Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition.

CRISPR-associated transposons (CASTs) are natural RNA-directed transposition systems. We demonstrate that transposon protein TniQ plays a central role in promoting R-loop formation by RNA-guided DNA-targeting modules. TniQ residues, proximal to CRISPR RNA (crRNA), are required for recognizing different crRNA categories, revealing an unappreciated role of TniQ to direct transposition into different classes of crRNA targets. To investigate adaptations allowing CAST elements to utilize attachment sites inaccessible to CRISPR-Cas surveillance complexes, we compared and contrasted PAM sequence requirements in both I-F3b CAST and I-F1 CRISPR-Cas systems. We identify specific amino acids that enable a wider range of PAM sequences to be accommodated in I-F3b CAST elements compared with I-F1 CRISPR-Cas, enabling CAST elements to access attachment sites as sequences drift and evade host surveillance. Together, this evidence points to the central role of TniQ in facilitating the acquisition of CRISPR effector complexes for RNA-guided DNA transposition.

Structures of the holo CRISPR RNA-guided transposon integration complex.

CRISPR-associated transposons (CAST) are programmable mobile genetic elements that insert large DNA cargos using an RNA-guided mechanism1-3. CAST elements contain multiple conserved proteins: a CRISPR effector (Cas12k or Cascade), a AAA+ regulator (TnsC), a transposase (TnsA-TnsB) and a target-site-associated factor (TniQ). These components are thought to cooperatively integrate DNA via formation of a multisubunit transposition integration complex (transpososome). Here we reconstituted the approximately 1 MDa type V-K CAST transpososome from Scytonema hofmannii (ShCAST) and determined its structure using single-particle cryo-electon microscopy. The architecture of this transpososome reveals modular association between the components. Cas12k forms a complex with ribosomal subunit S15 and TniQ, stabilizing formation of a full R-loop. TnsC has dedicated interaction interfaces with TniQ and TnsB. Of note, we observe TnsC-TnsB interactions at the C-terminal face of TnsC, which contribute to the stimulation of ATPase activity. Although the TnsC oligomeric assembly deviates slightly from the helical configuration found in isolation, the TnsC-bound target DNA conformation differs markedly in the transpososome. As a consequence, TnsC makes new protein-DNA interactions throughout the transpososome that are important for transposition activity. Finally, we identify two distinct transpososome populations that differ in their DNA contacts near TniQ. This suggests that associations with the CRISPR effector can be flexible. This ShCAST transpososome structure enhances our understanding of CAST transposition systems and suggests ways to improve CAST transposition for precision genome-editing applications.

eIF2α controls memory consolidation via excitatory and somatostatin neurons.

An important tenet of learning and memory is the notion of a molecular switch that promotes the formation of long-term memory1-4. The regulation of proteostasis is a critical and rate-limiting step in the consolidation of new memories5-10. One of the most effective and prevalent ways to enhance memory is by regulating the synthesis of proteins controlled by the translation initiation factor eIF211. Phosphorylation of the α-subunit of eIF2 (p-eIF2α), the central component of the integrated stress response (ISR), impairs long-term memory formation in rodents and birds11-13. By contrast, inhibiting the ISR by mutating the eIF2α phosphorylation site, genetically11 and pharmacologically inhibiting the ISR kinases14-17, or mimicking reduced p-eIF2α with the ISR inhibitor ISRIB11, enhances long-term memory in health and disease18. Here we used molecular genetics to dissect the neuronal circuits by which the ISR gates cognitive processing. We found that learning reduces eIF2α phosphorylation in hippocampal excitatory neurons and a subset of hippocampal inhibitory neurons (those that express somatostatin, but not parvalbumin). Moreover, ablation of p-eIF2α in either excitatory or somatostatin-expressing (but not parvalbumin-expressing) inhibitory neurons increased general mRNA translation, bolstered synaptic plasticity and enhanced long-term memory. Thus, eIF2α-dependent mRNA translation controls memory consolidation via autonomous mechanisms in excitatory and somatostatin-expressing inhibitory neurons.

Absorption Correction for 3D Elemental Distributions of Dental Composite Materials Using Laboratory Confocal Micro-X-ray Fluorescence Spectroscopy.

