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Plant Disease Nov 2023Soybean ( L.) is produced in over 70,000 ha in the Altillanura Region, eastern Colombia (Agronet 2023). From 2018 to 2020, foliar symptoms like green stem and foliar...
Soybean ( L.) is produced in over 70,000 ha in the Altillanura Region, eastern Colombia (Agronet 2023). From 2018 to 2020, foliar symptoms like green stem and foliar retention of soybean, which in Brazil can cause up to 100% soybean yield losses (Meyer et al. 2017), were observed in soybean fields in Colombia. During 2020, samples from symptomatic plants in reproductive stages (R1-R8) were collected from different commercial soybean fields in the Altillanura Region. Over 200 samples were processed, using an incubation method described in Coyne et al. (2014). Nematodes were recovered from photosynthetic leaf tissues and enlarged nodes/buds with population densities ranging from 13 to 132 and 36 to 936 nematodes/10g, respectively. Adult females were morphologically and molecularly characterized as (Oliveira et al. 2019; Subbotin et al. 2020). Female body length (n = 20) ranged from 653.3 to 806.3 μm (mean = 723 μm ± 52.7), stylet length from 11.0 to 12.3 μm (11.8 μm ± 0.3), body diameter from 14.8 to 17.9 μm (16.3 μm ± 1.1), post-uterine sac length from 38.7 to 51.9 μm (44.6 μm ± 5.1), vulva to anus from 145.5 to 223.2 μm (172.2 μm ± 22.4), and 26% of the vulva-anus distance. Genomic DNA was extracted (QIAGEN DNeasy® Blood & Tissue kit) from a pool of nematodes. The D2A/D3B (Tenente et al. 2004) primers were used to amplify and sequence the D2/D3 expansion region of the 28S rRNA gene. PCR product (~759 bp) was purified, sequenced, deposited in GenBank (OQ930285), and compared to previously deposited sequences (e.g., KX356756, KY510840, KY510839, KY510841, KT692694, KY510842, MH187565) by means of the BLAST algorithm. Similarly, 988F and 18SR-Burs (De Jesus et al. 2016) primers were used to amplify and sequence the near full-length 18S RNA gene (SSU). PCR product was purified, sequenced, deposited in GenBank (OQ954344), and compared to previously deposited sequences (e.g., KT454962, KT943534, KT943535, KY510835, KY510836, KY510837, KY510838, MH187565). Phylogenetic Bayesian analysis (Ronquist et al. 2012) of the of the D2/D3 and 18S regions placed this nematode from Colombia in the clade (PP = 100). To fulfill a modified Koch's postulates, the population described above was used in a greenhouse assay. In total, 120 soybean plants (cv. Flor Blanca) were infected with 200 (females + males)/plant. Briefly, at cotyledon stage (VC), 50 µl aliquot containing 50 was delivered onto each cotyledon and unifoliolate leaves (200 nematodes/plant). Sterile water was delivered to 80 plants which served as control. Plants were kept in the greenhouse at approximately 25°C and covered with clear plastic bag for 72 h to maintain over 90% relative humidity. After 15, 30, 45, and 60 days, soybean plants (n = 20) were processed, quantified, and the average reproduction factor (final population/initial population) was 0.1, 2.9, 14.0, and 1.8, respectively. Infected plants showed symptoms of blistering leaves with malformation (midrib vein twist), and was not observed in control plants. To our knowledge, this is the first report of parasitizing soybean buds and leaves in Colombia. Soybean is an important commodity for the Altillanura Region, and it is important to monitor the risk posed by this nematode. Furthermore, a better understanding of the nematode-host interaction and epidemiology in Colombia soybean producing regions is needed.
PubMed: 38085963
DOI: 10.1094/PDIS-06-23-1117-PDN -
Fluids and Barriers of the CNS Dec 2023Microdialysis is a technique that can be utilized to sample the interstitial fluid of the central nervous system (CNS), including in primary malignant brain tumors known...
BACKGROUND
Microdialysis is a technique that can be utilized to sample the interstitial fluid of the central nervous system (CNS), including in primary malignant brain tumors known as gliomas. Gliomas are mainly accessible at the time of surgery, but have rarely been analyzed via interstitial fluid collected via microdialysis. To that end, we obtained an investigational device exemption for high molecular weight catheters (HMW, 100 kDa) and a variable flow rate pump to perform microdialysis at flow rates amenable to an intra-operative setting. We herein report on the lessons and insights obtained during our intra-operative HMW microdialysis trial, both in regard to methodological and analytical considerations.
