Multiple Repeats Research Articles

Sleep patterns, global mental status and mortality risk among middle-aged urban adults.

Sleep, cognition, and mortality may be interdependent. We explored paths between sleep, cognition and mortality and potential interactions. The study examines the relationship among sleep, global mental status, and mortality risk using data from 1364 participants from the Healthy Aging in Neighborhood of Diversity across the Life Span (HANDLS) study. We used Cox proportional hazards models and four-way decomposition models to analyze sleep patterns and global mental status. After a median time at risk of 8.2 years, 172 deaths occurred, with rate of 16 per 1000 person-years. A 1-unit increase in the Pittsburgh Sleep Quality Index (PSQI) global score was linked to a 7% increase in mortality risk in the reduced model, but this effect was attenuated in the full model. In both reduced and fully adjusted models, the PSQI global score and sleep quality domains interacted with global mental status, with poor sleep generally associated with mortality risk in the group with better global mental status at first-visit. In four-way decomposition models, total effects (TE) of PSQI scores on mortality risk were positive and statistically significant, while being mostly controlled direct effects. However, among women, the inverse TE of global mental status on mortality risk was partially mediated by PSQI sleep latency and the PSQI global. Poor global mental status is associated with greater mortality risk at better sleep quality levels and vice versa. Further longitudinal studies with multiple sleep and cognitive performance repeats are needed to corroborate these findings.

The Challenge of Bacterial Strain Identification: Leptospira interrogans Serovars Australis in a Dog and Long-Term Clinical Follow-Up

Leptospirosis is a widespread disease throughout the world, presenting in severe clinical forms in dogs. The pathogenicity of the different serovars in field infections is not fully documented, and clinical diagnosis is often limited to a combination of serological tests and molecular analyses. The latter, although a fundamental tool, cannot identify the infecting strain without further analysis. This study reports the use of various indirect (microscopic agglutination test, MAT) and direct (microbiological culture, real-time PCR) laboratory techniques, followed by typing protocols (Multi-locus Sequence Typing (MLST), Multiple Loci Variable number tandem repeat Analysis (MLVA), serotyping) that allowed for the identification of the Leptospira serovar Australis in a symptomatic and previously vaccinated dog (vaccine containing heterologous strains). This study reports long-term clinical follow-up (0–640 days) and describes the possible role of the infection in the development of chronic renal failure. This study aims to highlight how a combination of different techniques can be useful to better characterise the environmental circulation of zoonotic agents. Therefore, the identification and isolation of circulating L. strains would facilitate the updating of epidemiological data, enhance the knowledge of pathogenicity and long-term clinical effects, and provide a valuable resource for improving the efficacy of a specific serovar vaccination.

Improved understanding of sequence polymorphisms at 42 Y chromosome short tandem repeats for the Chinese Han population

Y-chromosome short tandem repeat (Y-STR) is an important type of genetic markers in the human genome, widely used in molecular anthropology and forensic genetics. However, most Y-STR studies has been focused on the length-based variations resulting from differences in the number of repeat units. Less attention was paid to sequence-based Y-STR variations. Consequently, sequence-based variation characteristics of Y-STRs in Chinese populations remain insufficiently studied. In this study, targeted sequencing of 42 Y-STR loci was performed for 331 Chinese Han males (with an average sequencing depth of 612 ×), unveiling a total of 387 sequence allele types and their frequencies in the population. Repeat pattern variations were observed in seven loci containing multiple repeat units. Across all sequenced repeat and flanking regions, 46 single-nucleotide substitutions and insertion/deletion variations were identified, including 13 mutations not recorded in the dbSNP database. Twenty-seven previously unreported sequence-based alleles were identified. Additionally, differences in Y-STRs between the Chinese Han population and three American populations (African Americans, Caucasians, and Hispanics) were revealed from sequence-based data analysis. In summary, this study provides a detailed summary of the sequence features of 42 Y-STRs in the Chinese Han population, improving our understanding of Y-STRs and providing basic data of sequence variations for the application of Y-STRs.

HPB SO59 - How do Previous Biliary Interventions Affect the Operative and Postoperative Outcomes Of Patients Undergoing Laparoscopic Cholecystectomy (LC) and Bile Duct Exploration (LCBDE)?

