bluuebunny/crossref_metadata_2025 huggingface dataset:
The histone demethylase KDM3 prevents auto-immune piRNAs production in Drosophila
Authors: Casier Karine , Autaa Julie , Gueguen Nathalie , Delmarre Valérie , Pauline Marie P. , Ronsseray Stéphane , Carré Clément , Brasset Emilie , Teysset Laure , Boivin Antoine
Published: June 2022

In animals, genome integrity of the germ line is protected from transposable element (TE) activity by small, non-coding, dedicated RNAs acting as an immune system against TEs, and called PIWI-interacting RNAs (piRNAs) 1,2. In Drosophila, the production of piRNAs is initiated from heterochromatic loci containing remnants of TEs and enriched in histone H3 trimethylated on lysine 9 (H3K9me3) 3–5. These loci, called piRNA clusters, constitute a memory of past TE invasions. Little is known about how piRNA clusters are genetically defined. Using a genetic screen combined with a bimodal epigenetic state piRNA cluster (BX2), we identified the splicing factor Half pint (Hfp) and the histone demethylase KDM3 as being able to prevent BX2 piRNA production. Furthermore, we showed that Hfp is needed to splice Kdm3 transcripts. Germline expression of Kdm3 coding sequence (splicing-independent) rescued the hfp germline knock-down (GLKD) effect demonstrating that Kdm3 is sufficient to prevent BX2 piRNA production. Our data revealed that in the absence of Kdm3, dozens of gene-containing regions become bona fide germinal dual strand piRNA clusters. Indeed, they produce piRNAs originating from both DNA strands, become transcribed in a Moonshiner-dependent manner and enriched in di-and tri-methylation of lysine 9 of histone H3 (H3K9me2/3) and in Rhino, an HP1-like protein. Eggs laid by Kdm3 GLKD females do not hatch and show developmental defects phenocopying loss of function of genes included into the new piRNA clusters, suggesting an inheritance of functional ovarian “auto-immune” piRNAs. Our results demonstrate that some gene-containing regions are actively prevented for piRNA production by proteins that counteract piRNA cluster emergence. Hence, a non-piRNA-producing state is therefore not a “by default” state but rather a cellular lock that is actively controlled for some genomic loci.

KEY FACTS

Hfp regulates the expression of Kdm3 via its splicing

Kdm3 prevents genomic regions containing coding genes from becoming piRNA clusters

Embryos from Kdm3 mutant females show developmental phenotypes suggesting that auto-immune piRNAs are functional and alter the expression of genes embedded in newly established piRNA clusters
Differential vulnerability of neuronal subpopulations of the subiculum in a mouse model for mesial temporal lobe epilepsy
Authors: Franz Julia , Barheier Nicole , Tulke Susanne , Haas Carola A. , Häussler Ute
Published: June 2022

Selective loss of inhibitory interneurons (INs) that promotes a shift toward an excitatory predominance may have a critical impact on the generation of epileptic activity. While research on mesial temporal lobe epilepsy (MTLE) has mostly focused on hippocampal changes, including IN loss, the subiculum as the major output region of the hippocampal formation has received comparatively little attention. Although it has been shown to occupy a key position in the epileptic network, data on cellular changes in the subiculum are controversial. Using the intrahippocampal kainate (KA) mouse model for MTLE, which recapitulates main features of human MTLE such as hippocampal sclerosis and granule cell dispersion followingstatus epilepticus(SE), we identified cell loss in the subiculum and quantified changes in specific IN subpopulations along its dorsoventral axis.

We performed intrahippocampal recordings, FluoroJade C-staining for degenerating neurons shortly after SE and immunohistochemistry for neuronal nuclei (NeuN), parvalbumin (PV), neuropeptide Y (NPY), calretinin (CR) and calbindin (CB), andin situhybridization for glutamic acid decarboxylase(Gad) 67mRNA at 21 days after KA.

We observed remarkable cell loss in the ipsilateral subiculum shortly after SE which was reflected in lowered density of NeuN+ cells in the chronic stage when epileptic activity could be measured in the subiculum concomitant with the hippocampus. We show a position-dependent reduction ofGad67-expressing INs by ~50% which particularly affected the PV- and to a lesser extent CR-expressing INs, whereas CB-expressing cells were unchanged.

Interestingly, the density of NPY-positive neurons was increased, but double-labeling forGad67mRNA expression revealed that rather ade novoexpression of NPY in non-GABAergic cells instead of IN changes underlay this increase.

Our data reveal a position- and cell type-specific vulnerability of subicular INs in MTLE which might contribute to hyperexcitability of the subiculum, as reflected in the occurrence of epileptic activity.