METHODS
Intra-operative HMW microdialysis was performed during 15 clinically indicated glioma resections in fourteen patients, across three radiographically diverse regions in each patient. Microdialysates were analyzed via targeted and untargeted metabolomics via ultra-performance liquid chromatography tandem mass spectrometry.
RESULTS
Use of albumin and lactate-containing perfusates impacted subsets of metabolites evaluated via global metabolomics. Additionally, focal delivery of lactate via a lactate-containing perfusate, induced local metabolic changes, suggesting the potential for intra-operative pharmacodynamic studies via reverse microdialysis of candidate drugs. Multiple peri-operatively administered drugs, including levetiracetam, cefazolin, caffeine, mannitol and acetaminophen, could be detected from one microdialysate aliquot representing 10 min worth of intra-operative sampling. Moreover, clinical, radiographic, and methodological considerations for performing intra-operative microdialysis are discussed.
CONCLUSIONS
Intra-operative HMW microdialysis can feasibly be utilized to sample the live human CNS microenvironment, including both metabolites and drugs, within one surgery. Certain variables, such as perfusate type, must be considered during and after analysis. Trial registration NCT04047264.
Topics: Humans; Microdialysis; Glioma; Extracellular Fluid; Lactic Acid; Catheters; Tumor Microenvironment
PubMed: 38115038
DOI: 10.1186/s12987-023-00497-2 -
Cancers Nov 2023Our aim was to evaluate the concordance between the Myriad MyChoice and two alternative homologous recombination deficiency (HRD) assays (AmoyDx HRD Focus NGS Panel and...
Our aim was to evaluate the concordance between the Myriad MyChoice and two alternative homologous recombination deficiency (HRD) assays (AmoyDx HRD Focus NGS Panel and OncoScan™) in patients with epithelial ovarian cancer (EOC). Tissue samples from 50 patients with newly diagnosed EOC and known Myriad MyChoice HRD status were included. DNA aliquots from tumor samples, previously evaluated with Myriad MyChoice and centrally reassessed, were distributed to laboratories to assess their HRD status using the two platforms, after being blinded for the Myriad MyChoice CDx HRD status. The primary endpoint was the concordance between Myriad MyChoice and each alternative assay. Tumor samples were evaluated with an AmoyDx HRD Focus Panel ( = 50) and with OncoScan™ ( = 43). Both platforms provided results for all tumors. Analysis showed that correlation was high for the Myriad MyChoice GI score and AmoyDx HRD Focus Panel (r = 0.79) or OncoScan™ (r = 0.87) (continuous variable). The overall percent agreement (OPA) between Myriad MyChoice GI status (categorical variable) and each alternative assay was 83.3% (68.6-93.3%) with AmoyDx and 77.5% (61.5-89.2%) with OncoScan™. The OPA in HRD status between Myriad MyChoice and AmoyDx was 88.6% (75.4-96.2). False-positive rates were 31.6% (6/19) for AmoyDx GI status and 31.9% (7/22) for OncoScan™, while false-negative rates were 0% (0/28, AmoyDx) and 11.1% (2/18, OncoScan™) compared with the Myriad MyChoice GI status. While substantial concordance between Myriad MyChoice and alternative assays was demonstrated, prospective validation of the analytical performance and clinical relevance of these assays is warranted.
PubMed: 38067228
DOI: 10.3390/cancers15235525 -
BMC Genomics Jul 2023A common feature of single-cell RNA-seq (scRNA-seq) data is that the number of cells in a cell cluster may vary widely, ranging from a few dozen to several thousand. It...
BACKGROUND
A common feature of single-cell RNA-seq (scRNA-seq) data is that the number of cells in a cell cluster may vary widely, ranging from a few dozen to several thousand. It is not clear whether scRNA-seq data from a small number of cells allow robust identification of differentially expressed genes (DEGs) with various characteristics.
RESULTS
We addressed this question by performing scRNA-seq and poly(A)-dependent bulk RNA-seq in comparable aliquots of human induced pluripotent stem cells-derived, purified vascular endothelial and smooth muscle cells. We found that scRNA-seq data needed to have 2,000 or more cells in a cluster to identify the majority of DEGs that would show modest differences in a bulk RNA-seq analysis. On the other hand, clusters with as few as 50-100 cells may be sufficient for identifying the majority of DEGs that would have extremely small p values or transcript abundance greater than a few hundred transcripts per million in a bulk RNA-seq analysis.
CONCLUSION
Findings of the current study provide a quantitative reference for designing studies that aim for identifying DEGs for specific cell clusters using scRNA-seq data and for interpreting results of such studies.
