A Single Base Change in the csgD Promoter Resulted in Enhanced Biofilm in Swine-Derived Salmonella Typhimurium.

Pathogenic Salmonella strains causing gastroenteritis typically can colonize and proliferate in the intestines of multiple host species. They retain the ability to form red dry and rough (rdar) biofilms, as seen in Salmonella enterica serovar Typhimurium. Conversely, Salmonella serovar like Typhi, which can cause systemic infections and exhibit host restriction, are rdar-negative. In this study, duck-derived strains and swine-derived strains of S. Typhimurium locate on independent phylogenetic clades and display relative genomic specificity. The duck isolates appear more closely related to human blood isolates and invasive non-typhoidal Salmonella (iNTS), whereas the swine isolates were more distinct. Phenotypically, compared to duck isolates, swine isolates exhibited enhanced biofilm formation that was unaffected by the temperature. The transcriptomic analysis revealed the upregulation of csgDEFG transcription as the direct cause. This upregulation may be mainly attributed to the enhanced promoter activity caused by the G-to-T substitution at position -44 of the csgD promoter. Swine isolates have created biofilm polymorphisms by altering a conserved base present in Salmonella Typhi, iNTS, and most Salmonella Typhimurium (such as duck isolates). This provides a genomic characteristics perspective for understanding Salmonella transmission cycles and evolution.

Role of Graphene in Surface Plasmon Resonance-Based Biosensors.

This work explores the transformative role of graphene in enhancing the performance of surface plasmon resonance (SPR)-based biosensors. The motivation for this review stems from the growing interest in the unique properties of graphene, such as high surface area, excellent electrical conductivity, and versatile functionalization capabilities, which offer significant potential to improve the sensitivity, specificity, and stability of SPR biosensors. This review systematically analyzes studies published between 2010 and 2023, covering key metrics of biosensor performance. The findings reveal that the integration of graphene consistently enhances sensitivity. Specificity, although less frequently reported numerically, showed promising results, with high specificity achieved at sub-nanomolar concentrations. Stability enhancements are also significant, attributed to the protective properties of graphene and improved biomolecule adsorption. Future research should focus on mechanistic insights, optimization of integration techniques, practical application testing, scalable fabrication methods, and comprehensive comparative studies. Our findings provide a foundation for future research, aiming to further optimize and harness the unique physical properties of graphene to meet the demands of sensitive, specific, stable, and rapid biosensing in various practical applications.

Sex-Specific and Trimester-Specific Associations of Prenatal Exposure to Bisphenols, Parabens, and Triclosan with Neonatal Birth Size and Gestational Age.

Bisphenols, parabens, and triclosan (TCS) are common endocrine disrupters used in various consumer products. These chemicals have been shown to cross the placental barrier and affect intrauterine development of fetuses. In this study, we quantified serum levels of six bisphenols, five parabens, and TCS in 483 pregnant women from southern China. Quantile-based g-computation showed that combined exposure to bisphenols, parabens, and TCS was significantly (p < 0.05) and negatively associated with birth weight (ß = -39.9, 95% CI: -73.8, -6.1), birth length (ß = -0.19, 95% CI: -0.34, -0.04), head circumference (ß = -0.13, 95% CI: -0.24, -0.02), and thoracic circumference (ß = -0.16, 95% CI: -0.29, -0.04). An inverse correlation was also identified between mixture exposure and gestational age (ß = -0.12, 95% CI: -0.24, -0.01). Bisphenol A (BPA), bisphenol Z (BPZ), bisphenol AP (BPAP), propylparaben (PrP), and TCS served as the dominant contributors to the overall effect. In subgroup analyses, male newborns were more susceptible to mixture exposure than females, whereas the exposure-outcome link was prominent among pregnant women in the first and second trimesters. More evidence is warranted to elucidate the impacts of exposure to mixtures on birth outcomes, as well as the underlying mechanisms.

Introduction of a nationwide first-trimester anomaly scan in the Dutch national screening program.

