Evolution of Alternative Adaptive Immune Systems in Vertebrates.

Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucine-rich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases. B-like cells develop in the hematopoietic typhlosole and kidneys, whereas T-like cells develop in the thymoid, a thymus-equivalent region at the gill fold tips. Thus, the dichotomy between T-like and B-like cells and the presence of dedicated lymphopoietic tissues emerge as ancestral vertebrate features, whereas the somatic diversification of structurally distinct antigen receptor genes evolved independently in jawless and jawed vertebrates.

Efficient embryonic homozygous gene conversion via RAD51-enhanced interhomolog repair.

Searching for factors to improve knockin efficiency for therapeutic applications, biotechnology, and generation of non-human primate models of disease, we found that the strand exchange protein RAD51 can significantly increase Cas9-mediated homozygous knockin in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is a hallmark of meiosis but only occurs at low frequencies in somatic cells, and its occurrence in zygotes is controversial. Using multiple approaches, we provide evidence for an endogenous IHR mechanism in the early embryo that can be enhanced by RAD51. This process can be harnessed to generate homozygotes from wild-type zygotes using exogenous donors and to convert heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we identify additional IHR-promoting factors and describe features of IHR events. Together, our findings show conclusive evidence for IHR in mouse embryos and describe an efficient method for enhanced gene conversion.

Revisiting astrocyte to neuron conversion with lineage tracing in vivo.

In vivo cell fate conversions have emerged as potential regeneration-based therapeutics for injury and disease. Recent studies reported that ectopic expression or knockdown of certain factors can convert resident astrocytes into functional neurons with high efficiency, region specificity, and precise connectivity. However, using stringent lineage tracing in the mouse brain, we show that the presumed astrocyte-converted neurons are actually endogenous neurons. AAV-mediated co-expression of NEUROD1 and a reporter specifically and efficiently induces reporter-labeled neurons. However, these neurons cannot be traced retrospectively to quiescent or reactive astrocytes using lineage-mapping strategies. Instead, through a retrograde labeling approach, our results reveal that endogenous neurons are the source for these viral-reporter-labeled neurons. Similarly, despite efficient knockdown of PTBP1 in vivo, genetically traced resident astrocytes were not converted into neurons. Together, our results highlight the requirement of lineage-tracing strategies, which should be broadly applied to studies of cell fate conversions in vivo.

Age-Dependent Alterations in Meiotic Recombination Cause Chromosome Segregation Errors in Spermatocytes.

Faithful chromosome segregation in meiosis requires crossover (CO) recombination, which is regulated to ensure at least one CO per homolog pair. We investigate the failure to ensure COs in juvenile male mice. By monitoring recombination genome-wide using cytological assays and at hotspots using molecular assays, we show that juvenile mouse spermatocytes have fewer COs relative to adults. Analysis of recombination in the absence of MLH3 provides evidence for greater utilization in juveniles of pathways involving structure-selective nucleases and alternative complexes, which can act upon precursors to generate noncrossovers (NCOs) at the expense of COs. We propose that some designated CO sites fail to mature efficiently in juveniles owing to inappropriate activity of these alternative repair pathways, leading to chromosome mis-segregation. We also find lower MutLγ focus density in juvenile human spermatocytes, suggesting that weaker CO maturation efficiency may explain why younger men have a higher risk of fathering children with Down syndrome.

Therapeutic Potential of PTBP1 Inhibition, If Any, Is Not Attributed to Glia-to-Neuron Conversion.

A holy grail of regenerative medicine is to replenish the cells that are lost due to disease. The adult mammalian central nervous system (CNS) has, however, largely lost such a regenerative ability. An emerging strategy for the generation of new neurons is through glia-to-neuron (GtN) conversion in vivo, mainly accomplished by the regulation of fate-determining factors. When inhibited, PTBP1, a factor involved in RNA biology, was reported to induce rapid and efficient GtN conversion in multiple regions of the adult CNS. Remarkably, PTBP1 inhibition was also claimed to greatly improve behaviors of mice with neurological diseases or aging. These phenomenal claims, if confirmed, would constitute a significant advancement in regenerative medicine. Unfortunately, neither GtN conversion nor therapeutic potential via PTBP1 inhibition was validated by the results of multiple subsequent replication studies with stringent methods. Here we review these controversial studies and conclude with recommendations for examining GtN conversion in vivo and future investigations of PTBP1.

Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination.

Currently favored models for meiotic recombination posit that both noncrossover and crossover recombination are initiated by DNA double-strand breaks but form by different mechanisms: noncrossovers by synthesis-dependent strand annealing and crossovers by formation and resolution of double Holliday junctions centered around the break. This dual mechanism hypothesis predicts different hybrid DNA patterns in noncrossover and crossover recombinants. We show that these predictions are not upheld, by mapping with unprecedented resolution parental strand contributions to recombinants at a model locus. Instead, break repair in both noncrossovers and crossovers involves synthesis-dependent strand annealing, often with multiple rounds of strand invasion. Crossover-specific double Holliday junction formation occurs via processes involving branch migration as an integral feature, one that can be separated from repair of the break itself. These findings reveal meiotic recombination to be a highly dynamic process and prompt a new view of the relationship between crossover and noncrossover recombination.

Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells.

How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4+CD8+ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment. The transcription factor BCL11B, a critical regulator of T cell commitment, is associated with increased chromatin interaction, and Bcl11b deletion compromised chromatin interaction at its target genes. We propose that these large-scale and concerted changes in chromatin organization present an energy barrier to prevent the cell from reversing its fate to earlier stages or redirecting to alternatives and thus lock the cell fate into the T lineages.

Second Messenger cA4 Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.

Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cAn) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit. The generated cAn second messenger in turn targets the CARF domain of trans-acting RNase Csm6, triggering its HEPN domain-based RNase activity. We have undertaken cryo-EM studies on multi-subunit Thermococcus onnurineus Csm effector ternary complexes, as well as X-ray studies on Csm1-Csm4 cassette, both bound to substrate (AMPPNP), intermediates (pppAn), and products (cAn), to decipher mechanistic aspects of cAn formation and release. A network of intermolecular hydrogen bond alignments accounts for the observed adenosine specificity, with ligand positioning dictating formation of linear pppAn intermediates and subsequent cAn formation by cyclization. We combine our structural results with published functional studies to highlight mechanistic insights into the role of the Csm effector complex in mediating the cAn signaling pathway.

A hybrid photocatalytic system enables direct glucose utilization for methanogenesis.

Integration of methanogenic archaea with photocatalysts presents a sustainable solution for solar-driven methanogenesis. However, maximizing CH4 conversion efficiency remains challenging due to the intrinsic energy conservation and strictly restricted substrates of methanogenic archaea. Here, we report a solar-driven biotic-abiotic hybrid (biohybrid) system by incorporating cadmium sulfide (CdS) nanoparticles with a rationally designed methanogenic archaeon Methanosarcina acetivorans C2A, in which the glucose synergist protein and glucose kinase, an energy-efficient route for glucose transport and phosphorylation from Zymomonas mobilis, were implemented to facilitate nonnative substrate glucose for methanogenesis. We demonstrate that the photo-excited electrons facilitate membrane-bound electron transport chain, thereby augmenting the Na+ and H+ ion gradients across membrane to enhance adenosine triphosphate (ATP) synthesis. Additionally, this biohybrid system promotes the metabolism of pyruvate to acetyl coenzyme A (AcCoA) and inhibits the flow of AcCoA to the tricarboxylic acid (TCA) cycle, resulting in a 1.26-fold augmentation in CH4 production from glucose-derived carbon. Our results provide a unique strategy for enhancing methanogenesis through rational biohybrid design and reprogramming, which gives a promising avenue for sustainably manufacturing value-added chemicals.

