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At least 235 records · Page 13Linked to original sources

High-accuracy extrapolated ab initio thermochemistry. II. Minor improvements to the protocol and a vital simplification.

The recently developed high-accuracy extrapolated ab initio thermochemistry method for theoretical thermochemistry, which is intimately related to other high-precision protocols such as the Weizmann-3 and focal-point approaches, is revisited. Some minor improvements in theoretical rigor are introduced which do not lead to any significant additional computational overhead, but are shown to have a negligible overall effect on the accuracy. In addition, the method is extended to completely treat electron correlation effects up to pentuple excitations. The use of an approximate treatment of quadruple and pentuple excitations is suggested; the former as a pragmatic approximation for standard cases and the latter when extremely high accuracy is required. For a test suite of molecules that have rather precisely known enthalpies of formation {as taken from the active thermochemical tables of Ruscic and co-workers [Lecture Notes in Computer Science, edited by M. Parashar (Springer, Berlin, 2002), Vol. 2536, pp. 25-38; J. Phys. Chem. A 108, 9979 (2004)]}, the largest deviations between theory and experiment are 0.52, -0.70, and 0.51 kJ mol(-1) for the latter three methods, respectively. Some perspective is provided on this level of accuracy, and sources of remaining systematic deficiencies in the approaches are discussed.

Journal Article↗

On the possibility of constructive neutral evolution.

The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level," relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here with regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of these are instances of a more general scheme of "constructive neutral evolution" that invokes biased variation, epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or operations. The directional and constructive outcomes of these models are due not to neutral allele fixations per se, but to these other factors. Neutral models of this type may help to clarify the poorly understood role of nonselective factors in evolutionary innovation and directionality.

Amino Acid Sequence↗

Occurence of Veillonella and Neisseria in the niches of the human oral cavity.

Samples collected from the dental surface, gingival sulcus, dorsum of the tongue and from the cheek of ten adults (18 to 32 years) were investigated to identify the Veillonella and Neisseria species present by applying the taxonomic criteria suggested in the latest edition of Bergey's Manual. The various niches contain both V. parvula and V. alcalescens, but with the predominance of strains which do not fit precisely the described catalase and putrescine requirements. Eighty-nine out of 100 isolated strains of Gram negative oxidase positive cocci could be identified as N. sicca and N. subflava; about 11 unidentified strains exhibited characteristics of N. flavescens species.

Adolescent↗

Advances in the Application of Adenine Base Editor (ABE) in Biology and Medicine: Prospects and Challenges.

Adenine base editors (ABEs), which achieve A·T to G·C conversions in the genome precisely, symbolize a groundbreaking development in genetic engineering across animal, plant, and microbial systems. This review systematically summed up the research progress and current challenges of ABE in medical and biological applications: it outlined the historical context and pivotal milestones of its technological development; it emphasized major therapeutic advances for genetic diseases including spinal muscular atrophy, mitochondrial genetic disorders, and hyperlipidemia; it provided a comprehensive overview of its prospective uses for enhancing genetic traits in agricultural crops, including grains and fruits; this review conducted a multidimensional assessment of ABE performance through systematic comparison with other base editing technologies, comprehensively evaluating both editing efficiency and inherent limitations. It specifically addresses biosecurity risks such as off-target effects and genomic instability. Finally, safety concerns were proposed as the central challenge hindering its clinical translation, although ABE holds immense promise for precision medicine and agricultural breeding. Unlike previous reviews that mainly summarized early ABE development and general applications, this review particularly emphasizes recently engineered ABE systems, translational bottlenecks, delivery strategies, comparative clinical feasibility, and unresolved biosafety challenges that currently limit broader therapeutic and agricultural applications.

Adenine base editors↗

Cell-type-specific response to silicon treatment in soybean leaves revealed by single-nucleus RNA sequencing and targeted gene editing.

Mineral nutrient uptake and deposition profoundly influence plant development, stress resilience, and productivity. Silicon (Si), though classified as a non-essential element, significantly influences a plant's physiology, particularly in fortifying defense responses and mitigating stress. While the genetic and molecular mechanisms of Si uptake and transport are well studied in monocots, particularly rice, their role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. In this study, we utilized single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. We identified distinct cellular populations, including a unique Si-induced or Si-associated cell cluster within vascular cells, suggesting a specialized mechanism of Si distribution. Si treatment notably induced the expression of defense-related genes, with a pronounced enrichment in vascular cells, underscoring their pivotal role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in phytoalexin biosynthesis, salicylic acid, and immune receptor signaling, suggesting transcriptional priming of genes involved in defense responses. Further investigation of Si transporters revealed precise expression of an Si efflux gene in epidermal cells in response to Si treatment. We also validated the role of efflux Si transporters using a Xenopus oocyte assay and CRISPR/Cas9 genome editing of composite soybean plant roots. This study provides critical insights into the biotic stress regulatory networks influenced by Si treatment in soybean leaves at the single-cell level, thus laying the foundation for enhancing stress tolerance through optimized mineral nutrient uptake.

