title: Integrative Omics Reveals Subtle Molecular Perturbations Following Ischemic Conditioning in a Porcine Kidney Transplant Model

abstract:
BackgroundRemote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls.

MethodsKidney pairs (n = 8+8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed a modern integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC.

ResultsIn kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (p<0.05).

ConclusionsOur data identifies subtle molecular phenotypes in porcine kidneys following RIC and this knowledge could potentially aid optimization of remote ischemic conditioning protocols in renal transplantation.


title: Augmentation of CD47-SIRPα signaling protects cones in genetic models of retinal degeneration

abstract: Inherited retinal diseases such as retinitis pigmentosa (RP) can be caused by thousands of different mutations, a small number of which have been successfully treated with gene replacement. However, this approach has yet to scale and may be infeasible in many cases, highlighting the need for interventions that could benefit more patients. Here, we found that microglial phagocytosis is upregulated during cone degeneration in RP, suggesting that expression of "dont eat me" signals such as CD47 might confer protection to cones. To test this, we delivered an adeno-associated viral (AAV) vector expressing CD47 on cones, which promoted cone survival in three mouse models of RP and preserved visual function. Cone rescue with CD47 required signal regulatory protein alpha (SIRP) but not microglia or thrombospondin-1 (TSP1), suggesting that CD47 interacts with SIRP on non-microglial cells to alleviate degeneration. These findings establish augmentation of CD47-SIRP signaling as a potential treatment strategy for RP and possibly other forms of neurodegeneration.

category: neuroscience


title: A key role of astrocytic calcium dynamics to link neuronal activity with the BOLD signal

abstract: Functional magnetic resonance imaging (fMRI) relies on the coupling between neuronal and vascular activity, but the mechanisms behind this coupling are still under discussion. Recent experimental evidence suggests that calcium signaling may play a significant role in neurovascular coupling. However, it is still controversial where this calcium signal is located (in neurons or elsewhere), how it operates and how relevant is its role. In this paper we introduce a biologically plausible model of the neurovascular coupling and we show that calcium signaling in astrocytes can explain the main aspects of the dynamics of the coupling. We find that calcium signaling can explain so-far unrelated features such as the linear and non-linear regimes, the negative vascular response (undershoot) and the emergence of a (calcium-driven) Hemodynamic Response Function. These features are reproduced here for the first time by a single model of the detailed neuronal-astrocyte-vascular pathway. Furthermore, we analyze how information is coded and transmitted from the neuronal to the vascular system and we find that frequency modulation of astrocytic calcium dynamics plays a key role in this process. Finally, our work provides a framework to link neuronal activity to the BOLD signal, and vice-versa, where neuronal activity can be inferred from the BOLD signal. This opens new ways to link known alterations of astrocytic calcium signaling in neurodegenerative diseases (e.g. Alzheimers and Parkinsons diseases) with detectable changes in neurovascular coupling.


title: Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees

abstract: The drastic rise in the number of cases in Maharashtra, India has created a matter of concern for public health experts. Twelve isolates of VUI lineage B.1.617 were propagated in VeroCCL81 cells and characterized. Convalescent sera of the COVID-19 cases and recipients of BBV152 (Covaxin) were able to neutralize VUI B.1.617.

category: immunology


title: Ebola virus disease outbreak in the Republic of Guinea 2021: hypotheses of origin.

abstract:
In 2013-2016, a large-scale Ebola virus diseas (EVD) outbreak hit the countries of West Africa for the first time. Thus provoking a health crisis. The most affected countries were Sierra Leone, Liberia and the Republic of Guinea. Since the end of the outbreak in 2016, there have been no new cases until recently. In February 2021, the Republic of Guinea announced about laboratory-confirmed EVD cases in its territory.

By April 12, 2021, an Ebola virus disease outbreak in the province of NZerekore (Gueke sub-prefecture) of the Republic of Guinea had affected 16 people, 9 of whom had died. The origin of this outbreak is still unknown. This paper considers various hypotheses of its emergence. Within the frames of the study sequencing and analysis of the whole genome sequence of the strain that initiated the epidemic process have been carried out. The most likely cause of this outbreak, according to the results obtained, should be deemed a long-term persistence of the virus in the body of survivors, followed by a relapse of the disease and transmission among contact persons.

category: microbiology


title: Topical TMPRSS2 inhibition prevents SARS-CoV-2 infection in differentiated primary human airway cells

abstract:
BackgroundThere are limited effective prophylactic treatments for SARS-CoV-2 infection, and limited early treatment options. Viral cell entry requires spike protein binding to the ACE2 receptor and spike cleavage by TMPRSS2, a cell surface serine protease. Targeting of TMPRSS2 by either androgen blockade or direct inhibition is already in clinical trials in early SARS-CoV-2 infection.

MethodsThe likely initial cells of SARS-CoV-2 entry are the ciliated cells of the upper airway. We therefore used differentiated primary human airway epithelial cells maintained at the air-liquid interface (ALI) to test the impact of targeting TMPRSS2 on the prevention of SARS-CoV-2 infection.

ResultsWe first modelled the systemic delivery of compounds. Enzalutamide, an oral androgen receptor antagonist, had no impact on SARS-Cov-2 infection. By contrast, camostat mesylate, an orally available serine protease inhibitor, blocked SARS-CoV-2 entry. However, camostat is rapidly metabolised in the circulation in vivo, and systemic bioavailability after oral dosing is low. We therefore modelled local airway administration by applying camostat to the apical surface of the differentiated ALI cultures. We demonstrated that a brief exposure to topical camostat is effective at restricting SARS-CoV-2 viral infection.

ConclusionThese experiments demonstrate a potential therapeutic role for topical camostat for pre- or post-exposure prophylaxis of SARS-CoV-2, which can now be evaluated in a clinical trial.


title: Precursor types predict the stability of neuronal branches

abstract: Branches are critical for neuron function, generating the morphological complexity required for functional networks. They emerge from different, well-described, cytoskeletal precursor structures that elongate to branches. While branches are thought to be maintained by shared cytoskeletal regulators, our data from mouse hippocampal neurons indicate that the precursor structures trigger alternative branch maintenance mechanisms with differing stabilities. While branches originating from lamellipodia or growth cone splitting events collapse soon after formation, branches emerging from filopodia persist. Furthermore, compared to other developing neurites, axons stabilise all branches and preferentially initiate branches from filopodia. These differences explain the decreased stability of branches we observe in neurons lacking the plasma membrane protein phospholipid phosphatase related protein 3 (PLPPR3/PRG2). Rather than altering branch stability directly, PLPPR3 boosts a  filopodia branch program on axons, thereby indirectly initiating more long-lived branches. We propose that studies on branching should distinguish overall stabilising effects from effects on precursor types, ideally using multifactorial statistical models as exemplified in this study.

category: cell biology


title: Hydrosphere occupancy modeling ({psi}) and Akaike (AIC) habitat model selection of urban amphibian in West Java landscape

abstract: Amphibians are animal that requires combinations of hydrosphere (riparian vegetation, water body) and vegetation (trees) microhabitats. In urban settings, those microhabitats are scarce and disappearing. One of areas that still have sufficient microhabitats to support amphibian populations is located in an 88.9 Ha urban forests of Universitas Indonesia Campus in West Java. Here, this paper aims to assess and model the several amphibian species occupancy ({Psi}) with vegetation covers, riparian vegetation, and water bodies based on Akaike habitat selection (AIC) indices. The studied amphibian species include Bufo melanosticus, Hylarana nicobariensis, Fejervarya limnocharis, and Polypedates leucomystax. For modeling, 7 microhabitat models were developed and tested for amphibian species occupancy with covariates including vegetation cover, riparian vegetation, and water body microhabitats. The Principle Component Analysis (PCA) shows that the occupancies of amphibian were influenced mostly by the presences of water bodies followed by riparian vegetation, and vegetation covers. According to the values of {Psi} and AIC, Polypedates leucomystax and Fejervarya limnocharis were species that have high occupancy in riparian vegetation microhabitats with {Psi} values of -14.18 and -12.59. Likewise, Hylarana nicobariensis has an equal occupancy in vegetation, riparian vegetation, and water body microhabitats. While Bufo melanosticus shows high occupancy in vegetated microhabitats ({Psi} = -14.18) rather than in riparian vegetation and water bodies ({Psi} = -8.79). The combinations of riparian vegetation and water bodies show higher occupancy ({Psi} = -8.00) rather than {Psi}(vegetation cover+water body = -5.64) and {Psi}(vegetation cover+ riparian vegetation = -4.36) combinations.

