Low Copy Research Articles

Copy number variations at the Rhg1 locus and their relationship with resistance to soybean cyst nematode (Heterodera glycines)

Soybean cyst nematode (SCN, Heterodera glycines) is a devastating pest affecting soybean production worldwide. Host resistance is one of the primary practices used to manage SCN. The Rhg1 locus contributes to the strong and effective SCN resistance, with resistance levels predominantly governed by copy number variations (CNVs) and, to lesser extent, sequence variations. This study assessed the host resistance of 100 soybean breeding lines to SCN populations HG type 2.5.7 (S1) and HG type 7 (S2). Two controlled growth chamber experiments involved inoculating plants with 2,000 SCN eggs and juveniles, followed by counting SCN white females and calculating the female index (FI) to classify resistance responses. To determine CNVs at the Rhg1, a SYBR Green-based quantitative PCR (qPCR) assay was optimized and validated using 12 soybean accessions with known copy numbers. The qPCR assay demonstrated 94.36% efficiency for the target gene at Rhg1 locus, Glyma18g02590, with copy number detected by the assay correlating strongly (r=0.994) with whole genome sequencing data in previous study. Copy number of each line was determined using 2−ΔΔCq method relative to Williams 82 (single copy) and correlated with the resistance response. One line, ND20-16996(GT) was resistant (FI<10%) to S2 in both runs, while none were resistant to S1. Copy number among the breeding lines ranged from 1 to 11, with higher copy numbers correlating negatively with female index, indicating greater resistance. The breeding lines with copy number ≥ 9 were either resistant or moderately resistant to S2, and mostly moderately resistant to S1, with few being moderately susceptible (FI=30 to <60%). The lines with low copy numbers (≤3) were mostly susceptible (FI≥60%) to S1, while moderately susceptible or susceptible to S2. These results show the importance of Rhg1 CNVs in determining levels of SCN resistance and selecting resistant soybean lines.

T-SRE: Transformer-based semantic Relation extraction for contextual paraphrased plagiarism detection

Plagiarism has become a pervasive issue in academics and professionals to safeguard academic integrity and intellectual property rights. The escalating sophistication of plagiarized content through semantic manipulation and structural reorganization poses significant challenges to existing detection systems that rely primarily on lexical similarity measures. The proposed T-SRE (Transformer-based Semantic Relation Extraction), a novel framework addresses the limitations of traditional n-gram and string-matching approaches by leveraging deep semantic analysis. The proposed framework combines Dependency Parsing (DP) for syntactic relationship mapping and Named Entity Recognition (NER) for contextual entity identification, augmented by a transformer-based neural network that captures long-range contextual dependencies. This learning methodology incorporates three key components: a position-aware word reordering algorithm, Levenshtein distance metric for structural similarity, and contextual word embeddings for semantic preservation detection. The proposed T-SRE enhances text structure recognition by combining position-aware reordering with semantic preservation through ensemble learning. The system implements a hierarchical classification scheme that quantifies plagiarism severity through a four-tier taxonomy: heavy, low, non-plagiarized and verbatim copy. The Udacity benchmark dataset showcases the model’s superior detection capabilities, achieving 92% precision, 89% recall, and an F1-score of 90.5%, particularly in lightweight textual modifications.The framework achieves a granularity score of 1.28, outperforming existing approaches.

Abstract A035: A real-time PCR method for the detection of cancer-specific methylation patterns in cfDNA