Topics: Humans; Gene Expression Profiling; Single-Cell Gene Expression Analysis; Induced Pluripotent Stem Cells; RNA-Seq; Single-Cell Analysis; Sequence Analysis, RNA
PubMed: 37394518
DOI: 10.1186/s12864-023-09487-y -
Journal of Proteomics Oct 2023Here we introduce hyperthermoacidic archaeal proteases (HTA-Proteases©) isolated from organisms that thrive in nearly boiling acidic volcanic springs and investigate...
Here we introduce hyperthermoacidic archaeal proteases (HTA-Proteases©) isolated from organisms that thrive in nearly boiling acidic volcanic springs and investigate their use for bottom-up proteomic experiments. We find that HTA-Proteases have novel cleavage specificities, show no autolysis, function in dilute formic acid, and store at ambient temperature for years. HTA-Proteases function optimally at 70-90 °C and pH of 2-4 with rapid digestion kinetics. The extreme HTA-Protease reaction conditions actively denature sample proteins, obviate the use of chaotropes, are largely independent of reduction and alkylation, and allow for a one-step/five-minute sample preparation protocol without sample manipulation, dilution, or additional cleanup. We find that brief one-step HTA-Protease protocols significantly increase proteome and protein sequence coverage with datasets orthogonal to trypsin. Importantly, HTA-Protease digests markedly increase coverage and identifications for ribonucleoproteins, histones, and mitochondrial membrane proteins as compared to tryptic digests alone. In addition to increased coverage in these classes, HTA-Proteases and simplified one-step protocols are expected to reduce technical variability and advance the fields of clinical and high-throughput proteomics. This work reveals significant utility of heretofore unavailable HTA-Proteases for proteomic workflows. We discuss some of the potential for these remarkable enzymes to empower new proteomics methods, approaches, and biological insights. SIGNIFICANCE: Here we introduce new capabilities for bottom-up proteomics applications with hyperthermoacidic archaeal proteases (HTA-Proteases©). HTA-Proteases have novel cleavage specificity, require no chaotropes, and allow simple one-step/five-minute sample preparations that promise to reduce variability between samples and laboratories. HTA-Proteases generate unique sets of observable peptides that are non-overlapping with tryptic peptides and significantly increase sequence coverage and available peptide targets relative to trypsin alone. HTA-Proteases show some bias for the detection and coverage of nucleic acid-binding proteins and membrane proteins relative to trypsin. These new ultra-stable enzymes function optimally in nearly boiling acidic conditions, show no autolysis, and do not require aliquoting as they are stable for years at ambient temperatures. Used independently or in conjunction with tryptic digests, HTA-Proteases offer increased proteome coverage, unique peptide targets, and brief one-step protocols amenable to automation, rapid turnaround, and high-throughput approaches.
Topics: Peptide Hydrolases; Trypsin; Proteome; Proteomics; Workflow; Peptides; Membrane Proteins
PubMed: 37634627
DOI: 10.1016/j.jprot.2023.104992 -
Journal of Dairy Science Jul 2023The objectives of this study were to evaluate the abundance and viability of leukocytes, the abundance of microRNA, and the activity of the complement pathway in (1)...
The objectives of this study were to evaluate the abundance and viability of leukocytes, the abundance of microRNA, and the activity of the complement pathway in (1) colostrum following heat-treatment or freezing, and (2) colostrum, transition milk, and mature milk. In experiment 1, composite colostrum samples were harvested from individual cows (n = 14) on a commercial dairy farm in NY and split into 3 aliquots using single-use colostrum bags. One aliquot was immediately cooled on ice following harvest (RAW) and stored at 4°C overnight, one was heat-treated for 60 min at 60°C (HT) before being cooled on ice and stored at 4°C overnight, and one was frozen at -20°C overnight (FR). The following morning, all samples were warmed to 40°C before further processing. In experiment 2, cows were sampled in a longitudinal study where composite samples were collected from colostrum (first milking, n = 23), transition milk (3 to 4 d postpartum, n = 13), and mature milk (6 to 7 d postpartum, n = 13). In both experiments colostrum was harvested from the first milking within 8 h of calving and samples were processed within 14 h of collection. Colostral leukocytes were isolated before viability was determined by trypan blue exclusion and manual differential cell counts were performed. Extracellular vesicles were isolated from whey by ultracentrifugation to isolate and quantify microRNA. Activity of the alternative complement pathway was determined in casein-depleted whey by semi-solid phase hemolysis assay. Somatic cell counts were determined for all raw samples. Macrophages and neutrophils made up the greatest proportion of leukocytes in colostrum followed by lymphocytes. Lymphocyte proportion increased as colostrum transitioned to mature milk, but overall somatic cell numbers declined concurrently. Viable cells were not isolated from HT or FR samples. Abundance of microRNA isolated from transition and mature milk was decreased compared with colostrum, did not differ between HT and RAW, but was increased in FR compared with RAW. Alternative complement pathway activity was decreased in HT, but not FR compared with RAW, and was not measurable in transition or mature milk. Postharvest heat-treatment and freezing of colostrum eliminated viable colostral leukocytes and affected microRNA abundance and complement activity. Leukocyte proportions, microRNA abundance, and complement activity changed as colostrum transitioned to mature milk. Although there were clear changes in the colostral components under study in relation to treatment and transition to mature milk, the biological significance of the described treatment effects and temporal changes were not investigated here.