Glycine max↗

A simple microcomputer-based three-dimensional serial section reconstruction system (MICROS).

We have developed a computer system which enters and aligns serial sections and displays the completed reconstructions at different rotations in space. The system uses commercially available hardware, including a Hewlett-Packard 9845T microcomputer and an H-P 9874A digitizer. The software for the system is written in the BASIC language. The system consists of two programs, one for section digitization, the other for rotation and display of the reconstructions. Sections are digitized directly from micrographs or back-projected slides. The outlines of cells or other structures are traced from these media using a hand-held cursor on the digitizer. The positions of elements (inputs) which contact the structure and fiducials are also digitized. The sections are aligned by simultaneously displaying two consecutive sections on the graphics CRT screen. The sections are coarsely superimposed by centering around screen center using a centering algorithm. They are precisely aligned by rotating and translating the images with a reference cursor. Special functions for inserting and deleting sections and rapid section scanning are available for editing. The aligned sections are stored using a linked-list file structure on either floppy disks or tape cartridges. The rotation program replots the completed reconstructions on the graphics CRT or digital plotter. The program will reproduce the reconstructions at any scale and at any rotation in the x-, y- or z-planes. A hidden line algorithm removes hidden lines to give a 3-dimensional (3-D) perspective to the reconstructions. The positions of inputs and fiducials are represented by symbols. We use the system to reconstruct cells and neural processes. The 3-D reconstructions allow us to: (a) examine the spatial distribution and density of synaptic contacts on neurons; (b) study complex neuronal shapes; (c) examine the vectors of neural processes. The computer reconstruction system, which is moderately priced, should also prove useful for reconstructing many other types of biological profile.

Animals↗

Evolving conservation: The role of unconventional approaches to restore contemporary vertebrate populations and genomic biodiversity.

Conservation biology and restoration ecology are two essential yet distinct disciplines that address the growing challenge of biodiversity loss. Traditionally, these fields have relied on ecological principles and management practices aimed at protecting or reestablishing natural systems. The crisis is no longer just ecological; it is evolutionary and genomic. The accelerating pace of environmental change has outstripped the capacity of conventional approaches, creating a pressing need for innovative solutions. Biotechnology offers potentially transformative tools that can enhance the effectiveness and precision of both conservation and restoration efforts, especially for species where conventional conservation approaches have proved insufficient. Techniques such as genetic rescue, synthetic biology, and gene editing are increasingly being explored to address critical challenges, such as invasive species control, genetic diversity loss, and habitat fragmentation, to both invigorate endangered species and restore historical biodiversity. Despite its promise, the integration of biotechnology into conservation and restoration has raised ethical, ecological, and regulatory concerns. These include ecological unpredictability and public resistance to genetic interventions in wild populations. This perspective examines the current landscape of biotechnological applications in conservation and restoration, highlighting successful case studies, ongoing controversies, and optimism for additional progress. We argue that thoughtful, transparent integration of biotechnology that is grounded in ecological knowledge and stakeholder engagement can reconcile the goals of conservation and restoration. As ecosystems face mounting pressures, biotech-enabled strategies may prove essential for fostering resilience and ensuring long-term ecological sustainability.

Conservation of Natural Resources↗

Initial observations on effect of vigabatrin on in vivo 1H spectroscopic measurements of gamma-aminobutyric acid, glutamate, and glutamine in human brain.

Recent developments involving 1H nuclear magnetic resonance (NMR) spectroscopic editing techniques have allowed noninvasive measurements of gamma-aminobutyric acid (GABA) in human cerebrum. The additional information gained from GABA and macromolecule measurements permitted more precise glutamate (Glu) and glutamine (Gln) measurements. Occipital lobe GABA in 10 nonepileptic, healthy subjects was 1.0 mumol/g brain [95% confidence interval (CI) 0.9-1.1]. Vigabatrin (VGB) is a safe and effective antiepileptic drug (AED) that irreversibly inhibits neuronal and glial GABA-transaminase. GABA levels were increased in all patients treated with VGB. With a standard dose of 3-6 g/day, GABA levels were 2.6 mumol/g (95% CI 2.3-2.8). Mean occipital GABA level measured in epileptic patients not receiving VGB was 0.9 mumol/g (95% CI 0.7-1.1). Gln was increased by 1.9 mumol/g and Glu was decreased by 0.8 mumol/g in patients receiving VGB as compared with patients receiving standard medications alone.

