title: Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine

abstract:
The first pandemic of the 21st century was caused by an H1N1 influenza A virus (IAV) introduced from pigs into humans, highlighting the importance of swine as reservoirs for pandemic viruses. Two major lineages of swine H1 circulate in North America: the 1A classical swine lineage (including the 2009 pandemic H1N1) and 1B human seasonal-like lineage. Here, we investigated the evolution of these H1 IAV lineages in North American swine and their potential pandemic risk. We assessed the antigenic distance between the HA of representative swine H1 and human seasonal vaccine strains (1978-2015) in hemagglutination inhibition (HI) assays using a panel of monovalent anti-sera raised in pigs. Antigenic cross-reactivity varied by strain but was associated with genetic distance. Generally, swine 1A lineage viruses that seeded the 2009 H1 pandemic were antigenically most similar to H1 pandemic vaccine strains, with the exception of viruses in the genetic clade 1A.1.1.3 that had a two-amino acid deletion mutation near the receptor-binding site, dramatically reducing antibody recognition. The swine 1B lineage strains, which arose from previously circulating (pre-2009 pandemic) human seasonal viruses, were more antigenically similar to pre-2009 human seasonal H1 vaccine viruses than post-2009 strains. Human population immunity was measured by cross-reactivity in HI assays to representative swine H1 strains. There was a broad range of titers against each swine strain that was not associated with age, sex, or location. However, there was almost no cross-reactivity in human sera to the 1A.1.1.3 and 1B.2.1 genetic clades of swine viruses, and the 1A.1.1.3 and 1B.2.1 clades were also the most antigenically distant from all human vaccine strains. Our data demonstrate that antigenic distances of representative swine strains from human vaccine strains represent a rational assessment of swine IAV for zoonotic risk research and pandemic preparedness prioritization.

ImportanceHuman H1 influenza A viruses (IAV) spread to pigs in North America, resulting in sustained circulation of two major groups of H1 viruses in swine. We quantified the genetic diversity of H1 in swine and measured antigenic phenotypes. We demonstrated that swine H1 lineages were significantly different from human vaccine strains and this antigenic dissimilarity increased over time as the viruses evolved in swine. Pandemic preparedness vaccine strains for human vaccines also demonstrated a loss in similarity with contemporary swine strains. Human sera revealed a range of responses to swine IAV, including two groups of viruses with little to no immunity. Surveillance and risk assessment of IAV diversity in pig populations are essential to detect strains with reduced immunity in humans, providing critical information for pandemic preparedness.


title: Plasmodium falciparum genetic diversity in coincident human and mosquito hosts

abstract:
Population genetic diversity of P. falciparum antigenic loci is high despite large bottlenecks in population size during the parasite life cycle. The extent of this diversity in human blood-stage infections, following expansion from a small number of liver-stage schizonts, has been well described. However, little is known about parasite genetic diversity in the vector, where a similar bottleneck and expansion occurs following parasite mating and where parasite genotypes from several different human infections may accumulate. We assessed parasite genetic diversity within human and mosquito P. falciparum infections collected from the same households during a 14-month longitudinal cohort study using amplicon deep sequencing of two antigenic gene fragments (ama1 and csp). To a prior set of infected humans (n=1175/2813; 86.2% sequencing success) and mosquito abdomens (n=199/1448; 95.5% sequencing success), we added sequences from infected mosquito heads (n=134/1448; 98.5% sequencing success). Across all sample types we observed 456 ama1 and 289 csp unique haplotypes. While both hosts contained many rare haplotypes, population genetic metrics indicated that the overall and sample-level parasite populations were more diverse in mosquitoes than in humans, and infections were more likely to harbor a dominant haplotype in humans than in mosquitoes (based on relative read abundance). Finally, within a given mosquito there was little overlap in genetic composition of abdomen and head infections, suggesting that infections may be cleared from the abdomen during a mosquitos lifespan. Taken together, our observations provide evidence for the role of the mosquito vector in maintaining sequence diversity of malaria parasite populations.

Significance statementConcurrent infections with multiple strains of Plasmodium falciparum, the leading causative agent of death due to malaria, are common in highly endemic regions. During transitions within and between the parasites mosquito and human hosts, population bottlenecks occur, and distinct parasite strains may have differential fitness in the various environments encountered. These bottlenecks and fitness differences may lead to differences in strain prevalence and diversity between hosts. We investigated differences in genetic diversity between P. falciparum parasites in human and mosquito hosts and found that, compared to human parasite populations and infections, mosquito populations and infections were more diverse. This suggests that the mosquito vector may play a role in in maintaining sequence diversity in malaria parasite populations.

category: microbiology


title: Controls of SAR11 subclade abundance, diversity, and growth in two Mid-Atlantic estuaries

abstract:
SAR11 is a dominant bacterial clade in marine oligotrophic ecosystems. SAR11 can also be dominant in estuarine systems, where they are not well-studied. We examined the effects of season, nutrient concentrations, and salinity in shaping SAR11 subclade abundance, diversity, function, and growth in two Mid-Atlantic estuaries, the Delaware and Chesapeake Bays. Using metagenome-assembled genomes, we identified twelve distinct genomospecies within the Ia, II, IIIa, and V subclades, which made up to 60% of the total bacterial community. The functional potential of all SAR11 genomospecies varied, especially in carbohydrate metabolism, transporters, and one-carbon metabolic pathways. Predicted growth rates, estimated by the Peak to Trough method, varied by season and genomospecies. SAR11 growth rates negatively correlated in the spring but positively correlated in the summer with chlorophyll a concentrations and bacterial production, as well as phosphate and ammonium concentrations. Genomospecies in Ia.1, IIIa.2, and IIIa.4 subclades had low growth rates, while genomospecies in Ia.3, Ia.5, Ia.6, II, and V subclades had higher and more variable growth rates that were positively correlated with phosphate concentrations and temperature. Growth rate variation between subclades was associated with carbohydrate metabolic gene repertoires, especially glycolysis and number of transporters. While total transcript to genome ratios generally mirrored growth rates, transcription of genes involved in phosphate and nitrogen transport were negatively associated with growth rates. These data suggest that SAR11 genomospecies abundance varies in these estuaries because of differences in growth rates and metabolic capacities in response to changes in environmental conditions.

ImportanceThe SAR11 clade is one of the most abundant bacterial groups in marine systems, including many estuaries. From the Delaware Bay and Chesapeake Bay environmental metagenomes, we reconstructed nearly complete SAR11 metagenome-assembled genomes representing ten genomospecies in four subclades, of which at least one is novel. Growth rate estimates of genomospecies correlated with functional gene repertoires of carbohydrate transporter and metabolism. Different SAR11 genomospecies dominated among the seasons, depending on their growth rates, biological productivity, and nutrient concentrations. Our RNAseq approach facilitated an understanding of the environmental controls on the abundance of SAR11 genomospecies in their natural habitat. This study is the first to combine multiple measures of diversity, abundance, functional potential, growth rates and activity of this important group, demonstrating a direct link between SAR11 genomospecies abundance and growth in the context of its environment.


title: An attempt to find the correlations between body weight and the composition of gut microbiota in Zhejiang and Shanghai

abstract: Previous studies showed that the human gut microbiota was associated with metabolic diseases, but the interaction and mechanism between the gut microbiota and metabolic disease are still unclear. In this study, the gut microbiota of 58 persons living in Zhejiang and Shanghai area will be analyzed. Then, the potential contribution of the human gut microbiota to obesity/high Body Mass Index (BMI) will be explored. The gut microbiota was studied by high throughput sequencing analysis of bacterial 16S rRNA gene fragments, and the gut microbiota samples with different BMI were compared. Meanwhile, some gut microorganisms from faeces of a healthy individual were cultivated and isolated, and the classification was identified by 16S rRNA sequencing. The main microbes in human gut microbiota were assigned to the phyla of Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Moreover, four strains were isolated from an individual fecal sample, of which one species was assigned to Escherichia fergusonii and the other three strains were assigned to Weissella cibaria. These four species belong to both abundant and low-abundant species revealed by high throughput sequencing. It was found that individuals with different BMI have different gut microbiota; while the differences are not significant. Also, the Firmicutes/Bacteroidetes ratio increases with the decrease of BMI, which is corresponding to previous results. In the future, more cohort gut microbiota in Zhejiang and Shanghai area will be collected and recovered, and the gut microbiota database of Zhejiang and Shanghai area will be built up in order to provide the basis for future gut microbiota modulation in this area.


title: Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

abstract:
Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 hours while excreting a dark brown component to the medium, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.