BACKGROUND: A significant proportion of major fetal structural anomalies can be detected in the first trimester by ultrasound examination. However, the test performance of the first-trimester anomaly scan (FTAS) performed in a low-risk population as part of a nationwide prenatal screening program is unknown. Potential benefits of the FTAS include early detection of fetal anomalies, providing parents with more time for reproductive decision-making. OBJECTIVES: To investigate the uptake, test performance and time to a final prenatal diagnosis after referral. STUDY DESIGN: A nationwide implementation study was conducted in the Netherlands (November 2021-November 2022). The FTAS was performed between 12+3 and 14+3 weeks gestation by certified sonographers using a standard protocol. Women were referred to a tertiary care center if anomalies were suspected. Uptake, test performance and time to a final prenatal diagnosis (days between referral and date of final diagnosis/prognosis for reproductive decision-making) were determined. Test performance was calculated for first-trimester major congenital anomalies, such as anencephaly and holoprosencephaly and all diagnosed anomalies <24 weeks gestation. RESULTS: The FTAS uptake was 74.9% (129 704/173 129). In 1.0% (1 313/129 704), an anomaly was suspected, of which 54.9% (n=721) had abnormal findings on the detailed first-trimester diagnostic scan and 44.6% (n=586) showed normal results. In 0.5% (n=6), intra-uterine fetal death occurred. In the total group of 721 cases with abnormal findings, 332 structural anomalies, 117 genetic anomalies, 82 other findings (abnormal fetal biometry, sonomarkers, placental/umbilical cord anomaly, an-/oligohydramnios) and 189 cases with transient findings (defined as ultrasound findings which resolved <24 weeks gestation) were found, with one case having an unknown outcome. 0.9% (n=1164) of all cases with a normal FTAS were diagnosed with a fetal anomaly in the second trimester. Test performance included a sensitivity of 84.6% (126/149) for first-trimester major congenital anomalies and 31.6% (537/1701) for all types of anomalies. Specificity for all anomalies was 99.2% (98 055/98 830); positive predictive value 40.9% (537/1 312); negative predictive value 98.8% (98 055/99 219); positive likelihood ratio 40.3; negative likelihood ratio 0.7; false positive rate 0.8% (775/98 830) and false negative rate 68.4% (1 164/1 701). The median time to diagnosis for structural anomalies was 20 days (6-43 days; median GA 16+3), for genetic anomalies 17 days (8.5-27.5 days; median GA 15+6 weeks) and for first-trimester major congenital anomalies 9 days (5-22 days; median GA 14+6 weeks). CONCLUSIONS: The performance of a newly introduced nationwide FTAS in a low-risk population showed a high sensitivity for first-trimester major congenital anomalies and a lower sensitivity for all anomalies combined. The program was accompanied by a referral rate of 1.0%, of which 59.1% involved cases where anomalies were either not confirmed or resolved before 24 weeks gestation. Timing of diagnosis was around 16 weeks gestation for referred cases. To evaluate the balance between benefits and potential harm of the FTAS within a nationwide prenatal screening program, it is essential to assess the effectiveness of the program over time and to consider the perspectives of both women and their partners, as well as healthcare professionals.

Utility of an in-line somatic cell count sensor for selecting cows for dry-cow therapy.

