title: A Systematic Strategy for Identifying Causal Single Nucleotide Polymorphisms and Their Target Genes on Juvenile Arthritis Risk Haplotypes

abstract:
IntroductionAlthough genome-wide association studies (GWAS) multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes.

MethodsWe used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180 bp oligonucleotide reporters ("oligos") in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve >20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs.

ResultsWe identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total = 84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants.

ConclusionUsing MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.


title: Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan

abstract: Metabolism is fundamentally intertwined with the ageing process. We here report that a key determinant of cellular lifespan is not only nutrient supply and intracellular metabolism, but also metabolite exchange interactions that occur between cells. Studying chronological ageing in yeast, we observed that metabolites exported by young, exponentially growing, cells are re- imported during the stationary phase when cells age chronologically, indicating the existence of cross-generational metabolic interactions. We then used self-establishing metabolically cooperating communities (SeMeCos) to boost cell-cell metabolic interactions and observed a significant lifespan extension. A search for the underlying mechanisms, coupling SeMeCos, metabolic profiling, proteomics and genome-scale metabolic modelling, attributed a specific role to methionine consumer cells. These cells were enriched over time, adopted glycolytic metabolism and increased export of protective metabolites. Glycerol, in particular, accumulated in the communal metabolic environment and extended the lifespan of all cells in the community in a paracrine fashion. Our results hence establish metabolite exchange interactions as a determinant of the ageing process and show that metabolically cooperating cells shape their metabolic environment to achieve lifespan extension.

category: biochemistry


title: Promising Antimalarials targeting Apicoplast DNA Polymerase from Plasmodium falciparum

abstract: Malaria is caused by the parasite Plasmodium falciparum, which contains an essential non-photosynthetic plastid called the apicoplast. A single DNA polymerase, apPOL, is targeted to the apicoplast, where it replicates and repairs the genome. apPOL has no direct orthologs in mammals and is considered a promising drug target for the treatment and/or prevention of malaria. We previously reported screening the Malaria Box to identify MMV666123 as an inhibitor of apPOL. Herein we extend our studies and report structure-activity relationships for MMV666123 and identify key structural motifs necessary for inhibition. Although attempts to crystallize apPOL with the inhibitor were not fruitful, kinetic analysis and crystal structure determinations of WT and mutant apo-enzymes, facilitated model building and provided insights into the putative inhibitor binding site. Our results validate apPOL as an antimalarial target and provide an avenue for the design of high potency, specific inhibitors of apPOL and other A-family DNA polymerases.


title: Intermittent Fasting Activates AMP-Kinase to Restructure Right Ventricular Lipid Metabolism and Microtubules in Rodent Pulmonary Arterial Hypertension

abstract: Intermittent fasting (IF) extends lifespan via pleotropic mechanisms, but one important molecular mediator of the beneficial effects of IF is AMP-kinase (AMPK). AMPK enhances lipid metabolism and modulates microtubule dynamics. Dysregulation of these two molecular pathways causes right ventricular (RV) failure in pulmonary arterial hypertension (PAH). In rodent PAH, IF activates RV AMPK, which restores mitochondrial and peroxisomal density and restructures mitochondrial and peroxisomal lipid metabolism protein regulation. In addition, IF increases electron transport chain (ETC) protein abundance and activity in the RV. Echocardiographic and hemodynamic measures of RV function are positively associated with fatty acid oxidation and ETC protein levels in correlational heatmapping analyses. IF also combats heightened microtubule density, which normalizes t-tubule structure. In summation, we demonstrate IF-mediated AMPK signaling counteracts two key molecular drivers of RV failure. Thus, IF may be a novel treatment approach for RV dysfunction, a currently untreatable and lethal consequence of PAH.


title: A short ERAP2 that binds IRAP is expressed in macrophages independently from gene variation

abstract: The M1 zinc metalloproteases ERAP1, ERAP2 and IRAP play a role in HLA-I antigen presentation by refining the peptidome either in the ER (ERAP1 and ERAP2) or in the endosomes (IRAP). They have been also entrusted with other, although less defined, functions such as the regulation of the angiotensin system and blood pressure. In humans, ERAP1 and IRAP are commonly expressed. ERAP2 instead has evolved under balancing selection that maintains two haplotypes one of which undergoing RNA splicing leading to nonsense-mediated decay and loss of protein. Hence, likewise in rodents in which the ERAP2 gene is missing, about a quarter of the human population does not express ERAP2. We report here that macrophages, but not monocytes or other mononuclear blood cells, express and secrete an ERAP2 shorter form independently from the haplotype. The generation of this "short" ERAP2 is due to an autocatalytic cleavage within a distinctive structural motif and requires an acidic microenvironment. Remarkably, ERAP2 "short" binds IRAP and the two molecules are co-expressed in the endosomes as well as in the cell membrane. Of note, the same phenomenon could be observed in some cancer cells. These data prompt to reconsider the role of ERAP2 which might have been maintained in humans because fulfilling a relevant function as "short" form in specialized cells.


title: An affinity-matured DLL4 ligand for broad-spectrum activation and inhibition of Notch signaling

abstract: The Notch pathway regulates cell fate decisions and is an emerging target for regenerative and cancer therapies. Recombinant Notch ligands are attractive candidates for modulating Notch signaling; however, their intrinsically low receptor-binding affinity restricts their utility in biomedical applications. To overcome this limitation, we evolved variants of the ligand Delta-like 4 (DLL4) with enhanced affinity and cross-reactivity. A consensus variant with maximized binding affinity, DeltaMAX, engages human and murine Notch receptors with 500- to 1000-fold increased affinity compared to wild-type human DLL4. DeltaMAX also potently activates human Notch in plate-bound, bead-bound, and cellular formats. When administered as a soluble decoy, DeltaMAX inhibits Notch activation in response to either Delta-like (DLL) or Jagged (Jag) ligands, highlighting its utility as both an agonist and antagonist. Finally, we demonstrate that DeltaMAX stimulates increased proliferation and expression of effector mediators in primary activated human T cells. Taken together, our data defines DeltaMAX as a versatile biotechnological tool for broad-spectrum activation or inhibition of Notch signaling.

category: bioengineering


title: A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome

abstract: The central function of the large subunit of the ribosome is to catalyze peptide bond formation. This biochemical reaction is conducted at the peptidyl transferase center (PTC). Experimental evidence shows that the catalytic activity is affected by the electrostatic environment around the peptidyl transferase center. The electrostatic field originates from the particular 3-dimensional space distribution in the phosphate moieties of the 23S (archea and bacteria) or 28S (eukarya) rRNA of the large ribosomal subunit as well as the funnel shape of the cavity at its connection with the ribosome exit tunnel. Here, we set up a minimal geometrical model fitting the available x-ray solved structure of the ribonucleoproteic cavity around the catalytic center of the large subunit of the ribosome. The purpose of this phenomenological model is to estimate quantitatively the electrostatic potential and electric field that are experienced during the peptidyl transfer reaction. At least two reasons motivate the need for developing this quantification. First, we inquire whether the electric field in this particular catalytic environment, made only of nucleic acids, is of the same order of magnitude as the one prevailing in catalytic centers of the proteic enzymes counterparts. Second, the protein synthesis rate is dependent on the nature of the amino acid sequentially incorporated in the nascent chain. The activation energy of the catalytic reaction and its detailed kinetics are expected to be dependent on the mechanical work exerted on the amino acids by the electric field, especially when one of the four charged amino acid residues (R, K, E, D) is newly incorporated in the nascent chain. Physical values of the electric field will provide quantitative knowledge of mechanical work, activation energy and kinetics of the peptide bond formation catalysed by the ribosome.

category: biophysics


title: Nuclear lamina strain states revealed by intermolecular force biosensor

abstract: We developed an intramolecular FRET-based strain biosensor using nanobodies capable of measuring the mechanical strain of lamin filaments. Using this sensor, we were able to show that the nuclear lamina is subjected to significant strains. These strains are dependent on nuclear volume, actomyosin contractility, functional LINC complex, chromatin condensation state, cell cycle, and EMT. Overall, we demonstrate that nanobody-based approach allows construction of novel force biosensors for mechanobiology studies.


title: Surface interaction patches link non-specific binding and phase separation of antibodies

abstract: Non-specificity is a key challenge in the successful development of therapeutic antibodies. The tendency for non-specific binding in antibodies is often difficult to reduce via judicious design and, instead, it is necessary to rely on comprehensive screening campaigns. A better understanding of the molecular origins that drive antibody non-specificity is therefore highly desirable in order to prevent non-specific off-target binding. Here, we perform a systematic analysis of the impact of surface patch properties on antibody non-specificity using a designer antibody library as a model system and DNA as a non-specificity ligand. Using an in solution microfluidics approach, we discover patches of surface hydrogen bonding to be causative of the observed non-specificity under physiological salt conditions and suggest them to be a vital addition to the molecular origins of non-specificity. Moreover, we find that a change in formulation conditions leads to DNA-induced antibody liquid-liquid phase separation as a manifestation of antibody non-specificity. We show that this behaviour is driven by a cooperative electrostatic network assembly mechanism enabled by mutations that yield a positively charged surface patch. Together, our study provides a direct link between molecular binding events and macroscopic liquid-liquid phase separation. These findings highlight a delicate balance between surface interaction patches and their crucial role in conferring antibody non-specificity.


title: The CIpP activator, TR-57, is highly effective as a single agent and in combination with venetoclax against CLL cells in vitro.

abstract:
Despite advances in treatment, a significant proportion of patients with chronic lymphocytic leukaemia (CLL) will relapse with drug-resistant disease.

