bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational design of genes encoding completely overlapping protein domains: Influence of genetic code and taxonomic rank
Authors: Wichmann Stefan , Scherer Siegfried , Ardern Zachary
Published: September 2020

Overlapping genes (OLGs) with long protein-coding overlapping sequences are often excluded by genome annotation programs, with the exception of virus genomes. A recent study used a novel algorithm to construct OLGs from arbitrary protein domain pairs and concluded that virus genes are best suited for creating OLGs, a result which fitted with common assumptions. However, improving sequence evaluation using Hidden Markov Models shows that the previous result is an artifact originating from dataset-database biases. When parameters for OLG design and evaluation are optimized we find that 94.5% of the constructed OLG pairs score at least as highly as naturally occurring sequences, while 9.6% of the artificial OLGs cannot be distinguished from typical sequences in their protein family. Constructed OLG sequences are also indistinguishable from natural sequences in terms of amino acid identity and secondary structure, while the minimum nucleotide change required for overprinting an overlapping sequence can be as low as 1.8% of the sequence. Separate analysis of datasets containing only sequences from either archaea, bacteria, eukaryotes or viruses showed that, surprisingly, virus genes are much less suitable for designing OLGs than bacterial or eukaryotic genes. An important factor influencing OLG design is the structure of the standard genetic code. Success rates in different reading frames strongly correlate with their code-determined respective amino acid constraints. There is a tendency indicating that the structure of the standard genetic code could be optimized in its ability to create OLGs while conserving mutational robustness. The findings reported here add to the growing evidence that OLGs should no longer be excluded in prokaryotic genome annotations. Determining the factors facilitating the computational design of artificial overlapping genes may improve our understanding of the origin of these remarkable genetic constructs and may also open up exciting possibilities for synthetic biology.
Sex, Age, and Parental Harmonic Convergence Behavior Affect the Immune Performance ofAedes aegyptiOffspring
Authors: Reitmayer Christine M , Pathak Ashutosh K , Harrington Laura C , Brindley Melinda A. , Cator Lauren J , Murdock Courtney C
Published: September 2020

Aedes aegyptiis an important vector of several pathogenic arboviruses including dengue, chikungunya and Zika. Innovative approaches to controlAedespopulations, involving synthetic transgenic modifications as well asWolbachiabacteria, appear promising. For the various techniques requiring offspring inheritance of a trait, released males must successfully compete for mating partners against wildtype males. However, very little is known about mechanisms of mate selection in mosquitoes in general and in particular about potential correlations between mating success and offspring immune performance.

Harmonic convergence signals have been proposed as a cue for females to predict male quality. We investigated whether offspring of converging parental pairs showed differences in immune competence compared to offspring derived from non-converging parental pairs using three different types of immune assays. We found that offspring immune responses (melanization response and response to a bacterial challenge) differed between offspring from converging and non-converging parents. However, immune responses were shaped by several interacting factors such as sex, age, reproductive status, and parental mating behavior. Parental mating behavior had a stronger effect on the immune response of male offspring than on female offspring. Further, a population of female offspring derived from converging parental pairs reached their peak dengue virus dissemination rate earlier compared to a population of offspring derived from non-converging parental pairs. Our results provide insight into a wide range of selective pressures shaping mosquito immune function. Evolutionary trade-offs between naturally and sexually selected traits can have important implications for disease transmission and control and should be considered in the development of reproductive control strategies.
Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis a virus (HAV) isolates from the West Bank, Palestine during the period between 2014 and 2016
Authors: Dumaidi Kamal , Qaraqe Hayah , Al-Jawabreh Amer , Abu-Helu Rasmi , Samarah Fekri , Al-Jawabreh Hanan
Published: September 2020

Background

HAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.

Aims

the aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West bank, Palestine.

Study design

a cohort of 161 clinically and laboratory confirmed HAV (IgM-positive) cases and 170 IgM negative individuals from all the districts of the West Bank, Palestine during the period of 2014-2016 were tested for VP3/VP1 junction of the HAV genome using RT-PCR and sequence analysis. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.

