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Streptococcus pneumoniae is a major human pathogen and rising resistance to β-lactam antibiotics, such as penicillin, is a significant threat to global public health. Mutations occurring in the penicillin-binding proteins (PBPs) can confer high-level penicillin resistance but other poorly understood genetic factors are also important. Here, we combined strictly controlled laboratory experiments and population analyses to identify a new penicillin resistance pathway that is independent of PBP modification. Initial laboratory selection experiments identified high-frequency pde1 mutations conferring S. pneumoniae penicillin resistance. The importance of variation at the pde1 locus was confirmed in natural and clinical populations in an analysis of >7,200 S. pneumoniae genomes. The pde1 mutations identified by these approaches reduce the hydrolytic activity of the Pde1 enzyme in bacterial cells and thereby elevate levels of cyclic-di-adenosine monophosphate and penicillin resistance. Our results reveal rapid de novo loss of function mutations in pde1 as an evolutionary gateway conferring low-level penicillin resistance. This relatively simple genomic change allows cells to persist in populations on an adaptive evolutionary pathway to acquire further genetic changes and high-level penicillin resistance. [ABSTRACT FROM AUTHOR]

Background: Breast-conserving surgery (BCS) is a mainstay for breast cancer management, and obtaining negative margins is critical. Some have advocated for the use of preoperative magnetic resonance imaging (MRI) in reducing positive margins after BCS. We sought to determine whether preoperative MRI was associated with reduced positive margins. Patients and Methods: The SHAVE/SHAVE2 trials were multicenter trials in ten US centers with patients with stage 0–3 breast cancer undergoing BCS. Use of preoperative MRI was at the discretion of the surgeon. We evaluated whether or not preoperative MRI was associated with margin status prior to randomization regarding resection of cavity with shave margins. Results: A total of 631 patients participated. Median age was 64 (range 29–94) years, with a median tumor size of 1.3 cm (range 0.1–9.3 cm). Patient factors included 26.1% of patients (165) had palpable tumors, and 6.5% (41) received neoadjuvant chemotherapy. Tumor factors were notable for invasive lobular histology in 7.0% (44) and extensive intraductal component (EIC) in 32.8% (207). A preoperative MRI was performed in 193 (30.6%) patients. Those who underwent preoperative MRI were less likely to have a positive margin (31.1% versus 38.8%), although this difference was not statistically significant (p = 0.073). On multivariate analysis, controlling for patient and tumor factors, utilization of preoperative MRI was not a significant factor in predicting margin status (p = 0.110). Rather, age (p = 0.032) and tumor size (p = 0.040) were the only factors associated with margin status. Conclusion: These data suggest that preoperative MRI is not associated margin status; rather, patient age and tumor size are the associated factors. [ABSTRACT FROM AUTHOR]

Background: Molecular subtype in invasive breast cancer guides systemic therapy. It is unknown whether molecular subtype should also be considered to tailor surgical therapy. The present investigation was designed to evaluate whether breast cancer subtype impacted surgical margins in patients with invasive breast cancer stage I through III undergoing breast-conserving therapy.Methods: Data from 2 randomized trials evaluating cavity shave margins (CSM) on margin status in patients undergoing partial mastectomy (PM) were used for this analysis. Patients were included if invasive carcinoma was present in the PM specimen and data for all 3 receptors (ER, PR, and HER2) were known. Patients were classified as luminal if they were ER and/or PR positive; HER2 enriched if they were ER and PR negative but HER2 positive; and TN if they were negative for all 3 receptors. The impact of subtype on the margin status was evaluated at completion of standard PM, prior to randomization to CSM versus no CSM. Non-parametric statistical analyses were performed using SPSS Version 26.Results: Molecular subtype was significantly correlated with race (P = .011), palpability (P = .007), and grade (P < .001). Subtype did not correlate with Hispanic ethnicity (P = .760) or lymphovascular invasion (P = .756). In this cohort, the overall positive margin rate was 33.7%. This did not vary based on molecular subtype (positive margin rate 33.7% for patients with luminal tumors vs 36.4% for those with TN tumors, P = .425).Discussion: Molecular subtype does not predict margin status. Therefore, molecular subtype should not, independent of other factors, influence surgical decision-making. [ABSTRACT FROM AUTHOR]