Abstract Non-invasive liquid biopsy tests are proving to be the next frontier in cancer diagnostics with methylation emerging as a reliable biomarker for low levels of circulating tumor DNA (ctDNA). There is a rising interest in sensitive, low-cost liquid biopsy assays to detect low copies of hypermethylated ctDNA in an excess background of non-cancer-associated hypomethylated cell- free DNA (cfDNA). Real-time quantitative methylation-specific PCR (qMSP) allows for the detection of low abundance methylated fragments. qMSP approaches have previously been developed but are predominantly designed to target a specific CpG site. To date we are not aware of any qMSP approaches that target pan-cancer-associated methylation patterns across multiple CpG sites. Harbinger Health has developed a qMSP method with locked nucleic acid (LNA) blockers that target methylation haplotypes, allowing for multiplex enrichment and quantification of cancer-specific methylation patterns. Using targeted bisulfite sequencing, we identified ten pan-cancer-informative CpG-dense regions which showed consistent contiguous elevated methylation states in cancer cfDNA and low levels of methylation in non-cancer cfDNA. We designed qMSP assays for these regions and LNA blockers which bind to unmethylated target CpG sites, outcompeting the hydrolysis probe through a high Tm differential. This prevented non-specific probe hybridization. The qMSP-LNA assays were evaluated in simplex and multiplex using cell line DNA in a titration of hypermethylated “ctDNA” spiked into hypomethylated “cfDNA” to simulate varying ctDNA levels, and then validated with cancer and non-cancer cfDNA samples at 5 ng input, equivalent to 1450 haploid copies. The percentage of methylated DNA was estimated by the ratio of methylated copies (qMSP-LNA) to total copies (internal reference), which were quantified by standard curves. The qMSP-LNA assays detected low abundance methylated DNA fragments down to 23 target copies. LNA blockers completely depleted background signal originating from unmethylated DNA with high specificity, showing no inhibition of methylated DNA detection. When tested in cfDNA samples which varied in conversion efficiency, discordant methylation states, and methylation abundance, the assays reproducibly amplified and detected highly methylated fragments which correspond to cancer signal. Harbinger Health has developed qMSP-LNA assays for contiguous CpG biomarkers which differentiate cancer and non-cancer samples from only ten pan-cancer-informative regions. The qMSP-LNA method detected low abundance fragments with specific methylation patterns with high specificity and sensitivity. The assay reproducibly detected methylated DNA in cfDNA samples that represent a clinically relevant range of methylation signal and will be further validated in a larger cohort of cancer and non-cancer cfDNA samples. Due to the high specificity and sensitivity, this cost-effective PCR method may provide utility and improve access for early cancer detection and monitoring. Citation Format: Emily Neaga, Caitlin Gilley, Sarah Falotico, Mayur Gurnani, Zhenyu Zhang, Jocelyn Charlton, Miguel Williams, Anthony Shuber. A real-time PCR method for the detection of cancer-specific methylation patterns in cfDNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A035.

Multiple paralogues and recombination mechanisms contribute to the high incidence of 22q11.2 Deletion Syndrome.

The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why the incidence of 22q11.2DS is much greater than that of other genomic disorders remains unknown. Short read sequencing cannot resolve the complex segmental duplicon structure to provide direct confirmation of the hypothesis that the rearrangements are caused by nonallelic homologous recombination between the low copy repeats on Chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping in LCR22 regions, we combined fiber-FISH optical mapping with whole genome (ultra-)long read sequencing or rearrangement-specific long-range PCR on 24 duos (22q11.2DS patient and parent-of-origin) comprising several different LCR22-mediated rearrangements. Unexpectedly, we demonstrate that not only different paralogous segmental duplicon but also palindromic AT-rich repeats (PATRR) are driving 22q11.2 rearrangements. In addition, we show the existence of two different inversion polymorphisms preceding rearrangement, and somatic mosaicism. The existence of different recombination sites and mechanisms in paralogues and PATRRs which are copy number expanding in the human population are a likely explanation for the high 22q11.2DS incidence.

Abstract A020: Enhanced cell-free RNA (cfRNA) recovery for liquid biopsy applications: Comparative analysis using controlled RNA samples for early and advanced cancer detection