Results

Overall, all the 34 sequences of the HAV was found to be HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%) with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h=8), but low haplotype (gene) diversity (Hd=0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n=10) and closer to haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, poor hand washing and drinking of un-treated water was considered the major HAV risk factors in the present study.

Conclusion

HAV-IB subgentype is endemic in Palestine. HAV showed low genetic variation and nucleotide diversity. Furthermore, haplotype network analysis revealed haplotype variation among the Palestinian sequences.
FisB relies on homo-oligomerization and lipid-binding to catalyze membrane fission in bacteria
Authors: Landajuela Ane , Braun Martha , Rodrigues Christopher D. A. , Martínez-Calvo Alejandro , Doan Thierry , Horenkamp Florian , Andronicos Anna , Shteyn Vladimir , Williams Nathan D. , Lin Chenxiang , Wingreen Ned S. , Rudner David Z. , Karatekin Erdem
Published: September 2020

Little is known about mechanisms of membrane fission in bacteria despite their requirement for cytokinesis. The only known dedicated membrane fission machinery in bacteria, FisB, is expressed during sporulation inBacillus subtilisand is required to release the developing spore into the mother cell cytoplasm. Here we characterized the requirements for FisB-mediated membrane fission. FisB forms mobile clusters of ∼12 molecules that give way to an immobile cluster at the engulfment pole containing ∼40 proteins at the time of membrane fission. Analysis of FisB mutants revealed that binding to acidic lipids and homo-oligomerization are both critical for targeting FisB to the engulfment pole and membrane fission. Experiments using artificial membranes and filamentous cells suggest FisB does not have an intrinsic ability to sense or induce membrane curvature but can bridge membranes. Finally, modeling suggests homo-oligomerization and trans interactions with membranes are sufficient to explain FisB accumulation at the membrane neck that connects the engulfment membrane to the rest of the mother cell membrane during late stages of engulfment. Together, our results show that FisB is a robust and unusual membrane fission protein that relies on homo-oligomerization, lipid-binding and the unique membrane topology generated during engulfment for localization and membrane scission, but surprisingly, not on lipid microdomains, negative-curvature lipids, or curvature-sensing.
Rapid behavioural response of urban birds to COVID-19 lockdown
Authors: Gordo Oscar , Brotons Lluís , Herrando Sergi , Gargallo Gabriel
Published: September 2020

Biodiversity is threatened by the growth of urban areas. However, it is still poorly understood how animals can cope with and adapt to these rapid and dramatic transformations of natural environments. The COVID-19 pandemic provides us with a unique opportunity to unveil the mechanisms involved in this process. Lockdown measures imposed in most countries are causing an unprecedented reduction of human activities giving us an experimental setting to assess the effects of our lifestyle on biodiversity. We studied the birds’ response to the population lockdown by using more than 126,000 bird records collected by a citizen science project in north eastern Spain. We compared the occurrence and detectability of birds during the spring 2020 lockdown with baseline data from previous years in the same urban areas and dates. We found that birds did not increase their probability of occurrence in urban areas during the lockdown, refuting the hypothesis that nature has recovered its space in human emptied urban areas. However, we found an increase in bird detectability, especially during early morning, suggesting a rapid change in the birds’ daily routines in response to quieter and less crowded cities. In conclusion, urban birds showed high behavioural plasticity to rapidly adjust to novel environmental conditions, as those imposed by the COVID-19.
Loss of RNF43/ZNRF3 predisposes to Hepatocellular carcinoma by impairing liver regeneration and altering liver fat metabolism
Authors: Mastrogiovanni Gianmarco , Pacini Clare , Kakava Sofia , Arnes-Benito Robert , Bradshaw Charles R , Davies Susan , Saeb-Parsy Kourosh , Koo Bon-Kyoung , Huch Meritxell
Published: September 2020

