Systematic characterization of immunoglobulin loci and deep sequencing of the expressed repertoire in the Atlantic cod (Gadus morhua).

BACKGROUND: The Atlantic cod is a prolific species in the Atlantic, despite its inconsistent specific antibody response. It presents a peculiar case within vertebrate immunology due to its distinct immune system, characterized by the absence of MHCII antigen presentation pathway, required for T cell-dependent antibody responses. Thorough characterisation of immunoglobulin loci and analysis of the antibody repertoire is necessary to further our understanding of the Atlantic cod's immune response on a molecular level. RESULTS: A comprehensive search of the cod genome (gadmor3.0) identified the complete set of IgH genes organized into three sequential translocons on chromosome 2, while IgL genes were located on chromosomes 2 and 5. The Atlantic cod displayed a moderate germline V gene diversity, comprising four V gene families for both IgH and IgL, each with distinct chromosomal locations and organizational structures. 5'RACE sequencing revealed a diverse range of heavy chain CDR3 sequences and relatively limited CDR3 diversity in light chains. The analysis highlighted a differential impact of V-gene germline CDR3 length on receptor CDR3 length between heavy and light chains, underlining different recombination processes. CONCLUSIONS: This study reveals that the Atlantic cod, despite its inconsistent antibody response, maintains a level of immunoglobulin diversity comparable to other fish species. The findings suggest that the extensive recent duplications of kappa light chain genes do not result in increased repertoire diversity. This research provides a comprehensive view of the Atlantic cod's immunoglobulin gene organization and repertoire, necessary for future studies of antibody responses at the molecular level.

Suppressed thermal transport in silicon nanoribbons by inhomogeneous strain.

Nanoscale structures can produce extreme strain that enables unprecedented material properties, such as tailored electronic bandgap1-5, elevated superconducting temperature6,7 and enhanced electrocatalytic activity8,9. While uniform strains are known to elicit limited effects on heat flow10-15, the impact of inhomogeneous strains has remained elusive owing to the coexistence of interfaces16-20 and defects21-23. Here we address this gap by introducing inhomogeneous strain through bending individual silicon nanoribbons on a custom-fabricated microdevice and measuring its effect on thermal transport while characterizing the strain-dependent vibrational spectra with sub-nanometre resolution. Our results show that a strain gradient of 0.112% per nanometre could lead to a drastic thermal conductivity reduction of 34 ± 5%, in clear contrast to the nearly constant values measured under uniform strains10,12,14,15. We further map the local lattice vibrational spectra using electron energy-loss spectroscopy, which reveals phonon peak shifts of several millielectron-volts along the strain gradient. This unique phonon spectra broadening effect intensifies phonon scattering and substantially impedes thermal transport, as evidenced by first-principles calculations. Our work uncovers a crucial piece of the long-standing puzzle of lattice dynamics under inhomogeneous strain, which is absent under uniform strain and eludes conventional understanding.

One-Dimensional MoS2 Nanoscrolls as Miniaturized Memories.

Dimensionality of materials is closely related to their physical properties. For two-dimensional (2D) semiconductors such as monolayer molybdenum disulfide (MoS2), converting them from 2D nanosheets to one-dimensional (1D) nanoscrolls could contribute to remarkable electronic and optoelectronic properties, yet the rolling-up process still lacks sufficient controllability, which limits the development of their device applications. Herein we report a modified solvent evaporation-induced rolling process that halts at intermediate states and achieve MoS2 nanoscrolls with high yield and decent axial uniformity. The accordingly fabricated nanoscroll memories exhibit an on/off ratio of ∼104 and a retention time exceeding 103 s and can realize multilevel storage with pulsed gate voltages. Such open-end, high-curvature, and hollow 1D nanostructures provide new possibilities to manipulate the hysteresis windows and, consequently, the charge storage characteristics of nanoscale field-effect transistors, thereby holding great promise for the development of miniaturized memories.

Change pattern and stability of oasisization land in Mu Us Sandy Land.

