Simultaneous quantification of the most common and proteolytic Pseudomonas species in raw milk by multiplex qPCR.

The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high temperature (UHT) milk and milk products. To enable rapid detection and quantification of seven frequent and proteolytic Pseudomonas species (P. proteolytica, P. gessardii, P. lactis, P. fluorescens, P. protegens, P. lundensis, and P. fragi) in raw milk, we developed two triplex qPCR assays taking into account species-dependent differences in AprX activity. Besides five species-specific hydrolysis probes, targeting the aprX gene, a universal rpoB probe was included in the assay to determine the total Pseudomonas counts. For all six probes, linear regression lines between Cq value and target DNA concentration were obtained in singleplex as well as in multiplex approaches, yielding R2 values of > 0.975 and amplification efficiencies of 85-97%. Moreover, high specificity was determined using genomic DNA of 75 Pseudomonas strains, assigned to 57 species, and 40 other bacterial species as templates in the qPCR. Quantification of the target species and total Pseudomonas counts resulted in linear detection ranges of approx. 103-107 cfu/ml, which correspond well to common Pseudomonas counts in raw milk. Application of the assay using 60 raw milk samples from different dairies showed good agreement of total Pseudomonas counts calculated by qPCR with cell counts derived from cultivation. Furthermore, a remarkably high variability regarding the species composition was observed for each milk sample, whereby P. lundensis and P. proteolytica/P. gessardii were the predominant species detected. KEY POINTS: • Multiplex qPCR for quantification of seven proteolytic Pseudomonas species and total Pseudomonas counts in raw milk • High specificity and sensitivity via hydrolysis probes against aprX and rpoB • Rapid method to determine Pseudomonas contamination in raw milk and predict spoilage potential.

Patient-Derived Organoids of Cholangiocarcinoma.

Cholangiocarcinoma (CC) is an aggressive malignancy with an inferior prognosis due to limited systemic treatment options. As preclinical models such as CC cell lines are extremely rare, this manuscript reports a protocol of cholangiocarcinoma patient-derived organoid culture as well as a protocol for the transition of 3D organoid lines to 2D cell lines. Tissue samples of non-cancer bile duct and cholangiocarcinoma were obtained during surgical resection. Organoid lines were generated following a standardized protocol. 2D cell lines were generated from established organoid lines following a novel protocol. Subcutaneous and orthotopic patient-derived xenografts were generated from CC organoid lines, histologically examined, and treated using standard CC protocols. Therapeutic responses of organoids and 2D cell lines were examined using standard CC agents. Next-generation exome and RNA sequencing was performed on primary tumors and CC organoid lines. Patient-derived organoids closely recapitulated the original features of the primary tumors on multiple levels. Treatment experiments demonstrated that patient-derived organoids of cholangiocarcinoma and organoid-derived xenografts can be used for the evaluation of novel treatments and may therefore be used in personalized oncology approaches. In summary, this study establishes cholangiocarcinoma organoids and organoid-derived cell lines, thus expanding translational research resources of cholangiocarcinoma.

Anatomical changes with needle length are correlated with leaf structural and physiological traits across five Pinus species.

The genus Pinus has wide geographical range and includes species that are the most economically valued among forest trees worldwide. Pine needle length varies greatly among species, but the effects of needle length on anatomy, function, and coordination and trade-offs among traits are poorly understood. We examined variation in leaf morphological, anatomical, mechanical, chemical, and physiological characteristics among five southern pine species: Pinus echinata, Pinus elliottii, Pinus palustris, Pinus taeda, and Pinus virginiana. We found that increasing needle length contributed to a trade-off between the relative fractions of support versus photosynthetic tissue (mesophyll) across species. From the shortest (7 cm) to the longest (36 cm) needles, mechanical tissue fraction increased by 50%, whereas needle dry density decreased by 21%, revealing multiple adjustments to a greater need for mechanical support in longer needles. We also found a fourfold increase in leaf hydraulic conductance over the range of needle length across species, associated with weaker upward trends in stomatal conductance and photosynthetic capacity. Our results suggest that the leaf size strongly influences their anatomical traits, which, in turn, are reflected in leaf mechanical support and physiological capacity.

C-type natriuretic peptide/cGMP/FoxO3 signaling attenuates hyperproliferation of pericytes from patients with pulmonary arterial hypertension.