The homologous E3 ubiquitin ligases RNF43/ZNRF3 negatively regulate WNT signalling activation. Recently, both genes have been found mutated in several types of cancers. Specifically, loss-of-function mutations result in adenoma formation in mouse small intestine. However, their role in liver cancer has not been explored yet. Here we describe that hepatocyte-specific deletion of bothRnf43/Znrf3results in altered lipid metabolism and a non-alcoholic steatohepatitis (NASH) phenotype in mouse, in the absence of exogenous fat supplementation. The effect is cell-autonomous, as evidenced by the intracellular lipid accumulation detected in mutant liver organoids. Upon chronic liver damage,Rnf43/Znrf3deletion results in impaired hepatocyte regeneration, subsequent to an imbalance between hepatocyte differentiation and proliferation, which leads to hepatocellular carcinoma. Remarkably, hepatocellular carcinoma patients with mutations in ZNRF3 also present altered lipid metabolism and poorer survival. Our findings imply that Wnt activation through the RNF43/ZNRF3 module predisposes to liver cancer by altering the liver lipid metabolic ground-state and impairing liver regeneration, which combined, facilitate the progression towards malignancy. Our results highlight the requirement for personalized therapeutic or dietary interventions for those RNF43/ZNRF3 mutated individuals at risk of developing steatosis, NASH and/or liver cancer.
LAP2alpha maintains a mobile and low assembly state of A-type lamins in the nuclear interior
Authors: Naetar Nana , Georgiou Konstantina , Knapp Christian , Bronshtein Irena , Zier Elisabeth , Fichtinger Petra , Dechat Thomas , Garini Yuval , Foisner Roland
Published: September 2020

Lamins form stable filaments at the nuclear periphery in metazoans. Unlike B-type lamins, lamins A and C localize also in the nuclear interior, where they interact with lamin-associated polypeptide 2 alpha (LAP2α). We show that lamin A in the nuclear interior is formed from newly expressed pre-lamin A during processing and from soluble mitotic mature lamins in a LAP2α-independent manner. Binding of LAP2α to lamins A/C in the nuclear interior during interphase inhibits formation of higher order structures of lamin A/Cin vitroandin vivo, keeping lamin A/C in a mobile low assembly state independent of lamin A/C S22 phosphorylation. Loss of LAP2α causes formation of larger, less mobile and biochemically stable lamin A/C structures in the nuclear interior, which reduce the mobility of chromatin. We propose that LAP2α is essential to maintain a mobile lamin A/C pool in the nuclear interior, which is required for proper nuclear functions.
Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication
Authors: Begum Tina , Serrano-Serrano Martha Liliana , Robinson-Rechavi Marc
Published: September 2020

Despite the importance of gene function to evolutionary biology, the applicability of comparative methods to gene function is poorly known. A specific case which has crystalized methodological questions is the “ortholog conjecture”, the hypothesis that function evolves faster after duplication (i.e., in paralogs), and conversely is conserved between orthologs. Since the mode of functional evolution after duplication is not well known, we investigate under which reasonable evolutionary scenarios phylogenetic independent contrasts or pairwise comparisons can recover a putative signal of different functional evolution between orthologs and paralogs.

We investigate three different simulation models, which represent reasonable but simplified hypotheses about the evolution of a gene function trait. These are time dependent trait acceleration, correlated changes in rates of both sequence and trait evolution, and asymmetric trait jump. For each model we tested phylogenetic independent contrasts and an improved pairwise comparison method which accounts for interactions between events and node age.

Both approaches lose power to detect the trend of functional evolution when the functional trait accelerates for a long time following duplication for trees with many duplications, with better power of phylogenetic contrasts under intermediate scenarios. Concomitant increase in evolutionary rates of sequence and of trait after duplication can lead to both an incorrect rejection of the null under null simulations of trait evolution, and a false rejection of the ortholog conjecture under ortholog conjecture simulations, by phylogenetic independent contrasts. Improved pairwise comparisons are robust to this bias. Both approaches perform equally well under rapid shifts in traits.