Recent studies demonstrate that the imipridones ONC-201 and ONC-212 and the more potent TR-compounds are effective against a range of different cancers, including acute myeloid leukaemia and tumours of the brain, breast, and prostate. These drugs induce cell death through inhibition of mitochondrial function and activation of the mitochondrial protease, caseinolytic protease (CIpP), and the unfolded protein response (UPR).

Here we demonstrate that a drug in this class, TR-57, has efficacy as a single agent and is synergistic with venetoclax against CLL cells cultured under in vitro conditions that mimic the tumour microenvironment. The inhibitory effects of TR-57 on cell survival, proliferation and migration were irrespective of poor-risk features, including aberrations of TP53. Changes in protein expression suggest the mechanisms of action of TR-57 and its synergy with venetoclax involve activation of the UPR, inhibition of the AKT and ERK1/2 pathways and a pro-apoptotic shift in expression of proteins of the BCL-2 family.

The study suggests TR-57, as a single agent and in combination with venetoclax, may represent an effective treatment option for CLL, including for patients with poor-risk disease.

category: cancer biology


title: SOYBEAN RESPONSE TO INITIAL STAGE OF Fusarium virguliforme INFECTION

abstract: Fusarium virguliforme causes the Sudden Death Syndrome, an important disease in soybean crops. In this work, we investigated the defensive response mechanisms in soybean root, at cell wall level, during F. virguliforme infection using an in vitro culture system. We measured total root lignin content by the acetyl bromide method and estimated the in-situ lignin and suberin deposition by confocal microscopy on local and systemic root tissues, i.e. adjacent and distant to the pathogen entry site respectively. Moreover, the expression dynamics of phenylalanine ammonia lyase (PAL), shikimate/quinate hydroxycinnamoyltransferase (HCT) and cinnamyl alcohol dehydrogenase (CAD) was evaluated by real-time quantitative PCR. The results showed that, although the most significant increment of lignin deposition was observed in the epidermal cells of local tissues, F. virguliforme also induced lignin deposition changes in a sistemic fashion. In fact, inoculated plants presented a higher deposition of lignin in hypodermis and cortex than the control ones, independently of the distance from the inoculum source, while suberin deposition was higher in local zones. Moreover, the gene expression analysis showed an up-regulation of PAL, HCT and CAD genes after the inoculation with the pathogen, which correlates with the cell wall modifications observed in the local tissues. The results presented here suggest that the increase in lignin and suberin deposition during soybean root/F. virguliforme interaction is probably a strategy not only to stop the pathogen entrance, but to provide the plant more time to prepare its defences as well.

category: plant biology


title: Global phylogeography of marine Synechococcus in coastal areas reveals strikingly different communities than in the open ocean

abstract: Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome dataset of the Ocean Sampling Day (June 21st 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study tackles the main differences between open-ocean and coastal communities worldwide.

category: microbiology


title: Incomplete bunyavirus particles contribute to within-host spread and between-host transmission

abstract: Bunyaviruses lack a specific mechanism to ensure the incorporation of a complete set of genome segments into each virion, explaining the generation of incomplete virus particles lacking one or more genome segments. Such incomplete virus particles, which may represent the majority of particles produced, are generally considered to interfere with virus infection and spread. Using the three-segmented Rift Valley fever virus as a model bunyavirus, we here show that two distinct incomplete virus particle populations that are unable to spread autonomously, are able to efficiently complement each other in both mammalian and insect cells following co-infection. We further show that incomplete virus particles are capable of co-infecting mosquitoes, resulting in the rescue of infectious virus that is able to disseminate to the mosquito salivary glands. Our findings reveal a significant role of incomplete particles in within-host spread and between-host transmission, reminiscent of the life cycle of multipartite viruses.


title: Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly

abstract:
The nucleosome remodeling complexes (CRs) SWI/SNF, RSC, and Ino80C cooperate in evicting or repositioning nucleosomes to produce nucleosome depleted regions (NDRs) at the promoters of many yeast genes induced by amino acid starvation. We analyzed mutants depleted of the catalytic subunits of these CRs for binding of transcriptional activator Gcn4 and recruitment of TATA-binding protein (TBP) during preinitiation complex (PIC) assembly. RSC and Ino80 were found to enhance Gcn4 binding to both UAS elements in NDRs upstream of promoters and to unconventional binding sites within nucleosome- occupied coding sequences; and SWI/SNF contributes to UAS binding when RSC is depleted. All three CRs are actively recruited by Gcn4 to most UAS elements and appear to enhance Gcn4 binding by reducing nucleosome occupancies at the binding motifs, indicating a positive regulatory loop. SWI/SNF acts unexpectedly in WT cells to prevent excessive Gcn4 binding at many UAS elements, indicating a dual mode of action that is modulated by the presence of RSC. RSC and SWI/SNF collaborate to enhance TBP recruitment at Gcn4 target genes, together with Ino80C, in a manner associated with nucleosome eviction at the TBP binding sites. Cooperation among the CRs in TBP recruitment is also evident at the highly transcribed ribosomal protein genes, while RSC and Ino80C act more broadly than SWI/SNF at the majority of other constitutively expressed genes to stimulate this step in PIC assembly. Our findings indicate a complex interplay among the CRs in evicting promoter nucleosomes to regulate activator binding and stimulate PIC assembly.

AUTHOR SUMMARYATP-dependent chromatin remodelers (CRs), including SWI/SNF and RSC in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes, and we recently implicated the CR Ino80C in this process as well. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently via evicting nucleosomes from the Gcn4 binding motifs. At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. The CRs in turn are recruited by Gcn4 to establish positive or negative feedback loops that control Gcn4 binding. The three CRs also cooperate to enhance TBP recruitment, again involving nucleosome depletion, at both Gcn4 target and highly expressed ribosomal protein genes, whereas only RSC and Ino80C act broadly throughout the genome to enhance this key step in preinitiation complex assembly. Our findings illuminate functional cooperation among multiple CRs in regulating activator binding and promoter activation.

category: molecular biology


title: Sizing up spotted lanternfly nymphs for instar determination and growth allometry

abstract: A major ongoing research effort seeks to understand the behavior, ecology and control of the spotted lanternfly (SLF) (Lycorma delicatula), a highly-invasive pest in the U.S. and South Korea. These insects undergo four nymphal stages (instars) before reaching adulthood, and appear to shift host plant preferences, feeding, dispersal and survival patterns, anti-predator behaviors, and response to traps and chemical controls, with each stage. However, categorizing SLF lifestage is challenging for the first three instars, which have the same coloration and shape, because no comprehensive allometric datasets exist. We present a dataset of body mass and length for SLF nymphs throughout a growing season and compare our results with published ranges of instar body lengths based on small samples. An ontogenetic allometric analysis found that SLF nymph body mass scales isometrically with body length (exponent c = 3.05 [2.95,3.15]). An analysis using two clustering methods also revealed that first through third instar body mass and length fell into distinct clusters (Dyars rule), supporting using these two metrics to stage nymphs during a single growing season. The ranges for 2nd and 3rd instars were not consistent between our results and those from earlier studies for diverse locations. Using previously-published data, we also found that tarsal claw and arolia (adhesive footpad) dimensions scale in proportion to body length and mass, respectively, indicating that adhesive ability does not decrease with age, as posited in some previous studies. Conversely, mouthpart dimensions do not correlate with body length, consistent with predictions that these features should reflect preferred host plant characteristics rather than body size. We suggest extending these methods to study how SLF instar development depends on factors such as hatch date, host plant, temperature, and geographic location, using citizen scientist networks to collect morphometric data for a wide range of locations and environmental conditions.

category: zoology


title: Alnustone inhibits Streptococcus pneumoniae virulence by targeting pneumolysin and sortase A

abstract: Streptococcus pneumoniae (S. pneumoniae) is a significant Gram-positive opportunistic pathogen responsible for a variety of lethal infections. This bacterium accounts for more deaths from diseases than any other single pathogen worldwide. Distinctively, these symptoms arise despite effective antibiotic therapy. This study unveiled a novel mechanism of resistance to S. pneumoniae infection by targeting pneumolysin (PLY) and sortase A (Srt A), the key virulence factors of S. pneumoniae. Through protein phenotype assays, we found alnustone to be a potent drug that inhibits both PLY and Srt A. Using a PLY-mediated hemolysis assay, we found that albumin can effectively reduce Srt A peptidase activity by blocking PLY oligomerization, thereby directly inhibiting PLY-expressing cytolysis. Co-incubation of S. pneumoniae D39 Srt A with small-molecule inhibitors reduces cell wall-bound Nan A (pneumococcal-anchored surface protein Srt A), inhibits biofilm formation, and significantly reduces biomass. But more interestingly, the protective effect of invasive pneumococcal disease (IPD) on murine streptococcus pneumoniae was further demonstrated. Our study proposes a detailed bacteriostatic mechanism of pneumococcal and highlights the major translational potential of targeting circulating PLY and Srt A to protect against pneumococcal infections. Our results suggest that the antiviral strategy of directly targeting PLY and Srt A with alnustone is a promising treatment option for Streptococcus pneumoniae and that alnustone can be used as an effective inhibitor of PLY and Srt A.