Pericyte dysfunction, with excessive migration, hyperproliferation, and differentiation into smooth muscle-like cells contributes to vascular remodeling in Pulmonary Arterial Hypertension (PAH). Augmented expression and action of growth factors trigger these pathological changes. Endogenous factors opposing such alterations are barely known. Here, we examine whether and how the endothelial hormone C-type natriuretic peptide (CNP), signaling through the cyclic guanosine monophosphate (cGMP) -producing guanylyl cyclase B (GC-B) receptor, attenuates the pericyte dysfunction observed in PAH. The results demonstrate that CNP/GC-B/cGMP signaling is preserved in lung pericytes from patients with PAH and prevents their growth factor-induced proliferation, migration, and transdifferentiation. The anti-proliferative effect of CNP is mediated by cGMP-dependent protein kinase I and inhibition of the Phosphoinositide 3-kinase (PI3K)/AKT pathway, ultimately leading to the nuclear stabilization and activation of the Forkhead Box O 3 (FoxO3) transcription factor. Augmentation of the CNP/GC-B/cGMP/FoxO3 signaling pathway might be a target for novel therapeutics in the field of PAH.

Lumbar Spondylodiscitis Mimicking Cholecystitis: A Case Report and Review of Literature.

BACKGROUND: Lower back pain is a frequent cause of emergency department visits and one of the leading causes of the disease burden worldwide. The purpose of this case report and literature review was to discuss atypical abdominal entities mimicking spinal diseases typically presenting with lower back pain. METHODS: A 79-year-old man presented with lower back pain and urinary incontinence after receiving a non-image-guided lumbar infiltration treatment 4 weeks prior to admission. The magnetic resonance imaging (MRI) highlighted multisegmental hyperintensities in the intervertebral disk spaces of the lumbar spine indicative for spondylodiscitis. Antibiotic treatment over a week did not lead to significant clinical improvement. Blood cultures, cardiologic, otorhinolaryngologic, and dental examinations turned out negative for a focus of infection. A computed tomography (CT) guided biopsy was indicated after discontinuation of antibiotic treatment for less than 24 hours. Rapid clinical deterioration with concomitant onset of abdominal pain resulted in the diagnosis of cholecystitis, which required cholecystectomy. We performed a systematic literature review using the Pubmed database for the keywords "spondylodiscitis," "spine," "abdominal," and "cholecystitis," to identify abdominal diseases that mimic spine pathologies and spinal diseases that mimic abdominal pathologies. RESULTS: No other report in English literature of cholecystitis associated with initial onset of lower back pain was identified. Eighteen reports referred to abdominal conditions that mimic spinal diseases, among them a patient with cyclic lumbar back pain who received a lumbar spinal fusion who, after persisting symptoms led to further diagnostic procedures, was ultimately diagnosed with endometriosis. Spinal symptoms included paraplegia and urinary incontinence as results of acute aortic pathologies. Eleven reports presented spinal pain mimicking abdominal conditions including abdominal pain and diarrhea as well as have had surgical procedures such as an appendectomy before the spinal condition was discovered. CONCLUSION: Clinical symptoms of the spine such as lower back pain can be unspecific and lead to false conclusions in the presence of concomitant pathologies in MRI. Only clinical deterioration in our case patient prompted correction of the diagnosis on day 7. Initial workup for alternative common infectious foci such as lung and urinary tract was performed, but further abdominal workup despite the absence of abdominal symptoms may have led to an earlier diagnosis. Our literature review found several cases of misdiagnosed spinal and abdominal conditions. Some had undergone unnecessary surgical procedures before the right diagnosis was made. Because of the high incidence of symptoms such as lumbar back pain and abdominal pain, considering optimal patient care as well as economic aspects, it would be essential to conduct an interdisciplinary clinical management to avoid errors in the early stage of diagnostics.

Weekday-dependent long-term outcomes in gastrointestinal cancer surgery: a German population-based retrospective cohort study.

BACKGROUND: For most solid cancers, surgery represents the mainstay of curative treatment. Several studies investigating the effects of the weekday of surgery (WOS) on patient outcomes have yielded conflicting results. Barmer, the second-largest health insurance company in Germany, serves roughly 10% of the German population. The authors have used the Barmer database to evaluate how the weekday on which the surgery is performed influences long-term oncologic outcomes. METHODS: For this retrospective cohort study, the Barmer database was used to investigate the effect of the WOS (Monday-Friday) on outcomes following oncological resections of the colorectum ( n =49 003), liver ( n =1302), stomach ( n =5027), esophagus ( n =1126), and pancreas ( n =6097). In total, 62 555 cases from 2008 to 2018 were included in the analysis. The endpoints were overall survival (OS), postoperative complications, and the necessity for therapeutic interventions or reoperations. The authors further examined whether the annual caseload or certification as a cancer center influenced the weekday effect. RESULTS: The authors observed a significantly impaired OS for patients receiving gastric or colorectal resections on a Monday. Colorectal surgery performed on Mondays was associated with more postoperative complications and a higher probability of reoperations. The annual caseload or a certification as a colorectal cancer center had no bearing on the observed weekday effect. There is evidence that hospitals schedule older patients with more comorbidities earlier in the week, possibly explaining these findings. CONCLUSION: This is the first study investigating the influence of the WOS on long-term survival in Germany. Our findings indicate that, in the German healthcare system, patients undergoing colorectal cancer surgery on Mondays have more postoperative complications and, therefore, require significantly more reoperations, ultimately lowering the OS. This surprising finding appears to reflect an attempt to schedule patients with higher postoperative risk earlier in the week as well as semi-elective patients admitted on weekends scheduled for surgery on the next Monday.

