Non-core Region Research Articles

RAG1 and RAG2 non-core regions are implicated in leukemogenesis and off-target V(D)J recombination in BCR-ABL1-driven B-cell lineage lymphoblastic leukemia.

The evolutionary conservation of non-core RAG regions suggests significant roles that might involve quantitative or qualitative alterations in RAG activity. Off-target V(D)J recombination contributes to lymphomagenesis and is exacerbated by RAG2' C-terminus absence in Tp53-/- mice thymic lymphomas. However, the genomic stability effects of non-core regions from both Rag1c/c and Rag2c/c in BCR-ABL1+ B-lymphoblastic leukemia (BCR-ABL1+ B-ALL), the characteristics, and mechanisms of non-core regions in suppressing off-target V(D)J recombination remain unclear. Here, we established three mouse models of BCR-ABL1+ B-ALL in mice expressing full-length RAG (Ragf/f), core RAG1 (Rag1c/c), and core RAG2 (Rag2c/c). The Ragc/c (Rag1c/c and Rag2c/c) leukemia cells exhibited greater malignant tumor characteristics compared to Ragf/f cells. Additionally, Ragc/c cells showed higher frequency of off-target V(D)J recombination and oncogenic mutations than Ragf/f. We also revealed decreased RAG cleavage accuracy in Ragc/c cells and a smaller recombinant size in Rag1c/c cells, which could potentially exacerbate off-target V(D)J recombination in Ragc/c cells. In conclusion, these findings indicate that the non-core RAG regions, particularly the non-core region of RAG1, play a significant role in preserving V(D)J recombination precision and genomic stability in BCR-ABL1+ B-ALL.

Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis.

ELYS is a nucleoporin that localizes to the nuclear side of the nuclear pore complex (NPC) in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate post-mitotic NPC assembly. Here we identify ELYS as a major binding partner of the membrane protein VAPB during mitosis. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which mediates interaction with the MSP (major sperm protein)-domain of VAPB. Binding assays using recombinant proteins or cell lysates and co-immunoprecipitation experiments show that VAPB binds the FFAT motif of ELYS in a phosphorylation-dependent manner. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB results in prolonged mitosis, slow progression from meta- to anaphase and in chromosome segregation defects. Together, our results suggest a role of VAPB in mitosis upon recruitment to or release from ELYS at the non-core region of the chromatin in a phosphorylation-dependent manner.

Population-land spatial coupling in urban non-core region and environmental pollution: evidence from urbanization in China

Urban non-core region land exploitation and population immigration toward urban non-core areas, two fundamentals of urbanization in China, challenge the environment; however, the pollution effect remains unclear. Using prefecture-level data in China between 2003 and 2020, our study investigates the pollution effect of population-land spatial coupling in the urban non-core region. The empirical results demonstrate that excessive urban non-core region land expansion alone negatively impacts the environment. Meanwhile, outward spatial population distribution in a town, primarily measured by the relative proportion of the urban non-core region population size, directly aggravates environmental pollution on the one hand and indirectly improves the environment by alleviating the adverse effect of land-led urbanization. These findings remain robust under various regional heterogeneity analyses and still stand regardless of the investigated pollutants. The practical implications suggest that breaking through the population-land spatial coupling when the urban core region is small is advisable; meanwhile, efforts in maintaining the coupling, especially for areas with sizeable peripheral land exploitation, should be held.

Developing non-core regions by establishing new universities

ABSTRACT We explore the regional engagement of universities in non-core regions in a Global South context and uncover how new universities form and institutionalize regional ties. Through case studies of five new universities in India, we identify three routes – personal, organizational and brokered – through which new universities form regional ties, and four logics – incrementalism, social responsibility, legitimation and rationalization – through which these ties become embedded. We unpack and combine each of the routes and logics into a framework that explains how new ties are formed and developed between a new university and its surrounding non-core region.

Metabolomics integrated with machine learning to discriminate the geographic origin of Rougui Wuyi rock tea

The geographic origin of agri-food products contributes greatly to their quality and market value. Here, we developed a robust method combining metabolomics and machine learning (ML) to authenticate the geographic origin of Wuyi rock tea, a premium oolong tea. The volatiles of 333 tea samples (174 from the core region and 159 from the non-core region) were profiled using gas chromatography time-of-flight mass spectrometry and a series of ML algorithms were tested. Wuyi rock tea from the two regions featured distinct aroma profiles. Multilayer Perceptron achieved the best performance with an average accuracy of 92.7% on the training data using 176 volatile features. The model was benchmarked with two independent test sets, showing over 90% accuracy. Gradient Boosting algorithm yielded the best accuracy (89.6%) when using only 30 volatile features. The proposed methodology holds great promise for its broader applications in identifying the geographic origins of other valuable agri-food products.

