Rearrangement In Region Research Articles

The impact of geopolitical transformations on the settlement of the Nagorno-Karabakh conflict: self-determination or genocide?

ABSTRACT Geopolitical transformations have drastic effects in many spheres of public life. Their most prominent manifestations are observed with regard to ethno-political conflicts and their settlement processes, particularly when they are accompanied by serious regional rearrangements. The Nagorno-Karabakh conflict and the process of its settlement are among the most typical cases in this regard. After the 2018 change of power in Armenia, the normally developing process of the Nagorno-Karabakh conflict settlement within the framework of the main principles of international law ended up in sharp upheavals, succumbing to the logic of the sharply heated West-Russia geopolitical confrontation. The formation of antagonistic relations between the Co-Chair states of the OSCE Minsk Group undermined their mediation efforts, leaving two options for the resolution of the conflict: the realization of people’s right to self-determination with the support of international community or the genocide of the Nagorno-Karabakh people. The article considers the threats of a catastrophic development of events due to changes in the positions of powerful actors regarding the conflict settlement under the influence of geopolitical transformations, as well as the possibility of preventing such a development.

Improving resistant starch content of cassava starch by pulsed electric field-assisted esterification

This study aims to investigate the effect of pulsed electric field (PEF) assisted OSA esterification treatment on the multi-scale structure and digestive properties of cassava starch and structure-digestion relationships. The degree of substitution (DS) of starch dually modified at 1.5–4.5 kV/cm was 37.6–55.3 % higher than that of starch modified by the conventional method. Compared with native starch, the resistant starch (RS) content of esterified starch treated with 3 kV/cm significantly increased by 17.13 %, whereas that of starch produced by the conventional method increased by only 5.91 %. Furthermore, assisted esterification at low electric fields (1.5–3 kV/cm) promotes ester carbonyl grafting on the surface of starch granules, increases steric hindrance and promotes the rearrangement of the amorphous regions of starch, which increases the density of the double-helical structure. These structural changes slow down starch digestion and increase the RS content. Therefore, this study presents a potential method for increasing the RS content of starch products using PEF to achieve the desired digestibility.

Tailored gradient nanocrystallization in bulk metallic glass via ultrasonic vibrations

To advance materials with superior performance, the construction of gradient structures has emerged as a promising strategy. In this study, a gradient nanocrystalline-amorphous structure was induced in Zr46Cu46Al8 bulk metallic glass (BMG) through ultrasonic vibration (UV) treatment. Applying a 20 kHz ultrasonic cyclic loading in the elastic regime, controllable gradient structures with varying crystallized volume fractions can be achieved in less than 2 s by adjusting the input UV energy. In contrast to traditional methods of inducing structural gradients in BMGs, this novel approach offers distinct advantages: it is exceptionally rapid, requires minimal stress, and allows for easy tuning of the extent of structural gradients through precise adjustment of processing parameters. Nanoindentation tests reveal higher hardness near the struck surface, attributed to a greater degree of nanocrystal formation, which gradually diminishes with depth. As a result of the gradient dispersion of nanocrystals, an increased plasticity was found after UV treatment, characterized by the formation of multiple shear bands. Microstructural investigations suggest that UV-induced nanocrystallization originates from local atomic rearrangements in phase-separated Cu-rich regions with high diffusional mobility. Our study underscores the tunability of structural gradients and corresponding performance improvements in BMGs through ultrasonic energy modulation, offering valuable insights for designing advanced metallic materials with tailored mechanical properties.

Mapping recurrent mosaic copy number variation in human neurons

When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, “CNV neurons”), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes.

A water-stable high-voltage P3-type cathode for sodium-ion batteries

The Na-deficient P3-type layered oxide cathode material usually experience complex in-plane Na+/vacancy ordering rearrangement and undesirable P3-O3 phase transitions in the high-voltage region, leading to inferior cycling performance. Additionally, they exhibit unsatisfactory stability when exposed to water for extended periods. To address these challenges, we propose a Cu/Ti co-doped P3-type cathode material (Na0.67Ni0.3Cu0.03Mn0.6Ti0.07O2), which effectively mitigates Na+/vacancy ordering and suppresses P3-O3 phase transitions at high voltages. As a result, the as-prepared sample exhibited outstanding cyclic performance, with 81.9% retention after 500 cycles within 2.5–4.15 V, and 75.7% retention after 300 cycles within 2.5–4.25 V. Meanwhile, it demonstrates enhanced Na+ transport kinetics during desodiation/sodiation and reduced growth of charge transfer impedance (Rct) after various cycles. Furthermore, the sample showed superb stability against water, exhibiting no discernible degradation in structure, morphology, or electrochemical performance. This co-doping strategy provides new insights for innovative and prospective cathode materials.