Keypoints (3-5)

The subiculum develops epileptic activity after intrahippocampal kainate injection in mice

Gad67-mRNA expressing interneurons are reduced in the subiculum in the intrahippocampal kainate model for mesial temporal lobe epilepsy

Parvalbumin- and calretinin-expressing interneurons are particularly vulnerable in epilepsy

Neuropeptide Y upregulation in non-GABAergic cells in the subiculum indicates compensatory processes
Ensemble-specific deficit in neuronal intrinsic excitability in aged mice
Authors: Chen Lingxuan , Francisco Taylor R. , Baggetta Austin M. , Zaki Yosif , Ramirez Steve , Clem Roger L. , Shuman Tristan , Cai Denise J.
Published: June 2022

With the prevalence of age-related cognitive deficits on the rise, it is essential to identify cellular and circuit alterations that contribute to age-related memory impairment. Increased intrinsic neuronal excitability after learning is important for memory consolidation, and changes to this process could underlie memory impairment in old age. Some studies find age-related deficits in hippocampal neuronal excitability that correlate with memory impairment but others do not, possibly due to selective changes only in activated neural ensembles. Thus, we tagged CA1 neurons activated during learning and recorded their intrinsic excitability 5 hours or 7 days post-training. Adult mice exhibited increased neuronal excitability 5 hours after learning, specifically in ensemble (learning-activated) CA1 neurons. As expected, ensemble excitability returned to baseline 7 days post-training. In aged mice, there was no ensemble-specific excitability increase after learning, which was associated with impaired hippocampal memory performance. These results suggest that CA1 may be susceptible to age-related impairments in post-learning ensemble excitability and underscore the need to selectively measure ensemble-specific changes in the brain.
Optimization of a Translational Murine Model of Closed-head Traumatic Brain Injury
Authors: Mace Brian E. , Lassiter Eric , Arulraja Evangeline Kamalini , Chaparro Eduardo , Cantillana Viviana , Gupta Rupali , Faw Timothy D. , Laskowitz Daniel T. , Kolls Brad J
Published: June 2022

Traumatic brain injury (TBI) from closed-head trauma is a leading cause of disability with limited effective interventions. Many TBI models impact brain parenchyma directly following craniotomy, and are limited by the fact that these forces do not recapitulate clinically relevant closed head injury. However, applying clinically relevant injury mechanics to an intact skull may lead to variability and as a result, modeling TBI remains a challenge. Moreover, current models often do not explore sex differences in TBI, which is critically important for translation to clinical practice. We systematically investigated sources of variability in a murine model of closed-head TBI and developed a framework to reduce variability across severity and sex. We manipulated pressure, dwell time, and displacement to determine effects on vestibulomotor performance, spatial learning, and neuronal damage in 10-week-old male and female mice. Increasing pressure beyond 70psi had a ceiling effect on cellular and behavioral outcomes, while manipulating dwell time only affected behavioral performance. Increasing displacement precisely graded injury severity in both sexes across all outcomes. Physical signs of trauma occurred more frequently at higher displacements. Females performed worse than males when injured at 2.7mm displacement, and had greater mortality at higher displacements. Stratifying severity based on day-1 rotarod performance retained cellular injury relationships and separated both sexes into injury severity cohorts with distinct behavioral recovery. Utilizing this stratification strategy, within-group rotarod variability over 6 days post-injury was reduced by 50%. These results have important implications for translational research in TBI and provide a framework for using this clinically relevant translational injury model in both male and female mice.
Lysosomal dysfunction in Down Syndrome and Alzheimer mouse models is caused by selective v-ATPase inhibition by Tyr682phosphorylated APP βCTF
Authors: Im Eunju , Jiang Ying , Stavrides Philip , Darji Sandipkumar , Erdjument-Bromage Hediye , Neubert Thomas A. , Choi Jun Yong , Wegiel Jerzy , Lee Ju-Hyun , Nixon Ralph A.
Published: June 2022

Lysosome dysfunction arises early and propels Alzheimer’s Disease (AD). Herein, we show that amyloid precursor protein (APP), linked to early-onset AD in Down Syndrome (DS), acts directly via its β-C-terminal fragment (βCTF) to disrupt lysosomal v-ATPase and acidification. In human DS fibroblasts, the phosphorylated682YENPTY internalization motif of APP-βCTF binds selectively within a pocket of the v-ATPase V0a1 subunit cytoplasmic domain and competitively inhibits association of the V1 subcomplex of v-ATPase, thereby reducing its activity. Lowering APP-βCTF Tyr682phosphorylation restores v-ATPase and lysosome function in DS fibroblasts andin vivoin brains of DS model mice. Notably, lowering APP-βCTF Tyr682phosphorylation below normal constitutive levels boosts v-ATPase assembly and activity, suggesting that v-ATPase may also be modulated tonically by phospho-APP-βCTF. Elevated APP-βCTF Tyr682phosphorylation in two mouse AD models similarly disrupts v-ATPase function. These findings offer new insight into the pathogenic mechanism underlying faulty lysosomes in all forms of AD.
Multiple particle tracking (MPT) using PEGylated nanoparticles reveals heterogeneity within murine lymph nodes and between lymph nodes at different locations
Authors: Ramirez Ann , Merwitz Brooke , Lee Hannah , Vaughan Erik , Maisel Katharina
Published: June 2022