category: ecology


title: Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection

abstract: SARS-CoV-2 can cause a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of the host factors mediating viral infection or restriction is critical to elucidate SARS-CoV-2 host-pathogen interactions and the progression of COVID-19. To this end, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. These screens uncovered proviral and antiviral host factors across highly interconnected host pathways, including components implicated in clathrin transport, inflammatory signaling, cell cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high-molecular weight glycoproteins, as a prominent viral restriction network. We demonstrate that multiple membrane-anchored mucins are critical inhibitors of SARS-CoV-2 entry and are upregulated in response to viral infection. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and suggests interactions between SARS-CoV-2 and airway mucins of COVID-19 patients as a host defense mechanism.

category: genetics


title: Prefusion conformation of SARS-CoV-2 receptor-binding domain favors interactions with human receptor ACE2

abstract: A new coronavirus pandemic COVID-19, caused by Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2), poses a serious threat across continents, leading the World Health Organization to declare a Public Health Emergency of International Concern. In order to block the entry of the virus into human host cells, major therapeutic and vaccine design efforts are now targeting the interactions between the SARS-CoV-2 spike (S) glycoprotein and the human cellular membrane receptor angiotensin-converting enzyme, hACE2. By analyzing cryo-EM structures of SARS-CoV-2 and SARS-CoV-1, we report here that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) that binds with hACE2 has expanded in size, undergoing a large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits higher intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction has caused a significant structural rigidification, favoring proteolytic processing of S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification in the RBD dynamics and their likely impact on infectivity.

category: bioinformatics


title: Torsions-Driven Root Helical Growth, Waving And Skewing In Arabidopsis

abstract:
Helical growth broadly exists in immobile plants to support their limited movement, and Arabidopsis seedling root exhibiting natural left-handedness helical growth is considered as a simplified model for investigating this interesting behavior. Efforts have been made for understanding the mechanism of root helical growth and consequent root waving and skewing on tilted and impenetrable surface, and several models have been established. Here, previous reports are reviewed and a straightforward torsions-driven mechanism has been emphasized, and additional experiments have been performed to fill up the gaps of this theory in our study.

This study implies that, torsions originating from handedness of both cortical microtubules and cellulose microfibrils play central role in root handed helical growth. Different from torsions directly provided by handed assembled cortical microtubules, torsions originating from right-handed assembled cellulose microfibrils are relaxed by their cross-linking with pectin within cell wall, but only exhibited when their cross-linking is interrupted due to damaged cell wall integrity. To topologically relax these torsions, supercoils of cortical microtubules and/or cellulose microfibrils exhibiting as oblique alignments are formed in root cells, which alter the orientation of root cell files and generate handed helical roots. Working together with gravitropic response, relaxation of torsions originating from helical roots drives roots to elongate with handedness, which therefore produces waved and skewed roots on tilted and impenetrable surface.

category: plant biology


title: Beta-band desynchronization reflects uncertainty in effector selection during motor planning

abstract:
While beta-band activity during motor planning is known to be modulated by uncertainty about where to act, less is known about its modulations to uncertainty about how to act. To investigate this issue, we recorded oscillatory brain activity with EEG while human participants (n = 17) performed a hand choice reaching task. The reaching hand was either predetermined or of participants choice, and the target was close to one of the two hands or at about equal distance from both. To measure neural activity in a motion-artifact-free time window, the location of the upcoming target was cued 1000-1500 ms before the presentation of the target, whereby the cue was valid in 50% of trials. As evidence for motor planning during the cueing phase, behavioral observations showed that the cue affected later hand choice. Furthermore, reaction times were longer in the choice than in the predetermined trials, supporting the notion of a competitive process for hand selection. Modulations of beta-band power over central cortical regions, but not alpha-band or theta-band power, were in line with these observations. During the cueing period, reaches in predetermined trials were preceded by larger decreases in beta-band power than reaches in choice trials. Cue direction did not affect reaction times or beta-band power, which may be due to the cue being invalid in 50% of trials, retaining effector uncertainty during motor planning. Our findings suggest that effector uncertainty, similar to target uncertainty, selectively modulates beta-band power during motor planning.

New & NoteworthyWhile reach-related beta-band power in central cortical areas is known to modulate with the number of potential targets, here we show, using a cueing paradigm, that the power in this frequency band, but not in the alpha or theta-band, is also modulated by the uncertainty of which hand to use. This finding supports the notion that multiple possible effector-specific actions can be specified in parallel up to the level of motor preparation.


title: Wnt-dependent activation of ERK mediates repression of chondrocyte fate during calvarial development.

abstract: Wnt signaling regulates cell fate decisions in diverse contexts during development, and loss of Wnt signaling in the cranial mesenchyme results in a robust and binary cell fate switch from cranial bone to ectopic cartilage. The Extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) and Wnt signaling pathways are activated during calvarial osteoblast cell fate selection. Here, we test the hypothesis that ERK signaling is a mediator of Wnt-dependent cell fate decisions in the cranial mesenchyme. First, we show that loss of Erk1/2 in the cranial mesenchyme results in a diminished domain of osteoblast marker expression and increased expression of cartilage fate markers and ectopic cartilage formation in the frontal bone primordia. Second, we show that mesenchyme Wnt/{beta}-catenin signaling and Wntless are required for ERK activation in calvarial osteoblasts. Third, we demonstrate that Wnt and ERK signaling pathways function together to repress Sox9 expression in mouse cranial mesenchyme. Our results demonstrate a link between the Wnt and ERK signaling pathways in regulating lineage selection in a subset of calvarial cells and provide new insights into Wnt-dependent cell fate decisions.

category: developmental biology


title: Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients

abstract:
Risk factors for COVID-19 disease severity are still poorly understood. Considering the pivotal role of gut microbiota on host immune and inflammatory functions, we investigated the association between changes in gut microbiota composition and the clinical severity of COVID-19. We conducted a multicentre cross-sectional study prospectively enrolling 115 COVID-19 patients categorized according to: 1) WHO Clinical Progression Scale - mild 19 (16.5%), moderate 37 (32.2%) or severe 59 (51.3%); and 2) location of recovery from COVID-19 - ambulatory 14 (household isolation; 12.2%), hospitalized in ward 40 (34.8%) or intensive care unit 61 (53.0%). Gut microbiota analysis was performed through 16S rRNA gene sequencing and data obtained was further related with clinical parameters of COVID-19 patients. Risk factors for COVID-19 severity were identified by univariate and multivariable logistic regression models.

In comparison with mild COVID-19 patients, the gut microbiota of moderate and severe patients has: a) lower Firmicutes/Bacteroidetes ratio, b) higher abundance of Proteobacteria; and c) lower abundance of beneficial butyrate-producing bacteria such as Roseburia and Lachnospira genera. Multivariable regression analysis showed that Shannon index diversity (odds ratio [OR] 2.85 [95% CI 1.09-7.41]; p=0.032) and C-Reactive Protein (OR 3.45 [95% CI 1.33-8.91]; p=0.011) were risk factors for COVID-19 severe disease (a score of 6 or higher in WHO clinical progression scale).

In conclusion, our results demonstrated that hospitalised moderate and severe COVID-19 patients have microbial signatures of gut dysbiosis and for the first time, the gut microbiota diversity is pointed out as a prognostic biomarker for COVID-19 disease severity.


title: Computational investigation reveals that the mutant strains of SARS-CoV2 are highly infectious than wildtype

abstract: Remarkable infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) is due to the rapid emergence of various strains, thus enable the virus to rule the world. Over the course of SARS-CoV2 pandemic, the scientific communities worldwide are responding to newly emerging genetic variants. However, the mechanism behind the persistent infection of these variants is still not known due to the paucity of study of these variants at molecular level. In this scenario, computational methods have immense utility in understanding the molecular and functional properties of different variants. Therefore, in this study various mutants (MTs) of SpikeS1 receptor binding domain (RBD) of highly infectious SARS-CoV2 strains were carried and elucidated the protein structure and dynamics using molecular dynamics (MD) approach. MD simulation study showed that all MTs exhibited stable structures with altered functional properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed through protein-protein docking and observed that MTs showed high binding affinities than WT. Hence, this study shed light on the molecular basis of infection caused by different variants of SARS-CoV2, which might play an important role in to cease the transmission and pathogenesis of virus and also implicate in rational designing of a specific drug.


title: Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances

abstract:
PREMISEThe genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it.

METHODSWe sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference.

RESULTSOur results indicate that the inclusion of all plastid genome partitions is needed to infer fully resolved phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia.