Karyotype and LTR-RTs analysis provide insights into oak genomic evolution

BackgroundWhole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests.ResultsKaryotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes.ConclusionChromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.

Nanopore sequencing with T2T-CHM13 for accurate detection and preventing the transmission of structural rearrangements in highly repetitive heterochromatin regions in human embryos.

Structural rearrangements in highly repetitive heterochromatin regions can result in miscarriage or foetal malformations; however, detecting and preventing the transmission of these rearrangements has been challenging. Recently, the completion of sequencing of the complete human genome (T2T-CHM13) has made it possible to accurately characterise structural rearrangements in these regions. We developed a method based on T2T-CHM13 and nanopore sequencing to detect and block structural rearrangements in highly repetitive heterochromatin sequences. T2T-CHM13-based "Mapping Allele with Resolved Carrier Status" was performed for couples who carry structural rearrangements in heterochromatin regions. Using nanopore sequencing and the T2T-CHM13 reference genome, the precise breakpoints of inversions and translocations close to the centromere were detected and haplotypes were constructed using flanking single-nucleotide polymorphisms (SNPs). Haplotype linkage analysis was then performed by comparing consistent parental SNPs with embryonic SNPs to determine whether the embryos carried hereditary inversions or balanced translocations. Based on copy number variation and haplotype linkage analysis, we transplanted normal embryos, which were further verified by an amniotic fluid test. To validate this approach, we used nanopore sequencing of families with inversions and reciprocal translocations close to the centromere. Using the T2T-CHM13 reference genome, we accurately detected inversions and translocations in centromeres, constructed haplotypes and prevented the transmission of structural rearrangements in the offspring. This study represents the first successful application of T2T-CHM13 in human reproduction and provides a feasible protocol for detecting and preventing the transmission of structural rearrangements of heterochromatin in embryos.

The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis

Parthenium hysterophorus, a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadripartite structure commonly found in chloroplast genomes, including inverted repeat regions (IR) of 25,085 bp, a small single copy (SSC) region of 18,052 bp, and a large single copy (LSC) region of 83,588 bp. A total of 129 unique genes were identified in P. hysterophorus chloroplast genomes, including 85 protein-coding genes, 36 tRNAs, and eight rRNAs genes. Comparative analysis of the P. hysterophorus plastome with those of related species from the tribe Heliantheae revealed both conserved structures and intriguing variations. While many structural elements were shared among the species, we identified a rearrangement in the large single-copy region of P. hysterophorus. Moreover, our study highlighted notable gene divergence in several specific genes, namely matK, ndhF, clpP, rps16, ndhA, rps3, and ndhD. Phylogenetic analysis based on the 72 shared genes placed P. hysterophorus in a distinct clade alongside another species, P. argentatum. Additionally, the estimated divergence time between the Parthenium genus and Helianthus (sunflowers) was approximately 15.1 million years ago (Mya). These findings provide valuable insights into the evolutionary history and genetic relationships of P. hysterophorus, shedding light on its divergence and adaptation over time.

Concurrent Testing of Spatially Separated Tissue Samples and Circulating Tumor DNA Reveals Substantial Intra-Patient Genetic Heterogeneity in Relapsed/Refractory Follicular Lymphoma