Abstract Background Laparoscopic biliary surgery is perceived to be difficult in patients who had undergone previous biliary interventions; ERCP, cholecystostomy or cholecystectomy. Our objective was to evaluate the referral pattern, the preoperative characteristics and operative and postoperative outcomes in such patients. Method Analysis of prospectively collected data from patients treated by a specialist biliary unit dedicated to index admission LC and single session laparoscopic management of bile duct stones. In spite of a policy of no preoperative endoscopic clearance of bile duct stones the unit inevitably received some patients who had had previous ERCP at other hospitals prior to referral or were initially unfit when admitted to the base hospital and required ERCP. In a series of 6140 LC and LCBDE 158 patients (2.57%) had already undergone ERCP and 31 (0.5%) had undergone cholecystectomies (18), cholecystostomies (9) or attempted cholecystectomy. Results Of 158 pre-referral ERCPs, 130 (82.3%) were referred from other hospitals, 36 (22.8%) having had more than one ERCP. 83.5% had suspected CBD stones. LC difficulty grade was IV to V in 48.7%. 112 patients (70.9%) required LCBDE. There were 10.1% biliary related complications, 3 re-operations, one conversion and one mortality. of 31 patients with previous biliary interventions, 58% came from other units or hospitals. A third had already undergone ERCP. 61.3% had LC difficulty grades IV or V. The 18 un-cholecystectomised patients needed LCBDE with no conversions or bile duct injuries. There were only 2 (6.5%) biliary related complications. Conclusion While previous biliary interventions understandably increased the difficulty of LC they did not adversely affect operative and postoperative outcomes. Such surgery should be undertaken in the specialist setting as 70.9% of those with previous endoscopic and 58.1% of those with previous surgical or radiologically guided biliary interventions require LCBDE. Implementing definitive surgical interventions during the index admission can achieve a substantial reduction in re-admission rates, and overall decrease in hospital episodes without significant morbidity, re-interventions or mortality. This enhances the quality of life for patients who would otherwise be subjected to multiple repeat ERCPs and yields significant cost benefits.

Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7

The intrinsically disordered carboxy-terminal domain (CTD) of the largest subunit of RNA Polymerase II (RNAPII) consists of multiple tandem repeats of the consensus heptapeptide Y1-S2-P3-T4-S5-P6-S7. The CTD promotes liquid-liquid phase-separation (LLPS) of RNAPII in vivo. However, understanding the role of the conserved heptad residues in LLPS is hampered by the lack of direct biochemical characterization of the CTD. Here, we generated a systematic array of CTD variants to unravel the sequence-encoded molecular grammar underlying the LLPS of the human CTD. Using in vitro experiments and molecular dynamics simulations, we report that the aromaticity of tyrosine and cis-trans isomerization of prolines govern CTD phase-separation. The cis conformation of prolines and β-turns in the SPXX motif contribute to a more compact CTD ensemble, enhancing interactions among CTD residues. We further demonstrate that prolines and tyrosine in the CTD consensus sequence are required for phosphorylation by Cyclin-dependent kinase 7 (CDK7). Under phase-separation conditions, CDK7 associates with the surface of the CTD droplets, drastically accelerating phosphorylation and promoting the release of hyperphosphorylated CTD from the droplets. Our results highlight the importance of conformationally restricted local structures within spacer regions, separating uniformly spaced tyrosine stickers of the CTD heptads, which are required for CTD phase-separation.

Rapid growth rate of Enterobacter sp. SM3 determined using several methods

BackgroundBacterial growth rate, commonly reported in terms of doubling time, is frequently determined by one of two techniques: either by measuring optical absorption of a growing culture or by taking samples at different times during their growth phase, diluting them, spreading them on agar plates, incubating them, and counting the colonies that form. Both techniques require measurements of multiple repeats, as well careful assessment of reproducibility and consistency. Existing literature using either technique gives a wide range of growth rate values for even the most extensively studied species of bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. This work aims to apply several methods to reliably determine the growth rate of a recently identified species of Enterobacteriaceae, called Enterobacter sp. SM3, and to compare that rate with that of a well-known wildtype E. coli strain KP437.ResultsWe extend conventional optical density (OD) measurements to determine the growth rate of Enterobacter sp. SM3. To assess the reliability of this technique, we compare growth rates obtained by fitting the OD data to exponential growth, applying a relative density method, and measuring shifts in OD curves following set factors of dilution. The main source of error in applying the OD technique is due to the reliance on an exponential growth phase with a short span. With proper choice of parameter range, however, we show that these three methods yield consistent results. We also measured the SM3 division rate by counting colony-forming units (CFU) versus time, yielding results consistent with the OD measurements. In lysogeny broth at 37oC, SM3 divides every 21 ± 3 min, notably faster than the RP437 strain of E. coli, which divides every 29 ± 2 min.ConclusionThe main conclusion of this report is that conventional optical density (OD) measurements and the colony-forming units (CFU) method can yield consistent values of bacterial growth rate. However, to ensure the reproducibility and reliability of the measured growth rate of each bacterial strain, different methods ought to be applied in close comparison. The effort of checking for consistency among multiple techniques, as we have done in this study, is necessary to avoid reporting variable values of doubling time for particular species or strains of bacteria, as seen in the literature.