Understanding land structure change and stability in the process of oasisization is particularly important for the desertification control in sandy land. Based on land use data of eight periods from 1980 to 2020, we extracted the spatial distribution information of oasis land in Mu Us Sandy Land, and analyzed the spatio-temporal variations of land transformation patterns and stability of oasis land with overlay analysis and grid analysis. The results showed that desertification in the Mu Us Sandy Land had reversed, with a significant process of oasis. The area of forest and grassland increased from 10.2% in 1980 to 73.7% in 2020, while the area of oasisization land increased from 32500 km2 in 1980 to 33900 km2 in 2020. The area of extremely severe, severe, and moderate desertification significantly decreased, while the area of non-desertification and mild desertification obviously increased. The four patterns of oasisization land transformation, including stability, fluctuation, expansion, and retreat, which accounted for 78.7%, 12.2%, 6.2%, and 2.9% of the oasisization land area in 2020, respectively. The oasisization land with low change intensity (the cumulative change intensity less than 0.12) in the Mu Us Sandy Land accounted for 82.7% of the total oasisization area, and the oasisization land in the sandy land was generally stable. Zoning management strategies should be applied according to the stability of sand belt and transformation pattern of oasisization land to achieve the goal of efficient system management and improvement, including eliminating sand hazards at desertification expansion areas with strong wind and sand activities, consolidating sand resources at oasisization areas where ecologically fragile desertification was frequent, and sustainably managing and utilizing sand resources at stable expansion of oases in forest- and grass-rich oasisization areas.

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method.

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

Gluten-Free Diet Induces Rapid Changes in Phenotype and Survival Properties of Gluten-Specific T Cells in Celiac Disease.

BACKGROUND & AIMS: The treatment of celiac disease (CeD) with gluten-free diet (GFD) normalizes gut inflammation and disease-specific antibodies. CeD patients have HLA-restricted, gluten-specific T cells persisting in the blood and gut even after decades of GFD, which are reactivated and disease driving upon gluten exposure. Our aim was to examine the transition of activated gluten-specific T cells into a pool of persisting memory T cells concurrent with normalization of clinically relevant biomarkers during the first year of treatment. METHODS: We followed 17 CeD patients during their initial GFD year, leading to disease remission. We assessed activation and frequency of gluten-specific CD4+ blood and gut T cells with HLA-DQ2.5:gluten tetramers and flow cytometry, disease-specific serology, histology, and symptom scores. We assessed gluten-specific blood T cells within the first 3 weeks of GFD in 6 patients and serology in an additional 9 patients. RESULTS: Gluten-specific CD4+ T cells peaked in blood at day 14 while up-regulating Bcl-2 and down-regulating Ki-67 and then decreased in frequency within 10 weeks of GFD. CD38, ICOS, HLA-DR, and Ki-67 decreased in gluten-specific cells within 3 days. PD-1, CD39, and OX40 expression persisted even after 12 months. IgA-transglutaminase 2 decreased significantly within 4 weeks. CONCLUSIONS: GFD induces rapid changes in the phenotype and number of gluten-specific CD4+ blood T cells, including a peak of nonproliferating, nonapoptotic cells at day 14. Subsequent alterations in T-cell phenotype associate with the quiescent but chronic nature of treated CeD. The rapid changes affecting gluten-specific T cells and disease-specific antibodies offer opportunities for clinical trials aiming at developing nondietary treatments for patients with newly diagnosed CeD.

Key technology of vector removal decoupling in a slope-based figuring model and application in continuous phase plate fabrication.

For the high-precision fabrication of a continuous phase plate (CPP), a combined decoupling algorithm of single-step decoupling based on the Clairaut-Schwarz theorem and global decoupling by stagewise iteration is proposed. It attempts to address the problem of the low accuracy and limitation of the existing slope-based figuring (SF) model in two-dimensional applications caused by the vector removal coupling between the tool slope influence function and the material removal slope due to the inherent convolution effect in the SF model. The shortcomings of CPP interferometry and the application bottleneck of the Hartmann test in traditional height-based figuring model are studied. The generation mechanism of vector removal coupling is analyzed and compensated. A CPP of 85m m×85m m was successfully machined by the decoupled slope-based figuring model, and the root mean square (RMS) of the surface height error accounted for 6.01% of the RMS of the design value. The research results can effectively improve the convergence and certainty of CPP fabrication using the slope-based figuring model.

Source-oriented risk assessment of heavy metal(loid)s in agricultural soils around a multimetal smelting area near the Yellow River, China.