Background: Scrutiny of genetic heterogeneity in follicular lymphoma (FL) patients has been mainly limited to the investigation of single-site biopsies in previous studies, while the potential of circulating cell-free DNA (cfDNA) to resolve intra-patient heterogeneity has not been fully exploited in FL. Therefore, we aimed to characterize spatiotemporal heterogeneity in relapsed/refractory (R/R) FL by performing comprehensive genomic profiling of spatially separated tissue samples with matching cfDNA samples collected throughout the disease course. Methods: We performed ultra-deep targeted sequencing of 63 tumor tissue DNA (tisDNA), 28 cfDNA and paired germline DNA samples collected from 22 R/R FL patients. Sequencing libraries were prepared using a SureSelectXT HS (Agilent, USA) panel encompassing 173 genes recurrently mutated in FL, as well as rearrangement regions for immunoglobulin V(D)J repertoire profiling. Sequencing was performed on a NovaSeq6000 or NextSeq2000 (Illumina, USA) platform reaching a median deduplicated depth of 5,419x and 1,695x for cfDNA and tisDNA samples, respectively. We called short somatic variants using GATK Mutect2 (v.4.1.7.0), copy number alterations using PureCN (v.1.20.0) and CNVKit (v.0.9.9), as well as immunoglobulin repertoire using the whole-mark module of ARResT/Interrogate. Results: Median 6 and 8 non-silent variants were detected in cfDNA and tisDNA samples, respectively, affecting KMT2D (52%), CREBBP (45%) and TNFRSF14 (33%) most frequently in both sample types. Non-silent variants were detected in 21 of 24 (87.5%) pretreatment cfDNA samples. Comparing tisDNA samples with matching pretreatment cfDNA samples median 63.6% of variants were shared, yet unique variants were identified in cfDNA in 13/20 sample pairs, involving a median 14.3% of the variants. Studying the phylogenetic evolution of tumor samples pointed to early branching in majority of the patients, with ubiquitously present mutations detected in all samples constituting a median 24.3% of variants, although late branching was also observed in a subset (2/22) of the patients with at least 50% of variants detected in all samples. Most conserved variants were detectable in KMT2D and CREBBP, with notable exceptions of a lower mutation prevalence, but a high conservation rate in ATP6V1B2 and STAT6 genes. Subclonal clustering of variants and hierarchy analysis of samples from patients (n=5) with 2 tisDNA collected at separate lymphoma sites and a matching pretreatment cfDNA indicated that spatially discordant variants formed the same subclone, that could be also recovered in cfDNA in 4/5 patients (80%). An additional patient presented with almost identical tisDNA samples, but further unique mutations in cfDNA (PAT-FL-20)(Figure 1.). Investigating the prognostic significance of ctDNA level in the relapsed setting revealed that higher ctDNA levels were significantly associated with poor response to therapy (p=0.023, Kruskal-Wallis test), yet when we stratified patients by the median pretreatment ctDNA level (1.44x10 5 haploid genome equivalent/mL plasma) progression free survival in the subsequent treatment line was not substantially different between the two arms (p=0.11, log-rank test). Conclusion: Based on our results, R/R FL is characterized by remarkable intra-patient genetic heterogeneity. Although the founder clone harboring pathogenic KMT2D and CREBBP mutations can be identified in majority of the samples, expansion of tumor subclones between lymphoma sites confers divergent evolution, leaving genetic alterations unidentified during single-site based genetic testing. We also provide preliminary evidence, that multitarget high-throughput sequencing of cfDNA can uncover spatially restricted subclones that play a role in disease progression in R/R FL and that pretreatment ctDNA level might have a predictive value in the relapsed setting of FL. Figure 1. Molecular alterations in FL patients with tisDNA samples from two separate lymphoma sites and a matching cfDNA. KMT2D and CREBBP variants show high conservation, yet further variants are often spatially restricted, which can be resolved by cfDNA profiling. Copy number alterations (CNA) show lower concordance, yet recurrent CNA-s can be recovered in a subset of the cases. Identical immunoglobulin heavy and light chain usage can be detected in all samples of 3 patients and in paired tisDNA in 2 patients.

Epidemiology of PAX6 Gene Pathogenic Variants and Expected Prevalence of PAX6-Associated Congenital Aniridia across the Russian Federation: A Nationwide Study.

This study investigates the distribution of PAX6-associated congenital aniridia (AN) and WAGR syndrome across Russian Federation (RF) districts while characterizing PAX6 gene variants. We contribute novel PAX6 pathogenic variants and 11p13 chromosome region rearrangements to international databases based on a cohort of 379 AN patients (295 families, 295 probands) in Russia. We detail 100 newly characterized families (129 patients) recruited from clinical practice and specialized screening studies. Our methodology involves multiplex ligase-dependent probe amplification (MLPA) analysis of the 11p13 chromosome, PAX6 gene Sanger sequencing, and karyotype analysis. We report novel findings on PAX6 gene variations, including 67 intragenic PAX6 variants and 33 chromosome deletions in the 100 newly characterized families. Our expanded sample of 295 AN families with 379 patients reveals a consistent global PAX6 variant spectrum, including CNVs (copy number variants) of the 11p13 chromosome (31%), complex rearrangements (1.4%), nonsense (25%), frameshift (18%), and splicing variants (15%). No genetic cause of AN is defined in 10 patients. The distribution of patients across the Russian Federation varies, likely due to sample completeness. This study offers the first AN epidemiological data for the RF, providing a comprehensive PAX6 variants spectrum. Based on earlier assessment of AN prevalence in the RF (1:98,943) we have revealed unexamined patients ranging from 55% to 87%, that emphases the need for increased awareness and comprehensive diagnostics in AN patient care in Russia.

