Search Results (76)

Retained products of conception (RPOC) represent a significant cause of morbidity in the post-abortive and postpartum periods, potentially leading to abnormal uterine bleeding, pelvic pain, infections, and intrauterine adhesions. Accurate diagnosis is crucial to avoid unnecessary surgical interventions and to preserve future fertility. Transvaginal ultrasound constitutes the primary imaging modality for identifying RPOC, but the lack of standardized diagnostic criteria complicates clinical decision-making. This narrative review explores the current literature on sonographic findings associated with RPOC, focusing on the diagnostic value of endometrial thickness (ET), the presence of intrauterine echogenic masses, and the use of Color Doppler imaging. Although an ET ≥15 mm is frequently used to suspect RPOC, the variability in cut-off thresholds and limited specificity reduce its diagnostic reliability. The detection of an echogenic intrauterine mass appears to be the most sensitive and specific sonographic feature. Color Doppler assessment, particularly the presence of enhanced myometrial vascularity (EMV) and classification systems like the Gutenberg score, offers further insight by stratifying hemorrhagic risk and guiding therapeutic choices. However, vascular parameters such as peak systolic velocity (PSV) and resistive index (RI) demonstrate a substantial overlap between benign and pathological conditions, limiting their stand-alone utility. The review also addresses the differential diagnosis of RPOC, including blood clots, arteriovenous malformations, placental polyps, gestational trophoblastic disease, and endometrial osseous metaplasia. The role of three-dimensional ultrasound remains limited in clinical practice, offering no significant advantage over two-dimensional imaging. Finally, the timing of follow-up ultrasound after medical treatment with misoprostol is critical: delayed assessment reduces overtreatment by allowing time for spontaneous resolution. In conclusion, despite advances in ultrasound technology, the diagnosis of RPOC remains challenging due to heterogeneity in imaging findings and inter-observer variability. A multimodal approach integrating grayscale and Doppler ultrasound with clinical evaluation is essential for optimal management. Full article

The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical crops (actinidia, feijoa, citrus, and tea). A total of 47 accessions (elite cultivars, forms, and breeding lines) of these four genera were included in the study. The efficiency of the following universal primers was assessed using Sanger sequencing: ITS-p5/ITS-u4, ITS-p5/ITS-u2, ITS-p3/ITS-u4, 23S,4.5S&5S, 16S, petB/petD, rpl23/rpl2.l, rpl2 intron, rpoC1 intron, trnK intron, and trnE-UUC/trnT-GUU. Among these primers, trnE-UUC/trnT-GUU showed greater intraspecific polymorphisms, while rpl2 intron and 16S displayed the lowest polymorphism levels in all crops. In addition, the 23S,4.5S & 5S, and rpoC1 intron were efficient for intraspecific analysis of tea and actinidia species. Using five efficient chloroplast primers, a total of 22/6 SNPs/InDels were observed in tea accessions, 45/17 SNPs/InDels in actinidia, 23/3 SNPs/InDels in mandarins, and 5/4 SNPs/InDels in feijoa. These results will be useful for the further development of DNA barcodes of related accessions. Full article

DNA barcoding of intraspecific diversity of agricultural crops is important to develop the genetic passports of valuable genotypes and cultivars. The advantage of DNA-barcoding as compared to traditional genotyping of cultivars is that the procedure can be unified and applied for the broad range of accessions. This not only makes it cost efficient, but also allows to develop open access genetic databases to accumulate information of the world’s germplasm collections of different crops. In this regard, the aim of the review was to analyze the latest research in this field, including the selection of loci, universal primers, strategies of amplicons analysis, bioinformatic tools, and the development of databases. We reviewed the advantages and disadvantages of each strategy with the focus of cultivars identification. The data indicates that following chloroplast loci are the most prominent for the intraspecific diversity analysis: (trnE-UUC/trnT-GUU, rpl23/rpl2.l, psbA-trnH, trnL-trnF, trnK, rpoC1, ycf1-a, rpl32-trnL, trnH-psbA and matK). We suggest that the combination of three or four of these loci can be a sufficient DNA barcode for cultivar-level identification. This combination has to be selected for each crop. Advantages and disadvantages of different approaches of amplicons analysis are discussed. The bioinformatic tools and databases for the plant barcoding are reviewed. This review will be useful for selecting appropriate strategies for barcoding of intraspecific diversity of agricultural crops to develop genetic passports of valuable cultivars in germplasm collections worldwide. Full article