Streptococcus pneumoniae (the pneumococcus) is a major human pathogen causing invasive disease, including community-acquired bacteraemia, and remains a leading cause of global mortality. Understanding the role of phagocytes in killing bacteria is still limited, especially in vivo. In this study, we established a zebrafish model to study the interaction between intravenously administered pneumococci and professional phagocytes such as macrophages and neutrophils, to unravel bacterial killing mechanisms employed by these immune cells. Our model confirmed the key role of polysaccharide capsule in promoting pneumococcal virulence through inhibition of phagocytosis. Conversely, we show pneumococci lacking a capsule are rapidly internalised by macrophages. Low doses of encapsulated S. pneumoniae cause near 100% mortality within 48 hours postinfection (hpi), while 50 times higher doses of unencapsulated pneumococci are easily cleared. Time course analysis of in vivo bacterial numbers reveals that while encapsulated pneumococcus proliferates to levels exceeding 105 CFU at the time of host death, unencapsulated bacteria are unable to grow and are cleared within 20 hpi. Using genetically induced macrophage depletion, we confirmed an essential role for macrophages in bacterial clearance. Additionally, we show that upon phagocytosis by macrophages, phagosomes undergo rapid acidification. Genetic and chemical inhibition of vacuolar ATPase (v-ATPase) prevents intracellular bacterial killing and induces host death indicating a key role of phagosomal acidification in immunity to invading pneumococci. We also show that our model can be used to study the efficacy of antimicrobials against pneumococci in vivo. Collectively, our data confirm that larval zebrafish can be used to dissect killing mechanisms during pneumococcal infection in vivo and highlight key roles for phagosomal acidification in macrophages for pathogen clearance. [ABSTRACT FROM AUTHOR]

The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation (1-3). Although the divergence observed at some host-resistance (4-6) and parasite-infectivity (7-9) genes is consistent with this, the long time periods typically required to study co-evolution have so far prevented any direct empirical test. Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Φ2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. Coevolution also resulted in far greater genetic divergence between replicate populations, which was correlated with the range of hosts that coevolved phage were able to infect. Consistent with this, the most rapidly evolving phage genes under coevolution were those involved in host infection. These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species., According to the Red Queen hypothesis, biotic interactions are a fundamental driver of molecular evolution (2). The Red Queen hypothesis posits that for a given species, its effective environment is [...]

We studied the two mreB genes, encoding actinlike cytoskeletal elements, in the predatory bacterium Bdellovibrio bacteriovorus. This bacterium enters and replicates within other Gram-negative bacteria by attack-phase Bdellovibrio squeezing through prey outer membrane, residing and growing filamentously in the prey periplasm forming an infective 'bdelloplast,' and septating after 4 h, once the prey contents are consumed. This lifestyle brings challenges to the Bdellovibrio cytoskeleton. Both mreB genes were essential for viable predatory growth, but C-terminal green fluorescent protein tagging each separately with monomeric teal-fluorescent protein (mTFP) gave two strains with phenotypic changes at different stages in predatory growth and development. MreB1-mTFP cells arrested growth early in bdelloplast formation, despite successful degradation of prey nucleoid. A large population of stalled bdelloplasts formed in predatory cultures and predation proceeded very slowly. A small proportion of bdelloplasts lysed after several days, liberating MreB1-mTFP attack-phase cells of wild-type morphology; this process was aided by subinhibitory concentrations of an MreB-specific inhibitor, A22. MreB2-mTFP, in contrast, was predatory at an almost wild-type rate but yielded attack-phase cells with diverse morphologies, including spherical, elongated, and branched, the first time such phenotypes have been described. Wild-type predatory rates were seen for all but spherical morphotypes, and septation of elongated morphotypes was achieved by the addition of A22. doi: 10.1128/JB.01157-09

Kinetic resolution provided a highly enantioselective method to access a range of 3-aryl-3,4-dihydro-2 H -1,4-benzoxazines using n -butyllithium and the chiral ligand sparteine. The enantioenrichment remained high on removing the tert -butoxycarbonyl (Boc) protecting group. The intermediate organolithium undergoes ring opening to an enamine. The kinetic resolution was extended to give enantiomerically enriched substituted 1,2,3,4-tetrahydroquinoxalines and was applied to the synthesis of an analogue of the antibiotic levofloxacin that was screened for its activity against the human pathogen Streptococcus pneumoniae. [ABSTRACT FROM AUTHOR]

Abstract Background Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome. Results To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired. Conclusions The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

The advent of fully autonomous vehicles (AVs) raises many questions. While some appear purely technical, others engage matters of public policy, sometimes with a prominent ethical component. Our expertise lies in law and applied ethics, and so our inquiry will focus heavily on legal or ethical issues arising from a widespread adoption of AVs and their response in emergency situations involving animals. By "animals" we do not mean all other animals than humans. We will concentrate on interest-bearing animals. These are animals who possess a welfare or wellbeing, animals whose lives can fare well or badly from their perspective. [ABSTRACT FROM AUTHOR]