Lymph nodes (LNs) are highly structured lymphoid organs that compartmentalize B and T cells in the outer cortex and inner paracortex, respectively, and are supported by a collagen-rich reticular network. Tissue material properties like viscoelasticity and diffusion of materials within extracellular spaces and their implications on cellular behavior and therapeutic delivery have been a recent topic of investigation. Here, we developed a nanoparticle system to investigate the rheological properties, including pore size and viscoelasticity, through multiple particle tracking (MPT) combined with LN slice cultures. Dense coatings with polyethylene glycol (PEG) allow nanoparticles to diffuse within the LN extracellular spaces. Despite differences in function in B and T cell zones, we found that extracellular tissue properties and mesh spacing do not change significantly in the cortex and paracortex, though nanoparticle diffusion was slightly reduced in B cell zones. Interestingly, our data suggest that LN pore sizes are smaller than the previously predicted 10 – 20 μm, with pore sizes ranging from 500 nm - 1.5 μm. Our studies also confirm that LNs exhibit viscoelastic properties, with an initial solid-like response followed by stress-relaxation at higher frequencies. Finally, we found that nanoparticle diffusion is dependent on LN location, with nanoparticles in skin draining LNs exhibiting a higher diffusion coefficient and pore size compared to mesenteric LNs. Our data shed new light onto LN interstitial tissue properties, pore size, and define surface chemistry parameters required for nanoparticles to diffuse within LN interstitium. Our studies also provide both a tool for studying LN interstitium and developing design criteria for nanoparticles targeting LN interstitial spaces.

Abbreviations

LNs, FBS, EDC, NHS, ECM, PEG
Engineered Wnt7a ligands rescue blood brain barrier and neurobehavioral deficits in a mouse model of COVID-19
Authors: Trevino Troy N. , Fogel Avital B. , Class Jacob , Sanborn Mark A. , Vanhollebeke Benoit , Rehman Jalees , Tai Leon M. , Richner Justin M. , Lutz Sarah E.
Published: June 2022

Respiratory infection with SARS-CoV-2 causes systemic vascular inflammation and cognitive impairment. We sought to identify the underlying mechanisms mediating vascular dysfunction and inflammation following mild respiratory SARS-CoV-2 infection. To this end, we conduced unbiased transcriptional analysis to identify brain endothelial cell signaling pathways dysregulated by SARS-CoV-2in vivo. This analysis revealed significant suppression of Wnt/β-catenin signaling, a critical regulator of blood brain barrier integrity. We therefore hypothesized that enhancing cerebrovascular Wnt/β-catenin activity would offer protection against BBB permeability, neuroinflammation, and neurological signs in acute infection. Indeed, we found that delivery of cerebrovascular-targeted, engineered Wnt7a ligands protected blood brain barrier integrity, reduced T cell infiltration of the brain, and reduced microglial activation in SARS-CoV-2 infection. Importantly, this therapeutic strategy also mitigated SARS-CoV-2 induced deficits in the novel object recognition assay for learning and memory and the pole descent task for bradykinesia. These observations suggest that enhancement of Wnt/β-catenin signaling or its downstream effectors could be potential interventional strategies for restoring cognitive health following acute viral infections.
Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize
Authors: He Juan , Xu Chi , You Chenjiang , Mo Beixin , Chen Xuemei , Gao Lei , Liu Lin
Published: June 2022

MicroRNAs (miRNAs) are endogenous 20-to 24-nucleotide (nt) noncoding RNAs that play important regulatory roles in many biological processes in eukaryotes. miRNAs modulate the expression of target genes at the post-transcriptional level by transcript cleavage or translational inhibition. Identification of miRNA target genes have been extensively investigated in Arabidopsis and rice, but an in-depth global analysis of miRNA-mediated target regulation is still lacking in maize. Here, we report a transcriptome-wide identification of miRNA targets by analyzing Parallel Analysis of RNA Ends (PARE) datasets derived from nine different tissues at five developmental stages of the maize (Zea mays L.) B73 cultivar. 246 targets corresponding to 60 miRNAs from 25 families were identified, including transcription factors and other genes. In addition, PARE analysis revealed that miRNAs guide specific target transcript cleavage in a tissue-preferential manner. Interestingly, primary transcripts of MIR159c and MIR169e were found to be cleaved by mature miR159 and miR169, respectively, indicating a positive-feedback regulatory mechanism in miRNA biogenesis. Moreover, several new miRNA-target gene pairs involved in seed germination were identified and experimentally validated. Our PARE analyses generated a wide and detailed miRNA-target interaction atlas, which provides a valuable resource for investigating the roles of miRNAs and their targets in maize.
Natural strongyle infection reduces relative abundance of inflammation-inducingPrevotellain wild primates
Authors: Cizauskas Carrie A. , Washburne Alex D. , Knelman Joseph E. , Hansen Christina B. , Nderitu Antony Mwangi , Esinyon Peter Lokwamo , Dobson Andrew P. , Graham Andrea L.
Published: June 2022

Microbes living within the mammalian gastrointestinal tract affect the metabolization and extraction of dietary nutrients, immune function, colonization by pathogens, and risk of autoimmune disease. While most microbiome studies focus on sequences of the 16S gene shared by Bacteria and Archaea, these are not the only regular inhabitants of mammalian guts. Macroparasites such as helminths are nearly ubiquitous in wildlife, and a quarter of the world’s human population harbors helminths; these worms affect host physiology as they compete with microbiota over host resources while also affecting host immunity, and changing the host microbiome. Little is understood about how helminths interact with microbiomes to affect host disease states, and few studies have examined these interactions in natural systems in genetically diverse hosts experiencing coinfections and other stressors.

