Type I-F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity

This is the final version. Available from the publisher via the DOI in this record.Type I CRISPR-Cas systems are abundant and widespread adaptive immune systems in bacteria and can greatly enhance bacterial survival in the face of phage infection. Upon phage infection, some CRISPR-Cas immune responses result in bacterial dormancy or slowed growth, which suggests the outcomes for infected cells may vary between systems. Here we demonstrate that type I CRISPR immunity of Pectobacterium atrosepticum leads to suppression of two unrelated virulent phages, ɸTE and ɸM1. Immunity results in an abortive infection response, where infected cells do not survive, but viral propagation is severely decreased, resulting in population protection due to the reduced phage epidemic. Our findings challenge the view of CRISPR-Cas as a system that protects the individual cell and supports growing evidence of abortive infection by some types of CRISPR-Cas systems

Transient eco-evolutionary dynamics early in a phage epidemic have strong and lasting impact on the long-term evolution of bacterial defences

This is the final version. Available on open access from Public Library of Science (PLoS) via the DOI in this recordData Availability: Data and code are available online https://doi.org/10.5281/zenodo.8193506Organisms have evolved a range of constitutive (always active) and inducible (elicited by parasites) defence mechanisms, but we have limited understanding of what drives the evolution of these orthogonal defence strategies. Bacteria and their phages offer a tractable system to study this: Bacteria can acquire constitutive resistance by mutation of the phage receptor (surface mutation, sm) or induced resistance through their CRISPR-Cas adaptive immune system. Using a combination of theory and experiments, we demonstrate that the mechanism that establishes first has a strong advantage because it weakens selection for the alternative resistance mechanism. As a consequence, ecological factors that alter the relative frequencies at which the different resistances are acquired have a strong and lasting impact: High growth conditions promote the evolution of sm resistance by increasing the influx of receptor mutation events during the early stages of the epidemic, whereas a high infection risk during this stage of the epidemic promotes the evolution of CRISPR immunity, since it fuels the (infection-dependent) acquisition of CRISPR immunity. This work highlights the strong and lasting impact of the transient evolutionary dynamics during the early stages of an epidemic on the long-term evolution of constitutive and induced defences, which may be leveraged to manipulate phage resistance evolution in clinical and applied settings.Natural Environment Research Council (NERC)European Research Council (ERC)Biotechnology and Biological Sciences Research Council (BBSRC

Denitrification as a source of nitric oxide emissions from incubated soil cores from a UK grassland

Agricultural soils are a major source of nitric oxide (NO) and nitrous oxide (N2O), which are produced and consumed by biotic and abiotic soil processes. The dominant sources of NO and N2O are microbial nitrification and denitrification. While N2O emissions have been attributed to both processes, depending on the environmental conditions such as substrate availability, pH and water filled pore space (WFPS), NO emissions are thought to predominantly derive from nitrification. Although attributing gaseous emissions to specific processes is still difficult, recent findings challenge the latter of those assumptions. Using the gas-flow-soil-core method, i.e soil cores incubated under a He/O2 atmosphere at constant surface gas flow, combined with 15N labelled isotopic techniques, the present study investigated the role of denitrification on NO, N2O and N2 emissions in a UK grassland soil under high soil moisture and an aerobic headspace atmosphere. With the application of KNO3 and glucose to support denitrification, denitrification was the source of N loss of between 0.61 and 0.67% of the added N via NO emissions, 1.60–1.68% via N2O and 0.03–0.05% via N2 emissions. Overall, our study showed that denitrification has been overlooked as a source of NO emissions

Coevolution between bacterial CRISPR-Cas systems and their bacteriophages

This is the author accepted manuscript. The final version is available from Cell Press via the DOI in this record CRISPR-Cas systems provide bacteria and archaea with adaptive, heritable immunity against their viruses (bacteriophages and phages) and other parasitic genetic elements. CRISPR-Cas systems are highly diverse, and we are only beginning to understand their relative importance in phage defense. In this review, we will discuss when and why CRISPR-Cas immunity against phages evolves, and how this, in turn, selects for the evolution of immune evasion by phages. Finally, we will discuss our current understanding of if, and when, we observe coevolution between CRISPR-Cas systems and phages, and how this may be influenced by the mechanism of CRISPR-Cas immunity.VENIBiotechnology and Biological Sciences Research CouncilBiotechnology and Biological Sciences Research Counci

Mental States Are Like Diseases

While Quine’s linguistic behaviorism is well-known, his Kant Lectures contain one of his most detailed discussions of behaviorism in psychology and the philosophy of mind. Quine clarifies the nature of his psychological commitments by arguing for a modest view that is against ‘excessively restrictive’ variants of behaviorism while maintaining ‘a good measure of behaviorist discipline…to keep [our mental] terms under control’. In this paper, I use Quine’s Kant Lectures to reconstruct his position. I distinguish three types of behaviorism in psychology and the philosophy of mind: ontological behaviorism, logical behaviorism, and epistemological behaviorism. I then consider Quine’s perspective on each of these views and argue that he does not fully accept any of them. By combining these perspectives we arrive at Quine’s surprisingly subtle view about behaviorism in psychology

