ChloroDBPFinder: Machine Learning-Guided Recognition of Chlorinated Disinfection Byproducts from Nontargeted LC-HRMS Analysis

High-resolution mass spectrometry (HRMS) is a prominent analytical tool that characterizes chlorinated disinfection byproducts (Cl-DBPs) in an unbiased manner. Due to the diversity of chemicals, complex background signals, and the inherent analytical fluctuations of HRMS, conventional isotopic pattern (37Cl/35Cl), mass defect, and direct molecular formula (MF) prediction are insufficient for accurate recognition of the diverse Cl-DBPs in real environmental samples. This work proposes a novel strategy to recognize Cl-containing chemicals based on machine learning. Our hierarchical machine learning framework has two random forest-based models: the first layer is a binary classifier to recognize Cl-containing chemicals, and the second layer is a multiclass classifier to annotate the number of Cl present. This model was trained using ∼1.4 million distinctive MFs from PubChem. Evaluated on over 14,000 unique MFs from NIST20, this machine learning model achieved 93.3% accuracy in recognizing Cl-containing MFs (Cl-MFs) and 92.9% accuracy in annotating the number of Cl for Cl-MFs. Furthermore, the trained model was integrated into ChloroDBPFinder, a standalone R package for the streamlined processing of LC-HRMS data and annotating both known and unknown Cl-containing compounds. Tested on existing Cl-DBP data sets related to aspartame chlorination in tap water, our ChloroDBPFinder efficiently extracted 159 Cl-containing DBP features and tentatively annotated the structures of 10 Cl-DBPs via molecular networking. In another application of a chlorinated humic substance, ChloroDBPFinder extracted 79 high-quality Cl-DBPs and tentatively annotated six compounds. In summary, our proposed machine learning strategy and the developed ChloroDBPFinder provide an advanced solution to identifying Cl-containing compounds in nontargeted analysis of water samples. It is freely available on GitHub (https://github.com/HuanLab/ChloroDBPFinder).

Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression

Colorectal cancer (CRC) is driven by genomic alterations in concert with dietary influences, with the gut microbiome implicated as an effector in disease development and progression. While meta-analyses have provided mechanistic insight into patients with CRC, study heterogeneity has limited causal associations. Using multi-omics studies on genetically controlled cohorts of mice, we identify diet as the major driver of microbial and metabolomic differences, with reductions in α diversity and widespread changes in cecal metabolites seen in high-fat diet (HFD)-fed mice. In addition, non-classic amino acid conjugation of the bile acid cholic acid (AA-CA) increased with HFD. We show that AA-CAs impact intestinal stem cell growth and demonstrate that Ileibacterium valens and Ruminococcus gnavus are able to synthesize these AA-CAs. This multi-omics dataset implicates diet-induced shifts in the microbiome and the metabolome in disease progression and has potential utility in future diagnostic and therapeutic developments.

P2457Left atrial strain parameters predict clinical outcomes in patients with HFmrEF and HFpEF

Background

Heart failure with preserved ejection fraction (HFpEF) and with mid-range ejection fraction (HFmrEF) are conditions sharing similar diagnostic criteria and symptoms. Left ventricular (LV) diastolic dysfunction has often been considered central to the pathophysiology of both, as determined by current conventional echocardiographic measures of elevated filling pressure and/or an increased in left atrial (LA) volume. However, the independent prognostic importance of LA function, beyond clinical predictors and LV features, in those groups remains unclear.

Aims

To evaluate the prognostic value of LA function measured by speckle tracking echocardiography in patients with new diagnosis of HFpEF and HFmrEF.

Methods

A total of 171 consecutive patients diagnosed with HFpEF with an Ejection Fraction (EF) ≥50%, or HFmrEF with an EF of 40–49% were prospectively enrolled and followed up. Follow-up was completed in 134 patients with HFpEF (n=100) and HFmrEF (n=34) for a median period of 57 months. Baseline characteristic and comorbidities were recorded, as well as conventional resting echocardiographic parameters of systolic and diastolic function. Left atrial phasic function was analysed using 2D-Specle Tracking. Peak-atrial longitudinal strain (PALS) and peak-atrial contraction strain (PACS) were measured, reflecting LA reservoir and pump function respectively. We looked at the relationship of traditional parameters of systolic and diastolic function and LA strain, with the following cardiovascular (CV) events: acute coronary syndromes, new atrial fibrillation, cerebrovascular events, HF-related admissions and cardiac deaths.