Clinical Features and Outcomes in Large Granular Lymphocyte Leukemia-Associated Pure Red Cell Aplasia with STAT3 Mutation

Background Large granular lymphocyte leukemia (LGLL) is a rare disease frequently complicated with pure red cell aplasia (PRCA) [1, 2]. STAT3 mutations have been describled in 30-40% of LGLL patients [3]. The aim of this work was to evaluate whether STAT3 mutations might be associated with specific clinical features and outcomes in LGLL-associated PRCA. Methods and results From January 2016 to July 2023, 81 patients with LGLL-associated PRCA were enrolled in the China Eastern Cooperation Group for Anemia (CECGA) database (ChiCTR2100043485). As an initial step in the STAT3 mutational analysis, we screened all patients with Sanger sequencing or Next-generation sequencing (NGS). The initial dose of CsA was 3-5mg/kg/day, and the serum concentration was adjusted to be 150-200ng/mL based on adverse reactions. After 12 months of maintenance, the dosage was slowly reduced. Cyclophosphamide combined with prednisone (CP) regimen was used as a salvage therapy for patients who failed to CsA. The initial dose of cyclophosphamide and prednisone were 100mg/day and 0.5-1mg/kg/day, respectively. Among the 81 cases, 26% of them were positive for STAT3 mutations. The clinical characteristics of patients with or without STAT3 mutation were summarized in Table 1. Patients with STAT3 mutations had a higher reticulocyte percentage (0.88% vs 0.28%, P=0.039) and red cell distribution width-coefficient of variation (18.8% vs 15.8%, P=0.008) than patients without STAT3 mutations. Y640F mutation were found in 9 of 21 cases. Subgroup analysis showed that patients with Y640F mutation were associated with younger age (44 vs 65 years old, P=0.007) and higer lymphocyte percentage in peripheral blood (63.7% vs 34.4%, P=0.033). Deep sequencing of rearranged T-cell receptor Vβ complementarity-determining region 3 by NGS was conducted in 61 patients. The predominant V-gene of LGLL clonotypes belonged to the TRBV06 family gene was detected in 12 (25%) patients. The expression of TRBV06 family gene was a litter lower in patients with STAT3 mutation than non-mutant groups (8% vs 31%, P=0.189). The complete response rate (CRR) [31% (5/16) vs 33% (19/58), P=0.909] and overall response rate (ORR) [56% (9/16) vs 50% (29/58), P=0.658] of cyclosporine (CsA) treatment were similar in patients with STAT3 mutations or not. In STAT3 mutant group, the CRR [54% (7/13) vs 31% (5/16), P=0.274] and ORR [85% (11/13) vs 56% (9/16), P=0.130] of CP regimen tended to be better than CsA . 6 patients (67%) relapsed among the 9 patients who responded to CsA in STAT3 mutant group. In patients without STAT3 mutation, 19 of 29 (66%) CsA-responders relapsed. There was no siginificant difference in the relapse-free survival between the two group (Figure 1). Discussion/Conclusions In summary, STAT3 mutation was frequently recognized in LGLL-associated PRCA, and the hotspot site was Y640F. Patients with STAT3 mutations responded to CsA as well as those without the mutation. CP regimen could be used as a salvage therapy for patients who failed to CsA. Reference 1. Balasubramanian SK, Sadaps M, Thota S, et al. Rational management approach to pure red cell aplasia. Haematologica. 2018, 103(2): 221-230. 2. Wu X, Cheng L, Liu X, et al. Clinical characteristics and outcomes of 100 adult patients with pure red cell aplasia. Ann Hematol. 2022, 101(7):1493-1498. 3. Barilà G, Teramo A, Calabretto G, et al. Stat3 mutations impact on overall survival in large granular lymphocyte leukemia: a single-center experience of 205 patients. Leukemia. 2020, 34: 1116-1124.