HighlightsO_LIParacetamol was fully degraded by activated sludge from hospital wastewater.
C_LIO_LILow paracetamol concentrations were removed by a diverse microbial community.
C_LIO_LIPseudomonas sp. dominated cultures with high paracetamol concentration.
C_LIO_LIUncharacterized amidases are probably involved in degrading paracetamol in WWTPs.
C_LIO_LIDeaminases and dioxygenases might be degrading paracetamol transformation products.
C_LI


title: VanRS and CroRS cross-talk revealed by coevolutionary modeling regulates antibiotic resistance in VanA-type vancomycin-resistant Enterococcus faecalis

abstract:
Enterococcus faecalis is an opportunistic pathogen that can cause bacteremia and endocarditis. Previous studies have shown that concurrent treatment with cephalosporin and vancomycin antibiotics exhibit synergy in vancomycin-resistant E. faecalis to render the bacterium susceptible to antibiotic treatment whereas treatment with each antibiotic separately was not successful. Proteins responsible for mediating vancomycin and cephalosporin resistance are classified as two-component systems (TCS). TCS consist of a histidine kinase that phosphorylates a response regulator after environmental activation. These signaling networks have been shown to exhibit cross-talk interactions, and through direct coupling analysis, we identify encoded specificity between vancomycin resistance TCS, which are horizontally acquired, and cephalosporin resistance TCS, which are endogenous to E. faecalis. To verify cross-talk between these pathways is responsible for vancomycin and cephalosporin synergy, we use RNA-Seq to identify differentially expressed genes in VanA- and VanB-type vancomycin resistant enterococci after treatment with the cephalosporin antibiotic, ceftriaxone, and also with vancomycin. We find that cross-talk between VanSA and CroR in strain HIP11704 may be responsible for synergy, demonstrating that horizontally acquired TCS can have large impacts on pre-existing signaling networks. The presence of encoded specificity between exogenous TCS and endogenous TCS show that the systems co-evolve, and cross-talk between these systems may be exploited to engineer genetic elements that disrupt antibiotic resistance TCS pathways.

Author SummaryBacteria may transmit genetic elements to other bacteria through the process known as horizontal gene transfer. In some enterococci, vancomycin resistance genes are acquired this way. Proteins encoded within the bacterial genome can interact with proteins acquired through horizontal gene transfer. The interaction that occurs between proteins VanSA and VanRA is known to mediate vancomycin antibiotic resistance in VanA-type vancomycin resistant enterococci (VRE), and the interaction between proteins CroS and CroR is an important pathway in cephalosporin antibiotic resistance. We show that the VanSA, which is obtained through horizontal gene transfer, inhibits CroR under treatment with antibiotics vancomycin and ceftriaxone. This interaction is responsible for the observed synergy between vancomycin and ceftriaxone in VanA-type VREs. These findings demonstrate how horizontally acquired genes may produce proteins that interrupt known protein interactions, including antibiotic resistance signaling pathways in bacteria. Furthermore, the specific mechanism found for VanA-type VREs provides a basis for engineering of horizontally acquired proteins that disrupt antibiotic resistance pathways.


title: Availability of abundant thiamine determines efficiency of thermogenic activation in human neck area derived adipocytes

abstract:
ObjectiveBrown/beige adipocytes are characterized by expression of uncoupling protein-1 (UCP1) that enables them to dissipate energy as heat instead of generating ATP. The activation of this process can alleviate obesity as it augments energy expenditure. Human brown adipose tissue is interspersed in distinct anatomical regions including the deep neck area. We found that UCP1 enriched adipocytes differentiated from progenitors of this depot highly expressed ThTr2 transporter of thiamine, the precursor of thiamine pyrophosphate (TPP) cofactor for mitochondrial fuel generating enzymes, and aimed to investigate the importance of thiamine availability during thermogenic activation.

MethodsHuman adipocytes were differentiated from subcutaneous and deep neck precursors and activated for thermogenesis by the cell permeable dibutyryl-cAMP, which mimics adrenergic stimulation. Proton leak respiration reflecting heat generation was monitored by Seahorse XF analyzer. Direct mitochondrial effect of TPP was observed in flux assay of permeabilized adipocytes. Expression of thermogenic genes and proteins was analyzed by RT-qPCR and immunoblotting, respectively.

ResultsInhibition of ThTr2 during thermogenic activation of deep and subcutaneous neck derived adipocytes by cAMP led to decreased proton leak respiration reflecting lower uncoupling activity. In the absence of thiamine, cAMP-induced elevation of proton leak respiration was diminished but restored by thiamine addition reaching highest levels in deep neck adipocytes and at concentrations larger than present in human blood plasma. Addition of TPP to permeabilized adipocytes increased proton leak respiration fueled by one of the TPP-dependent enzymes, pyruvate dehydrogenase. ThTr2 inhibition also hampered cAMP-dependent induction of UCP1, PGC1a and other browning marker genes, along with mitochondrial complex subunits, and thermogenic induction of these genes was potentiated by thiamine in a concentration dependent manner.

ConclusionOur study has revealed the importance of amply supplied thiamine during thermogenic activation in human adipocytes. Thiamine may increase heat generation by providing TPP for TPP-dependent enzymes which lack this cofactor and by potentiating the induction of UCP1 and other thermogenic genes.

HighlightO_LIAbundant thiamine is required for efficient activation of UCP1 dependent thermogenesis in human deep neck derived adipocytes
C_LIO_LIInhibition of thiamine transporters leads to decreased thermogenic response
C_LIO_LIIn stimulated adipocytes, thiamine supply provides extra thiamine pyrophosphate for increasing pyruvate dehydrogenase activity to generate sufficient fuel of UCP1 dependent respiration.
C_LIO_LIAdrenergic stimulation of thermogenic gene expression is potentiated by thiamine in a concentration dependent manner
C_LI

category: cell biology


title: Inflammatory stress signaling via NF-kB alters accessible cholesterol to upregulate SREBP2 transcriptional activity in endothelial cells

abstract: There is a growing appreciation that a tight relationship exists between cholesterol homeostasis and immunity in leukocytes, however, this relationship has not been deeply explored in the vascular endothelium. Endothelial cells (ECs) rapidly respond to extrinsic signals, such as tissue damage or microbial infection, by upregulating factors to activate and recruit circulating leukocytes to the site of injury and aberrant activation of ECs leads to inflammatory based diseases, such as multiple sclerosis and atherosclerosis. Here, we studied the role of cholesterol and its master regulator, SREBP2, in the EC responses to inflammatory stress. Treatment of ECs with pro-inflammatory cytokines upregulates SREBP2 cleavage and cholesterol biosynthetic gene expression within the late phase of the acute inflammatory response. Furthermore, SREBP2 activation was dependent on NF-{kappa}B DNA binding and canonical SCAP-SREBP2 processing. Mechanistically, inflammatory activation of SREBP was mediated by a reduction in accessible cholesterol, leading to heightened sterol sensing and downstream SREBP2 cleavage. Detailed analysis of NF-{kappa}B inducible genes that may impact sterol sensing resulted in the identification of a novel RELA-inducible target, STARD10, that mediates accessible cholesterol homeostasis in ECs. Thus, this study provides an in-depth characterization of the relationship between cholesterol homeostasis and the acute inflammatory response in EC.


title: The mechanism underlying redundant functions of the YTHDF proteins

abstract: The YTH N6-methyladenosine RNA binding proteins (YTHDFs) mediate the functional effects of N6-methyladenosine (m6A) on RNA. Recently, a report proposed that all YTHDFs work redundantly to facilitate RNA decay, raising questions about the exact functions of individual YTHDFs, especially YTHDF1 and YTHDF2. We show that YTHDF1 and YTHDF2 differ in their low-complexity domains (LCDs) and exhibit different behaviors in condensate formation and subsequent physiological functions. Biologically, we also find that the global stabilization of RNA after depletion of all YTHDFs is driven by increased P-body formation and is not strictly m6A dependent.


title: Senescent Preosteoclast Secretome Promotes Metabolic Syndrome Associated Osteoarthritis through Cyclooxygenase 2

abstract:
BackgroundMetabolic syndrome-associated osteoarthritis (MetS-OA) is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. The aim of this study was to determine the role of cellular senescence in the development of MetS-OA.

MethodsAnalysis of the human osteoarthritis initiative (OAI) dataset was conducted to investigate the MRI subchondral bone features of MetS-human OA participants. Joint phenotype and senescent cells were evaluated in two MetS-OA mouse models: high-fat diet (HFD)-challenged mice and STR/Ort mice. In addition, the molecular mechanisms by which preosteoclasts become senescent as well as how the senescent preosteoclasts impair subchondral bone microenvironment were characterized using in vitro preosteoclast culture system.

ResultsHumans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. MetS-OA mice exhibited a rapid increase in joint subchondral bone plate and trabecular thickness before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence at the pre- or early-osteoarthritis stage and acquire a unique secretome to stimulate osteoblast differentiation and inhibit osteoclast differentiation. Antagonizing preosteoclast senescence markedly mitigates pathological subchondral alterations and osteoarthritis progression in MetS-OA mice. At the molecular level, preosteoclast secretome activates COX2-PGE2, resulting in stimulated differentiation of osteoblast progenitors for subchondral bone formation. Administration of a selective COX2 inhibitor attenuated subchondral bone alteration and osteoarthritis progression in MetS-OA mice. Longitudinal analyses of the human Osteoarthritis Initiative (OAI) cohort dataset also revealed that COX2 inhibitor use, relative to non-selective nonsteroidal anti-inflammatory drug use, is associated with less progression of osteoarthritis and subchondral bone marrow lesion worsening in participants with MetS-OA.

ConclusionsOur findings suggest a central role of a senescent preosteoclast secretome-COX2/PGE2 axis in the pathogenesis of MetS-OA, in which selective COX2 inhibitors may have disease-modifying potential.

