The predictive value of sonographic images of follicular lesions – a comparison with nodules unequivocal in FNA – single centre prospective study

Background

To determine the diagnostic efficacy of ultrasonographic malignancy risk features (UMRFs) in follicular lesions (FL) in a population with low risk of malignancy in FL and to compare it with a similar analysis in a group of patients with unequivocal cytology (UC): benign lesion (BL) or malignant neoplasm (MN).

Methods

Presence of UMRFs (hypoechogenicity, solid echostructure, taller-than-wide shape, pathological vascularization, irregular margins, microcalcifications and macrocalcifications) and their sets were assessed in 322 FL: 202 follicular lesions of undetermined significance (FLUS) and 120 suspicious for follicular neoplasm (SFN) and 300 nodules with UC: 200 BL and 100 MN, subsequently evaluated histopathologically.

Results

Cancers were confirmed in 100% nodules in MN group (89.0% of them were papillary carcinomas - PTC), in 6.4% FLUS nodules (69.2% PTC), and in 10.8% SFN nodules (30.8% PTC). In the UC group all UMRFs occurred more frequently in cancers than in benign lesions. In the FL group only calcifications were found in cancers more frequently – macro and microcalcifications together: 34.6 vs. 11.5% (p?=?0.001) and isolated macrocalcifications: 26.0 vs. 6.8% (p?=?0.001); the presence of those features increased the basic risk of malignancy in FL more than 2 times. The presence of at least 2 of the following URMFs: hypoechogenicity, solid echostructure, any type of calcifications and suspected shape, additionally improved sensitivity.

Conclusions

Evaluation of UMRFs in FLs is less effective than in nodules with UC, and its effectiveness decreases parallel to the decrease in percentage of PTCs among malignant neoplasms and to the increase of the percentage of adenomas among benign nodules. The presence of macrocalcifications in such FLs significantly increases the basic risk of malignancy in these nodules.

     

Functional role of metalloproteins in genome stability

Cells contain a large number of metalloproteins that commonly harbor at least one metal ion cofactor. In metalloproteins, metal ions are usually coordinated by oxygen, sulfur, or nitrogen centers belonging to amino acid residues in the protein. The presence of the metal ion in metalloproteins allows them to take part in diverse biological processes, such as genome stability, metabolic catalysis, and cell cycle progression. Clinically, alteration of the function of metalloproteins in mammals is genetically associated with diseases characterized by DNA damage and repair defects. The present review focuses on the current perspectives of metal ion homeostasis in different organisms and summarizes the most recent understanding on magnesium, copper, iron, and manganese-containing proteins and their functional involvement in the maintenance of genome stability.     

A comparative study of <Emphasis Type="Italic">k</Emphasis>-spectrum-based error correction methods for next-generation sequencing data analysis

Background

Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of distinction between true biological variants and sequence error alterations during downstream analysis. Many error correction methods have been developed to correct erroneous NGS reads before further analysis, but independent evaluation of the impact of such dataset features as read length, genome size, and coverage depth on their performance is lacking. This comparative study aims to investigate the strength and weakness as well as limitations of some newest k-spectrum-based methods and to provide recommendations for users in selecting suitable methods with respect to specific NGS datasets.

Methods

Six k-spectrum-based methods, i.e., Reptile, Musket, Bless, Bloocoo, Lighter, and Trowel, were compared using six simulated sets of paired-end Illumina sequencing data. These NGS datasets varied in coverage depth (10× to 120×), read length (36 to 100 bp), and genome size (4.6 to 143 MB). Error Correction Evaluation Toolkit (ECET) was employed to derive a suite of metrics (i.e., true positives, false positive, false negative, recall, precision, gain, and F-score) for assessing the correction quality of each method.

Results

Results from computational experiments indicate that Musket had the best overall performance across the spectra of examined variants reflected in the six datasets. The lowest accuracy of Musket (F-score?=?0.81) occurred to a dataset with a medium read length (56 bp), a medium coverage (50×), and a small-sized genome (5.4 MB). The other five methods underperformed (F-score?<?0.80) and/or failed to process one or more datasets.

Conclusions

This study demonstrates that various factors such as coverage depth, read length, and genome size may influence performance of individual k-spectrum-based error correction methods. Thus, efforts have to be paid in choosing appropriate methods for error correction of specific NGS datasets. Based on our comparative study, we recommend Musket as the top choice because of its consistently superior performance across all six testing datasets. Further extensive studies are warranted to assess these methods using experimental datasets generated by NGS platforms (e.g., 454, SOLiD, and Ion Torrent) under more diversified parameter settings (k-mer values and edit distances) and to compare them against other non-k-spectrum-based classes of error correction methods.