Statistical model of synchronized cooperative motion in glass-forming liquids

This paper presents a theoretical framework describing the tendency for synchronized positional rearrangements of any two structural species in a multicomponent glass-forming liquid. Such correlated motions are especially important as the glass-forming liquid approaches the glass transition. It is established that the expected cage-breaking probability of a structural unit is proportional to the dynamical propensity of the structural unit calculated via the isoconfigurational ensemble method. This theoretical framework supports the notion that spatial heterogeneities in composition result in dynamical heterogeneities, enabled by synchronized positional rearrangements. Using this model, an alkali borosilicate glass is investigated as an example, and results indicate that structural species with large differences in enthalpy might inhibit the expansion of cooperative rearranging regions and increase the number of such regions. The physical impact on relaxation time distribution and configurational entropy are also discussed.

Exploring the Relationship between Fusion Genes and MicroRNAs in Cancer.

Fusion genes are key cancer driver genes that can be used as potential drug targets in precision therapies, and they can also serve as accurate diagnostic and prognostic biomarkers. The fusion genes can cause microRNA (miRNA/miR) aberrations in many types of cancer. Nevertheless, whether fusion genes incite miRNA aberrations as one of their many critical oncogenic functionalities for driving carcinogenesis needs further investigation. Recent discoveries of miRNA genes that are present within the regions of genomic rearrangements that initiate fusion gene-based intronic miRNA dysregulation have brought the fusion genes into the limelight and revealed their unexplored potential in the field of cancer biology. Fusion gene-based 'promoter-switch' event aberrantly activate the miRNA-related upstream regulatory signals, while fusion-based coding region alterations disrupt the original miRNA coding loci. Fusion genes can potentially regulate the miRNA aberrations regardless of the protein-coding capability of the resultant fusion transcript. Studies on out-of-frame fusion and nonrecurrent fusion genes that cause miRNA dysregulation have attracted the attention of researchers on fusion genes from an oncological perspective and therefore could have potential implications in cancer therapies. This review will provide insights into the role of fusion genes and miRNAs, and their possible interrelationships in cancer.

Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa.

The origin of new genes has long been a central interest of evolutionary biologists. However, their novelty means that they evade reconstruction by the classical tools of evolutionary modelling. This evasion of deep ancestral investigation necessitates intensive study of model species within well-sampled, recently diversified, clades. One such clade is the model genus Neurospora, members of which lack recent gene duplications. Several Neurospora species are comprehensively characterized organisms apt for studying the evolution of lineage-specific genes (LSGs). Using gene synteny, we documented that 78% of Neurospora LSG clusters are located adjacent to the telomeres featuring extensive tracts of non-coding DNA and duplicated genes. Here, we report several instances of LSGs that are likely from regional rearrangements and potentially from gene rebirth. To broadly investigate the functions of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co-regulatory modules using Weighted Gene Correlation Network Analysis, revealing that LSGs are widely but peripherally involved in known regulatory machinery for diverse functions. The ancestral status of the LSG mas-1, a gene with roles in cell-wall integrity and cellular sensitivity to antifungal toxins, was investigated in detail alongside its genomic neighbours, indicating that it arose from an ancient lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes. Our discoveries illuminate a "rummage region" in the N. crassa genome that enables the formation of new genes and functions to arise via gene duplication and relocation, followed by fast mutation and recombination facilitated by sequence repeats and unconstrained non-coding sequences.

Analysis of copy number variation in AZF region of Y chromosome in patients with spermatogenic failure