We surveyed the microbiomes and helminth parasites of wild primates and found strong associations between helminths and microbes in the bacterial microbiome. Notably, we find that the presence of a strongyle we hypothesize to be hookworm is correlated strongly with decreased relative abundance ofPrevotellaspecies, a lineage associated with inflammatory bowel disease humans. This observed decline inPrevotellarelative abundance, a genus implicated in several host autoimmune and inflammatory disorders, motivates future research on whether the mixed results of helminthic therapy (i.e., “infecting” patients with gastrointestinal nematodes to treat various diseases) stem from the mixed causes of inflammation, and whether inflammation specifically correlated withPrevotella-driven dysbiosis can be mediated through mechanisms mimicking how hookworms and other nematodes behave in the gastrointestinal ecosystem of their hosts. Our findings lend ground-truthed support to previous lab-based studies and limited/restricted human trials showing potential benefits, via microbial modulation, of nematode therapy in treating inflammatory bowel disease. Our study adds statistical weight to a link between helminths and a specific lineage of microbes associated with inflammation.
Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes
Authors: Feng Huijuan , Lu Xiang-Jun , Liu Linxi , Ustianenko Dmytro , Zhang Chaolin
Published: June 2022

UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes despite our poor understanding on the mechanisms of photo-crosslinking. This knowledge gap is due to the challenge to precisely map the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we developed PxR3D-map, a computational method to analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. PxR3D-map reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. We found that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different types of RNA-binding domains. Our work suggests protein-RNA photocrosslinking is highly selective in the cellular environment, which can guide interpretation of data generated by UV-crosslinking-based assays and further technology development.
An integrated approach to evaluate the functional effects of disease-associated NMDA receptor variants
Authors: Moody Gabrielle , Musco Angela , Bennett Joseph , Wollmuth Lonnie P.
Published: June 2022

The NMDA receptor (NMDAR) is a ubiquitously expressed glutamate-gated ion channel that plays key roles in brain development and function. Not surprisingly, a variety of disease-associated variants have been identified in genes encoding NMDAR subunits. A critical first step to assess whether these variants contribute to their associated disorder is to characterize their effect on receptor function. However, the complexity of NMDAR function makes this challenging, with most variants typically altering multiple functional properties. At synapses, NMDARs encode presynaptic activity to carry a charge transfer that alters membrane excitability and a Ca2+ influx that has both short- and long-term signaling actions. Here, we characterized epilepsy-associated variants in GluN1 and GluN2A subunits with various phenotypic severity. To capture the dynamics of NMDAR encoding, we applied 10 glutamate pulses at 10 Hz to derive a charge integral. This encoding assay is advantageous since it incorporates multiple gating parameters – activation, deactivation, and desensitization – into a single value. We then integrated this encoding with Mg2+ block and Ca2+ influx using fractional Ca2+ currents to generate indices of charge transfer and Ca2+ transfer over wide voltage ranges. This approach yields consolidated parameters that can be used as a reference to normalize allosteric modulation and has the potential to speed up future bench to bedside methods of investigating variants to determine patient treatment.
Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility
Authors: Kerr Peter J , Cattadori Isabella M , Sim Derek , Liu June , Holmes Edward C. , Read Andrew F.
Published: June 2022

To characterize the ongoing evolution of myxoma virus in Australian rabbits we used experimental infections of laboratory rabbits to determine the virulence and disease phenotypes of recent virus isolates. The viruses, collected between 2012-2015, fell into three lineages, one of which, lineage c, experienced a punctuated increase in evolutionary rate. All viruses were capable of causing acute death with aspects of neutropenic septicaemia, characterized by minimal signs of myxomatosis, the occurrence of pulmonary oedema and bacteria invasions throughout internal organs, but with no inflammatory response. For the viruses of highest virulence all rabbits usually died at this point. In more attenuated viruses some rabbits died acutely while others developed an amyxomatous phenotype. Rabbits that survived for longer periods developed greatly swollen cutaneous tissues with very high virus titres. This was particularly true of lineage c viruses. Unexpectedly, we identified a line of laboratory rabbits with some innate resistance to myxomatosis and used these in direct comparisons with the fully susceptible rabbit line. Importantly, the same disease phenotype occurred in both susceptible and resistant rabbits, although virulence was shifted towards more attenuated grades in resistant animals. We propose that selection against inflammation at cutaneous sites prolongs virus replication and enhances transmission, leading to the amyxomatous phenotype. In some virus backgrounds this creates an immunosuppressive state that predisposes to high virulence and acute death. The alterations in disease pathogenesis, particularly the overwhelming bacterial invasions that characterize the modern viruses, suggest that their virulence grades are not directly comparable with earlier studies.