Minimizing the use of antimicrobials at the end of lactation (dry cow therapy, DCT) requires categorization of cows as likely infected or uninfected. While microbiology is the gold standard for such categorization, the costs of doing so mean that indirect tests such as somatic cell count (SCC) are commonly used. An in-line SCC sensor (SenseHub In Line Somatic Cell Count, in-line SCC) is commercially available but its utility to differentiate cows eligible for dry cow therapy has not been assessed. This prospective diagnostic accuracy study was undertaken to define the sensitivity (Se) and specificity (Sp) of SenseHub SCC against cow-composite milk samples submitted for conventional microbiology. A secondary objective was to assess the utility of SenseHub SCC compared with the maximum (max DHI SCC) or last (last DHI SCC) SCC determined from cow-composite milk samples collected as part of routine herd production recording at monthly intervals throughout lactation. Cows (n = 1,544) from 4 spring-calving, predominantly pasture-fed dairy herds from 3 regions of New Zealand had cow-composite milk samples collected following aseptic teat end preparation immediately before or after the final milking of lactation. These samples were submitted for routine microbiology. The microbiology data from approximately half the cows (n = 770; training data set) were randomly selected after blocking for intramammary infection (IMI) status within herd and these data were used to determine the optimal predictor for indicating IMI from the in-line SCC data by maximizing the area under the receiver operator curve (AUC). The average of the in-line SCC over the final 12 weeks of lactation (in-line 12wSCC) was found to be the best predictor and used for further analyses. The Se and Sp of the in-line SCC for any IMI or for a major pathogen IMI (defined as presence of Staphylococcus aureus, Streptococcus dysgalactiae or Streptococcus uberis) was calculated using the test data set (n = 774). The AUC for the maximum and last DHI SCC were compared with that of the in-line 12wSCC. The cow-level prevalence of any IMI or a major IMI across the entire population was 50.6% and 14.2%, respectively. At a cutpoint of 150,000 cells/mL, Se and Sp of the in-line 12wSCC for any IMI was 0.68 (95%CI 0.64-0.72) and 0.71 (95% CI 0.65-76), respectively, and the Se and Sp for a major pathogen IMI was 0.89 (95%CI 0.82-0.95) and 0.51 (95% CI 0.47-0.55), respectively. The AUC for a major pathogen IMI was 0.82 (95% CI 0.79-0.86), 0.82 (95% CI 0.78-0.86) and 0.84 (95% CI 0.90-0.97) for in-line 12wSCC, max DHI SCC and last DHI SCC, respectively. These AUC did not differ and the AUC for the in-line 12wSCC was non-inferior to that of the last and maximum HT SCC (both P < 0.001). It was concluded that the in-line 12wSCC had an AUC, Se and Sp not different from DHI SCC data and hence this test has utility in selecting cows for different dry cow therapy treatments.

Combination of Capture-SELEX and Post-SELEX for procymidone-specific aptamer selection and broad-specificity aptamer discovery, and development of aptamer-based lateral flow assay.

BACKGROUND: Due to its wide application, procymidone has become one of the pesticides with high detection rates in supervision and sampling. Therefore, it is necessary to establish a rapid and efficient method for the detection of procymidone. However, an important bottleneck restricting the development of rapid detection methods of procymidone is that its specific recognition elements are rarely reported. In this work, Capture-SELEX and post-SELEX were used in aptamer screening, and the obtained aptamers were used to construct an aptamer-based lateral flow assay (LFA). RESULTS: Firstly, a specific aptamer Seq15 was obtained for procymidone by Capture-SELEX, and its dissociation constant (Kd) was 24.22 nM. Secondly, post-SELEX was used to analyze and modify Seq15 to improve its performance, and the Kd of the truncated sequence Seq15-2 was 21.28 nM. In addition to this, the broad-specificity aptamer Seq17-1 was obtained via post-SELEX. Seq17-1 could broadly recognize dicarboximide fungicides (procymidone, iprodione, chlozolinate, dimethachlon and vinclozolin) and their metabolic derivative (3,5-dichloroaniline). Finally, the specific aptamer-based LFA of procymidone was constructed, and the limit of detection (LOD) was 0.79 ng/mL. Meanwhile, the LODs of dicarboximide fungicides and their metabolic derivative were 0.62, 0.64, 0.71, 0.69, 0.64 and 0.66 ng/mL, respectively. The above LFAs were highly specific and stable, and had been successfully used for the detection of vegetable samples. SIGNIFICANCE: Under the combination of Capture-SELEX and Post-SELEX, this study not only provides specific recognition elements for rapid detection of procymidone, but also provides new ideas for the discovery of broad-specificity aptamers. Combining broad-specificity primary detection and single-specificity quantification, a composite aptamer-based LFA detection platform has been developed, which significantly improves detection efficiency.

Do extracellular vesicles have specific target cells?; Extracellular vesicle mediated embryo maternal communication.