Heavy metal(loid) (HM) contamination in agricultural soils, particularly in areas severely impacted by smelting industries, has attracted worldwide attention. In this study, agricultural soils were collected in a flourishing multimetal smelting area near the Yellow River in central China. By an integrated approach encompassing the positive matrix factorization model, ordinary kriging interpolation and hierarchical clustering analysis (PMF-OK-HC), a total of four major sources and their mass contributions were identified, namely, soil parent material (56.6%), industrial waste and Mo smelting (24.0%), metal smelting and traffic emissions (12.8%), and coal combustion (6.7%). On this basis, the health risk of HMs was evaluated by Monte Carlo simulations and showed that a higher risk, with a higher proportion of exceeding-thresholds risk, was observed for children than for adults in terms of both noncarcinogenic and carcinogenic risks. Exposure pathways of oral ingestion in children could result in a higher attributed risk than other pathways. Furthermore, source-oriented risk assessment (SORA) revealed that the sources of coal combustion, industrial waste and Mo smelting had the highest contributions to noncarcinogenic and carcinogenic risks. Overall, for effective environmental management in agricultural soil, the framework of SORA was verified as an effective tool in the identification of the priority control of HMs and their sources.

Identification of a pharyngeal mucosal lymphoid organ in zebrafish and other teleosts: Tonsils in fish?

The constant exposure of the fish branchial cavity to aquatic pathogens causes local mucosal immune responses to be extremely important for their survival. Here, we used a marker for T lymphocytes/natural killer (NK) cells (ZAP70) and advanced imaging techniques to investigate the lymphoid architecture of the zebrafish branchial cavity. We identified a sub-pharyngeal lymphoid organ, which we tentatively named "Nemausean lymphoid organ" (NELO). NELO is enriched in T/NK cells, plasma/B cells, and antigen-presenting cells embedded in a network of reticulated epithelial cells. The presence of activated T cells and lymphocyte proliferation, but not V(D)J recombination or hematopoiesis, suggests that NELO is a secondary lymphoid organ. In response to infection, NELO displays structural changes including the formation of T/NK cell clusters. NELO and gill lymphoid tissues form a cohesive unit within a large mucosal lymphoid network. Collectively, we reveal an unreported mucosal lymphoid organ reminiscent of mammalian tonsils that evolved in multiple teleost fish families.

3D reconstruction method based on the multi-polarization superposition coding phase pattern of LRR objects.

Conventional research in structured light measurements has utilized light intensity as a channel for information. The polarization of light can be used as an additional channel of information. In this paper, a method based on the superposition of multiple polarization states is proposed to encode structured light. By building a polarization model between the color of light and the polarization states, polarized structured light containing phase information is obtained without rotating the polarizer. It is demonstrated that the method improves the waveform quality of stripes and the accuracy of the 3D reconstruction results when measuring highly reflective objects.

Design method of an ultra-thin two-dimensional geometrical waveguide near-eye display based on forward-ray-tracing and maximum FOV analysis.

A two-dimensional geometrical waveguide enables ultra-thin augmented reality (AR) near-eye display (NED) with wide field of view (FOV) and large exit-pupil diameter (EPD). A conventional design method can efficiently design waveguides that meet the requirements, but is unable to fully utilize the potential display performance of the waveguide. A forward-ray-tracing waveguide design method with maximum FOV analysis is proposed, enabling two-dimensional geometrical waveguides to achieve their maximum FOV while maintaining minimum dimensions. Finally, the designed stray-light-suppressed waveguide NED has a thickness of 1.7 mm, a FOV of 50.00°H × 29.92°V, and an eye-box of 12 mm × 12 mm at an eye-relief of 18 mm.

Heat Flow Guiding and Modulation by Kinks in a Silicon Nanoribbon.

Tailoring heat flow in solids has profound implications for the innovation of functional thermal devices. However, the current methods face technological challenges related to system complexity, material stability, and operating temperature. In this study, we demonstrated efficient heat flow modulation in a single material without a phase transition, using a simple and entirely material-independent strategy, kinked nanostructure patterning, at near-ambient temperature. By carefully controlling the kink arm length and kink angle of the Si nanoribbons, we achieved a thermal conductivity modulation of up to ∼20%. Our theoretical modeling showed that this modulation results from the competing roles of phonon backscattering and open view channels on heat transport. We also build a regime map based on the existence of an open view channel and provide concrete design guidelines for thermal conductivity modulation considering the kink angle and arm length. This study opens up new opportunities for efficient heat flow manipulation through nanostructure patterning.