CONCLUSIONSThe concatenation and combined analysis of all plastid genome partitions and the construction of manually curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of strongly supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence datasets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.


title: The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection

abstract: MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.

category: systems biology


title: Alprazolam modulates persistence energy during emotion processing in first-degree relatives of individuals with schizophrenia: a network control study

abstract: Schizophrenia is marked by deficits in facial affect processing associated with abnormalities in GABAergic circuitry, deficits also found in first-degree relatives. Facial affect processing involves a distributed network of brain regions including limbic regions like amygdala and visual processing areas like fusiform cortex. Pharmacological modulation of GABAergic circuitry using benzodiazepines like alprazolam can be useful for studying this facial affect processing network and associated GABAergic abnormalities in schizophrenia. Here, we use pharmacological modulation and computational modeling to study the contribution of GABAergic abnormalities toward emotion processing deficits in schizophrenia. Specifically, we apply principles from network control theory to model persistence energy - the control energy required to maintain brain activation states - during emotion identification and recall tasks, with and without administration of alprazolam, in a sample of first-degree relatives and healthy controls. Here, persistence energy quantifies the magnitude of theoretical external inputs during the task. We find that alprazolam increases persistence energy in relatives but not in controls during threatening face processing, suggesting a compensatory mechanism given the relative absence of behavioral abnormalities in this sample of unaffected relatives. Further, we demonstrate that regions in the fusiform and occipital cortices are important for facilitating state transitions during facial affect processing. Finally, we uncover spatial relationships (i) between regional variation in differential control energy (alprazolam versus placebo) and (ii) both serotonin and dopamine neurotransmitter systems, indicating that alprazolam may exert its effects by altering neuromodulatory systems. Together, these findings reveal differences in emotion-processing circuitry associated with genetic vulnerability to schizophrenia.


title: Inactivation of SARS-CoV-2 by β-propiolactone Causes Aggregation of Viral Particles and Loss of Antigenic Potential

abstract: Inactivated viral preparations are important resources in vaccine and antisera industry. Of the many vaccines that are being developed against COVID-19, inactivated whole-virus vaccines are also considered effective. {beta}-propiolactone (BPL) is a widely used chemical inactivator of several viruses. Here, we analyze various concentrations of BPL to effectively inactivate SARS-CoV-2 and their effects on the biochemical properties of the virion particles. BPL at 1:2000 (v/v) concentrations effectively inactivated SARS-CoV-2. However, higher BPL concentrations resulted in the loss of both protein content as well as the antigenic integrity of the structural proteins. Higher concentrations also caused substantial aggregation of the virion particles possibly causing undesirable outcomes including a potential immune escape by infectious virions, and a loss in antigenic potential. We also identify that the viral RNA content in the culture supernatants can be a direct indicator of their antigenic content. Our findings may have important implications in the vaccine and antisera industry during COVID-19 pandemic.


title: Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea

abstract:
BackgroundRetrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons become temporarily active during epigenetic reprogramming and cellular stress response, which may accelerate host genome evolution. In fungal pathogens, a positive role has been attributed to retrotransposons when shaping genome architecture and expression of genes encoding pathogenicity factors; thus, retrotransposons are known to influence pathogenicity.

ResultsWe here uncovered a hitherto unknown role of fungal retrotransposons as being pathogenicity factors, themselves. Studying the aggressive fungal plant pathogen Botrytis cinerea, that is known to deliver some long-terminal repeat (LTR) deriving regulatory trans-species small RNAs (BcsRNAs) into plant cells to suppress host gene expression for infection we found that naturally occurring, less aggressive B. cinerea strains possess considerably lower copy numbers of LTR retrotransposons and had lost retrotransposon BcsRNA production. By a transgenic proof-of-concept approach, we reconstituted retrotransposon expression in a BcsRNA-lacking B. cinerea strain, which resulted in enhanced aggressiveness in a retrotransposon and BcsRNA expression-dependent manner. Moreover, retrotransposon expression in B. cinerea led to suppression of plant defence-related genes during infection.

ConclusionsWe propose that retrotransposons are pathogenicity factors that manipulate host plant gene expression by encoding trans-species BcsRNAs. Taken together, the novelty that retrotransposons are pathogenicity factors will have general impact on studies of host-microbe interactions and pathology.

category: genomics


title: Memes: an R interface to the MEME Suite

abstract: Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we present memes, an R package which provides a seamless R interface to the MEME Suite. memes provides a novel "data aware" interface to these tools, enabling rapid and complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools, memes leverages existing R/Bioconductor data structures to store the complex, multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally, memes provides data visualization capabilities to facilitate communication of results. memes is available as a Bioconductor package at https://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.


title: Narrative Event Segmentation in the Cortical Reservoir

abstract: During continuous perception of movies or stories, awake humans display cortical activity patterns that reveal hierarchical segmentation of event structure. Sensory areas like auditory cortex display high frequency segmentation related to the stimulus, while semantic areas like posterior middle cortex display a lower frequency segmentation related to transitions between events (Baldassano et al. 2017). These hierarchical levels of segmentation are associated with different time constants for processing. Chien and Honey (2020) observed that when two groups of participants heard the same sentence in a narrative, preceded by different contexts, neural responses for the groups were initially different and then gradually aligned. The time constant for alignment followed the segmentation hierarchy: sensory cortices aligned most quickly, followed by mid-level regions, while some higher-order cortical regions took more than 10 seconds to align. These hierarchical segmentation phenomena can be considered in the context of processing related to comprehension. Uchida et al. (2021) recently described a model of discourse comprehension where word meanings are modeled by a language model pre-trained on a billion word corpus (Yamada et al 2020). During discourse comprehension, word meanings are continuously integrated in a recurrent cortical network. The model demonstrates novel discourse and inference processing, in part because of two fundamental characteristics: real-world event semantics are represented in the word embeddings, and these are integrated in a reservoir network which has an inherent gradient of functional time constants due to the recurrent connections. Here we demonstrate how this model displays hierarchical narrative event segmentation properties. The reservoir produces activation patterns that are segmented by the HMM of Baldassano et al (2017) in a manner that is comparable to that of humans. Context construction displays a continuum of time constants across reservoir neuron subset, while context forgetting has a fixed time constant across these subsets. Virtual areas formed by subgroups of reservoir neurons with faster time constants segmented with shorter events, while those with longer time constants preferred longer events. This neurocomputational recurrent neural network simulates narrative event processing as revealed by the fMRI event segmentation algorithm of Baldassano et al (2017), and provides a novel explanation of the asymmetry in narrative forgetting and construction observed by Chien and Honey (2020). The model extends the characterization of online integration processes in discourse to more extended narrative, and demonstrates how reservoir computing provides a useful model of cortical processing of narrative structure.


title: Fourier SPoC: A costumised machine-learning analysis pipeline for auditory beat-based entrainment in the MEG

abstract:
We propose here (the informed use) of a customised, data-driven machine-learning pipeline to analyse magnetoencephalography (MEG) in a theoretical source space, with respect to the processing of a regular beat. This hypothesis- and data-driven analysis pipeline allows us to extract the maximally relevant components in MEG source-space, with respect to the oscillatory power in the frequency band of interest and, most importantly, the beat-related modulation of that power. Our pipeline combines Spatio-Spectral Decomposition as a first step to seek activity in the frequency band of interest (SSD, [1]) with a Source Power Co-modulation analysis (SPoC; [2]), which extracts those components that maximally entrain their activity with the given target function, that is here with the periodicity of the beat in the frequency domain (hence, f-SPoC). MEG data (102 magnetometers) from 28 participants passively listening to a 5-min long regular tone sequence with a 400 ms beat period (the "target function" for SPoC) were segmented into epochs of two beat periods each to guarantee a sufficiently long time window. As a comparison pipeline to SSD and f-SpoC, we carried out a state-of-the-art cluster-based permutation analysis (CBPA, [3]). The time-frequency analysis (TFA) of the extracted activity showed clear regular patterns of periodically occurring peaks and troughs across the alpha and beta band (8-20 Hz) in the f-SPoC but not in the CBPA results, and both the depth and the specificity of modulation to the beat frequency yielded a significant advantage. Future applications of this pipeline will address target the relevance to behaviour and inform analogous analyses in the EEG, in order to finally work toward addressing dysfunctions in beat-based timing and their consequences.

Author summaryWhen listening to a regular beat, oscillations in the brain have been shown to synchronise with the frequency of that given beat. This phenomenon is called entrainment and has in previous brain-imaging studies been shown in the form of one peak and trough per beat cycle in a range of frequency bands within 15-25 Hz (beta band). Using machine-learning techniques, we designed an analysis pipeline based on Source-Power Co-Modulation (SPoC) that enables us to extract spatial components in MEG recordings that show these synchronisation effects very clearly especially across 8-20 Hz. This approach requires no anatomical knowledge of the individual or even the average brain, it is purely data driven and can be applied in a hypothesis-driven fashion with respect to the "function" that we expect the brain to entrain with and the frequency band within which we expect to see this entrainment. We here apply our customised pipeline using "f-SPoC" to MEG recordings from 28 participants passively listening to a 5-min long tone sequence with a regular 2.5 Hz beat. In comparison to a cluster-based permutation analysis (CBPA) which finds sensors that show statistically significant power modulations across participants, our individually extracted f-SPoC components find a much stronger and clearer pattern of peaks and troughs within one beat cycle. In future work, this pipeline can be implemented to tackle more complex "target functions" like speech and music, and might pave the way toward rhythm-based rehabilitation strategies.


title: Coagulation disorders in patients with severe hemophagocytic lymphohistiocytosis

abstract:
BackgroundCoagulation disorders are common in patients with hemophagocytic lymphohistiocytosis (HLH), associated with an increased risk of bleeding and death. We aim to investigate coagulation disorders and their outcome implications in critically ill patients with HLH.

