bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel truncating mutations inCTNND1cause a dominant craniofacial and cardiac syndrome
Authors: Alharatani Reham , Ververi Athina , Beleza-Meireles Ana , Ji Weizhen , Mis Emily , Patterson Quinten T. , Griffin John N. , Bhujel Nabina , Chang Caitlin A. , Dixit Abhijit , Konstantino Monica , Healy Christopher , Hannan Sumayyah , Neo Natsuko , Cash Alex , Li Dong , Bhoj Elizabeth , Zackai Elaine H. , Cleaver Ruth , Baralle Diana , McEntagart Meriel , Newbury-Ecob Ruth , Scott Richard , Hurst Jane A. , Billie Au Ping Yee , Hosey Marie Therese , Khokha Mustafa , Marciano Denise K. , Lakhani Saquib A. , Liu Karen J.
Published: July 2019

CTNND1encodes the p120-catenin (p120) protein, which has a wide range of functions, including the maintenance of cell-cell junctions, regulation of the epithelial-mesenchymal transition and transcriptional signaling. Due to advances in next generation sequencing,CTNND1has been implicated in human diseases including cleft palate and blepharocheilodontic syndrome (BCD) albeit only recently. In this study, we identify eight novel protein-truncating variants, sixde novo,in thirteen participants presenting with craniofacial dysmorphisms including cleft palate and hypodontia, as well as congenital cardiac anomalies, limb dysmorphologies and neurodevelopmental disorders. Using conditional deletions in mice as well as CRISPR/Cas9 approaches to targetCTNND1inXenopus, we identified a subset of phenotypes that can be linked to p120-catenin in epithelial integrity and turnover, and additional phenotypes that suggest mesenchymal roles ofCTNND1.We propose thatCTNND1variants have a wider developmental role than previously described, and that variations in this gene underlie not only cleft palate and BCD but may be expanded to a broader velocardiofacial-like syndrome.
Robust generation of erythroid and multilineage hematopoietic progenitors from human iPSCs using a scalable monolayer culture system
Authors: Ruiz Juan Pablo , Chen Guibin , Haro Mora Juan Jesus , Keyvanfar Keyvan , Liu Chengyu , Zou Jizhong , Beers Jeanette , Bloomer Hanan , Qanash Husam , Uchida Naoya , Tisdale John F. , Boehm Manfred , Larochelle Andre
Published: July 2019

One of the most promising objectives of clinical hematology is to derive engraftable autologous hematopoietic stem cells (HSCs) from human induced pluripotent stem cells (iPSCs). Progress in translating iPSC technologies to the clinic relies on the availability of scalable differentiation methodologies. In this study, human iPSCs were differentiated for 21 days using STEMdiff™, a monolayer-based approach for hematopoietic differentiation of human iPSCs that requires no replating, co-culture or embryoid body formation. Both monolayer and suspension cells were functionally characterized throughout differentiation. In the supernatant fraction, an early transient population of primitive CD235a+ erythroid cells first emerged, followed by hematopoietic progenitors with multilineage differentiation activity in vitro but no long-term engraftment potential in vivo. In later stages of differentiation, a nearly exclusive production of definitive erythroid progenitors was observed. In the adherent monolayer, we identified a prevalent population of mesenchymal stromal cells and limited arterial vascular endothelium (VE), suggesting that the cellular constitution of the monolayer may be inadequate to support the generation of HSCs with durable repopulating potential. Quantitative modulation of WNT/β-catenin and activin/nodal/TGFβ signaling pathways with CHIR/SB molecules during differentiation enhanced formation of arterial VE, definitive multilineage and erythroid progenitors, but was insufficient to orchestrate the generation of engrafting HSCs. Overall, STEMdiff™ provides a clinically-relevant and readily adaptable platform for the generation of erythroid and multilineage hematopoietic progenitors from human pluripotent stem cells.

Highlights

Robust, scalable and clinically-relevant monolayer-based culture system for hematopoietic differentiation of human iPSCs.

Successive emergence of primitive erythroid cells, definitive multilineage HSPCs and erythroid progenitors in the culture supernatant.

Abundant mesenchymal cells and limited arterial vascular endothelium in the culture monolayer.