IMPORTANCE

The evolution of the myxoma virus (MYXV) following its release as a biological control for European rabbits in Australia is the textbook example of the co-evolution of virus virulence and host resistance. However, most of our knowledge of MYXV evolution only covers the first few decades of its spread in Australia and often with little direct connection between how changes in virus phenotype relate to those in the underlying virus genotype. By conducting detailed experimental infections of recent isolates of MYXV in different lines of laboratory rabbits we examined the ongoing evolution of MYXV disease phenotypes. Our results reveal a wide range of phenotypes, including an amyxomatous type as well as the impact of invasive bacteria, that in part depended on the level of rabbit host resistance. These results provide a unique insight into the complex virus and host factors that combine to shape disease phenotype and viral evolution.
EFFECT OF ORGANIC AND CHEMICAL FERTILIZERS ON THE NUTRITIONAL COMPOSITION OF Amaranthus spinosus
Authors: Raman Deepa , Joshi Namita , Rana Pawan Singh
Published: June 2022

Organic and chemical fertilizers are used in agriculture as they improve the fertility of soil and the growth of plants. So, the present investigation was designed to determine the effect of different fertilizers on the nutritional value of Amaranthus spinosus plant. The quantity of different fertilizers was used as 500 kg h-1. Some selected parameters of soil such as temperature (29.50 C), moisture (3.5 %), Water holding capacity (74%), pH (8.17), organic carbon % (1.90) and organic matter % (3.28) were measured and analysed. There was no significant variation in these parameters under different fertilizers treatment. The phytochemicals of Organic fertilizers treated plant sample had higher concentration of Alkaloid (1.06), flavonoid (0.89), tannin (1.48) and saponin (1.67), ash (7.75), moisture (87.6) and protein (9.1), Fe (0.054), Zn (0.008), Cu (0.001), Na (0.0080), Ca (113) and Mg (93) when compared to the other fertilizer treatments. Inorganic fertilizer did not show any significant effect on plant growth, while the combination of organic and chemical fertilizers was found to have a significant effect. The results reveal that organic fertilizers or their combination with chemical fertilizer are better for the crops than chemical fertilizers.
Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities
Authors: Ushio Masayuki , Sado Tetsuya , Fukuchi Takehiko , Sasano Sachia , Masuda Reiji , Osada Yutaka , Miya Masaki
Published: June 2022

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species is practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths under field conditions remains poorly understood. We herein performed quantitative fish environmental DNA (eDNA) metabarcoding on 550 seawater samples that were collected twice a month from 11 coastal sites for two years in the Boso Peninsula, Japan, and analyzed eDNA monitoring data using nonlinear time-series analytical tools. We detected fish-fish interactions as information flow between eDNA time series, reconstructed interaction networks for the top 50 frequently detected species, and quantified pairwise, fluctuating interaction strengths. Although there was a large variation, water temperature influenced fish-fish interaction strengths. The impact of water temperature on interspecific interaction strengths varied among fish species, suggesting that fish species identity influences the temperature effects on interactions. For example, interaction strengths thatHalichoeres tenuispinisandMicrocanthus stringatusreceived strongly increased with water temperature, while those ofEngraulis japonicusandGirella punctatadecreased with water temperature. An increase in water temperature induced by global climate change may change fish interactions in a complex way, which consequently influences marine community dynamics and stability. Our research demonstrates a practical research framework to study the effects of environmental variables on interaction strengths of marine communities in nature, which would contribute to understanding and predicting natural marine ecosystem dynamics.
Genomic epidemiology revealed the emergence and worldwide dissemination of ST383 carbapenem-resistant hypervirulent Klebsiella pneumoniae and hospital acquired infections of ST196 Klebsiella quasipneumoniae in Qatar
Authors: Tsui Clement Kin-Ming , Abid Fatma Ben , McElheny Christi Lee , Almuslamani Muna , Omrani Ali S. , Doi Yohei
Published: June 2022

The emergence of carbapenem-resistant (CR) hypervirulent Klebsiella pneumoniae (hvKp) is a new threat to healthcare. In this study, we studied the molecular epidemiology of CR Klebsiella isolates in Qatar using whole genome sequence data. We also characterised the prevalence and genetic basis of hypervirulent phenotypes, and established the virulence potential using a Galleria mellonella model. One hundred CR Klebsiella isolates were recovered, and NDM and OXA-48 were the most common carbapenemases. Phylogenetic analysis indicated the presence of diverse sequence types and clonal lineages; one of them belonged to K. quaisipneumoniae ST196 that may be disseminated among several health care centres. Ten K. pneumoniae isolates carrying rmpA and/or rmpA2, and 2 isolates belonged to KL2, indicating the prevalence of classical hypervirulent (hv) isolates was not high. Isolates carrying CR and hv genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated the blaNDM was located on an IncHI1B type plasmid (pFQ61_ST383_NDM-5), which also harbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from inversion and recombination events. In contrast, blaOXA-48 was located in an IncL-type plasmid. Comparative genomes indicated the recent evolution and emergence of CR-hv Kp ST383 via the acquisition of hybrid plasmids with both carbapenemase and virulence genes. CR-hv K. pneumoniae ST383 pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.
Characterization of prohibitins as novel target to block asexual and sexual stage growth of Plasmodium falciparum
Authors: Saini Monika , Ngwa Che Julius , Marothia Manisha , Vandana  , Pandey Kailash C. , Pati Soumya , Ranganathan Anand , Pradel Gabriele , Singh Shailja
Published: June 2022