title: Algae community structure and relation to environmental factors in the Hulanhe Wetland, Northeast China

abstract: The distribution characteristic of algae community was evaluated in eight sampling sites based on a monthly survey during May to October 2020 and 2021 in the Hulanhe Wetland, Northeast China. Algae and water environmental factors including water temperature (T), pH, Conductivity (Cond.), biochemical oxygen demand (BOD), chemical oxygen demand (COD), total organic carbons (TOC), total phosphorus (TP) and nitrogen (TN) were investigated, and a total of 216 taxa were identified by microscope. The algae community was dominated by Bacillariophyta, Chlorophyta and Euglenophyta. Species such as Melosira granulate, Cyclotella meneghiniana, Navicula cryptocephala and Pandorina morum were the most common species. Significant difference of the algae composition and abundance were found in the different sampling sites. Species composition in H8 were different variously with other sites, provide a good chance for us to study the tolerance of the species, compared with other sites, several pollution indicator species were observed. According to canonical correspondence analysis (CCA), TN and TP were the main environmental factors affecting the distribution of algae. Furthermore, temperature and dissolved oxygen were also important to the algae community. It is suggested that the relationship between algae community and environmental factors can point to new directions in future studies on the water quality and habitat conditions in a wetland.

category: ecology


title: Distribution of Critical Areas for Ecological Conservation in Multiple Scenarios ---- Emphasizing the Impact of Human Activities

abstract: Determining critical ecological protected areas at the city (county) spatial scale is crucial for coordinating regional ecological environment management, control, and governance. It is a recognized consensus in academia that human activities significantly impact natural ecosystems. Many scholars ignore this point in the research process and only use several factors to characterize human influence. Therefore, this study takes Aksu City and Wensu County, important cities and towns in southern Xinjiang, as examples, focusing on the impact of human activities on the distribution of critical ecological protection areas. First, we simulated the range, intensity, and local natural conditions of human activities in the study area using geospatial data. We created corresponding resistance surfaces (human activity resistance surface and natural landscape resistance surface). We then assign different weights to the two resistance surfaces based on several possible scenarios, resulting in different synthetic resistance surfaces. Finally, we used the Linkage Mapper plugin to identify critical ecological reserves and compared several results. The results show that: Human activities have greatly interfered with the migration and dispersal of species, affecting the distribution of critical ecological reserves. The specific performance is that in the urban center area with high intensity of human activities, the number and location of the surrounding ecological corridors change significantly with the increase in the proportion of human activity resistance and the total area remains unchanged; As part of the ecological corridors, the ecological pinch points changes with the location of the corridor, and the whole area remains unchanged; The threshold range of the restoration value of ecological barrier points is reduced. The maximum value generated by the restoration of ecological barrier points is reduced, which shows that the restoration value of ecological barrier points decreases with increased human activities.


title: Female Zebrafish (Danio rerio) Demonstrate Stronger Preference for Established Shoals over Newly-Formed Shoals in the Three-Tank Open-Swim Preference Test

abstract: Zebrafish (Danio rerio) share a considerable amount of biological similarity with mammals, including identical or homologous gene expression pathways, neurotransmitters, hormones, and cellular receptors. Zebrafish also display complex social behaviors like shoaling and schooling, making them an attractive model for investigating normal social behavior as well as exploring impaired social function conditions such as autism spectrum disorders. Newly-formed and established shoals exhibit distinct behavior patterns and inter-member interactions that can convey the groups social stability. We used a three-chamber open-swim preference test to determine whether individual zebrafish show a preference for an established shoal over a newly-formed shoal. Results indicated that both sexes maintained greater proximity to arena zones nearest to the established shoal stimulus. In addition, we report the novel application of Shannon entropy to discover sex differences in systematicity of responses not revealed by unit-based measurements; male subjects spent more time investigating between the two shoals than female subjects. This novel technique using established versus newly-formed shoals can be used in future studies testing transgenics and pharmacological treatments that mimic autism spectrum disorder and other disorders that affect social interaction.

category: animal behavior and cognition


title: Gender-based disparities and biases in science: observational study of a virtual conference

abstract: Success in STEM (Science, Technology, Engineering, and Math) remains influenced by race, gender, and socioeconomic status. Here, we focus on the impact of gender on question-asking behavior during the 2021 JOBIM virtual conference (Journees Ouvertes en Biologie et Mathematiques). We gathered quantitative and qualitative data including: demographic information, question asking motivations, live observations and interviews of participants. Quantitative analyses include unprecedented figures such as the fraction of the audience identifying as LGBTQIA+ and an increased attendance of women in virtual conferences. Although parity was reached in the audience, women asked half as many questions as men. This under-representation persisted after accounting for seniority of the asker. Interviews of participants highlighted several barriers to oral expression encountered by women and gender minorities: negative reactions to their speech, discouragement to pursue a career in research, and gender discrimination/sexual harassment. Informed by the study, guidelines for conference organizers have been written.

category: scientific communication and education


title: The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

abstract: The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the genes numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

category: systems biology


title: Automated reconstruction of dendritic and axonal arbors reveals molecular correlates of neuroanatomy

abstract: Neuronal anatomy is central to the organization and function of brain cell types. However, anatomical variability within apparently homogeneous populations of cells can obscure such insights. Here, we report large-scale automation of arbor reconstruction on a dataset of 802 inhibitory neurons characterized using the Patch-seq method, which enables measurement of multiple properties from individual neurons, including local morphology and transcriptional signature. We demonstrate that these automated reconstructions can be used in the same manner as manual reconstructions to understand the relationship between many cellular properties used to define cell types. We uncover molecular correlates of laminar innervation on multiple molecularly defined neuronal subclasses and types. In particular, our results reveal molecular correlates of the variability in Layer 1 (L1) innervation even in a transcriptomically defined subpopulation of Martinotti cells in the adult mouse neocortex.

category: neuroscience


title: Skeletal Muscle Proteostasis Promotes Central Nervous System Rejuvenation and Reduces Neuroinflammation during Aging and Neurodegenerative Disease

abstract: Skeletal muscle has recently arisen as a novel regulator of Central Nervous System (CNS) function and aging, secreting bioactive molecules known as myokines with proteostasis and metabolism-modifying functions in targeted tissues, including the CNS. Here we report the generation of a novel transgenic mouse with enhanced skeletal muscle proteostasis via moderate overexpression of master regulator of proteostasis and lysosomal function Transcription Factor E-B. We have discovered that the resulting enhanced muscle proteostasis function significantly ameliorates proteotoxicity, reduces neuroinflammation and promotes transcriptional remodeling of the aging CNS, preserving cognition and memory in aging mice. Enhancing skeletal muscle proteostasis also reduces neuroinflammation and accumulation of tau-associated pathological hallmarks in a mouse model of tau pathology. Our results implicate maintenance of skeletal muscle proteostasis throughout aging to direct regulations of the aging CNS metabolism and function, and suggest that skeletal-muscle originating factors may act as novel therapeutic targets against age-associated neurodegenerative diseases.


title: Reconstitution of Kinetochore and Microtubule Dynamics Reveals a Role for a Kinesin-8 in Establishing End-on Attachments

abstract: During mitosis, individual microtubules make attachments to chromosomes via a specialized protein complex called the kinetochore to faithfully segregate the chromosomes to daughter cells. Translocation of kinetochores on the lateral surface of the microtubule has been proposed to contribute to high fidelity chromosome capture and alignment at the mitotic midzone, but has been difficult to observe in vivo because of spatial and temporal constraints. To overcome these barriers, we used total internal reflection fluorescence (TIRF) microscopy to track the interactions between endogenously tagged tubulin, kinetochore proteins, and other microtubule-associated proteins in lysates from metaphase-arrested Saccharomyces cerevisiae. Using both TIRF microscopy and cryo-correlative light microscopy and electron tomography, we successfully reconstituted microtubule-bound, intact kinetochores. These kinetochores translocate on the lateral microtubule surface toward the microtubule plus end and transition to end-on attachment, whereupon microtubule depolymerization commences. The directional kinetochore movement is dependent on the highly processive kinesin-8, Kip3. We propose that Kip3 facilitates stable kinetochore attachment to microtubule plus ends through its abilities to move the kinetochore laterally on the surface of the microtubule and to regulate microtubule plus end dynamics.

category: cell biology


title: An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs

abstract:
BackgroundA genome-wide association study (GWAS) correlates variation in the genotype with variation in the phenotype across a cohort, but the causal gene mediating that impact is often unclear. When the phenotype is protein abundance, a reasonable hypothesis is that the gene encoding that protein is the causal gene. However, as variants impacting protein levels can occur thousands or even millions of base pairs from the gene encoding the protein, it is unclear at what distance this simple hypothesis breaks down.