     

Adsorption of heavy metal from aqueous solution by dehydrated root powder of long-root Eichhornia crassipes

The root powder of long-root Eichhornia crassipes, as a new kind of biodegradable adsorbent, has been tested for aqueous adsorption of Pb, Zn, Cu, and Cd. From FT-IR, we found that the absorption peaks of phosphorous compounds, carbonyl, and nitrogenous compounds displayed obvious changes before and after adsorption which illustrated that plant characteristics may play a role in binding with metals. Surface properties and morphology of the root powders have been characterized by means of SEM and BET. Energy spectrum analysis showed that the metals were adsorbed on root powders after adsorption. Then, optimum quantity of powder, pH values, and metal ion concentrations in single-system and multi-system were detected to discuss the characteristics and mechanisms of metal adsorption. Freundlich model and the second-order kinetics equation could well describe the adsorption of heavy metals in single-metal system. The adsorption of Pb, Zn, and Cd in the multi-metal system decreased with the concentration increased. At last, competitive adsorption of every two metals on root powder proved that Cu and Pb had suppressed the adsorption performance of Cd and Zn.     

寄主植物挥发物对梨小食心虫受孕雌虫的引诱作用初探

梨小食心虫Grapholita molesta(Busck),是一种世界性的蛀果害虫。利用产卵选择试验研究了15种寄主植物挥发物对梨小食心虫受孕雌虫的产卵引诱活性。室内试验表明:受孕雌虫对不同挥发物的产卵选择趋性不同,其中对叶醇和己酸丁酯表现出明显的产卵选择趋性。为验证寄主挥发物对受孕雌虫的实际诱捕效果,进行了田间诱捕试验。结果发现,挥发物中己酸丁酯、苯甲腈、叶醇、E-2-己烯醛以及乙酸己酯诱捕到的雌虫均为受孕雌虫,显著高于空白对照及其他物质,其中己酸丁酯的平均诱捕量最多,苯甲腈次之,E-2-己烯醛、乙酸己酯这两种物质的平均诱捕量分别为第三、第四,叶醇的诱捕量低于乙酸己酯,其余物质的诱捕量均较低。综合室内及田间试验结果发现,寄主植物挥发物对受孕雌虫的引诱作用也随它们之间的作用距离表现出一定的差异性。     

Immobilized Metal Affinity Chromatography Coupled to Multiple Reaction Monitoring Enables Reproducible Quantification of Phospho-signaling

A major goal in cell signaling research is the quantification of phosphorylation pharmacodynamics following perturbations. Traditional methods of studying cellular phospho-signaling measure one analyte at a time with poor standardization, rendering them inadequate for interrogating network biology and contributing to the irreproducibility of preclinical research. In this study, we test the feasibility of circumventing these issues by coupling immobilized metal affinity chromatography (IMAC)-based enrichment of phosphopeptides with targeted, multiple reaction monitoring (MRM) mass spectrometry to achieve precise, specific, standardized, multiplex quantification of phospho-signaling responses. A multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay targeting phospho-analytes responsive to DNA damage was configured, analytically characterized, and deployed to generate phospho-pharmacodynamic curves from primary and immortalized human cells experiencing genotoxic stress. The multiplexed assays demonstrated linear ranges of ≥3 orders of magnitude, median lower limit of quantification of 0.64 fmol on column, median intra-assay variability of 9.3%, median inter-assay variability of 12.7%, and median total CV of 16.0%. The multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay enabled robust quantification of 107 DNA damage-responsive phosphosites from human cells following DNA damage. The assays have been made publicly available as a resource to the community. The approach is generally applicable, enabling wide interrogation of signaling networks.Cell signaling research is faced with the challenging task of interrogating increasingly large numbers of analytes in “systems biology” approaches, while maintaining the high standards of integrity and reproducibility traditionally associated with the scientific approach. For example, studies interrogating complex systems, such as protein signaling networks, require quantification technologies capable of sensitive, specific, multiplexable, and reproducible application. However, recent reports have highlighted alarmingly high rates of irreproducibility in fundamental biological and pre-clinical studies (1, 2), as well as poor performance of affinity reagents used in traditional proteomic assay and detection platforms (3, 4). There is an imminent need for high quality assays, including highly characterized standards and detailed documentation of processes and procedures (5). To improve the translation of cell signaling discoveries into clinical application, we need reproducible and transferable technologies that enable higher throughput quantification of protein phosphorylation.Signaling dynamics through post-translational modifications (e.g. phosphorylation) are predominantly measured by Western blotting. Although this technique has led to many discoveries and is the de facto “gold standard,” it suffers from many drawbacks. Western blotting is a low throughput approach applied to individual analytes (i.e. no multiplexing) and is susceptible to erroneous interpretation when applied quantitatively (6). Alternative immunoassay platforms have emerged (e.g. immunohistochemistry, ELISA, mass cytometry, and bead-based or planar arrays), but suffer from similar limitations, namely specificity issues (because of cross-reactivity of antibodies), poor standardization, and difficulties in multiplexing.One alternative for quantifying phosphorylation is targeted, multiple reaction monitoring (MRM)¹ MS, a widely deployed technique in clinical laboratories for quantification of small molecules (7, 8). MRM is now also well established for precise and specific quantification of endogenous, proteotypic peptides relative to spiked-in stable isotope-labeled internal standards (9–11), and MRM can be applied to phosphopeptides (12–18). MRM assays can be run at high multiplex levels (19–21) and can be standardized to be highly reproducible across laboratories (22–24), even on an international stage (25). Because phosphorylation typically occurs at sub-stoichiometric levels and because phosphopeptides must compete for ionization with more abundant peptides, mass spectrometry-based analysis of phosphorylation requires an analyte enrichment step. Immuno-affinity enrichment approaches using anti-phospho-tyrosine antibodies (26) or panels of antibodies targeting signaling nodes (27) have been implemented with shotgun mass spectrometry. Although anti-peptide antibodies can also be used to enrich individual phosphopeptides upstream of MRM (28), the generation of these reagents is time-consuming and costly, limiting widespread uptake.Phosphopeptide enrichment based on metal affinity chromatography has recently matured into a reproducible approach (29). Immobilized metal affinity chromatography (IMAC) is widely used in discovery phosphoproteomic studies to enrich phosphopeptides upstream of shotgun-based mass spectrometry (30, 31). We hypothesized that a subset of the cellular phosphoproteome with favorable binding characteristics to the IMAC resin might be reproducibly recovered for quantification when coupled with quantitative MRM mass spectrometry, enabling robust IMAC-MRM assays without the need for an antibody.In this report, we: (1) demonstrate the feasibility of generating analytically robust, multiplex IMAC-MRM assays for quantifying cellular phospho-signaling, (2) present a semi-automated, 96-well format magnetic bead-based protocol for IMAC enrichment, (3) provide a catalogue of phosphopeptides that are highly amenable to IMAC-MRM quantification, and (4) make publicly available standard operating protocols (SOP) and fit-for-purpose analytical validation data for IMAC-MRM assays targeting 107 phospho-analytes, providing a community resource for study of the DNA damage response. The data suggest that the IMAC-MRM approach is generally applicable to signaling pathways, enabling wider interrogation of signaling networks.     