Prohibitins (PHBs) are highly conserved pleiotropic proteins as they have been shown to mediate key cellular functions. Here, we characterize PHBs encoding putative genes of Plasmodium falciparum by exploiting different orthologous models. We demonstrated that PfPHB1 (PF3D7_0829200) and PfPHB2 (PF3D7_1014700) are expressed in asexual and sexual blood stages of the parasite. Immunostaining indicated these proteins as mitochondrial residents as they were found to be localized as punctate foci. We further validated PfPHBs as organellar proteins residing in the Plasmodium mitochondria, where they interact with each other. Functional characterization was done in Saccharomyces cerevisiae orthologous model by expressing PfPHB1 and PfPHB2 in cells harboring respective mutants. The PfPHBs functionally complemented the yeast PHB1 and PHB2 mutants, where the proteins were found to be involved in stabilizing the mitochondrial DNA, retaining mitochondrial integrity and rescuing yeast cell growth. Further, Rocaglamide (Roc-A), a known inhibitor of PHBs and anti-cancerous agent, was tested against PfPHBs and as an antimalarial. Roc-A treatment retarded the growth of PHB1, PHB2, and ethidium bromide petite yeast mutants. Moreover, Roc-A inhibited growth of yeast PHBs mutants that were functionally complemented with PfPHBs, validating P. falciparum PHBs as one of the molecular targets for Roc-A. Roc-A treatment led to growth inhibition of artemisinin-sensitive (3D7), artemisinin-resistant (R539T) and chloroquine-resistant (RKL-9) parasites in nanomolar ranges. The compound was able to retard gametocyte growth with significant morphological aberrations. Based on our findings, we propose the presence of functional mitochondrial PfPHB1 and PfPHB2 in P. falciparum and their druggability to block parasite growth.
An Analysis of PCR Ct Scores and Distributions from the ONS Community Infection Survey during the COVID Second Wave in the UK
Authors: Johnson Keith , Hammer Steven J , Klymenko Tanya
Published: June 2022

This work presents an analysis of PCR cycle threshold (Ct) scores and their distributions, i.e. the probabilities that a test is positive with a score Ct, P(Ct), derived from the survey during the second COVID wave in the UK. Their relation to gene target breakdown is exemplified. Thus a significant parameter for tracking the course of COVID in the second wave is the percentage of positive tests with Ct < 25, %Ct <25, which is obtained by plotting weekly percentiles from the survey against Ct to construct the ogive or cumulative frequency curve (CMF). The biological basis for studying this parameter is the strong correlation between %Ct < 25 and the percentage of positive tests comprising target genes ORF1ab+N and ORF1ab+N+S, or %Inf.

Furthermore, the probability distributions, obtained by differentiating the ogives, were found to be predominantly bimodal with a hot peak at Ct = 20.31+/- 4.65 and a cold peak with Ct = 32.95+/-1.11. These closely match the peaks found for the target genes ORF1ab+N, viz. Ct=18.54+/-2.31 and Ct=32.02+/-0.49 as well as in Walker et al [12]. Similar results were found in [13] and [14]. The cold peak seems likely to be associated with residue from a previous infection. The distributions for gene targets in cfvroc Pillar 2 [15,16] are also bimodal but the peaks occur at lower values of Ct. This suggests the results are machine/sample dependent and emphasises the need for calibration, if quality control in PCR testing is to be improved.
A cross-sectional analysis of factors associated with the development of refeeding syndrome in children 0 – 59 months diagnosed with severe acute malnutrition in a South African setting
Authors: Heydenrych Natalie , De Maayer Tim , Nel Mariette , van den Berg Louise
Published: June 2022

Background

Refeeding syndrome (RFS) is a life-threatening, underdiagnosed, and under-researched complication in treating children with severe acute malnutrition (SAM). This study aimed to determine the incidence and onset of RFS and identify biochemical abnormalities, clinical signs, and complications associated with RFS development in children 0–59 months treated in a South African public hospital setting.

Methods

A retrospective cohort study was performed on hospital files of children diagnosed with SAM at Rahima Moosa Mother and Child Hospital, Johannesburg, from 1/10/2014 to 31/12/2018. A total of 148 files could be retrieved from the hospital archives. The diagnosis of SAM based on the World Health Organization definition was confirmed in 126 of these children, and they were included in the study. The onset of RFS among the children included in the study was diagnosed based on published criteria for RFS. Children who developed RFS and those who did not were compared concerning biochemistry and clinical signs and symptoms on admission.

Results

The median age of the 126 children (63% male) with confirmed SAM was 34 months (IQR: 26.0 to 48.4 months). The mortality rate was 18.2%. Of these children, 8.7% were retrospectively diagnosed as having developed RFS during their recorded hospital stay, despite implementing the WHO treatment guidelines for SAM. A significantly higher percentage of the children that developed RFS presented on admission with hypophosphatemia (p=0.04), severe hypokalemia (p=0.0005), hyponatremia (p=0.004), an international normalized ratio (INR) of above 1.7 (p=0.049), diarrhea (p=0.04), dehydration (p=0.02) and urinary tract infection (UTI) (p=0.04) than those that did not. Edema was more prevalent on admission in children who developed RFS than those who did not (63.6% vs 39.1%), though the difference was not statistically significant (p=0.20). Children who developed RFS stayed in hospital significantly longer than those who did not (18 vs 12 days) (p=0.003).