Confocal micro-X-ray fluorescence (micro-XRF) spectroscopy facilitates three-dimensional (3D) elemental imaging of heterogeneous samples in the micrometer range. Laboratory setups using X-ray tube excitation render the method accessible for diverse research fields but interpretation of results and quantification remain challenging. The attenuation of X-rays in composites depends on the photon energy as well as on the composition and density of the material. For confocal micro-XRF, attenuation severely impacts elemental distribution information, as the signal from deeper layers is distorted by superficial layers. Absorption correction and quantification of fluorescence measurements in heterogeneous composite samples have so far not been reported. Here, an absorption correction approach for confocal micro-XRF combining density information from microcomputed tomography (micro-CT) data with laboratory X-ray absorption spectroscopy (XAS) and synchrotron transmission measurements is presented. The energy dependency of the probing volume is considered during the correction. The methodology is demonstrated on a model composite sample consisting of a bovine tooth with a clinically used restoration material.

"Dissolve-on-Demand" 3D Printed Materials: Polymerizable Eutectics for Generating High Modulus, Thermoresponsive and Photoswitchable Eutectogels.

Solvent-free photopolymerization of vinyl monomers to produce high modulus materials with applications in 3D printing and photoswitchable materials is demonstrated. Polymerizable eutectic (PE) mixtures are prepared by simply heating and stirring various molar ratios of N-isopropylacrylamide (NIPAM), acrylamide (AAm) and 2-hydroxyethyl methacrylate (HEMA). The structural and thermal properties of the resulting mixtures are evaluated by 1D and 2D NMR spectroscopy as well as differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). UV photocuring kinetics of the PE mixtures is evaluated via in situ photo-DSC and photorheology measurements. The PE mixtures cure rapidly and display storage moduli that are orders of magnitude greater than equivalent copolymers cured in an aqueous medium. The versatility of these PE systems is demonstrated through the addition of a photoswitchable spiropyran acrylate monomer, as well as applying the PE formulation as a stereolithography (SLA)-based 3D printing resin. Due to the hydrogen-bonding network in PE systems, 3D printing of the eutectic resin is possible in the absence of crosslinkers. The addition of a RAFT agent to reduce average polymer chain length enables 3D printing of materials which retain their shape and can be dissolved on demand in appropriate solvents.

Marine fish parasites in the Cat Ba Archipelago, Vietnam: the results of 2010-2023 field surveys.

Between 2010 and 2023, a longitudinal study was undertaken to uncover the diversity of the parasite fauna of marine fishes in the Cat Ba Archipelago, a world biosphere reserve, in Vietnam. A total of 1,042 specimens representing 80 different fish species were collected and examined. Of these, 68 fish species, represented by 994 specimens (95.39%), were infected with parasites. A total of 162 parasitic species were discovered, including 54 trematodes, 37 monogeneans, 27 crustaceans, 15 myxozoans, 10 acanthocephalans, 10 nematodes, 7 cestodes, and 2 hirudineans. Over the course of the survey, twenty new species were described, including 7 acanthocephalans and 13 trematodes. Additionally, twenty species were recorded for the first time from the Cat Ba Archipelago and twenty-two species had new host records reported. The prevalence and mean intensity of parasite infection were found to be unaffected by season. These data on the parasitic fauna of Cat Ba Archipelago not only expand our knowledge of the diversity of Vietnam, but also provide strong baseline data for measuring future change resulting from environmental perturbations.

Linkage-specific ubiquitin chain formation depends on a lysine hydrocarbon ruler.

Virtually all aspects of cell biology are regulated by a ubiquitin code where distinct ubiquitin chain architectures guide the binding events and itineraries of modified substrates. Various combinations of E2 and E3 enzymes accomplish chain formation by forging isopeptide bonds between the C terminus of their transiently linked donor ubiquitin and a specific nucleophilic amino acid on the acceptor ubiquitin, yet it is unknown whether the fundamental feature of most acceptors-the lysine side chain-affects catalysis. Here, use of synthetic ubiquitins with non-natural acceptor site replacements reveals that the aliphatic side chain specifying reactive amine geometry is a determinant of the ubiquitin code, through unanticipated and complex reliance of many distinct ubiquitin-carrying enzymes on a canonical acceptor lysine.