CHIR/SB molecules increase arterial vascular endothelium formation, suppress primitive hematopoiesis and promote definitive multilineage and erythroid progenitors.
Facile discovery of isonitrile natural products via tetrazine based click reactions
Authors: Huang Yaobing , Cai Wenlong , Rio Flores Antonio Del , Twigg Frederick , Zhang Wenjun
Published: July 2019

A facile method for the quick discovery and quantification of isonitrile compounds from microbial cultures was established based on the isonitrile-tetrazine click reaction. A in situ reduction further enabled bioorthogonal ligation of primary and secondary isonitriles for the first time.
Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
Authors: De Kegel Barbara , Ryan Colm J.
Published: July 2019

What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have revealed that paralog genes are less likely to be essential than singleton genes and that this can partially be attributed to the ability of paralogs to buffer each other’s loss. However, the essentiality of a gene is not a fixed property and can vary significantly across different genetic backgrounds. It is unclear to what extent paralogs contribute to this variation, as most studies have analyzed genes identified as essential in a single genetic background. Here, using gene essentiality profiles of 558 genetically heterogeneous tumor cell lines, we analyze the contribution of paralogy to variable essentiality. We find that, compared to singleton genes, paralogs are less frequently essential and that this is more evident when considering genes with multiple paralogs or with highly sequence similar paralogs. We determine that paralogs derived from whole genome duplication exhibit more variable essentiality than those derived from small-scale duplications. We estimate that in 13-17% of cases the variable essentiality of paralogs can be attributed to buffering relationships between paralog pairs, as evidenced by synthetic lethality. Paralog pairs derived from whole genome duplication and pairs that function in protein complexes are significantly more likely to display such synthetic lethal relationships. Overall we find that many of the observations made using a single strain of budding yeast can be extended to understand patterns of essentiality in genetically heterogeneous cancer cell lines.
Specialization of theDrosophilanuclear export family protein, Nxf3, for piRNA precursor export
Authors: Kneuss Emma , Munafò Marzia , Eastwood Evelyn L. , Deumer Undine-Sophie , Preall Jonathan B. , Hannon Gregory J. , Czech Benjamin
Published: July 2019

The piRNA pathway is a conserved, small RNA-based immune system that protects animal germ cell genomes from the harmful effects of transposon mobilisation. InDrosophilaovaries, most piRNAs originate from dual-strand clusters, which generate piRNAs from both genomic strands. Dual-strand clusters use non-canonical transcription mechanisms. Although transcribed by RNA polymerase II, cluster transcripts lack splicing signatures and poly(A) tails. mRNA processing is important for general mRNA export mediated by Nuclear export factor 1. Although UAP56, a component of the transcription and export complex, has been implicated in piRNA precursor export, it remains unknown how dual-strand cluster transcripts are specifically targeted for piRNA biogenesis by export from the nucleus to cytoplasmic processing centers. Here we report that dual-strand cluster transcript export requires CG13741/Bootlegger and theDrosophilaNuclear export factor family protein, Nxf3. Bootlegger is specifically recruited to piRNA clusters and in turn brings Nxf3. We find that Nxf3 specifically binds to piRNA precursors and is essential for their export to piRNA biogenesis sites, a process that is critical for germline transposon silencing. Our data shed light on how dual-strand clusters compensate for a lack of canonical features of mature mRNAs to be specifically exported via Nxf3, ensuring proper piRNA production.
An acute session of motor imagery training induces use-dependent plasticity
Authors: Ruffino Célia , Gaveau Jérémie , Papaxanthis Charalambos , Lebon Florent
Published: July 2019

Motor imagery, defined as the mental representation of an action without movement-related sensory inputs, is a well-known intervention to improve motor performance. In the current study, we tested whether use-dependent plasticity, a mechanism underlying motor learning, could be induced by an acute session of motor imagery. By means of transcranial magnetic stimulation (TMS) over the left primary motor cortex, we evoked isolated thumb movements in the right hand and assessed corticospinal excitability in the flexor and extensor pollicis brevis muscles. We measured the mean TMS-induced movement direction before and after an acute session of motor imagery practice. In a first experiment, participants of the imagery group were instructed to repeatedly imagine their thumb moving in a direction deviated by 90° from the pre-test movement. This group, but not the control group, deviated the post-training TMS-induced movements toward the training target direction (+44° ±62° and −1° ±23°, respectively). Interestingly, the deviation magnitude was driven by the corticospinal excitability increase in the agonist muscle. In a second experiment, we found that post-training TMS-induced movements were proportionally deviated toward the trained direction and returned to baseline 30 minutes after the motor imagery training. These findings suggest that motor imagery induces use-dependent plasticity and, this neural process is accompanied by corticospinal excitability increase in the agonist muscle.
AtDAT1 is a key enzyme of D-amino acid stimulated ethylene production inArabidopsis thaliana
Authors: Suarez Juan , Hener Claudia , Lehnhardt Vivien-Alisa , Hummel Sabine , Stahl Mark , Kolukisaoglu Üner
Published: July 2019