Extracellular vesicles (EVs) serve as messengers for intercellular communication, yet the precise mechanisms by which recipient cells interpret EV messages remain incompletely understood. In this study, we explored how the origin of EVs, their protein cargo, and the recipient cell type influence the cellular response to EVs within an embryo implantation model. We treated two types of EVs to 6 different recipient cell types and expression of zinc finger protein 81 (ZNF81) gene expression in the recipient cells were quantified using quantitative polymerase chain reaction (qPCR). The proteomic contents of the EV cargos were also analyzed. The results showed that downregulation of the ZNF81 gene was a specific cellular response of receptive endometrial epithelial cells to trophoblast derived EVs. Protein cargo analysis revealed that the proteomic profile of EVs depends on their cell of origin and therefore may affect the recipient cell response to EVs. Furthermore, trophoblastic EVs were found to be specifically enriched with transcription factors such as CTNNB1 (catenin beta-1), HDAC2 (histone deacetylase 2), and NOTCH1 (neurogenic locus notch homolog protein 1), which are known regulators of ZNF81 gene expression. The current study provided compelling evidence supporting the existence of EV specificity, where the characteristics of both the EVs and the recipient cell type collectively contribute to regulating EV target specificity. Additionally, EV protein cargo analysis suggested a potential association between transcription factors and the specific functionality of trophoblastic EVs. This in vitro embryo implantation model and ZNF81 read-out provides a unique platform to study EV specific functionality in natural cell-cell communication.

Unleashing the Power of Evolution in Xylanase Engineering: Investigating the Role of Distal Mutation Regulation.

The drive to enhance enzyme performance in industrial applications frequently clashes with the practical limitations of exhaustive experimental screening, underscoring the urgency for more refined and strategic methodologies in enzyme engineering. In this study, xylanase Xyl-1 was used as the model, coupling evolutionary insights with energy functions to obtain theoretical potential mutants, which were subsequently validated experimentally. We observed that mutations in the nonloop region primarily aimed at enhancing stability and also encountered selective pressure for activity. Notably, mutations in this region simultaneously boosted the Xyl-1 stability and activity, achieving a 65% success rate. Using a greedy strategy, mutant M4 was developed, achieving a 12 °C higher melting temperature and doubled activity. By integration of spectroscopy, crystallography, and quantum mechanics/molecular mechanics molecular dynamics, the mechanism behind the enhanced thermal stability of M4 was elucidated. It was determined that the activity differences between M4 and the wild type were primarily driven by dynamic factors influenced by distal mutations. In conclusion, the study emphasizes the pivotal role of evolution-based approaches in augmenting the stability and activity of the enzymes. It sheds light on the unique adaptive mechanisms employed by various structural regions of proteins and expands our understanding of the intricate relationship between distant mutations and enzyme dynamics.

Host range of naturally and artificially evolved symbiotic bacteria for a specific host insect.

Diverse insects are intimately associated with specific symbiotic bacteria, where host and symbiont are integrated into an almost inseparable biological entity. These symbiotic bacteria usually exhibit host specificity, uncultivability, reduced genome size, and other peculiar traits relevant to their symbiotic lifestyle. How host-symbiont specificity is established at the very beginning of symbiosis is of interest but poorly understood. To gain insight into the evolutionary issue, we adopted an experimental approach using the recently developed evolutionary model of symbiosis between the stinkbug Plautia stali and Escherichia coli. Based on the laboratory evolution of P. stali-E. coli mutualism, we selected ΔcyaA mutant of E. coli as an artificial symbiont of P. stali that has established mutualism by a single mutation. In addition, we selected a natural cultivable symbiont of P. stali of relatively recent evolutionary origin. These artificial and natural symbiotic bacteria of P. stali were experimentally inoculated to symbiont-deprived newborn nymphs of diverse stinkbug species. Strikingly, the mutualistic E. coli was unable to establish infection and support growth and survival of all the stinkbug species except for P. stali, uncovering that host specificity can be established at a very early stage of symbiotic evolution. Meanwhile, the natural symbiont was able to establish infection and support growth and survival of several stinkbug species in addition to P. stali, unveiling that a broader host range of the symbiont has evolved in nature. Based on these findings, we discuss what factors are relevant to the establishment of host specificity in the evolution of symbiosis.IMPORTANCEHow does host-symbiont specificity emerge at the very beginning of symbiosis? This question is difficult to address because it is generally difficult to directly observe the onset of symbiosis. However, recent development of experimental evolutionary approaches to symbiosis has brought about a breakthrough. Here we tackled this evolutionary issue using a symbiotic Escherichia coli created in laboratory and a natural Pantoea symbiont, which are both mutualistic to the stinkbug Plautia stali. We experimentally replaced essential symbiotic bacteria of diverse stinkbugs with the artificial and natural symbionts of P. stali and evaluated whether the symbiotic bacteria, which evolved for a specific host, can establish infection and support the growth and survival of heterospecific hosts. Strikingly, the artificial symbiont showed strict host specificity to P. stali, whereas the natural symbiont was capable of symbiosis with diverse stinkbugs, which provide insight into how host-symbiont specificity can be established at early evolutionary stages of symbiosis.

Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.

In vitro assessments for the prediction of pharmacokinetic (PK) behavior of biotherapeutics can help identify corresponding liabilities significantly earlier in the discovery timeline. This can minimize the need for extensive early in vivo PK characterization, thereby reducing animal usage and optimizing resources. In this study, we recommend bolstering classical developability workflows with in vitro measures correlated with PK. In agreement with current literature, in vitro measures assessing nonspecific interactions, self-interaction, and FcRn interaction are demonstrated to have the highest correlations to clearance in hFcRn Tg32 mice. Crucially, the dataset used in this study has broad sequence diversity and a range of physicochemical properties, adding robustness to our recommendations. Finally, we demonstrate a computational approach that combines multiple in vitro measurements with a multivariate regression model to improve the correlation to PK compared to any individual assessment. Our work demonstrates that a judicious choice of high throughput in vitro measurements and computational predictions enables the prioritization of candidate molecules with desired PK properties.

Interpretation of results of PCR and B-D-glucan for the diagnosis of Pneumocystis Jirovecii Pneumonia in immunocompromised adults with acute respiratory failure.

BACKGROUND: The accuracy of a diagnostic test depends on its intrinsic characteristics and the disease incidence. This study aims to depict post-test probability of Pneumocystis pneumonia (PJP), according to results of PCR and Beta-D-Glucan (BDG) tests in patients with acute respiratory failure (ARF). MATERIALS AND METHODS: Diagnostic performance of PCR and BDG was extracted from literature. Incidence of Pneumocystis pneumonia was assessed in a dataset of 2243 non-HIV immunocompromised patients with ARF. Incidence of Pneumocystis pneumonia was simulated assuming a normal distribution in 5000 random incidence samples. Post-test probability was assessed using Bayes theorem. RESULTS: Incidence of PJP in non-HIV ARF patients was 4.1% (95%CI 3.3-5). Supervised classification identified 4 subgroups of interest with incidence ranging from 2.0% (No ground glass opacities; 95%CI 1.4-2.8) to 20.2% (hematopoietic cell transplantation, ground glass opacities and no PJP prophylaxis; 95%CI 14.1-27.7). In the overall population, positive post-test probability was 32.9% (95%CI 31.1-34.8) and 22.8% (95%CI 21.5-24.3) for PCR and BDG, respectively. Negative post-test probability of being infected was 0.10% (95%CI 0.09-0.11) and 0.23% (95%CI 0.21-0.25) for PCR and BDG, respectively. In the highest risk subgroup, positive predictive value was 74.5% (95%CI 72.0-76.7) and 63.8% (95%CI 60.8-65.8) for PCR and BDG, respectively. CONCLUSION: Although both tests yield a high intrinsic performance, the low incidence of PJP in this cohort resulted in a low positive post-test probability. We propose a method to illustrate pre and post-test probability relationship that may improve clinician perception of diagnostic test performance according to disease incidence in predefined clinical settings.

Short-term memory, attentional control and brain size in primates.

Brain size variability in primates has been attributed to various domain-specific socio-ecological factors. A recently published large-scale study of short-term memory abilities in 41 primate species (ManyPrimates 2022 Anim. Behav. Cogn. 9, 428-516. (doi:10.26451/abc.09.04.06.2022)) did not find any correlations with 11 different proxies of external cognitive demands. Here, we found that the interspecific variation in test performance shows correlated evolution with total brain size, with the relationship becoming tighter as species with small sample sizes were successively removed, whereas it was not predicted by the often-used encephalization quotient. In a subsample, we also found that the sizes of brain regions thought to be involved in short-term memory did not predict performance better than overall brain size. The dependence on brain size suggests that domain-general cognitive processes underlie short-term memory as tested by ManyPrimates. These results support the emerging notion that comparative studies of brain size do not generally identify domain-specific cognitive adaptations but rather reveal varying selections on domain-general cognitive abilities. Finally, because attentional processes beyond short-term memory also affect test performance, we suggest that the delayed response test can be refined.