Low-speed gas knife protection for the large aperture optical component in high-power laser systems

In high-power laser systems, fused silica aerosols produced by laser-induced damage to optical components impede further improvement in operation efficiency. To mitigate aerosol threats, low-speed gas knives are an attractive online option. Herein, we investigate the protective mechanism of a low-speed gas knife (<20 m/s) against aerosol invasion on the optical component. First, aerosol particles invaded the surface experimentally in two ways and were detected both in the core and non-core regions, depending on the coverage area of the protection flow. Particle sedimentation percentages can directly reflect the protection capability of the gas knife flow. Since a “midstream defect” is readily apparent, a CFD model was developed to explain the phenomenon from the perspective of velocity distribution. Additionally, the Euler-Lagrange method was used to track airflow particle motions and reappear the protective process. The numerical and experimental results on protection efficiency are closely correlated. The numerical calculation indicates that the “midstream defect” manifested in the core region is possibly attributed to the turbulent dispersion and anisotropic near-wall effects of particles of various diameters, while in the non-core region, the mechanism differs. This work provides a framework for airflow clean designs inside high-power laser systems.

Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T.

Flavobacteria are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of Flavobacterium faecale WV33T, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of F. faecale WV33T represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of F. faecale WV33T contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 Flavobacterium type strains, including F. faecale WV33T, tend to be very plastic, and Flavobacterium strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 Flavobacterium-type strains showed that F. faecale WV33T was positioned in a unique clade in the evolutionary tree.

The peripheral and core regions of virus-host network of COVID-19.

Two thousand nineteen novel coronavirus SARS-CoV-2, the pathogen of COVID-19, has caused a catastrophic pandemic, which has a profound and widespread impact on human lives and social economy globally. However, the molecular perturbations induced by the SARS-CoV-2 infection remain unknown. In this paper, from the perspective of omnigenic, we analyze the properties of the neighborhood perturbed by SARS-CoV-2 in the human interactome and disclose the peripheral and core regions of virus-host network (VHN). We find that the virus-host proteins (VHPs) form a significantly connected VHN, among which highly perturbed proteins aggregate into an observable core region. The non-core region of VHN forms a large scale but relatively low perturbed periphery. We further validate that the periphery is non-negligible and conducive to identifying comorbidities and detecting drug repurposing candidates for COVID-19. We particularly put forward a flower model for COVID-19, SARS and H1N1 based on their peripheral regions, and the flower model shows more correlations between COVID-19 and other two similar diseases in common functional pathways and candidate drugs. Overall, our periphery-core pattern can not only offer insights into interconnectivity of SARS-CoV-2 VHPs but also facilitate the research on therapeutic drugs.

Volitional Modulation of the Left DLPFC Neural Activity Based on a Pain Empathy Paradigm-A Potential Novel Therapeutic Target for Pain.

The ability to perceive and feel another person' pain as if it were one's own pain, e.g., pain empathy, is related to brain activity in the “pain-matrix” network. A non-core region of this network in Dorsolateral Prefrontal Cortex (DLPFC) has been suggested as a modulator of the attentional-cognitive dimensions of pain processing in the context of pain empathy. We conducted a neurofeedback experiment using real-time functional magnetic resonance imaging (rt-fMRI-NF) to investigate the association between activity in the left DLPFC (our neurofeedback target area) and the perspective assumed by the participant (“first-person”/“Self” or “third-person”/“Other” perspective of a pain-inducing stimulus), based on a customized pain empathy task. Our main goals were to assess the participants' ability to volitionally modulate activity in their own DLPFC through an imagery task of pain empathy and to investigate into which extent this ability depends on feedback. Our results demonstrate participants' ability to significantly modulate brain activity of the neurofeedback target area for the “first-person”/”Self” and “third-person”/”Other” perspectives. Results of both perspectives show that the participants were able to modulate (with statistical significance) the activity already in the first run of the session, in spite of being naïve to the task and even in the absence of feedback information. Moreover, they improved modulation throughout the session, particularly in the “Self” perspective. These results provide new insights on the role of DLPFC in pain and pain empathy mechanisms and validate the proposed protocol, paving the way for future interventional studies in clinical populations with empathic deficits.