Considering our ignorance of gene function evolution, and the potential for bias under simple models, we recommend methodological pluralism in studying gene family evolution. Functional phylogenomics is complex and results supported by only one method should be treated with caution.
Local PI(4,5)P2pool dynamics detected by the coincidence biosensor tubbyCT maintain the integrity of ER-PM junctions during PLC signaling
Authors: Thallmair Veronika , Schultz Lea , Evers Saskia , Goecke Christian , Thallmair Sebastian , Leitner Michael G. , Oliver Dominik
Published: September 2020

Phosphoinositides (PIs) are important signaling molecules and determinants of membrane identity in the eukaryotic plasma membrane, where they multi-task in divergent signaling pathways. Signaling pleiotropy likely depends on distinct PI pools in the same membrane, although the physical definition of such pools has remained ambiguous. PI(4,5)P2, specifically, is also the precursor for the second messengers in the Gq/PLC pathway, IP3and DAG, and is broken down by PLCβ during signaling. Endoplasmic reticulum-plasma membrane contact sites (ER-PM junctions) have emerged as central hubs for lipid transport between both membranes, and specifically for PI homeostasis by supplying the PM with phosphatidylinositol.

Here we show that the tubby protein, by virtue of its C-terminal tubby-domain, preferentially localizes to ER-PM junctions by binding to both PI(4,5)P2and the ER-PM tether E-Syt3. Under conditions of vigorous PI(4,5)P2consumption by PLCβ, additional recruitment of tubby revealed an increase of a local PI(4,5)P2pool fed by local synthesis through PI kinases. Inhibition of this pool-filling process led to the release of the ER-PM tethers, E-Syts, from the membrane and hence to loss of integrity of the ER-PM contact sites.

We conclude that spatiotemporal metabolic channeling of PI synthesis initiated by non-vesicular transport in the ER-PM junctions specifies a local pool of PI(4,5)P2that is pivotal for the maintenance of homeostatic functions during global depletion of PI(4,5)P2. The findings further suggest that the tubby-like proteins (TULPs), so far known to impact on energy homeostasis and obesity through primary cilia signaling, have an additional function at ER-PM junctions.

HIGHLIGHTS

The tubby domain preferentially assembles into ER-PM junctions due to coincidence detection of PI(4,5)P2and E-Syt3

Tubby recruitment reveals an increase of a local pool of PI(4,5)P2in ER-PM junctions during PLCβ signaling

Junctional PI(4,5)P2dynamics require local synthesis of PI(4,5)P2

Local PI(4,5)P2supply is required for integrity of ER-PM junctions during PLCβ activity.
Population dynamics of GC-changing mutations in humans and great apes
Authors: Bergman Juraj , Schierup Mikkel Heide
Published: September 2020

Background

The nucleotide composition of the genome is a balance between origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and among great ape species.

Results

We report a stronger correlation between GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC. We show that the strength of gBGC differs for transitions and transversions but that its overall strength is positively correlated with effective population sizes of human populations and great ape species, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. We study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to hypermutability of specific nucleotide contexts.

Conclusions

Differences in GC-biased gene conversion are evident between different mutation types, and dependent on sex-specific recombination, population size and flanking nucleotide context. Our results therefore highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.
Processing of novel food reveal payoff and rank-biased social learning in a wild primate
Authors: Canteloup C. , Cera M.B. , Barrett B.J. , van de Waal E.
Published: September 2020

Social learning – learning from others – is the basis for behavioural traditions. Different social learning strategies (SLS), where individuals biasedly learn behaviours based on their content or who demonstrates them, may increase an individual’s fitness and generate behavioural traditions. While SLS have been mostly studied in isolation, their interaction and the interplay between individual and social learning is less understood. We performed a field-based open diffusion experiment in a wild primate. We provided two groups of vervet monkeys with a novel food, unshelled peanuts, and documented how three different peanut opening techniques spread within the groups. We analysed data using hierarchical Bayesian dynamic learning models that explore the integration of multiple SLS with individual learning. We i) report evidence of social learning compared to strictly individual learning, ii) show that vervets preferentially socially learn the technique that yields the highest observed payoff and iii) also bias attention toward individuals of higher rank. This shows that behavioural preferences can arise when individuals integrate social information about the efficiency of a behaviour alongside cues related to the rank of a demonstrator. When these preferences converge to the same behaviour in a group, they may result in stable behavioural traditions.
A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas)
Authors: Peñaloza Carolina , Gutierrez Alejandro P. , Eory Lel , Wang Shan , Guo Ximing , Archibald Alan L. , Bean Tim P. , Houston Ross D.
Published: September 2020