ResultsBy making the simple assumption that cis-pQTLs should be distance dependent while trans-pQTLs are distance independent, we arrive at a simple and empirical distance cutoff separating cis- and trans-pQTLs. Analyzing a recent large-scale pQTL study (Pietzner, 2021) we arrive at an estimated distance cutoff of 944 kilobasepairs (kbp) (95% confidence interval: 767-1,161) separating the cis and trans regimes.

ConclusionsWe demonstrate that this simple model can be applied to other molecular GWAS traits. Since much of biology is built on molecular traits like protein, transcript and metabolite abundance, we posit that the mathematical models for cis and trans distance distributions derived here will also apply to more complex phenotypes and traits.

category: genetics


title: Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing

abstract: The accumulation of protein damage is one of the major drivers of replicative ageing, describing a cells reduced ability to reproduce over time even under optimal conditions. Reactive oxygen and nitrogen species are precursors of protein damage and therefore tightly linked to ageing. At the same time, they are an inevitable by-product of the cells metabolism. Cells are able to sense high levels of reactive oxygen and nitrogen species and can subsequently adapt their metabolism through gene regulation to slow down damage accumulation. However, the older or damaged a cell is the less flexibility it has to allocate enzymes across the metabolic network, forcing further adaptions in the metabolism. To investigate changes in the metabolism during replicative ageing, we developed an multi-scale mathematical model using budding yeast as a model organism. The model consists of three interconnected modules: a Boolean model of the signalling network, an enzyme-constrained flux balance model of the central carbon metabolism and a dynamic model of growth and protein damage accumulation with discrete cell divisions. The model can explain known features of replicative ageing, like average lifespan and increase in generation time during successive division, in yeast wildtype cells by a decreasing pool of functional enzymes and an increasing energy demand for maintenance. We further used the model to identify three consecutive metabolic phases, that a cell can undergo during its life, and their influence on the replicative potential, and proposed an intervention span for lifespan control.


title: Erbb4 deletion from fast-spiking interneurons causes psychosis-relevant neuroimaging phenotypes

abstract: Converging lines of evidence suggest that dysfunction of cortical parvalbumin-expressing (PV+) GABAergic interneurons is a core feature of psychosis. This dysfunction is thought to underlie neuroimaging abnormalities commonly found in patients with psychosis, particularly in the hippocampus. These include increases in resting cerebral blood flow (CBF) and levels of glutamatergic metabolites, and decreases in binding of GABAA 5 receptors and the synaptic density marker synaptic vesicle glycoprotein 2A (SV2A). However, direct links between PV+ interneuron dysfunction and these neuroimaging readouts have yet to be established. Conditional deletion of a schizophrenia susceptibility gene, the tyrosine kinase receptor Erbb4, from cortical and hippocampal PV+ interneurons leads to several synaptic, behavioral and cognitive phenotypes relevant to psychosis in mice. Here, we investigated how this PV+ interneuron disruption affects the hippocampal in vivo neuroimaging readouts in the Erbb4 model. Adult Erbb4 conditional mutant mice (Lhx6-Cre;Erbb4F/F, n=12) and their wild-type littermates (Erbb4F/F, n=12) were scanned in a 9.4T magnetic resonance scanner to quantify CBF and glutamatergic metabolite levels (glutamine, glutamate, GABA). Subsequently, we assessed GABAA receptors and SV2A density using quantitative autoradiography. Erbb4 mutant mice showed significantly elevated CBF and glutamine levels, as well as decreased SV2A density compared to wild-type littermates. No significant GABAA receptor density differences were identified. These findings demonstrate that specific disruption of cortical PV+ interneurons in mice recapitulate some of the key neuroimaging findings in psychosis patients, and link PV+ interneuron deficits to non-invasive, translational measures of brain function and neurochemistry that can be used across species.


title: A two-stage framework for neural processing of biological motion

abstract: It remains to be understood how biological motion is hierarchically computed, from discrimination of local "life motion" animacy to global dynamic body perception. Here, we addressed this functional separation of the correlates of the perception of life motion, defined as characteristic for the local motion of parts of living beings, from perception of global motion of a body. We hypothesized that life motion processing can be isolated, by using a single dot motion perceptual decision paradigm featuring the biomechanical details of local realistic motion of a single joint. To ensure that we were indeed tackling processing of biological motion properties we used a discrimination instead of detection task. We discovered using representation similarity analysis that two key early dorsal and two ventral stream regions (visual motion selective hMT+ and V3A, extrastriate body area EBA and a region within fusiform gyrus FFG) showed robust and separable signals related to encoding of life motion and global motion. These signals reflected two independent processing stages, as revealed by representation dissimilarity analysis and deconvolution of fMRI responses to each motion pattern. This study showed that higher level pSTS encodes both classes of biological motion in a similar way, revealing a higher-level integrative stage, reflecting scale independent biological motion perception. Our results reveal a two-stage framework for neural computation of biological motion, with an independent contribution of dorsal and ventral regions for the initial stage.


title: Modulation of brain activity by psycholinguistic information during naturalistic speech comprehension and production

abstract: Language processing requires the integration of diverse sources of information across multiple levels of processing. A range of psycholinguistic properties have been documented in previous studies as having influence on brain activation during language processing. However, most of those studies have used factorial designs to probe the effect of one or two individual properties using highly controlled stimuli and experimental paradigms. Little is known about the neural correlates of psycholinguistic properties in more naturalistic discourse, especially during language production. The aim of our study is to explore the above issues in a rich fMRI dataset in which participants both listened to recorded passages of discourse and produced their own narrative discourse in response to prompts. Specifically, we measured 13 psycholinguistic properties of the discourse comprehended or produced by the participants, and we used principal components analysis (PCA) to address covariation in these properties and extract a smaller set of latent language characteristics. These latent components indexed vocabulary complexity, sensory-motor and emotional language content, discourse coherence and speech quantity. A parametric approach was adopted to study the effects of these psycholinguistic variables on brain activation during comprehension and production. We found that the pattern of effects across the cortex was somewhat convergent across comprehension and production. However, the degree of convergence varied across language properties, being strongest for the component indexing sensory-motor language content. We report the full, unthresholded effect maps for each psycholinguistic variable, as well as mapping how these effects change along a large-scale cortical gradient of brain function. We believe that our findings provide a valuable starting point for future, confirmatory studies of discourse processing.


title: Anti-spike antibody response to natural infection with SARS-CoV-2 and its activity against emerging variants

abstract:
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has substantially impacted human health globally. Spike-specific antibody response plays a major role in protection against SARS-CoV-2. Here, we demonstrated that acute SARS-CoV-2 infection elicits rapid and robust spike-binding and ACE2-blocking antibody responses, which wane approximately 11 months after infection. Serological responses were found to be correlated with the frequency of spike-specific memory B cell responses to natural infections. Further, significantly higher spike-binding, ACE2-blocking, and memory B cell responses were detected in patients with fever and pneumonia. Spike-specific antibody responses were found to be greatly affected by spike mutations in emerging variants, especially the Beta and Omicron variants. These results warrant continued surveillance of spike-specific antibody responses to natural infections and highlight the importance of maintaining functional anti-spike antibodies through immunization.

ImportanceAs spike protein-specific antibody responses play a major role in protection against SARS-CoV-2, we examined the spike-binding and ACE2-blocking antibody responses in SARS-CoV-2 infection at different time points. We found robust responses following acute infection, which waned approximately 11 months after infection. Further, the serological responses were correlated with the frequency of spike-specific memory B cell responses to natural infections. Patients with fever and pneumonia showed significantly stronger spike-binding, ACE2-blocking antibody, and memory B cell responses. Moreover, the spike-specific antibody responses were substantially affected by the emerging variants, especially the Beta and Omicron variants. These results warrant continued surveillance of spike-specific antibody responses to natural infections and highlight the importance of maintaining functional anti-spike antibodies through immunization.

category: immunology


title: Characterization of Cysteine-rich protein families of Giardia lamblia and their role during antigenic variation.

abstract:
Giardia lamblia encode several families of cysteine-rich proteins. Among these families are the Variant-specific Surface Proteins (VSPs), which are involved in the process of antigenic variation. In addition to VSPs, other Cys-rich proteins have been described, such as High Cysteine Membrane Proteins (HCMPs), High Cysteine Proteins (HCPs) and Tenascin-like Proteins (TLPs). However, these proteins are less characterized and there is no consensus on their subcellular localization, function, expression, and relationship with the VSPs. Although numerous efforts have been made to determine the distinctive characteristics of VSPs and the number of VSP genes present in the genome of Giardia, a clear profile of the VSP repertoire is still lacking. Here, we performed an exhaustive analysis of the Cys-rich families in the recently updated version of the Giardia genome, including their organization, characteristic features, evolution and levels of expression, by combining simple pattern searches and predictions with massive sequencing techniques, integrating and reanalyzing as much omics data as possible. We propose a new classification for the Cys-rich protein-encoding genes and pseudogenes that better describes their involvement in the parasite biology and define unique characteristics of the VSPs that include, besides their known features, an Initiator element/Kozak-like sequence, an extended polyadenylation signal and a unique pattern of mutually exclusive transcript accumulation. Our findings also imply that the HCMPs (now named Cys-Rich Membrane Proteins, CRMPs) are upregulated under stress conditions and might protect the parasite during VSP switching. These results contribute to a better understanding of the process of antigenic variation in this pathogen.

