A survey of BWT variants for string collections.

MOTIVATION: In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have been developed for computing the BWT of string collections. While the focus has been on improving efficiency, both in space and time, the exact definition of the BWT employed has not been at the center of attention. As we show in this paper, the different tools in use often compute non-equivalent BWT variants: the resulting transforms can differ from each other significantly, including the number r of runs, a central parameter of the BWT. Moreover, with many tools, the transform depends on the input order of the collection. In other words, on the same dataset, the same tool may output different transforms if the dataset is given in a different order. RESULTS: We studied 18 dedicated tools for computing the BWT of string collections and were able to identify 6 different BWT variants computed by these tools. We review the differences between these BWT variants, both from a theoretical and from a practical point of view, comparing them on 8 real-life biological datasets with different characteristics. We find that the differences can be extensive, depending on the datasets, and are largest on collections of many similar short sequences. The parameter r, the number of runs of the BWT, also shows notable variation between the different BWT variants; on our datasets, it varied by a multiplicative factor of up to 4.2. AVAILABILITY: Source code and scripts to replicate the results and download the data used in the article are available at https://github.com/davidecenzato/BWT-variants-for-string-collections. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1.

cAMP response element-binding protein (CREB) regulated transcriptional coactivator 2 (CRTC2) is a critical transcription factor that maintains glucose homeostasis by activating CREB. Energy homeostasis is maintained through multiple pathways; therefore, CRTC2 may interact with other transcription factors, particularly under metabolic stress. CRTC2 liver-specific KO mice were created, and the global proteome, phosphoproteome, and acetylome from liver tissue under high-fat diet conditions were analyzed using liquid chromatography-tandem mass spectrometry and bioinformatics analysis. Differentially regulated proteins (DRPs) were enriched in metabolic pathways, which were subsequently corroborated through animal experiments. The consensus DRPs from these datasets were used as seed proteins to generate a protein-protein interaction network using STRING, and GeneMANIA identified fatty acid synthase as a mutually relevant protein. In an additional local-protein-protein interaction analysis of CRTC2 and fatty acid synthase with DRPs, sterol regulatory element binding transcription factor 1 (SREBF1) was the common mediator. CRTC2-CREB and SREBF1 are transcription factors, and DNA-binding motif analysis showed that multiple CRTC2-CREB-regulated genes possess SREBF1-binding motifs. This indicates the possible induction by the CRTC2-SREBF1 complex, which is validated through luciferase assay. Therefore, the CRTC2-SREBF1 complex potentially modulates the transcription of multiple proteins that fine-tune cellular metabolism under metabolic stress.

The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland.

To date, very few mass spectrometry (MS)-based proteomics studies are available on the anterior and posterior lobes of the pituitary. In the past, MS-based investigations have focused exclusively on the whole pituitary gland or anterior pituitary lobe. In this study, for the first time, we performed a deep MS-based analysis of five anterior and five posterior matched lobes to build the first lobe-specific pituitary proteome map, which documented 4090 proteins with isoforms, mostly mapped into chromosomes 1, 2, and 11. About 1446 differentially expressed significant proteins were identified, which were studied for lobe specificity, biological pathway enrichment, protein-protein interaction, regions specific to comparison of human brain and other neuroendocrine glands from Human Protein Atlas to identify pituitary-enriched proteins. Hormones specific to each lobe were also identified and validated with parallel reaction monitoring-based target verification. The study identified and validated hormones, growth hormone and thyroid-stimulating hormone subunit beta, exclusively to the anterior lobe whereas oxytocin-neurophysin 1 and arginine vasopressin to the posterior lobe. The study also identified proteins POU1F1 (pituitary-specific positive transcription factor 1), POMC (pro-opiomelanocortin), PCOLCE2 (procollagen C-endopeptidase enhancer 2), and NPTX2 (neuronal pentraxin-2) as pituitary-enriched proteins and was validated for their lobe specificity using parallel reaction monitoring. In addition, three uPE1 proteins, namely THEM6 (mesenchymal stem cell protein DSCD75), FSD1L (coiled-coil domain-containing protein 10), and METTL26 (methyltransferase-like 26), were identified using the NeXtProt database, and depicted tumor markers S100 proteins having high expression in the posterior lobe. In summary, the study documents the first matched anterior and posterior pituitary proteome map acting as a reference control for a better understanding of functional and nonfunctional pituitary adenomas and extrapolating the aim of the Human Proteome Project towards the investigation of the proteome of life.