Topics: Pregnancy; Female; Cattle; Animals; Milk; Colostrum; Hot Temperature; MicroRNAs; Freezing; Ice; Longitudinal Studies; Leukocytes; Lactation
PubMed: 37164855
DOI: 10.3168/jds.2022-22876 -
Animals : An Open Access Journal From... Oct 2023Semen delivery practice is crucial to the efficiency of artificial insemination using high-quality boar sperm. The present study aimed to evaluate the effect of a common...
Semen delivery practice is crucial to the efficiency of artificial insemination using high-quality boar sperm. The present study aimed to evaluate the effect of a common semen delivery method, a Styrofoam box, under elevated temperatures on boar sperm quality and functionality and to investigate the underlying molecular responses of sperm to the temperature rise. Three pooled semen samples from 10 Duroc boars (3 ejaculates per boar) were used in this study. Each pooled semen sample was divided into two aliquots. One aliquot was stored at a constant 17 °C as the control group. Another one was packaged in a well-sealed Styrofoam box and placed in an incubator at 37 °C for 24 h to simulate semen delivery on hot summer days and subsequently transferred to a refrigerator at 17 °C for 3 days. The semen temperature was continuously monitored. The semen temperature was 17 °C at 0 h of storage and reached 20 °C at 5 h, 30 °C at 14 h, and 37 °C at 24 h. For each time point, sperm quality and functionality, apoptotic changes, expression levels of phosphorylated AMPK, and heat shock proteins HSP70 and HSP90 were determined by CASA, flow cytometry, and Western blotting. The results showed that elevated temperature during delivery significantly deteriorated boar sperm quality and functionality after 14 h of delivery. Storage back to 17 °C did not recover sperm motility. An increased temperature during delivery apparently promoted the conversion of sperm early apoptosis to late apoptosis, showing a significant increase in the expression levels of Bax and Caspase 3. The levels of phosphorylated AMPK were greatly induced by the temperature rise to 20 °C during delivery but reduced thereafter. With the temperature elevation, expression levels of HSP70 and HSP90 were notably increased. Our results indicate that a temperature increase during semen delivery greatly damages sperm quality and functionality by promoting sperm apoptosis. HSP70 and HSP90 could participate in boar sperm resistance to temperature changes by being associated with AMPK activation and anti-apoptotic processes.
PubMed: 37893927
DOI: 10.3390/ani13203203 -
Scientific Reports Feb 2024Postural Orthostatic Tachycardia Syndrome (POTS) reflects an autonomic dysfunction, which can occur as a complication to COVID-19. Our aim was to examine...
Postural Orthostatic Tachycardia Syndrome (POTS) reflects an autonomic dysfunction, which can occur as a complication to COVID-19. Our aim was to examine gastrointestinal symptoms and gut microbiota composition in patients with POTS and post-acute COVID-19 syndrome (PACS), compared with controls. POTS patients (n = 27), PACS patients (n = 32) and controls (n = 39) delivered fecal samples and completed a 4-day food diary, irritable bowel syndrome-severity scoring system (IBS-SSS), and visual analog scale for IBS (VAS-IBS). A total of 98 DNA aliquots were sequenced to an average depth of 28.3 million (M) read pairs (Illumina 2 × 150 PE) per sample. Diversity and taxonomic levels of the microbiome, as well as functional abundances were calculated for POTS and PACS groups, then compared with controls. There were several differences in taxonomic composition between POTS and controls, whereas only the abundance of Ascomycota and Firmicutes differed between PACS and controls. The clinical variables total IBS-SSS, fatigue, and bloating and flatulence significantly correlated with multiple individual taxa abundances, alpha diversity, and functional abundances. We conclude that POTS, and to a less extent PACS, are associated with differences in gut microbiota composition in diversity and at several taxonomic levels. Clinical symptoms are correlated with both alpha diversity and taxonomic and functional abundances.