Adult↗

[Histologic classification of epithelial salivary gland tumors].

A precise and reproducible histopathological classification, in combination with grading and staging, is the basis for determining the prognosis and treatment of salivary gland tumors. The 2nd edition of WHO Histological Typing of Salivary Gland Tumors, as well as the staging according to UICC 1989, is oriented towards the routine work of surgical pathologists. Knowledge about the important entities of this classification is an indispensable foundation for successful therapy and interdisciplinary cooperation.

Adenoma↗

Dual-gRNA CRISPR/Cas9 Deletion of CsDMR6 in Sweet Orange Supported by Improved In Vitro Regeneration.

Huanglongbing (HLB), caused by Candidatus Liberibacter spp., remains the most destructive disease affecting citrus worldwide. To support host-directed genome-editing strategies aimed at reducing susceptibility, we optimized key regeneration steps in Citrus sinensis and validated a dual-gRNA CRISPR/Cas9 approach targeting the susceptibility gene CsDMR6. Juvenile explants of 'Valencia' and hybrid genotypes (CsH1-CsH3) were successfully established in vitro, and shoot elongation was markedly improved by supplementing Citrus Shoot Multiplication (CiSM) medium with 1 mg L-1 GA3. Callus induction was most efficient in Citrus Callus Induction (CiCM) medium under dark conditions, while a 48 h NAA pulse (100 µM) significantly enhanced rooting, increasing efficiencies to 37.1% in 'Valencia' and 52.9% in CsH1. Two guide RNAs targeting conserved regions of CsDMR6 were designed and shown to be identical across all evaluated genotypes. The dual-gRNA cassette was assembled into a CRISPR/Cas9 geminivirus-based vector and transiently delivered into sweet orange leaf tissue via Agrobacterium. GFP fluorescence verified construct expression, and PCR amplification across the target region produced a diagnostic ~447 bp fragment corresponding to the expected ~5.8 kb deletion. Sanger sequencing confirmed precise junction formation between the two cut sites. These results demonstrate efficient large-fragment deletion of CsDMR6 in sweet orange and establish an experimentally validated, genotype-compatible regeneration and editing platform. This study provides a transient validation of the dual-gRNA system and establishes the technical foundation required for future stable, non-transgenic edited lines. Together, these advances support the downstream functional evaluation of CsDMR6 loss-of-function alleles under HLB pressure.

CRISPR/Cas9↗

Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces?

Biologically important joining of RNA pieces in cells, as exemplified by splicing and some classes of RNA editing, is posttranscriptional, whereas in RNA viruses it is generally believed to occur during viral RNA polymerase-dependent RNA synthesis. Here, we demonstrate the assembly of precise genome of an RNA virus (poliovirus) from its cotransfected fragments, which does not require specific RNA sequences, takes place before generation of the viral RNA polymerase, and occurs in different ways: Apparently unrestricted ligation of the terminal nucleotides, joining of any one of the two entire fragments with the relevant internal nucleotide of its partner, or internal crossovers within the overlapping sequence. Incorporation of the entire 5' or 3' partners into the recombinant RNA is activated by the presence of terminal 3'-phosphate and 5'-OH, respectively. Such postreplicative reactions, fundamentally differing from the known site-specific and structurally demanding cellular RNA rearrangements, might contribute to the origin and evolution of RNA viruses and could generate new RNA species during all stages of biological evolution.

3' Untranslated Regions↗

Medical staff and hospital administration uses of discharge abstract data.

In summary, this article suggests several useful approaches whereby physicians and hospital administrators can efficiently sort through large amounts of discharge abstract data to identify problem areas, particularly those concerning quality of care and utilization of services, and to formulate strategies for improvement. Approaches and steps suggested include: . Review objectives-determining variables of greatest concern; . Standards-determining acceptable values or levels of performance; . Focus of review-determining the unit of review, such as specific departments, diseases, or physicians; and . Quality and reliability of discharge abstract data-determining the data to use by undertaking four levels of edits: technical edits, logical edits, ratio edits, and categorical edits. A model flowchart provided in this article serves as a conceptual framework by which potential problem areas can be studied during a patient's hospitalization to precisely identify the interaction, the time, and the cause/association of the problem.

Decision Making↗

Non-redundancy of cytidine deaminases in class switch recombination.