Results

During a median follow up period of 57 months (range 11.10), of 134 patients, 42 (31%) had at least one CV event, 10 (8%) out of whom had at least one HF-related hospitalization and 5 (4%) had cardiac death. 92 patients (69%) remained event-free. In univariate analysis, lower PALS and PACS were associated with increased risk for the composite endpoint of all CV-events (PALS OR=0.92 p<0.01 and PACS OR=0.92 p<0.05), but only PALS predicted HF admissions (PALS OR=0.86 p<0.05). In multivariate analysis after adjusting for LV EF, E/e' and LAVi, PALS remained significant at predicting CV-events (OR=0.91 p<0.05) and HF admissions (OR=0.85 p<0.05), but PACS did not. Amongst all echocardiographic parameters measured, PALS had the greatest Area Under the Curve at Receiver Operating Characteristics analysis (AUC=0.78 p<0.05) and a PALS value of <23% best predicted future HF-related admissions (sensitivity 0.9, specificity 0.6).

Conclusion

LA dysfunction in HFpEF and HFmrEF is associated with a higher risk of CV events and HF hospitalizations. The association of LA strain with HF hospitalization remained significant after adjustment for systolic and diastolic parameters.

Assessing Potential Habitat and Carrying Capacity for Reintroduction of Plains Bison (Bison bison bison) in Banff National Park

Interest in bison (Bison bison, B. bonasus) conservation and restoration continues to grow globally. In Canada, plains bison (B. b. bison) are threatened, occupying less than 0.5% of their former range. The largest threat to their recovery is the lack of habitat in which they are considered compatible with current land uses. Fences and direct management make range expansion by most bison impossible. Reintroduction of bison into previously occupied areas that remain suitable, therefore, is critical for bison recovery in North America. Banff National Park is recognized as historical range of plains bison and has been identified as a potential site for reintroduction of a wild population. To evaluate habitat quality and assess if there is sufficient habitat for a breeding population, we developed a Habitat Suitability Index (HSI) model for the proposed reintroduction and surrounding areas in Banff National Park (Banff). We then synthesize previous studies on habitat relationships, forage availability, bison energetics and snowfall scenarios to estimate nutritional carrying capacity. Considering constraints on nutritional carrying capacity, the most realistic scenario that we evaluated resulted in an estimated maximum bison density of 0.48 bison/km². This corresponds to sufficient habitat to support at least 600 to 1000 plains bison, which could be one of the largest 10 plains bison populations in North America. Within Banff, there is spatial variation in predicted bison habitat suitability and population size that suggests one potential reintroduction site as the most likely to be successful from a habitat perspective. The successful reintroduction of bison into Banff would represent a significant global step towards conserving this iconic species, and our approach provides a useful template for evaluating potential habitat for other endangered species reintroductions into their former range.

Mechanisms of dendritic spine remodeling in a rat model of traumatic brain injury

Traumatic brain injury (TBI), a leading cause of death and disability in the United States, causes potentially preventable damage in part through the dysregulation of neural calcium levels. Calcium dysregulation could affect the activity of the calcium-sensitive phosphatase calcineurin (CaN), with serious implications for neural function. The present study used both an in vitro enzymatic assay and Western blot analyses to characterize the effects of lateral fluid percussion injury on CaN activity and CaN-dependent signaling in the rat forebrain. TBI resulted in an acute alteration of CaN phosphatase activity and long-lasting alterations of its downstream effector, cofilin, an actin-depolymerizing protein. These changes occurred bilaterally in the neocortex and hippocampus, appeared to persist for hours after injury, and coincided with synapse degeneration, as suggested by a loss of the excitatory post-synaptic protein PSD-95. Interestingly, the effect of TBI on cofilin in some brain regions was blocked by a single bolus of the CaN inhibitor FK506, given 1 h post-TBI. Overall, these findings suggest a loss of synapse stability in both hemispheres of the laterally-injured brain, and offer evidence for region-specific, CaN-dependent mechanisms.