Sensitivity and Specificity of a Screening Test for the Detection of Deficiencies in Visuo-Perceptual Skills.

This study determines the sensitivity and specificity of a screening test to detect perceptual abnormalities and whether there are differences between gender. Vision is a complex process involving visual perception. Any alterations can affect learning, so having a screening test in Spanish that is easy to use and reliable for timely diagnosis will reduce the percentage of visuo-perceptual interference during learning process. A total of 200 subjects participated, aged between 8 and 15 years old, with good visual acuity, and no strabismus, amblyopia, ocular pathology, or neurological damage. The Petrosyan questionnaire (screening test) was employed to identify symptoms associated with perceptual impairment, and a subsequent assessment was conducted to evaluate perceptual abilities. The mean age was 11.5 years (57% male; 44% female). The screening test indicated that 30% of the subjects were suspected of having perceptual alteration, while 24% were diagnosed with a real alteration in perceptual abilities. The sensitivity was 1 and the specificity was 0.92. The Spanish version of the Petrosyan questionnaire has high sensitivity and specificity values and is therefore considered very accurate for identifying the need for a perceptual assessment. There are statistically significant differences in perceptual abilities according to gender. The female group shows more symptomatology and a higher percentage of alteration in perceptual skills.

Comprehensive Study of the IBMP ELISA IgA/IgM/IgG COVID-19 Kit for SARS-CoV-2 Antibody Detection.

COVID-19 laboratory diagnosis primarily relies on molecular tests, highly sensitive during early infection stages with high viral loads. As the disease progresses, sensitivity decreases, requiring antibody detection. Since the beginning of the pandemic, serological tests have been developed and made available in Brazil, but their diagnostic performance varies. This study evaluated the IBMP ELISA IgA/IgM/IgG COVID-19 kit performance in detecting SARS-CoV-2 antibodies. A total of 90 samples, including 64 from COVID-19 patients and 26 pre-pandemic donors, were assessed based on time post symptom onset (0-7, 8-14, and 15-21 days). The kit showed 61% sensitivity, 100% specificity, and 72% accuracy overall. Sensitivity varied with time, being 25%, 57%, and 96% for 0-7, 8-14, and 15-21 days, respectively. Similar variations were noted in other commercial tests. The Gold ELISA COVID-19 (IgG/IgM) had sensitivities of 31%, 71%, and 100%, while the Anti-SARS-CoV-2 NCP ELISA (IgG) and Anti-SARS-CoV-2 NCP ELISA (IgM) showed varying sensitivities. The IBMP ELISA kit displayed high diagnostic capability, especially as the disease progressed, complementing COVID-19 diagnosis. Reproducibility assessment revealed minimal systematic and analytical errors. In conclusion, the IBMP ELISA IgA/IgM/IgG COVID-19 kit is a robust tool for detecting anti-SARS-CoV-2 antibodies, increasing in efficacy over the disease course, and minimizing false negatives in RT-PCR COVID-19 diagnosis.

The Strong Activation of p53 Tumor Suppressor Drives the Synthesis of the Enigmatic Isoform of DUSP13 Protein.

The p53 tumor suppressor protein activates various sets of genes depending on its covalent modifications, which are controlled by the nature and intensity of cellular stress. We observed that actinomycin D and nutlin-3a (A + N) collaborate in inducing activating phosphorylation of p53. Our recent transcriptomic data demonstrated that these substances strongly synergize in the upregulation of DUSP13, a gene with an unusual pattern of expression, coding for obscure phosphatase having two isoforms, one expressed in the testes and the other in skeletal muscles. In cancer cells exposed to A + N, DUSP13 is expressed from an alternative promoter in the intron, resulting in the expression of an isoform named TMDP-L1. Luciferase reporter tests demonstrated that this promoter is activated by both endogenous and ectopically expressed p53. We demonstrated for the first time that mRNA expressed from this promoter actually produces the protein, which can be detected with Western blotting, in all examined cancer cell lines with wild-type p53 exposed to A + N. In some cell lines, it is also induced by clinically relevant camptothecin, by nutlin-3a acting alone, or by a combination of actinomycin D and other antagonists of p53-MDM2 interaction-idasanutlin or RG7112. This isoform, fused with green fluorescent protein, localizes in the perinuclear region of cells.