To explore the characteristics of copy number variation (CNV) within the Y chromosome azoospermia factor (AZF) region in patients with spermatogenesis disorders in the Shenzhen area. A total of 123 patients with spermatogenesis disorders who had visited Shenzhen People's Hospital from January 2016 to October 2022 (including 73 patients with azoospermia and 50 patients with oligozoospermia) and 100 normal semen males were selected as the study subjects. The AZF region was detected with multiplex ligation-dependent probe amplification (MLPA), and the correlation between the CNV in the AZF region and spermatogenesis disorders was analyzed using the chi-square test or Fisher's exact test. 19 CNV were detected among 53 patients from the 223 samples, including 20 cases (27.40%, 20/73) from the azoospermia group, 19 cases (38%, 19/50) from the oligozoospermia group, and 14 cases (14%, 14/100) from the normal control group. In the azoospermia, oligozoospermia, and normal control groups, the detection rates for CNV related to the AZFa region (including AZFab and AZFabc) were 5.48% (4/73), 2.00% (1/50), and 0 (0/100), respectively. The detection rates for the AZFb region (including the AZFbc region) were 6.85% (5/73), 0 (0/50), and 0 (0/100), respectively. The detection rates for gr/gr deletions in the AZFc region were 2.74% (2/73), 6.00% (3/50), and 9.00% (9/100), respectively, and those for b2/b4 deletions in the AZFc region were 2.74% (2/73), 10.00% (5/50), and 0 (0/100), respectively. The detection rates for complex rearrangements in the AZFc region were 6.85% (5/73), 18.00% (9/50), and 3.00% (3/100), respectively. Statistical analysis showed no significant difference in the detection rate of gr/gr deletions between the three groups (Fisher's Exact Test value = 2.712, P = 0.249); the differences in the detection rate of b2/b4 deletions between the three groups were statistically significant (Fisher's Exact Test value = 9.489, P = 0.002); the differences in the detection rate of complex rearrangements in the AZFc region between the three groups were statistically significant (Fisher's Exact Test value = 9.493, P = 0.006). In this study, a rare AZFa region ARSLP1 gene deletion (involving SY86 deletion) was detected in a patient with oligozoospermia. CNV in the AZFa and AZFb regions have a severe impact on spermatogenesis, but partial deletion in the AZFa region (ARSLP1 gene deletion) has a minor impact on spermatogenesis. The b2/b4 deletion and complex rearrangement in the AZFc region may be risk factors for male infertility. The gr/gr deletion may not serve as a risk factor for male infertility in the Shenzhen area.

Optimization of cooling condition and energy parameters during laser bending of Duplex-2205

ABSTRACT In this study, the impact of process parameters on bend angle was explored under varying cooling conditions. Optimization of process parameters and cooling conditions was performed to maximize bend angle with minimum energy input. A regression fit function was generated and experimentally validated, and the mechanical and metallurgical properties at the optimum condition were analyzed. The study revealed that forced cooling at the lower surface significantly improved the bend angle, achieving a 35.2% increase compared to natural cooling. Process parameters were found to have varying effects at different cooling conditions. Optimization using Pareto front optimality and genetic algorithm resulted in a 7.5% increase in bend angle and a 22.14% improvement in bend angle per line energy rate. The tensile strength and hardness of the bend specimen at the optimum condition were increased at the expense of ductility, attributed to phase distribution rearrangement in the laser irradiation region.

In Situ Spatial Analysis of Metabolic Heterogeneity in Single Living Tumor Spheroids Using Nanocapillary-Based Electrospray Ionization Mass Spectroscopy.

Spatial metabolomic analysis of individual tumor spheroids can help investigate metabolic rearrangements in different cellular regions of a spheroid. In this work, a nanocapillary-based electrospray ionization mass spectroscopy (ESI-MS) method is established that could realize the spatial sampling of cellular components in different regions of a single living tumor spheroid and the subsequent MS analysis for a metabolic study. During the penetration of the nanocapillary into the spheroid for sampling, this "wound surface" at the outer layer of the spheroid takes only 0.1% of the whole area that maximally maintains the cellular activity inside the spheroid for the metabolic analysis. Using the ESI-MS analysis, different metabolic activities in the inner and outer (upper and lower) layers of a single spheroid are revealed, giving a full investigation of the metabolic heterogeneity inside one living tumor spheroid for the first time. In addition, the metabolic activities between the outer layer of the spheroid and two-dimensional (2D)-cultured cells show obvious differences, which suggests more frequent cell-cell and cell-extracellular environment interactions during the culture of the spheroid. This observation not only establishes a powerful tool for the in situ spatial analysis of the metabolic heterogeneity in single living tumor spheroids but also provides molecular information to elucidate the metabolic heterogeneity in this three-dimensional (3D)-cultured cell model.