Three Important Considerations in Posttraumatic Rhinoplasty

Introduction:

Many factors must be considered when performing a posttraumatic rhinoplasty. Since nasal fractures are the most common fractures in the adult facial skeleton, many patients who suffer midface trauma also suffer from nasal deformity/deviation and nasal airflow impedance. There are three specific regions within the nose which may impede airflow: nasal septum, internal nasal valves, and inferior turbinates. Each component of functional and posttraumatic rhinoplasty has been studied independently. However, a review of posttraumatic rhinoplasty procedures in which multiple regions of the nasal anatomy were addressed, when indicated, has not been elucidated much in the literature.

Materials and Methods:

A retrospective review of the medical charts and operative reports of 42 consecutive patients who underwent a post-traumatic rhinoplasty from July 2002 to December 2006 by the same surgeon was undertaken to determine which specific regions of the nose required secondary repair. Postoperative results were then reviewed to determine objective complications and subjective complaints. The specific techniques employed in the each operative procedure were then analyzed and objective complications and subjective complaints were recorded.

Results:

The most common preoperative patient complaint included difficulty breathing and nasal complex deformity followed by difficulty breathing alone and isolated deviation/deformity. The most common preoperative objective findings included airflow obstruction and nasal deformity, followed by isolated airflow obstruction, and isolated deviation/deformity with no air flow disturbance. All patients underwent a secondary posttraumatic septorhinoplasty. Septoplasty was performed in 78.6% of the patients; spreader grafts were used in 74% of the patients, and inferior turbinate surgery was done in 62% of the patients. Postoperatively, subjective findings revealed no complaints in 38 patients (90.5%). Two patients had complaints of persistent nasal deformity and air flow obstruction; 1 patient had persistent nasal deformity, and another patient had persistent air flow obstruction. Objectively, 5 patients had persistent nasal deformity, 2 patients had persistent air flow obstruction, and two patients had persistent airflow obstruction and nasal deformity.

Conclusion:

When indicated, by appropriately addressing the key regions of the nasal complex, including the septum, internal nasal valves, and inferior turbinates, the majority of patients (90.5%) will have no subjective complaints of difficulty breathing or a nasal complex deformity.

The Mycobacterium avium-intracellulare complex dnaB locus and protein intein splicing

Intein is a protein sequence mebedded in-frame within a precursor protein and is posttranslationally excised by a self-catalytic protein splicing process. Protein splicing is believed to follow a pathway requiring Cys, Ser, or Thr residues at the intein N-terminus and substitutions other than Cys, Ser, or Thr residues prevent splicing. We show that the dnaB locus in some strains of M. avium-intracellulare complex (MAC) contains intein and that the intein N-terminal amino acid is Ala [Ala-type]. We demonstrate that the M. avium DnaB precursor protein undergoes posttranslational proteolytic processing producing proteins corresponding to the sizes of the DnaB and intein. Further, by Western analysis we detect a protein corresponding to the size of the spliced DnaB protein in MAC cell extracts. Together, these results indicate that the Ala-type MAC DnaB inteins can splice and provide another example that points to an interesting alternative splicing mechanism (Southworth, M. W., Benner, J., and Perler, F. B., EMBO J. 19, 5019-5026, 2000).

Tumor-targeted Salmonella. Highly selective delivery vectors

Genetically engineered Salmonella offer an intriguing new approach to selectively target solid tumors, including melanoma, lung, colon, breast, kidney and liver. These bacteria target tumors after systemic administration and selectively replicate within them. Specificity for tumors is often more than 1,000 times greater than for any other tissue. Auxotrophic mutations make these bacteria highly safe and form the basis for maintaining tumor specificity. An altered lipid greatly reduces the potential for septic shock yet also retains the antitumor properties of these bacteria. These bacteria have innate antitumor activity towards both primary and metastatic tumors and the ability to deliver proteins capable of activating chemotherapeutic agents directly within tumors. The delay in tumor growth results in mice that survive up to twice as long. These bacteria are susceptible to a wide range of antibiotics, allowing external control of the vector after administration. The combination of these features within a single vector seems specially surprising considering their unlikely source.