Author SummaryThe most common cause of parasite-induced diarrhea is Giardia lamblia. This intestinal parasite causes 180 million cases of symptomatic disease (giardiasis) yearly but also many asymptomatic infections, resulting in that more than 0.5 billion people are currently colonized by the parasite. One key virulence mechanism of G. lamblia, resulting in long-term infections and frequent re-infections, is antigenic variation of Variant-specific Surface Proteins (VSPs). The cysteine-rich VSP proteins are encoded by a multi-gene family but until now the number of genes and how they are regulated has been unclear. Here a recently assembled Giardia reference genome was analyzed using different bioinformatic analyses and this revealed that there are 136 VSP genes in the Giardia genome. The analyses revealed that there are additional cysteine rich proteins in gene families with fewer members that are related to VSPs but with other roles than antigenic variation. A large number of incomplete VSP genes were also identified and they can function as a sequence reservoir for generation of VSP variability. The VSP genes have unique regulatory elements in the upstream and downstream regions, suggesting a role in regulation. Several gene expression data sets were re-analyzed and it showed that one major VSP is expressed per cell. This study is the first to reveal the organization of VSPs in Giardia and it will be the basis for further studies of the mechanism of antigenic variation in this important intestinal parasite.


title: Intra-membrane client recognition potentiates the chaperone functions of Calnexin

abstract:
One third of the human proteome are membrane proteins. They are particularly vulnerable to misfolding, often requiring assistance by molecular chaperones. Calnexin (CNX), one of the most abundant ER chaperones, plays an important role in membrane protein biogenesis and engages clients via its sugar-binding lectin domain.

Using mass spectrometric analyses, we show that Calnexin (CNX) interacts with a large number of non-glycosylated membrane proteins, suggesting additional binding modes. We find that misfolded membrane proteins are preferentially bound by CNX and that CNX uses its single transmembrane domain (TMD) for client recognition. Combining experimental and computational approaches, we systematically dissect signatures for intramembrane client recognition by CNX and identify sequence motifs within the CNX TMD region that mediate client binding. Building on this, we show that intramembrane client binding potentiates the chaperone functions of CNX.

Together, this study reveals a widespread role of CNX client recognition in the lipid bilayer, which synergizes with its established lectin-based substrate binding. Molecular chaperones thus can combine different interaction modes to support the biogenesis of the diverse eukaryotic membrane proteome.


title: Status of susceptibility of the visceral leishmaniasis vector, Phlebotomus argentipes (Diptera: Psychodidae: Phlebotominae), to insecticides used for vector control in Nepal

abstract:
BackgroundVisceral leishmaniasis (VL) is targeted for elimination as a public health problem in Nepal by 2023. For nearly three decades, the core vector control intervention in Nepal has been indoor residual spraying (IRS) with pyrethroids. Considering the long-term use of pyrethroids and possible development of resistance of the vector Phlebotomus argentipes sand flies, we monitored susceptibility status of their field populations to the insecticides of different classes, in villages with and without IRS activities in recent years.

Methodology/Principal findingsSand flies were collected from villages with and without IRS in five VL endemic districts from August 2019 to November 2020. The WHO susceptibility test procedure was adopted using filter papers impregnated at the discriminating concentrations of insecticides of the following classes: pyrethroids (alpha-cypermethrin 0.05%, deltamethrin 0.05% and lambda-cyhalothrin 0.05%), carbamates (bendiocarb 0.1%) and organophosphates (malathion 5%). Pyrethroid resistance intensity bioassays with papers impregnated with 5x of the discriminating concentrations, piperonyl butoxide (PBO) synergist-pyrethroid bioassays and DDT cross resistance bioassays were also performed. In the IRS villages, the vector sand flies were resistant (mortality rate <90%) to alpha-cypermethrin and possibly resistant (mortality rate 90-97%) to deltamethrin and lambda-cyhalothrin, while susceptibility to these insecticides was variable in the non-IRS villages. The vector was fully susceptible to bendiocarb and malathion in all villages. A delayed knockdown time (KDT50) with pyrethroids was observed in all villages. The pyrethroid resistance intensity was low, and the susceptibility improved at 5x of the discriminating concentrations. Enhanced pyrethroid susceptibility after pre-exposure to PBO and the DDT-pyrethroid cross-resistance were evident.

Conclusions/SignificanceOur investigation showed that P. argentipes sand flies have emerged with pyrethroid resistance, suggesting the need to switch to alternative classes of insecticides such as organophosphates for IRS. We strongly recommend for the regular and systematic monitoring of insecticide resistance in sand flies to optimize the efficiency of vector control interventions to sustain VL elimination efforts in Nepal.

Author summaryVisceral leishmaniasis (VL), transmitted by P. argentipes sand flies, is endemic in South-East Asian countries such as Bangladesh, India and Nepal, and is on the verge of elimination as a public health problem in Nepal by 2023. As part of the WHO Global Vector Control Response, entomological surveillance including insecticide resistance monitoring is one of the four main pillars of this strategy. In the early 1990s, the historical use of DDT for sand fly vector control was replaced with deltamethrin or alpha-cypermethrin, which have now been in use for almost three decades in Nepal. Suspecting that this long-term use of pyrethroids might have selected resistance in sand fly populations which would jeopardize control efforts, we conducted the first comprehensive survey to generate contemporary evidence of insecticide resistance in Nepal. For this, we performed WHO susceptibility tests in five VL endemic districts and found strong evidence of pyrethroid resistance in vector populations from the areas receiving IRS. Resistance mechanisms involved would probably be kdr mutations and monooxygenase. This study also endorses regular insecticide resistance monitoring to inform evidence-based decisions on insecticide use for vector control and to maintain the effectiveness of vector control measures as a core intervention in the fight against VL.


title: A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities

abstract:
Microbial communities contain a broad phylogenetic diversity of organisms, however the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems, and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include fungal ITS data, we compared five candidate DNA extraction kits against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon and shotgun metagenomics sequencing. We present results considering a diverse panel of host-associated and environmental sample types, and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection, and microbial community composition among protocols.

Accession numbersRaw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub (github.com/justinshaffer/Extraction_kit_testing).

Methods summaryTo allow for downstream applications involving fungi in addition to bacteria and archaea, we compared five DNA extraction kits with our previously established, standardized protocol for extracting DNA for microbial community analysis. Across ten diverse sample types, we found one extraction kit to perform comparably or better than our standardized protocol. Our conclusion is based on per-sample comparisons of DNA yield, the number of quality-filtered sequences generated, the limit of detection of microbial cells, microbial community alpha-diversity, beta-diversity, and taxonomic composition, and extent of well-to-well contamination.


title: Human repair-related Schwann cells adopt functions of antigen-presenting cells in vitro

abstract:
The plastic potential of Schwann cells (SCs) is increasingly recognized to play a role after nerve injury and in diseases of the peripheral nervous system. In addition, reports on the interaction between SCs and immune cells indicate their involvement in inflammatory processes. However, data about the immunocompetence of human SCs are primarily derived from neuropathies and it is currently unknown whether SCs directly regulate an adaptive immune response after nerve injury.

Here, we performed a comprehensive analysis of the immunomodulatory capacities of human repair-related SCs (hrSCs), which recapitulate SC response to nerve injury in vitro. We used our previously established protocol for the culture of primary hrSCs from human peripheral nerves and analyzed the transcriptome, secretome, and cell surface proteins for signatures and markers relevant in innate and adaptive immunity, performed phagocytosis assays, and monitored T-cell subset activation in co-cultures with autologous human T-cells.

Our findings show that hrSCs are highly phagocytic, which is in line with high MHCII expression. In addition, hrSCs express co-regulatory molecules, such as CD40, CD80, B7H3, CD58, CD86, HVEM, release a plethora of chemoattractants, matrix remodelling proteins and pro- as well as anti-inflammatory cytokines, and upregulate the T-cell inhibiting PD-L1 molecule upon pro-inflammatory stimulation with IFN{gamma}. Furthermore, hrSC contact reduced the number and activation status of allogenic CD4+ and CD8+ T-cells.

This study demonstrates that hrSCs possess features and functions typical for professional antigen presenting cells in vitro, and suggest a new role of these cells as negative regulators of T-cell immunity during nerve regeneration.