Research on Laser-Induced Damage Post-Restoration Morphology of Fused Silica and Optimization of Patterned CO2 Laser Repair Strategy.

Fused silica has become the preferred optical material in the field of inertial confinement fusion (ICF) due to its excellent performance; however, these costly optical elements are vulnerable, and their manufacture is time-consuming. Therefore, the restoration of laser-induced damage for these optical elements is of great value. To restrain the post-restoration raised rim problem in the CO2 laser repair process to improve the restoration quality, the separate influences of key parameters of laser power, irradiation duration, and laser beam diameter on post-restoration pit morphology are compared in combined simulation and experimental studies. An optimized, patterned CO2 laser strategy is proposed and verified; the results indicate that, with the strategy, the rim height decreases from 2.6 µm to 1.52 µm, and maximal photo thermal absorption is decreased from 784.2 PPM to 209.43 PPM.

Combined polishing process of a sapphire aspherical component based on temperature-controlled magnetorheological processing.

In view of the problems of large surface roughness and low removal efficiency caused by the existing sapphire processing process, a combined polishing process based on temperature control computer controlled optical surfacing-magnetic rheology is proposed. The polishing removal mechanism of sapphire material polishing and the law of processing surface roughness change are studied. The optimal process parameters are obtained by designing the orthogonal experiments. Under this parameter, a sapphire aspherical component with good surface quality is obtained, and the temperature has a significant amount of influence on the removal efficiency. Finally, the optimum temperature of sapphire material under magnetorheological polishing was determined to be 75°C. The results greatly improve the manufacturing efficiency of high sapphire surface quality.

Lymphocyte subsets in Atlantic cod (Gadus morhua) interrogated by single-cell sequencing.

Atlantic Cod (Gadus morhua) has lost the major histocompatibility complex class II presentation pathway. We recently identified CD8-positive T cells, B cells, and plasma cells in cod, but further characterisation of lymphocyte subsets is needed to elucidate immune adaptations triggered by the absence of CD4-positive T lymphocytes. Here, we use single-cell RNA sequencing to examine the lymphocyte heterogeneity in Atlantic cod spleen. We describe five T cell subsets and eight B cell subsets and propose a B cell trajectory of differentiation. Notably, we identify a subpopulation of T cells that are CD8-negative. Most of the CD8-negative T lymphocytes highly express the homologue of monocyte chemotactic protein 1b, and another subset of CD8-negative T lymphocytes express the homologue of the scavenger receptor m130. Uncovering the multiple lymphocyte cell sub-clusters reveals the different immune states present within the B and T cell populations, building a foundation for further work.

Stereotyped B-cell responses are linked to IgG constant region polymorphisms in multiple sclerosis.

Clonally related B cells infiltrate the brain, meninges, and cerebrospinal fluid of MS patients, but the mechanisms driving the B-cell response and shaping the immunoglobulin repertoires remain unclear. Here, we used single-cell full-length RNA-seq and BCR reconstruction to simultaneously assess the phenotypes, isotypes, constant region polymorphisms, and the paired heavy- and light-chain repertoires in intrathecal B cells. We detected extensive clonal connections between the memory B cell and antibody-secreting cell (ASC) compartments and observed clonally related cells of different isotypes including IgM/IgG1, IgG1/IgA1, IgG1/IgG2, and IgM/IgA1. There was a strong dominance of the G1m1 allotype constant region polymorphisms in ASCs, but not in memory B cells. Tightly linked to the G1m1 allotype, we found a preferential pairing of the immunoglobulin heavy-chain variable (IGHV)4 gene family with the κ variable (IGKV)1 gene family. The IGHV4-39 gene was most used and showed the highest frequency of pairing with IGKV1-5 and IGKV1(D)-33. These results link IgG constant region polymorphisms to stereotyped B-cell responses in MS and indicate that the intrathecal B-cell response in these patients could be directed against structurally similar epitopes.

TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences.

