Quantifying Protein-Nucleic Acid Interactions for Engineering Useful CRISPR-Cas9 Genome-Editing Variants.

Numerous high-specificity Cas9 variants have been engineered for precision genome editing. These variants typically harbor multiple mutations designed to alter the Cas9-single guide RNA (sgRNA)-DNA complex interactions for reduced off-target cleavage. By dissecting the contributions of individual mutations, we attempt to derive principles for designing high-specificity Cas9 variants.

Adolescent pregnancy, maternal and child anaemia: Empirical analysis from India, Bangladesh, and Nigeria.

Early childbearing poses several potential risks to maternal and child health. This paper empirically analyses the association between teenage pregnancy and child nutritional status, maternal and child anaemia in three countries (Nigeria, India and Bangladesh) that account for the highest proportion of teenage births and/or total number of malnourished teenage mothers and children. Data were sourced from nine waves of Demographic and Health Surveys conducted in Bangladesh, India, and Nigeria from 2005-2018, covering a sample of 27,705 children from Bangladesh, 266,308 children from India and 54,719 children from Nigeria.

Structural insights into the assembly pathway of the Helicobacter pylori CagT4SS outer membrane core complex.

Cag type IV secretion system (CagT4SS) translocates oncoprotein cytotoxin-associated gene A (CagA) into host cells and plays a key role in the pathogenesis of Helicobacter pylori. The structure of the outer membrane core complex (OMCC) in CagT4SS consists of CagX, CagY, CagM, CagT, and Cag3 in a stoichiometric ratio of 1:1:2:2:5 with 14-fold symmetry. However, the assembly pathway of OMCC remains elusive.

Light-Activated Nanodiamond-Based Drug Delivery Systems for Spatiotemporal Release of Antisense Oligonucleotides.

Nanodiamonds (NDs) are considered promising delivery platforms, but inaccurate and uncontrolled release of drugs at target sites is the biggest challenge of NDs in precision medicine. This study presents the development of phototriggerable ND-based drug delivery systems, utilizing -nitrobenzyl (-NB) molecules as photocleavable linkers between drugs and nanocarriers. UV irradiation specifically cleaved -NB molecules and then was followed by releasing antisense oligonucleotides from ND-based carriers in both buffer and cellular environments.

Continuum of care in maternal and child health in Indonesia.

Aim: This paper aims to empirically analyze the socioeconomic and demographic correlates of maternal and child health (MCH) care utilization in Indonesia using the (CoC) concept.

Background: The concept of CoC has emerged as an important guiding principle in reproductive, maternal, newborn, and child health. Indonesia's maternal mortality rate, neonatal mortality, and under-five mortality rates are among the highest in the Southeast Asian region.

Accurate top protein variant discovery via low-N pick-and-validate machine learning.

A strategy to obtain the greatest number of best-performing variants with least amount of experimental effort over the vast combinatorial mutational landscape would have enormous utility in boosting resource producibility for protein engineering. Toward this goal, we present a simple and effective machine learning-based strategy that outperforms other state-of-the-art methods. Our strategy integrates zero-shot prediction and multi-round sampling to direct active learning via experimenting with only a few predicted top variants.

Ultra-stable threose nucleic acid-based biosensors for rapid and sensitive nucleic acid detection and in vivo imaging.

The human genome's nucleotide sequence variation, such as single nucleotide mutations, can cause numerous genetic diseases. However, detecting nucleic acids accurately and rapidly in complex biological samples remains a major challenge. While natural deoxyribonucleic acid (DNA) has been used as biorecognition probes, it has limitations like poor specificity, reproducibility, nuclease-induced enzymatic degradation, and reduced bioactivity on solid surfaces.

High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2.