The number of Fritillaria species native to the Alps has long been debated, and observational biases due to the short flowering periods and the scattered distributions of endemic Fritillaria populations along the mountain range have probably made the task of botanists more complicated. Moreover, previous phylogenetic studies in Fritillaria have considered alpine taxa only marginally. To test species boundaries within the F. tubaeformis species complex and to study their phylogenetic relationships, intra- and inter-specific genetic variability of sixteen samples belonging to four Fritillaria species was carried out in different localities of the Maritime and Ligurian Alps, with extensions to the rest of the Alpine arc. The combined use of five plastid DNA markers (matK, ndhF, rpl16, rpoC1, and petA-psbJ) and nrITS showed that F. tubaeformis and F. burnatii are phylogenetically independent taxa, fully confirming morphological and morphometric divergences and, that F. burnatii is not related phylogenetically to the central European F. meleagris. Our phylogenetic study also supports the separation of F. tubaeformis from F. moggridgei, pointing to environment/ecological constraints or reproductive barriers as possible causes of their distinct evolutionary status. Our analysis also showed that the mountain endemic F. involucrata is not closely related to F. tubaeformis, contrasting with previous studies. The phylogenetic analysis of the nrITS region supports a close relationship between F. burnatii and F. moggridgei, but with low statistical support. Full article

Background/Objectives: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding. Methods: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties. Results: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine–cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers. Conclusions: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera. Full article

Background: Artemisia is a large and complex genus comprising about 500 species. Currently, only a limited number of plastomes (the chloroplast genome) of Artemisia are available. Their structures have not been comparatively analyzed, and a phylogenetic backbone based on plastome-scale data is still lacking. This situation has greatly hindered our understanding of the plastome variation patterns and infra-generic relationships of the genus. Methods: We newly sequenced 34 Artemisia plastomes representing 30 species and three varieties. Combining this with previously published plastomes, we comparatively analyzed their structure and constructed phylogenetic relationships using the protein-coding sequences (CDS) of plastomes. Results: Our analyses indicated that the Artemisia plastomes are conserved in terms of their structure, GC content, gene number, and order. The sequence divergence is higher in the LSC and SSC regions than in the IR regions. Three protein-coding genes and four non-coding regions, i.e., accD, petG, ycf1, rpoC1-rpoC2, rpoC2-rps2, trnG(UCC)-trnfM(CAU), and ndhG-ndhI, were highly diverse and could be chosen as candidates of DNA barcodes. Phylogenetic trees were divided into several clades, and all four main subgenera were not monophyletic. Additionally, the phylogenetic position of A. stracheyi is still controversial. Conclusions: Plastomes can provide important information for phylogenetic constructions. This study provides insights into the infra-generic relationships within Artemisia and also lays a foundation for future evolutionary studies of this genus. Full article

In this study, a global response analysis was performed to explore the mechanism of action of Usnic acid and its synergy with Norfloxacin, a well-known quinolone antibiotic to which MRSA clinical isolates showed resistance (MIC, 500 µg/mL). A microdilution assay, a growth kinetics analysis, a microscopic analysis, and cell-based assays consistently showed that Usnic acid possesses strong anti-staphylococcal activity (MIC, 7.8 µg/mL), causes cell leakage, modulates efflux pump activity, and synergizes with Norfloxacin against the multi-drug-resistant clinical isolate MRSA 2071. Whole-cell proteome profiling using gel-free proteomics-based nano-LC-ESI-QTOF-MS/MS revealed several proteins whose expression was significantly modulated by Usnic acid and Norfloxacin alone or in combination. Usnic acid downregulated the abundance of RNA polymerase subunits (RpoB and RpoC), carbamoyl phosphate synthase large subunit (PyrAB), chaperone (GroEL), and adenylosuccinate synthetase (PurA). Interestingly, proteins found to be upregulated in the presence of Usnic acid and Norfloxacin included oxidative-stress-related proteins such as peroxidase (Tpx), alkyl hydroperoxide reductase (AphC), and general stress protein (UspA). This study clearly shows that Usnic acid affects numerous cellular targets and can potentiate the action of Norfloxacin. Furthermore, an in vivo study showed that UA at low concentrations prevents body weight gain, but changes in other tested toxicological parameters were found to be within normal limits. Thus, UA at low doses appears to be a promising candidate for repurposing old antibiotics through combination therapy against MRSA infections. Full article