RETRACTED ARTICLE: Kernalized average entropy and density based spatial clustering with noise

Image clustering is one of the key technologies for image processing. Most image clustering methods based on density algorithms encountered with challenges including robust salient region extraction, cluster centre identification and noise. To address these issues, different density-based clustering methods were used. To accommodate this constraint, this paper proposes a method named Kernalized Average Entropy and Density-based Spatial Clustering (KAE-DSC). The KAE-DSC method efficiently extracts the robust salient region for texture and image database using Spatial Candidate Region Detection. Finally, Spatial Density-based Clustering with Noise is used to differentiate between core, non-core and noisy region for grouping similar region. By identifying the three different regions, efficient prediction is said to be made for the given texture and medical images. KAE-DSC method is compared with several other methods based on several evaluation indexes to testify that the proposed KAE-DSC is outperformed. Abundant experimental results proved that KAE-DSC is robust to parameters, which can automatically determine the number of clustering and improve the accuracy of clustering with minimum time complexity.

A Novel ENSO Monitoring Method using Precipitable Water Vapor and Temperature in Southeast China

Southeast China, a non-core region influenced by the El Niño–Southern Oscillation (ENSO), has been seldom investigated before. However, the occurrence of ENSO will affect the redistribution of precipitation and the temperature (T) spatial pattern on a global scale. This condition will further lead to flood or drought disasters in Southeast China. Therefore, the method of monitoring the occurrence of ENSO is important and is the focus of this paper. The spatiotemporal characteristics of precipitable water vapor (PWV) and T are first analyzed during ENSO using the empirical orthogonal function (EOF). The results showed that a high correlation spatiotemporal consistency exist between PWV and T. The response thresholds of PWV and T to ENSO are determined by moving the window correlation analysis (MWCA). If the sea surface temperature anomaly (SSTA) at the Niño 3.4 region exceeded the ranges of (−1.17°C, 1.04°C) and (−1.15°C, 1.09°C), it could cause the anomalous change of PWV and T in Southeast China. Multichannel singular spectral analysis (MSSA) is introduced to analyze the multi-type signals (tendency, period, and anomaly) of PWV and T over the period of 1979–2017. The results showed that the annual abnormal signal and envelope line fluctuation of PWV and T agreed well in most cases with the change in SSTA. Therefore, a standard PWV and T index (SPTI) is proposed on the basis of the results to monitor ENSO events. The PWV and T data derived from the grid-based European Center for Medium-Range Weather Forecasting (ECMWF) reanalysis products and GNSS/RS stations in Southeast China were used to validate the performance of the proposed SPTI. Experimental results revealed that the time series of average SPTI calculated in Southeast China corresponded well to that of SSTA with a correlation coefficient of 0.66 over the period of 1979–2017. The PWV values derived from the Global Navigation Satellite System (GNSS) and radiosonde data at two specific stations (WUHN and 45004) were also used to calculate the SPTI. The results showed that the correlation coefficients between SPTI and SSTA were 0.73 and 0.71, respectively. Such results indicate the capacity of the proposed SPTI to monitor the ENSO in Southeast China.

Anomaly Variation of Vegetation and Its Influencing Factors in Mainland China During ENSO Period

Considering the noncore region influenced by El Nino-Southern Oscillation (ENSO) events, China is hardly investigated in terms of the vegetation variation during the ENSO period.Therefore, this study focused on increasing knowledge of vegetation growth and variation during the ENSO period.The novelty of this paper is introduced the moving window correlation analysis method to determine the thresholds of vegetation response to sea surface temperature anomaly (SSTa) and southern oscillation index (SOI) and analyze the main reasons for such variations.China was divided into seven areas based on different weather conditions, and the variations in vegetation growth in various areas during the ENSO period were analyzed. The response of vegetation to ENSO events in China was analyzed from the perspectives of precipitable water vapor (PWV), temperature, and precipitation, thereby revealing the interplay of multi-factors on vegetation growth.The main conclusions include (1) a positive vegetation response to El Nino exists all over China with thresholds of SSTa ≥ 1.87°C and SOI ≤ -3.27hPa, whereas a negative response of vegetation variation to La Nina exists with thresholds of SSTa ≤ -1.05°C and SOI ≥ 1.7hPa; (2) the correlations (p <; 0.05) of PWV to normalized difference vegetation index (NDVI) (PWV-NDVI), temperature-NDVI, and precipitation-NDVI reached 0.84, 0.86, and 0.68, respectively, and PWV, temperature, and precipitation were negatively/positively abnormal during El Nino/La Nina periods; (3) in coastal areas of Southeast China, correlations between NDVI and PWV/temperature/ precipitation are poor and the opposite anomalies of PWV/temperature/ precipitation existed when compared to other areas of China.