Adaptive Signal Modulation Evolved by the Inherent Nonlinearity of Phase-Change Quantum-Dot String.

To simulate a topological neural network handling weak signals via stochastic resonance (SR), it is necessary to introduce an inherent nonlinearity into nanoscale devices. We use the self-assembly method to successfully fabricate a phase-change quantum-dot string (PCQDS) crossing Pd/Nb:AlNO/AlNO/Nb:AlNO/Pd multilayer. The inherent nonlinearity of phase change couples with electron tunneling so that PCQDS responds to a long signal sequence in a modulated output style, in which the pulse pattern evolves to that enveloped by two sets of periodic wave characterized by neural action potential. We establish an SR mode consisting of several two-state systems in which dissipative tunneling is coupled to environment. Size oscillations owing to NbO QDs adaptively adjust barriers and wells, such that tunneling can be periodically modulated by either asymmetric energy or local temperature. When the external periodic signals are applied, the system first follows the forcing frequency. Subsequently, certain PCQDs oscillate independently and consecutively to produce complicated frequency and amplitude modulations.

Studying the O-GlcNAcome of human placentas using banked tissue samples.

O-GlcNAcylation is a dynamic modulator of signaling pathways, equal in magnitude to the widely studied phosphorylation. With the rapid development of tools for its detection at the single protein level, the O-GlcNAc modification rapidly emerged as a novel diagnostic and therapeutic target in human diseases. Yet, mapping the human O-GlcNAcome in various tissues is essential for generating relevant biomarkers. In this study, we used human banked tissue as a sample source to identify O-GlcNAcylated protein targets relevant to human diseases. Using human term placentas, we propose (1) a method to clean frozen banked tissue of blood proteins; (2) an optimized protocol for the enrichment of O-GlcNAcylated proteins using immunoaffinity purification; and (3) a bioinformatic workflow to identify the most promising O-GlcNAc targets. As a proof-of-concept, we used 45 mg of banked placental samples from two pregnancies to generate intracellular protein extracts depleted of blood protein. Then, antibody-based O-GlcNAc enrichment on denatured samples yielded over 2000 unique HexNAc PSMs and 900 unique sites using 300 µg of protein lysate. Due to efficient sample cleanup, we also captured 82 HexNAc proteins with high placental expression. Finally, we provide a bioinformatic tool (CytOVS) to sort the HexNAc proteins based on their cellular localization and extract the most promising O-GlcNAc targets to explore further. To conclude, we provide a simple 3-step workflow to generate a manageable list of O-GlcNAc proteins from human tissue and improve our understanding of O-GlcNAcylation's role in health and diseases.

Mitochondrial dysfunction in the pathophysiology of renal diseases.

Mitochondria are essential organelles in the human body, serving as the metabolic factory of the whole organism. When mitochondria are dysfunctional, it can affect all organs of the body. The kidney is rich in mitochondria, and its function is closely related to the development of kidney diseases. Studying the relationship between mitochondria and kidney disease progression is of great interest. In the past decade, scientists have made inspiring progress in investigating the role of mitochondria in the pathophysiology of renal diseases. This article discusses various mechanisms for maintaining mitochondrial quality, including mitochondrial energetics, mitochondrial biogenesis, mitochondrial dynamics, mitochondrial DNA repair, mitochondrial proteolysis and the unfolded protein response, mitochondrial autophagy, mitochondria-derived vesicles, and mitocytosis. The article also highlights the cross talk between mitochondria and other organelles, with a focus on kidney diseases. Finally, the article concludes with an overview of mitochondria-related clinical research.