Mapping mutations and discovering cellular determinants that cause the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce infected cells to form syncytia would facilitate the development of strategies for blocking the formation of such cell-cell fusion. Here we describe high-throughput screening methods based on droplet microfluidics and the size-exclusion selection of syncytia, coupled with large-scale mutagenesis and genome-wide knockout screening via clustered regularly interspaced short palindromic repeats (CRISPR), for the large-scale identification of determinants of cell-cell fusion. We used the methods to perform deep mutational scans in spike-presenting cells to pinpoint mutable syncytium-enhancing substitutions in two regions of the spike protein (the fusion peptide proximal region and the furin-cleavage site).

Parallel engineering and activity profiling of a base editor system.

Selecting the most suitable existing base editors and engineering new variants for installing specific base conversions with maximal efficiency and minimal undesired edits are pivotal for precise genome editing applications. Here, we present a platform for creating and analyzing a library of engineered base editor variants to enable head-to-head evaluation of their editing performance at scale. Our comprehensive comparison provides quantitative measures on each variant's editing efficiency, purity, motif preference, and bias in generating single and multiple base conversions, while uncovering undesired higher indel generation rate and noncanonical base conversion for some of the existing base editors.

Versatile nanodiamond-based tools for therapeutics and bioimaging.

Nanodiamonds (NDs) are a remarkable class of carbon-based nanoparticles in nanomedicine which have recently become a hot topic of research due to their unique features including functionalization versatility, tunable opto-magnetic properties, chemical stability, minimal cytotoxicity, high affinity to biomolecules and biocompatibility. These attractive features make NDs versatile tools for a wide range of biologically relevant applications. In this feature article, we discuss the opto-magnetic properties of negatively charged nitrogen vacancy (NV) centres in NDs as fluorescence probes.

Wavelength-Dependent, Orthogonal Photoregulation of DNA Liberation for Logic Operations.

In this study, we synthesized two phosphoramidites based on 2,7-bis-{4-nitro-8-[3-(2-propyl)-styryl]}-9,9-bis-[1-(3,6-dioxaheptyl)]-fluorene (BNSF) and 4,4'-bis-{8-[4-nitro-3-(2-propyl)-styryl]}-3,3'-di-methoxybiphenyl (BNSMB) structures as visible light-cleavable linkers for oligonucleotide conjugation. In addition to the commercial ultraviolet (UV) photocleavable (PC) linker, the BNSMB linker was further applied as a building component to construct photoregulated DNA devices as duplex structures, which are functionalized with fluorophores and quenchers. Selective cleavage of PC and BNSMB is achieved in response to ultraviolet (UV) and visible light irradiations as two inputs, respectively.

Childhood immunization and age-appropriate vaccinations in Indonesia.

Background: Childhood immunization is a cost-effective way to protect individuals against communicable diseases. However, although there is a large literature on childhood immunization in Indonesia, there is a paucity of research on the age-appropriateness on measles and DTwP-3 vaccination, and the inequities in immunization coverage across Indonesia.

Methods: In this paper, using seven waves of data from the nationally representative Indonesia Demographic and Health Surveys (DHS) covering the period 1991- 2017, we empirically analyse the socio-economic and demographic factors influencing the uptake of four routine vaccines (BCG, Polio-3, DTwP-3, and Measles).

Ramadan exposure and child nutrition.

In this study, we empirically analyse whether exposure to the Ramadan fasting period is negatively associated with child nutrition. The data for the analyses come from a retrospective assessment of 759,799 children from 103 Demographic and Health Surveys (DHS) across 56 countries during 2003-2020. Considering the month-long Ramadan exposure as a natural experiment, we implement an framework, comparing stunting and underweight among children aged 0-5 years who were exposed to Ramadan fasting at any time with those who were not exposed.

Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities.

The genome-editing Cas9 protein uses multiple amino-acid residues to bind the target DNA. Considering only the residues in proximity to the target DNA as potential sites to optimise Cas9's activity, the number of combinatorial variants to screen through is too massive for a wet-lab experiment. Here we generate and cross-validate ten in silico and experimental datasets of multi-domain combinatorial mutagenesis libraries for Cas9 engineering, and demonstrate that a machine learning-coupled engineering approach reduces the experimental screening burden by as high as 95% while enriching top-performing variants by ∼7.