Description of the complete rDNA repeat unit structure of Coturnixjaponica Temminck et Schlegel, 1849 (Aves).

Ribosomal RNA (18S, 5.8S, 28S) gene clusters in genomes form regions that consist of multiple tandem repeats. They are located on a single or several pairs of chromosomes and play an important role in the formation of the nucleolus responsible for the assembly of ribosome subunits. The rRNA gene cluster sequences are widely used for taxonomic studies, however at present, complete information on the avian rDNA repeat unit structure including intergenic spacer sequence is available only for the chicken (Gallusgallusdomesticus Linnaeus, 1758). The GC enrichment and high-order repeats peculiarities within the intergenic spacer described for the chicken rDNA cluster may be responsible for these failures. The karyotype of the Japanese quail (Coturnixjaponica Temminck et Schlegel, 1849) deserves close attention because, unlike most birds, it has three pairs of nucleolar organizer bearing chromosomes, two of which are microchromosomes enriched in repeating elements and heterochromatin that carry translocated terminal nucleolar organizers. Here we assembled and annotated the complete Japanese quail ribosomal gene cluster sequence of 21166 base pairs (GenBank under the registration tag BankIt2509210 CoturnixOK523374). This is the second deciphered avian rDNA cluster after the chicken. Despite the revealed high similarity with the chicken corresponding sequence, it has a number of specific features, which include a slightly lower degree of GC content and the presence of bendable elements in the content of both the transcribed spacer I and the non-transcribed intergenic spacer.

SHANK3 depletion leads to ERK signalling overdose and cell death in KRAS-mutant cancers

The KRAS oncogene drives many common and highly fatal malignancies. These include pancreatic, lung, and colorectal cancer, where various activating KRAS mutations have made the development of KRAS inhibitors difficult. Here we identify the scaffold protein SH3 and multiple ankyrin repeat domain 3 (SHANK3) as a RAS interactor that binds active KRAS, including mutant forms, competes with RAF and limits oncogenic KRAS downstream signalling, maintaining mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) activity at an optimal level. SHANK3 depletion breaches this threshold, triggering MAPK/ERK signalling hyperactivation and MAPK/ERK-dependent cell death in KRAS-mutant cancers. Targeting this vulnerability through RNA interference or nanobody-mediated disruption of the SHANK3–KRAS interaction constrains tumour growth in vivo in female mice. Thus, inhibition of SHANK3–KRAS interaction represents an alternative strategy for selective killing of KRAS-mutant cancer cells through excessive signalling.

Monitoring Apoptosis and Myeloid Differentiation of Acridine Orange-Mediated Sonodynamic Therapy-Induced Human Promyelocytic Leukemia HL60 Cells.

In the treatment of acute myeloid leukemia (AML), conventional therapies can lead to severe side effects and drug resistance. There is a need for alternative treatments that do not cause treatment resistance and have minimal or no side effects. Sonodynamic therapy (SDT), due to its noninvasive, multiple repeatability, localized treatment feature and do not cause treatment resistance, emerges as an alternative treatment option. However, it has not received sufficient attention in the treatment of AML especially acute promyelocytic leukemia (APL). The aim of the study was to investigate the potential differentiation and antileukemic effects of acridine orange (AO)-mediated SDT on HL60 cells. Cell viability was determined by the 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT)method in the control, ultrasound, AO concentrations, and ultrasound-exposed AO concentrations groups. Transmission electron microscopy (TEM) was used to determine morphology, and flow cytometry was used to determine apoptosis, DNA cycle, cell volume, mitochondria membrane potential (Δψm), reactive oxygen species (ROS) production, and differentiation markers (CD11b and CD15) expressions. Additionally, toluidine blue staining for semithin sections was used to determine differentiation. The cytotoxicity of AO-mediated SDT on HL60 cells was significantly higher than other groups, and TEM images showed that it caused various morphological changes typical for apoptosis. Flow cytometry results showed the presence of early apoptosis, subG1 arrest, loss of Δψm, increase of intracellular ROS production, decreased cell volume, and increased expression of CD11b (1.3-fold) antigen and CD15 (1.2-fold) antigen. Data showed that AO-mediated SDT significantly induced apoptosis in HL60 cells. Increased expression of CD11b and CD15 antigens and morphological findings demonstrated that AO-mediated SDT contributes to granulocytic differentiation in HL60 cells. AO-mediated SDT has potential as an alternative treatment of APL.