Topics: Humans; Postural Orthostatic Tachycardia Syndrome; Irritable Bowel Syndrome; Gastrointestinal Microbiome; Post-Acute COVID-19 Syndrome; COVID-19
PubMed: 38336892
DOI: 10.1038/s41598-024-53784-9 -
BMC Infectious Diseases Jul 2023Chikungunya is associated with high morbidity and the natural history of symptomatic infection has been divided into three phases (acute, post-acute, and chronic)...
Multicenter study of the natural history and therapeutic responses of patients with chikungunya, focusing on acute and chronic musculoskeletal manifestations - a study protocol from the clinical and applied research in Chikungunya (REPLICK network).
BACKGROUND
Chikungunya is associated with high morbidity and the natural history of symptomatic infection has been divided into three phases (acute, post-acute, and chronic) according to the duration of musculoskeletal symptoms. Although this classification has been designed to help guide therapeutic decisions, it does not encompass the complexity of the clinical expression of the disease and does not assist in the evaluation of the prognosis of severity nor chronic disease. Thus, the current challenge is to identify and diagnose musculoskeletal disorders and to provide the optimal treatment in order to prevent perpetuation or progression to a potentially destructive disease course.
METHODS
The study is the first product of the Clinical and Applied Research Network in Chikungunya (REPLICK). This is a prospective, outpatient department-based, multicenter cohort study in Brazil. Four work packages were defined: i. Clinical research; ii) Translational Science - comprising immunology and virology streams; iii) Epidemiology and Economics; iv) Therapeutic Response and clinical trials design. Scheduled appointments on days 21 (D21) ± 7 after enrollment, D90 ± 15, D120 ± 30, D180 ± 30; D360 ± 30; D720 ± 60, and D1080 ± 60 days. On these visits a panel of blood tests are collected in addition to the clinical report forms to obtain data on socio-demographic, medical history, physical examination and questionnaires devoted to the evaluation of musculoskeletal manifestations and overall health are performed. Participants are asked to consent for their specimens to be maintained in a biobank. Aliquots of blood, serum, saliva, PAXgene, and when clinically indicated to be examined, synovial fluid, are stored at -80° C. The study protocol was submitted and approved to the National IRB and local IRB at each study site.
DISCUSSION
Standardized and harmonized patient cohorts are needed to provide better estimates of chronic arthralgia development, the clinical spectra of acute and chronic disease and investigation of associated risk factors. This study is the largest evaluation of the long-term sequelae of individuals infected with CHIKV in the Brazilian population focusing on musculoskeletal manifestations, mental health, quality of life, and chronic pain. This information will both define disease burden and costs associated with CHIKV infection, and better inform therapeutic guidelines.
Topics: Humans; Chikungunya Fever; Cohort Studies; Prospective Studies; Quality of Life; Chronic Disease; Multicenter Studies as Topic
PubMed: 37507666
DOI: 10.1186/s12879-023-08292-y -
Diagnostics (Basel, Switzerland) Jan 2024Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA...
Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA (ecDNA) in plasma, could be a promising biomarker for oral or systemic diseases. In contrast to genetics, the quantity of salivary ecDNA is of importance and can be affected by the pre-analytical processing of samples, but the details are not known. The aim of our study was to analyze the effects of centrifugation and freezing of saliva on the concentration of ecDNA in saliva. Fifteen healthy volunteers, free of any known systemic or oral diseases, were asked to collect unstimulated saliva samples. Aliquots were centrifuged at 1600× and frozen or directly processed. The fresh or thawed cell-free saliva samples underwent subsequent centrifugation at 16,000× . The supernatants were used for DNA isolation and quantification using fluorometry and real-time PCR. While freezing had minimal effects on the salivary ecDNA concentration, another centrifugation step decreased ecDNA considerably in both fresh and frozen samples (by 97.8% and 98.4%, respectively). This was mirrored in the quantitative PCR targeting a nuclear (decrease by 93.5%) and mitochondrial (decrease by 97.7%) ecDNA sequence. In conclusion, in this first study focusing on the technical aspects of salivary ecDNA quantitation, we show that, regardless of its subcellular origin, the concentration of ecDNA in saliva is mainly affected by additional centrifugation and not by the freezing of centrifuged cell-free saliva samples. This suggests that most salivary ecDNA likely is associated with cell debris and apoptotic bodies. Which fraction is affected by a particular disease should be the focus of further targeted studies.
PubMed: 38337765
DOI: 10.3390/diagnostics14030249