A Study of Problem Solving Using Blocks Vehicle in a STEAM Course for Lower Elementary Levels

STEAM education is currently one of the most important parts of the elementary school curriculum. If STEAM learning can cultivate good problem-solving ability, it will also help improve judgment and thinking abilities. Several voices in the literature have argued for cooperative learning in STEAM courses. Although the effectiveness of course learning often is evaluated using course feedback forms, there is comparatively little emphasis on whether a course succeeds in realizing cooperative learning. For a course involving self-propelled toy-brick cars, there is little research on the application of low-grade pupils. Therefore, based on the integration of STEAM courses into self-propelled toy-brick car learning, this study applied two learning strategies of cooperative learning and individual learning to low-grade pupils in the second grade in elementary schools. After completing the course problem-solving ability indicators were measured and analyzed using the problem-solving ability test. The results show that the mean score of the experimental group in the problem-solving ability test was higher than that of the control group. In the problem-solving ability test, the scores of the two groups were also significantly different, which suggests that cooperative learning is more effective than individual learning strategies.acceptedVersio

A novel isolator-based system promotes viability of human embryos during laboratory processing

In vitro fertilisation (IVF) and related technologies are arguably the most challenging of all cell culture applications. The starting material is a single cell from which one aims to produce an embryo capable of establishing a pregnancy eventually leading to a live birth. Laboratory processing during IVF treatment requires open manipulations of gametes and embryos, which typically involves exposure to ambient conditions. To reduce the risk of cellular stress, we have developed a totally enclosed system of interlinked isolator-based workstations designed to maintain oocytes and embryos in a physiological environment throughout the IVF process. Comparison of clinical and laboratory data before and after the introduction of the new system revealed that significantly more embryos developed to the blastocyst stage in the enclosed isolator-based system compared with conventional open-fronted laminar flow hoods. Moreover, blastocysts produced in the isolator-based system contained significantly more cells and their development was accelerated. Consistent with this, the introduction of the enclosed system was accompanied by a significant increase in the clinical pregnancy rate and in the proportion of embryos implanting following transfer to the uterus. The data indicate that protection from ambient conditions promotes improved development of human embryos. Importantly, we found that it was entirely feasible to conduct all IVF-related procedures in the isolator-based workstations

Benefits and risks of the hormetic effects of dietary isothiocyanates on cancer prevention

The isothiocyanate (ITC) sulforaphane (SFN) was shown at low levels (1-5 µM) to promote cell proliferation to 120-143% of the controls in a number of human cell lines, whilst at high levels (10-40 µM) it inhibited such cell proliferation. Similar dose responses were observed for cell migration, i.e. SFN at 2.5 µM increased cell migration in bladder cancer T24 cells to 128% whilst high levels inhibited cell migration. This hormetic action was also found in an angiogenesis assay where SFN at 2.5 µM promoted endothelial tube formation (118% of the control), whereas at 10-20 µM it caused significant inhibition. The precise mechanism by which SFN influences promotion of cell growth and migration is not known, but probably involves activation of autophagy since an autophagy inhibitor, 3-methyladenine, abolished the effect of SFN on cell migration. Moreover, low doses of SFN offered a protective effect against free-radical mediated cell death, an effect that was enhanced by co-treatment with selenium. These results suggest that SFN may either prevent or promote tumour cell growth depending on the dose and the nature of the target cells. In normal cells, the promotion of cell growth may be of benefit, but in transformed or cancer cells it may be an undesirable risk factor. In summary, ITCs have a biphasic effect on cell growth and migration. The benefits and risks of ITCs are not only determined by the doses, but are affected by interactions with Se and the measured endpoint

Intramedullary melanotic schwannoma

We present a case of an intramedullary melanotic schwannoma (IMS) of the thoracic spinal cord. To our knowledge, this is the seventh reported case of an IMS of the central nervous system. Schwannomas are benign nerve sheath tumors of neural crest origin composed entirely of well differentiated Schwann cells that typically occur in peripheral nerves. Both the intramedullary location and the melanotic component of the reported lesion make it exceedingly rare. We will present our case, theories as to the origin of these tumors, clues in radiographic identification, and current clinical follow-up recommendations

Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer.

The early detection of breast cancer is the best means to minimise disease-related mortality. Current screening techniques have limited sensitivity and specificity. Breast nipple aspirate fluid can be obtained noninvasively and contains proteins secreted from ductal and lobular epithelia. Nipple aspirate fluid proteins are breast specific and generally more concentrated than corresponding blood levels. Proteomic analysis of 1 microl of diluted nipple aspirate fluid over a 5-40 kDa range from 20 subjects with breast cancer and 13 with nondiseased breasts identified five differentially expressed proteins. The most sensitive and specific proteins were 6500 and 15 940 Da, found in 75-84% of samples from women with cancer but in only 0-9% of samples from normal women. These findings suggest that (1) differential expression of nipple aspirate fluid proteins exists between women with normal and diseased breasts, and (2) analysis of these proteins may predict the presence of breast cancer