Abstract Introduction: Extracting cfRNA from biological samples is crucial in liquid biopsy applications, particularly for detecting low-frequency mutations like KRAS G12V, essential for early cancer diagnosis and minimal residual disease (MRD) monitoring. Traditional cfRNA extraction methods involve multiple transfer steps, aliquoting, and pooling, leading to cfRNA loss and affecting mutation detection sensitivity and accuracy. The nRichDX Revolution cfTNA Max 20 kit, with its innovative nRicher cartridge, simplifies the extraction process by eliminating these extra steps, potentially enhancing yield and efficiency. This study evaluates the cfRNA recovery efficiency of the nRichDX kit compared to the Qiagen Circulating Total Nucleic Acid kit. Methods: Plasma samples (5 mL each) were spiked with RNA containing KRAS G12V mutation at concentrations ranging from 100 to 2 million copies, mimicking early-stage cancer detection and MRD monitoring, where low copy numbers represent early disease and high copy numbers reflect advanced cancer stages. cfRNA was extracted using the nRichDX and Qiagen kits, with each condition tested in triplicate. cfRNA recovery efficiency was assessed using quantitative reverse transcription PCR (qRT-PCR) to quantify KRAS G12V RNA copies recovered. High-sensitivity RNA ScreenTape Analysis was also used to evaluate cfRNA profile quality. Results: The nRichDX kit recovered significantly higher cfRNA yields than Qiagen across all concentrations. Recovery rates were consistent and reproducible, with over 70% of input RNA recovered, even at lower inputs (100 to 100,000 copies), where recovery rates were approximately 70-85%. High Sensitivity RNA ScreenTape Analysis showed a linear increase in 18S and 28S ribosomal peaks and high RNA Integrity Number (RIN) scores in nRichDX profiles. The ability to robustly recover low copy numbers is significant for early cancer detection and MRD monitoring. In contrast, the kit’s effectiveness in high copy number samples reflects its ability to monitor advanced cancer stages accurately. Conclusion: The nRichDX cfTNA kit demonstrates exceptional efficiency in cfRNA extraction from plasma samples across a broad dynamic range, from as few as 100 copies to as many as 2 million copies of the KRAS G12V mutation. Its versatility makes it suitable for various cancer detection and monitoring applications. The streamlined process offered by the nRicher cartridge minimizes sample handling and reduces cfRNA loss, enhancing performance. This translates to more accurate and sensitive detection of early-stage and high-burden mutations associated with advanced cancer. The high-quality profiles indicated by RNA ScreenTape Analysis further validate the reliability of the nRichDX kit, making it a valuable tool for liquid biopsy applications, with significant advantages in early cancer detection and monitoring disease progression. Citation Format: Nafiseh Jafari, Mayer Saidian, Jason Saenz, Andrew Dunnigan, Carlos Hernandez, Leila Aghili. Enhanced cell-free RNA (cfRNA) recovery for liquid biopsy applications: Comparative analysis using controlled RNA samples for early and advanced cancer detection [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A020.

Development of a LAMP assay for the rapid visual detection of the emerging tick-borne Songling virus

BackgroundSongling virus (SGLV) within the genus Orthonairovirus, family Nairoviridae, is an emerging tick-borne virus associated with human febrile illness. However, no rapid detection method for SGLV has been established.MethodsIn this study, four primer sets targeting the nucleocapsid protein gene of SGLV were designed for use in the LAMP assay and evaluated to identify the optimal primer set. Recombinant plasmids were constructed and utilized for assessing the sensitivity of the assay. Tacheng tick virus 1 (TcTV-1)-, Beiji nairovirus (BJNV)-, Yezo virus (YEZV)-, severe fever with thrombocytopenia syndrome virus (SFTSV)-, and tick-borne encephalitis virus (TBEV)-positive tick samples were utilized to assess the specificity. Field-collected ticks were also evaluated as biological specimens to validate the assay.ResultsA SGLV-specific LAMP assay was established with a detection limit of 1 × 10–2 copies/μl and could be visually confirmed by a color change from purple to blue in SGLV-positive samples. No cross-reactivity was observed in the detection of TcTV-1, BJNV, YEZV, SFTSV, and TBEV using the LAMP assay. In addition to the detection of the same seven high-copy numbers of SGLV as the SYBR Green quantitative RT-PCR assay within a reduced timeframe, the developed LAMP method also effectively identified an additional sample with a low copy number in the field-collected tick samples.ConclusionsWe successfully developed a sensitive, specific, and cost-effective visual method for the rapid detection of SGLV using the LAMP assay, which can be applied in pathogenesis and epidemiological surveillance studies of SGLV.Graphical

Effect of the B chromosome-located long non-coding RNAs on gene expression in maize