Tumor-Targeted Salmonella: Strain Development and Expression of the HSV-tK Effector Gene

Gene therapy approaches to cancer treatment have been limited by the ability of the delivery vectors to achieve specific high-level expression within tumor cells or the tumor environment following systemic administration. Numerous physical barriers exist in the delivery of therapeutic agents (including drugs, viruses, and liposomes) to solid tumors that can compromise the effectiveness (1), thus stimulating the search for alternative methods of delivery. Whereas it has been known for some time that spores of anaerobic Clostridium can germinate within the necrotic spaces of human tumors, they are limited to larger hypoxic tumors and are inaccessible to smaller metastases (2,3). The ability of motile, facultatively anaerobic Salmonella to target tumors following systemic administration, preferentially amplify within them, and express effector genes such as the herpes simplex virus thymidine kinase (HSV-TK) makes them an attractive alternative to Clostridia, liposome and viral-based delivery vectors (4). These Salmonella were attenuated by poly-auxotrophic mutations, which limited their pathogenesis in normal tissues, but retained high-level replication within tumors, resulting in tumor suppression of both primary and metastatic tumors (4,5). The attenuating mutations were added stepwise following in vitro and in vivo selection and screening methods. Although live-attenuated vectors for use in humans requires defined genetic mutations, our experience has shown that combinations of point-mutations and frame-shift mutations allows for rapid isolation of strains with multiple mutations having desirable properties, which can later be defined and/ or stabilized. Bearing this in mind, we present the basic methodology for the development of tumor-targeting facultative anaerobes with effector gene delivery capabilities that we applied to Salmonella.

Principles for Sustainable Governance of the Oceans

Pressures being exerted on the ocean ecosystems through overfishing, pollution, and environmental and climate change are increasing. Six core principles are proposed to guide governance and use of ocean resources and to promote sustainability. Examples of governance structures that embody these principles are given.

Glycoproteins of the aspartyl proteinase gene family secreted by the developing placenta

Pregnancy in cattle and sheep can be diagnosed by the presence of placentally-derived antigens (pregnancy-associated glycoproteins or PAG-1) in maternal serum soon after implantation begins at about Day 20 following conception. Molecular cloning of their cDNA has revealed that PAG-1 belong to the aspartic proteinase gene family and have about 50% amino acid sequence identity to pepsin. However, critical amino acid substitutions at the active site regions suggest that both bovine and ovine PAG-1 are enzymatically inactive. PAG-1 expression has been shown by in situ hybridization and immunocytochemistry to be localized to the trophoblast binucleate cells, which invade maternal uterine endometrium during implantation. The glycoproteins are concentrated in dense cytoplasmic granules that are discharged after the binucleate cells have migrated to the maternal side of the placental barrier. We suggest, therefore, that the PAG-1 might have an endocrine function either as carriers of other bioactive peptides or by acting as hormones themselves. Recently screening of placental libraries with nucleic acid probes has identified additional cDNA that are very abundant and code for polypeptides (PAG-2 and PAG-3) related to, but antigenically and structurally distinct from PAG-1 described above. These molecules have sequences of amino acids at their catalytic centers that are consistent with their being potentially functional proteinases but their role during pregnancy, like that of PAG-1, is unclear.

Pyogenic psoas abscess

In a 12-month period, five cases of pyogenic psoas abscess presented to the Townsville General Hospital. These cases are presented, together with a review of the literature to illustrate the clinical features of this condition and the therapeutic challenge it may pose.

Regulation of biosynthesis of aminoacyl-transfer RNA synthetases and of transfer-RNA in Escherichia coli

We have isolated temperature resistant revertants from temperature sensitive E. coli strains containing either a thermolabile glutaminyl-tRNA synthetase or leucyl-tRNA synthetase. Among the revertants which still contained the thermolabile leucyl-tRNA synthetase we found two classes of regulatory mutants (leuX and leu Y) which have elevated levels of this enzyme. The leuX mutation specifies an operator-promoter region adjacent to the structural gene (leuS) for the enzyme. The leuY gene maps away from the leuS gene and codes for a protein. Using these mutants we demonstrated that the levels of leucyl-tRNA are related to the derepression of the leucine and isoleucine-valine operons. Among the revertants which still contained the thermolabile glutaminyl-tRNA synthetase were characterized three classes of mutants, glnT, glnU, and glnR. The glnT and glnU mutants contain elevated levels of tRNAgln, while the glnR mutant possesses elevated levels of glutaminyl-tRNA synthetase. The level of glutamine synthetase, the enzyme responsible for the formation of glutamine, is also derepressed in the glnT and glnR mutants.