CRISPR/Cas12a powered sandwich aptamer assay coupled with effective DNA self-assembly amplification for sensitive detection of immunoglobulin E

Sensitive and accurate detection of protein biomarkers is of significance for disease diagnosis. Recently, CRISPR/Cas system has emerged as a powerful signal amplifier in the field of sensing technology. We report a CRISPR/Cas12a powered sandwich aptamer assay (CAPSA) for protein analysis coupled with effective DNA self-assembly amplifications. The target protein is sandwiched between the capture antibody on the microplate and the aptamer detection probe. The aptamer is engineered with a specific initiator to trigger streptavidin (SA)-biotin-based dendritic amplification reaction, yielding a DNA polymer with multiple repeats of active DNA (acDNA) as Cas12a recognition sites. With the addition of Cas12a reporter system, the acDNA activates Cas12a to cleave DNA reporters, producing amplified fluorescence signals. Particularly, we also describe an innovative one-step DNA self-assembly amplification strategy to meet the demands for fast point-of-care testing, which can be directly integrated into the CAPSA without additional operation steps. The proposed methods were demonstrated by detecting immunoglobulin E (IgE), which plays a vital role in allergic reactions. Our proposed one-step DNA self-assembly amplified CAPSA enabled us to detect IgE as low as 0.6 pM, exhibiting high selectivity and satisfactory performance in complex sample analysis. Collectively, this method combines the efficient signal amplification of DNA self-assembly with the high trans-cleavage activity of Cas12a, offering a simple, universal, and double-amplified approach for sensitive analysis of protein biomarkers.

Altered neural recruitment despite dual task performance recovery in athletes with repeat concussion.

Sports-related concussions (SRCs) pose significant challenges to college-aged athletes, eliciting both immediate symptoms and subacute cognitive and motor function impairment. While most symptoms and impairments resolve within weeks, athletes with repeat SRCs may experience heightened risk for prolonged recovery trajectories, future musculoskeletal injuries, and long-term neurocognitive deficits. This includes impaired dual task performance and altered neurophysiology that could persist across the lifespan and elicit future pathophysiology and neurodegeneration. Thus, it is imperative to improve our understanding of neurophysiology after SRC. This study aimed to investigate the impact of repeat SRCs on dual task performance and associated neural recruitment using functional near-infrared spectroscopy (fNIRS). A total of 37 college-aged athletes (ages 18-24) participated in this cross-sectional observational study. Among these athletes, 20 had a history of two or more SRCs, while 17 had never sustained a SRC and served as controls. Participants completed the Neuroimaging-Compatible Dual Task Screen (NC-DTS) while fNIRS measured neural recruitment in the frontoparietal attention network and the primary motor and sensory cortices. Behavioral analysis revealed that athletes with repeat SRCs exhibited comparable single task and dual task performance to control athletes. Additionally, dual task effects (DTE), which capture performance declines in dual tasks versus single tasks, did not significantly differ between groups. Notably, the cohort of athletes with repeat SRC in this study had a longer time since their last SRC (mean = 1.75 years) than majority of previous SRC studies. Neuroimaging results indicated altered neural recruitment patterns in athletes with multiple repeat SRCs during both single and dual tasks. Specifically, athletes with repeat SRCs demonstrated increased prefrontal cortex (PFC) activation during single motor tasks compared to controls (P < 0.001, d = 0.47). Conversely, during dual tasks, these same athletes exhibited reduced PFC activation (P < 0.001, d = 0.29) and primary motor cortex (M1) activation (P = 0.038, d = 0.16) compared to their single task activation. These findings emphasize the complex relationship between SRC history, dual task performance, and changes in neurophysiology. While athletes with repeat SRCs demonstrate recovery in behavioral dual task performance, persistent alterations in neural recruitment patterns suggest ongoing neurophysiological changes, possibly indicating compensatory neural strategies and inefficient neural resource allocation, even beyond symptom resolution and medical clearance. Understanding the compensatory neural recruitment strategies that support behavioral performance following repeat SRCs can inform return-to-play decisions, future musculoskeletal injury risk, and the long-term impact of SRCs on neurocognitive function.