GOFAST: an integrated approach for efficient and comprehensive membrane proteome analysis.

Membrane proteomics, the large-scale analysis of membrane proteins, is often constrained by the difficulties of achieving fully resolvable separation and resistance to proteolysis, both of which could lead to low recovery and low identification rates of membrane proteins. Here, we introduce a novel integrated approach, GELFrEE Optimized FASP Technology (GOFAST) for large-scale and comprehensive membrane proteins analysis. Using an array of sample preparation techniques including gel-eluted liquid fraction entrapment electrophoresis (GELFrEE), filter-aided sample preparation (FASP), and microwave-assisted on-filter enzymatic digestion, we identified 2 090 proteins from the membrane fraction of a leukemia cell line (K562). Of these, 37% are annotated as membrane proteins according to gene ontology analysis, resulting in the largest membrane proteome of leukemia cells reported to date. Our approach combines the advantages of GELFrEE high-loading capacity, gel-free separation, efficient depletion of detergents, and microwave-assisted on-filter digestion, minimizing sample losses and maximizing MS-detectable sequence coverage of individual proteins. In addition, this approach also shows great potential for the identification of alternative splicing products.

Examining the frequency of crenulated premolars and their association with crenulated molars.

Crenulated occlusal surfaces have previously been described on maxillary and mandibular molars; however, the occurrence of crenulations on premolars is only anecdotally supported. This study applies a modified version of a recordation scale developed for molar crenulations to record the frequency of crenulated premolars on the maxillary and mandibular premolars of modern individuals from a variety of populations: African, African American, Asian, Australian, European American, Latino, and Malay (n = 1238). Crenulations on the molars of the same individuals were also recorded to assess the relationship between occurrences on premolars and molars. Observations were compiled into frequency tables and analyzed using chi-square tests and correspondence analysis; relationships among teeth were quantified with polychoric correlation coefficients. Although crenulated premolars are observed rarely overall, the frequency of occurrence is significantly associated with group membership. Crenulated premolars occur most frequently in African, African American, and Australian samples and are observed least often among European American and Malay samples. Additionally, there is a strong relationship between third and fourth premolars, particularly within a jaw, and between fourth premolars and the molars in the same jaw. Interestingly, crenulations in premolars are most strongly associated with Grade 2 crenulations on molars. The observed differences between populations, and the associations between crenulated premolars and molars are evaluated with respect to function, tooth size, and dental development. Based on the results presented here, we recommend the addition of premolar crenulations to existing dental morphological traits used to study human population variation.

Language use in ancestry research and estimation.

Recent discussions have revolved around the concept of ancestry and ancestry estimation; however, the associated terminology and its theoretical underpinnings have not been similarly examined. This research evaluates the concepts (e.g., race, ancestry, ethnicity) currently in use, examines if they are consistent with the groups employed to illustrate them (e.g., Black, European, Hispanic), and looks for patterns in language usage. Articles in the Anthropology, Odontology, and General sections of the Journal of Forensic Sciences between 2009 and 2019 were evaluated for ancestry-related language use. For each article, the concepts, examples, and bibliographic information were recorded, and the relationship between concept and example was examined. These data were cross-tabulated to evaluate relationships between the variables. Cramer's V was used to assess the strength of association of these relationships. In this sample, ancestry predominates, especially recently The concept used is significantly associated with all variables except publication date and authors' institution(s). Despite the prevalence of the ancestry concept, racially based terms for individual groups were common. The use of ancestry, over race, in forensic contexts has been suggested to be a primarily linguistic change; these results may support that assertion. Inconsistent language usage leads to a lack of clarity in meaning among researchers and misinterpretation of the data. It is critical to recognize that inconsistencies exist, but also to understand why they exist. These results underscore the long overdue need for the inclusion of diverse perspectives in forensic anthropology, especially in the current conversations surrounding ancestry and ancestry estimation.

Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk.

Psychrotolerant Pseudomonas species are a main cause of proteolytic spoilage of ultra-high temperature (UHT) milk products due to the secretion of the heat-resistant metallopeptidase AprX, which is encoded by the first gene of the aprX-lipA2 operon. While the proteolytic property has been characterized for many different Pseudomonas isolates, the underlying aprX-lipA2 gene organization was only described for a few strains so far. In this study, the phylogenomic analysis of 185 Pseudomonas type strains revealed that the presence of aprX is strongly associated to a monophylum composed of 81 species, of which 83% carried the aprX locus. Furthermore, almost all type strains of known milk-relevant species were shown to be members of the three monophyletic groups P. fluorescens, P. gessardii, and P. fragi. In total, 22 different types of aprX-lipA2 genetic organizations were identified in the genus, whereby 31% of the species tested carried the type 1 operon structure consisting of eight genes (aprXIDEF prtAB lipA2). Other genetic structures differed from type 1 mainly in the presence and location of genes coding for two lipases (lipA1 and lipA2) and putative autotransporters (prtA and prtB). The peptidase activity of 129 strains, as determined on skim milk agar and in UHT-milk, correlated largely with different aprX-lipA2 gene compositions. Particularly, isolates harboring the type 1 operon were highly proteolytic, while strains with other operon types, especially ones lacking prtA and prtB, exhibited significantly lower peptidase activities. In conclusion, the phylogenomic position and the aprX-lipA2 gene organization specify the proteolytic potential of Pseudomonas isolates. In addition, however, an interplay of several environmental factors and intrinsic traits influences production and activity of AprX, leading to strain-specific proteolytic phenotypes.

Ultra-Structure database design methodology for managing systems biology data and analyses.

BACKGROUND: Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). RESULTS: We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. CONCLUSION: We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era.

Tooth Crown Morphology in Turner and Klinefelter Syndrome Individuals from a Croatian Sample.

OBJECTIVE: Turner syndrome (TS) and Klinefelter syndrome (KS) represent the two most common X chromosome aneuploidies, each associated with systemic disruptions to growth and development. Effects of these conditions on tooth crown morphology are explored in a sample of Croatian individuals. MATERIALS AND METHODS: The sample included 57 TS, 37 KS and 88 control individuals. Dental crown morphology was scored on dental casts according to the Turner-Scott Dental Anthropology System. RESULTS: Incisor shoveling and the hypocone were significantly different between TS individuals and both control and KS individuals. Individuals with TS exhibit lower grades of expression than either group. Furthermore, the number of lingual cusps on the mandibular premolars, the hypoconulid on the mandibular second molar, and cusp 7 on the mandibular first molar were significantly different, though pair-wise comparisons did not elucidate these differences. Tuberculum dentale, distal accessory ridge, and Carabelli's trait were expressed similarly to the control. KS individuals were not significantly different from control individuals for any trait, though this may be related to sample size. CONCLUSIONS: Previous studies suggest the loss of an X chromosome has a reducing effect on dental crown morphology, which is confirmed in this research. TS individuals exhibit generally simpler dental morphology compared to the control sample, though some traits are expressed comparably to the control sample. The effects of KS are less clear. Though previous studies suggest that the presence of an extra X chromosome increases dental crown dimensions, there was no notable effect on crown morphology in this study.

A Versatile Toolbox for the Control of Protein Levels Using Nε-Acetyl-l-lysine Dependent Amber Suppression.

The analysis of the function of essential genes in vivo depends on the ability to experimentally modulate levels of their protein products. Current methods to address this are based on transcriptional or post-transcriptional regulation of mRNAs, but approaches based on the exploitation of translation regulation have so far been neglected. Here we describe a toolbox, based on amber suppression in the presence of Nε-acetyl-l-lysine (AcK), for translational tuning of protein output. We chose the highly sensitive luminescence system LuxCDABE as a reporter and incorporated a UAG stop codon into the gene for the reductase subunit LuxC. The system was used to measure and compare the effects of AcK- and Nε-(tert-butoxycarbonyl)-l-lysine (BocK) dependent amber suppression in Escherichia coli. We also demonstrate here that, in combination with transcriptional regulation, the system allows protein production to be either totally repressed or gradually adjusted. To identify sequence motifs that provide improved translational regulation, we varied the sequence context of the amber codon and found that insertion of two preceding prolines drastically decreases luminescence. In addition, using LacZ as a reporter, we demonstrated that a strain encoding a variant with a Pro-Pro amber motif can only grow on lactose when AcK is supplied, thus confirming the tight translational regulation of protein output. In parallel, we constructed an E. coli strain that carries an isopropyl ß-d-1-thiogalactopyranoside (IPTG)-inducible version of the AcK-tRNA synthetase (AcKRS) gene on the chromosome, thus preventing mischarging of noncognate substrates. Subsequently, a diaminopimelic acid auxotrophic mutant (ΔdapA) was generated demonstrating the potential of this strain in regulating essential gene products. Furthermore, we assembled a set of vectors based on the broad-host-range pBBR ori that enable the AcK-dependent amber suppression system to control protein output not only in E. coli, but also in Salmonella enterica and Vibrio cholerae.