Abstract Background Phages are thought to play a crucial role in the maintenance of diversity in natural bacterial communities. Theory suggests that phages impose density dependent regulation on bacterial populations, preventing competitive dominants from excluding less competitive species. To test this, we constructed experimental communities containing two bacterial species (Pseudomonas fluorescens and Pseudomonas aeruginosa) and their phage parasites. Communities were propagated at two environmental temperatures that reversed the outcome of competition in the absence of phage. Results The evenness of coexistence was enhanced in the presence of a phage infecting the superior competitor and in the presence of phage infecting both competitors. This occurred because phage altered the balance of competitive interactions through reductions in density of the superior competitor, allowing concomitant increases in density of the weaker competitor. However, even coexistence was not equally stable at the two environmental temperatures. Conclusion Phage can alter competitive interactions between bacterial species in a way that is consistent with the maintenance of coexistence. However, the stability of coexistence is likely to depend upon the nature of the constituent bacteria-bacteriophage interactions and environmental conditions.

The predatory bacterium B. bacteriovorus grows and divides inside the periplasm of Gram-negative bacteria, forming a structure known as a bdelloplast. Cell division of predators inside the dead prey cell is not by binary fission but instead by synchronous division of a single elongated filamentous cell into odd or even numbers of progeny cells. Bdellovibrio replication and cell division processes are dependent on the finite level of nutrients available from inside the prey bacterium. The filamentous growth and division process of the predator maximizes the number of progeny produced by the finite nutrients in a way that binary fission could not. To learn more about such an unusual growth profile, we studied the role of DivIVA in the growing Bdellovibrio cell. This protein is well known for its link to polar cell growth and spore formation in Gram-positive bacteria, but little is known about its function in a predatory growth context. We show that DivIVA is expressed in the growing B. bacteriovorus cell and controls cell morphology during filamentous cell division, but not the number of progeny produced. Bacterial Two Hybrid (BTH) analysis shows DivIVA may interact with proteins that respond to metabolic indicators of amino-acid biosynthesis or changes in redox state. Such changes may be relevant signals to the predator, indicating the consumption of prey nutrients within the sealed bdelloplast environment. ParA, a chromosome segregation protein, also contributes to bacterial septation in many species. The B. bacteriovorus genome contains three ParA homologs; we identify a canonical ParAB pair required for predatory cell division and show a BTH interaction between a gene product encoded from the same operon as DivIVA with the canonical ParA. The remaining ParA proteins are both expressed in Bdellovibrio but are not required for predator cell division. Instead, one of these ParA proteins coordinates gliding motility, changing the frequency at which the cells reverse direction. Our work will prime further studies into how one bacterium can co-ordinate its cell division with the destruction of another bacterium that it dwells within. [ABSTRACT FROM AUTHOR]

I will discuss how animal laboratory research can be ethically analyzed using Donaldson and Kymlicka's political theory of animal rights. To accomplish this, I will not presuppose their strong animal rights framework. Donaldson and Kymlicka's approach revolves around some basic human-animal relationships, reflecting the relational turn in applied ethics writ large. However, they do not discuss laboratory animal research in any detail, and so an extension to that domain of animal use is in order. Donaldson and Kymlicka's emphasis on human-animal relationships is useful for reminding ourselves that in laboratories various staff or personnel can develop bonds with captive animals that make it difficult to follow certain protocols as well as create a deep and lasting negative impression. Though, when suitably modified, Donaldson and Kymlicka's political theory can apply to animal research ethics, it can only do so if we ask more from all members of our society. [ABSTRACT FROM AUTHOR]

Human and animal research both operate within established standards. In the United States, criticism of the human research environment and recorded abuses of human research subjects served as the impetus for the establishment of the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research, and the resulting Belmont Report. The Belmont Report established key ethical principles to which human research should adhere: respect for autonomy, obligations to beneficence and justice, and special protections for vulnerable individuals and populations. While current guidelines appropriately aim to protect the individual interests of human participants in research, no similar, comprehensive, and principled effort has addressed the use of (nonhuman) animals in research. Although published policies regarding animal research provide relevant regulatory guidance, the lack of a fundamental effort to explore the ethical issues and principles that should guide decisions about the potential use of animals in research has led to unclear and disparate policies. Here, we explore how the ethical principles outlined in the Belmont Report could be applied consistently to animals. We describe how concepts such as respect for autonomy and obligations to beneficence and justice could be applied to animals, as well as how animals are entitled to special protections as a result of their vulnerability. [ABSTRACT FROM AUTHOR]