Main pointsO_LIHuman repair-related Schwann cells (hrSC) function as professional antigen presenting cells.
C_LIO_LIHrSCs up-regulate PD-L1 upon pro-inflammatory IFN{gamma} stimulation.
C_LIO_LIHrSCs hamper CD4+ and CD8+ T-cell activation.
C_LI

Graphical abstract

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title: Excitatory and inhibitory D-serine binding to the NMDA receptor

abstract: N-methyl-D-aspartate receptors (NMDARs) uniquely require binding of two different neurotransmitter agonists for synaptic transmission. D-serine and glycine bind to one subunit, GluN1, while glutamate binds to the other, GluN2. These agonists bind to the receptors bi-lobed ligand-binding domains (LBDs), which close around the agonist during receptor activation. To better understand the unexplored mechanisms by which D-serine contributes to receptor activation, we performed multi-microsecond molecular dynamics simulations of the GluN1/GluN2A LBD dimer with free D-serine and glutamate agonists. Surprisingly, we observed D-serine binding to both GluN1 and GluN2A LBDs, suggesting that D-serine competes with glutamate for binding to GluN2A. This mechanism is confirmed by our electrophysiology experiments, which show that D-serine is indeed inhibitory at high concentrations. Although free energy calculations indicate that D-serine stabilizes the closed GluN2A LBD, its inhibitory behavior suggests that it either does not remain bound long enough or does not generate sufficient force for ion channel gating. We developed a workflow using pathway similarity analysis to identify groups of residues working together to promote binding. These conformation-dependent pathways were not significantly impacted by the presence of N-linked glycans, which act primarily by interacting with the LBD bottom lobe to stabilize the closed LBD.


title: Integrated analysis of Wnt signalling system component gene expression

abstract: Wnt signalling controls patterning and differentiation across many tissues and organs of the developing embryo via temporally and spatially restricted expression of multi-gene families encoding ligands, receptors, pathway modulators and intracellular components. Here we report an integrated analysis of key encoding genes in the 3D space of the mouse embryo across multiple stages of development. We applied a method for 3D/3D image transformation to map all gene expression patterns to a single reference embryo for each stage providing both visual analysis and volumetric mapping allowing computational methods to interrogate the combined expression patterns. We identify novel territories where multiple Wnt and Fzd genes are co-expressed and cross-compare all patterns, including all seven Wnt paralogous gene pairs. The comprehensive analysis allows regions in the embryo where no Wnt or Fzd gene expression is detected, and where single Wnt genes are uniquely expressed, to be revealed. This work provides insight into a level of organisation of the patterns not previously possible, as well as presenting a resource that can be utilised further by the research community for whole system analysis.

category: developmental biology


title: Biodiversity effects on seedling biomass growth are modulated by light environment across functional groups

abstract:
O_LITree biodiversity has the potential to ensure consistency in the functioning of forest ecosystems, not just over space, but over long-timescales by maintaining composition through recruitment. However, for continued buffering in the face of global environmental change, the sensitivity of biodiversity-ecosystem functioning relationships to heterogeneous environments needs to be understood.
C_LIO_LISeedling recruitment in carbon-rich tropical forests is a result of biotic and abiotic drivers but their combined outcomes at the community-level remain poorly understood. Although biodiversity in seedling communities can potentially increase their growth and biomass accumulation, abiotic drivers like light can alter this effect through divergent effects on constituent species and functional groups. In forests with high baseline heterogeneity in microclimates, these processes can enhance or constrain regeneration.
C_LIO_LIWe tested the effects and interactions between species richness and canopy cover on the growth of seedling communities consisting of tropical broad-leaved evergreen and deciduous forest species using a fully crossed manipulated experiment in the Andaman Islands, India and compared these with field observations from a long-term forest plot in the same landscape.
C_LIO_LIWe show that in the critical seedling establishment phase, species richness and light increase community biomass independently. Accounting for variation across species, individual species on average accumulated more biomass in communities with both higher light and higher diversity.
C_LIO_LIWe also show that overyielding in species rich communities fits expectations from a model of complementarity with non-random overyielding than selection or spatial insurance effects.
C_LIO_LISynthesis Taken together, our results show that the potential for biodiversity to increase ecosystem functioning in seedling communities is modulated by light. Further understanding on the interaction of biodiversity with multiple abiotic drivers and their effect on regeneration dynamics is crucial for predicting future ecosystem functioning.
C_LI


title: Community structure determines the predictability of population collapse

abstract:
O_LIEarly warning signals (EWS) are phenomenological tools that have been proposed as predictors of the collapse of biological systems. Whilst a growing body of work has shown the utility of EWS based on either statistic derived from abundance data or shifts in phenotypic traits such as body size, so far this work has largely focused on single species populations.
C_LIO_LIHowever, in order to predict reliably the future state of ecological systems which inherently could consist of multiple species, understanding how reliable such signals are in a community context is critical.
C_LIO_LIHere, reconciling quantitative genetics and Lotka-Volterra equations which allow us to track both abundance and mean traits, we simulate the collapse of populations embedded in mutualistic and multi-trophic predator-prey communities. Using these simulations and warning signals derived from both population- and community-level data, we show that the utility of abundance-based EWS as well as metrics derived from stability-landscape theory (e.g., width and depth of the basin of attraction) are fundamentally linked, and thus the depth and width of the stability landscape could be used to identify which species should exhibit the strongest EWS of collapse.
C_LIO_LIThe probability a species displays both trait and abundance based EWS is dependent on its position in a community, with some species able to act as indicators species. In addition, our results also demonstrate that in general trait-based EWS appear less reliable in comparison to abundance-based EWS in forecasting species collapses in our simulated communities. Furthermore, community-level abundance-based EWS were fairly reliable in comparison to their species-level counterparts in forecasting species level collapses.
C_LIO_LIOur study suggests a holistic framework that combines abundance-based EWS and metrics derived from stability-landscape theory that may help in forecasting species loss in a community context.
C_LI


title: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

abstract: The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is more typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK, and the imposition of new restrictions, in particular the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages which preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically-infected individual. We conclude that the last hypothesis provides the best explanation of the observed behaviour and dynamics of the variant, although we find that the individual need not be immunocompromised, as persistently-infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs to each other, and identify that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations, and its lack of rapid evolutionary rate on the ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms) it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.

category: evolutionary biology


title: The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep

abstract: Understanding the genetic architecture underpinning quantitative traits in wild populations is pivotal to understanding the processes behind trait evolution. The  animal model is a popular method for estimating quantitative genetic parameters such as heritability and genetic correlation and involves fitting an estimate of relatedness between individuals in the study population. Genotypes at genome-wide markers can be used to estimate relatedness; however, relatedness estimates vary with marker density, potentially affecting results. Increasing density of markers is also expected to increase the power to detect quantitative trait loci (QTL). We estimated heritability and performed genome-wide association studies (GWAS) on five body size traits in an unmanaged population of Soay sheep using two different SNP densities: a dataset of 37,037 genotyped SNPs, and an imputed dataset of 417,373 SNPs. Heritability estimates did not differ between the two SNP densities, but the high-density imputed SNP dataset revealed five new SNP-trait associations that were not found with the lower density dataset. Conditional GWAS analyses after fitting the most significant SNPs revealed two more novel SNP-trait associations.

category: genomics


title: Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs

abstract: The fungus Botrytis cinerea is a polyphagous pathogen that encompasses multiple host-specialized lineages. While several secreted proteins, secondary metabolites and retrotransposons-derived small RNAs have been characterized as virulence factors, their role in host specialization remain unknown. The aim of this study was to identify the genomic correlates of host-specialization in populations of B. cinerea associated with grapevine and tomato. Using PacBio sequencing, we produced complete assemblies of the genomes of strains Sl3 and Vv3 that represent the French populations T and G1 of B. cinerea, specialized on tomato and grapevine, respectively. Both assemblies revealed 16 core chromosomes that were highly syntenic with chromosomes of the reference strain B05.10. The main sources of variation in gene content were the subtelomeric regions and the accessory chromosomes, especially the chromosome BCIN19 of Vv3 that was absent in Sl3 and B05.10. The repertoires and density of transposable elements were clearly different between the genomes of Sl3 and Vv3 with a larger number of subfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5% coverage). An Helitron-like element was found in almost all subtelomeric regions of the Vv3 genome, in particular in the flanking regions of a highly duplicated gene encoding a Telomere-Linked Helicase, while both features were absent from the Sl3 and B05.10 genomes. Different retrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets of small RNAs. Finally, extending the study to additional strains indicated that the accessory chromosome BCIN19 and the small RNAs producing retrotransposons Copia_4 and Gypsy_7 are common features of the G1 population that are scarcely if ever found in strains isolated from other populations. This research reveals that accessory chromosomes, repertoires of transposons and their derived small RNAs differ between populations of B. cinerea specialized on different hosts. The genomic data characterized in our study pave the way for further studies aiming at investigating the molecular mechanisms underpinning host specialization in a polyphagous pathogen.