D-enantiomers of proteinogenic amino acids (D-AAs) are found ubiquitously, but the knowledge about their metabolism and functions in plants is scarce. A long forgotten phenomenon in this regard is the D-AA-stimulated ethylene production in plants. As a starting point to investigate this effect theArabidopsisaccession Landsberg erecta (Ler) got into focus as it was found defective in metabolizing D-AAs. Combining genetics and molecular biology of T-DNA lines and natural variants together with biochemical and physiological approaches we could identify AtDAT1 as a major D-AA transaminase inArabidopsis. Atdat1loss-of-function mutants andArabidopsisaccessions with defectiveAtDAT1alleles were not able to produce D-Ala, D-Glu and L-Met, the metabolites of D-Met, anymore. This result corroborates the biochemical characterization of AtDAT1, which showed highest activity using D-Met as substrate. Germination of seedlings in light and dark led to enhanced growth inhibition ofatdat1mutants on D-Met. Ethylene measurements revealed an enhanced D-AA stimulated ethylene production in these mutants. According to initial working models of this phenomenon D-Met is preferentially malonylated instead of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). This decrease of ACC degradation should then lead to the increase of ethylene production. We could observe in our studies a reciprocal relation of malonylated methionine and ACC upon D-Met application and even significantly more malonyl-methionine inatdat1mutants. Unexpectedly, the malonyl-ACC levels did not differ between mutants and wild type in these experiments. With AtDAT1, the first central enzyme of plant D-AA metabolism was characterized biochemically and physiologically. The specific effects of D-Met on ACC metabolization, ethylene production and plant development ofdat1mutants unraveled the impact of AtDAT1 on these processes, but they are not in full accordance to previous working models. Instead, our results imply the influence of additional candidate factors or processes on D-AA-stimulated ethylene production which await to be uncovered.
Meiosis Initiates In The Fetal Ovary Of Mice Lacking All Retinoic Acid Receptor Isotypes
Authors: Vernet Nadège , Mark Manuel , Condrea Diana , Féret Betty , Klopfenstein Muriel , Alunni Violaine , Teletin Marius , Ghyselinck Norbert B.
Published: July 2019

Gametes are generated through a specialized cell differentiation process, meiosis which, in most mammals, is initiated in ovaries during fetal life. It is widely admitted that all-transretinoic acid (ATRA) is the molecular signal triggering meiosis initiation in mouse female germ cells, but a genetic approach in which ATRA synthesis is impaired disputes this proposal. In the present study, we investigated the contribution of endogenous ATRA to meiosis by analyzing fetuses lacking all RARs ubiquitously, obtained through a tamoxifen-inducible cre recombinase-mediated gene targeting approach. Efficient ablation of RAR-coding genes was assessed by the multiple congenital abnormalities displayed by the mutant fetuses. Unexpectedly, their germ cells robustly expressed STRA8, REC8, SYCP1 and SYCP3, showing that RAR are actually dispensable up to the zygotene stage of meiotic prophase I. Thus our study goes against the current model according to which meiosis is triggered by endogenous ATRA in the developing ovary and revives the identification of the meiosis-preventing substance synthesized by CYP26B1 in the fetal testis.
Higher quality de novo genome assemblies from degraded museum specimens: a linked-read approach to museomics
Authors: Colella Jocelyn P. , Tigano Anna , MacManes Matthew D.
Published: July 2019

Abstract

High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historic specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges. Linked-read or ‘synthetic long-read’ sequencing technologies, such as 10X Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded specimens. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four published genomes assembled from a single shotgun library and four deer mouse (Peromyscus spp.) genomes assembled using 10X Genomics technology. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher quality, measured by larger N50 values and greater gene content. Although not without caveats, our results suggest that linked-read sequencing technologies may represent a viable option to build de novo genomes from historic museum specimens, which may prove particularly valuable for extinct, rare, or difficult to collect taxa.
Shaky Scaffolding: Age Differences In Cerebellar Activation Revealed Through Activation Likelihood Estimation Meta-Analysis
Authors: Bernard Jessica A. , Nguyen An D. , Hausman Hanna K. , Maldonado Ted , Ballard Hannah K. , Jackson T. Bryan , Eakin Sydney M. , Lokshina Yana , Goen James R.M.
Published: July 2019

Cognitive neuroscience research has provided foundational insights into aging, but has focused primarily on the cerebral cortex. However, the cerebellum is subject to the effects of aging. Given the importance of this structure in the performance of motor and cognitive tasks, cerebellar differences stand to provide critical insights into age differences in behavior. But, our understanding of cerebellar functional activation in aging is limited. Thus, we completed a meta-analysis of neuroimaging studies across task domains. Unlike in the cortex where an increase in bilateral activation is seen during cognitive task performance with advanced age, there is less overlap in cerebellar activation across tasks in older adults relative to young. Conversely, we see an increase in activation overlap in older adults during motor tasks. We propose that this is due to inputs for comparator processing in the context of control theory (cortical and spinal) that may be differentially impacted in aging. These findings advance our understanding of the aging mind and brain.
Decelerated carbon cycling by ectomycorrhizal fungi is controlled by substrate quality and community composition
Authors: Fernandez Christopher W. , See Craig R. , Kennedy Peter G.
Published: July 2019

