Comment on “the IS6 family, a clinically important group of insertion sequences including IS26” by Varani and co-authors

The insertion sequence IS26 has long been known to play a major role in the recruitment of antibiotic resistance genes into the mobile resistance gene pool of Gram-negative bacteria and IS26 also plays a major role in their subsequent broad dissemination. Related IS, IS431/257 and IS1216 are important in the same roles in Gram positive bacteria. However, until recently the properties of IS26 movement that could potentially explain this ability had not been explored. A much needed insight has come from our recent demonstration that IS26 uses a novel targeted mechanism that is conservative. The targeted conservative mechanism is much more efficient than the known replicative mechanism, which is now more accurately called copy-in. A recent review “The IS6 family, a clinically important group of insertion sequences including IS26” by Varani, He, Siguier, Ross and Chandler published in Mobile DNA has substantially misrepresented the recent studies on the targeted conservative mechanism and at the same time incorrectly implied that any mechanism established for IS26 can be assumed to apply to a range of IS that are at best very distantly related. A few of the most important issues are examined in this comment. Readers are advised to consult the original literature to check facts before drawing firm conclusions.

A Method to Compute the Schrieffer–Wolff Generator for Analysis of Quantum Memory

Quantum illumination uses entangled light that consists of signal and idler modes to achieve higher detection rate of a low-reflective object in noisy environments. The best performance of quantum illumination can be achieved by measuring the returned signal mode together with the idler mode. Thus, it is necessary to prepare a quantum memory that can keep the idler mode ideal. To send a signal towards a long-distance target, entangled light in the microwave regime is used. There was a recent demonstration of a microwave quantum memory using microwave cavities coupled with a transmon qubit. We propose an ordering of bosonic operators to efficiently compute the Schrieffer–Wolff transformation generator to analyze the quantum memory. Our proposed method is applicable to a wide class of systems described by bosonic operators whose interaction part represents a definite number of transfer in quanta.

Multiple macroecological laws do characterize various aspects of microbiota dynamics

In this letter we address the potential confusion related to our recent demonstration that multiple macroecological laws describe short- and long-term dynamics of microbial communities. Specifically, we clarify that these laws, similarly to many other relationships observed in nature, are characterized not just by the existence of scaling, but also by certain characteristic values of the scaling exponents. By performing proper statistical analysis, we demonstrate that the relationships sensitive to temporal bacterial dynamics are not reproduced in the shuffled data. We also discuss that there is no clear evidence in the data that macroecological relationships in microbiota are primarily driven by external or environmental factors. Proper statistical analyses of the data suggest that the dynamics of gut microbiota, even on a constant diet, contains rich temporal structure. Therefore, it is likely that complex and non-linear internal dynamics may be primarily responsible for the observed macroecological laws in microbiota and other ecological communities.

Advances in understanding of mycorrhizal-like associations in bryophytes

Mutually beneficial associations between plants and soil fungi, mycorrhizas, are one of the most important terrestrial symbioses. These partnerships are thought to have propelled plant terrestrialisation some 500 million years ago and today they play major roles in ecosystem functioning. It has long been known that bryophytes harbour, in their living tissues, fungal symbionts, recently identified as belonging to the three mycorrhizal fungal lineages Glomeromycotina, Ascomycota and Basidiomycota. Latest advances in understanding of fungal associations in bryophytes have been largely driven by the discovery, nearly a decade ago, that early divergent liverwort clades, including the most basal Haplomitriopsida, and some hornworts, engage with a wider repertoire of fungal symbionts than previously thought, including endogonaceous members of the ancient sub-phylum Mucoromycotina. Subsequent global molecular and cytological studies have revealed that Mucoromycotina symbionts, alongside Glomeromycotina, are widespread in both complex and simple thalloid liverworts and throughout hornworts, with physiological studies confirming that, in liverworts at least, these associations are mycorrhizal-like, and highlighting important functional differences between Mucoromycotina and Glomeromycotina symbioses. Whether a more prominent role of Mucoromycotina symbionts in plant nitrogen nutrition, as identified in liverworts, extends to other plant lineages, including the flowering plants, is a major topic for future research. The latest finding that ascomycete symbionts of leafy liverworts are not restricted to one fungus, Rhizoscyphus ericae, but include species in the genus Meliniomyces, as shown here in Mylia anomala, together with the recent demonstration that R. ericae forms nutritional mutualisms with the rhizoids of Cephalozia bicuspidata, fill other major gaps in our growing knowledge of fungal associations across land plants.

Therapeutic targeting of Lyn kinase to treat chorea-acanthocytosis

Chorea-Acanthocytosis (ChAc) is a devastating, little understood, and currently untreatable neurodegenerative disease caused by VPS13A mutations. Based on our recent demonstration that accumulation of activated Lyn tyrosine kinase is a key pathophysiological event in human ChAc cells, we took advantage of Vps13a−/− mice, which phenocopied human ChAc. Using proteomic approach, we found accumulation of active Lyn, γ-synuclein and phospho-tau proteins in Vps13a−/− basal ganglia secondary to impaired autophagy leading to neuroinflammation. Mice double knockout Vps13a−/− Lyn−/− showed normalization of red cell morphology and improvement of autophagy in basal ganglia. We then in vivo tested pharmacologic inhibitors of Lyn: dasatinib and nilotinib. Dasatinib failed to cross the mouse brain blood barrier (BBB), but the more specific Lyn kinase inhibitor nilotinib, crosses the BBB. Nilotinib ameliorates both Vps13a−/− hematological and neurological phenotypes, improving autophagy and preventing neuroinflammation. Our data support the proposal to repurpose nilotinib as new therapeutic option for ChAc patients.