Nucleic Acids and Their Analogues for Biomedical Applications.

Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells.

High-fidelity KKH variant of Staphylococcus aureus Cas9 nucleases with improved base mismatch discrimination.

The Cas9 nuclease from Staphylococcus aureus (SaCas9) holds great potential for use in gene therapy, and variants with increased fidelity have been engineered. However, we find that existing variants have not reached the greatest accuracy to discriminate base mismatches and exhibited much reduced activity when their mutations were grafted onto the KKH mutant of SaCas9 for editing an expanded set of DNA targets. We performed structure-guided combinatorial mutagenesis to re-engineer KKH-SaCas9 with enhanced accuracy.

Facilitating Machine Learning-Guided Protein Engineering with Smart Library Design and Massively Parallel Assays.

Protein design plays an important role in recent medical advances from antibody therapy to vaccine design. Typically, exhaustive mutational screens or directed evolution experiments are used for the identification of the best design or for improvements to the wild-type variant. Even with a high-throughput screening on pooled libraries and Next-Generation Sequencing to boost the scale of read-outs, surveying all the variants with combinatorial mutations for their empirical fitness scores is still of magnitudes beyond the capacity of existing experimental settings.

A Combinatorial CRISPR-Cas9 Screen Identifies Ifenprodil as an Adjunct to Sorafenib for Liver Cancer Treatment.

Systematic testing of existing drugs and their combinations is an attractive strategy to exploit approved drugs for repurposing and identifying the best actionable treatment options. To expedite the search among many possible drug combinations, we designed a combinatorial CRISPR-Cas9 screen to inhibit druggable targets. Coblockade of the N-methyl-d-aspartate receptor (NMDAR) with targets of first-line kinase inhibitors reduced hepatocellular carcinoma (HCC) cell growth.

Publisher Correction: Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9.

The combined effect of multiple mutations on protein function is hard to predict; thus, the ability to functionally assess a vast number of protein sequence variants would be practically useful for protein engineering. Here we present a high-throughput platform that enables scalable assembly and parallel characterization of barcoded protein variants with combinatorial modifications. We demonstrate this platform, which we name CombiSEAL, by systematically characterizing a library of 948 combination mutants of the widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease to optimize its genome-editing activity in human cells.

Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing.

Background: Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown.

Long-Term Prognostic Implications of Cerebral Microbleeds in Chinese Patients With Ischemic Stroke.

Background: This study was performed to determine the clinical correlates and long-term prognostic implications of microbleed burden and location in Chinese patients with ischemic stroke.

Methods And Results: We recruited 1003 predominantly Chinese patients with ischemic stroke who received magnetic resonance imaging at the University of Hong Kong. We determined the clinical correlates of microbleeds and the long-term risks (3126 patient-years of follow-up) of recurrent ischemic stroke and intracerebral hemorrhage (ICH) by microbleed burden (0 versus 1, 2-4, and ≥5) and location, adjusting for age, sex, and vascular risk factors and stratified by antithrombotic use.

From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants.

Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds.

Neuroprotective effect of honokiol and magnolol, compounds from Magnolia officinalis, on beta-amyloid-induced toxicity in PC12 cells.

Amyloid β peptide (Aβ) induced toxicity is a well-established pathway of neuronal cell death which might play a role in Alzheimer's disease. In this regard, the toxic effect of Aβ on a cultured Aβ-sensitive neuronal cell line was used as a primary screening tool for potential anti-Alzheimer's therapeutic agents. The effects of nine pure compounds (vitamin E, α-asarone, salidroside, baicolin, magnolol, gastrodin, bilobalide, honokiol and β-asarone) from selected Chinese herbs on neuronal cell death induced by Aβ in NGF-differentiated PC12 cells were examined.