As the most diverse genus of Salicaceae, Salix is primarily distributed in the temperate zone of the Northern Hemisphere, encompassing 350–500 species worldwide. The genus’s evolutionary history is complex due to significant genetic differentiation. Chloroplast genes, being highly conserved, serve as effective tools for studying uniparental inheritance and evolution. In this study, we sequenced and assembled the chloroplast genomes of five representative Salix species. Phylogenetic relationships were constructed using chloroplast genome data, and structural differences among lineages were compared. These Salix chloroplast genomes exhibited a typical quadripartite structure, with lengths ranging from 154,444 to 155,725 bp. We successfully annotated 131 genes, including 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Clade I showed higher variability in the SSC region, identifying five highly variable regions: petA-psbJ, rps16-rps3, ndhD, ccsA-ndhD, and ndhG-ndhI. Two rapidly evolving genes, ndhI and ycf4, were also identified. The total length of insertions and deletions (InDels) in Clade I was 1046 bp. Clade II exhibited greater variability in the LSC region, with four highly variable regions being identified: trnK-trnQ, ndhC-trnV, trnV, and psdE-petL. Four rapidly evolving genes—infA, rpoC1, rps18, and ycf1—were identified. The total length of InDels in Clade II was 1282 bp. Therefore, this study elucidated the chloroplast genome evolution across different Salix lineages, thereby providing deeper insights into intrageneric phylogenetic relationships. Full article

Brownlowia tersa and Brownlowia argentata are two true mangroves in the genus Brownlowia in Malvaceae, and they are a near-threatened and a data-deficient species, respectively. However, the genomic resources of Brownlowia have not been reported for studying their phylogeny and evolution. Here, we report the chloroplast genomes of B. tersa and B. argentata based on stLFR data that were 159,478 and 159,510 base pairs in length, respectively. Both chloroplast genomes contain 110 unique genes and one infA pseudogene. Sixty-eight RNA-editing sites were detected in 26 genes in B. argentata. A comparative analysis with related species showed similar genome sizes, genome structures, and gene contents as well as high sequence divergence in non-coding regions. Abundant SSRs and dispersed repeats were identified. Five hotspots, psbI-trnS, trnR-atpA, petD-rpoA, rpl16-rps3, and trnN-ndhF, were detected among four species in Brownlowioideae. One hotspot, rps14-psaB, was observed in the two Brownlowia species. Additionally, phylogenetic analysis supported that the Brownlowia species has a close relationship with Pentace triptera. Moreover, rpoC2 was a candidate gene for adaptive evolution in the Brownlowia species compared to P. triptera. Thus, these chloroplast genomes present valuable genomic resources for further evolutionary and phylogenetic studies of mangroves and plant species in Malvaceae. Full article

Citrus huanglongbing (HLB) is one of the most severe diseases affecting the citrus industry, with Diaphorina citri (Hemiptera: Liviidae) serving as its primary natural vector. To understand the genetic diversity and population structure of D. citri in the context of HLB diffusion, we analyzed 13 populations from the HLB diffusion frontier and 25 populations from epidemic areas in China. The HLB diffusion frontier areas refer to the peripheral regions of HLB distribution in China, including the western Zhejiang, southern Jiangsu, northern Jiangxi, northern Hunan, and eastern Sichuan provinces. In contrast, the HLB epidemic areas represent regions in China where HLB is actively widespread and causing significant impacts. We utilized mitochondrial genes (COI, ND5, and Cytb) of D. citri and housekeeping genes (dnaQ, rpoC, and argH) of its endosymbiont Candidatus Carsonella ruddii (Ca. C. ruddii) for this analysis. Our findings revealed that the D. citri and Ca. C. ruddii in different regions showed low haplotype diversity and nucleotide diversity. While the genetic variation in D. citri populations primarily occurred within populations, the endosymbiont showed contrasting patterns in the HLB epidemic areas. We identified three dispersal paths: (1) migration of the Yunnan population to Sichuan, Guizhou, and Guangxi; (2) movement of the Guangdong population to Fujian, Jiangxi, and Zhejiang; and (3) dispersal of the Guangdong population to Hunan and Guangxi. Our study suggests that D. citri populations at the HLB diffusion frontier are predominantly transmitted from neighboring epidemic areas. Full article

The Hypericaceae family, comprising nine genera and over seven hundred species, includes Hypericum plants traditionally used for medicinal purposes. In this study, we performed high-throughput sequencing on three Hypericum species: Hypericum acmosepalum, Hypericum addingtonii, and Hypericum beanii, and conducted comparative genomic analyses with related species. The chloroplast genome sizes were 152,654 bp, 122,570 bp, and 137,652 bp, respectively, with an average GC content of 37.9%. All genomes showed a quadripartite structure, with significant variations in IR regions (3231–26,846 bp). The total number of genes ranged from 91 to 129. SSRs were predominantly located in the LSC region, with mononucleotide repeats being dominant. Comparative analysis identified several hotspot regions, including accD, rpoC2, rpoB, and rpl22 in the LSC region and matK, rpl32, rpl33, and rps4 in the SSC region. Nucleotide polymorphism analysis revealed eight highly variable regions and eleven gene loci, providing potential molecular markers for species identification. Phylogenetic analysis indicated that Triadenum and Cratoxylum are closely related to Hypericum, with H. acmosepalum and H. beanii being closest relatives and Hypericum hookerianum as their sister species. These findings provide molecular tools for species identification and insights for conservation strategies of medicinal Hypericum species. Full article