Palate Shape and Depth: A Shape-Matching and Machine Learning Method for Estimating Ancestry from Human Skeletal Remains.

In the past, assessing ancestry relied on the naked eye and observer experience; however, replicability has become an important aspect of such analysis through the application of metric techniques. This study examines palate shape and assesses ancestry quantitatively using a 3D digitizer and shape-matching and machine learning methods. Palate curves and depths were recorded, processed, and tested for 376 individuals. Palate shape was an accurate indicator of ancestry in 58% of cases. Cluster analysis revealed that the parabolic, hyperbolic, and elliptical shapes are discrete from one another. Preliminary results indicate that palate depth in Hispanic individuals is greatest. Palate shape appears to be a useful indicator of ancestry, particularly when assessed by a computer. However, these data suggest that palate shape is not useful for assessing ancestry in Hispanic individuals. Although ancestry may be determined from palate shape, the use of multiple features is recommended and more reliable.

[2.2.2]Paracyclophane-Trienes-Attractive Monomers for ROMP.

Three derivatives of 4,7-substituted [2.2.2]paracyclophane-trienes were synthesized and used in ring-opening metathesis polymerization (ROMP), resulting in well-soluble poly(para-phenylenevinylene)s (PPV). The paracyclophane-trienes were prepared using an iterative buildup of a phenylene-ethynylene backbone, followed by a cis selective Grignard reduction and an intramolecular McMurry reaction. The monomers were applied in ROMP to result in well-soluble PPV derivatives with an unusual substituent pattern. The PPVs were spin-coated into amorphous, highly fluorescent films. To the best of our knowledge, we are the first to synthesize 4,7-substituted [2.2.2]paracyclophane-trienes and use them as ROMP monomers.

Epiphyseal union of the cervical vertebral centra: its relationship to skeletal age and maturation of thoracic vertebral centra.

Epiphyseal union stages for cervical vertebral centra (ring epiphyses) were documented for 55 individuals (females and males, ages 14-27 years) from the Terry Collection, using the Albert and Maples method 1, to examine both its relationship to age at death and to thoracic data collected from the same individuals using the same method. Results showed a moderate correlation between cervical ring union and age (r = 0.63, p = 0.000), and a fairly low correlation between cervical and thoracic ring union (r = 0.41, p = 0.002). Paired samples t-tests yielded a statistically significant difference between cervical and thoracic union mean values (p = 0.01). Union progressed earlier in cervical vertebrae and in females. Results indicated fairly substantial variation in both sexes. Findings may serve as a basic guideline for estimating a general age range at death for unknown skeletal remains and to corroborate findings from other skeletal age indicators.

Epstein-Barr virus activates beta-catenin in type III latently infected B lymphocyte lines: association with deubiquitinating enzymes.

beta-Catenin is a multifunctional protein, stabilization of which is a critical step in its functional activity. Stabilization can be conferred through several means, including mutations in beta-catenin, common in many carcinomas. In this article, we explore the effect of viral infection on the beta-catenin signaling pathway in B lymphocytes, including cell lines derived from lymphomas. Infection by the human tumor virus Epstein-Barr virus (EBV) generates several types of latency with different spectra of latent gene expression that are associated with different malignancies. In type III latency, exemplified by EBV lymphoproliferative diseases, the full range of these viral proteins is expressed, whereas in type I latency, only the EBNA1 protein is expressed and functional. We show that beta-catenin is rapidly degraded in type I B lymphocytic lines but it is stabilized in type III B cell lines, and that beta-catenin/T cell factor transcriptional activity is significantly higher in type III cells. Also we show the association of free cytoplasmic beta-catenin with deubiquitinating enzymes, which may play a role in beta-catenin stabilization. Activation of the beta-catenin/T cell factor pathway by EBV may contribute to the lymphoproliferation characteristic of type III latency.