RAG2 localization and dynamics in the pre-B cell nucleus.

RAG2 of the V(D)J recombinase is essential for lymphocyte development. Within the RAG2 noncore region is a plant homeodomain (PHD) that interacts with the modified histone H3K4me3, and this interaction is important for relieving inhibition of the RAG recombinase for V(D)J recombination. However, the effect of the noncore region on RAG2 localization and dynamics in cell nuclei is poorly understood. Here, we used cell imaging to measure the effect of mutating the RAG2 noncore region on properties of the full length protein. We measured GFP-labeled full length RAG2 (FL), the RAG2 core region alone (Core), and a T490A mutant in the noncore region, which has unique regulatory properties. This showed that FL, T490A, and Core localized to nuclear domains that were adjacent to DAPI-rich heterochromatin, and that contained the active chromatin marker H3K4me3. Within the RAG2-enriched regions, T490A exhibited greater colocalization with H3K4me3 than either FL or Core. Furthermore, colocalization of H3K4me3 with FL and T490A, but not Core, increased in conditions that increased H3K4me3 levels. Superresolution imaging showed H3K4me3 was distributed as puncta that RAG2 abutted, and mobility measurements showed that T490A had a significantly lower rate of diffusion within the nucleus than either FL or Core proteins. Finally, mutating Trp453 of the T490A mutant (W453A,T490A), which blocks PHD-dependent interactions with H3K4me3, abolished the T490A-mediated increased colocalization with H3K4me3 and slower mobility compared to FL. Altogether, these data show that Thr490 in the noncore region modulates RAG2 localization and dynamics in the pre-B cell nucleus, such as by affecting RAG2 interactions with H3K4me3.

Migration Patterns of University Spin-offs: Case Study of Region Twente, a Non-Core Region in the Netherlands

Migration Patterns of University Spin-offs: Case Study of Region Twente, a Non-Core Region in the Netherlands

Feature-dependent intrinsic functional connectivity across cortical depths in the human auditory cortex

Frequency preference and spectral tuning are two cardinal features of information processing in the auditory cortex. However, sounds should not only be processed in separate frequency bands because information needs to be integrated to be meaningful. One way to better understand the integration of acoustic information is to examine the functional connectivity across cortical depths, as neurons are already connected differently across laminar layers. Using a tailored receiver array and surface-based cortical depth analysis, we revealed the frequency–preference as well as tuning–width dependent intrinsic functional connectivity (iFC) across cortical depths in the human auditory cortex using functional magnetic resonance imaging (fMRI). We demonstrated feature-dependent iFC in both core and noncore regions at all cortical depths. The selectivity of frequency–preference dependent iFC was higher at deeper depths than at intermediate and superficial depths in the core region. Both the selectivity of frequency–preference and tuning–width dependent iFC were stronger in the core than in the noncore region at deep cortical depths. Taken together, our findings provide evidence for a cortical depth-specific feature-dependent functional connectivity in the human auditory cortex.

Visualization of binding of RAG2 to H3K4me3 regulated by its noncore domain.

Abstract Association of RAG2 with the epigenetic marker H3K4me3 through a PHD domain in its noncore region is important for activating the RAG1 component of the RAG recombinase complex for V(D)J recombination. However, immunofluorescence staining of RAG2 expressed in thymocytes suggests RAG2 is localized principally to the nuclear periphery, away from sites of H3K4 modification. To further test for interactions between RAG2 and separate epigenetic markers, we used confocal microscopy to measure full length RAG2 labeled with GFP at its N-terminus (GFP-FL) and expressed in RAG2−/−pro-B cells. Cross-correlation analysis of cells immunostained with antibodies to H3K4me3 and H3K9me3 showed that RAG2 colocalization with H3K4me3 was significantly greater than with H3K9me3. Furthermore, blocking histone demethylation by treating cells with 2,4-pyridinedicarboxylic acid increased colocalization of GFP-FL with H3K4me3, but not its colocalization with H3K9me3. Interestingly, a GFP-labeled T490A mutant of full length RAG2 (GFP-T490A) showed significantly greater colocalization with H3K4me3 than the labeled wild-type RAG2. GFP-labeled RAG2 core alone (GFP-core) exhibited the poorest colocalization with H3K4me3 of the constructs that we measured. Finally, nanoscale resolution using structured illumination microscopy showed that RAG2 was unevenly distributed in the nucleus, containing dispersed RAG2-rich and RAG2-poor regions. Furthermore, RAG2 interactions with H3K4me3 were restricted to interfaces between H3K4me3-enriched puncta and the RAG2. Altogether, these data provide visualization of RAG2 binding to the epigenetic marker H3K4me3, and that Thr490 of RAG2 regulates this interaction.