Peran Anggota Kepolisian Dalmas Polda Bali dalam Penegakan Hukum terhadap Penanganan Unjuk Rasa Tolak Reklamasi Teluk Benoa

Every citizen has the right to express an opinion in accordance with Law Number 9 of 1998 concerning Freedom of Expressing Opinions in Public. Freedom of opinion is generally carried out by demonstrations. The recent demonstration in Bali is a demonstration against the reclamation of Benoa Bay. This is of particular concern to members of the Bali Police Dalmas as the main party in the handling of this demonstration. In handling it, the Bali Police Dalmas is guided to enforce the law against each of these demonstrations. Based on this background, this research was conducted with the aim of describing how the role of members of the Bali Police Dalmas police in law enforcement against the Benoa Bay protest against the Benoa Bay reclamation and what factors hindered the implementation of handling the Benoa Bay reclamation protest action by members of the Bali Police Dalmas. This study used an empirical legal research method. The results of this study indicated that the role of the Bali Police Dalmas in enforcing the law against the protest against Benoa Bay reclamation was carried out based on pre-emptive, preventive, and repressive actions based on statutory regulations and the police chief regulations regarding the handling of demonstrations. In addition, the factors that hindered the implementation of the protest against the reclamation of Benoa Bay by members of the Bali Police Dalmas include internal and external factors. the internal factor is factor of Dalmas members themselves, both from a mental perspective, professionalism, and knowledge about how to handle protests. Meanwhile, the external factor is generally the mass of protesters who do not understand the provisions that apply to the implementation of a demonstration.

Mineralocorticoid Dysfunction during Critical Illness

The recent demonstration of the significant reduction in mortality in patients with septic shock treated with adjunctive glucocorticoids combined with fludrocortisone and the effectiveness of angiotensin II in treating vasodilatory shock have renewed interest in the role of the mineralocorticoid axis in critical illness. Glucocorticoids have variable interactions at the mineralocorticoid receptor. Similarly, mineralocorticoid receptor–aldosterone interactions differ from mineralocorticoid receptor–glucocorticoid interactions and predicate receptor–ligand interactions that differ with respect to cellular effects. Hyperreninemic hypoaldosteronism or selective hypoaldosteronism, an impaired adrenal response to increasing renin levels, occurs in a subgroup of hemodynamically unstable critically ill patients. The suggestion is that there is a defect at the level of the adrenal zona glomerulosa associated with a high mortality rate that may represent an adaptive response aimed at increasing cortisol levels. Furthermore, cross-talk exists between angiotensin II and aldosterone, which needs to be considered when employing therapeutic strategies.

12. Global Growth, Inequality, and Poverty:

This chapter argues that economists have oversold the virtues of globalization, displaying confidence in derived policy prescriptions well beyond the evidence. The most spectacular recent demonstration of hubris is the failure of almost the whole of the mainstream economics profession in the few years before 2007–8 to forecast a major recession. The chapter then outlines the neo-liberal world view and its application in the form of the development recipe known as the Washington Consensus. Since the 1980s, the Western economic policy ‘establishment’ has espoused a doctrine of ‘best economic policy’ for the world which says, put too simply, that ‘more market and less state’ should be the direction of travel for developed and developing countries. This overarching neo-liberal ideology embraces globalization as a major component, relating to the nature of integration into the international economy. The chapter then looks at trends in world income distribution and poverty, bearing in mind the optimistic claims of the globalization argument.

Transcription-coupled repair in Drosophila melanogaster is independent of the mismatch repair pathway

Transcription-coupled repair (TCR) removes base damage on the transcribed strand of a gene to ensure a quick resumption of transcription. Based on the absence of key enzymes for TCR and empirical evidence, TCR was thought to be missing in Drosophila melanogaster. The recent demonstration of TCR in S2 cells raises the question about the involved genes. Since the mismatch repair (MMR) pathway serves a central role in TCR, at least in Escherichia coli, we studied the mutational signatures in flies with a deletion of the MMR gene spellchecker1 (spel1), a MutS homolog. Whole-genome sequencing of mutation accumulation (MA) lines obtained 7,345 new single nucleotide variants (SNVs) and 5,672 short indel mutations, the largest data set from an MA study in D. melanogaster. Based on the observed mutational strand-asymmetries, we conclude that TCR is still active without spel1. The operation of TCR is further confirmed by a negative association between mutation rate and gene expression. Surprisingly, the TCR signatures are detected for introns, but not for exons. We propose that an additional exon-specific repair pathway is masking the signature of TCR. This study presents the first step towards understanding the molecular basis of TCR in Drosophila melanogaster.

Release of a Seaglider from an AutoNaut surface vehicle: demonstration mission in the Eurec4a project

<p>This PICO presentation describes a recent demonstration mission of our wave-propelled autonomous vehicle, an AutoNaut named Caravela. Caravela has been designed and built to carry and deploy a profiling ocean glider at a specified location and time. This has applications for example in transporting an ocean glider to a remote location without use of a research vessel, or initiating a glider campaign at a particular time such as prior to a hurricane or the spring bloom.</p><p> </p><p>In January-February 2020 we participated in the international Eurec4a field campaign in the tropical Atlantic to the east of Barbados. Caravela was deployed from Barbados and carried a Seaglider to release at the study site. The observational campaign was designed to occupy a time series site with three Seagliders (making intensive measurements of upper ocean properties) and the AutoNaut (making continuous measurements of surface meteorology, radiation and surface ocean currents).  Here we describe the technological challenges, the field campaign and the preliminary results of the scientific observations from Caravela and the Seagliders. The aim is to use the observations to calculate the air-sea fluxes and ultimately to close a mixed layer heat budget for the observation site.</p>