Some genetic consequences of changes in the level of recA gene function in Escherichia coli K-12

Genetic recombination was studied in E. coli mutants that carry lesions in the recA gene but retain some capacity for generating recombinant progeny. We observed that recombination was detectable only at a very low level during the incubation of leaky RecA- merozygotes in broth. However, recombination appeared to occur at much higher frequencies when recombinant progeny were assayed by selection on minimal agar. Analysis of the recombinants obtained with Hfr donors revealed a deficiency of multiple exchanges per unit length of DNA in leaky RecA- strains. In many of these crosses recombinants that inherited donor alleles close to the transfer origin were much reduced in frequency, except when the recipient was also RecB-.

Tetrapyrrole biosynthesis: N-methyl-N'-nitrosoguanidine-induced mutants of Propionibacterium shermanii

An isolation method forN-methyl-N′-nitrosoguanidine-induced catalase negative mutants ofP. shermaniibased on replica plating is described. In contrast to previous methods, it extends to the early stages of tetrapyrrole biosynthesis which are common in both corrins and porphyrins. It may thus aid in elucidating the mechanism and control of porphyrin and corrin biosynthesis. Some preliminary results are discussed.

Isolation and characterization of lambda transducing bacteriophages for the su1+ (supD minus) amber suppressor of Escherichia coli

Specialized lambda transducing phages for the sul+ (supD-) amber suppressor in Escherichia coli K-12 have been isolated, using a secondary site lambda-cI857 lysogen in which we have shown the prophage to be closely linked to sul+.sul+ transducing particles were detected frequently, at 10-5 per plaque-forming unit, in lysates prepared from the secondary-site lysogens. High-frequency transducing lysates were obtained from several independently isolated sul+ transductants and were analyzed by CsCl equilibrium density gradient centrifugation. The transducing phages are defective; marker rescue analysis indicates that the lambda-N gene is not present. In lambda-cI857DELTANdSul+, a bio-type transducing phage, the genes specifying recombination and excision functions have been replaced by bacterial deoxyribonucleic acid.

Isolation and characterization of an Escherichia coli K-12 mutant with a temperature-sensitive recA- phenotype

A mutation that causes a temperature-sensitive RecA(-) phenotype was identified in a derivative of a PolA(-) strain that failed to grow at high temperature. The mutant allele (recA200) was shown to be linked to cysC, conferred a sharply temperature-sensitive, ultraviolet-sensitive Rec(-) phenotype in the range 35 to 42 C, and in crosses failed to show complementation at 42 C with Hfr's that transferred recA(-). Double mutants that carried both recA200 and polA were examined for ability to grow and synthesize DNA at restrictive temperatures.

Isolation and characterization of a regulatory mutant of an aminoacyl-transfer ribonucleic acid synthetase in Escherichia coli K-12

From Escherichia coli strain K28, which is temperature sensitive for growth because of a mutation in its seryl-transfer ribonucleic acid (tRNA) synthetase gene (serS), temperature-resistant mutants were selected which were found to have a fivefold higher level of seryl-tRNA synthetase than the parent strain. The "high-level" character was found to be genetically stable and is due to a mutation in a locus denoted serO. This locus was found to be very closely linked to serS on the genetic map, and the relative gene order was concluded to be serS-serO-serC. In a serO(-) strain, the normal dependence of seryl-tRNA synthetase (SerRS) activity on changes of exogenous serine concentration was not observed. In a stable heterozygous merodiploid, the serO(-) mutation is still expressed, i.e., it is cis dominant. These results strongly suggest that serO is an operator site involved in the control of the serS gene.

Close linkage of the genes serC (for phosphohydroxy pyruvate transaminase) and serS (for seryl-transfer ribonucleic acid synthetase) in Escherichia coli K-12

Escherichia coli strain K28, isolated after nitrosoguanidine mutagenesis, was found to be auxotrophic for serine. It was also temperature sensitive for growth as a result of producing an altered seryl-transfer ribonucleic acid (tRNA) synthetase (EC 6.1.1.11, l-serine: tRNA ligase [AMP]). The auxotrophy was caused by a mutation in the structural gene for phosphohydroxy-pyruvate transaminase (serC), which was distinct from, but closely linked to, the structural gene for seryl-tRNA synthetase (serS). We conclude that the relevant genes are in the order gal-serS-serC-aroA.