Multi-scale modeling and simulation of tunnel excavation in sand-gravel strata

In sand-gravel strata, the deformation and mechanical behavior of soil mass as well as tunnel structure are mainly controlled by excavation disturbance degree and mesoscopic distribution of soil-rock-mixture in excavation disturbance area. Considering the mesoscopic structure of soil-rock-mixture, a multi-scale analysis approach for tunnel excavation in sand-gravel strata is proposed. Then, three key issues of the method, mainly about the determination of core region and non-core region, the determination of rock size that can be homogenized, equivalent method of soil-rock-mixture, are discussed. The basic thought of the multi-scale analysis approach can be expressed as follows. Firstly, the tunnel excavation model in sand-gravel strata is divided into core region and non-core region. In core region, the soil-rock-mixture is treated as the two-phase composite composed by rock block and soil, while in non-core region, the soil-rock-mixture is viewed as macroscopic homogeneous material. On this basis, the simulation and analysis of tunnel excavation are carried out. From the view of surrounding rock deformation and pressure, the results are compared with meso-analysis model and macro-analysis model of tunnel excavation, and the analysis showed that the simulation results of multi-scale analysis approach are coincidence with meso-analysis model. More importantly, the proposed method greatly reduces the computational work and modeling work, improved the computation efficiency observably.

RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2.

The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a plant homeodomain (PHD) finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused and dependent on ‘non-core’ portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity and reveals a novel role for the RAG1 non-core region in RAG1 targeting.

Disruption of the RAG2 zinc finger motif impairs protein stability and causes immunodeficiency

Although the RAG2 core domain is the minimal region required for V(D)J recombination, the noncore region also plays important roles in the regulation of recombination, and mutations in this region are often related to severe combined immunodeficiency. A complete understanding of the functions of the RAG2 noncore region and the potential contributions of its individual residues has not yet been achieved. Here, we show that the zinc finger motif within the noncore region of RAG2 is indispensable for maintaining the stability of the RAG2 protein. The zinc finger motif in the noncore region of RAG2 is highly conserved from zebrafish to humans. Knock-in mice carrying a zinc finger mutation (C478Y) exhibit decreased V(D)J recombination efficiency and serious impairment in T/B-cell development due to RAG2 instability. Further studies also reveal the importance of the zinc finger motif for RAG2 stability. Moreover, mice harboring a RAG2 noncore region mutation (N474S), which is located near C478 but is not zinc-binding, exhibit no impairment in either RAG2 stability or T/B-cell development. Taken together, our findings contribute to defining critical functions of the RAG2 zinc finger motif and provide insights into the relationships between the mutations within this motif and immunodeficiency diseases.

An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex.

V(D)J recombination assembles functional antigen receptor genes during lymphocyte development. Formation of the recombination complex containing the recombination activating proteins, RAG1 and RAG2, is essential for the site-specific DNA cleavage steps in V(D)J recombination. However, little is known concerning how complex formation leads to a catalytically-active complex. Here, we combined limited proteolysis and mass spectrometry methods to identify regions of RAG1 that are sequestered upon association with RAG2. These results show that RAG2 bridges an interdomain boundary in the catalytic region of RAG1. In a second approach, mutation of RAG1 residues within the interdomain boundary were tested for disruption of RAG1:RAG2 complex formation using fluorescence-based pull down assays. The core RAG1 mutants demonstrated varying effects on complex formation with RAG2. Interestingly, two mutants showed opposing results for the ability to interact with core versus full length RAG2, indicating that the non-core region of RAG2 participates in binding to core RAG1. Significantly, all of the RAG1 interdomain mutants demonstrated altered stoichiometries of the RAG complexes, with an increased number of RAG2 per RAG1 subunit compared to the wild type complex. Based on our results, we propose that interaction of RAG2 with RAG1 induces cooperative interactions of multiple binding sites, induced through conformational changes at the RAG1 interdomain boundary, and resulting in formation of the DNA cleavage active site.