Interactions between symbiotic ectomycorrhizal (EM) and free-living saprotrophs can result in significant deceleration of leaf litter decomposition. While this phenomenon is widely cited, its generality remains unclear, as both the direction and magnitude of EM fungal effects on leaf litter decomposition have been shown to vary among studies. Here we explicitly examine how contrasting leaf litter types and EM fungal communities may lead to differential effects on C and N cycling. Specifically, we measured the response of soil nutrient cycling, litter decay rates, litter chemistry and fungal community structure to the reduction of EM fungi (via trenching) with a reciprocal litter transplant experiment in adjacentPinus- orQuercus-dominated sites. We found clear evidence of EM fungal suppression of C and N cycling in thePinus-dominated site, but no suppression in theQuercus-dominated site. Additionally, in thePinus-dominated site, only thePinuslitter decay rates were decelerated by EM fungi and were associated with decoupling of litter C and N cycling. Our results support the hypothesis that EM fungi can decelerate C cycling via N competition, but strongly suggest that the ‘Gadgil effect’ is dependent on both substrate quality and EM fungal community composition. We argue that understanding tree host traits as well as EM fungal functional diversity is critical to a more mechanistic understanding of how EM fungi mediate forest soil biogeochemical cycling.
Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data
Authors: Ignjatovic Vera , Geyer Philipp E , Palaniappan Krishnan K , Chaaban Jessica E , Omenn Gilbert S , Baker Mark S , Deutsch Eric W , Schwenk Jochen M
Published: July 2019

The proteomic analyses of human blood and blood-derived products (e.g. plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g. inter-individual variability), analysis of biospecimen (e.g. sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest whilst enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.

Abstract Figure
Perturbing neural representations of working memory with task-irrelevant interruption
Authors: Hakim Nicole , Feldmann-Wüstefeld Tobias , Awh Edward , Vogel Edward K.
Published: July 2019

Working memory maintains information so that it can be used in complex cognitive tasks. A key challenge for this system is to maintain relevant information in the face of task-irrelevant perturbations. In this series of experiments, we investigated the impact of task-irrelevant interruptions on neural representations of working memory. We recorded electroencephalogram (EEG) activity in humans while they performed a working memory task. On a subset of trials, we interrupted participants with salient, but task-irrelevant objects. To track the impact of these task-irrelevant interruptions on neural representations of working memory, we measured two well-characterized, temporally sensitive EEG markers that reflect active, prioritized working memory representations: the contralateral delay activity (CDA) and lateralized alpha power (8-12hz). Following interruption, we found that CDA momentarily sustained, but was gone by the end of the trial. Lateralized alpha power was immediately influenced by the interrupters, but recovered by the end of the trial. This suggests that dissociable neural processes contribute to the maintenance of working memory information. Additionally, we found that task expectancy modulated the timing and magnitude of how these two neural signals responded to task-irrelevant interruptions, suggesting that the brain’s response to task-irrelevant interruption is shaped by task context. The distinct time courses of and influence of task context on these two neural signatures of working memory have many interesting theoretical implications about how information is actively maintained in working memory.

Significance statement

Working memory plays a central role in intelligent behaviors because it actively maintains relevant information that is easily accessible and manipulatable. In everyday life, we are often interrupted while performing such complex cognitive tasks. Therefore, understanding how working memory responds to and overcomes momentary task-irrelevant interruptions is critical for us to understand how complex cognition works. Here, we unveil how two distinct neural signatures of working memory respond to task-irrelevant interruptions by recording electroencephalogram activity in humans. Our findings raise long-standing theoretical questions about how different neural and cognitive processes contribute to the maintenance of information in working memory.
Replication Timing and Transcription Identifies a Novel Fragility Signature Under Replication Stress
Authors: Sarni Dan , Sasaki Takayo , Miron Karin , Tur-Sinai Michal Irony , Rivera-Mulia Juan Carlos , Magnuson Brian , Lungman Mats , Gilbert David M. , Kerem Batsheva
Published: July 2019