FundingThis work was supported by the National Institutes of Health grant R01AG068226 and R01AG072090 to M.W., R01AR079620 to S.D., and P01AG066603 to X.C.


title: An endolysosome membrane transformation process for engulfment of autophagosomes independently of ESCRT

abstract: Endolysosome, usually regarded as the cellular recycling bin, digests materials from multiple origins. The materials from different origins are delivered to endolysosome through the vesicle fusion, kiss-and-run mechanisms, CMA or microautophagy. However, it remains unknown whether endolysosome can receive cargo via other ways. Here, we reported another endolysosomal process for receiving materials. In this, endolysosome receives materials by extending two arms which embraces autophagosomes and engulfs the autophagosomes ultimately, but not via the conventional fusion of autophagosomes with endolysosomes. We named this process as LEA (lysosome eats autophagosome) and the endolysosome arms as LF (endolysosome filopodia) provisionally. The endolysosomes with engulfed autophagosomes (LEA endolysosomes) get more autophagosomes via the fusion with other LEA endolysosomes. The engulfed autophagosomes are labelled by F-actin on their membranes and have ER protein Sec61{beta} and peroxisome protein Pex14 inside their lumens, but mitochondria are excluded outside endolysosome. Our discovery of LEA and LF reveal an unidentified endolysosome transformation process which is responsible for receiving cargoes.


title: Net-shaped DNA nanostructure designed for rapid/sensitive detection and potential inhibition of SARS-CoV-2 virus

abstract: We present a net-shaped DNA nanostructure (called "DNA Net" herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive ([~] $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1x103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

category: bioengineering


title: Network Thermodynamics of Biological Systems: A Bond Graph Approach

abstract: Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to come. This paper brings together and summarises the seminal work of his group in applying energy-based bond graph methods to biological systems. In particular, this paper: (a) motivates the need to consider energy in modelling biology; (b) introduces bond graphs as a methodology for achieving this; (c) describes extensions to modelling electrochemical transduction; (d) outlines how bond graph models can be constructed in a modular manner and (e) describes stoichiometric approaches to deriving fundamental properties of reaction networks. These concepts are illustrated using a new bond graph model of photosynthesis in chloroplasts.

category: systems biology


title: Temporal and spatial patterns of vertebrate extinctions during the Anthropocene

abstract: The human-induced annihilation of modern biodiversity is dragging the planet into a mass extinction that has already altered patterns of life globally. Among vertebrates, over 500 species have become extinct or possibly extinct in the last five centuries - an extinction rate that would have taken several millennia without human intervention. Vertebrate extinctions have often been quantified as cumulative counts that reveal sharp increases in losses over time. Here, we quantify global tetrapod extinctions since the 1400s using numbers of species losses across successive and independent time periods until present. Our results reveal that extinctions were low and fundamentally restricted to islands in pre-industrial times, experiencing a significant increase and spread over continental mainland following the onset of the industrial revolution. Recent amphibian extinctions alarmingly exceed the extinctions of all tetrapods, while extinctions of island birds account for a third of all extinctions. Finally, we quantified the relationship between human population growth (HPG, as a proxy for aggregate human effects on the environment) and extinctions between 1800-2000, to then predict that an estimated 838 tetrapod species will go extinct between 2030-2100 based on United Nations HPG projections. These findings further warn humanity about the need to sustainably control HPG and the destructive impacts of rapid environmental change on ecosystems worldwide.

category: ecology


title: The characteristics of high-dark-diversity habitats derived from lidar

abstract: A key aspect of nature conservation is knowledge of which aspects of nature to conserve or restore to favor the characteristic diversity of plants in a given area. Here, we used a large plant dataset with > 40.000 plots combined with airborne laser scanning (lidar) data to reveal the local characteristics of habitats having a high plant dark diversity - i.e., absence of suitable species - at national extent (> 43.000 km2). Such habitats have potential for reaching high realized diversity levels and hence are important in a conservation context. We calculated 10 different lidar based metrics (both terrain and vegetation structure) and combined these with 7 different field-based measures (soil chemistry and species indicators). We then used Integrated Nested Laplace Approximation for modelling plant dark diversity across 33 North European habitat types (open landscapes and forests) selected by the European communities to be important. In open habitat types high-dark-diversity habitats had relatively low pH, high nitrogen content, tall homogenous vegetation and overall relatively homogenous terrains (high terrain openness) although with a rather high degree of local microtopographical variations. High-dark-diversity habitats in forests had relatively tall vegetation, few natural-forest indicators, low potential solar radiation input and a low cover of small woody plants. Our results highlight important vegetation, terrain and soil related factors that managers and policymakers should be aware of in conservation and restoration projects to ensure a natural plant diversity, for example low nutrient loads, natural microtopography and open forests with old-growth elements such as dead wood and rot attacks.


title: Acoustic cues and season affect mobbing responses in a bird community

abstract: Heterospecific communication is common for birds when mobbing a predator. However, joining the mob should depend on the number of callers already enrolled, as larger mobs imply lower individual risks for the newcomer. In addition, some  community informant species seem more reliable regarding the information transferred in mobbing calls. Birds should therefore rely on both the number of callers and the species identity of the caller(s) when mobbing. Given the large differences in social organization and environment throughout the year in passerine communities, the response to acoustic cues could be impacted by the season. In the present study, we tested the potential interaction between the number of callers, the species identity of the caller (i.e., coal tit or crested tit), and the season on birds mobbing response using a factorial playback experiment. Overall, we found that soundtracks with three callers triggered more mobbing than soundtracks with one caller and that soundtracks with coal tits calls triggered more mobbing than soundtracks with crested tits calls. However, this effect interacted with the season: in spring, only soundtracks with three coal tits triggered a mobbing response. We therefore confirm the hypothesis that birds consider both the species and the number of callers when joining a mobbing chorus. Moreover, our study demonstrates how seasonal context interacts with acoustic cues and illustrates the dynamic properties of heterospecific communication.


title: Parental care allows genetic variation to accumulate by relaxing selection

abstract: Benign social environments are thought to relax selection against deleterious mutations, enabling them to accumulate in the genome. However, it has not proved straightforward to demonstrate causality in this relationship. We allowed burying beetle populations to evolve with and without the benign effects of parental care for over 20 generations, before inbreeding lineages that were seeded from these experimental populations to expose any differences in their mutation load. We found that inbred lineages with a history of parental care went extinct most quickly, indicating that they harboured more recessive deleterious alleles.

category: evolutionary biology


title: Rapid evolutionary change in trait correlations of a single protein

abstract: Many organismal traits are genetically determined and covary in evolving populations. The resulting trait correlations can either help or hinder evolvability - the ability to bring forth new and adaptive phenotypes. The evolution of evolvability requires that trait correlations themselves must be able to evolve, but we know little about this ability. To learn more about it, we here study one of the simplest evolvable systems, a gene encoding a single protein, and two traits of this protein, namely the ability to emit yellow and green light. We show that correlations between these two traits can evolve rapidly through both mutation and selection on short evolutionary time scales. In addition, we show that these correlations are driven by a proteins ability to fold, because single mutations that alter foldability can dramatically change trait correlations. Since foldability is important for most proteins and their traits, mutations affecting protein folding may alter trait correlations mediated by many other proteins. Thus, mutations that affect protein foldability may also help shape the correlations of complex traits that are affected by hundreds of proteins.


title: Loss of CD24 promotes radiation- and chemo-resistance by inducing stemness properties associated with a hybrid E/M state in breast cancer cells

abstract: There is compelling evidence that cancer stem cells (CSCs) play an essential role in failure of conventional antitumor therapy. In breast cancer, CD24-/low/CD44+ phenotype as well as a high aldehyde dehydrogenase activity (ALDH+) are widely associated with CSC subtypes. Furthermore, CD24-/low/CD44+ pattern is also characteristic of the mesenchymal cells generated by an epithelial-mesenchymal transition (EMT). CD24 is a surface marker expressed in many tumor types, however, its biological functions and role in cancer progression and treatment resistance remain poorly documented. We have previously shown that loss of CD24 expression in breast cancer cells is associated with radiation resistance, in relationship with the control of oxidative stress. Because ROS are known to mediate the effects of anticancer drugs as well as ionizing radiation, we investigated if CD24 could be defined as an actor of both radiation- and chemo-resistance of breast cancer cells. Using the HMLE breast cancer cell model, we observed that loss of CD24 expression induces stemness properties associated with the acquisition of a hybrid E/M phenotype. The CD24-/low cells were intrinsically more resistant than CD24+ cells. The resistance was linked to a lower level of ROS, and CD24 controlled ROS levels through the regulation of mitochondrial functions independently of antioxidant activity. Together, these results suggest a key role of CD24 in de-differentiation process of breast cancer cells, promoting acquisition of therapeutic resistance properties.

category: cancer biology


title: Mechanistic target of rapamycin (mTOR) regulates self-sustained quiescence, tumor indolence and late clinical metastasis in a Beclin-1-dependent manner.

abstract:
Self-sustained quiescence (SSQ) has been characterized as a stable but reversible non-proliferative cellular state that limits the cloning of cultured cancer cells. By developing refined clonogenic assays, we showed here that cancer cells in SSQ can be selected with anticancer agents and that culture at low cell density induced SSQ in pancreas and prostate adenocarcinoma cells. Pre-culture of cells in 3D or their pretreatment with pharmacological inhibitors of mechanistic target of rapamycin (mTOR) synergize with low cell density for induction of SSQ in a Beclin-1-dependent manner. Dissociated pancreatic adenocarcinoma (PAAD) cells rendered defective for SSQ by down-regulating Beclin-1 expression exhibit higher tumor growth rate when injected subcutaneously into mice. Conversely, dissociated PAAD cells in SSQ promote the formation of small indolent tumors that eventually transitioned to a rapid growth phase. Ex vivo clonogenic assays showed that up to 40% of clonogenic cancer cells enzymatically dissociated from resected growing mouse tumors could enter SSQ, suggesting that SSQ could significantly impact the proliferation of cancer cells naturally dispersed from tumors. Remarkably, the kinetics of clinical metastatic recurrence in 124 patients with pancreatic adenocarcinoma included in the TGCA-PAAD project could be predicted from the mRNA levels of Beclin-1 and Cyclin-A2, a marker of both cell proliferation and mTOR complex 1 activity, in their primary tumor. Overall, our data show that SSQ is likely to promote the late development of clinical metastases and provide a rationale for a better selection of patients eligible for intensive adjuvant chemotherapy. Additionally, they suggest that identifying new agents targeting cancer cells in SSQ could help improve patient survival.