Adaptive cooling strategy via human hair: High optothermal conversion efficiency of solar radiation into thermal dissipation.

Natural species have developed complex nanostructures in a hierarchical pattern to control the absorption, reflection, or transmission of desired solar and infrared wavelengths. This bio-inspired structure is a promising method to manipulating solar energy and thermal management. In particular, human hair is used in this article to highlight the optothermal properties of bio-inspired structures. This study investigated how melanin, an effective solar absorber, and the structural morphology of aligned domains of keratin polymer chains, leading to a significant increase in solar path length, which effectively scatter and absorb solar radiation across the hair structure, as well as enhance thermal ramifications from solar absorption by fitting its radiative wavelength to atmospheric transmittance for high-yield radiative cooling with realistic human body thermal emission.

Deforestation impacts soil biodiversity and ecosystem services worldwide.

Deforestation poses a global threat to biodiversity and its capacity to deliver ecosystem services. Yet, the impacts of deforestation on soil biodiversity and its associated ecosystem services remain virtually unknown. We generated a global dataset including 696 paired-site observations to investigate how native forest conversion to other land uses affects soil properties, biodiversity, and functions associated with the delivery of multiple ecosystem services. The conversion of native forests to plantations, grasslands, and croplands resulted in higher bacterial diversity and more homogeneous fungal communities dominated by pathogens and with a lower abundance of symbionts. Such conversions also resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Responses of the microbial community to deforestation, including bacterial and fungal diversity and fungal guilds, were predominantly regulated by changes in soil pH and total phosphorus. Moreover, we found that soil fungal diversity and functioning in warmer and wetter native forests is especially vulnerable to deforestation. Our work highlights that the loss of native forests to managed ecosystems poses a major global threat to the biodiversity and functioning of soils and their capacity to deliver ecosystem services.

Direct solar energy conversion on zinc-air battery.

A concept of solar energy convertible zinc-air battery (SZAB) is demonstrated through rational design of an electrode coupled with multifunction. The multifunctional electrode is fabricated using nitrogen-substituted graphdiyne (N-GDY) with large π-conjugated carbonous network, which can work as photoresponsive bifunctional electrocatalyst, enabling a sunlight-promoted process through efficient injection of photoelectrons into the conduction band of N-GDY. SZAB enables direct conversion and storage of solar energy during the charging process. Such a battery exhibits a lowered charge voltage under illumination, corresponding to a high energy efficiency of 90.4% and electric energy saving of 30.3%. The battery can display a power conversion efficiency as high as 1.02%. Density functional theory calculations reveal that the photopromoted oxygen evolution reaction kinetics originates from the transition from the alkyne bonds to double bonds caused by the transfer of excited electrons, which changes the position of highest occupied molecular orbital and lowest unoccupied molecular orbital, thus greatly promoting the formation of intermediates to the conversion process. Our findings provide conceptual and experimental confirmation that batteries are charged directly from solar energy without the external solar cells, providing a way to manufacture future energy devices.

Enriching surface-ordered defects on WO3 for photocatalytic CO2-to-CH4 conversion by water.

Defect engineering has been widely applied in semiconductors to improve photocatalytic properties by altering the surface structures. This study is about the transformation of inactive WO3 nanosheets to a highly effective CO2-to-CH4 conversion photocatalyst by introducing surface-ordered defects in abundance. The nonstoichiometric WO3-x samples were examined by using aberration-corrected electron microscopy. Results unveil abundant surface-ordered terminations derived from the periodic {013} stacking faults with a defect density of 20.2%. The {002} surface-ordered line defects are the active sites for fixation CO2, transforming the inactive WO3 nanosheets into a highly active catalyst (CH4: O2 = 8.2: 16.7 µmol h-1). We believe that the formation of the W-O-C-W-O species is a critical step in the catalytic pathways. This work provides an atomic-level comprehension of the structural defects of catalysts for activating small molecules.