Gene-gene interaction network analysis indicates CNTN2 is a candidate gene for idiopathic generalized epilepsy.

Twin and family studies have established the genetic contribution to idiopathic generalized epilepsy (IGE). The genetic architecture of IGE is generally complex and heterogeneous, and the majority of the genetic burden in IGE remains unsolved. We hypothesize that gene-gene interactions contribute to the complex inheritance of IGE. CNTN2 (OMIM* 615,400) variants have been identified in cases with familial adult myoclonic epilepsy and other epilepsies. To explore the gene-gene interaction network in IGE, we took the CNTN2 gene as an example and investigated its co-occurrent genetic variants in IGE cases. We performed whole-exome sequencing in 114 unrelated IGE cases and 296 healthy controls. Variants were qualified with sequencing quality, minor allele frequency, in silico prediction, genetic phenotype, and recurrent case numbers. The STRING_TOP25 gene interaction network analysis was introduced with the bait gene CNTN2 (denoted as A). The gene-gene interaction pair mode was presumed to be A + c, A + d, A + e, with a leading gene A, or A + B + f, A + B + g, A + B + h, with a double-gene A + B, or other combinations. We compared the number of gene interaction pairs between the case and control groups. We identified three pairs in the case group, CNTN2 + PTPN18, CNTN2 + CNTN1 + ANK2 + ANK3 + SNTG2, and CNTN2 + PTPRZ1, while we did not discover any pairs in the control group. The number of gene interaction pairs in the case group was much more than in the control group (p = 0.021). Taking together the genetic bioinformatics, reported epilepsy cases, and statistical evidence in the study, we supposed CNTN2 as a candidate pathogenic gene for IGE. The gene interaction network analysis might help screen candidate genes for IGE or other complex genetic disorders.

Detection of Helicobacter pylori Infection in Human Gastric Fluid Through Surface-Enhanced Raman Spectroscopy Coupled With Machine Learning Algorithms.

Diagnostic methods for Helicobacter pylori infection include, but are not limited to, urea breath test, serum antibody test, fecal antigen test, and rapid urease test. However, these methods suffer drawbacks such as low accuracy, high false-positive rate, complex operations, invasiveness, etc. Therefore, there is a need to develop simple, rapid, and noninvasive detection methods for H. pylori diagnosis. In this study, we propose a novel technique for accurately detecting H. pylori infection through machine learning analysis of surface-enhanced Raman scattering (SERS) spectra of gastric fluid samples that were noninvasively collected from human stomachs via the string test. One hundred participants were recruited to collect gastric fluid samples noninvasively. Therefore, 12,000 SERS spectra (n = 120 spectra/participant) were generated for building machine learning models evaluated by standard metrics in model performance assessment. According to the results, the Light Gradient Boosting Machine algorithm exhibited the best prediction capacity and time efficiency (accuracy = 99.54% and time = 2.61 seconds). Moreover, the Light Gradient Boosting Machine model was blindly tested on 2,000 SERS spectra collected from 100 participants with unknown H. pylori infection status, achieving a prediction accuracy of 82.15% compared with qPCR results. This novel technique is simple and rapid in diagnosing H. pylori infection, potentially complementing current H. pylori diagnostic methods.

Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

A knowledge-based grouping of genes into pathways or functional units is essential for describing and understanding cellular complexity. However, it is not always clear a priori how and at what level of specificity functionally interconnected genes should be partitioned into pathways, for a given application. Here, we assess and compare nine existing and two conceptually novel functional classification systems, with respect to their discovery power and generality in gene set enrichment testing. We base our assessment on a collection of nearly 2000 functional genomics datasets provided by users of the STRING database. With these real-life and diverse queries, we assess which systems typically provide the most specific and complete enrichment results. We find many structural and performance differences between classification systems. Overall, the well-established, hierarchically organized pathway annotation systems yield the best enrichment performance, despite covering substantial parts of the human genome in general terms only. On the other hand, the more recent unsupervised annotation systems perform strongest in understudied areas and organisms, and in detecting more specific pathways, albeit with less informative labels.

Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany.

BACKGROUND: Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany. METHODS: A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared. RESULTS: WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains. CONCLUSIONS: Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.

Are comparable studies really comparable? Suggestions from a problem-solving experiment on urban and rural great tits.

Performance in tests of various cognitive abilities has often been compared, both within and between species. In intraspecific comparisons, habitat effects on cognition has been a popular topic, frequently with an underlying assumption that urban animals should perform better than their rural conspecifics. In this study, we tested problem-solving ability in great tits Parus major, in a string-pulling and a plug-opening test. Our aim was to compare performance between urban and rural great tits, and to compare their performance with previously published problem solving studies. Our great tits perfomed better in string-pulling than their conspecifics in previous studies (solving success: 54%), and better than their close relative, the mountain chickadee Poecile gambeli, in the plug-opening test (solving success: 70%). Solving latency became shorter over four repeated sessions, indicating learning abilities, and showed among-individual correlation between the two tests. However, the solving ability did not differ between habitat types in either test. Somewhat unexpectedly, we found marked differences between study years even though we tried to keep conditions identical. These were probably due to small changes to the experimental protocol between years, for example the unavoidable changes of observers and changes in the size and material of test devices. This has an important implication: if small changes in an otherwise identical set-up can have strong effects, meaningful comparisons of cognitive performance between different labs must be extremely hard. In a wider perspective this highlights the replicability problem often present in animal behaviour studies.

Colorectal eversion technique combined with modified single-stapled double-purse-string low colorectal anastomosis.

AIM: Total mesorectal excision with adequate free margins is the gold standard for rectal surgery. Applying a linear stapler in a narrow pelvis can be challenging and the proper distal margin difficult to assess. In selected cases the colorectal eversion technique combined with single-stapled double-purse-string anastomosis (SSDP) can be a practical solution. METHOD: Eleven patients, six men and five women, mean body mass index 27 ± 1.3 kg/m2, underwent total mesorectal excision with the colorectal eversion technique combined with modified SSDP between September 2022 and January 2023. RESULTS: The mean operative time was 190 min. The mean hospital stay was 4 days. There were no postoperative complications. The final histology showed complete mesorectal resection, circumferential resection margin negative, free distal resection margin, anastomotic doughnuts negative. At 7 ± 3 months follow-up there was no evidence of local recurrence or distant metastasis. CONCLUSION: The colorectal eversion technique combined with modified SSDP is a reproducible and safe technique in selected patients. Prospective randomized trials with large patient series are needed to confirm our preliminary results.

Comparison of purse-string technique vs linear suture for skin closure after ileostomy reversal. A randomized controlled trial.

BACKGROUND: Protective stoma after rectal surgery has been associated with important complications. The most common is surgical site infection (SSI) high rates after stoma reversal reported in literature. Our study compared the rate of SSI of two skin closure techniques, linear closure, and purse string closure. METHODS: We carried out a single center, prospective, randomized controlled trial in the Department of Colorectal Surgery of Fondazione Policlinico Campus Bio-Medico of Rome between January 2018 through December 2021, to compare LC vs PS closure of ileostomy sites. RESULTS: A total of 117 patients (53.84% male) with a mean age of 65.68 ± 14.33 years were finally evaluated in the study. 58 patients were included in the PS group and 59 patients in the LC one. There was a marked difference in the SSI rate between the two arms of the study: 3 of 58 patients in the purse-string arm versus 11 of 59 in the control arm (p = 0.043). The outcome of cosmesis was also higher in PS, with a statistical significance (mean ± DS 4,01 ± 0,73 for PS group vs mean ± DS 2,38 ± 0,72 for LC group, p < 0,001). CONCLUSION: Our study demonstrated that the PS technique had a significantly lower incidence of stoma site SSI compared with LC technique. Our findings are in line with other randomized studies and suggest that PS closure could be considered as standard of care for wound closure after ileostomy reversal.