Class switch recombination (CSR), somatic hypermutation, and gene conversion are immunoglobulin diversification mechanisms that are strictly dependent on the activity of the activation-induced cytidine deaminase (AID). The precise role and substrate(s) of AID in these processes remain to be well defined. The closest homologue of AID is APOBEC-1, a bona fide mRNA-editing enzyme, which shares with AID the ability to deaminate cytidines within single-stranded DNA in vitro and in prokaryotic cells. To determine whether APOBEC-1 can therefore substitute for AID in activated B cells, we expressed human AID, a catalytic mutant thereof, and rat APOBEC-1 in AID-deficient murine B cells. Whereas AID rescued CSR, neither the inactive mutant nor APOBEC-1 could complement AID deficiency. This indicates that cytidine deaminase activity is necessary but not sufficient to initiate CSR, and suggests that AID is specifically targeted to its cognate substrate, the immunoglobulin genes or a distinct mRNA, by an as-yet-unknown mechanism.

APOBEC-1 Deaminase↗

Contextual alignment of biological sequences (Extended abstract).

We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.

Algorithms↗

Visualizing the conformational landscape of CRISPR-Cas9 through kinetics-informed structural studies.

CRISPR-Cas9 has transformed genome editing through its programmability and versatility. Its DNA cleavage activity involves dynamic conformational changes during gRNA binding, DNA recognition, R-loop formation, and endonuclease activation. Understanding these molecular transitions is critical for improving the specificity and efficiency of Cas9, but this remains challenging precisely due to these rapid structural rearrangements. Early structural studies provided foundational insights but were limited to static states under catalytically inactive conditions. Cryo-EM has since enabled visualization of the dynamic nature of active Cas9, by enriching for specific conformations. This chapter introduces a kinetics-informed cryo-EM approach to capture the stepwise activation of Cas9 in real time. With thorough kinetic analyses, such as stopped-flow measurements of R-loop formation, we describe how to identify optimal timepoints to visualize key conformational states with cryo-EM. Integration of kinetic and structural data enables precise mapping of the conformational landscape of Cas9 and other dynamic enzymes, advancing our understanding of their molecular mechanisms and providing a framework for engineering enhanced variants.

Cryoelectron Microscopy↗

SETOR: hardware-lighted three-dimensional solid model representations of macromolecules.

SETOR is designed to exploit the hardware lighting capabilities of the IRIS-4D series graphics workstations to render high-quality raster images of macromolecules that can undergo rotation and translation interactively. SETOR can render standard all-atom and backbone models of proteins or nucleic acids, but focuses on displaying protein molecules by highlighting elements of secondary structure. The program has a very friendly user interface that minimizes the number of input files by allowing the user to interactively edit parameters, such as colors, lighting coefficients, and descriptions of secondary structure via mouse activated dialogue boxes. The choice of polymer chain representation can be varied from standard vector models and van der Waal models, to a B-spline fit of polymer backbones that yields a smooth ribbon that approximates the polymer chain, to strict Cardinal splines that interpolate the smoothest curve possible that will precisely follow the polymer chain. The program provides a photograph mode, save/restore facilities, and efficient generation of symmetry-related molecules and packing diagrams. Additionally, SETOR is designed to accept commands and model coordinates from the standard input stream, and to control standard output. Ancillary programs provide a method to interactively edit hardcopy plots of all vector and many solid models generated by SETOR, and to produce standard HPGL or PostScript files. Examples of figures rendered by SETOR of a number of macromolecules of various classes are presented.

Computer Graphics↗

[Studies on a handheld computer system for perinatal care].

The present paper demonstrates a handheld computer system for use in perinatal care. The features of the system are as follows: The gestational age and fetal body weight were determined by analyzing the data from ultrasonography with the high-order regressive equation. The combined use of the linear regressive equation and Ott's equation was more useful in precisely calculating the fetal abdominal circumference. In order to decrease input error, attempts were made to minimize key-operations for data-entry. The use of the screen edition system also made it easier to correct input error. It was concluded that this system was practical and easy to handle, and would be a useful aid in clinical care.

Body Weight↗

LV chamber extraction from 3-D CT images--accuracy and precision.

Measurement of left ventricular (LV) chamber volume and shape from three-dimensional (3-D) CT images, generated by the fast X-ray CT scanner known as the dynamic spatial reconstructor, has previously been done using manual slice-image editing. To reduce the exorbitant operator analysis time and operator-dependent measurement variations of manual slice-image editing, we have devised a semiautomatic method for LV-chamber extraction. The method draws upon a minimum requirement for selective manual slice-image editing and mostly makes use of automatic image-analysis operations. Detailed validation results over a wide range of hemodynamic and image-analysis conditions show that the measurements of the semiautomatic method strongly correlate with those made via manual slice-image editing and exhibit a lower intertrial variability. Further, the method reduces operator interaction time by nearly an order of magnitude over that of manual slice-image editing, but provides more detailed 3-D structural definition.

Animals↗