Enhanced charge-carrier dynamics and efficient solar-to-urea conversion on Si-based photocathodes.

Photoelectrochemical (PEC) coupling of CO2 and nitrate can provide a useful and green source of urea, but the process is affected by the photocathodes with poor charge-carrier dynamics and low conversion efficiency. Here, a NiFe diatomic catalysts/TiO2 layer/nanostructured n+p-Si photocathode is rationally designed, achieving a good charge-separation efficiency of 78.8% and charge-injection efficiency of 56.9% in the process of PEC urea synthesis. Compared with the electrocatalytic urea synthesis by using the same catalysts, the Si-based photocathode shows a similar urea yield rate (81.1 mg·h-1·cm-2) with a higher faradic efficiency (24.2%, almost twice than the electrocatalysis) at a lower applied potential under 1 sun illumination, meaning that a lower energy-consumption method acquires more aimed productions. Integrating the PEC measurements and characterization results, the synergistic effect of hierarchical structure is the dominating factor for enhancing the charge-carrier separation, transfer, and injection by the matched band structure and favorable electron-migration channels. This work provides a direct and efficient route of solar-to-urea conversion.

Identification of a robust DNA methylation signature for Fanconi anemia.

Fanconi anemia (FA) is a clinically variable and genetically heterogeneous cancer-predisposing disorder representing the most common bone marrow failure syndrome. It is caused by inactivating predominantly biallelic mutations involving >20 genes encoding proteins with roles in the FA/BRCA DNA repair pathway. Molecular diagnosis of FA is challenging due to the wide spectrum of the contributing gene mutations and structural rearrangements. The assessment of chromosomal fragility after exposure to DNA cross-linking agents is generally required to definitively confirm diagnosis. We assessed peripheral blood genome-wide DNA methylation (DNAm) profiles in 25 subjects with molecularly confirmed clinical diagnosis of FA (FANCA complementation group) using Illumina's Infinium EPIC array. We identified 82 differentially methylated CpG sites that allow to distinguish subjects with FA from healthy individuals and subjects with other genetic disorders, defining an FA-specific DNAm signature. The episignature was validated using a second cohort of subjects with FA involving different complementation groups, documenting broader genetic sensitivity and demonstrating its specificity using the EpiSign Knowledge Database. The episignature properly classified DNA samples obtained from bone marrow aspirates, demonstrating robustness. Using the selected probes, we trained a machine-learning model able to classify EPIC DNAm profiles in molecularly unsolved cases. Finally, we show that the generated episignature includes CpG sites that do not undergo functional selective pressure, allowing diagnosis of FA in individuals with reverted phenotype due to gene conversion. These findings provide a tool to accelerate diagnostic testing in FA and broaden the clinical utility of DNAm profiling in the diagnostic setting.

Mechanistic View and Genetic Control of DNA Recombination during Meiosis.

Meiotic recombination is essential for fertility and allelic shuffling. Canonical recombination models fail to capture the observed complexity of meiotic recombinants. Here, by combining genome-wide meiotic heteroduplex DNA patterns with meiotic DNA double-strand break (DSB) sites, we show that part of this complexity results from frequent template switching during synthesis-dependent strand annealing that yields noncrossovers and from branch migration of double Holliday junction (dHJ)-containing intermediates that mainly yield crossovers. This complexity also results from asymmetric positioning of crossover intermediates relative to the initiating DSB and Msh2-independent conversions promoted by the suspected dHJ resolvase Mlh1-3 as well as Exo1 and Sgs1. Finally, we show that dHJ resolution is biased toward cleavage of the pair of strands containing newly synthesized DNA near the junctions and that this bias can be decoupled from the crossover-biased dHJ resolution. These properties are likely conserved in eukaryotes containing ZMM proteins, which includes mammals.

Deep reaction network exploration of glucose pyrolysis.