MethodsWe prospectively evaluated 47 critically ill patients with HLH (median age of 54 years [42-67]) between April 2015 and December 2018. Coagulation assessments were performed at day 1. Abnormal standard coagulation was defined as prothrombin time (PT) <50% and/or fibrinogen <2g/L. HLH aetiology was mostly ascribed to haematological malignancies (74% of patients).

ResultsCoagulation disorders and severe bleeding events were frequent, occurring in 30 (64%) and 11 (23%) patients respectively. At day 1, median fibrinogen level was 2{middle dot}65g/L [1.61-5.66]. Fibrinolytic activity was high as suggested by increased median levels of D-dimers, fibrin monomers, PAI-1 (plasminogen activator inhibitor) and tPA (tissue plasminogen activator). Forty-one (91%) patients had a decreased ADAMTS13 activity (A Disintegrin-like And Metalloproteinase with ThromboSpondin type 1 repeats, member 13). By multivariable analysis, the occurrence of a severe bleeding (OR 3.215 [1.194-8.653], p=0{middle dot}021) and SOFA score (Sepsis-Related Organ Failure Assessment) at day 1 (OR 1.305 per point [1.146-1.485], p<0{middle dot}001) were independently associated with hospital mortality. No early biological marker was associated with severe bleeding.

ConclusionsHyperfibrinolysis may be the primary mechanism responsible for hypofibrinogenemia and may also participate in ADAMTS13 degradation. Targeting the plasmin system appears as a promising approach in severe HLH-related coagulation disorders.


title: Limiting factors for queen conch (Lobatus gigas) reproduction: A simulation-based evaluation

abstract: Queen conch are among the most economically, socially, and culturally important fishery resources in the Caribbean. Despite a multitude of fisheries management measures enacted across the region, populations are depleted and failing to recover. It is believed that queen conch are highly susceptible to depensatory processes, impacting reproductive success and contributing to the lack of recovery. We developed a model of reproductive dynamics to evaluate how variations in biological factors such as population density, movement speeds, movement restrictions, rest periods between mating events, sexual facilitation, and perception of conspecifics affect reproductive success and overall reproductive output. We compared simulation results to empirical observations of mating and spawning frequencies from conch populations in the central Bahamas and Florida Keys. Our results confirm that low probability of mate finding associated with decreased population density is the primary driver behind observed breeding behavior in the field, although additional factors also play important roles. In particular, sexual facilitation and perception of conspecifics may explain observed lack of mating at low densities and differences between mating frequencies in the central Bahamas and Florida Keys, respectively. Our simulations suggest densities greater than 200 adults/ha are needed for high levels of spawning output, supporting the suggestion that effective management strategies for queen conch should aim to protect high-density reproductive aggregations and critical breeding habitats.


title: Redefining the PTEN Promoter: Identification of Two Upstream Transcription Start Regions

abstract: Germline mutation of PTEN is causally observed in Cowden syndrome (CS) and is one of the most common genetic causes of autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are found to be PTEN-mutation negative. Reassessment of PTEN promoter regulation may help explain abnormal PTEN dosage, as only the minimal promoter and coding regions are currently included in diagnostic PTEN mutation analysis. We reanalyzed the architecture of the PTEN promoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional TSRs at -2052 and -1907 basepairs from the start of PTEN, thus redefining the PTEN promoter and extending the PTEN 5UTR. The upstream TSRs described are active in cancer cell lines and human cancer and normal tissue. Further, these TSRs can produce novel PTEN transcripts due to the introduction of new splice sites. Evaluation of transcription factor binding specific to the upstream TSRs shows overrepresentation of TFs involved in inflammatory processes. Together, these data suggest that potentially clinically relevant promoter variants upstream of the known promoter may be overlooked in indivduals considered PTEN germline mutation-negative and may also explain lack of PTEN expression in sporadic neoplasias without PTEN somatic structural defects.


title: Automated Raman micro-spectroscopy of epithelial cells for the high-throughput classification.

abstract: Raman micro-spectroscopy is a powerful technique for the identification and classification of cancer cells and tissues. In recent years, the application of Raman spectroscopy to detect bladder, cervical, and oral cytological samples has been reported to have an accuracy that is greater than standard pathology. However, despite being entirely non-invasive and relatively inexpensive, the slow recording time, and lack of reproducibility, have prevented the clinical adoption of the technology. Here we present an automated Raman cytology system that can facilitate high-throughput screening and improve reproducibility. The proposed system is designed to be integrated directly into the standard pathology clinic, taking into account their methodologies and consumables. The system employs image processing algorithms and integrated hardware/software architectures in order to achieve automation and is tested using the ThinPrep standard, including the use of glass slides, and a number of bladder cancer cell lines. The entire automation process is implemented using the open source Micro-Manager platform, and is made freely available. We believe this code can be readily integrated into existing commercial Raman micro-spectrometers.

category: pathology


title: Dravet variant SCN1AA1783V impairs interneuron firing predominantly by altered channel activation

abstract:
Dravet syndrome (DS) is a developmental epileptic encephalopathy mainly caused by functional NaV1.1 haploinsufficiency in interneurons (IN). Recently, a new conditional mouse model expressing the recurrent human p.A1783V missense variant has become available. Here we provide an electrophysiological characterization of this variant in tsA201 cells, revealing both altered voltage-dependence of activation and slow inactivation without reduced sodium peak current density. Simulating IN excitability in a Hodgkin-Huxley one-compartment model suggested surprisingly similar firing deficits for Scn1aA1783V and full haploinsufficiency as caused by heterozygous truncation variants. Impaired NaVA1783V channel activation was predicted to have a significantly larger impact on channel function than altered slow inactivation and is therefore proposed as the main mechanism underlying IN dysfunction. The computational model was validated in cortical organotypic slice cultures derived from conditional Scn1aA1783V mice. Pan-neuronal activation of the p.A1783V variant in vitro confirmed the predicted IN firing deficit while demonstrating normal excitability of pyramidal neurons. Taken together these data demonstrate that despite maintained physiological peak currents density LOF gating properties may match effects of full haploinsufficiency on neuronal level, thereby causing DS.

HighlightsNaV1.1A1783V alters voltage-dependence of activation and slow inactivation while not affecting fast inactivation.
Depolarizing and hyperpolarizing shifts of activation and slow inactivation curves result in combined channel loss of function (LOF).
Simulations of NaV1.1A1783V interneuronal properties indicate reduced action potential firing rates comparable to full SCN1A haploinsufficiency, which is often found in Dravet syndrome.
In silico modelling identifies impaired channel activation as the predominant mechanism of channel LOF.
Panneuronal induction of Scn1a+/A1783V in a cortical slice culture model confirms restriction of loss of function and its restriction to interneurons.


title: Small Extracellular Vesicles Secreted by Region-specific Astrocytes Ameliorate the Mitochondrial Function in a Cellular Model of Parkinson's Disease

abstract: Extracellular vesicles (EVs) are emerging as powerful players in cell-to-cell communication both in health and diseased brain. In Parkinsons disease (PD) - characterized by selective dopaminergic (DAergic) neuron death in ventral midbrain (VMB) and degeneration of DAergic terminals in striatum (STR) - astrocytes (AS) exert dual harmful/protective functions. When activated by chemokine CCL3, AS promote a robust DAergic neuroprotection both in cellular and pre-clinical models of PD, with mechanisms not fully elucidated. Here we used a combination of techniques to characterize AS-EVs derived from VMB and STR, and investigated their potential to exert neuroprotection. First, we show that: (i) AS of both regions secrete small EVs of ~100 nm; (ii) VMB-AS release more EVs per cell than STR-AS under basal conditions; and (iii) only VMB-AS respond to CCL3 by producing more EVs, suggesting differential AS-EV secretion rate according to PD brain region. Next, addressing AS-EV potential against oxidative stress and mitochondrial toxicity, we found that AS-EVs, especially CCL3-AS-EVs, fully counteract H2O2-induced caspase-3 activation. Furthermore, using high resolution respirometry, we demonstrated that AS-EVs rescue the neuronal mitochondrial complex I function impaired by MPP+, with VMB-AS-EVs fully restoring ATP production in MPP+-injured neurons, highlighting a regional diversity of AS-EVs with neuroprotective implications for PD.


title: Sero-Prevalence and Risk Factor of  Peste Des Petits Ruminants in Sheep and Goats of Ethiopia: Systematic Review and Meta- Analysis

abstract:
BackgroundPeste des petits ruminant (PPR) is the most common prevalent viral disease of sheep and goats that impacts productivity and international animal trade in the world and also in Ethiopia. Despite the huge economic consequences related to PPR, little is known about the sero-prevalence of this disease at the country levels. The objective of this systematic review and meta-analysis was to estimate a single-group summary for sero-prevalence of PPR disease in small ruminants of Ethiopia and assess the potential risk factor to contribute the sero-prevalence estimate.