T-cell receptor (TCR) sequencing has enabled the development of innovative diagnostic tests for cancers, autoimmune diseases and other applications. However, the rarity of many T-cell clonotypes presents a detection challenge, which may lead to misdiagnosis if diagnostically relevant TCRs remain undetected. To address this issue, we developed TCRpower, a novel computational pipeline for quantifying the statistical detection power of TCR sequencing methods. TCRpower calculates the probability of detecting a TCR sequence as a function of several key parameters: in-vivo TCR frequency, T-cell sample count, read sequencing depth and read cutoff. To calibrate TCRpower, we selected unique TCRs of 45 T-cell clones (TCCs) as spike-in TCRs. We sequenced the spike-in TCRs from TCCs, together with TCRs from peripheral blood, using a 5' RACE protocol. The 45 spike-in TCRs covered a wide range of sample frequencies, ranging from 5 per 100 to 1 per 1 million. The resulting spike-in TCR read counts and ground truth frequencies allowed us to calibrate TCRpower. In our TCR sequencing data, we observed a consistent linear relationship between sample and sequencing read frequencies. We were also able to reliably detect spike-in TCRs with frequencies as low as one per million. By implementing an optimized read cutoff, we eliminated most of the falsely detected sequences in our data (TCR α-chain 99.0% and TCR ß-chain 92.4%), thereby improving diagnostic specificity. TCRpower is publicly available and can be used to optimize future TCR sequencing experiments, and thereby enable reliable detection of disease-relevant TCRs for diagnostic applications.

Innate lymphoid cell characterization in the rat and their correlation to gut commensal microbes.

Innate lymphoid cells (ILCs) are important for tissue immune homeostasis, and are thoroughly characterized in mice and humans. Here, we have performed in-depth characterization of rat ILCs. Rat ILCs were identified based on differential expression of transcription factors and lack of lineage markers. ILC3s represented the major ILC population of the small intestine, while ILC2s were infrequent but most prominent in liver and adipose tissue. Two major subsets of group 1 ILCs were defined. Lineage- T-bet+ Eomes+ cells were identified as conventional NK cells, while lineage- T-bet+ Eomes- cells were identified as the probable rat counterpart of ILC1s based on their selective expression of the ILC marker CD200R. Rat ILC1s were particularly abundant in liver and intestinal tissues, and were functionally similar to NK cells. Single-cell transcriptomics of spleen and liver cells confirmed the main division of NK cells and ILC1-like cells, and demonstrated Granzyme A as an additional ILC1 marker. We further report differential distributions of NK cells and ILCs along the small and large intestines, and the association of certain bacterial taxa to frequencies of ILCs. In conclusion, we provide a framework for future studies of ILCs in diverse rat experimental models, and novel data on the potential interplay between commensals and intestinal ILCs.

A virtual sequencer reveals the dephasing patterns in error-correction code DNA sequencing.

An error-correction code (ECC) sequencing approach has recently been reported to effectively reduce sequencing errors by interrogating a DNA fragment with three orthogonal degenerate sequencing-by-synthesis (SBS) reactions. However, similar to other non-single-molecule SBS methods, the reaction will gradually lose its synchronization within a molecular colony in ECC sequencing. This phenomenon, called dephasing, causes sequencing error, and in ECC sequencing, induces distinctive dephasing patterns. To understand the characteristic dephasing patterns of the dual-base flowgram in ECC sequencing and to generate a correction algorithm, we built a virtual sequencer in silico. Starting from first principles and based on sequencing chemical reactions, we simulated ECC sequencing results, identified the key factors of dephasing in ECC sequencing chemistry and designed an effective dephasing algorithm. The results show that our dephasing algorithm is applicable to sequencing signals with at least 500 cycles, or 1000-bp average read length, with acceptably low error rate for further parity checks and ECC deduction. Our virtual sequencer with our dephasing algorithm can further be extended to a dichromatic form of ECC sequencing, allowing for a potentially much more accurate sequencing approach.

Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq.

Gluten-specific CD4+ T cells drive the pathogenesis of celiac disease and circulating gluten-specific T cells can be identified by staining with HLA-DQ:gluten tetramers. In this first single-cell RNA-seq study of tetramer-sorted T cells from untreated celiac disease patients blood, we found that gluten-specific T cells showed distinct transcriptomic profiles consistent with activated effector memory T cells that shared features with Th1 and follicular helper T cells. Compared to non-specific cells, gluten-specific T cells showed differential expression of several genes involved in T-cell receptor signaling, translational processes, apoptosis, fatty acid transport, and redox potentials. Many of the gluten-specific T cells studied shared T-cell receptor with each other, indicating that circulating gluten-specific T cells belong to a limited number of clones. Moreover, the transcriptional profiles of cells that shared the same clonal origin were transcriptionally more similar compared with between clonally unrelated gluten-specific cells.