Identification of Wheat Glutamate Synthetase Gene Family and Expression Analysis under Nitrogen Stress.

Nitrogen (N), as the main component of biological macromolecules, maintains the basic process of plant growth and development. GOGAT, as a key enzyme in the N assimilation process, catalyzes α-ketoglutaric acid and glutamine to form glutamate. In this study, six GOGAT genes in wheat (Triticum aestivum L.) were identified and classified into two subfamilies, Fd-GOGAT (TaGOGAT2s) and NADH-GOGAT (TaGOGAT3s), according to the type of electron donor. Subcellular localization prediction showed that TaGOGAT3-D was localized in mitochondria and that the other five TaGOGATs were localized in chloroplasts. Via the analysis of promoter elements, many binding sites related to growth and development, hormone regulation and plant stress resistance regulations were found on the TaGOGAT promoters. The tissue-specificity expression analysis showed that TaGOGAT2s were mainly expressed in wheat leaves and flag leaves, while TaGOGAT3s were highly expressed in roots and leaves. The expression level of TaGOGATs and the enzyme activity of TaGOGAT3s in the leaves and roots of wheat seedlings were influenced by the treatment of N deficiency. This study conducted a systematic analysis of wheat GOGAT genes, providing a theoretical basis not only for the functional analysis of TaGOGATs, but also for the study of wheat nitrogen use efficiency (NUE).

Revealing Differential RNA Editing Specificity of Human ADAR1 and ADAR2 in Schizosaccharomyces pombe.

Adenosine-to-inosine (A-to-I) RNA editing is an important post-transcriptional modification mediated by the adenosine deaminases acting on RNA (ADAR) family of enzymes, expanding the transcriptome by altering selected nucleotides A to I in RNA molecules. Recently, A-to-I editing has been explored for correcting disease-causing mutations in RNA using therapeutic guide oligonucleotides to direct ADAR editing at specific sites. Humans have two active ADARs whose preferences and specificities are not well understood. To investigate their substrate specificity, we introduced hADAR1 and hADAR2, respectively, into Schizosaccharomyces pombe (S. pombe), which lacks endogenous ADARs, and evaluated their editing activities in vivo. Using transcriptome sequencing of S. pombe cultured at optimal growth temperature (30 °C), we identified 483 A-to-I high-confident editing sites for hADAR1 and 404 for hADAR2, compared with the non-editing wild-type control strain. However, these sites were mostly divergent between hADAR1 and hADAR2-expressing strains, sharing 33 common sites that are less than 9% for each strain. Their differential specificity for substrates was attributed to their differential preference for neighboring sequences of editing sites. We found that at the -3-position relative to the editing site, hADAR1 exhibits a tendency toward T, whereas hADAR2 leans toward A. Additionally, when varying the growth temperature for hADAR1- and hADAR2-expressing strains, we observed increased editing sites for them at both 20 and 35 °C, compared with them growing at 30 °C. However, we did not observe a significant shift in hADAR1 and hADAR2's preference for neighboring sequences across three temperatures. The vast changes in RNA editing sites at lower and higher temperatures were also observed for hADAR2 previously in budding yeast, which was likely due to the influence of RNA folding at these different temperatures, among many other factors. We noticed examples of longer lengths of dsRNA around the editing sites that induced editing at 20 or 35 °C but were absent at the other two temperature conditions. We found genes' functions can be greatly affected by editing of their transcripts, for which over 50% of RNA editing sites for both hADAR1 and hADAR2 in S. pombe were in coding sequences (CDS), with more than 60% of them resulting in amino acid changes in protein products. This study revealed the extensive differences in substrate selectivity between the two active human ADARS, i.e., ADAR1 and ADAR2, and provided novel insight when utilizing the two different enzymes for in vivo treatment of human genetic diseases using the RNA editing approach.