MethodologyArticle on PPR in sheep and goats were searched in PubMed, Web of Science, Google Scholar, reference lists and African online source of articles that had been conducted between 1994 to 2020 and using inclusion and exclusion criteria with restricted to those studies published in English language.

ResultsA total of 13 published papers containing 46 district level studies were included for analyses. The single-group summary of PPR disease sero-prevalence in small ruminant was estimated to be 27.71% (95 % CI: 21.46 - 33.96). Overall, the estimated pooled sero-prevalence at country level in sheep was 33.56% (95% CI: 18.72-48.41) and in goats 25.14% (95% CI: 15.68-34.59). Significant heterogeneity (I2 > 80%) was noted in all pooled estimates. The visual inspection of the funnel plot demonstrated the presence of possible publication bias which could be associated with the small number of studies and longtime interval.

ConclusionsThis quantitative review showed that the pooled sero-prevalence to be high and regional prevalence estimates of PPR presented here will be useful in raising awareness and advocating the Governments to engage in initiatives PPR control and prevention.


title: OPTIMIZED PROTOCOL FOR CYANOBACTERIAL 16S rRNA ANALYSIS IN DANUBE DELTA LAKES

abstract: Molecular biology protocols have been more and more accessible to researchers for ecological investigations, however, these protocols always require optimization steps for the analysis of specific types of samples. The purpose of this study was to optimize a molecular protocol for the analysis of cyanobacterial 16S rRNA in Danube Delta shallows lakes. In this regard, several commercial DNA extraction kits were tested in comparison with potassium ethyl xanthogenate extraction method on different matrices. The obtained DNA was further used for 16S rRNA PCR optimization. Finally, an optimized protocol is proposed for the molecular analysis of cyanobacteria group in freshwater samples. The best DNA extraction method was the potassium xanthogenate extraction from dried cyanobacterial biomass. A dynamic in total genomic eDNA was observed, reflecting the seasonal difference in phytoplankton biomass from the studied lakes. The PCR protocol optimized by us can be successfully applied for the identification of a broad range of cyanobacterial genetic markers.


title: A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide

abstract: In response to environmental stress, cellular defense strategies may be divided into two categories: those, as in homeostatic systems, that seek to maintain cell proliferation by degrading the stressor (i.e., resistance); and those that ensure cell survival (i.e. tolerance), even if this is often at the expense of cell proliferation. In this study, we have explored the genetic bases of the antagonism between resistance and tolerance during the response to hydrogen peroxide (H2O2) in budding yeast. We show that inactivation of protein kinase A (PKA) by H2O2 signaling induces an abrupt transition from normal homeostatic function to a stress-tolerant state by protecting the growth machinery, hence maximizing cellular fitness in a changing environment. This model system paves the way for developing antiproliferative strategies that target both resistance and tolerance mechanisms to prevent relapse.


title: The genetic population structure of Lake Tanganyika's Lates species flock, an endemic radiation of pelagic top predators

abstract: Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species--particularly that of L. mariae--which may be important for conservation and management of this culturally and economically important clade of fish.

category: evolutionary biology


title: Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

abstract:
IntroductionBiomedical research has grown increasingly cooperative, with several large consortia compiling and sharing epigenomic data. Since data are typically preprocessed by consortia prior to distribution, the implementation of new pipelines can lead to different versions of the same dataset. Analytic frameworks also constantly evolve to incorporate cutting-edge methods and shifting best practices. However, it remains unknown how differences in data and analytic versions alter the results of epigenome-wide analyses, which has broad implications for the replicability of epigenetic associations. Thus, we assessed the impact of these changes using a subsample of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort.

MethodsWe analyzed two versions of DNA methylation data, processed using separate preprocessing and analytic pipelines, to examine associations between childhood adversity and prenatal smoking exposure on DNA methylation at age 7. We performed two sets of analyses: (1) epigenome-wide association studies (EWAS); (2) Structured Life Course Modeling Approach (SLCMA), a two-stage method that models time-dependent effects. We also compared results from the SLCMA using more recent methodological recommendations.

ResultsDifferences between ALSPAC data versions impacted both EWAS and SLCMA analyses, yielding different sets of associations at conventional p-value thresholds. However, the magnitude and direction of associations was generally consistent between data versions, regardless of significance thresholds. Updating the SLCMA analytic version similarly altered top associations, but time-dependent effects remained concordant.

ConclusionsChanges to data and analytic versions influenced the results of epigenome-wide studies, particularly when using p-value thresholds as reference points for successful replication and stability.


title: Generalization of Cortical Multivariate Genome-Wide Associations Within and Across Samples

abstract: Genome-Wide Association studies have typically been limited to single phenotypes, given that high dimensional phenotypes incur a large multiple comparisons burden: ~1 million tests across the genome times the number of phenotypes. Recent work demonstrates that a Multivariate Omnibus Statistic Test (MOSTest) is well powered to discover genomic effects distributed across multiple phenotypes. Applied to cortical brain MRI morphology measures, MOSTest has resulted in a drastic improvement in power to discover loci when compared to established approaches (min-P). One question that arises is how well these discovered loci replicate in independent data. Here we perform 10 times cross validation within 35,644 individuals from UK Biobank for imaging measures of cortical area, thickness and sulcal depth (>1,000 dimensionality for each). By deploying a replication method that aggregates discovered effects distributed across multiple phenotypes, termed PolyVertex Score (PVS), we demonstrate a higher replication yield and comparable replication rate of discovered loci for MOSTest (# replicated loci: 348-845, replication rate: 94-95%) in independent data when compared with the established min-P approach (# replicated loci: 31-68, replication rate: 65-80%). An out-of-sample replication of discovered loci was conducted with a sample of 8,336 individuals from the Adolescent Brain Cognitive Development(R) (ABCD) study, who are on average 50 years younger than UK Biobank individuals. We observe a higher replication yield and comparable replication rate of MOSTest compared to min-P. This finding underscores the importance of using well-powered multivariate techniques for both discovery and replication of high dimensional phenotypes in Genome-Wide Association studies.


title: Generalization of Cortical MOSTest Genome-Wide Associations Within and Across Samples


title: PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum

abstract: Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. With the recent accumulation of RNA-seq data sets, the construction of RNA-seq-based GCNs has now become possible. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to humanity and contribute significantly to our food supply. However, co-expression network tools for these plants are outdated or lacking. In this study, we constructed global GCNs for barley and sorghum using 500 and 774 RNA-seq data sets, respectively. In addition, we curated the meta-information of these RNA-seq data sets and categorized them into four main tissue types, leaf, root, shoot, and flower/seed, and built tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus, offering an immersive environment for the exploration and visualization of gene expressions and co-expressions of barley and sorghum at the global and tissue-specific levels. PlantNexus is freely available at https://plantnexus.ohio.edu/.


title: CONET: Copy number event tree model of evolutionary tumor history for single-cell data

abstract: Copy number alterations constitute important phenomena in tumor evolution. Whole genome single cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an efficient MCMC procedure to search the space of possible model structures and parameters and utilizes both per-bin and per-breakpoint data. We introduce a range of model priors and penalties for efficient regularization. CONET achieves excellent performance on simulated data and for 260 cells from xenograft breast cancer sample.


title: Image-based Motion Artifact Reduction on Liver Dynamic Contrast Enhanced MRI

abstract: Liver MRI images often suffer degraded quality from ghosting or blurring artifact caused by patient respiratory or bulk motion. In this study, we developed a two-stage deep learning model to reduce motion artifact on dynamic contrast enhanced (DCE) liver MRIs. The stage-I network utilized a deep residual network with a densely connected multi-resolution block (DRN-DCMB) network to remove the majority of motion artifacts. The stage-II network applied the perceptual loss to preserve image structural features by updating the parameters of the stage-I network via backpropagation. The stage-I network was trained using small image patches simulated with five types of motion, i.e., rotational, sinusoidal, random, elastic deformation and through-plane, to mimic actual liver motion patterns. The stage-II network training used full-size images with the same types of motion as the stage-I network. The motion reduction deep learning model was testing using simulated motion images and images with real motion artifacts. The resulted images after two-stage processing demonstrated substantially reduced motion artifacts while preserved anatomic details without image blurriness. This model outperformed existing methods of motion reduction artifact on liver DCE-MRI.


title: PINAWeb: A web-based tool for the comparison of Protein-Protein Interaction Networks Aligners

abstract:
MotivationSeveral protein-protein interaction networks (PPIN) aligners have been developed during the last 15 years. One of their goals is to help the functional annotation of proteins and the prediction of protein-protein interactions. A correct aligner must preserve the networks topology as well as the biological coherence. However, this is a trade-off that is hard to achieve. In addition, most aligners require a considerable effort to use in practice and many researchers must choose an aligner without the opportunity to previously compare the performance of different aligners.