Using artificial chromosomes in maize breeding allows for site-specific integration of multigene stacks, effectively overcoming the limitations of conventional transgenic approaches. The maize B chromosome, which is dispensable and highly heterochromatic, has minimal impact on phenotypes at low copy numbers, making it a promising platform for engineering artificial chromosomes. However, recent studies have demonstrated that the maize B chromosome can impact gene expression and recombination on the A chromosome. Understanding the genic characteristics of the B chromosomes and their impact on gene expression is essential for their application in artificial chromosome construction. Despite advancements in elucidating how the B chromosome affects A chromosome expression, the role of long non-coding RNAs (lncRNAs) in this context remains unclear. In this study, we analyzed the RNA-seq data from leaf tissue of plants with 0 to 7 B chromosomes, identifying a total of 1614 lncRNAs, including 1516 A chromosome-located and 98 B chromosome-located lncRNAs, 72 of which are specific to the B chromosome. While A-located lncRNAs show greater dependence on the mere presence of the B chromosome, the expression of B-located lncRNAs is significantly affected by the number of B chromosomes present. Regulatory networks constructed in this study suggest that B-located lncRNAs may drive the differential expression of A chromosome-located transcription factors and genes associated with circadian rhythm regulation, indicating their regulatory role in A chromosome gene expression.

Cumulative effects of mutation accumulation on mitochondrial function and fitness

The impact of mutations on the mitochondria deserves specific interest due to the crucial role played by these organelles on numerous cellular functions. This study examines the effects of repeated bottlenecks on mitochondrial function and fitness. Daphnia pulex mutation accumulation lines (MA) lines were maintained for over 120 generations under copper and no copper conditions. Following the MA propagation, Daphnia from MA lines were raised under optimal and high temperatures for two generations before assessing mitochondrial and phenotypic traits. Spontaneous mutation accumulation under copper led to a later age at maturity and lowered fecundity in the MA lines. Mitochondrial respiration was found to be 10% lower in all mutation accumulation (MA) lines as compared to the non-MA control. MtDNA copy number was elevated in MA lines compared to the control under optimal temperature suggesting a compensatory mechanism. Three MA lines propagated under low copper had very low mtDNA copy number and fitness, suggesting mutations might have affected genes involved in mtDNA replication or mitochondrial biogenesis. Overall, our study suggests that mutation accumulation had an impact on life history traits, mtDNA copy number, and mitochondrial respiration. Some phenotypic effects were magnified under high temperatures. MtDNA copy number appears to be an important mitigation factor to allow mitochondria to cope with mutation accumulation up to a certain level beyond which it can no longer compensate.

Status of sperm mitochondrial functions and DNA methylation in infertile men with clinical varicocele before and after treatment

Varicocele has been associated with reduced male fertility potential. Treatment modalities for varicocele improve semen parameters, yet more than 50% of cases remain infertile. Varicocele-induced heat and hypoxia stress may affect sperm mitochondrial functions, possibly leading to aberrant epigenetic modifications. This study includes 30 fertile men and 40 infertile men with clinical varicocele. The effect of varicocele treatment (antioxidant supplementation and or varicocelectomy) was evaluated after 3 months of treatment. Mitochondrial membrane potential (MMP) and intracellular reactive oxygen species (iROS) were measured by flow cytometry using JC-1 and DCFDA, respectively. mtDNA copy number and deletions were determined by PCR. DNA methylation was analysed by pyrosequencing. Present investigations suggest that infertile men with varicocele have abnormal semen parameters; significantly low MMP, high iROS, and high mtDNA copy number. Semen parameters were improved in a subset of men of both the treatment modalities; however, it was noted that varicocelectomy helped better in improving sperm parameters compared to antioxidant treatment. Both treatment modalities helped in reducing iROS and mtDNA copy number significantly; however, they were noneffective in improving MMP. Altered DNA methylation at mitochondria D loop and mitochondrial structure and function genes UQCRC2, MIC60, TOM22, and LETM1 (promoter region) were observed in varicocele group. The DNA methylation levels were restored after varicocele treatment; however, the restoration was not consistent at all CpG sites. Both the treatment modalities helped in restoring the altered DNA methylation levels of mitochondrial genes but the restoration is nonhomogeneous across the studied CpG sites.