Economic evaluation of a community health worker model for tuberculosis care in Ho Chi Minh City, Viet Nam: a mixed-methods Social Return on Investment Analysis.

BACKGROUND: There is extensive evidence for the cost-effectiveness of programmatic and additional tuberculosis (TB) interventions, but no studies have employed the social return on investment (SROI) methodology. We conducted a SROI analysis to measure the benefits of a community health worker (CHW) model for active TB case finding and patient-centered care. METHODS: This mixed-method study took place alongside a TB intervention implemented in Ho Chi Minh City, Viet Nam, between October-2017 - September-2019. The valuation encompassed beneficiary, health system and societal perspectives over a 5-year time-horizon. We conducted a rapid literature review, two focus group discussions and 14 in-depth interviews to identify and validate pertinent stakeholders and material value drivers. We compiled quantitative data from the TB program's and the intervention's surveillance systems, ecological databases, scientific publications, project accounts and 11 beneficiary surveys. We mapped, quantified and monetized value drivers to derive a crude financial benefit, which was adjusted for four counterfactuals. We calculated a SROI based on the net present value (NPV) of benefits and investments using a discounted cash flow model with a discount rate of 3.5%. A scenario analysis assessed SROI at varying discount rates of 0-10%. RESULTS: The mathematical model yielded NPVs of US$235,511 in investments and US$8,497,183 in benefits. This suggested a return of US$36.08 for each dollar invested, ranging from US$31.66-US39.00 for varying discount rate scenarios. CONCLUSIONS: The evaluated CHW-based TB intervention generated substantial individual and societal benefits. The SROI methodology may be an alternative for the economic evaluation of healthcare interventions.

Visible-Light-Induced Control over Reversible Single-Chain Nanoparticle Folding.

We introduce a class of single-chain nanoparticles (SCNPs) that respond to visible light (λmax =415 nm) with complete unfolding from their compact structure into linear chain analogues. The initial folding is achieved by a simple esterification reaction of the polymer backbone constituted of acrylic acid and polyethylene glycol carrying monomer units, introducing bimane moieties, which allow for the photochemical unfolding, reversing the ester-bond formation. The compaction and the light driven unfolding proceed cleanly and are readily followed by size exclusion chromatography (SEC) and diffusion ordered NMR spectroscopy (DOSY), monitoring the change in the hydrodynamic radius (RH ). Importantly, the folding reaction and the light-induced unfolding are reversible, supported by the high conversion of the photo cleavage. As the unfolding reaction occurs in aqueous systems, the system holds promise for controlling the unfolding of SCNPs in biological environments.

Ultra-Deep Sequencing of Plasma-Circulating DNA for the Detection of Tumor- Derived Mutations in Patients with Nonmetastatic Colorectal Cancer.

Identification of tumor-derived mutation (TDM) in liquid biopsies (LB), especially in early-stage patients, faces several challenges, including low variant-allele frequencies, interference by white blood cell (WBC)-derived mutations (WDM), benign somatic mutations and tumor heterogeneity. Here, we addressed the above-mentioned challenges in a cohort of 50 nonmetastatic colorectal cancer patients, via a workflow involving parallel sequencing of paired WBC- and tumor-gDNA. After excluding potential false positive mutations, we detected at least one TDM in LB of 56% (28/50) of patients, with the majority showing low-patient coverage, except for one TDM mapped to KMT2D that recurred in 30% (15/30) of patients.

Wavelength Orthogonal Photodynamic Networks.

The ability of light to remotely control the properties of soft matter materials in a dynamic fashion has fascinated material scientists and photochemists for decades. However, only recently has our ability to map photochemical reactivity in a finely wavelength resolved fashion allowed for different colors of light to independently control the material properties of polymer networks with high precision, driven by monochromatic irradiation enabling orthogonal reaction control. The current concept article highlights the progress in visible light-induced photochemistry and explores how it has enabled the design of polymer networks with dynamically adjustable properties. We will explore current applications ranging from dynamic hydrogel design to the light-driven adaptation of 3D printed structures on the macro- and micro-scale. While the alternation of mechanical properties via remote control is largely reality for soft matter materials, we herein propose the next frontiers for adaptive properties, including remote switching between conductive and non-conductive properties, hydrophobic and hydrophilic surfaces, fluorescent or non-fluorescent, and cell adhesive vs. cell repellent properties.