The Pacific oyster (Crassostrea gigas) is a marine bivalve species with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available forC. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously publishedC. gigasassembly. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying 30K putative protein coding genes, with an average of 3.9 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density, and identified putative centromeres of the metacentric chromosomes. An enrichment ofHelitronrolling circle transponsable elements was observed, suggesting their potential role in shaping the evolution of theC. gigasgenome. This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for genetic improvement ofC. gigasin aquaculture breeding programmes.
Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins
Authors: De Zitter Elke , Hugelier Siewert , Duwé Sam , Vandenberg Wim , Tebo Alison G. , Van Meervelt Luc , Dedecker Peter
Published: September 2020

Photochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.
LSD1 promotes secretory cell specification to driveBRAFmutant colorectal cancer
Authors: Miller Samuel A. , Policastro Robert A. , Sriramkumar Shruthi , Lai Tim , Huntington Thomas D. , Ladaika Christopher A , Zentner Gabriel E. , O’Hagan Heather M.
Published: September 2020

Despite the connection to distinct mucus-containing colorectal cancer (CRC) histological subtypes, the role of secretory cells, including goblet and enteroendocrine (EEC) cells, in CRC progression has been underexplored. Analysis of TCGA and single cell RNA sequencing data demonstrates that multiple secretory progenitor populations are enriched inBRAF-mutant CRC patient tumors and cell lines. Enrichment of EEC progenitors inBRAF-mutant CRC is maintained by DNA methylation and silencing ofNEUROD1, a key gene required for differentiation of EECs. Mechanistically, secretory cells and the factors they secrete, such as Trefoil factor 3, are shown to promote colony formation and activation of cell survival pathways in the entire cell population. We further identify LSD1 as a critical regulator of secretory cell specificationin vitroand in a colon orthotopic xenograft model, where LSD1 loss reduces tumor growth and metastasis. This work establishes EEC progenitors, in addition to goblet cells, as targetable populations inBRAF-mutant CRC and identifies LSD1 as a therapeutic target in secretory lineage-containing CRC.
Host immune responses after suprachoroidal delivery of AAV8 in nonhuman primate eyes
Authors: Chung Sook Hyun , Mollhoff Iris Natalie , Mishra Alaknanda , Sin Tzu-Ni , Ngo Taylor , Ciulla Thomas , Sieving Paul , Thomasy Sara M. , Yiu Glenn
Published: September 2020

The suprachoroid is a potential space located between the sclera and choroid of the eye which provides a novel route for ocular drug or viral vector delivery. Suprachoroidal injection of AAV8 using transscleral microneedles enables widespread transgene expression in eyes of nonhuman primates, but may cause intraocular inflammation. We characterized the host humoral and cellular immune responses after suprachoroidal delivery of AAV8 expressing green fluorescent protein (GFP) in rhesus macaques, and found that it can induce a mild chorioretinitis that resolves after systemic corticosteroid administration, with recovery of photoreceptor morphology but persistent immune cell infiltration after 3 months. Suprachoroidal AAV8 triggered B-cell and T-cell responses against GFP, but only mild antibody responses to the viral capsid as compared to intravitreal injections of the same vector and dose. Systemic biodistribution studies showed lower AAV8 levels in liver and spleen after suprachoroidal injection compared with intravitreal delivery. Our findings suggest that suprachoroidal AAV8 primarily triggers host immune responses to GFP, likely due to sustained transgene expression in scleral fibroblasts outside the blood-retinal barrier, but elicits less humoral immune reactivity to the viral capsid than intravitreal delivery due to lower egress into systemic circulation. Thus, suprachoroidal AAV delivery of human transgenes may have significant translational potential for retinal gene therapy.
RNA helicase DDX5 enables STAT1 mRNA translation and interferon signaling in hepatitis B virus replicating hepatocytes
Authors: Sun Jiazeng , Wu Guanhui , Wang Wen-Hung , Zhang Zhengtao , Merle Philippe , Hui Lijian , Yang Danzhou , Andrisani Ourania
Published: September 2020

Objective

RNA helicase DDX5 is downregulated during hepatitis B virus (HBV) replication, and poor prognosis HBV-related hepatocellular carcinoma (HCC). The objective of this study is to understand the significance of DDX5 downregulation during HBV infection and poor prognosis HCC, as it pertains to therapy of chronically HBV-infected patients with HCC. IFN-α therapy is effective only for a subgroup of HBV-infected patients, for reasons not understood. Herein, we investigated a novel mechanism of STAT1 translational control, involving DDX5-mediated resolution of a G-quadruplex structure, located at the 5’UTR of STAT1 mRNA, enabling STAT1 translation.