Increased Susceptibility of Cardiac Tissue to PM2.5-Induced Toxicity in Uremic Cardiomyopathic Rats Is Linked to Elevated Levels of Mitochondrial Dysfunction.

Patients with chronic kidney disease (CKD) frequently develop uremic cardiomyopathy, characterized by mitochondrial dysfunction as one of its pathologically significant mediators. Given that PM2.5 specifically targets cardiac mitochondria, exacerbating toxicity, this study addresses the potential alterations in the severity of PM2.5 toxicity in the context of CKD conditions. Female Wistar rats were exposed to PM2.5 at a concentration of 250 μg/m3 daily for 3 h for 21 days after which an adenine-induced CKD model was developed. While both PM2.5 exposure and the induction of CKD in rats lead to cardiomyopathy, the CKD animals exposed to PM2.5 exhibited a notably severe extent of myocardial hypertrophy and fibrosis. ECG recordings in CKD+ PM2.5 animals revealed a depressed ST segment and prolonged QRS interval, with both PM2.5 and CKD animals displaying an elevated ST segment. Subcellular level analysis confirmed a significantly low mitochondrial copy number and a severe decline in mitochondrial bioenergetic function in the CKD+ PM2.5 group. The prominent decline in PGC1-α further affirmed the severe mitochondrial functional deterioration in CKD+ PM2.5 animals compared to other experimental groups. Additionally, myocardial calcification was enhanced in CKD+ PM2.5 animals, heightening the susceptibility of CKD animals to PM2.5 toxicity. In summary, our findings suggest that the increased vulnerability of CKD myocardium to PM2.5-induced toxicity may be attributed to severe mitochondrial damage and increased calcification in the myocardium.

Clinicopathologic Characteristics and Follow-Up Outcomes of Invasive Breast Carcinoma With Different Positive HER2 Fluorescence In Situ Hybridization Patterns: Experience From a Single Academic Institution

Human epidermal growth factor receptor 2 (HER2)-positive breast carcinoma (BC) encompasses a spectrum of molecular subtypes, characterized by varying HER2/CEP17 ratios and HER2 copy numbers, influencing responses to anti-HER2 therapy. This study stratified HER2 fluorescence in situ hybridization (FISH)-positive patients into 3 distinct groups—group 1 with high copy number (G1-HC: ratio ≥2, copy number ≥6), group 1 with low copy number (G1-LC: ratio ≥2, copy number ≥4 and <6), and group 3 (G3: ratio <2.0, copy number ≥6.0)—and evaluated their clinicopathologic features, response to anti-HER2 therapy, and outcomes. In a cohort of 2702 continuous primary BCs, G1-HC BCs accounted for 304 cases (11.3%), G1-LC for 37 cases (1.4%), and G3 for 75 cases (2.8%). G1-HC BCs were associated with younger age, higher tumor grade, and estrogen receptor negativity compared with G1-LC BCs. Furthermore, G1-HC BCs exhibited increased progesterone receptor negativity and HER2 immunohistochemistry 3+ compared with G1-LC and G3 BCs. Analysis of the subgroup of HER2 immunohistochemistry 2+-only cases (n = 166) showed similar results. Notably, G1-HC patients exhibited significantly enhanced responses to anti-HER2 neoadjuvant chemotherapy compared with G1-LC and G3 patients. Conversely, G1-LC patients displayed a lower likelihood of disease-free status compared with G1-HC and G3 patients, albeit with no significant differences in overall survival, distant metastasis, or local recurrence among the groups. These findings offer valuable clinicopathologic insights into different HER2 FISH positive subgroups, potentially informing future criteria for interpreting HER2 FISH results.

Mitochondrial DNA copy number and neurocognitive outcomes in children.