Multimodal analysis of ctDNA methylation and fragmentomic profiles enhances detection of nonmetastatic colorectal cancer.

Aims: Early detection of colorectal cancer (CRC) provides substantially better survival rates. This study aimed to develop a blood-based screening assay named SPOT-MAS ('screen for the presence of tumor by DNA methylation and size') for early CRC detection with high accuracy. Methods: Plasma cell-free DNA samples from 159 patients with nonmetastatic CRC and 158 healthy controls were simultaneously analyzed for fragment length and methylation profiles. We then employed a deep neural network with fragment length and methylation signatures to build a classification model. Results: The model achieved an area under the curve of 0.989 and a sensitivity of 96.8% at 97% specificity in detecting CRC. External validation of our model showed comparable performance, with an area under the curve of 0.96. Conclusion: SPOT-MAS based on integration of cancer-specific methylation and fragmentomic signatures could provide high accuracy for early-stage CRC detection.

A novel blood test for early detection of colorectal cancer. Colorectal cancer is a cancer of the colon or rectum, located at the lower end of the digestive tract. The early detection of colorectal cancer can help people with the disease have a higher chance of survival and a better quality of life. Current screening methods can be invasive, cause discomfort or have low accuracy; therefore newer screening methods are needed. In this study we developed a new screening method, called SPOT-MAS, which works by measuring the signals of cancer DNA in the blood. By combining different characteristics of cancer DNA, SPOT-MAS could distinguish blood samples of people with colorectal cancer from those of healthy individuals with high accuracy.

Inhibitory interneurons mediate autism-associated behaviors via 4E-BP2.

Translational control plays a key role in regulation of neuronal activity and behavior. Deletion of the translational repressor 4E-BP2 in mice alters excitatory and inhibitory synaptic functions, engendering autistic-like behaviors. The contribution of 4E-BP2-dependent translational control in excitatory and inhibitory neurons and astrocytic cells to these behaviors remains unknown. To investigate this, we generated cell-type-specific conditional 4E-BP2 knockout mice and tested them for the salient features of autism, including repetitive stereotyped behaviors (self-grooming and marble burying), sociability (3-chamber social and direct social interaction tests), and communication (ultrasonic vocalizations in pups). We found that deletion of 4E-BP2 in GABAergic inhibitory neurons, defined by Gad2, resulted in impairments in social interaction and vocal communication. In contrast, deletion of 4E-BP2 in forebrain glutamatergic excitatory neurons, defined by Camk2a, or in astrocytes, defined by Gfap, failed to cause autistic-like behavioral abnormalities. Taken together, we provide evidence for an inhibitory-cell-specific role of 4E-BP2 in engendering autism-related behaviors.

Real-Time Intraoperative Surface-Enhanced Raman Spectroscopy-Guided Thermosurgical Eradication of Residual Microtumors in Orthotopic Breast Cancer.

Residual microtumors following surgical resection are the major cause for lethal cancer recurrence. However, it remains challenging to completely eliminate these residual microtumors. Here, we report an integrated strategy for image-guided surgical resection of tumors and intraoperative surface-enhanced Raman spectroscopy (SERS) guided thermosurgical elimination of residual microtumors using a "three-in-one" theranostic nanoprobe, termed the Au nanostar-based photoacoustic (PA), SERS, and thermosurgical (starPART) probe. This starPART probe, comprising an Au nanostar core, a Raman molecule layer, and a silica outer layer, draws upon the significant advantages of PA imaging, SERS detection, and photothermal tumor ablation. These prominent features enable preoperative PA imaging for surgical resection of tumors and intraoperative SERS-guided thermosurgery for complete elimination of residual microtumors. In vivo experiments confirm complete eradication of microtumors without local recurrence and with a 100% tumor-free survivability. This work therefore offers a robust platform for real-time intraoperative eradication of residual microtumors with significant improvement of surgical outcomes.

Wavelength-Orthogonal Stiffening of Hydrogel Networks with Visible Light.