SignificanceThis study reveals that a particular state of cancer cell quiescence could largely determine delayed clinical metastasis, challenging current models of cancer cell persistence and offering new avenues for improving adjuvant chemotherapy.


title: Hypoxia promotes an inflammatory phenotype of fibroblasts in pancreatic cancer

abstract: Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extensive fibroinflammatory stroma and often experiences conditions of insufficient oxygen availability, or hypoxia. Cancer-associated fibroblasts (CAF) are a predominant and heterogeneous population of stromal cells within the pancreatic tumor microenvironment. Here, we uncover a previously unrecognized role for hypoxia in driving an inflammatory phenotype in PDAC CAFs. We identify hypoxia as a strong inducer of tumor IL1 expression, which is required for inflammatory CAF (iCAF) formation. Notably, iCAFs preferentially reside in hypoxic regions of PDAC. Our data implicate hypoxia as a critical regulator of CAF heterogeneity in PDAC.


title: NPC1 confers metabolic flexibility in Triple Negative Breast Cancer

abstract: Triple negative breast cancer (TNBC) often undergoes at least partial epithelial-to-mesenchymal transition (EMT) to facilitate metastasis. Identifying EMT-associated characteristics can reveal novel dependencies that may serve as therapeutic vulnerabilities in this aggressive breast cancer subtype. We find that NPC1, which encodes the lysosomal cholesterol transporter Niemann-Pick Type C1 is highly expressed in TNBC as compared to estrogen receptor-positive (ER+) breast cancer and is significantly elevated in high grade disease. We demonstrate that NPC1 is directly targeted by microRNA-200c (miR-200c) a potent suppressor of EMT, providing a mechanism for its differential expression in breast cancer subtypes. Silencing of NPC1 in TNBC causes an accumulation of cholesterol-filled lysosomes and drives decreased growth on soft agar and invasive capacity. Conversely, overexpression of NPC1 in an ER+ cell line increases growth on soft agar. We further identify TNBC cell lines as cholesterol auxotrophs, however, they do not solely depend on NPC1 for adequate cholesterol supply. Genetic inhibition of NPC1 in TNBC cell lines led to altered mitochondrial function and morphology, suppression of mTOR signaling, and accumulation of autophagosomes. A small-molecule inhibitor of NPC1, U18666A, decreased TNBC proliferation and synergized with the chemotherapeutic drug, Paclitaxel. This work suggests that NPC1 promotes aggressive characteristics in TNBC and identifies NPC1 as a potential therapeutic target.


title: Extensive patient-to-patient single nuclei transcriptome heterogeneity in pheochromocytomas and paragangliomas

abstract: Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors of varied genetic makeup, associated with high cardiovascular morbidity and a variable risk of malignancy. The source of the transcriptional heterogeneity of the disease and the underlying biological processes determining the outcome in PCPG remains largely unclear. We focused on PCPG tumors with germline SDHB and RET mutations, representing distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients and found high patient-to-patient transcriptome heterogeneity of the neuroendocrine tumor cells. The tumor microenvironment also showed heterogeneous profiles mainly contributed by macrophages of the immune cell clusters and Schwann cells of the stroma. Performing non-negative matrix factorization we identified common transcriptional programs active in RET and SDHB as well as distinct modules including neuronal development, hormone synthesis and secretion, and DNA replication. Comparison of the SDHB and RET transcriptomes with that of developmental stages of adrenal gland formation suggests different developmental stages at which PC and PG tumors appear to be arrested.


title: Reconstructing the decline of Atlantic Cod with the help of environmental variability in the Scotia Shelf of Canada

abstract:
Ignoring environmental variability can lead to imprecise and inaccurate estimates of abundance and distribution of organisms. Fully embracing environmental variability can improve precision and accuracy of estimates of abundance and distribution, especially when it can be measured with lower costs. Using the example of Atlantic cod in the Scotian Shelf of the northwest Atlantic Ocean, we demonstrate the improved clarity of their historical population trends when such informative features are included. Further, the use of Bayesian spatiotemporal Conditional autoregressive models substantially improves our ability to understand the role of ecosystem variability upon cod, even when samples are incomplete or missing. Finally, by decomposing biomass into number, weight and a Hurdle process to estimate habitat conditions, we can extract much more information on what has occurred in the past and make reasoned inference on processes.

One-Sentence SummaryDeconstructing and reconstructing cod with environmental variability


title: Resetting of H3K4me2 during mammalian parental-to-zygote transition

abstract:
Upon sperm and oocyte fertilization, drastic histone modification reprograming occurs during preimplantation development. However, the global H3K4me2 landscape and its dynamics reprogramming in this period remains largely unknown. Herein we investigate the erasure and re-establishment of H3K4me2 in mouse GV, MII and embryos using an improved approach called Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for histone modification with high-throughput sequencing. We find H3K4me2 extensively exists as a non-canonical pattern in mouse GV oocytes and early embryos. Interestingly, H3K4me2 is erased in MII oocyte and re-established in late 2-cell stage. Importantly, mouse embryos acquire widespread H3K4me2 in CpG-rich and hypomethylated regulatory regions in 4-cell stage, as well as 8-cell stage, but drastic changes happen upon ICM, these CpG-rich H3K4me2 regulatory regions then resolve to either active or repressed states. In summary, our study not only unveil that H3K4me2 transition from parental to zygote, but also provide a H3K4me2 profile during early embryo development, and this will enhance our comprehension to epigenetic reprogramming during mouse early development and in vitro fertilization.

HighlightO_LIH3K4me2 present differential patterns in sperm and oocytes, as no-canonical pattern in GV oocytes but canonical of sperm in mouse.
C_LIO_LIGV H3K4me2 peaks were almost erased in MII oocytes, and reconstructed accompanying ZGA occurred, the first landscape of H3K4me2 during early mammalian development was provided.
C_LIO_LINon-canonical H3K4me2 in mammalian embryos and pervasive H3K4me2 in CpG-rich regulatory regions in 4 and 8-cell embryos.
C_LIO_LICpG-rich H3K4me2 regulatory regions resolve to either active or repressed states in ICM.
C_LI

category: genetics


title: Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

abstract: Despite extensive efforts to address it, the vastness of uncharacterized  dark matter microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28x N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.

category: genomics


title: Autonomous untethered microinjectors for gastrointestinal delivery of insulin

abstract: The delivery of macromolecular drugs via the gastrointestinal (GI) tract is challenging. Macromolecular drugs display low stability and poor absorption across the intestinal epithelium. While permeation-enhancing drug delivery methods can increase the bioavailability of low molecular weight drugs, the effective delivery of high molecular weight drugs across the tight epithelial cell junctions remains a formidable challenge. Here, we describe autonomous microinjectors that can efficiently penetrate the GI mucosa and deliver insulin systemically. In addition, we performed in vitro studies to characterize insulin release and the penetration capacity of microinjectors and measure in vivo release of insulin in live rats. We found that the microinjectors administered within the luminal GI tract could deliver insulin trans-mucosally to the systemic circulation at similar levels to intravenously administered insulin. Due to their small size, tunability in sizing and dosing, wafer-scale fabrication, and parallel, autonomous operation, we anticipate that these novel microinjectors could significantly advance drug delivery across the GI tract mucosa to the systemic circulation.


title: A Self-Healing, Viscoelastic Hydrogel Promotes Healing of Brain Lesions

abstract: Brain lesions can arise from traumatic brain injury, infection, and craniotomy. Although injectable hydrogels show promise for promoting healing of lesions and health of surrounding tissue, enabling cellular ingrowth and restoring neural tissue continue to be challenging. We hypothesized that these challenges arise in part from viscoelastic mismatch between the hydrogel and the brain parenchyma, and tested this hypothesis by developing and evaluating a self-healing hydrogel that mimicked both the composition and viscoelasticity of native brain parenchyma. The hydrogel was crosslinked by dynamic boronate ester bonds between phenylboronic acid grafted hyaluronic acid (HA-PBA) and dopamine grafted gelatin (Gel-Dopa). This HA-PBA/Gel-Dopa hydrogel could be injected into a lesion cavity in a shear-thinning manner with rapid hemostasis, high tissue adhesion and efficient self-healing. We tested this in an in vivo mouse model of brain lesions and found the hydrogel to support neural cell infiltration, decrease astrogliosis and glial scars, and close the lesions. The results suggest a role for viscoelasticity in brain lesion healing, and motivate additional experimentation in larger animals as the technology progresses towards potential application in humans.