title: Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting

abstract: SARS-CoV-2 is currently causing an unprecedented pandemic. While vaccines are massively deployed, we still lack effective large-scale antiviral therapies. In the quest for antivirals targeting conserved structures, we focused on molecules able to bind viral RNA secondary structures. Aminoglycosides are a class of antibiotics known to interact with the ribosomal RNA of both prokaryotes and eukaryotes and have previously been shown to exert antiviral activities by interacting with viral RNA. Here we show that the aminoglycoside geneticin is endowed with antiviral activity against all tested variants of SARS-CoV-2, in different cell lines and in a respiratory tissue model at non-toxic concentrations. The mechanism of action is an early inhibition of RNA replication and protein expression mediated by direct interaction with the -1 programmed ribosomal frameshift (PRF) signal. Using in silico modeling, we have identified a potential binding site of geneticin in the pseudoknot of frameshift RNA motif. Moreover, we have selected, through virtual screening, additional RNA binding compounds, interacting with the same site with increased potency.


title: Ependymal cell maturation is heterogeneous and ongoing in the mouse spinal cord and dynamically regulated in response to injury

abstract: The spinal cord neural stem cell potential resides within the ependymal cells lining the central canal. These cells are, however, heterogeneous, and we know little about the biological diversity this represents. Here we use single-cell RNA-sequencing to profile adult mouse spinal cord ependymal cells. We uncover transcriptomes of known subtypes and a new mature ependymal cell state, that becomes more prominent with age. Comparison of ependymal cell transcriptomes from the brain and spinal cord revealed that ongoing cell maturation distinguishes spinal cord ependymal cells from their postmitotic brain counterparts. Using an ex vivo model of spinal cord injury, we show that ependymal cell maturation is reversible but also highly regulated. We revisit ependymal cell identities in adult human spinal cord and uncover evidence for their maturation and surprising ventralisation with age. This first in-depth characterisation of spinal cord ependymal cells paves the way to manipulation of distinct ependymal subtypes, provides insights into ependymal cell maturation dynamics and informs strategies for coaxing ependymal cell-driven spinal cord repair.


title: Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes

abstract:
The spatial heterogeneity of soils microhabitats warrants the study of ecological patterns and community assembly processes in the context of community coalescence, or the combining and restructuring of communities and their environment. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of mixing disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor less richness, dominated by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred ecological processes, estimated richness and differential abundance, calculated compositional dissimilarity, and constructed co-occurrence networks. Findings supported our hypotheses, with >20% decrease in soil bacterial richness in well-mixed soil. While soil mixing resulted in increasingly dissimilar communities compared to unmixed soil (Bray-Curtis dissimilarity; 0.75 vs. 0.25), well-mixed soil communities were increasingly self-similar. Our results imply that vast soil diversity may be attributed to the unmixed and spatially heterogeneous nature of soil, and also provide insight into soil communities following coalescence events. By isolating and better understanding the effect of spatial heterogeneity and dysconnectivity on soil microbial communities, we may better extrapolate how anthropogenic disturbances, such as climate change or land use change, may affect broad soil functions.

One sentence summarySoil mixing decreases bacterial richness as several taxa dominate the community, providing evidence for homogenizing community assembly processes.


title: Phenotypic Variation from Waterlogging in Multiple Perennial Ryegrass Varieties under Climate Change Conditions

abstract: Identifying how various components of climate change will influence ecosystems and vegetation subsistence will be fundamental to mitigate negative effects. Climate change-induced waterlogging is understudied in comparison to temperature and CO2. Grasslands are especially vulnerable through the connection with global food security, with perennial ryegrass dominating many flood-prone pasturelands in North-western Europe. We investigated the effect of long-term waterlogging on phenotypic responses of perennial ryegrass using four varieties grown in atmospherically controlled growth chambers (ambient vs 2050, +2{degrees}C and eCO2) during two months of peak growth. Using image analysis and PCA methodologies, we assess how multiple predictors (phenotypic, environmental, genetic and temporal) influence overall plant performance and productivity. Long-term waterlogging was found to reduce leaf-colour intensity, with younger plants having purple hues indicative of anthocyanins. Plant performance and yield was lower in waterlogged plants, with tetraploid varieties coping better than diploid ones. The climate change treatment was found to reduce colour intensities further. Flooding was found to reduce plant productivity via reductions in colour pigments and root proliferation. These effects will have negative consequences for global food security from facing extreme weather events and flooding. Our approach can be adapted as plant health diagnostics tools via remote sensing and drone-technology.


title: The genomic landscapes of desert birds are structured by contemporary features

abstract: Spatial models show that genetic differentiation can be explained by factors ranging from geographic distance to environmental resistance across the landscape. However, genomes exhibit a landscape of differentiation, which could indicate that multiple factors better explain divergence in different portions of the genome. We test whether the best-predictors of intraspecific differentiation vary across the genome in ten bird species that co-occur in Sonoran and Chihuahuan deserts. Using population-level genomic data, we characterized the genomic landscapes across species and modeled five predictors that represented historical and contemporary mechanisms. The extent of genomic landscapes differed across the ten species, influenced by varying levels of population structuring and admixture between deserts. General dissimilarity matrix modeling indicated that the best-fit models differed from the whole genome and partitions along the genome. The most important predictors of genetic distance were environment and contemporary demography, which each explained 25-38% of observed variation, with paleoclimate and the position of the biogeographic barrier explaining 14-16%, and distance only explaining 9%. In particular, the genome was best explained by the biogeographic barrier in regions where the genome showed high fixation between populations. Similar levels of heterogeneity were observed among species and phenotypic divergence within species. These results illustrate that the genomic landscape of differentiation was influenced by alternative spatial factors operating on different portions of the genome.


title: Structural analogue-based protein structure domain assembly assisted by deep learning

abstract:
MotivationWith the breakthrough of AlphaFold2, the protein structure prediction problem has made a remarkable progress through end-to-end deep learning techniques, in which correct folds could be built for nearly all single-domain proteins. However, the full-chain modelling appears to be lower on average accuracy than that for the constituent domains and requires higher demand on computing hardware, indicating the performance of full-chain modelling still needs to be improved. In this study, we investigate whether the predicted accuracy of full-chain model can be further improved by domain assembly assisted by deep learning.

ResultsIn this article, we developed a structural analogue-based protein structure domain assembly method assisted by deep learning, named SADA. In SADA, a multi-domain protein structure database (MPDB) was constructed for the full-chain analogue detection using individual domain models. Starting from the initial model constructed from the analogue, the domain assembly simulation was performed to generate the full-chain model through a two-stage differential evolution algorithm guided by the physics-based force field and an inter-residue distance potential predicted by deep learning. SADA was compared with the state-of-the-art domain assembly methods on 356 benchmark proteins, and the average TM-score of SADA models is 8.1% and 27.0% higher than that of DEMO and AIDA, respectively. We also assembled full-chain models of 20 human multi-domain proteins using individual domain models independently predicted by AlphaFold2, where the SADA full-chain models obtained a 4.8% higher average TM-score than full-chain models directly predicted by AlphaFold2 and fewer computing resources were required. In addition, we also find that the domains often interact in the similar way in the quaternary orientations if the domains have similar tertiary structures. Furthermore, homologous templates and structural analogues are complementary for multi-domain protein full-chain modelling.

AvailabilityThe SADA web server are freely available at http://zhanglab-bioinf.com/SADA.

category: bioinformatics


title: Integrative analysis to identify shared mechanisms between schizophrenia and bipolar disorder and their comorbidities

abstract: Schizophrenia and bipolar disorder are characterized by highly similar neuropsychological signatures, implying shared neurobiological mechanisms between these two disorders. These disorders also have comorbidities with other indications, such as type 2 diabetes mellitus (T2DM). To date, an understanding of the mechanisms that mediate the link between these two disorders remains incomplete. In this work, we identify and investigate shared patterns across multiple schizophrenia, bipolar disorder and T2DM gene expression datasets through multiple strategies. Firstly, we investigate dysregulation patterns at the gene-level and compare our findings against disease-specific knowledge graphs (KGs). Secondly, we analyze the concordance of co-expression patterns across datasets to identify disease-specific as well as common pathways. Thirdly, we examine enriched pathways across datasets and disorders to identify common biological mechanisms between them. Lastly, we investigate the correspondence of shared genetic variants between these two disorders and T2DM as well as the disease-specific KGs. In conclusion, our work reveals several shared candidate genes and pathways, particularly those related to the immune and nervous systems, which we propose mediate the link between schizophrenia and bipolar disorder and its shared comorbidity, T2DM.