I will discuss how animal laboratory research can be ethically analyzed using Donaldson and Kymlicka's political theory of animal rights. To accomplish this, I will not presuppose their strong animal rights framework. Donaldson and Kymlicka's approach revolves around some basic human-animal relationships, reflecting the relational turn in applied ethics writ large. However, they do not discuss laboratory animal research in any detail, and so an extension to that domain of animal use is in order. Donaldson and Kymlicka's emphasis on human-animal relationships is useful for reminding ourselves that, in laboratories, various staff or personnel can develop bonds with captive animals that make it difficult to follow certain protocols as well as create a deep and lasting negative impression. Though, when suitably modified, Donaldson and Kymlicka's political theory can apply to animal research ethics, it can only do so if we ask more from all members of our society. [ABSTRACT FROM AUTHOR]

Though there is a burgeoning interest in applied Buddhist ethics, Buddhist animal research ethics remains an underdeveloped area. In this paper I will explore how some central Buddhist ethical considerations can usefully engage our use of other animals (henceforth, animals) in science. As the scientific use of animals is broad, I will narrow my focus to laboratory science. I will show that, though a Buddhist abolitionism would not be unmotivated, it is possible to reject it. While doing so, it will be important to resist emphasizing elements of Buddhist thought that merely provide reasons to adopt the dominant ethical framework governing laboratory animal research ethics, known as the 3Rs. Though I will suggest how a Buddhist animal research ethics can sometimes permit the use of animals in harmful research, it will also require ethical constraints that resonate with some of the more progressive elements in 'Western' bioethics. [ABSTRACT FROM AUTHOR]

Background: Prior traumatic experiences have been associated with poorer coping strategies, greater distress, and more posttraumatic stress disorder (PTSD) symptoms following a subsequent cancer diagnosis affecting their survival. However, the impact of prior physical traumatic injury on cancer survival has not been examined. Methods: The present study matched patients from the same Level 1 Trauma center who appeared in both the trauma and cancer registries. A total of 498 patients met the criteria between 1998 and 2014 who have experienced both a diagnosis of cancer and a physical traumatic injury. The survival between the patients who had physical trauma before cancer (TBC) versus those that had physical trauma after the cancer diagnosis (TAC) were compared. Results: The TBC group had a higher percentage of males (48 % vs 33 % p = 0.001) and motor vehicle collisions (18 % vs 7 %, p < 0.001), than the TAC group. TBC patients were also significantly younger than TAC patients at the time of the physical traumatic event (68.7 ± 14.6 vs 76.2 ± 12.0 years, p < 0.001), and longer length of time between the cancer diagnosis and physical traumatic injury (2.9 ± 2.9 vs 1.7 ± 2.6 years, p < 0.001). The overall probability of survival for the entire sample was 68 %. Percent survival for the TBC (n = 251) and TAC (n = 247) groups was 56 and 80 % respectively (p < 0.001). Results were consistent regardless of stage of cancer at diagnosis (hazard ratio (HR (Standard Error)). After adjusting for comorbidities Charlson comorbidity index (CCI) (HR = 1.2 (0.06), p = 0.009)), cancer stage (HR = 2.8 (0.12), p < 0.001)), lung cancer (HR = 1.7 (0.25), p < 0.001) and bladder cancer (HR = 3.5 (0.55), p = 0.02), experiencing a prior physical traumatic injury was associated with an increased HR for mortality of 4.6 (0.93), p < 0.001). Conclusions: A physical traumatic episode before cancer diagnosis (TBC) increased the risk of death 4.6 fold compared to the TAC group even after adjusting for CCI, stage of cancer at diagnosis, lung cancer, and bladder cancer. These findings suggest considering a history of physical traumatic injury in cancer patients as a possible risk factor for faster cancer progression and mortality. [ABSTRACT FROM AUTHOR]

Previous analyses of empirical food webs (the networks of who eats whom in a community) have revealed that parasites exert a strong influence over observed food web structure and alter many network properties such as connectance and degree distributions. It remains unclear, however, whether these community-level effects are fully explained by differences in the ways that parasites and free-living species interact within a food web., To rigorously quantify the interrelationship between food web structure, the types of species in a web and the distinct types of feeding links between them, we introduce a shared methodology to quantify the structural roles of both species and feeding links. Roles are quantified based on the frequencies with which a species (or link) appears in different food web motifs - the building blocks of networks., We hypothesized that different types of species (e.g. top predators, basal resources, parasites) and different types of links between species (e.g. classic predation, parasitism, concomitant predation on parasites along with their hosts) will show characteristic differences in their food web roles., We found that parasites do indeed have unique structural roles in food webs. Moreover, we demonstrate that different types of feeding links (e.g. parasitism, predation or concomitant predation) are distributed differently in a food web context. More than any other interaction type, concomitant predation appears to constrain the roles of parasites. In contrast, concomitant predation links themselves have more variable roles than any other type of interaction., Together, our results provide a novel perspective on how both species and feeding link composition shape the structure of an ecological community and vice versa. [ABSTRACT FROM AUTHOR]