Low mitochondria DNA copy number (mtDNAcn) has been linked to cognitive decline. However, the role of mtDNAcn in healthy cognitive development is unclear. We hypothesized early-life mtDNAcn would be associated with children's learning and memory. We quantified mtDNAcn in umbilical cord blood and child blood at ages 5-7 from participants in a prospective birth cohort. We administered the Children's Memory Scale (CMS) at ages 9-14 (N = 342) and the Wechsler Intelligence Scale for Children (WISC-IV) at ages 7 and 9 (N = 457). Associations between mtDNAcn tertiles and CMS and WISC were evaluated with linear regression and linear mixed-effects models, respectively. We examined non-linear associations using generalized additive mixed models. Relative to the middle tertile of mtDNAcn, lower childhood mtDNAcn was associated with lower WISC Working Memory (β = -2.65, 95% CI [-5.24, -0.06]) and Full-Scale IQ (β = -3.71 [-6.42, -1.00]), and higher CMS Visual Memory (β = 4.70 [0.47, 8.93]). Higher childhood mtDNAcn was linked to higher CMS Verbal Memory (β = 7.75 [2.50, 13.01]). In non-linear models, higher childhood mtDNAcn was associated with lower WISC Verbal Comprehension. Our study provides novel evidence that mtDNAcn measured in childhood is associated with children's neurocognitive performance. mtDNAcn may be a marker of healthy child development. Mitochondrial DNA copy number (mtDNAcn) may serve as a biomarker for early-life neurocognitive performances in the children's population. Both low and high mtDNAcn may contribute to poorer neurocognition, reflected through learning and memory abilities. This research elucidated the importance of investigating mitochondrial biomarkers in healthy populations and facilitated advancements of future studies to better understand the associations between mitochondrial markers and adverse children's health outcomes.

Direct genome sequencing of respiratory viruses from low viral load clinical specimens using the target capture sequencing technology.

The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging-especially in the case of respiratory viruses-due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2,000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/µL of SARS-CoV-2 or 625.1 copies/µL of influenza A virus. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/µL, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.IMPORTANCETarget capture sequencing has been developed and applied for direct genome sequencing of viruses in clinical specimens to overcome the low detection sensitivity of metagenomic next-generation sequencing. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A, focusing on clinical specimens containing low copy numbers of viral genomes. Our results showed that the target capture sequencing yielded dramatically higher read counts than metagenomic sequencing for both viruses. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with other viruses, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.

ExoSloNano: Multi-Modal Nanogold Tags for identification of Macromolecules in Live Cells & Cryo-Electron Tomograms.

In situ cryo-Electron Microscopy (cryo-EM) enables the direct interrogation of structure-function relationships by resolving macromolecular structures in their native cellular environment. Tremendous progress in sample preparation, imaging and data processing over the past decade has contributed to the identification and determination of large biomolecular complexes. However, the majority of proteins are of a size that still eludes identification in cellular cryo-EM data, and most proteins exist in low copy numbers. Therefore, novel tools are needed for cryo-EM to identify the vast majority of macromolecules across multiple size scales (from microns to nanometers). Here, we introduce and validate novel nanogold probes that enable the detection of specific proteins using cryo-ET (cryo-Electron Tomography) and resin-embedded correlated light and electron microscopy (CLEM). We demonstrate that these nanogold probes can be introduced into live cells, in a manner that preserves intact molecular networks and cell viability. We use this system to identify both cytoplasmic and nuclear proteins by room temperature EM, and resolve associated structures by cryo-ET. We further employ gold particles of different sizes to enable future multiplexed labeling and structural analysis. By providing high efficiency protein labeling in live cells and molecular specificity within cryo-ET tomograms, we establish a broadly enabling tool that significantly expands the proteome available to electron microscopy.

An automated commercial open access assay for detection of Mycoplasma genitalium macrolide resistance.