Common fragile sties (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features characterizing CFSs have been associated with their instability, however, these features are prevalent across the genome and do not account for all known CFSs. Therefore, the molecular mechanism underlying CFS instability remains unclear. Here, we explored the transcriptional profile and temporal order of DNA replication (replication timing, RT) of cells under replication stress conditions. We show that the RT of only a small portion of the genome is affected by replication stress, and that CFSs are enriched for delayed RT. We identified a signature for chromosomal fragility, comprised of replication stress-induced delay in RT of early/mid S-phase replicating regions within actively transcribed large genes. This fragility signature enabled precise mapping of the core fragility region. Furthermore, the signature enabled the identification of novel fragile sites that were not detected cytogenetically, highlighting the improved sensitivity of our approach for identifying fragile sites. Altogether, this study reveals a link between altered DNA replication and transcription of large genes underlying the mechanism of CFS expression. Thus, investigating the RT and transcriptional changes in cancer may contribute to the understanding of mechanisms promoting genomic instability in cancer.
Experimental copper exposure, but not heat stress, leads to elevated intraovarian thyroid hormone levels
Authors: Suvi Ruuskanen , Giovanna Mottola , Katja Anttila
Published: July 2019

Climate change and pollution are some of the greatest anthropogenic threats to wild animals. Transgenerational plasticity – when parental exposure to environmental stress leads to changes in offspring phenotype – has been recently highlighted as a potential mechanism to respond to various environmental and anthropogenic changes across taxa. Transgenerational effects may be mediated via multiple mechanisms, such as transfer of maternal hormones to eggs/fetus. However, sources of variation in hormone transfer are poorly understood in fish, and thus the first step is to characterize whether environmental challenges alter transfer of maternal hormones to eggs. To this end, we explored the genetic and environmental variation (in response to temperature and endocrine disrupting copper) in maternal thyroid hormone (TH), transfer to offspring in a common fish model species, the three-spined stickleback (Gasterosteus aculeatus) using multiple approaches: (i) We compared ovarian TH levels among six populations across a wide geographical range in the Baltic Sea, including two populations at high water temperature areas (discharge water areas of nuclear power plants) and we experimentally exposed fish to (ii) environmentally relevant heat stress and (iii) copper for 7 days. We found that populations did not differ in intraovarian TH levels, and short-term heat stress did not influence intraovarian TH levels. However, copper exposure increased both T4 and T3 levels in ovaries. The next step would be to evaluate if such alterations would lead to changes in offspring phenotype.

Capsule: We show that experimental copper exposure, but not heat stress (experimental or among-population variation), leads to elevated ovarian thyroid hormone levels in sticklebacks.
Hidden Aspects of the Research-ADOS are Bound to Affect Autism Science
Authors: Torres Elizabeth B , Rai Richa , Mistry Sejal , Gupta Brenda
Published: July 2019

The research-grade ADOS is a broadly used instrument that informs and steers much of the science of Autism. Despite its broad use, little is known about the empirical variability inherently present in the scores of the ADOS scale, or their appropriateness to define change, to repeatedly use this test to characterize neurodevelopmental trajectories. Here we examine the empirical distributions of research-grade ADOS scores from 1,324 records in a cross-section of the population comprising participants with autism between 5-65 years of age. We find that these empirical distributions violate the theoretical requirements of normality and homogeneous variance, essential for independence between bias and sensitivity. Further, we assess a subset of 52 typical controls vs. those with autism and find lack of proper elements to characterize neurodevelopmental trajectories in a coping nervous system changing at non-uniform, non-linear rates. Lastly, longitudinally repeating the assessments over 4 visits in a subset of the participants with autism for whom verbal criteria kept the same appropriate ADOS modules over the timespan of the 4 visits, reveals that switching the clinician, changes the cutoff scores, and consequently, influences the diagnosis, despite maintaining fidelity in the same test’s modules, room conditions and tasks’ fluidity per visit. Given the changes in probability distribution shape and dispersion of these ADOS scores, the lack of appropriate metric spaces, and the impact that these elements have on sensitivity-bias co-dependencies, and on longitudinal tracking of autism, we invite a discussion on the use of this test for scientific purposes.
Depression of substantia nigra dopamine transmission is driven by retrograde neurotensin release and is enhanced by methamphetamine self-administration
Authors: Tschumi Christopher W. , Sharma Ramaswamy , Lynch William B. , Sharpe Amanda L. , Beckstead Michael J.
Published: July 2019