ResultsWe developed PINAWeb, a user-friendly web-based tool to obtain and compare the results produced by the aligners: AligNet, HubAlign, L-GRAAL, PINALOG and SPINAL. PPINs can be uploaded either from the STRING database or from a user database. The source code of PINAWeb is freely available on GitHub to enable researchers to add other aligners, network databases or alignment score metrics. In addition, PINAWeb provides a report with the analysis for every alignment in terms of topological and functional information scores, as well as the visualization of the alignments comparison (agreement/differences) when more than one aligner are considered.

Availabilityhttps://bioinfo.uib.es/~recerca/PINAWeb


title: Jasmonate inhibits adventitious root initiation through transcriptional repression of CKX1 and activation of RAP2.6L transcription factor in Arabidopsis

abstract: Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI


title: The cannabinoid agonist CB-13 produces peripherally mediated analgesia in mice but elicits tolerance and signs of CNS activity with repeated dosing

abstract: Activation of cannabinoid receptor type 1 (CB1) produces analgesia in a variety of preclinical models of pain; however, engagement of central CB1 receptors is accompanied by unwanted side effects, such as tolerance and dependence. Efforts to develop novel analgesics have focused on targeting peripheral CB1 receptors to circumvent central CB1-related side effects. In the present study, we evaluated the effects of acute and repeated dosing with the peripherally selective CB1-preferring agonist CB-13 on nociception and central CB1-related phenotypes in an inflammatory model of pain in mice. We also evaluated cellular mechanisms underlying CB-13-induced antinociception in vitro using cultured mouse dorsal root ganglion (DRG) neurons. CB-13 reduced inflammation-induced mechanical allodynia in a peripheral CB1 receptor-dependent manner and relieved inflammatory thermal hyperalgesia. In cultured mouse DRG neurons, CB-13 reduced TRPV1 sensitization and neuronal hyperexcitability induced by the inflammatory mediator prostaglandin E2, providing potential mechanistic explanations for the analgesic actions of peripheral CB1 receptor activation. With acute dosing, phenotypes associated with central CB1 receptor activation occurred only at a dose of CB-13 approximately 10-fold the ED50 for reducing allodynia. Strikingly, repeated dosing resulted in both analgesic tolerance and CB1 receptor dependence, even at a dose that did not produce central CB1 receptor-mediated phenotypes on acute dosing. This suggests repeated CB-13 dosing leads to increased CNS exposure and unwanted engagement of central CB1 receptors. Thus, caution is warranted regarding therapeutic use of CB-13 with the goal of avoiding CNS side effects. Nonetheless, the clear analgesic effect of acute peripheral CB1 receptor activation suggests that peripherally restricted cannabinoids are a viable target for novel analgesic development.


title: Annual dynamics of Zymoseptoria tritici populations in wheat cultivar mixtures: a compromise between the efficiency and durability of a recently broken-down resistance gene?

abstract: Cultivar mixtures slow polycyclic epidemics but may also affect the evolution of pathogen populations by diversifying the selection pressures exerted by their plant hosts at field scale. We compared the dynamics of natural populations of the fungal pathogen Zymoseptoria tritici in pure stands and in three binary mixtures of wheat cultivars (one susceptible cultivar and one cultivar carrying the recently broken-down Stb16q gene) over two annual field epidemics. We combined analyses of population  size based on disease severity, and of population  composition based on changes in the frequency of virulence against Stb16q in seedling assays with more than 3000 strains. Disease reductions were observed in mixtures late in the epidemic, at the whole canopy scale and on both cultivars, suggesting the existence of a reciprocal  protective effect. The three cultivar proportions in the mixtures (0.25, 0.5 and 0.75) modulated the decrease in (i) the size of the pathogen population relative to the two pure stands, (ii) the size of the virulent subpopulation, and (iii) the frequency of virulence relative to the pure stand of the cultivar carrying Stb16q. Our findings suggest that optimal proportions may differ slightly between the three indicators considered. We argued potential trade-offs that should be taken into account when deploying a resistance gene in cultivar mixtures: between the dual objectives  efficacy and  durability, and between the  size and  frequency of the virulent subpopulation. Based on current knowledge, it remains unclear whether virulent subpopulation size or frequency has the largest influence on interepidemic virulence transmission.


title: An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes

abstract: Penelope-like elements (PLEs) are an enigmatic clade of retroelements whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical EN+ PLEs encodes RT and a C-terminal GIY-YIG endonuclease (EN) that enables intrachromosomal integration, while EN-PLEs lack endonuclease and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, while EN-PLEs occur in several kingdoms. Here we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY-YIG endonuclease is linked to a C-terminal RT by a short domain with a characteristic Zn-finger-like motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune and Nematis clades, and show insertion bias for microsatellites, but lack hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiad clade is found in numerous invertebrate phyla, where they can reach tens of thousands of copies per genome. Naiads in spiders and clams independently evolved to encode selenoproteins. Chlamys, which lack the CCHH motif universal to PLE endonucleases, occur in green algae, spike mosses (targeting ribosomal DNA) and the slime mold Physarum. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain, strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, distribution and abundance is comparable to non-LTR and LTR-retrotransposons.

category: molecular biology


title: Blebs Promote Cell Survival by Assembling Oncogenic Signaling Hubs

abstract:
For most human cells, anchorage is a key necessity for survival. Cell-substrate adhesion activates diverse signaling pathways, without which cells undergo anoikis - a form of programmed cell death1. Acquisition of anoikis resistance is a pivotal step in cancer disease progression, as metastasizing cancer cells often lose firm attachment to surrounding tissue2-5. In these poorly attached states, cells often adopt rounded morphologies and form small hemispherical plasma membrane protrusions called blebs6-13. Bleb function has long been investigated in the context of amoeboid migration but is far less deeply examined in other scenarios14-19. Here we show by quantitative subcellular 3D imaging and manipulation of cell morphological states that blebbing triggers the formation of membrane-proximal signaling hubs that initiate signaling cascades leading to anoikis resistance. Specifically, in melanoma cells we discovered that blebbing generates plasma membrane contours that recruit curvature sensing septin proteins, which scaffold constitutively active mutant NRAS and effectors, driving the upregulation of ERK and PI3K signaling. Inhibition of blebs or septins has little effect on the survival of well-adhered cells, but in detached cells causes NRAS mislocalization, reduced MAPK and PI3K signaling, and ultimately, death. These data unveil an unanticipated morphological requirement for mutant NRAS to operate as an effective oncoprotein, suggesting novel clinical targets for the treatment of NRAS-driven melanoma. Furthermore, they define an unforeseen role for blebs as potent signaling organelles capable of integrating myriad cellular information flows into concerted signaling responses, in this case granting robust anoikis resistance.

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title: A gene duplication of a septin provides a developmentally-regulated filament length control mechanism

abstract: Septins are a family of conserved filament-forming proteins that function in a variety of processes including cell cycle progression, cell morphogenesis and autophagy. Despite their conservation from yeast to humans, the number of septin genes within an organism varies and higher eukaryotes express many septin isoforms due to alternative splicing. It is unclear how variability in septin complex composition influences the biophysical properties of septin polymers. Here we report that a complex duplication event within the CDC11 locus in the fungus, Ashbya gossypii, gave rise to two similar, but distinct Cdc11 proteins, Cdc11a and Cdc1b. CDC11b transcription is developmentally regulated producing different ratios of Cdc11a and b complexes during Ashbyas lifecycle. Moreover, deletion of either CDC11a or CDC11b results in distinct cell polarity defects. Remarkably, despite substantial identity in amino acid sequence, Cdc11a and Cdc11b complexes have distinct biophysical properties with clear filament length and membrane-binding ability differences. Thus, septin subunit composition has functional consequences for filament properties and such functional plasticity can be exploited for distinct biophysical properties and cell functions.


title: Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2

abstract: Cell cycle gene expression programs fuel proliferation and are dysregulated in many cancers. The retinoblastoma-family proteins, RB, p130/RBL2 and p107/RBL1, coordinately repress cell cycle gene expression, inhibiting proliferation and suppressing tumorigenesis. Ubiquitin-dependent protein degradation is essential to cell cycle control, and numerous proliferative regulators, tumor suppressors, and oncoproteins are ubiquitinated. However, little is known about the role of ubiquitin signaling in controlling RB-family proteins. A systems genetics analysis of several hundred CRISPR/Cas9 loss-of-function screens suggested the potential regulation of the RB-network by cyclin F, a substrate recognition receptor for the SCF family of E3 ligases. We demonstrate that RBL2/p130 is a direct substrate of SCFcyclin F. We map a cyclin F regulatory site to a flexible linker in the p130 pocket domain, and show that this site mediates binding, stability, and ubiquitination. Expression of a non-degradable p130 represses cell cycle gene expression and strongly reduces proliferation. These data suggest that SCFcyclin F plays a key role in the CDK-RB network and raises the possibility that aberrant p130 degradation could dysregulate the cell cycle in human cancers.