title: Single-cell genomic analysis of triple-negative breast cancer fibroblasts uncovers evolutionarily conserved features and potential therapeutic targets

abstract: To explore cancer associated fibroblasts (CAFs) in triple-negative breast cancers (TNBC), we performed scRNA-seq analysis of fibroblasts from murine and human TNBCs. We observed three distinct CAF subtypes in mouse TNBC: two that are intermingled and adjacent to tumor cells, and one that is more distal. We present evidence that progression of CAFs from normal resident fibroblasts/pericytes involves upregulation of their Pdgf and Tgfb receptors along with reciprocal ligand upregulation in other cells within the tumor microenvironment. Additionally, extracellular matrix, glycolytic, and mitochondrial respiratory genes are strongly upregulated in all CAFs. Activation of extracellular matrix genes specifically in CAFs and not in normal fibroblasts provides numerous targets for CAF-based therapeutics, many of which are conserved in CAFs from human TNBC. In contrast, the subtype structure of CAFs was less conserved, which along with their transcriptional heterogeneity suggests that molecular targeting of CAFs is more practical than targeting CAF subtypes.


title: Design and validation of the first family of photo-activatable ligands for melatonin receptors

abstract: Melatonin is a neurohormone released in a circadian manner with peak levels during the night. In mammals, melatonin mediates its effects mainly through G protein-coupled MT1 and MT2 receptors. Drugs acting on melatonin receptors are indicated for circadian rhythm- and sleep-related disorders and major depression. Pharmacological tools to study the activation of these receptors with high temporal resolution are lacking. Here, we synthesized a family of light-activatable caged melatonin compounds by covalently attaching o-nitrobenzyl (o-NB) or coumarin photocleavable groups to the N-position of melatonin. All caged compounds showed the expected decrease in binding affinity for MT1 and MT2. Among them, the o-NB derivative MCS-0382 showed the best uncaging and biological properties upon light activation with a significant increase (2.5 log left-shift) in affinity and potency in melatonin receptor binding and signaling, respectively. Generation of biologically active melatonin from MCS-0382 was further demonstrated by its ability to modulate the excitation of SCN neurons in rat brain slices. MCS-0382 is now available to study melatonin effects in a temporally controlled manner in cellular and physiological settings.

category: pharmacology and toxicology


title: A new, Critically Endangered species of Impatiens (Balsaminaceae) from the coastal plain of the Republic of Congo

abstract: Impatiens moutsambotei is described from a herbarium specimen collected at a waterfall in forest on the coastal plain, below the Mayombe Mts of the Republic of Congo. Sharing many distinctive characters with Impatiens floretii of the Doudou Mts of Gabon, it is abundantly distinguished inter alia by the leaf-blades which are lanceolate or narrowly elliptic, not ovate, their bases acute, not obtuse or broadly rounded to truncate; the reduced, peduncular bracts bearing long, filiform setae, and not entire; the proximal (upper) of the lateral united petals are entire, not bifid; the spur is curved at the base and overlaps the lower sepal, not curved through its length to describe a semi-circle and held below the lower sepal. Both species are placed in the Impatiens macroptera species aggregate. Impatiens moutsambotei is known from a single site, where it was collected nearly 30 years ago and not seen since. The new species is assessed as Critically Endangered due to threats of habitat clearance from mining and road widening, and may be already be extinct.

category: plant biology


title: Generating variability from motor primitives during infant locomotor development

abstract: Motor variability is a fundamental feature of developing systems allowing motor exploration and learning. In human infants, leg movements involve a small number of basic coordination patterns called locomotor primitives, but whether and when motor variability could emerge from these primitives remains unknown. Here we longitudinally followed 10 neonates ([~]4 days old) until walking onset ([~]14 months old) and recorded the activity of their leg muscles during locomotor or rhythmic movements. Using unsupervised machine learning, we show that the structure of trial-to-trial variability changes during early development. In the neonatal period, infants own a minimal number of motor primitives but generate a maximal motor variability across trials thanks to variable activations of these primitives. A few months later, toddlers generate significantly less variability despite the existence of more primitives, due to more regularity within their activation. These results suggest that human neonates initiate motor exploration as soon as birth by variably activating a few basic locomotor primitives that later fraction and become more consistently activated by the motor system.

category: neuroscience


title: Get the gist of the story: Neural map of topic keywords in multi-speaker environment

abstract: Neural representation of lexico-semantics in speech processing has been revealed in recent years. However, to date, how the brain makes sense of the higher-level semantic gist (topic keywords) of a continuous speech remains mysterious. Capitalizing on a generative probabilistic topic modelling algorithm on speech materials to which participants listened while their brain activities were recorded by Magnetoencephalography (MEG), here we show spatio-temporal neural representation of topic keywords in a multi-speaker environment where task-relevant (attended) and -irrelevant (unattended) speech co-exits. We report the difference of neural representation between salient and less salient semantic gist of both attended and unattended speech. Moreover, we show that greater sensitivity to semantically salient unattended speech in the left auditory and motor cortices negatively mediates attended speech comprehension.


title: Sigh breathing rhythm depends on intracellular calcium oscillations in a population of inspiratory rhythmogenic preBötzinger complex neurons in mice

abstract:
The preBotzinger Complex (preBotC) of the lower brainstem generates two breathing-related rhythms: one for inspiration on a timescale of seconds and another that produces larger amplitude sighs on the order of minutes. Their underlying mechanisms and cellular origins remain incompletely understood. We resolve these problems via a joint experiment and modeling approach. Blocking purinergic gliotransmission does not perturb either rhythm and imaging experiments show that both rhythms emanate from the same glutamatergic neuron population. We hypothesized that these two disparate rhythms emerge in tandem wherein recurrent excitation gives rise to inspiratory rhythm while a calcium oscillator generates sighs; there is no obligatory role for gliotransmission, hyperpolarization activated mixed cationic current (Ih) in neurons, or synaptic inhibition-mediated coupling of separate populations. We developed a mathematical model that instantiates our working hypothesis. Tests of model predictions validate the single-population rhythmogenic framework, reproducing disparate breathing-related frequencies and the ability for inspiratory and sigh rhythms to be separately regulated in support of respiration under a wide array of conditions. Here we show how a single neuron population exploits two cellular tool-kits: one involving voltage-dependent membrane properties and synaptic excitation for inspiratory breathing (eupnea) and an intracellular biochemical oscillator for sighs, which ventilate and maintain optimal function in the compliant mammalian lung.

SIGNIFICANCE STATEMENTBreathing consists of two vital rhythms: one for eupnea that serves periodic physiological gas exchange and the other for sighs, which are larger breaths that occur minutes apart and serve to optimize pulmonary function. These rhythms with disparate frequencies emerge via a mechanism that is simpler than previously envisaged: it results from one neuron population (not two as previously thought) without need for gliotransmission or synaptic inhibition-mediated coupling of neuronal populations. We show that a low-frequency intracellular calcium oscillation underlies sighs and functions in parallel with the higher-frequency voltage-dependent network oscillation that drives eupnea. Exploiting two separate cellular tool kits enables quasi-independent breathing rhythms, which are unique features of breathing in mammals with compliant lungs.


title: Hierarchical cue control of drug seeking in the face of cost

abstract: Addiction is characterized by intermittent drug seeking despite rising costs. This behavior is heavily influenced by environmental stimuli that signal drug availability and reinforce seeking. We aimed to establish the relationship between three key aspects of human drug use in rats: the intermittent, binge nature of drug intake, the motivational conflict of drug seeking in the face of escalating negative costs, and the ability of different drug cues to interact to modulate relapse. Rats were trained to self administer cocaine on an intermittent access schedule, where brief drug availability states were signaled by a shift in the ambient lighting of the environment and cocaine delivery was signaled by a separate proximal cue. Rats then went through a conflict procedure, where foot shock intensity associated with cocaine seeking was escalated until intake was suppressed. We completed relapse tests where the drug delivery cue was non contingently presented alone, or in the context of dynamic drug availability state transitions. Intermittent access spurred psychomotor sensitization and binge-like cocaine intake. The intensity of binge-like drug taking during training was predictive of later drug seeking despite escalating costs. In relapse tests, the ability of a proximal drug cue to trigger relapse was gated by the presence of a global cue signaling drug-availability state transitions. Our results suggest that the pattern of drug intake plays a role in many features of addiction, including modifying an individuals willingness to endure high costs associated with drug seeking. Further, our results indicate that drug-related sensory information can be hierarchically organized to exert a dynamic modulating influence on drug-seeking motivation.


title: The ventral striatum contributes to energy balance

abstract: Obesity-related pathologies and anorexia nervosa are increasingly considered as opposite ends of eating disorders (ED) spectrum. Accordingly, accumulating evidence points to opposite dysregulations of common brain systems in these pathologies, the Nucleus Accumbens (NAc) in particular. However, to which extent alterations in NAc activity are sufficient to elicit ED-like behavioral dimensions remains to be established. Using acute, bidirectional, chemogenetic modulation of each NAc medium spiny neuron (MSN) subpopulation, we found that D1-MSNs and D2-MSNs oppositely regulate the balance between food intake and exercise-induced energy expenditure. As opposed to the limited effect of repeated chemogenetic manipulations of each MSN subpopulation, the concomitant manipulation of both MSN subpopulation had sustained effects. Repeated activation of D1-MSNs combined with repeated inhibition of D2-MSNs biased behavior toward activity-related energy expenditure leading to weight/fat loss, whilst the opposite manipulations favored energy intake and hence weight/fat gain. These results suggest that dysregulations of NAc dopaminoceptive MSN network might be at the core of EDs.