Investigations of carbapenem resistant and hypervirulent Klebsiella pneumoniae.

Hypervirulent Klebsiella pneumoniae is an emerging pathogen that has gained attention due to its increased ability to cause infections even in healthy individuals. The aim of this study is to investigate virulence factors in K. pneumoniae strains isolated from clinical specimens and their association with carbapenem resistance. The study was conducted on 260 isolates identified between 2018 and 2023 at the Mohammed V Military Teaching Hospital in Rabat, Morocco. The isolates were categorized based on their susceptibility to antibiotics. The hypermucoviscosity was determined by a string test, while the presence of capsular serotypes and virulence genes were identified by PCR. Among our strains, 6.2% (n = 16) exhibited hypervirulent characteristics, 56% were resistant to carbapenem. Notably, 5.7% (n = 6) of carbapenem-resistant isolates expressed the hypermucoviscous phenotype, while 1.5% (n = 2) of carbapenem-susceptible K. pneumoniae isolates exhibited the same trait. In our study, we found that a total of 10 isolates (3.8%) had virulent capsular serotypes, with K2 being the most prevalent 40% (n = 4) and K20 in 30% (n = 3). Furthermore, we detected the presence of the Aerobactin gene in 1.5% (n = 4) of the isolates examined. Based on our findings, it appears that there was no correlation between the presence of virulence factors and carbapenem resistance. In conclusion, identifying hypervirulent K. pneumoniae in clinical specimens and assessing their antibiotic resistance profiles are crucial to ensure effective therapy and to prevent outbreaks.

Use of high-pressure processing and low-temperature storage to extend the performance shelf-life of two types of String cheese.

The manufacturing method of String cheese is similar to Mozzarella, but the hot curd is extruded through narrow tubes or pipes, which align the protein fibers that provides the characteristic ability for consumers to pull strings from this cheese. Firmness is another important performance attribute for consumers who just bite into the String cheese without peeling off strings. There have only been a few studies on String cheese, but it is known that stringiness and firmness decrease during prolonged storage, which is a particular challenge for exporting String cheese. We explored 2 treatments to try to retain the stringiness and firmness of String cheese for longer storage periods. The techniques used were high pressure processing (HPP; 600 MPa for 3 min) and reduced storage temperature (0°C). In other cheese varieties, these techniques have helped extend the performance shelf-life. We tested these techniques using the 2 main types of commercial String cheese: direct acid (DASC) and cultured String cheese (CSC), that were obtained from 2 different manufacturing facilities. The DASC had higher fat (∼2.2%) and higher pH values (∼0.2 units) compared with the CSC. The CSC had higher protein content (∼3.4%), higher insoluble calcium content (∼8 mg insoluble Ca/g protein) and higher hardness values (∼4 N) compared with the DASC. Due to the compositional differences, the 2 varieties were statistically analyzed separately for all other attributes. In both cheese types, HPP caused an immediate reduction in stringiness, some solubilization of insoluble calcium, and a slight increase in the cheese pH values. HPP also caused a slight increase in the TPA hardness of the CSC samples until 14 d (possibly due to a slight increase in cheese pH). The use of the 0°C storage temperature reduced proteolysis and helped retain firmness during storage. Low temperature storage could help extend the performance shelf-life of String cheese by a couple of months, but HPP was not suitable as the process caused an immediate reduction in stringiness due to the disruption of the matrix induced by the HPP treatment.

Modified Q-type purse-string suture duodenal stump embedding method for laparoscopic gastrectomy for gastric cancer.