Azithromycin, a macrolide antibioticum, is the first-line treatment for Mycoplasma genitalium (MG), but resistant MG is an increasing problem. Macrolide resistance-mediated mutations (MRM) has been linked to point mutations in region V of the MG 23S rRNA gene. We have evaluated an open access analyzer (Panther Fusion, Hologic Inc) for detectability of MRM (mutations A2071G and A2072G) and MG wild type (WT) in clinical samples. Also, the agreement of the Panther Fusion assay results with a corresponding established In-house MRM-WT PCR (ABI 7500) was calculated. Left over material from 55 clinical samples positive for MG by the Aptima test (Hologic) based on transcription-mediated amplification (TMA), collected from January to February 2023 in Region Skåne, Sweden, was analyzed. Specific amplification curves were generated for positive controls of MG mutations (A2071G and A2072G) and WT by the Panther Fusion assay. The limit of detection (LOD) was 5.3 copies/mL for WT, 8.1 copies/mL for mutation A2071G, and 81 copies/mL for mutation A2072G. The overall concordance was 91% between the Panther Fusion and the In-house PCR (Kappa 0.621, 95% CI; 0.327-0.914) for detection of WT or MRM in MG-positive clinical samples. The Panther Fusion detected MRM in 20% (11/55) and WT in 62% (34/55) of the samples. The corresponding In-house PCR results were 25% (14/55) and 65% (36/55). In summary, the Panther Fusion assay demonstrated detection of low copy number of MRM and WT of MG. Among clinical samples substantial agreement between the Panther Fusion and In-house PCR results was observed. Integrating MG-analysis (TMA) and MRM-WT assay on the Panther platform could make MRM testing more readily available. However, the Panther Fusion had a lower success rate (82% vs 90%) for macrolide susceptibility testing, hence testing with a complementary method should be considered for samples where neither WT nor MRM MG are detectable.

Clinicopathologic Features and Digital Imaging Analysis of HER2 Protein in Breast Carcinomas With Different HER2 Fluorescence in Situ Hybridization Patterns

BackgroundHER2-targeted therapies have significantly improved outcomes for patients with HER2-positive breast cancer (BC), which represents 15% to 20% of all BC cases. HER2 status is assessed via immunohistochemistry (IHC) and/or in situ hybridization (ISH), dividing BCs into five groups (G1-G5). Patients and methodsIn a study of 2,702 primary BC cases, comprising 12.7% G1, 0.2% G2, 2.8% G3, 8.5% G4, and 75.9% G5, we analyzed clinicopathologic features and HER2 protein expression digitally for each ISH group. ResultsNotably, G5 cases had a higher proportion of lobular carcinoma (13.9%) compared to other groups. G3 cases showed the highest percentage of grade 3 tumors (56.9%), while G5 cases had the lowest (21.4%). Additionally, G5 cases had the highest rate of estrogen receptor (ER) positivity (84.6%), while G1-HC (high copy number) cases had the lowest (70.4%). Most G1-HC cases were HER2 IHC 3+ (76.1%), while most G5 cases were IHC 0/1+ (75.7%). IHC 2+ was most common in G1-LC (low copy number) and G3 cases (83.8% and 90.7%, respectively), with G4 cases predominantly IHC 2+ (56.3%) and IHC 1+ (30.1%). Discordant HER2 IHC and ISH results were observed in 12 cases (0.4%), including 7 G1-HC (2.3%), 4 G1-LC (10.8%), and 1 G5 case (0.1%). Digital quantification of HER2 IHC levels in all groups except G5 revealed that G1-HC tumors had the highest HER2 protein expression, followed by G3, with G4 showing the lowest. ConclusionThese findings offer valuable insights into the clinicopathologic characteristics and future management for different HER2 ISH groups.

Human hypofunctional NCF1 variants promote pulmonary fibrosis in the bleomycin-induced mouse model and patients with systemic sclerosis via expansion of SPP1+ monocytes-derived macrophages

ObjectiveWe assessed the role of a systemic lupus erythematosus causal hypofunctional variant, neutrophil cytosolic factor 1 (NCF1)-p.Arg90His (p.R90H) substitution, in systemic sclerosis (SSc).MethodsAssociation of NCF1-H90 with SSc was performed in...

CHAMP: A Centrifugal Microfluidics-Based CRISPR/Cas12b-Combined Real-Time LAMP One-Pot Method for Mycoplasma pneumoniae Infection Diagnosis.

