DNA lesions. 8-oxoguanine DNA glycosylases (Oggs) detect and excise 8-oxoG through a multiple-step process. To better understand the basis for estranged base recognition, we have solved the crystal structures of MBOgg1, the 8-oxoguanine DNA glycosylase of Thermoanaerobacter tengcongensis, in complex with DNA containing a tetrahydrofuranyl site (THF, a stable abasic site analog) paired with an estranged cytosine (MBOgg1/DNA(THF:C)) or thymine (MBOgg1/DNA(THF:T)). Different states of THF (extrahelical or intrahelical) are observed in the two complexes of the ASU of MBOgg1/DNA(THF:C) structure. Analyses of their different interaction modes reveal that variable contacts on the 5' region flanking the THF abasic site are correlated with the states of the THF. Comparison of MBOgg1/DNA(THF:T) with MBOgg1/DNA(THF:C) indicates that the non-preferred estranged T may affect MBOgg1's contacts with the 5' flank of the lesion strand. Furthermore, we identified a region in MBOgg1 that is rich in positive charges and interacts with the 5' region flanking the lesion. This region is conserved only in non-eukaryotic Oggs, and additional mutagenesis and biochemical assays reveal that it may contribute to the distinct estranged base specificities between eukaryotic and non-eukaryotic Oggs.

MSMEG_2731, an uncharacterized nucleic acid binding protein from Mycobacterium smegmatis, physically interacts with RPS1.

While the M. smegmatis genome has been sequenced, only a small portion of the genes have been characterized experimentally. Here, we purify and characterize MSMEG_2731, a conserved hypothetical alanine and arginine rich M. smegmatis protein. Using ultracentrifugation, we show that MSMEG_2731 is a monomer in vitro. MSMEG_2731 exists at a steady level throughout the M. smegmatis life-cycle. Combining results from pull-down techniques and LS-MS/MS, we show that MSMEG_2731 interacts with ribosomal protein S1. The existence of this interaction was confirmed by co-immunoprecipitation. We also show that MSMEG_2731 can bind ssDNA, dsDNA and RNA in vitro. Based on the interactions of MSMEG_2731 with RPS1 and RNA, we propose that MSMEG_2731 is involved in the transcription-translation process in vivo.