Design and Results

Molecular, pharmacologic, and biophysical assays were used together with cellular model of HBV replication, HCC cell lines, and HBV-related liver tumors. We observed, the protein level of DDX5 correlated with that of transcription factor STAT1. We show, DDX5 regulates STAT1 mRNA translation by resolving a G-quadruplex (rG4) RNA structure, proximal to the 5’ end of STAT1 5’UTR. We employed luciferase reporter assays comparing wild type (WT) vs. mutant (MT) rG4 sequence, rG4-stabilizing compounds, CRISPR/Cas9 editing of the rG4 sequence, and circular dichroism determination of rG4 structure. Ribonucleoprotein assays identified direct DDX5 binding to WT but not MT rG4. Importantly, liver cancer cell lines expressing low DDX5 exhibited reduced interferon response, while immunohistochemistry of HBV-related HCCs exhibiting absence of DDX5, also lacked STAT1.

Conclusion

DDX5 resolves a G-quadruplex structure in 5’UTR of STAT1 mRNA, enabling STAT1 translation. DDX5 is a key regulator of the dynamic range of interferon response during innate immunity and adjuvant IFN-α therapy.
Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression
Authors: Natri Heini M. , Hudjashov Georgi , Jacobs Guy , Kusuma Pradiptajati , Saag Lauri , Darusallam Chelzie Crenna , Metspalu Mait , Sudoyo Herawati , Cox Murray P. , Romero Irene Gallego , Banovich Nicholas E.
Published: September 2020

Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity on the region. In a comparison with a European dataset, we identify 166 uniquely Indonesia-specific eQTLs, highlighting the benefits of performing association studies on non-European populations. By combining local ancestry and archaic introgression inference eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits. Our findings illustrate how local ancestry and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations.
Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets
Authors: Hass Matthew R. , Brisette Daniel , Parameswaran Sreeja , Pujato Mario , Donmez Omer , Kottyan Leah C. , Weirauch Matthew T. , Kopan Raphael
Published: September 2020

Runt-related transcription factor 1 (Runx1) can act as both an activator and a repressor. Here we show that CRISPR-mediated deletion ofRunx1in an embryonic kidney-derived cell (mK4) results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci are enriched for Runx sites, remain bound by Runx2, but lose chromatin accessibility and expression inRunx1knockout cells. Unexpectedly, regions near upregulated genes are depleted of Runx sites and are instead enriched for Zeb transcription factor binding sites. Re-expressing Zeb2 inRunx1knockout cells restores suppression. These data confirm that Runx1 activity is uniquely needed to maintain open chromatin at many loci, and demonstrate that genome-scale derepression is an indirect consequence of losing Runx1-dependent Zeb expression.
Mg2+-binding shifts the IM30 activity from membrane protection to membrane destabilization
Authors: Junglas Benedikt , Axt Amelie , Siebenaller Carmen , Sonel Hilal , Hellmann Nadja , Weber Stefan A.L. , Schneider Dirk
Published: September 2020