To better understand host–phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host rpoC gene, which encodes the RNA polymerase β’ subunit. To examine the hypothesis that mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and rpoC_G17D mutant cultures infected with phage K, at different timepoints after infection. Infection of the WT host led to a steady increase of phage transcription relative to the host. Our analysis allowed us to define 53 transcriptional units and to categorize genes based on their temporal expression patterns. Predicted promoter sequences defined by conserved −35, −10, and, in some cases, extended −10 elements, were found upstream of early and middle genes. However, in many cases, sequences upstream of late genes did not contain clear, complete, canonical promoter sequences, suggesting that factors in addition to host RNA polymerase are required for their expression. Infection of the rpoC_G17D mutant host led to a transcriptional pattern that was similar to that of the WT at early timepoints. However, beginning at 20 min after infection, transcription of late genes (such as phage structural genes and host lysis genes) was severely reduced. Our data indicate that the rpoC_G17D mutation prevents the expression of phage late genes, resulting in a failed infection cycle for phage K. In addition to illuminating the global transcriptional landscape of phage K throughout the infection cycle, this study will inform our investigations into the basis of phage K’s control of its transcriptional program as well as mechanisms of phage resistance. Full article

Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes were chosen and samples were collected for the current study. For molecular analysis, gDNA was isolated from the fresh leaves, and the five most effective angiosperm-specific markers, ITS2, rbcLa, rbcLc, rpoC1, and UBE3, were utilized. Based on amplification, sequencing, and identification success rates, ITS2 and UBE3 were recorded as the most efficient markers followed by rbcLa, rbcLc, and rpoC1. Results: During phylogenetic analysis, the query genotype-1 based on ITS2 and genotype-2 based on UBE3 clustered with (KF454101.1-Juglans regia) and (KC870919.1-J. regia) with bootstraps of 56 and 100, respectively. Genotype-3 based on rbcla clustered in a major clade with J. regia L., cultivars (MN397935.1 J. regia ‘Vina’) and (MN397934.1-J. regia ‘Serr’), (MN397933.1 J. regia ‘Pedro’), (MN397932.1 J. regia ‘Lara’), (MN397931.1 J. regia ‘Howard’), and (MN397930.1 J. regia ‘Hartley’) with bootstrap of 100. Meanwhile, genotype-4 and genotype-5 based on rbclc and rpoC1 clustered with (MN397935.1 J. regia ‘Vina’) and (MN397934.1 J. regia ‘Serr’), across the database sequences. To clarify the taxonomic status of cryptic walnut genotypes, it is necessary to combine diverse DNA barcodes. The results of ITS2 and UBE3, followed by rbcL barcoding markers, are promising taxonomic tools for cryptic walnut genotypes in Pakistan. Conclusions: It has been determined that the genotypes of walnuts in the study area are both J. regia L. and its cultivars and that the accuracy of discrimination regarding the genus Juglans L. is greater than 90%. The reported DNA barcodes are recommended for the correct identification and genetic evaluation of Juglans taxa and its population. Full article

Background/Objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa. Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment. Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired. Full article

Background: Retained products of conception after childbirth or miscarriage are associated with an increased rate of maternal complications, such as abnormal vaginal bleeding and infections. Late complications may also include intrauterine adhesions, causing infertility. Surgical interventions carry a certain risk. Thus, conservative management is often discussed as an alternative. The aim of this study was to assess the clinical outcomes of patients with retained products of conception, comparing a primary surgical approach to conservative management. Methods: We conducted a retrospective cohort study of 88 patients diagnosed with retained products of conception after 23+0 weeks of gestation at the Medical University Vienna between 2014 and 2022. Results: Forty-seven (53.4%) patients underwent primary surgical management and 41 (46.6%) primary conservative management. After primary conservative treatment, a complication could be observed in 10 (24.4%) women. In contrast, complications occurred in 32 (68.1%) women in the group with primary surgical treatment (p < 0.001). The most common complication in both groups was the ongoing suspicion of retained products of conception. Patients after primary surgical treatment were significantly more likely to require a secondary change in treatment (p < 0.001). Ultimately, secondary conservative management was applied in 30 (63.8%) patients. In contrast, only nine (21.95%) patients with primary conservative management required secondary surgical management. Conclusions: Due to the high risk of complications and persistent retained products of conception, primary surgical management should only be prioritized in hemodynamically instable or septic patients. Full article