OBJECTIVE: This study introduced the modified Q-type purse-string suture duodenal stump embedding method, a convenient way to strengthen the duodenum, and compared it to the conventional one to assess its efficacy and safety. METHODS: This retrospective analysis examined 612 patients who received laparoscopic gastrectomy for gastric Cancer at a single center. The patients were divided into Not Reinforced Group (n = 205) and Reinforced Group (n = 407) according to the surgical approach to the duodenal stump. The reinforced group was further divided into a modified Q-type purse-string suture embedding method group (QM, n = 232) and a conventional suture duodenal stump embedding method group (CM, n = 175) according to the methods of duodenal stump enhancement. Clinicopathological characteristics, operative variables, and short-term complications were documented and analyzed. RESULTS: The incidence of duodenal stump leakage(DSL) in the Not Reinforced Group was higher compared to the Reinforced Group, although the difference was not statistically significant [2.4% (5/205) vs 0.7% (3/407), p = 0.339]. Additionally, the Not Reinforced Group exhibited a higher rate of Reoperation due to DSL compared to the Reinforced Group [2 (1.0%) vs. 0, p = 0.046], with one patient in the Not Reinforced Group experiencing mortality due to DSL [1 (0.5%) vs 0, p = 0.158]. Subgroup analysis within the Reinforced Group revealed that the modified Q-type purse-string suture embedding group (QM) subgroup demonstrated statistically significant advantages over the conventional suture embedding group (CM) subgroup. QM exhibited shorter purse-string closure times (4.11 ± 1.840 vs. 6.05 ± 1.577, p = 0.001), higher purse-string closure success rates (93.1% vs. 77.7%, p = 0.001), and greater satisfaction with purse-string closure [224 (96.6%) vs 157 (89.7%), p = 0.005]. No occurrences of duodenal stump leakage were observed in the QM subgroup, while the CM subgroup experienced two cases [2 (1.1%)], though the difference was not statistically significant. Both groups did not exhibit statistically significant differences in secondary surgery or mortality related to duodenal stump leakage. CONCLUSION: Duodenal Stump Leakage (DSL) is a severe but low-incidence complication. There is no statistically significant relationship between the reinforcement of the duodenal stump and the incidence of DSL. However, laparoscopic reinforcement of the duodenal stump can reduce the severity of fistulas and the probability of Reoperation. The laparoscopic Q-type purse-string suture duodenal stump embedding method is a simple and effective technique that can, to some extent, shorten the operation time and enhance satisfaction with purse-string closure. There is a trend towards reducing the incidence of DSL, thereby improving patient prognosis to a certain extent.

Stretchable Nanofiber-Based Felt as a String Electrode for Potential Use in Wearable Glucose Biosensors.

Nanofiber technology is leading the revolution of wearable technology and provides a unique capability to fabricate smart textiles. With the novel fabrication technique of electrospinning, nanofibers can be fabricated and then manufactured into a durable conductive string for the application of smart textiles. This paper presents an electrospun nanofiber mesh-based (NF-Felt) string electrode with a conducting polymer coating for an electrochemical enzymatic glucose sensor. The surface area of a nanofiber matrix is a key physical property for enhanced glucose oxidase (GOx) enzyme binding for the development of an electrochemical biosensor. A morphological characterization of the NF-Felt string electrode was performed using scanning electron microscopy (SEM) and compared with a commercially available cotton-polyester (Cot-Pol) string coated with the same conducting polymer. The results from stress-strain testing demonstrated high stretchability of the NF-Felt string. Also, the electrochemical characterization results showed that the NF-Felt string electrode was able to detect a glucose concentration in the range between 0.0 mM and 30.0 mM with a sensitivity of 37.4 µA/mM·g and a detection limit of 3.31 mM. Overall, with better electrochemical performance and incredible flexibility, the NF-Felt-based string electrode is potentially more suitable for designing wearable biosensors for the detection of glucose in sweat.

Comprehensive Characterization of the C3HC4 RING Finger Gene Family in Potato (Solanum tuberosum L.): Insights into Their Involvement in Anthocyanin Biosynthesis.