The Mycoplasma pneumoniae outbreak poses health risks to community residents. However, it still has limitations for current clinical diagnostic methods (qPCR nucleic acid assay or IgM immunoassay), including specialized handling, expensive equipment, prolonged turnaround time, and false positives and negatives, highlighting the need to improve clinical diagnostic methods. Herein, we present a novel centrifugal microfluidics-based method for rapidly diagnosing M. pneumoniae infections (CHAMP system). This user-friendly method combines CRISPR/Cas12b and real-time loop-mediated isothermal amplification (LAMP) in a one-pot reaction, offering high sensitivity, specificity, and simplicity for methodology. By adding fully automated nucleic acid magnetic bead-extracted samples to a prepackaged centrifugal microfluidics chip, 48 samples can be automated tested simultaneously within 15 to 60 min at 60 °C. 427 clinical nasopharyngeal swab specimens were used for validation, demonstrating good positive and negative predictive values and good diagnostic sensitivity, specificity, and significant time savings. This method is particularly suitable for detecting low nucleic acid copies of M. pneumoniae samples.

Association between mitochondrial DNA copy number and neurodevelopmental outcomes among black and white preterm infants up to two years of age.

Mitochondrial DNA copy number (mtDNAcn) is associated with mitochondrial function, with abnormal copy numbers having been linked to various disease states. Our study aims to understand the association between infant mtDNAcn and infant neurodevelopment, as well as the association with racial disparities. A longitudinal study was conducted with 55 preterm infants from whom a single blood sample was collected during their Neonatal intensive care unit (NICU) stay and used to analyze mtDNAcn. In addition, the NICU Network Neurobehavioral Scale at 36-38 postmenstrual age (PMA) and the Bayley Scale of Infant and Toddler Development (Bayley) Edition III at 1 and 2 years of corrected age were both conducted. Linear regression models were performed to investigate the relationship between infant clinical characteristics, infant neurobehavioral outcomes, and mtDNAcn. The majority of infants studied were white (72.73%), non-Hispanic (70.91%), males (54.55%), delivered through C-section (72.73%), and without preterm premature rupture of membrane (76.36%). Increased mtDNAcn was associated with younger birth gestational age (<30.57 wk, P < 0.001). In addition, the opposite associations between mtDNAcn and neurodevelopmental outcomes were observed between white and black infants up to 1 year of gestational age. Increased mtDNAcn in white infants, and decreased mtDNAcn in black infants may be considered significant predictors of poor early-life neurodevelopmental outcomes in infants. A better understanding of the underlying mechanisms contributing to infant disparity in mtDNAcn and how low or high copy number impacts infant outcomes is essential.

Dendritically localized RNAs are packaged as diversely composed ribonucleoprotein particles with heterogeneous copy number states.

Localization of mRNAs to dendrites is a fundamental mechanism by which neurons achieve spatiotemporal control of gene expression. Translationally repressed neuronal mRNA transport granules, also referred to as ribonucleoprotein particles (RNPs), have been shown to be trafficked as single or low copy number RNPs and as larger complexes with multiple copies and/or species of mRNAs. However, there is little evidence of either population in intact neuronal circuits. Using single molecule fluorescence in situ hybridization studies in the dendrites of adult rat and mouse hippocampus, we provide evidence that supports the existence of multi-transcript RNPs with the constituents varying in amounts for each RNA species. By competing-off fluorescently labeled probe with serial increases of unlabeled probe, we detected stepwise decreases in Arc RNP number and fluorescence intensity, suggesting Arc RNAs localize to dendrites in both low- and multiple-copy number RNPs. When probing for multiple mRNAs, we find that localized RNPs are heterogeneous in size and colocalization patterns that vary per RNA. Further, localized RNAs that are targeted by the same trans-acting element (FMRP) display greater levels of colocalization compared to an RNA not targeted by FMRP. Simultaneous visualization of a dozen FMRP-targeted mRNA species using highly multiplexed imaging demonstrates that dendritic RNAs are mostly trafficked as heteromeric cargoes of multiple types of RNAs (at least one or more RNAs). Moreover, the composition of these RNA cargoes, as assessed by colocalization, correlates with the abundance of the transcripts even after accounting for the expected differences in colocalization based on expression. Collectively, these results suggest that dendritic RNPs are packaged as heterogeneous co-assemblies of different mRNAs and that RNP contents may be driven, at least partially, by highly abundant dendritic RNAs; a model that favors efficiency over fine-tuned control for sustaining long-distance trafficking of thousands of messenger molecules.