Resolving the reaction networks associated with biomass pyrolysis is central to understanding product selectivity and aiding catalyst design to produce more valuable products. However, even the pyrolysis network of relatively simple [Formula: see text]-D-glucose remains unresolved due to its significant complexity in terms of the depth of the network and the number of major products. Here, a transition-state-guided reaction exploration has been performed that provides complete pathways to most significant experimental pyrolysis products of [Formula: see text]-D-glucose. The resulting reaction network involves over 31,000 reactions and transition states computed at the semiempirical quantum chemistry level and approximately 7,000 kinetically relevant reactions and transition states characterized with density function theory, comprising the largest reaction network reported for biomass pyrolysis. The exploration was conducted using graph-based rules to explore the reactivities of intermediates and an adaption of the Dijkstra algorithm to identify kinetically relevant intermediates. This simple exploration policy surprisingly (re)identified pathways to most major experimental pyrolysis products, many intermediates proposed by previous computational studies, and also identified new low-barrier reaction mechanisms that resolve outstanding discrepancies between reaction pathways and yields in isotope labeling experiments. This network also provides explanatory pathways for the high yield of hydroxymethylfurfural and the reaction pathway that contributes most to the formation of hydroxyacetaldehyde during glucose pyrolysis. Due to the limited domain knowledge required to generate this network, this approach should also be transferable to other complex reaction network prediction problems in biomass pyrolysis.

On a class of bimodal oscillations powered by a steady, zero-frequency force-Implications to energy conversion and structural stability.

I propose that there exists in natural and artificial environments a class of resonant oscillations that can be excited directly by a steady, zero-frequency force such as that of wind, water, electric field. A member of this class comprises two normally independent oscillating modes of a system, for example, a building or bridge, which, separately, cannot be driven by a zero-frequency force. Agreeing on terms of collaboration, the two modes engage in a joint oscillation powered by the steady zero-frequency force in which they drive each other, one directly and the other parametrically. I observed a bimodal vibration belonging to this class in a home shower where the two modes are the pendulum excursion and the torsional twisting of a freely suspended showerhead which break into a joint oscillation above a threshold value of the water flow rate. I advance a theoretical model which predicts and explains the main features of the observations. The model constitutes an extension to two modes of a proposal and demonstration in 1883 by Lord Rayleigh and Michael Faraday for the excitation of a single resonant mode by modulating a system parameter at twice the resonance frequency. The proposal is credited with the launching of parametric physics. The Experiments section of this report consists of three linked video clips photographed in the home shower which support the basic theoretical assumptions. The ubiquity of zero-frequency forces, such as that of wind, and their direct conversion to alternating on-resonance system vibrations endows the class with an amplified destructive potential with implications for structural stability.

A thermal receptor for nonvisual sunlight detection in myriapods.

Organisms from cyanobacteria to humans have evolved a wide array of photoreceptive strategies to detect light. Sunlight avoidance behavior is common in animals without vision or known photosensory genes. While indirect light perception via photothermal conversion is a possible scenario, there is no experimental evidence for this hypothesis. Here, we show a nonvisual and extraocular sunlight detection mechanism by identifying the broad-range thermal receptor 1 (BRTNaC1, temperature range = 33 to 48 °C) in centipede antennae. BRTNaC1, a heat-activated cation-permeable ion channel, is structurally related to members of the epithelial sodium channel family. At the molecular level, heat activation of BRTNaC1 exhibits strong pH dependence controlled by two protonatable sites. Physiologically, temperature-dependent activation of BRTNaC1 upon sunlight exposure comes from a striking photothermal effect on the antennae, where a slightly acidic environment (pH 6.1) of the body fluid leads to the protonation of BRTNaC1 and switches on its high thermal sensitivity. Furthermore, testosterone potently inhibits heat activation of BRTNaC1 and the sunlight avoidance behavior of centipedes. Taken together, our study suggests a sophisticated strategy for nonvisual sunlight detection in myriapods.

Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability.

Existing single-cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here, we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre- and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profiles. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of the epigenetic status of biological systems with complicated nature such as neurons and cancer cells.