title: Template-based assembly of proteomic short reads for de novo antibody sequencing and repertoire profiling

abstract: Antibodies can target a vast molecular diversity of antigens. This is achieved by generating a complementary diversity of antibody sequences though somatic recombination and hypermutation. A full understanding of the antibody repertoire in health and disease therefore requires dedicated de novo sequencing methods. Next generation cDNA sequencing methods have laid the foundation of our current understanding of the antibody repertoire, but these methods share one major limitation in that they target the antibody-producing B-cells, rather than the functional secreted product in bodily fluids. Mass spectrometry-based methods offer an opportunity to bridge this gap between antibody repertoire profiling and bulk serological assays, as they can access antibody sequence information straight from the secreted polypeptide products. In a step to meeting the challenge of MS-based antibody sequencing, we present a fast and simple software tool (Stitch) to map proteomic short reads to user-defined templates with dedicated features for both monoclonal antibody sequencing and profiling of polyclonal antibody repertoires. We demonstrate the use of Stitch by fully reconstructing 2 monoclonal antibody sequences with >98% accuracy (including I/L assignment); sequencing a Fab from patient serum isolated by reversed-phase LC fractionation against a high background of homologous antibody sequences; sequencing antibody light chains from urine of multiple-myeloma patients; and profiling the IgG repertoire in sera from patients hospitalized with COVID-19. We demonstrate that Stitch assembles a comprehensive overview of the antibody sequences that are represented in the dataset and provides an important first step towards analyzing polyclonal antibodies and repertoire profiling.


title: Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model

abstract:
Patient-derived organoid (PDO) cancer models are generated from epithelial tumor cells. Although they reflect the molecular tumor characteristics, they lack the complexity of the tumor microenvironment, which is a key driver of tumorigenesis and therapy response. Here, we present a colorectal cancer (CRC) organoid model that incorporates epithelial cells and stromal fibroblasts from the same patient. Molecular characterization of primary cancer associated fibroblasts (CAFs) and matched normal fibroblasts (NF) revealed proteomic, secretome and gene expression differences in pathways associated with tumor related fibroblast function. Further, CAFs retained higher motility compared to NFs in vitro. Importantly, both CAFs and NFs supported cancer cell proliferation in 3D co-cultures, without the addition of classical niche factors. PDOs grown together with fibroblasts displayed a larger cellular heterogeneity of tumor cells compared to mono-cultures, and closely resembled the in vivo tumor morphology. This was also confirmed by the calculation of cellular proportions of epithelial cell subtypes in organoid mono-versus co-cultures, which were inferred through bioinformatics deconvolution of bulk RNA sequencing data using published single cell RNA sequencing datasets from CRC tissues. Additionally, we observed a mutual crosstalk between tumor cells and fibroblasts in the co-cultures. This was manifested by majorly deregulated pathways such as cell-cell communication and extracellular matrix remodeling in the organoids. For the fibroblasts, we observed enhanced expression of tumor induced marker genes and cytokines characteristic for myo- and immunogenic fibroblasts. This model will be vital as a physiological personalized tumor model to study disease mechanisms and therapy response in CRC.

One Sentence SummaryPatient matched fibroblasts support tumor organoid growth in 3D co-culture and maintain intratumoral cellular heterogeneity and histo-morphology.

category: cancer biology


title: Belgian endive-derived biostimulants promote shoot and root growth in vitro.

abstract: Recovering biostimulant compounds from by-products of crops is a promising strategy to add value, enhance sustainability, and increase the environmental safety of the agricultural production chain. Here, we report consistent root and shoot growth-stimulating bioactivity present in water-based extracts from Belgian endive forced roots (Cichorium intybus var. foliosum) over two consecutive harvest years. The shoot and the primary root of in vitro cultivated Arabidopsis thaliana treated with Belgian endive extract were about 30% increased in size compared to plants grown under control conditions. The ornamental species Plectranthus esculentus also showed enhanced in vitro shoot and root growth, suggesting bioactivity on a broad range of species. Fractionation of the Belgian endive extracts into aqueous and organic subfractions coupled with bio-activity measurements showed that the principal root and shoot growth-promoting ingredients are primarily water-soluble. NMR-based characterization of the bioactive aqueous fractions revealed the presence of pre-dominantly sugars and organic acids. Malate and sugars were abundant and common to all water fractions, suggesting these molecules contributed to the growth stimulation phenotype. The findings indicate that Belgian endive roots are a source for the development of organic waste-derived biostimulants with potential for application in tissue culture and putatively for soil-grown crop production.

category: plant biology


title: Co-targeting B-RAF and PTEN enables sensory axons to regenerate across and beyond the spinal cord injury

abstract: Primary sensory axons in adult mammals fail to regenerate after spinal cord injury (SCI), in part due to insufficient intrinsic growth potential. Robustly boosting their growth potential continues to be a challenge. Previously, we showed that constitutive activation of B-RAF (rapidly accelerated fibrosarcoma kinase) markedly promotes axon regeneration after dorsal root and optic nerve injuries. The regrowth is further augmented by supplemental deletion of PTEN (phosphatase and tensin homolog). Here, we examined whether concurrent B-RAF activation and PTEN deletion promotes dorsal column axon regeneration after SCI. Remarkably, genetically targeting B-RAF and PTEN selectively in DRG neurons of adult mice enables many DC axons to enter, cross, and grow beyond the lesion site after SCI; some axons reach ~2 mm rostral to the lesion by 3 weeks post-injury. Co-targeting B-RAF and PTEN promotes more robust DC regeneration than a pre-conditioning lesion, which additively enhances the regeneration triggered by B-RAF/PTEN. We also found that post-injury targeting of B-RAF and PTEN enhances DC axon regeneration. These results demonstrate that co-targeting B-RAF and PTEN effectively enhances the intrinsic growth potential of DC axons after SCI and therefore may help to develop a novel strategy to promote robust long-distance regeneration of primary sensory axons.


title: PP2A phosphatase regulates cell-type specific cytoskeletal organization to drive dendritic diversification

abstract: Uncovering molecular mechanisms regulating dendritic diversification is essential to understanding the formation and modulation of functional neural circuitry. Transcription factors play critical roles in promoting dendritic diversity and here, we identify PP2A phosphatase function as a downstream effector of Cut-mediated transcriptional regulation of dendrite development. Mutant analyses of the PP2A catalytic subunit (mts) or the scaffolding subunit (PP2A-29B) reveal cell-type specific regulatory effects with the PP2A complex required to promote dendritic growth and branching in Drosophila Class IV (CIV) multidendritic (md) neurons, whereas in Class I (CI) md neurons, PP2A functions in restricting dendritic arborization. Cytoskeletal analyses reveal requirements for Mts in regulating microtubule stability/polarity and F-actin organization/dynamics. In CIV neurons, mts knockdown leads to reductions in dendritic localization of organelles including mitochondria and satellite Golgi outposts, while CI neurons show increased Golgi outpost trafficking along the dendritic arbor. Further, mts mutant neurons exhibit defects in neuronal polarity/compartmentalization. Finally, genetic interaction analyses suggest {beta}-tubulin subunit 85D is a common PP2A target in CI and CIV neurons, while FoxO is a putative target in CI neurons.


title: Simultaneous dual recordings from hair cells and their calyx afferents reveal the functional significance of these specialized endings in the vestibular periphery.

abstract: In the vestibular periphery, transmission via conventional synaptic boutons is supplemented by postsynaptic calyceal endings surrounding Type I hair cells. This review focusses on the multiple modes of communication between these receptors and their enveloping calyces as revealed by simultaneous dual-electrode recordings. Classic orthodromic transmission is accompanied by two forms of bidirectional communication enabled by the extensive cleft between the Type I hair cell and its calyx. The slowest cellular communication low-pass filters the transduction current with a time constant 10 -- 100 milliseconds: potassium ions accumulate in the synaptic cleft, depolarizing both the hair cell and afferent to potentials greater than necessary for rapid vesicle fusion in the receptor and potentially triggering action potentials in the afferent. On the millisecond timescale, conventional glutamatergic quantal transmission occurs when hair cells are depolarized to potentials sufficient for calcium influx and vesicle fusion. Depolarization also permits a third form of transmission which occurs over tens of microseconds, resulting from the large voltage- and ion-sensitive cleft-facing conductances in both the hair cell and the calyx that are open at their resting potentials. Current flowing out of either the hair cell or the afferent divides into the fraction flowing across the cleft into its cellular partner, and the remainder flowing out of the cleft and into the surrounding fluid compartment. These findings suggest multiple biophysical bases for the extensive repertoire of response dynamics seen in the population of primary vestibular afferent fibers. The results further suggest that evolutionary pressures drive selection for the calyx afferent.


title: Simultaneous dual recordings from vestibular hair cells and their calyx afferents demonstrate multiple modes of transmission at these specialized endings


title: Extraction of individual associative memory related dominant theta frequency for personalized transcranial brain stimulation

abstract: Non-invasive brain stimulation (NIBS) has gained increased interest in research and therapy of associative memory (AM) and its impairments. However, the one-size-fits-all approach yields inconsistent findings, thus putting forward the need for the development of personalized frequency-modulated NIBS protocols to increase the focality and the effectiveness of the interventions. There have been only a few attempts to deliver theta frequency-personalized tES. The current study explores the feasibility of determining dominant individual theta-band frequency (ITF) based on AM task evoked EEG activity. In a sample of 42 healthy young adults, we extracted the frequencies (2-15 Hz, in 0.5 Hz steps) with the highest event-related spectral perturbation from the EEG recorded during successful encoding in the AM task. The developed method for extraction of the dominant theta-band frequency based on the AM-evoked EEG changes is able to reliably determine the AM-related ITF and can be used for personalization of the oscillatory NIBS techniques.