The inner membrane-associated protein of 30 kDa (IM30) is essential in chloroplasts and cyanobacteria. The spatio-temporal cellular localization of the protein appears to be highly dynamic and triggered by internal as well as external stimuli, mainly light intensity. A soluble fraction of the protein is localized in the cyanobacterial cytoplasm or the chloroplast stroma, respectively. Additionally, the protein attaches to the thylakoid membrane as well as to the chloroplast inner envelope or the cyanobacterial cytoplasmic membrane, respectively, especially under conditions of membrane stress. IM30 is involved in thylakoid membrane biogenesis and/or maintenance, where it either stabilizes membranes and/or triggers membrane-fusion processes. These apparently contradicting processes have to be tightly controlled and separated spatiotemporally in chloroplasts and cyanobacteria. The latter process depends on Mg2+-binding to IM30; yet, it still is unclear how Mg2+-loaded IM30 interacts with membranes and promotes membrane fusion. Here we show that interaction of Mg2+with IM30 results in increased binding of IM30 to native as well as model membranes. Via Atomic Force Microscopy in liquid, IM30-induced bilayer defects were observed in solid-supported bilayers in presence of Mg2+. The observed interaction of IM30 with membrane surfaces differs dramatically from previously observed membrane-stabilizing, carpet-like structures in the absence of Mg2+. Mg2+-induced alterations of the IM30 structure switches the IM30 activity from a membrane-stabilizing to a membrane-destabilizing function, a crucial step in membrane fusion.
Variable inbreeding depression may explain associations between the mating system and herbicide resistance
Authors: Van Etten Megan , Soble Anah , Baucom Regina S
Published: September 2020

Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages ofIpomoea purpureaartificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field. We paired our examination of inbreeding depression in fitness-related traits with an examination of gene expression changes associated with the level of herbicide resistance, breeding history (inbred or outcrossed), and the interaction of the breeding system and the level of herbicide resistance. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to non-selected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.
Degeneracy and stability in neural circuits of dopamine and serotonin neuromodulators: A theoretical consideration
Authors: Behera Chandan K. , Joshi Alok , Wang Da-Hui , Sharp Trevor , Wong-Lin KongFatt
Published: September 2020

Degenerate neural circuits perform the same function despite being structurally different. However, it is unclear whether neural circuits with interacting neuromodulator sources can themselves be degenerate while maintaining the same neuromodulatory function. Here, we address this by computationally modelling the neural circuits of neuromodulators serotonin and dopamine, local glutamatergic and GABAergic interneurons, and their possible interactions, under reward/punishment-based conditioning tasks. The neural modelling is constrained by relevant experimental studies of the VTA or DRN system using e.g. electrophysiology, optogenetics, and voltammetry. We first show that a single parsimonious, sparsely connected neural circuit model can recapitulate several separate experimental findings that indicated diverse, heterogeneous, distributed and mixed DRN-VTA neuronal signalling in reward and punishment tasks. The inability for this model to recapitulate all observed neuronal signalling suggests potentially multiple circuits acting in parallel. Then using computational simulations and dynamical systems analysis, we demonstrate that several different stable circuit architectures can produce the same observed network activity profile, hence demonstrating degeneracy. Due to the extensive D2-mediated connections in the investigated circuits, we simulate D2 receptor agonist by increasing the connection strengths emanating from the VTA DA neurons. We found that the simulated D2 agonist can distinguish among sub-groups of the degenerate neural circuits based on substantial deviations in specific neural populations’ activities in reward and punishment conditions. This forms a testable model prediction using pharmacological means. Overall, this theoretical work suggests the plausibility of degeneracy within neuromodulator circuitry and has important implication for the stable and robust maintenance of neuromodulatory functions.
A unified theory for organic matter accumulation
Authors: Zakem Emily J. , Cael B. B. , Levine Naomi M.
Published: September 2020

Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. The new framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millenial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.
Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids
Authors: Harada Ryo , Inagaki Yuji
Published: September 2020

Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as “PolIBCD+”) have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via non-vertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.
Apoptosis is not conserved in plants as revealed by critical examination of a model for plant apoptosis-like cell death
Authors: Minina Elena A. , Dauphinee Adrian N. , Ballhaus Florentine , Gogvadze Vladimir , Smertenko Andrei P. , Bozhkov Peter V.
Published: September 2020

Background

Animals and plants diverged over one billion years ago and evolved unique mechanisms for many cellular processes, including cell death. One of the most well-studied cell-death programmes in animals, apoptosis, involves gradual cell dismantling and engulfment of cellular fragments, apoptotic bodies, through phagocytosis. However, rigid cell walls prevent plant cell fragmentation and thus apoptosis is not applicable for executing cell death in plants. Furthermore, plants are devoid of the key components of apoptotic machinery, including phagocytosis as well as caspases and Bcl-2 family proteins. Nevertheless, the concept of plant “apoptosis-like programmed cell death” (AL-PCD) is widespread. This is largely due to superficial morphological resemblances between plant cell death and apoptosis; in particular between protoplast shrinkage in plant cells killed by various stimuli and animal cell volume decrease preceding fragmentation into apoptotic bodies.