Midbrain dopamine neurons play central roles in reward learning and motivated behavior, and inhibition at somatodendritic dopamine D2 receptor (D2R) synapses blunts psychostimulant reinforcement. Release of the neuropeptide neurotensin in the midbrain increases following methamphetamine exposure and induces long-term depression of D2R synaptic currents (LTDDA), however the source of neurotensin that drives LTDDAis not known. Here we show that LTDDAis driven by neurotensin released by dopamine neurons. Optogenetic stimulation of dopamine neurons was sufficient to induce LTDDAin the substantia nigra, but not the ventral tegmental area, and was dependent on neurotensin receptors, postsynaptic calcium, and vacuolar-type H+-ATPase activity in the postsynaptic cell. Further, LTDDAwas enhanced in mice that had self-administered methamphetamine. These findings reveal a novel form of signaling between dopamine neurons involving release of the peptide neurotensin, which may act as a feed forward mechanism to increase dopamine neuron excitability and methamphetamine self-administration.
Reconciling a Model of Core Metabolism with Growth Yield Predicts Biochemical Mechanisms and Efficiency for a Versatile Chemoautotroph
Authors: McNichol Jesse , Sievert Stefan M.
Published: July 2019

Obligately chemoautotrophicCampylobacteriadominate productivity in dark, sulfidic, and oxygen-depleted environments. However, biochemical mechanisms underlying their growth remain poorly known, limiting understanding of their physiology, ecology, and biogeochemical impact. In this study, we used comparative genomics, conceptual modeling of core metabolism, and chemostat growth yields to derive a model of energy conservation consistent with experimental data for the versatile chemoautotrophSulfurimonas denitrificans. Our model rests on three core mechanisms: Firstly, to allow electrogenic sulfur-based denitrification, we predict that the campylobacterial-type sulfur oxidation enzyme complex must donate electrons to the membrane quinone pool, possibly via a sulfide:quinone oxidoreductase. Secondly, to account for the unexpectedly low growth efficiency of aerobic sulfur oxidation compared to denitrification, we posit the high-affinity campylobacterial-type cbb3cytochrome c oxidase has a relatively low H+/e− of 1, likely due to a lack of proton pumping under physiological conditions. Thirdly, we hypothesize that reductant for carbon fixation by the reverse tricarboxylic acid cycle is produced by a non-canonical complex I that reduces both ferredoxin and NAD(P)H. This complex is conserved among relatedCampylobacteriaand may have allowed for the radiation of organisms likeS. denitrificansinto sulfur-rich environments that became available after the great oxidation event. Our theoretical model has two major implications. Firstly, it sets the stage for future experimental work by providing testable hypotheses about the physiology, biochemistry, and evolution of chemoautotrophicCampylobacteria. Secondly, it provides constraints on the carbon fixation potential of chemoautotrophicCampylobacteriain sulfidic environments worldwide by predicting theoretical ranges of chemosynthetic growth efficiency.

Significance

ChemoautotrophicCampylobacteriaare abundant in many low-oxygen, high-sulfide environments where they contribute significantly to dark carbon fixation. Although the overall redox reactions they catalyze are known, the specific biochemical mechanisms that support their growth are mostly unknown. Our study combines conceptual modeling of core metabolic pathways, comparative genomics, and measurements of physiological growth yield in a chemostat to infer the most likely mechanisms of chemoautotrophic energy conservation in the model organismSulfurimonas denitrificans. The hypotheses proposed herein are novel, experimentally falsifiable, and will guide future biochemical, physiological, and environmental modelling studies. Ultimately, investigating the core mechanisms of energy conservation will help us better understand the evolution and physiological diversification of chemoautotrophicCampylobacteriaand their role in modern ecosystems.
Enhanced Population Control in Synthetic Bacterial Consortium by Interconnected Carbon Cross-Feeding
Authors: Losoi Pauli S. , Santala Ville P. , Santala Suvi M.
Published: July 2019

Engineered microbial consortia can provide several advantages over monocultures in terms of utilization of mixed substrates, resistance to perturbations, and division of labor in complex tasks. However, maintaining stability, reproducibility, and control over population levels in variable conditions can be challenging in multi-species cultures. In our study, we modeled and constructed a synthetic symbiotic consortium with a genetically encoded carbon cross-feeding system. The system is based on strains ofEscherichia coliandAcinetobacter baylyiADP1, both engineered to be incapable of growing on glucose on their own. In a culture supplemented with glucose as the sole carbon source, growth of the two strains is afforded by the exchange of gluconate and acetate, resulting in inherent control over carbon availability and population balance. We investigated the system robustness in terms of stability and population control under different inoculum ratios, substrate concentrations, and cultivation scales, both experimentally and by modeling. To illustrate how the system might facilitate division of genetic circuits among synthetic microbial consortia, a green fluorescent protein sensitive to pH and a slowly-maturing red fluorescent protein were expressed in the consortium as measures of a circuit’s susceptibility to external and internal variability, respectively. The symbiotic consortium maintained stable and linear growth and circuit performance regardless of the initial substrate concentration or inoculum ratios. The developed cross-feeding system provides simple and reliable means for population control without expression of non-native elements or external inducer addition, being potentially exploitable in consortia applications involving precisely defined cell tasks or division of labor.
Engineering and Evolution of Methanol Assimilation inSaccharomyces cerevisiae
Authors: Espinosa Monica I. , Gonzalez-Garcia Ricardo A. , Valgepea Kaspar , Plan Manuel , Scott Colin , Pretorius Isak S. , Marcellin Esteban , Paulsen Ian T. , Williams Thomas C.
Published: July 2019