Rapid mapping of conditional and auxotrophic mutations in Escherichia coli K-12

The approximate genetic map locations of auxotrophic and conditional lethal mutations of Escherichia coli can be rapidly determined with replica plating techniques. A set of patches of 15 streptomycin-sensitive (Str(S)) Hfr strains with points of origin distributed around the map is replica plated onto a recombinant-selective plate with a lawn of Str(R) cells which carry an unmapped mutation. The map interval defined by the Hfr points of origin which are closest to the mutant locus is seen by the presence or absence of heavy patches of recombinants produced by transfer of early wild-type genes from the Hfrs. An alternative method is to replicate patches of different mutant strains (100 per plate) onto Hfr lawns; in this case more than 1,000 different mutants can be mapped in a single experiment in a few days. In this way, many types of mutations with similar phenotypes can be grouped as to approximate location on the genetic map. For ordering mutations within groups, the same replica plating methods can be used to cross F-prime derivatives of mutants with other mutants of the same group. Relative merits of these and other mapping methods of E. coli are discussed.

Genetic location of certain mutations conferring recombination deficiency in Escherichia coli

Four mutations conferring recombination deficiency (recA1, recA13, rec-12, and rec-65) have been cotransduced with cysC and pheA; consequently they lie between 53 and 50 on the standard genetic map of Escherichia coli. The four mutations show different degrees of apparent dominance in transient rec(+)/rec(-) zygotes, and the degree of apparent dominance of a particular mutation was shown to be a characteristic of that mutation, not a reflection of other genetic differences in the original rec mutant strain. All four mutations map at similar distances from cysC and pheA and, despite the different degrees of apparent dominance, all may lie in the recA gene.

Inversion of transfer modes and sex factor-chromosome interactions in conjugation in Escherichia coli

A study was made of the mating properties of an unusual system of interconvertible donor strains of Escherichia coli K-12: Ra-1, Ra-2, and RaF(+). The Ra-1 and Ra-2 strains are Hfr strains whose origins are widely separated on the chromosome and whose transfer modes proceed in the opposite direction from one another. When Ra-1 cells were mated with females, a small fraction of the donors transferred markers via the Ra-2 mode. This effect was enhanced by preconjugal ultraviolet (UV) treatment of the Ra-1 cells. Among the survivors of UV-treated Ra-1 cells, a few stable Ra-2 cells were found. When Ra-2 cells were used as the donors, some of them were found to mate via the Ra-1 mode, in analogy with the Ra-1 to Ra-2 alteration with inversion of F mentioned above. Related experiments suggested that the inversion occurs by detachment of the F factor from one Hfr origin locus, followed by reassociation of the F factor with the other Hfr origin locus. Both the Ra-1 and Ra-2 strains reverted spontaneously to an F(+) strain, called RaF(+). Cultures of RaF(+) cells were found to mate primarily according to the Ra-1 and Ra-2 transfer modes, with smaller contributions also coming from transfer modes with origins elsewhere on the chromosome in a way which is similar to the transfer of markers from a normal F(+) strain. The RaF(+) sex factor was found to be wild type, whereas the chromosome was found to carry irregularities (sex factor affinity loci) at the locations of the Ra-1 and Ra-2 origins. Only about 10% of the donor capacity of the RaF(+) strain was due to stable spontaneous Hfr cells in cultures of RaF(+) cells.

Low recombination frequency for markers very near the origin in conjugation in E. coli

By performing matings using various Hfr strains having different origins of transfer, it has been observed that male chromosomal markers located very near the origin of transfer in conjugation inE. coliappear in recombinants with a lower frequency than expected from an extrapolation of the transfer gradient. The effect is greatest for markers closest to the origin, and becomes negligible for markers transferred more than 4–5 min. after the origin. The results suggest that in the zygote a random cross-over between male and female genomes is necessary somewhere between the origin and any male marker in order for that marker to appear in a viable recombinant. It was also deduced that the entry time for the origin itself occurs after a 3–5 min. delay after mixing male and female cells together.