Herein, we introduce the wavelength-orthogonal crosslinking of hydrogel networks using two red-shifted chromophores, i.e. acrylpyerene (AP, λactivation =410-490 nm) and styrylpyrido[2,3-b]pyrazine (SPP, λactivation =400-550 nm), able to undergo [2+2] photocycloaddition in the visible-light regime. The photoreactivity of the SPP moiety is pH-dependent, whereby an acidic environment inhibits the cycloaddition. By employing a spiropyran-based photoacid generator with suitable absorption wavelength, we are able to restrict the activation wavelength of the SPP moiety to the green light region (λactivation =520-550 nm), enabling wavelength-orthogonal activation of the AP group. Our wavelength-orthogonal photochemical system was successfully applied in the design of hydrogels whose stiffness can be tuned independently by either green or blue light.

Action Plots in Action: In-Depth Insights into Photochemical Reactivity.

Predicting wavelength-dependent photochemical reactivity is challenging. Herein, we revive the well-established tool of measuring action spectra and adapt the technique to map wavelength-resolved covalent bond formation and cleavage in what we term "photochemical action plots". Underpinned by tunable lasers, which allow excitation of molecules with near-perfect wavelength precision, the photoinduced reactivity of several reaction classes have been mapped in detail. These include photoinduced cycloadditions and bond formation based on photochemically generated o-quinodimethanes and 1,3-dipoles such as nitrile imines as well as radical photoinitiator cleavage. Organized by reaction class, these data demonstrate that UV/vis spectra fail to act as a predictor for photochemical reactivity at a given wavelength in most of the examined reactions, with the photochemical reactivity being strongly red shifted in comparison to the absorption spectrum. We provide an encompassing perspective of the power of photochemical action plots for bond-forming reactions and their emerging applications in the design of wavelength-selective photoresists and photoresponsive soft-matter materials.

A Self-Catalyzed Visible Light Driven Thiol Ligation.

We introduce a highly efficient ligation system based on a visible light-induced rearrangement affording a thiophenol which rapidly undergoes thiol-Michael additions. Unlike conventional light-triggered thiol-ene/yne systems, which rely on the use of photocaged bases/nucleophiles, (organo)-photo catalysts, or radical photoinitiators, our system provides a light-induced reaction in the absence of any additives. The ligation is self-catalyzed via the pyridine mediated deprotonation of the photochemically generated thiophenol. Subsequently, the thiol-Michael reaction between the thiophenol anion and electron deficient alkynes/alkenes proceeds additive-free. Hereby, the underlying photoinduced rearrangement of o-thiopyrinidylbenzaldehyde (oTPyB) generating the free thiol is described for the first time. We studied the influence of various reactions conditions as well as solvents and substrates. We exemplify our findings in a polymer end group modification and obtained macromolecules with excellent end group fidelity.

Socio-protective effects of active case finding on catastrophic costs from tuberculosis in Ho Chi Minh City, Viet Nam: a longitudinal patient cost survey.

BACKGROUND: Many tuberculosis (TB) patients incur catastrophic costs. Active case finding (ACF) may have socio-protective properties that could contribute to the WHO End TB Strategy target of zero TB-affected families suffering catastrophic costs, but available evidence remains limited. This study measured catastrophic cost incurrence and socioeconomic impact of an episode of TB and compared those socioeconomic burdens in patients detected by ACF versus passive case finding (PCF). METHODS: This cross-sectional study fielded a longitudinal adaptation of the WHO TB patient cost survey alongside an ACF intervention from March 2018 to March 2019. The study was conducted in six intervention (ACF) districts and six comparison (PCF) districts of Ho Chi Minh City, Viet Nam. Fifty-two TB patients detected through ACF and 46 TB patients in the PCF cohort were surveyed within two weeks of treatment initiation, at the end of the intensive phase of treatment, and after treatment concluded. The survey measured income, direct and indirect costs, and socioeconomic impact based on which we calculated catastrophic cost as the primary outcome. Local currency was converted into US$ using the average exchange rates reported by OANDA for the study period (VND1 = US$0.0000436, 2018-2019). We fitted logistic regressions for comparisons between the ACF and PCF cohorts as the primary exposures and used generalized estimating equations to adjust for autocorrelation. RESULTS: ACF patients were poorer than PCF patients (multidimensional poverty ratio: 16 % vs. 7 %; p = 0.033), but incurred lower median pre-treatment costs (US$18 vs. US$80; p < 0.001) and lower median total costs (US$279 vs. US$894; p < 0.001). Fewer ACF patients incurred catastrophic costs (15 % vs. 30 %) and had lower odds of catastrophic cost (aOR = 0.17; 95 % CI: [0.05, 0.67]; p = 0.011), especially during the intensive phase (OR = 0.32; 95 % CI: [0.12, 0.90]; p = 0.030). ACF patient experienced less social exclusion (OR = 0.41; 95 % CI: [0.18, 0.91]; p = 0.030), but more often resorted to financial coping mechanisms (OR = 5.12; 95 % CI: [1.73, 15.14]; p = 0.003). CONCLUSIONS: ACF can be effective in reaching vulnerable populations and mitigating the socioeconomic burden of TB, and can contribute to achieving the WHO End TB Strategy goals. Nevertheless, as TB remains a catastrophic life event, social protection efforts must extend beyond ACF.