Incremental Efficacy for Repeat Ablation Procedures for Catheter Ablation of Atrial Fibrillation: 5-Year Follow-Up

BackgroundCatheter ablation atrial fibrillation (AF) is effective, but 20% to 40% of patients will require a repeat ablation. The role of more than 1 repeat ablation is not well known. ObjectivesThe purpose of this study was to evaluate the effectiveness and incremental benefits of multiple repeat catheter ablations to treat AF in patients. MethodsWe retrospectively included patients who underwent their first, second, third, and fourth AF ablation between 2004 and 2019. They were monitored with a 24-to-48-hour Holter every 3 months postablation the first year and every 6 to 12 months thereafter. Recurrence was defined as documented atrial arrhythmia >30 seconds. Outcomes are analyzed by Kaplan-Meier curves and compared by log rank test. ResultsWe included a total of 2,194 patients (64% with paroxysmal and 36% with nonparoxysmal AF). Mean age was 71 ± 10 years; 67% were male. After 1 ablation, freedom from AF was 52%. Among those 1,052 patients who had recurrences, 576 (55%) underwent a second ablation, 103 (10%) underwent a third procedure, and 20 (2%) underwent a fourth. Success rates for the second, third, and fourth ablation were 57%, 60%, and 40%, respectively, at 5-year follow-up. After the second ablation, freedom from AF in our entire cohort increased from 52% to 66%, with marginal changes after the third (67%) and fourth (67%) procedures. ConclusionsAlthough repeated ablations demonstrated significant benefits at the individual level, the success rate may drop off after a third. The overall success of the initial cohort was not significantly influenced by the success rates of multiple follow-up ablations.

Poly-GR repeats associated with ALS/FTD gene C9ORF72 impair translation elongation and induce a ribotoxic stress response in neurons.

Hexanucleotide repeat expansion in the C9ORF72 gene is the most frequent inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansion results in multiple dipeptide repeat proteins, among which arginine-rich poly-GR proteins are highly toxic to neurons and decrease the rate of protein synthesis. We investigated whether the effect on protein synthesis contributes to neuronal dysfunction and degeneration. We found that the expression of poly-GR proteins inhibited global translation by perturbing translation elongation. In iPSC-differentiated neurons, the translation of transcripts with relatively slow elongation rates was further slowed, and stalled, by poly-GR. Elongation stalling increased ribosome collisions and induced a ribotoxic stress response (RSR) mediated by ZAKα that increased the phosphorylation of the kinase p38 and promoted cell death. Knockdown of ZAKα or pharmacological inhibition of p38 ameliorated poly-GR-induced toxicity and improved the survival of iPSC-derived neurons from patients with C9ORF72-ALS/FTD. Our findings suggest that targeting the RSR may be neuroprotective in patients with ALS/FTD caused by repeat expansion in C9ORF72.

Microbial Forensics: Comparison of MLVA Results According to NGS Methods, and Forensic DNA Analysis Using MLVA

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled &lt;i&gt;in silico&lt;/i&gt; anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General’s Mechanism(UNSGM)’s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were &lt;i&gt;B. anthracis&lt;/i&gt; through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of &lt;i&gt;B. anthracis&lt;/i&gt; were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of &lt;i&gt;B. anthracis&lt;/i&gt;, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as &lt;i&gt;B. anthracis&lt;/i&gt; strain A4564 which is associated with injectional anthrax isolates in heroin users.

Outcomes of Painful Hips After Hip Arthroscopy Surgery for Femoroacetabular Impingement.