title: A Multidimensional Approach to Understanding the Emergence of Sex Differences in Internalizing Symptoms in Adolescence

abstract: Women are more vulnerable to internalizing disorders (e.g., depression and anxiety). This study took an integrative, developmental approach to investigate multidimensional factors associated with the emergence of sex differences in internalizing symptoms, using data from the Adolescent Brain Cognitive Development (ABCD) study. Indices of sex hormone levels (dehydroepiandrosterone, testosterone, and estradiol), physical pubertal development, task-based functional brain activity, family conflict, and internalizing symptoms were drawn from the ABCD studys baseline sample (9-to 10-year-old; N = 11,844). Principal component analysis served as a data-driven dimensionality reduction technique on the internalizing subscales to yield a single robust measure of internalizing symptoms. Moderated mediation analyses assessed whether associations between known risk factors and internalizing symptoms vary by sex. Results revealed direct and indirect effects of physical pubertal development on internalizing symptoms through family conflict across sexes. No effects were found of sex hormone levels or amygdala response to fearful faces on internalizing symptoms. Females did not report overall greater internalizing symptoms relative to males, suggesting that internalizing symptoms have not yet begun to increase in females at this age. Findings provide an essential baseline for future longitudinal research on the endocrine, neurocognitive, and psychosocial factors associated with sex differences in internalizing symptoms.


title: STEREOLOGICAL EVALUATION OF TISSUE PRESERVATION AFTERNEUROPROTECTIVE TREATMENTS FOR TRAUMATIC SPINAL CORDINJURY

abstract: Spinal cord injury (SCI) is a major cause of permanent disability and its causes and pathophysiological effects are very variables between patients. The assessment of tissue damage extent and neurodegeneration degree correlated with the functional evaluation are the most accepted tools to diagnose and prognose the trauma severity. Animal models of SCI have been used for treatment development and in the present work we evaluate the potency of stereological tools to estimate damage degree for a diagnostic of neural degeneration and locomotor and sensorial disability after SCI and the efficacy of different types of therapeutic strategies.


title: Lymph node-targeted vaccine boosting of TCR-T cell therapy enhances anti-tumor 1 function and eradicates solid tumors

abstract:
While T cell receptor (TCR)-modified T cell therapies have shown promise against solid tumors, overall therapeutic benefits in clinical practice have been modest due in part to suboptimal T cell persistence and activation in vivo, alongside the possibility of tumor antigen escape. In this study, we demonstrate an approach to enhance the in vivo persistence and activation of TCR-T cells through combination with Amphiphile (AMP)-vaccination including cognate TCR-T peptides. AMP-modification improves lymph node targeting of conjugated tumor immunogens and adjuvants, thereby coordinating a robust T cell-priming endogenous immune response. Vaccine combination with TCR-T cell therapy provided simultaneous in vivo invigoration of adoptively transferred TCR-T cells and in situ priming of the endogenous anti-tumor T cell repertoire. The resulting induction of an adoptive and endogenous anti-tumor effect led to durable responses in established murine solid tumors refractory to TCR-T cell monotherapy. Protection against recurrence was associated with antigen spreading to additional tumor-associated antigens not targeted by vaccination. Enhanced anti-tumor efficacy was further correlated with pro-inflammatory lymph node transcriptional reprogramming and increased antigen presenting cell maturation, resulting in TCR-T cell expansion and functional enhancement in lymph nodes and solid tumor parenchyma without lymphodepletion. In vitro evaluation of AMP-peptides with matched human TCR-T cells targeting NY-ESO-1, mutant KRAS, and HPV16 E7 illustrated the clinical potential of AMP-vaccination to enhance human TCR-T cell proliferation, activation, and anti-tumor activity. Taken together, these studies provide rationale and evidence to support clinical evaluation of the combination of AMP-vaccination with TCR-T cell therapies to augment anti-tumor activity.

SummaryAMP-vaccination targets the lymph nodes to enhance TCR-T cell therapy resulting in solid tumor eradication and durable protection against recurrence.

category: immunology


title: Mechanical forces impair antigen discrimination by reducing differences in T cell receptor off-rates

abstract:
T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains unclear. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds), and this was confirmed by molecular dynamic simulations. Consistent with these findings, we show that the best characterized catch-bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination and we suggest this new force-shielding role for the adhesion receptors CD2 and LFA-1.

One sentence summaryMechanical forces disproportionately accelerate the off-rates of higher-affinity antigens reducing T cell antigen discrimination


title: Measurement of Accumulation of Small Molecules into Gram-negative Bacteria

abstract: Some of the most dangerous bacterial pathogens (Gram-negative and mycobacteria) deploy a formidable secondary membrane barrier to reduce the influx of exogenous molecules. For Gram-negative bacteria, this second exterior membrane is known as the Outer Membrane (OM) and its unique composition is generally what restricts the passive permeation of small molecules into bacterial cells. While it is well appreciated that the OM is a principal determinant of small molecule permeation, it has proven to be challenging to assess this feature in a robust and quantitative way. Herein, we describe the development of the Bacterial Chloro-Alkane Penetration Assay (BaCAPA), which employs the use of a genetically encoded protein called HaloTag, to measure the uptake and accumulation of molecules into Gram-negative bacteria. Directing the localization of the HaloTag protein to either the cytoplasm or periplasm of Escherichia coli (E. coli) enabled a compartmental analysis of permeation across individual cell membranes. Significantly, we also showed that BaCAPA can be used to analyze the permeation of molecules within the phagocytes of macrophages, which may prove critical in the analysis of intracellular pathogens. Together, our results show that BaCAPA can effectively report on the accumulation of molecules into bacterial cells and we anticipate that this will widen the set of tools available to generally measure permeability into bacterial cells.


title: The Ndc80-Cdt1-Ska1 complex constitute a minimal processive kinetochore-microtubule coupling unit

abstract: The Ndc80 kinetochore complex is essential for robust kinetochore-microtubule (k-MT) attachments during mitosis. Ndc80 has been shown to recruit the Ska1 complex to kinetochores, where Ska1 is thought to aid in k-MT coupling by Ndc80. Our previous work has shown that Cdt1, a DNA replication licensing factor, is a novel mitotic spindle-associated protein that is also recruited to kinetochores via Ndc80 and is required for stabilizing k-MT attachments. In this study, we developed auxin-induced degron (AID)-tagging to validate the previously demonstrated mitotic role of Cdt1. We demonstrate a direct interaction between Cdt1 and Ska1 that is essential for proper recruitment of Cdt1 to kinetochores and spindle microtubules. We find that Cdk1dependent phosphorylation of Cdt1 during mitosis is critical for Ska1-binding, consequently regulating the stabilization of metaphase k-MT attachments and normal mitotic progression. Total internal reflection fluorescence microscopy (TIR-FM) experiments reveal that Cdt1 synergizes with the Ndc80 and the Ska1 complexes for microtubule-binding. Further, we show that single Cdt1 molecules form diffusive tripartite complexes with Ndc80 and Ska1 that can processively track the ends of dynamic microtubules in vitro. Taken together our data identifies a minimal molecular unit responsible for bidirectional processive tip tracking of kinetochores.


title: GliaMorph: A modular image analysis toolkit to quantify Müller glial cell morphology

abstract:
Cell morphology is critical for all cell functions. This is particularly true for glial cells as they rely on their complex shape to contact and support neurons. However, methods to quantify complex glial cell shape accurately and reproducibly are lacking. To address this gap in quantification approaches, we developed an analysis pipeline called "GliaMorph". GliaMorph is a modular image analysis toolkit developed to perform (i) image pre-processing, (ii) semi-automatic region-of-interest (ROI) selection, (iii) apicobasal texture analysis, (iv) glia segmentation, and (v) cell feature quantification. Muller Glia (MG) are the principal retinal glial cell type with a stereotypic shape linked to their maturation and physiological status. We here characterized MG on three levels, including (a) global image-level, (b) apicobasal texture, and (c) apicobasal vertical-to-horizontal alignment. Using GliaMorph, we show structural changes occurring in the developing retina. Additionally, we study the loss of cadherin2 in the zebrafish retina, as well as a glaucoma mouse disease model. The GliaMorph toolkit enables an in-depth understanding of MG morphology in the developing and diseased retina.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=144 HEIGHT=200 SRC="FIGDIR/small/490765v1_ufig1.gif" ALT="Figure 1">
View larger version (73K):
org.highwire.dtl.DTLVardef@1b1dddaorg.highwire.dtl.DTLVardef@5c54b4org.highwire.dtl.DTLVardef@1bd3221org.highwire.dtl.DTLVardef@2628e8_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIGlial morphology is complex, making it challenging to accurately quantify 3D cell shape.
C_LIO_LIWe developed the GliaMorph toolkit for image pre-processing, glial segmentation, and quantification of Muller glial cells.
C_LIO_LIMuller glia elaborate their morphology and rearrange subcellular features during embryonic development.
C_LIO_LIGliaMorph accurately identifies subcellular changes in models with disrupted glia cells, including zebrafish cadherin2 loss of function and a mouse glaucoma model.
C_LI

category: developmental biology


title: Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism

abstract: Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously - from embryo through adulthood - in the nervous system. The functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component, design principle (Hox transcriptional autoregulation counterbalanced by negative UNC-3 feedback) for homeostatic control of Hox gene expression in adult MNs. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity.