Active-site mTOR inhibitors augment HSV1-dICP0 infection in cancer cells via dysregulated eIF4E/4E-BP axis.

Herpes Simplex Virus 1 (HSV1) is amongst the most clinically advanced oncolytic virus platforms. However, efficient and sustained viral replication within tumours is limiting. Rapamycin can stimulate HSV1 replication in cancer cells, but active-site dual mTORC1 and mTORC2 (mammalian target of rapamycin complex 1 and 2) inhibitors (asTORi) were shown to suppress the virus in normal cells. Surprisingly, using the infected cell protein 0 (ICP0)-deleted HSV1 (HSV1-dICP0), we found that asTORi markedly augment infection in cancer cells and a mouse mammary cancer xenograft. Mechanistically, asTORi repressed mRNA translation in normal cells, resulting in defective antiviral response but also inhibition of HSV1-dICP0 replication. asTORi also reduced antiviral response in cancer cells, however in contrast to normal cells, transformed cells and cells transduced to elevate the expression of eukaryotic initiation factor 4E (eIF4E) or to silence the repressors eIF4E binding proteins (4E-BPs), selectively maintained HSV1-dICP0 protein synthesis during asTORi treatment, ultimately supporting increased viral replication. Our data show that altered eIF4E/4E-BPs expression can act to promote HSV1-dICP0 infection under prolonged mTOR inhibition. Thus, pharmacoviral combination of asTORi and HSV1 can target cancer cells displaying dysregulated eIF4E/4E-BPs axis.

DNA methylation age is associated with an altered hemostatic profile in a multiethnic meta-analysis.

Many hemostatic factors are associated with age and age-related diseases; however, much remains unknown about the biological mechanisms linking aging and hemostatic factors. DNA methylation is a novel means by which to assess epigenetic aging, which is a measure of age and the aging processes as determined by altered epigenetic states. We used a meta-analysis approach to examine the association between measures of epigenetic aging and hemostatic factors, as well as a clotting time measure. For fibrinogen, we performed European and African ancestry-specific meta-analyses which were then combined via a random effects meta-analysis. For all other measures we could not estimate ancestry-specific effects and used a single fixed effects meta-analysis. We found that 1-year higher extrinsic epigenetic age as compared with chronological age was associated with higher fibrinogen (0.004 g/L/y; 95% confidence interval, 0.001-0.007; P = .01) and plasminogen activator inhibitor 1 (PAI-1; 0.13 U/mL/y; 95% confidence interval, 0.07-0.20; P = 6.6 × 10-5) concentrations, as well as lower activated partial thromboplastin time, a measure of clotting time. We replicated PAI-1 associations using an independent cohort. To further elucidate potential functional mechanisms, we associated epigenetic aging with expression levels of the PAI-1 protein encoding gene (SERPINE1) and the 3 fibrinogen subunit-encoding genes (FGA, FGG, and FGB) in both peripheral blood and aorta intima-media samples. We observed associations between accelerated epigenetic aging and transcription of FGG in both tissues. Collectively, our results indicate that accelerated epigenetic aging is associated with a procoagulation hemostatic profile, and that epigenetic aging may regulate hemostasis in part via gene transcription.