1684-P: Transgene Integration-Induced Genomic Rearrangement in a Noncoding Region of Chromosome 1 Leads to Spontaneous Obesity and Type 2 Diabetes in Mice

Obesity is a critical risk factor for type 2 diabetes (T2D) and has become a global health issue. We found that a mouse line (C57/B6J) of Floxed-stop over expression of IF1 (ATPase Inhibitory Factor 1) (hereon called FEI) develops spontaneous obesity without induction of transgenic expression. Targeted-Locus-Amplification (TLA) analyses revealed a rearrangement in upstream sequences of the transgene integration site, and a duplication downstream in a non-coding region of chromosome 1. Male and female FEI mice show early dyslipidemia before weight gain at two months, reaching 50-60 grams at 6-8 months. Body composition revealed FEI mice have markedly increased fat mass and modestly increased lean mass, consistent with morphometric findings of substantially increased peripheral fat pads. FEI mice were hyperphagic. When subjected to pair-feeding, they reverted to comparable WT body weight levels, then gained weight again when fed ad libidum. Adult FEI mice maintain comparable physical activity levels to their WT counterparts, but indirect metabolic levels among FEI mice declined. These mice exhibited glucose and insulin tolerance at six weeks of age, as well as hyperglycemia, hyper-insulinemia, and hyper-leptinemia. Histology H&E staining revealed markedly enlarged adipocytes with crown-like structures on visceral white adipose tissue sections, and increased fat deposition in liver sections. RNAseq analyses from subcutaneous white adipose tissues of 5-month-old FEI mice demonstrate upregulation of adipogenic and inflammatory genes. Isolated FEI preadipocytes exhibited increased proliferation but impaired lipid deposition. RT-PCR revealed upregulation of inflammatory genes (IFI202b, TNF-α, and IL6). Together, we show FEI mice are a novel obese mouse model. Preclinical studies using this model may help yield insights into novel pathogenic mechanisms and effective treatments for obesity. Disclosure D.White: None. S.Alahari: None. E.D.Lazartigues: None. Q.Yang: None. J.Wu: None. S.Kang: None. L.Lauterboeck: None. P.Mobasheran: None. F.Paliarin: None. T.Nguyen: None. M.Elgazzaz: None. R.Maiya: None. Funding American Diabetes Association (1-17-IBS-184 to Q.Y.)

Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions.

DNA inverted repeats (IRs) are widespread across many eukaryotic genomes. Their ability to form stable hairpin/cruciform secondary structures is causative in triggering chromosome instability leading to several human diseases. Distance and sequence divergence between IRs are inversely correlated with their ability to induce gross chromosomal rearrangements (GCRs) because of a lesser probability of secondary structure formation and chromosomal breakage. In this study, we demonstrate that structural parameters that normally constrain the instability of IRs are overcome when the repeats interact in single-stranded DNA (ssDNA). We established a system in budding yeast whereby>73 kb of ssDNA can be formed in cdc13-707fs mutants. We found that in ssDNA, 12 bp or 30 kb spaced Alu-IRs show similarly high levels of GCRs, while heterology only beyond 25% suppresses IR-induced instability. Mechanistically, rearrangements arise after cis-interaction of IRs leading to a DNA fold-back and the formation of a dicentric chromosome, which requires Rad52/Rad59 for IR annealing as well as Rad1-Rad10, Slx4, Msh2/Msh3 and Saw1 proteins for nonhomologous tail removal. Importantly, using structural characteristics rendering IRs permissive to DNA fold-back in yeast, we found that ssDNA regions mapped in cancer genomes contain a substantial number of potentially interacting and unstable IRs.

The brittle-to-ductile transition in aluminosilicate glasses is driven by topological and dynamical heterogeneity

Amorphous materials can exhibit varying degrees of nanoscale ductility depending on their atomic structure. Despite its critical importance for applications, the physical origin that controls ductility remains largely unknown. Here, by using molecular dynamics simulations, we investigate the ductile-to-brittle transition of oxide glasses as a function of the connectivity of the atomic network. Interestingly, based on topological constraint theory, we show that the structural origin of the ductile-to-brittle transition is the rigidity transition caused by the percolation of stressed-rigid atomic clusters. Our further analysis of four-point correlation functions reveals that, similar to the case of supercooled liquids, the plastic dynamics of oxide glasses at room temperature are strongly correlated and spatially heterogeneous. Surprisingly, the dynamical length scale of plastic events significantly decreases when the stressed-rigid cluster percolates, resulting in a narrower transient plastic rearrangement region. These results provide physical insights into the relationship between the topological features of atomic structure, fracture behavior, and stress-induced dynamical heterogeneity of glasses.