Microbial fermentation for chemical production is becoming more broadly adopted as an alternative to petrochemical refining. Fermentation typically relies on sugar as a feedstock, however, one-carbon compounds like methanol are an attractive alternative as they can be derived from organic waste and natural gas. This study focused on engineering methanol assimilation in the yeastSaccharomyces cerevisiae.Three methanol assimilation pathways were engineered and tested: a synthetic xylulose monophosphate (XuMP), a ‘hybrid’ methanol dehydrogenase-XuMP, and a bacterial ribulose monophosphate (RuMP) pathway, with the latter identified as the most effective at assimilating methanol. Additionally,13C-methanol tracer analysis uncovered a native capacity for methanol assimilation inS. cerevisiae, which was optimized using Adaptive Laboratory Evolution. Three independent lineages selected in liquid methanol-yeast extract medium evolved premature stop codons inYGR067C, which encodes an uncharacterised protein that has a predicted DNA-binding domain with homology to theADR1transcriptional regulator. Adr1p regulates genes involved in ethanol metabolism and peroxisomal proliferation, suggestingYGR067Chas a related function. When one of the evolvedYGR067Cmutations was reverse engineered into the parental CEN.PK113-5D strain, there were up to 5-fold increases in13C-labelling of intracellular metabolites from13C-labelled methanol when 0.1 % yeast extract was a co-substrate, and a 44 % increase in final biomass. Transcriptomics and proteomics revealed that the reconstructedYGR067Cmutation results in down-regulation of genes in the TCA cycle, glyoxylate cycle, and gluconeogenesis, which would normally be up-regulated during growth on a non-fermentable carbon source. Combining the synthetic RuMP and XuMP pathways with the reconstructed Ygr067cp truncation led to further improvements in growth. These results identify a latent methylotrophic metabolism inS. cerevisiaeand pave the way for further development of native and synthetic one-carbon assimilation pathways in this model eukaryote.
Study on shape retention properties of filament/staple fiber composite yarns and fabrics
Authors: Song Juan , Su Xuzhong , Liu Xinjin
Published: July 2019

Purpose

With the improvement of living standards and acceleration of working pace, the shape retention property of textiles has attracted more attention. Yarn spinning is the first fundamental process in making textiles and apparel, and the properties of yarn influence the performance of textiles directly. Filament/staple fiber composite yarn is a kind of yarn spun by filament and staple fiber, and comprehensive qualities of yarn can be improved. Therefore, the purpose of this paper is to study the shape retention properties of filament/staple fiber composite yarns and corresponding fabrics.

Design/methodology/approach

Four kinds of composite yarn, core-spun yarn with one 50D SPH filament feeding, sirofil wrapped yarn with one 50D SPH filament feeding from left, sirofil wrapped yarn with one 50D SPH filament feeding from right, sirofil wrapped yarn with two 25D SPH filaments feeding from two sides, were spun. The qualities of spun yarns were measured. Then, corresponding two kinds of twill fabrics were woven by core-spun yarn and sirofil wrapped yarn with two filaments, respectively. The handle parameters, crease recovery, appearance leveling after washing, dimensional change rate after washing, strength and elongation and tensile elasticity were tested by using corresponding test instruments.

Findings

The tested results of spun yarn qualities show that comparing with the core-spun yarn, the evenness of sirofil wrapped yarn is improved, the hairiness is reduced, and the breaking strength and elongation are increased. Comparing with sirofil wrapped yarn with one filament, the evenness of sirofil wrapped yarn with two filaments is improved. The measured results of fabrics properties show that under the same weaving process, comparing to the fabric woven by core-spun yarn, the dimension of fabric woven by sirofil wrapped yarn is small after desizing, and warp and weft density is large. The possible reason is that the shrinkage of the SPH filament outside the sirofil wrapped yarn happens after desizing, which also makes the dimensional change rate after washing of the corresponding fabric large, and crease recovery poor.