The New SH3b_T Domain Increases the Structural and Functional Variability Among SH3b-Like CBDs from Staphylococcal Phage Endolysins.

Endolysins, proteins encoded by phages to lyse their hosts and release their progeny, have evolved to adapt to the structural features of each host. The endolysins from Staphylococcus-infecting phages typically feature complex architectures with two enzymatically active domains (EADs) and one cell wall-binding domain (CBD) belonging to the bacterial SH3 (SH3b) superfamily. This study focuses on three SH3b-like CBDs from representative staphylococcal phage endolysins (LysRODI, LysC1C and LysIPLA5) that were structurally and functionally characterized. While RODI_CBD and C1C_CBD were assigned to the well-known SH3_5 family, a new family, SH3b_T (PF24246), was identified using the CBD from LysIPLA5 as a model. GFP-fused CBDs were created to assess their differential binding to a collection of staphylococcal strains. IPLA5_CBD showed enhanced binding to Staphylococcus epidermidis, while RODI_CBD and C1C_CBD exhibited distinct binding profiles, with RODI_CBD targeting Staphylococcus aureus specifically and C1C_CBD displaying broad binding. Sequence comparisons suggested that a few differences in key amino acids could be responsible for the latter binding difference. The CBDs modulated the activity spectrum of synthetic EAD-CBD combinations in accordance with the previous binding profiles, but in a manner that was also dependent on the EAD present in the fusion protein. These results serve as a context for the diversity and versatility of SH3b domains in staphylococcal endolysins, providing insights on how (i) the CBDs from this superfamily have diverged to adapt to diverse bacterial ligands in spite of sharing a common fold; and (ii) the evolution of specificity relies on the EAD-CBD combination rather than solely the CBD.

Deep venous thrombosis (DVT) diagnostics: gleaning insights from point-of-care ultrasound (PoCUS) techniques in emergencies: a systematic review and meta-analysis.

BACKGROUND: The assessment of deep venous thrombosis (DVT) is clinically difficult diagnosis. The "gold standard test" for DVT diagnosis is venography; however, various point-of-care ultrasound (POCUS) protocols have been suggested for DVT evaluation in the emergency department. AIMS: This review evaluated the role of different POCUS protocols in diagnosing DVT in the emergency department. METHODS: A systematic review and meta-analysis was conducted based of PRISMA guideline and registered on PROSEPRO (CRD42023398871). An electronic database search in Embase, PubMed, ScienceDirect, and Google scholar and a manual search were performed to identify eligible studies till February 2023. Quality Assessment of Diagnostic Accuracy Studies tool (QUADAS-2) was used to assess the risk of bias in included studies. Quantitative analysis was carried out using STATA 16 and Review Manager software (RevMan 5.4.1). Sensitivity, specificity of POCUS protocols for DVT diagnosis compared to reference standard test was calculated. RESULTS: Heterogeneity was identified between 26 included studies for review. The pooled sensitivity, specificity, PPV, and NPV for the 2-point POCUS protocol were 92.32% (95% CI: 87.58-97.06), 96.86% (95% CI: 95.09-98.64), 88.41% (95% CI: 82.24-94.58) and 97.25% (95% CI: 95.51-98.99), respectively. Similarly, the pooled sensitivity, specificity, PPV, and NPV for 3-point POCUS were 89.15% (95% CI: 83.24-95.07), 92.71% (95% CI: 89.59-95.83), 81.27% (95% CI: 73.79-88.75), and 95.47% (95% CI: 92.93-98). The data pooled for complete compression ultrasound, and whole-leg duplex ultrasound also resulted in a sensitivity and specificity of 100% (95% CI: 98.21-100) and 97.05% (95% CI: 92.25-100), respectively. On the other hand, the time from triage to DVT diagnosis was significantly shorter for emergency physician-performed POCUS than diagnostic tests performed by radiologists. CONCLUSION: The diagnostic performance of POCUS protocols performed by emergency physicians was excellent. Combined with the significant reduction in time to diagnosis. POCUS can be used as the first-line imaging tool for DVT diagnosis in the emergency department. We also recommended that attending emergency physicians with POCUS training are present during DVT diagnosis to improve diagnostic performance even though high diagnostic performance is observed even with the minimum training.

Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis.

Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.