Conclusion

In this population of children with SAM treated in a South African public hospital setting, the presence on hospital admission of low levels of electrolytes, elevated INR, dehydration, diarrhea, and UTI was significantly associated with developing RFS. Recognizing these as possible red flags for developing RFS in children admitted with SAM might contribute to improved outcomes and needs further investigation.
Climate change and the rising incidence of dengue in Argentina
Authors: López MS , Gómez A , Müller G , Walker E , Robert MA , Estallo EL
Published: June 2022

BACKGROUND

One of the most important consequences of climate change is the increased spread of dengue from tropical and subtropical regions to temperate areas around the world. Climate variables such as temperature and precipitation influence the dengue vector’s biology, physiology, abundance, and life cycle. Thus, an analysis is needed of climate changes and their possible links with the growing occurrence of epidemics recorded in recent decades.

OBJECTIVES

To assess the increasing incidence of dengue driven by climate change at the southern limits of dengue virus transmission in South America.

METHODS

We analyze the evolution of climate, epidemiological, and biological variables, comparing a period without the presence of dengue cases to a more recent period with the occurrence of cases and, consequently, of important epidemics. Temperature and precipitation are the climate variables evaluated, the total number of cases and incidence of dengue are the epidemiological variables, and finally, the optimal temperature ranges for transmission of the dengue vector is the biological variable.

RESULTS

The presence of dengue cases and epidemic outbreaks are observed to be consistent with positive temperature trends and anomalies. Dengue cases do not seem to be associated with precipitation trends and anomalies. The number of days with optimal temperatures for dengue transmission increased from the period without dengue cases to the period with the presence of dengue cases. However, the number of months with optimal transmission temperatures was the same in both periods.

CONCLUSIONS

The higher incidence of dengue virus (DENV) and its expansion to different regions of Argentina seem to be associated with temperature increases in the country during the past decades. The active surveillance of both the vector and associated arboviruses will make it possible to assess and predict the occurrence of epidemics, based on the accelerated changes in climate. Such surveillance should go hand in hand with efforts to improve the understanding of the mechanisms driving the geographic expansion of dengue and other arboviruses beyond the current limits.
Cortical activation predicts posttraumatic improvement in youth treated with TF-CBT or CCT
Authors: Espil Flint M. , Balters Stephanie , Li Rihui , McCurdy Bethany H. , Kletter Hilit , Piccirilli Aaron , Cohen Judith A. , Weems Carl F. , Reiss Allan L. , Carrion Victor G.
Published: June 2022

Background

Identifying neural activation patterns that predict youths’ treatment response may aid in the development of imaging-based assessment of emotion dysregulation following trauma and foster tailored intervention. Changes in cortical hemodynamic activity measured with functional near-infrared spectroscopy (fNIRS) may provide a time and cost-effective option for such work. We examined youths’ PTSD symptom change following treatment and tested if previously identified activation patterns would predict treatment response.

Methods

Youth (N = 73, mean age = 12.97, SD = 3.09 years) were randomly assigned to trauma-focused cognitive behavioral therapy (TF-CBT), cue-centered therapy (CCT), or treatment as usual (TAU). Parents and youth reported on youth’s PTSD symptoms at pre-intervention, post-intervention, and follow-up. Neuroimaging data (N = 31) assessed at pre-intervention were obtained while youth engaged in an emotion expression task. Treatment response slopes were calculated for youth’s PTSD symptoms.

Results

Overall, PTSD symptoms decreased from pre-intervention through follow-up across conditions, with some evidence of relative benefit of TF-CBT and CCT over TAU but significant individual variation in treatment response. Cortical activation patterns were correlated with PTSD symptom improvement slopes (r = 0.53). In particular, cortical responses to fearful and neutral facial stimuli in six fNIRS channels in the bilateral dlPFC were important predictors of PTSD symptom improvement.

Conclusions

The use of fNIRS provides a method of monitoring and assessing cortical activation patterns in a relatively inexpensive and portable manner. Associations between functional activation and youths’ PTSD symptoms improvement may be a promising avenue for understanding emotion dysregulation in clinical populations.
Recovery of clinical, cognitive and cortical activity measures following mild traumatic brain injury (mTBI): a longitudinal investigation
Authors: Coyle Hannah L. , Bailey Neil W. , Ponsford Jennie , Hoy Kate E.
Published: June 2022

The mechanisms that underpin recovery following mild traumatic brain injury (mTBI) remain poorly understood. Identifying neurophysiological markers and their functional significance is necessary to develop diagnostic and prognostic indicators of recovery. The current study assessed 30 participants in the subacute phase of mTBI (10-31 days post-injury) and 28 demographically matched controls. Participants also completed 3 month (mTBI: N = 21, control: N = 25) and 6 month (mTBI: N = 15, control: N = 25) follow up sessions to track recovery. At each time point, a battery of clinical, cognitive, and neurophysiological assessments was completed. Neurophysiological measures included resting-state electroencephalography (EEG) and transcranial magnetic stimulation combined with EEG (TMS-EEG). Outcome measures were analysed using mixed linear models (MLM). Group differences in mood, post-concussion symptoms and resting-state EEG resolved by 3 months, and recovery was maintained at 6 months. On TMS-EEG derived neurophysiological measures of cortical reactivity, group differences ameliorated at 3 months but re-emerged at 6 months, while on measures of fatigue, group differences persisted across all time points. Persistent neurophysiological changes and greater fatigue in the absence of measurable cognitive impairment may suggest the impact of mTBI on neuronal communication may leads to increased neural effort to maintain efficient function. Neurophysiological measures to track recovery may help identify both temporally optimal windows and therapeutic targets for the development of new treatments in mTBI.
Characterization of non-human primate dura in health and neurodegeneration
Authors: Janson Christopher , Hauser Kyle , Muller Scott , Hansen Eric , Lam Cornelius , Kordower Jeffrey , Romanova Liudmila
Published: June 2022