The benefits of hip arthroscopic surgery for femoroacetabular impingement are well-established. Hip arthroscopic surgery rates have risen dramatically over the last decade. Some patients, however, may continue to experience hip symptoms after surgery and are dissatisfied with their inability to return to desired optimal activity levels. The purpose of the study is to understand the long-term outcomes of patients with painful hips after hip arthroscopy for femoroacetabular impingement. This is a retrospective study of the outcomes of painful hips after hip arthroscopy for femoroacetabular impingement, with four to 14-year follow-up from 2008 to 2022. A total of 84 hip arthroscopies were performed. Most of the patients had labral tear debridement and shaving of the aspherical femoral head also known as cam lesion, and five patients had repair for labral tear. There were eight patients who had bilateral hip involvement. There were 27 men and 57 females between the second to fifth decades. The electronic patient's records and radiological images were reviewed, and patient outcomes were graded as pain-free hip (asymptomatic) or painful hip (persistent pain and symptoms of instability). After hip arthroscopy surgery, 55% (46) of hips were graded pain-free in patients who were mostly in their 20s and 30s, while 45% (38) of hips had persistent pain. These patients were in their third or fifth decade. In the painful hip cohort, 33 patients had one hip arthroscopic surgery, while five patients had multiple repeat hip arthroscopies in the same hip over a three to six-year period. Bilateral hip arthroscopies were performed at different times in eight patients of which five individuals experienced painful hip outcomes. There were seven females and one male in their 30s and 40s. The labral tear was repaired in five patients, and two patients had painful hip outcomes. Both were females in their 20s and 30s. Patients with chronic painful hips after hip arthroscopic surgery were investigated to identify the cause of the pain. If no cause was established, then they were finally referred to pain specialist clinicians for pain management. This cohort had seven patients between 28 and 43 years. Six were female and one was male. Total hip replacement (THR) was performed in four patients (4.7%). Conversely, 95.3% of patients did not need THR during the study period of 14 years. Hip arthroscopy can be an effective treatment for femoroacetabular impingement. Careful patient selection and a holistic approach are vital for a good patient outcome. The success rate of the pain-free hip after hip arthroscopy decreases with increasing age of the patient, particularly in the female gender.Patients with grade II and more degenerative chondral changes do not perform well. Patients in their fourth and fifth decade can benefit from hip arthroscopy provided a comprehensive discussion of the expected outcomes is conducted prior to surgery. Overall, hip arthroscopy remains a valuable tool, but it is important to be conscious of its limitations and potential challenges.

Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination

Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.

Multiple locus variable number tandem repeat analysis genotype polymorphism of Bacillus anthracis in China

Objective: To analyze the multiple locus variable number tandem repeat analysis (MLVA) genotype polymorphism of Bacillus (B.) anthracis and establish a MLVA genotype database of B. anthracis in China. Methods: B. anthracis strains isolated from different sources in China since 1947 were collected. Genotype identification was carried out using the MLVA15 genotyping protocol based on 15 variable number tandem repeat loci. The genotypes were uniformly numbered and named. The distribution characteristics of the MLVA genotypes of strains were analyzed. Software Bionumerics was used to construct clustering diagrams to analyze the genetic relationships. Results: The MLVA15 clustering analysis subdivided the isolates into 4 major groups and 91 genotypes, 54 of which were unique to China. The genotypes from MLVA15-CHN1 to MLVA15-CHN6 were widely distributed throughout China and in all eras, while other genotypes were restricted to certain regions or eras. Conclusions: This study established a MLVA genotype database of B. anthracis, which provides basis for the understanding of MLVA genetic polymorphisms and the control and molecular source tracing of the anthrax outbreaks in China.

Molecular epidemiology and genomic features of Bordetella parapertussis in Shanghai, China, 2017-2022.