title: RanBP1 plays an essential role in directed migration of neural crest cells during development.

abstract: Collective cell migration is essential for embryonic development, tissue regeneration and repair, and has been implicated in pathological conditions such as cancer metastasis. It is, in part, directed by external cues that promote front-to-rear polarity in individual cells. However, our understanding of the pathways that underpin the directional movement of cells in response to external cues remains incomplete. To examine this issue we made use of neural crest cells (NC), which migrate as a collective during development to generate vital structures including bones and cartilage. Using a candidate approach, we found an essential role for Ran-binding protein 1 (RanBP1), a key effector of the nucleocytoplasmic transport pathway, in enabling directed migration of these cells. Our results indicate that RanBP1 is required for establishing front-to-rear polarity, so that NCs are able to chemotax. Moreover, our work suggests that RanBP1 function in chemotaxis involves the polarity kinase LKB1/PAR4. We envisage that regulated nuclear export of LKB1 through Ran/RanBP1 is a key regulatory step required for establishing front-to-rear polarity and thus chemotaxis, during NC collective migration.


title: Tbx2 is essential for cochlear inner hair cell development and regeneration

abstract: Atoh1 is essential for the development of outer hair cells (OHCs) and inner hair cells (IHCs) in the mammalian cochlea. Whereas Ikzf2 is necessary for OHC development, the key gene for IHC development remains unknown. We found that deleting Tbx2 in neonatal IHCs led to their trans-differentiation into OHCs, by repressing 26.7% of IHC and inducing 56.3% of OHC genes, including Ikzf2. More importantly, persistent expression of Tbx2 together with transient Atoh1 effectively reprogramed non-sensory supporting cells into new IHCs expressing functional IHC marker vGlut3. The differentiation status of these new IHCs is much more advanced than those previously reported. Thus, Tbx2 is essential for IHC development, and its co-upregulation with Atoh1 in supporting cells represents a new approach for treating IHC degeneration-related deafness.


title: Failure of digit tip regeneration in the absence of <Lmx1b> suggests Lmx1b functions disparate from dorsoventral polarity

abstract: Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of {Delta}LARM1/2 mutants that lack limb-specific Lmx1b enhancers fail to regenerate. To separate the nails effect from the lack of DV polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration and the nail requirement is supported. Transcriptomic comparison between wild-type and non-regenerative{Delta} LARM1/2 mutant blastemas reveals differential up-regulation of vascularization and connective tissue functional signatures in wild-type versus upregulation of inflammation in the mutant. These results, together with the finding of uniform Lmx1b expression in the wild-type blastema and in the dorsal dermis underneath the nail, indicate that, in addition of the nails effect, a direct role for Lmx1b in driving the progression of digit tip regeneration is likely.


title: Soil microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance

abstract:
O_LIPlants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes.
C_LIO_LIWe tested the role of a plant-beneficial soil bacterium (Acidovorax radicis) in altering eco-evolutionary interactions between sap-feeding aphid herbivores (Sitobion avenae) feeding on barley (Hordeum vulgare). We reared two aphid genotypes separately or together on three barley varieties that were inoculated with or without A. radicis bacteria. In the first experiment we counted the aphid number and plant biomass after 7, 14 and 21 days of aphid growth, while in a second experiment we counted and removed offspring every 1-2 days to assess aphid longevity and fecundity.
C_LIO_LIResults showed that A. radicis increased plant growth and suppressed aphids of both genotypes. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Fescue aphids experienced increased growth when they were sharing the plant with Sickte aphids on inoculated plants; this increase was not seen in the control plants without A. radicis and was only apparent after 14 days of aphid population growth.
C_LIO_LIPlant inoculation with A. radicis reduced aphid survival (reduced number of reproductive days) and fecundity (reduced daily reproductive output for surviving aphids). In the second experiment, when density was controlled, Fescue aphids did not experience increased reproduction in mixed populations, suggesting this is a density-dependent effect. Using Lotka-Volterra modelling, we demonstrated that A. radicis inoculation decreased aphid population stability as it increased inter-genotype competition but decreased the intra-genotype competition (likely through reduced population density).
C_LIO_LIOur work demonstrates the important role that plant-associated microbiomes can have in mediating eco-evolutionary interactions between herbivores and host plants.
C_LI


title: A quantitative eDNA-based method to monitor fish spawning in lakes: application to European perch and whitefish

abstract:
There is an urgent need to evaluate the effects of anthropogenic pressures and climatic change on fish populations dynamics. When monitored in lakes, the spawning of fish is generally assessed using traditional, mostly destructive or damaging, methods as gillnetting and collection of fertilized eggs.

Over the last decade, environmental DNA (eDNA) based methods have been widely developed for the detection of aquatic species, offering a non-invasive alternative method to conventional biomonitoring tools. In particular, the emergence of new methods as the droplet digital PCR (ddPCR) offer the possibility to quantify an absolute eDNA signal in a very sensitive way and at a low cost.

Here, we developed and implemented a quantitative eDNA method to monitor the spawning activity of two fish species, European perch and whitefish. ddPCR protocols were formalized based on existing and newly designed COI primers, and were applied during four spawning periods in lake Geneva.

The results demonstrate the efficiency of eDNA coupled with ddPCR to identify the timing and duration of the spawning periods, as well as the peak of the spawning activity for the targeted species. In addition, the use of a control species (i.e., quantification of the eDNA signal of a fish that does not reproduce during the monitoring period) was shown to be relevant to clearly discriminate fluctuations of the eDNA signal associated to the spawning activity from the baseline eDNA signal. For future implementation, we recommend using an integrative sampling strategy (e.g., pooled samples for a give station) to smooth the local variability of the eDNA signal. These results show that we reached an operational level to use these non-invasive eDNA methods to monitor the spawning periods of these two fish species in large lakes.


title: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa

abstract: Morphology often relates to ecology in a well-defined manner, enabling prediction of ecological roles for taxa that lack direct observations, such a fossils. Diet is a particularly important component of a species ecology. However, in order to predict diet it must first be codified, and establishing metrics that effectively summarize dietary variability without excessive information loss remains challenging. We employed a dietary item relative importance coding scheme to derive multivariate dietary classifications for a sample of extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether these scores could be predicted from a set of dental metrics, with body size as a covariate. There is no "one size fits all" model for predicting dietary item importance; different topographical features best predict different foods at different body sizes, and model-averaged estimates perform especially well. We show how models derived from living taxa can be used to provide novel insights into the dietary diversity of extinct carnivoran species. Our approach need not be limited to diet as an ecological trait of interest, to these phenotypic traits, or to carnivorans. Rather, this framework serves as a general approach to predicting multivariate ecology from phenotypic traits.


title: Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating

abstract: By providing additional opportunities for coalescence within families, the presence of consanguineous unions in a population reduces coalescence times relative to non-consanguineous populations. First-cousin consanguinity can take one of six forms differing in the configuration of sexes in the pedigree of the male and female cousins who join in a consanguineous union: patrilateral parallel, patrilateral cross, matrilateral parallel, matrilateral cross, bilateral parallel, and bilateral cross. Considering populations with each of the six types of first-cousin consanguinity individually and a population with a mixture of the four unilateral types, we examine coalescent models of consanguinity. We previously computed, for first-cousin consanguinity models, the mean coalescence time for X-chromosomal loci and the limiting distribution of coalescence times for autosomal loci. Here, we use the separation-of-time-scales approach to obtain the limiting distribution of coalescence times for X-chromosomal loci. This limiting distribution has an instantaneous coalescence probability that depends on the probability that a union is consanguineous; lineages that do not coalesce instantaneously coalesce according to an exponential distribution. We study the effects on the coalescence time distribution of the type of first-cousin consanguinity, showing that patrilateral-parallel and patrilateral-cross consanguinity have no effect on X-chromosomal coalescence time distributions and that matrilateral-parallel consanguinity decreases coalescence times to a greater extent than does matrilateral-cross consanguinity.


title: Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription

abstract:
To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly-spaced timepoints of macrophage activation. Enhancers and genes connected by loops exhibited stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. Changes in acetylation at looped distal enhancers preceded changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, while lost loops were often accompanied by high levels of transcription with the loop boundaries themselves. Taken together, these results are consistent with a reciprocal relationship in which loops can facilitate increased transcription by connecting promoters to distal enhancers while high levels of transcription can impede loop formation.