The C3HC4 RING finger gene (RING-HC) family is a zinc finger protein crucial to plant growth. However, there have been no studies on the RING-HC gene family in potato. In this study, 77 putative StRING-HCs were identified in the potato genome and grouped into three clusters based on phylogenetic relationships, the chromosome distribution, gene structure, conserved motif, gene duplication events, and synteny relationships, and cis-acting elements were systematically analyzed. By analyzing RNA-seq data of potato cultivars, the candidate StRING-HC genes that might participate in tissue development, abiotic stress, especially drought stress, and anthocyanin biosynthesis were further determined. Finally, a StRING-HC gene (Soltu.DM.09G017280 annotated as StRNF4-like), which was highly expressed in pigmented potato tubers was focused on. StRNF4-like localized in the nucleus, and Y2H assays showed that it could interact with the anthocyanin-regulating transcription factors (TFs) StbHLH1 of potato tubers, which is localized in the nucleus and membrane. Transient assays showed that StRNF4-like repressed anthocyanin accumulation in the leaves of Nicotiana tabacum and Nicotiana benthamiana by directly suppressing the activity of the dihydroflavonol reductase (DFR) promoter activated by StAN1 and StbHLH1. The results suggest that StRNF4-like might repress anthocyanin accumulation in potato tubers by interacting with StbHLH1. Our comprehensive analysis of the potato StRING-HCs family contributes valuable knowledge to the understanding of their functions in potato development, abiotic stress, hormone signaling, and anthocyanin biosynthesis.

The Characterization of a Novel PrMADS11 Transcription Factor from Pinus radiata Induced Early in Bent Pine Stem.

A novel MADS-box transcription factor from Pinus radiata D. Don was characterized. PrMADS11 encodes a protein of 165 amino acids for a MADS-box transcription factor belonging to group II, related to the MIKC protein structure. PrMADS11 was differentially expressed in the stems of pine trees in response to 45° inclination at early times (1 h). Arabidopsis thaliana was stably transformed with a 35S::PrMADS11 construct in an effort to identify the putative targets of PrMADS11. A massive transcriptome analysis revealed 947 differentially expressed genes: 498 genes were up-regulated, and 449 genes were down-regulated due to the over-expression of PrMADS11. The gene ontology analysis highlighted a cell wall remodeling function among the differentially expressed genes, suggesting the active participation of cell wall modification required during the response to vertical stem loss. In addition, the phenylpropanoid pathway was also indicated as a PrMADS11 target, displaying a marked increment in the expression of the genes driven to the biosynthesis of monolignols. The EMSA assays confirmed that PrMADS11 interacts with CArG-box sequences. This TF modulates the gene expression of several molecular pathways, including other TFs, as well as the genes involved in cell wall remodeling. The increment in the lignin content and the genes involved in cell wall dynamics could be an indication of the key role of PrMADS11 in the response to trunk inclination.

Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field.

An external electric field is an effective tool to induce the polymorphic transformation of molecular crystals, which is important practically in the chemical, material, and energy storage industries. However, the understanding of this mechanism is poor at the molecular level. In this work, two types of order parameters (OPs) were constructed for the molecular crystal based on the intermolecular distance, bond orientation, and molecular orientation. Using the K-means clustering algorithm for the sampling of OPs based on the Euclidean distance and density weight, the polymorphic transformation of TNT was investigated using a finite temperature string (FTS) under external electric fields. The potential of mean force (PMF) was obtained, and the essence of the polymorphic transformation between o-TNT and m-TNT was revealed, which verified the effectiveness of the FTS method based on K-means clustering to OPs. The differences in PMFs between the o-TNT and transition state were decreased under external electric fields in comparison with those in no field. The fields parallel to the c-axis obviously affected the difference in PMF, and the relationship between the changes in PMFs and field strengths was found. Although the external electric field did not promote the convergence, the time of the polymorphic transformation was reduced under the external electric field in comparison to its absence. Moreover, under the external electric field, the polymorphic transformation from o-TNT to m-TNT occurred while that from m-TNT to o-TNT was prevented, which was explained by the dipole moment of molecule, relative permittivity, chemical potential difference, nucleation work and nucleation rate. This confirmed that the polymorphic transformation orientation of the molecular crystal could be controlled by the external electric field. This work provides an effective way to explore the polymorphic transformation of the molecular crystals at a molecular level, and it is useful to control the production process and improve the performance of energetic materials by using the external electric fields.