Pertussis is a highly contagious respiratory illness mainly caused by Bordetella pertussis (BP). Bordetella parapertussis (BPP) can induce symptoms compatible with pertussis, but has been underdiagnosed and underreported. The current pertussis vaccines offer low protection against BPP. Herein, we aim to reveal the epidemiology and genomic evolution of BPP in Shanghai, China. Children diagnosed with BPP infection from January 2017 to December 2022 in Shanghai, China were enrolled. We performed antimicrobial susceptibility testing (AST), multiple locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing (WGS) analysis. A total of 260 international BPP genomes were chosen for comparison to investigate the genomic diversity and phylogenetic characteristics of Chinese strains within a global context. Sixty patients were diagnosed with BPP infection by culture, with the positive ratio of 3.5‰ (60/17337) for BPP in nasopharyngeal swap samples. The average age of patients was 4.5 ± 0.3 years. BPPs contained four MLVA types including MT6 (65.0%), MT4 (26.7%), untype-1 (6.7%) and MT5 (1.7%), and none of strains showed resistance to macrolides. All strains carried virulence genotype of ptxP37/ptxA13/ptxB3/ptxC3/ptxD3/ptxE3/fim2-2/fim3-10. MT4 and MT5 strains carried prn54, whereas MT6 and untype-1 BPPs expressed prn101. We identified two outbreaks after 2020 caused by MT4 and MT6 strains, each corresponding to distinct WGS-based phylogenetic lineages. The MT4-lineage is estimated to have originated around 1991 and has since spread globally, being introduced to China between 2005 and 2010. In contrast, the MT6-lineage was exclusively identified in China and is inferred to have originated around 2002. We revealed the genomic diversity of BPPs circulating in Shanghai, China, and reported the outbreaks of MT6 and MT4 BPPs after 2020. This is the first report on the emergence and regional outbreak of MT6 BPPs in the world, indicating that continuous surveillance on BPPs are thus required.

Applying auxiliary arrays for mainlobe blanking to counter mainlobe repeater jamming

Mainlobe repeater jamming exploits mainlobe gain of radar antenna and signal-processing gain to significantly disrupt the target detection performance of radar. The combination of multiple auxiliary radars to form a distributed array radar improves the radar system’s angle resolution, enabling the realization of traditional spatial jamming cancellation. However, the jamming cancellation method struggle to effectively suppress multiple mainlobe repeater jamming signals when their number exceeds that of auxiliary radars, resulting in pattern distortion and subsequent loss of target energy. To address this issue, the mainlobe blanking method with auxiliary radars is proposed based on the specific characteristics of the jamming signals being distributed in multiple discontinuous peaks at the same angle. This approach leverages the superior angular resolution to accurately differentiate between target and jamming signals based on their distance-angle characteristics. Moreover, specific jamming suppression methods are employed for each jamming signal based on whether it overlaps with the target in the time domain, minimizing the loss of target energy. Furthermore, the proposed method is capable of suppressing jamming even when the target and jamming signals overlap in the time domain, and is not constrained by the number of auxiliary radars available. Simulations and experiments are used to validate the effectiveness and correctness of the proposed method in suppressing mainlobe repeater jamming.

Ultrahigh stable heterometallic InCo-organic framework for efficiently catalyzing cycloaddition of CO2 with epoxides and Knoevenagel condensation

Due to versatile applications and fascinating topologies of heterometallic MOFs, developing new functional frameworks is of great significance and a great challenge. Inspired by this, we target to assemble rarely reported d-p heterometallic MOFs by using 4,4′-(4-(4-carboxyphenyl)pyridine-2,6-diyl)diisophthalic acid (H5CPPDA) as the organic linker, whose N and O donors have different affinities to d and p ions according to the soft-hard theory. Herein, a highly robust nanochannel-based InCo-organic framework of [InCo(CPPDA)(H2O)]·4DMF·6H2O}n (NUC-85) was successfully achieved under the acidic solvothermal condition. In the host framework of NUC-85, the ligand of CPPDA5− utilizes its five deprotonated carboxyl groups with three kinds of coordination modes (μ1-η1:η1, μ2-η1:η1 and μ3-η2:η1) as well as pyridine to combine In3+ and Co2+ ions into scarcely reported one-dimensional chains of [InCo(COO)5(H2O)]n, six of which are further arranged into hexagonal nano-channels (aperature ca. 14.5 Å). After thermal activation, the inner surface of channels in NUC-85a is functionalized by open metal sites of octa-coordinated In3+ and penta-coordinated Co2+ ions. Performed experiments prove that NUC-85a is an excellent heterogeneous catalyst for the cycloaddition of CO2 with epoxides under the mild conditions. Moreover, the Knoevenagel condensation with benzaldehyde and malononitrile as substrates can be efficiently catalyzed by NUC-85a. In the above two kinds of organic reactions, NUC-85a displays the satisfied chemical stability, high selectivity and multiple repeatability. This research demonstrates that nanostructure-based heterometallic MOFs have a bright future as a catalyst for Lewis acid/base supported organic reactions because of their congenital advantages such as sufficient active sites, high stability and convenient recyclability.