HIGHLIGHTSO_LILPS + IFN{gamma} triggers genome-wide changes in chromatin looping, enhancer acetylation, and gene expression
C_LIO_LILooped enhancer-promoter pairs exhibit ordered and correlated changes in acetylation and expression
C_LIO_LIChanges in gene expression exhibit a directional bias at differential loop anchors
C_LIO_LILost loops are associated with high levels of transcription within loop boundaries
C_LI


title: Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

abstract: Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, combining flow cytometry and high throughput sequencing, we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose nutrition sources. In addition to the well-known chromatin factors modulating transcriptional memory, we find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. We perform a genome-wide characterisation of this process and show that changes in nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that in addition to nuclear mRNA degradation, differences in cytoplasmic mRNA decay also modulate transcriptional memory and contribute to faster gene expression remodelling in primed cells. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.


title: Generalisation of early learned tutor song preferences in female zebra finches (Taeniopygia guttata)

abstract: Song learning is a prime example for a culturally transmitted mating signal. Local or individual song variants are socially learned early in life and adults sing and prefer these songs. An unresolved issue in this context is the question of how learned preferences for specific variants generalise to songs sufficiently similar to the original model. Here we asked whether female zebra finches would generalise early learned song preferences along a similarity gradient based on syllables sharing between test and tutor songs. For each female, this gradient consisted of their tutors (fathers) song (F), two variants of unfamiliar songs edited to share 2/3 (F2/3) and 1/3 (F1/3) of syllables with fathers song and an unfamiliar song (UF). Females preferences were measured in a 4-way operant choice arena where the birds could perch on different operant perches to trigger playbacks of the four different songs. Number and duration of perch visits were positively associated with the number of syllables that the assigned stimuli shared with fathers songs. These results suggest that female zebra finches generalise early learned song preferences to songs sharing syllables (and/or voice characteristics) with songs learned early in life.

category: animal behavior and cognition


title: The iron-sulfur cluster is critical for DNA binding by human DNA polymerase ϵ

abstract: DNA polymerase {varepsilon} (Pol{varepsilon}) is a key enzyme for DNA replication in eukaryotes. It is attached to a helicase and performs DNA synthesis on the leading strand. Recently it was shown that the catalytic domain of yeast Pol{varepsilon} (Pol{varepsilon}CD) contains a [4Fe-4S] cluster located at the base of the processivity domain (P-domain) and coordinated by four conserved cysteines. In this work, we have shown that human Pol{varepsilon}CD (hPol{varepsilon}CD) expressed in bacterial cells also contains an iron-sulfur cluster. In comparison, recombinant hPol{varepsilon}CD produced in insect cells contains an eight-fold-lower level of iron. Interestingly, the iron content correlates with the level of DNA-binding molecules, which suggests an important role of the iron-sulfur cluster in hPol{varepsilon} interaction with DNA. Indeed, mutation of two conserved cysteines that coordinate the cluster abolished template:primer binding and, therefore, DNA polymerase and proofreading exonuclease activities. We propose that the cluster regulates the conformation of the P-domain, which, like a gatekeeper, controls access to a DNA-binding cleft for a template:primer. In addition, we performed kinetic and binding studies of hPol{varepsilon}CD. The binding studies demonstrated low affinity of hPol{varepsilon}CD to DNA and a strong effect of salt concentration on stability of the hPol{varepsilon}CD/DNA complex. Pre-steady-state kinetic studies have shown a maximal polymerization rate constant of 51.5 s-1 and a relatively low affinity to incoming dNTP with an apparent KD of 105 M. This work provides notable insight into the role of a [4Fe-4S] cluster in Pol{varepsilon} function.

category: biochemistry


title: A microfluidic droplet array demonstrating high-throughput screening in individual lipid-producing microalgae

abstract: Microalgae are a group of photoautotrophic microorganisms which could use carbon dioxide for autosynthesis. They have been envisioned as one of the most prospective feedstock for renewable oil. However, great endeavors will still be needed to increase their economic feasibility; the screening of competitive species and suitable culture conditions are such issues. To greatly accelerate these rather laborious steps and also improve their experimental lump-sum-manner, we developed a microfluidic droplet-based 2x103 resolution "identification card", which allowed high throughput real-time monitoring of individual algae among population. A novel fluid-blocking-based droplet generating and trapping performance were integrated in the platform which made it excellent in operational simplicity, rapidity and stability and full of the potentials in single-cell-isolation/screening. The developed platform was successfully used to screen three unicellular algae, namely, Isochrysis zhanjiangensis, Platymonas subcordiformis and Platymonas helgolandica var. tsingtaoensis. In situ bioassays of the lipid accumulation and cell proliferation at single cell level for interspecies comparison were possible. Nitrogen stress condition can be indentified that induce positive-skewed frequency distribution of lipid content.


title: SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework

abstract:
Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed, even though maximum likelihood or Bayesian models are usually more consistent. Third, many methods utilize case-specific data, such as sampling times or infection exposure intervals. This impedes study of persistent infections in vulnerable groups, where such information has a limited use. Finally, most methods implicitly assume that transmission events are independent, while common source outbreaks violate this assumption.

We propose a maximum likelihood framework SOPHIE (SOcial and PHilogenetic Investigation of Epidemics) based on integration of phylogenetic and random graph models. It infers transmission networks from viral phylogenies and expected properties of inter-host social networks modelled as random graphs with given expected degree distributions. SOPHIE is scalable, accounts for intra-host diversity and accurately infers transmissions without case-specific epidemiological data. SOPHIE code is freely available at https://github.com/compbel/SOPHIE/

category: bioinformatics


title: MobsPy: A Meta-Species Language for Chemical Reaction Networks

abstract:
Chemical reaction networks are widely used to model biochemical systems. However, when the complexity of these systems increases, the chemical reaction networks are prone to errors in the initial modeling and subsequent updates of the model.

We present the Meta-species-oriented Biochemical Systems Language (MobsPy), a language designed to simplify the definition of chemical reaction networks in Python. MobsPy is built around the notion of meta-species, which are sets of species that can be multiplied to create higher-dimensional orthogonal characteristics spaces and inheritance of reactions. Reactions can modify these characteristics. For reactants, queries allow to select a subset from a meta-species and use them in a reaction. For products, queries specify the dimensions in which a modification occurs. We demonstrate the simplification capabilities of the MobsPy language at the hand of a running example and a circuit from literature. The MobsPy Python package includes functions to perform both deterministic and stochastic simulations, as well as easily configurable plotting. The MobsPy package is indexed in the Python Package Index and can thus be installed via pip.


title: Physical limits to acceleration of chemical reactions inside phase-separated compartments

abstract: We present a theoretical analysis of phase separated compartments as a means to facilitate chemical reactions. We find that the attractive interactions that concentrate reactants within the dense phase inhibit reactions by lowering the chemical potential and mobility of the reactants. Therefore, condensed phases are only beneficial if mobility in the condensed phase can be maintained. This can be achieved in multi-step reactions, where the proximity between enzymatic steps results in higher efficiency with less unreacted substrate, but does not increase the reaction rate. Alternatively, mobility can be maintained if recruitment to the condensed phase is driven by multiple attractive moieties that can bind and release independently. However, the spacers necessary to ensure independence between stickers are prone to entangle with the dense phase scaffold. We find an optimal sticker affinity that balances the need for rapid binding/unbinding kinetics and minimal entanglement. Reaction rates can be accelerated by shrinking the size of the dense phase with a corresponding increase in the number of stickers to enhance recruitment.

category: biophysics


title: Insights into Long-term Acclimation Strategies of Grapevines in Response to Multi-decadal Cyclical Drought

abstract: The Australian wine industry is currently under pressure to sustain its profitability due to climate change. Therefore, there is a pressing need to explore grapevine genetic diversity and identify superior clones with improved drought resistance. We previously characterised more than 15,000 dry-farmed (for over 65 years) Cabernet Sauvignon clones in a vineyard and identified three drought-tolerant (DT) clones, which can maintain significantly higher intrinsic water use efficiency (WUEi) under limited soil moisture than drought-sensitive (DS) clones. To understand whether DT clones grown under multi-decadal cyclical drought can prime their vegetatively-propagated clonal progenies for future drought events, in this study, all DT and DS vegetative progenies were propagated with commercial clones in the glasshouse. Their physiological and molecular responses were investigated under well-watered and two recurrent drought (D1 and D2) conditions. We observed that concentration of a natural priming agent, {gamma}-amino butyric acid (GABA), were significantly higher in all DT progenies relative to other progenies under drought. Both commercial and DT progenies exhibited improved gas exchange, photosynthetic performance and WUEi under recurrent drought events relative to DS progenies. Our results suggest that DT progenies have adapted to be in a "primed state" to withstand future drought events.

category: physiology


title: Lipodystrophy can be uncoupled from detrimental metabolic consequences

abstract: SUMMARYAdipose tissue has at least two major functions: storing metabolic energy as triacylglycerols (TG) and coordinating metabolism by secreting hormones, such as leptin. In lipodystrophies, defects of storing TG are typically accompanied by metabolic abnormalities, such as hepatic steatosis, and endocrine perturbations. Thus, the concept emerged that the endocrine function of adipose tissue is coordinated with, and requires, TG stores. To test this notion, we selectively depleted adipose TG stores by deleting the TG synthesis enzymes, DGAT1 and DGAT2, in murine adipose tissue (ADGAT DKO mice). Despite markedly reduced TG storage, ADGAT DKO mice maintained ample adipose tissue endocrine function and surprisingly did not develop metabolic perturbations, even when fed a high-fat diet, owing to increased energy expenditure and beiging of white adipose tissue. These findings, thus, reveal that adipose tissue performs TG storage and endocrine functions largely independently from each other.