High glucose concentration induces endothelial cell proliferation by regulating cyclin‐D2‐related miR‐98

Cyclin D2 is involved in the pathology of vascular complications of type 2 diabetes mellitus (T2DM). This study investigated the role of cyclin‐D2‐regulated miRNAs in endothelial cell proliferation of T2DM. Results showed that higher glucose concentration (4.5 g/l) significantly promoted the proliferation of rat aortic endothelial cells (RAOECs), and significantly increased the expression of cyclin D2 and phosphorylation of retinoblastoma 1 (p‐RB1) in RAOECs compared with those under low glucose concentration. The cyclin D2‐3′ untranslated region is targeted by miR‐98, as demonstrated by miRNA analysis software. Western blot also confirmed that cyclin D2 and p‐RB1 expression was regulated by miR‐98. The results indicated that miR‐98 treatment can induce RAOEC apoptosis. The suppression of RAOEC growth by miR‐98 might be related to regulation of Bcl‐2, Bax and Caspase 9 expression. Furthermore, the expression levels of miR‐98 decreased in 4.5 g/l glucose‐treated cells compared with those treated by low glucose concentration. Similarly, the expression of miR‐98 significantly decreased in aortas of established streptozotocin (STZ)‐induced diabetic rat model compared with that in control rats; but cyclin D2 and p‐RB1 levels remarkably increased in aortas of STZ‐induced diabetic rats compared with those in healthy control rats. In conclusion, this study demonstrated that high glucose concentration induces cyclin D2 up‐regulation and miR‐98 down‐regulation in the RAOECs. By regulating cyclin D2, miR‐98 can inhibit human endothelial cell growth, thereby providing novel therapeutic targets for vascular complication of T2DM.     

Microboring organisms in living stylasterid corals (Cnidaria,Hydrozoa)

Microboring or euendolithic microorganisms, which colonize and penetrate various carbonate substrates, are abundant in coral reef ecosystems and play a major role in reef carbonate dissolution. A few studies reported the presence of euendoliths in stylasterid coral skeletons but the biological identity, distribution and abundance of these microorganisms remain largely unknown. Observations of over 100 stylasterid colonies, collected in the Indo-Pacific area, revealed for the first time that the association between these corals and euendolith organisms appears to be quite common in shallow tropical waters. The most abundant euendolith was identified as a cryptic stage in the development of the rhodophyte Porphyra (Conchocelis stage). The euendoliths were observed in the skeletons of seven species of three genera (four Stylaster, two Distichopora and one Lepidotheca). The presence of euendoliths inside skeletons conferred a particular colour to the studied stylasterid corals. Distribution and abundance of microborings varied significantly among stylasterid species and among branches of a single colony and so did the colour of their skeletons. Colonization of skeletons and the associated colour distribution were almost uniform in some stylasterids, forming an upward gradually diminishing or sharply limited gradient. This study shows that patterns of euendolith colonization and growth in stylasterid skeletons may depend on the stage of the euendolith development as well as on their environmental requirements such as light exposure.