title: Homologous locus pairing is a transient, diffusion-mediated process in meiotic prophase

abstract:
The pairing of homologous chromosomes (homologs) in meiosis is essential for distributing the correct numbers of chromosomes into haploid gametes. In budding yeast, pairing depends on the formation of 150-200 Spo11-mediated double-strand breaks (DSBs) that are distributed among 16 homolog pairs, but it is not known if all, or only a subset of these DSBs, contribute to the close juxtaposition of homologs. Having established a system to measure the position of fluorescently tagged chromosomal loci in 3D space over time, we analyzed locus trajectories to determine how frequently, and how long, loci spend colocalized or apart. Continuous imaging revealed highly heterogeneous cell-to-cell behavior of foci, with the majority of cells exhibiting a "mixed" phenotype where foci move into and out of proximity, even at late stages of prophase, suggesting that the axial structures of the synaptonemal complex may be more dynamic than anticipated. The observed plateaus of the mean-squared change in distance (MSCD) between foci informed the development of a biophysical model of two diffusing polymers that captures the loss of centromere linkages as cells enter meiosis, nuclear confinement, and the formation of Spo11-dependent linkages. The predicted number of linkages per chromosome in our theoretical model closely approximates the small number (~2-4) of estimated synapsis-initiation sites, suggesting that excess DSBs have negligible effects on the overall juxtaposition of homologs. These insights into the dynamic in-terchromosomal behavior displayed during homolog pairing demonstrate the power of combining time-resolved in vivo analysis with modeling at the granular level.

Significance StatementEssential for sexual reproduction, meiosis is a specialized cell division required for the production of haploid gametes. Critical to this process is the pairing, recombination, and segregation of homologous chromosomes (homologs). While pairing and recombination are linked, it is not known how many linkages are sufficient to hold homologs in proximity. Here, we reveal that random diffusion and the placement of a small number of linkages are sufficient to establish the apparent "pairing" of homologs. We also show that colocalization between any two loci is more dynamic than anticipated. Our study is the first to provide observations of live interchromosomal dynamics during meiosis and illustrates the power of combining single-cell measurements with theoretical polymer modeling.


title: Diffusion and distal linkages govern interchromosomal dynamics during meiotic prophase

category: biophysics


title: Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome

abstract:
Short tandem repeat (STR) instability is causally linked to pathologic transcriptional silencing in a subset of repeat expansion disorders. In fragile X syndrome (FXS), instability of a single CGG STR tract is thought to repress FMR1 via local DNA methylation. Here, we report the acquisition of more than ten Megabase-sized H3K9me3 domains in FXS, including a 5-8 Megabase block around FMR1. Distal H3K9me3 domains encompass synaptic genes with STR instability, and spatially co-localize in trans concurrently with FMR1 CGG expansion and the dissolution of TADs. CRISPR engineering of mutation-length FMR1 CGG to normal-length preserves heterochromatin, whereas cut-out to pre-mutation-length attenuates a subset of H3K9me3 domains. Overexpression of a pre-mutation-length CGG de-represses both FMR1 and distal heterochromatinized genes, indicating that long-range H3K9me3-mediated silencing is exquisitely sensitive to STR length. Together, our data uncover a genome-wide surveillance mechanism by which STR tracts spatially communicate over vast distances to heterochromatinize the pathologically unstable genome in FXS.

One-Sentence SummaryHeterochromatinization of distal synaptic genes with repeat instability in fragile X is reversible by overexpression of a pre-mutation length CGG tract.


title: A Computational and Biochemical Study of -1 Ribosomal Frameshifting in Human mRNAs

abstract: -1 programmed ribosomal frameshifting (-1 PRF) is a translational recoding mechanism used by many viral and cellular mRNAs. -1 PRF occurs at a heptanucleotide slippery sequence and is stimulated by a downstream RNA structure, most often in the form of a pseudoknot. The utilization of -1 PRF to produce proteins encoded by the -1 reading frame is wide-spread in RNA viruses, but relatively rare in cellular mRNAs. In human, only three such cases of -1 PRF events have been reported, all involving retroviral-like genes and protein products. To evaluate the extent of -1 PRF utilization in the human transcriptome, we have developed a computational scheme for identifying putative pseudoknot-dependent -1 PRF events and applied the method to a collection of 43,191 human mRNAs in the NCBI RefSeq database. In addition to the three reported cases, our study identified more than two dozen putative -1 PRF cases. The genes involved in these cases are genuine cellular genes without a viral origin. Moreover, in more than half of these cases, the frameshift site locates far upstream (>250 nt) from the stop codon of the 0 reading frame, which is nonviral-like. Using dual luciferase assays in HEK293T cells, we confirmed that the -1 PRF signals in the mRNAs of CDK5R2 and SEMA6C are functional in inducing efficient frameshifting. Our findings have significant implications in expanding the repertoire of the -1 PRF phenomenon and the protein-coding capacity of the human transcriptome.

category: biochemistry


title: Exquisite Sensitivity to Dual BRG1/BRM ATPase Inhibitors Reveals Broad SWI/SNF Dependencies in Acute Myeloid Leukemia

abstract: Various subunits of mammalian SWI/SNF chromatin remodeling complexes display loss-of-function mutations characteristic of tumor suppressors in different cancers, but an additional role for SWI/SNF supporting cell survival in distinct cancer contexts is emerging. In particular, genetic dependence on the catalytic subunit BRG1/SMARCA4 has been observed in acute myeloid leukemia (AML), yet the feasibility of direct therapeutic targeting of SWI/SNF catalytic activity in leukemia remains unknown. Here, we evaluated the activity of dual BRG1/BRM ATPase inhibitors across a genetically diverse panel of cancer cell lines and observed that hematopoietic cancer cell lines were among the most sensitive compared to other lineages. This result was striking in comparison to data from pooled short hairpin RNA screens, which showed that only a subset of leukemia cell lines display sensitivity to BRG1 knockdown. We demonstrate that combined genetic knockdown of BRG1 and BRM is required to recapitulate the effects of dual inhibitors, suggesting that SWI/SNF dependency in human leukemia extends beyond a predominantly BRG1-driven mechanism. Through gene expression and chromatin accessibility studies, we show that the dual inhibitors act at genomic loci associated with oncogenic transcription factors, and observe a downregulation of leukemic pathway genes including MYC, a well-established target of BRG1 activity in AML. Overall, small molecule inhibition of BRG1/BRM induced common transcriptional responses across leukemia models resulting in a spectrum of cellular phenotypes. Our studies reveal the breadth of SWI/SNF dependency and support targeting SWI/SNF catalytic function as a potential therapeutic strategy in AML.

category: cancer biology


title: A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis

abstract: The OsTIR1/auxin-inducible degron (AID) system allows "on demand" selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. This new tool paves the way to studying the differential roles that target proteins may have in specific phases of the cell cycle.

category: synthetic biology


title: RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair

abstract: R-loops, consisting of ssDNA and DNA-RNA hybrids, are potentially vulnerable unless they are appropriately processed. Recent evidence suggests that R-loops can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. Yet, how the vulnerability of R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops and chromosome translocations and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end-joining dependent on BRCA1, Pol{theta}, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.


title: Protein Charge Neutralization is the Proximate Driver Dynamically Tuning a Nanoscale Bragg Reflector

abstract: Reflectin is a cationic, block copolymeric protein that mediates the dynamic fine-tuning of color and brightness of light reflected from nanostructured Bragg reflectors in iridocyte skin cells of squids. In vivo, neuronally activated phosphorylation of reflectin triggers its assembly, driving osmotic dehydration of the membrane-bounded Bragg lamellae containing the protein to simultaneously shrink the lamellar thickness and spacing while increasing its refractive index contrast, thus tuning the wavelength and increasing the brightness of reflectance. In vitro, we show that reduction in repulsive net charge of the purified, recombinant reflectin - either (for the first time) by generalized anionic screening with salt, or by pH titration - drives a finely tuned, precisely calibrated increase in size of the resulting multimeric assemblies. The calculated effects of phosphorylation in vivo are consistent with these effects observed in vitro. X-ray scattering analyses confirm the sphericity, size and low polydispersity of the assemblies. Precise proportionality between assembly size and charge-neutralization is enabled by the demonstrated rapid dynamic arrest of multimer growth. The resulting stability of reflectin assemblies with time ensures reciprocally precise control of the particle number concentration, thereby encoding a precise calibration between the extent of neuronal signaling, osmotic pressure, and the resulting optical changes. The results presented here strongly suggest that it is charge neutralization, rather than any change in aromatic content, that is the proximate driver of assembly, fine-tuning a colligative property-based nanostructured biological machine. A physical mechanism is proposed.