Results

Here, we provide a comprehensive spatio-temporal analysis of cytological and biochemical events occurring in plant cells subjected to heat shock at 40-55°C and 85°C, the experimental conditions typically used to trigger AL-PCD and necrotic cell death, respectively. We show that cell death under both conditions was not accompanied by membrane blebbing or formation of apoptotic bodies, as would be expected during apoptosis. Instead, we observed instant and irreversible permeabilization of the plasma membrane and ATP depletion. These processes did not depend on mitochondrial functionality or the presence of Ca2+and could not be prevented by an inhibitor of ferroptosis. We further reveal that the lack of protoplast shrinkage at 85°C, the only striking morphological difference between cell deaths induced by 40-55°C or 85°C heat shock, is a consequence of the fixative effect of the high temperature on intracellular contents.

Conclusions

We conclude that heat shock-induced cell death is an energy-independent process best matching definition of necrosis. Although the initial steps of this necrotic cell death could be genetically regulated, classifying it as apoptosis or AL-PCD is a terminological misnomer. Our work supports the viewpoint that apoptosis is not conserved across animal and plant kingdoms and demonstrates the importance of focusing on plant-specific aspects of cell death pathways.
The C-terminal domain of transcription factor RfaH: Folding, fold switching and energy landscape
Authors: Seifi Bahman , Wallin Stefan
Published: September 2020

We study the folding and fold switching of the C-terminal domain (CTD) of the transcription factor RfaH using a hybrid sequence-structure based model. We show that this model captures the essential thermodynamic behavior of this metamorphic domain, i.e., a switch in the global free energy minimum from anα-helical hairpin to a 5-strandedβ-barrel upon separating the CTD from the rest of the protein. Using this model and Monte Carlo sampling techniques, we analyze the energy landscape of the CTD in terms of progress variables for folding towards the two folds. We find that, below the folding temperature, the energy landscape is characterized by a single, dominant funnel to the nativeβ-barrel structure. The absence of a deep funnel to theα-helical hairpin state reflects a negligible population of this fold for the isolated CTD. We observe, however, a significantly higherα-helix structure content in the unfolded state compared to results from a similar but fold switch-incompetent version of our model. Moreover, in folding simulations started from an extended chain conformation we find transientα-helix structure that disappears as the chain progresses to the thermally stableβ-barrel state.
Eco product development combining eco design and life cycle assessment
Authors: Barbosa Ana Jamile Damasceno , Santos Vitor Hugo de Paiva , Araújo Priscilla Cavalcante de , Medeiros Felipe Lucas de , Otaviano Letícia Yasmin da Silva
Published: September 2020

Purpose

The paper aims to propose the development of an eco product to replace the traditional cotton swab that meets the expected needs, besides having a bias based on sustainability and economic viability.

Design/methodology/approach

The applied nature article opted for an exploratory and descriptive study, with the objective of seeking a solution to a real problem: to reduce the environmental impact in the disposal of cotton swabs. To test this hypothesis, the exploratory stage evaluated the literature on the principles of eco design and environmental marketing to understand market viability and environmental impacts. The descriptive phase presented a comparative analysis between the original product and the proposed one, in terms of production processes and impacts of the product life cycle. Thus, an alternative product was conceived and validated applying the life cycle analysis (LCA).

Findings

The paper provides a comparative analysis between the eco product and the traditional product in order to validate the hypothesis that the new proposal reduces the environmental impact. It was found that both productive processes have similar impacts; however, the raw material of the proposed eco product demonstrated a significant reduction in the impact caused on the environment, considering cradle to cradle analysis.

Originality/value

This paper conceives an eco product as an alternative to traditional cotton swab, presenting an innovative potential in line with worldwide sustainability trends.