Brain meninges and associated vasculature participate in brain clearance and are implicated in many neurological conditions such as Alzheimer’s disease, meningitis, multiple sclerosis, stroke, and traumatic brain injury. However, most of our knowledge concerning brain clearance via meninges is based on rodent data, and relevance to human disease remains unclear. One of the technical barriers in studies of meningeal physiology in health and disease is that existing imaging modalities are suboptimal for large and optically non-transparent meningeal tissue of humans and non-human primate (NHP) animal models. To address this barrier, we performed first characterization of NHP dura by high resolution confocal microscopy of clarified tissue. We investigated vascular structures and resident cells in normal monkeys and primate models of tauopathy and synucleinopathy. We demonstrated the presence of an extensive meningeal vascular network covering the entire tissue surface with resolution to the smallest capillaries. This is also the first work to map lymphatic vessels in the dura of non-human primate (NHP). Overall, the NHP lymphatic meningeal system resembles the anatomy found in rat dura, but it is more complex. Analysis of dura from NPH models of tauopathy and synucleinopathy revealed an association with disease-specific biomarkers (amyloid, tau, α-synuclein) with both the blood and lymphatic vasculature. This work has broad relevance to many brain diseases where solute accumulation and abnormal macromolecular clearance is a part of the pathogenesis.
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
Authors: Ravindran Vandana , Wagoner Jessica , Athanasiadis Paschalis , Den Hartigh Andreas B. , Sidorova Julia M. , Ianevski Aleksandr , Fink Susan L. , Frigessi Arnoldo , White Judith , Polyak Stephen J. , Aittokallio Tero
Published: June 2022

The ongoing coronavirus disease 2019 (COVID-19) pandemic has highlighted the need to better understand virus-host interactions. We developed a network-based algorithm that expands the SARS-CoV-2-host protein interaction network and identifies host targets that modulate viral infection. To disrupt the SARS-CoV-2 interactome, we systematically probed for potent compounds that selectively target the identified host proteins with high expression in cells relevant to COVID-19. We experimentally tested seven chemical inhibitors of the identified host proteins for modulation of SARS-CoV-2 infection in human cells that express ACE2 and TMPRSS2. Inhibition of the epigenetic regulators bromodomain-containing protein 4 (BRD4) and histone deacetylase 2 (HDAC2), along with ubiquitin specific peptidase (USP10), enhanced SARS-CoV-2 infection. Such proviral effect was observed upon treatment with compounds JQ1, vorinostat, romidepsin, and spautin-1, when measured by cytopathic effect and validated by viral RNA assays, suggesting that HDAC2, BRD4 and USP10 host proteins have antiviral functions. Mycophenolic acid and merimepodib, two inhibitors of inosine monophosphate dehydrogenase (IMPDH 1 and IMPDH 2), showed modest antiviral effects with no toxicity in mock-infected control cells. The network-based approach enables systematic identification of host-targets that selectively modulate the SARS-CoV-2 interactome, as well as reveal novel chemical tools to probe virus-host interactions that regulate virus infection.

Synopsis

Viruses exploit host machinery and therefore it is important to understand the virus-host dependencies to gain better insight of the key regulators of viral infection.

Using a context-specific SARS-COV-2 PPI network, a computational framework was developed to identify host modulators of viral infection.

Chromatin modifying host proteins HDAC2 and BRD4, along with deubiquitinating enzyme USP10, act as antiviral proteins.

IMPDH inhibitors mycophenolic acid and merimipodib showed modest antiviral response to SARS-COV-2 infection, and no toxic effects.

Cell context specificity is a critical factor when identifying selective modulators of viral infection and potential antiviral therapeutics.

Topology-based network models cannot distinguish between host-proteins, the inhibition of which leads to either virus suppressive or enhancing effects.
Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage
Authors: Martínez-García Belén , Dyson Sílvia , Segura Joana , Gutierrez-Escribano Pilar , Aragón Luís , Roca Joaquim
Published: June 2022

Condensin extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain DNA positive supercoils. However, in experimental conditions that sustain DNA loop extrusion, condensin restrains negative supercoils. Namely, upon ATP-mediated loading onto DNA, each condensin constrains a DNA linking number difference (ΔLk) of -0.4. This ΔLk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. These ΔLk values reflect the transient formation of a short left-handed loop of DNA, which is not the extruding loop. We conclude that, upon condensin ATPase-head engagement, a segment of DNA is pinched to form a short negatively supercoiled loop, which can be subsequently merged with the extruding loop. Such “pinch and merge” mechanism implies that the DNA is transferred between two dynamic DNA-binding sites while anchored at a third site.