title: Quorum sensing signals from epibiont mediate the induction of bioactive peptides in mat-forming cyanobacteria Nostoc

abstract:
The regulation of oligopeptides production is essential in understanding their ecological role in complex microbial communities including harmful cyanobacterial blooms. The role of chemical communication between the cyanobacterium and the microbial community harboured as epibionts within its phycosphere is at an initial stage of research and little is understood about its specificity. Herein, we present insight into the role of a bacterial epibiont in regulating production of cyanobacterial oligopeptides microviridins, well-known elastase inhibitors with presumed anti-grazing effects, in an ecologically important cyanobacterial genus Nostoc. Heterologous expression and identification of specific signal molecules from the epibiont suggest the role of a quorum sensing-based interaction. Further, physiological experiments show an increase in microviridin production without affecting cyanobacterial growth and photosynthetic activity. Simultaneously, oligopeptides presenting a selective inhibition pattern provide support for their specific function in response to the presence of cohabitant epibionts. Thus, the chemical interaction revealed in our study provides an example of an interspecies signalling pathway monitoring the bacterial flora around the cyanobacterial filaments and induction of intrinsic species-specific metabolic responses.

IMPORTANCEThe regulation of cyanopeptide production beyond microcystin is essential to understand their ecological role in complex microbial communities, e.g. harmful cyanobacterial blooms. The role of chemical communication between the cyanobacterium and the epibionts within its phycosphere is at an initial stage of research and little is understood about its specificity. The frequency of cyanopeptide occurrence also demonstrates the need to understand the contribution of cyanobacterial peptides to the overall biological impact of cyanopeptides on aquatic organisms and vertebrates including humans. Our results shed light on the epibiont control of cyanopeptide production via quorum sensing mechanisms and we posit that such mechanisms may be widespread in natural cyanobacterial bloom community regulation.


title: Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India

abstract:
As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being constantly used to investigate its transmissions and evolution. In the backdrop of the global emergence of "variants of concern" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches was undertaken to identify possible new variants and gauge the fitness of current circulating strains.

Phylogenetic analysis revealed that the predominant clade in circulation was a distinct newly identified lineage B.1.617 possessing common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R, in the spike protein including within the receptor binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R and E484Q along with P681R in the furin cleavage site, revealed that these may possibly result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility. The same two RBD mutations indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Experimental validation against a wider panel of mAbs, sera from vaccinees and those that recovered from natural infection needs to be studied.

The emergence of such local variants through the accumulation of convergent mutations during the COVID-19 second wave needs to be further investigated for their public health impact in the rest of the country and its possibility of becoming a VOC.


title: WRKY33-mediated indole glucosinolate metabolic pathway confers host resistance against Alternaria brassicicola

abstract:
The tryptophan (Trp)-derived plant secondary metabolites, including camalexin, 4-hydroxy-indole-3-carbonylnitrile (4OH-ICN), and indole glucosinolate (IGS), show broad-spectrum antifungal activity. However, the upstream regulators of these metabolic pathways among different plant species in response to fungus infection are rarely studied. In this study, our results revealed a positive role of WRKY33 in host resistance to Alternaria brassicicola by directly regulating the transcription of genes involved in the biosynthesis and atypical hydrolysis of IGS both in Arabidopsis and Chinese kale. Indole-3-yl-methylglucosinolate (I3G) and 4-methoxyindole-3-yl-methylglucosinolate (4MI3G) are the main components of IGS. WRKY33 induces the expression of MYB51 and CYP83B1 which promotes the biosynthesis of I3G, the precursor of 4MI3G. Moreover, it also directly activates the expression of CYP81F2, IGMT1, and IGMT2 to drive side chain modification of I3G to produce 4MI3G, which is in turn hydrolyzed by PEN2. However, Chinese kale showed a more severe symptom than Arabidopsis when infected by Alternaria brassicicola. Comparative analyses of the origin and evolution of Trp-metabolism indicate that the loss of camalexin biosynthesis in Brassica crops during evolution might attenuate the resistance of crops to Alternaria brassicicola. As a result, IGS metabolic pathway mediated by WRKY33 becomes essential for Chinese kale to deter Alternaria brassicicola. Our results highlight the differential regulation of Trp-derived camalexin and IGS biosynthetic pathways in plant immunity between Arabidopsis and Brassica crops.

One-sentence SummaryPathogen-responsive WRKY33 directly regulates indole glucosinolates biosynthesis and atypical hydrolysis, conferring to host resistance to Alternaria brassicicola in Arabidopsis and Brassica crops.


title: SAMBA controls the rate of cell division in maize development through APC/C interaction

abstract: SAMBA has been identified as a plant-specific regulator of the anaphase-promoting complex (APC/C) which controls unidirectional cell cycle progression in Arabidopsis, but so far its role was not studied in monocots. Here, the association of SAMBA with APC/C was shown to be conserved in maize. Two samba CRISPR alleles showed growth defects that aggravated with plant age such as dwarfed plants due to shortened upper leaf length, erect leaf architecture, and reduced leaf size due to an altered cell division rate and cell expansion. Despite the fact that in both alleles the frameshift occurred at the same position, the two alleles differed in the severity and developmental onset of the phenotypes, because samba-1 represented a knock-out allele, while translation re-initiation in samba-3 resulted in a truncated protein that was still able to interact with the APC/C and regulate its function, albeit with altered APC/C activity or efficiency. Our data are consistent with a dosage-dependent role for SAMBA to control developmental processes for which a change in growth rate is pivotal.


title: Afucosylated Plasmodium falciparum-specific IgG is induced by infection but not by subunit vaccination

abstract:
IgG specific for members of the Plasmodium falciparum erythrocyte membrane protein 1(PfEMP1) family, which mediates receptor- and tissue-specific sequestration of infected erythrocytes (IEs), is a central component of naturally acquired malaria immunity. PfEMP1-specific IgG is thought to protect via inhibition of IE sequestration, and through IgG-Fc Receptor (Fc{gamma}R) mediated phagocytosis and killing of antibody-opsonized IEs. The affinity of afucosylated IgG to Fc{gamma}RIIIa is elevated up to 40-fold compared to fucosylated IgG, resulting in enhanced antibody-dependent cellular cytotoxicity. Most IgG in plasma is fully fucosylated, but afucosylated IgG is elicited in response to enveloped viruses and to paternal alloantigens during pregnancy. Here we show that naturally acquired PfEMP1-specific IgG is likewise markedly afucosylated in a stable and exposure-dependent manner, and efficiently induces Fc{gamma}RIIIa-dependent natural killer (NK) cell degranulation. In contrast, immunization with a soluble subunit vaccine based on VAR2CSA-type PfEMP1 resulted in fully fucosylated specific IgG. These results have implications for understanding natural and vaccine-induced antibody-mediated protective immunity to malaria.

SummaryAfucosylated IgG has enhanced Fc-receptor affinity and functionality, and is formed specifically against membrane proteins of enveloped viruses. We show that this also applies to Plasmodium falciparum erythrocyte membrane-specific IgG induced by natural infection, but not by soluble PfEMP1 vaccination.

category: immunology


title: Dual adhesive unipolar polysaccharides synthesized by overlapping biosynthetic pathways in Agrobacterium tumefaciens

abstract:
Agrobacterium tumefaciens, is a member of the Alphaproteobacteria that pathogenizes plants, and associates with biotic and abiotic surfaces via a single cellular pole. A. tumefaciens produces the unipolar polysaccharide (UPP) at the site of surface contact. UPP production is normally surface-contact inducible, but elevated levels of the second messenger cyclic diguanylate monophosphate (cdGMP) bypass this requirement. Multiple lines of evidence suggest that the UPP has a central polysaccharide component. Using an A. tumefaciens derivative with elevated cdGMP and mutationally disabled for other dispensable polysaccharides, a series of related genetic screens have identified a large number of genes involved in UPP biosynthesis, most of which are Wzx-Wzy-type polysaccharide biosynthetic components. Extensive analyses of UPP production in these mutants have revealed that the UPP is comprised of two genetically, chemically and spatially discrete forms of polysaccharide, and that each requires a specific Wzy-type polymerase. Other important biosynthetic, processing and regulatory functions for UPP production are also revealed, some of which are common to both polysaccharides, and a subset of which are specific to each species. Many of the UPP genes identified are conserved among diverse rhizobia, whereas others are more lineage specific.

Plain language summaryBacteria attach to a wide variety of surfaces including host tissues, via externalized structures described as adhesins. We define a large set of genes involved in synthesis of a complex unipolar adhesin comprised of two distinct polysaccharides, that is required for surface attachment by the plant-associated pathogen Agrobacterium tumefaciens.

category: microbiology