Originality/value

In the paper, for improving the shape retention properties of the pure cotton woven fabric, one kind of SPH filament was added to the woven fabric by spinning filament/staple fiber composite yarns. Four kinds of composite yarn, core-spun yarn with one 50D SPH filament, sirofil wrapped yarn with one 50D SPH filament feeding from the left side, sirofil wrapped yarn with one 50D SPH filament feeding from the right side, sirofil wrapped yarn with two 25D SPH filaments feeding from two sides, were spun. Two kinds of twill fabrics were weaving by core-spun yarn and sirofil wrapped yarn with two filaments, respectively.
The response of root traits to precipitation change of herbaceous species in temperate steppes
Authors: Zhou Meng , Wang Jing , Bai Wenming , Zhang Yushi , Zhang Wen‐Hao
Published: July 2019

Plasticity of root traits plays an important role in plant growth and survival under changing climate. Shift in precipitation is one of the most pertinent global change factors driving changes in structure and function of grasslands. However, few studies have investigated intraspecific variation of root traits in response to precipitation change under field conditions.

We conducted a 10‐year simulated increased precipitation experiment in a temperate grassland and a 700‐km regional scale transect along a precipitation gradient ranging from 144.23 to 412.29 mm in northern China. The morphological, chemical and anatomical traits of the first two‐order roots were determined on 15 common herbaceous species in the manipulation experiment and two regionally common species (Leymus chinensis, Artemisia frigida) along a precipitation gradient.

We found that most of the root traits of the herbaceous species exhibited no significant responses to water addition. The two regionally common species adjusted their root traits at sites with the annual precipitation lower than certain value, that is 250 and 160 mm for L. chinensis and A. frigida, respectively. These results indicate that root traits of the herbaceous species exhibit little plasticity in response to precipitation change and that the adjustment of root traits occurs when the range of annual precipitation exceeds a certain threshold.

Root traits of L. chinensis and A. frigida varied differently both in manipulation experiment and along the precipitation gradient. Root traits of L. chinensis were relatively constant, while A. frigida adjusted their morphological root traits in response to water addition. Moreover, L. chinensis showed higher specific root length (SRL) and area, and root N contents at sites with annual precipitation lower than c. 250 mm. In contrast, A. frigida displayed thicker roots with lower SRL and area at sites with annual precipitation lower than c. 160 mm.

Our results showed that root traits of herbaceous species in temperate grasslands exhibited little plasticity and that different species have evolved diverse adaptive strategies in response to precipitation change. These novel findings provide valuable information to predict responses of temperate grasslands to future climate change.
Effects of topography on tropical forest structure depend on climate context
Authors: Muscarella Robert , Kolyaie Samira , Morton Douglas C. , Zimmerman Jess K. , Uriarte María
Published: July 2019

Topography affects abiotic conditions which can influence the structure, function and dynamics of ecological communities. An increasing number of studies have demonstrated biological consequences of fine‐scale topographic heterogeneity but we have a limited understanding of how these effects depend on the climate context.

We merged high‐resolution (1 m2) data on topography and canopy height derived from airborne lidar with ground‐based data from 15 forest plots in Puerto Rico distributed along a precipitation gradient spanningc. 800–3,500 mm/year. Ground‐based data included species composition, estimated above‐ground biomass (AGB), and two key functional traits (wood density and leaf mass per area, LMA) that reflect resource‐use strategies and a trade‐off between hydraulic safety and hydraulic efficiency. We used hierarchical Bayesian models to evaluate how the interaction between topography × climate is related to metrics of forest structure (i.e. canopy height and AGB), as well as taxonomic and functional alpha‐ and beta‐diversity.

Fine‐scale topography (characterized with the topographic wetness index, TWI) significantly affected forest structure and the strength (and in some cases direction) of these effects varied across the precipitation gradient. In all plots, canopy height increased with topographic wetness but the effect was much stronger in dry compared to wet forest plots. In dry forest plots, topographically wetter microsites also had higher levels of AGB but in wet forest plots, topographically drier microsites had higher AGB.

Fine‐scale topography influenced functional composition but had only weak or non‐significant effects on taxonomic and functional alpha‐ and beta‐diversity. For instance, community‐weighted wood density followed a similar pattern to AGB across plots. We also found a marginally significant association between variation of wood density and topographic heterogeneity that depended on climate context.

Synthesis. The effects of fine‐scale topographic heterogeneity on tropical forest structure and composition depend on the climate context. Our study demonstrates how a stronger integration of topographic heterogeneity across precipitation gradients could improve estimates of forest structure and biomass, and may provide insight to the ways that topography might mediate species responses to drought and climate change.
Plant phylogenetic history explains in‐stream decomposition at a global scale
Authors: LeRoy Carri J. , Hipp Andrew L. , Lueders Kate , Follstad Shah Jennifer J. , Kominoski John S. , Ardón Marcelo , Dodds Walter K. , Gessner Mark O. , Griffiths Natalie A. , Lecerf Antoine , Manning David W. P. , Sinsabaugh Robert L. , Webster Jack R.
Published: July 2019

Evolutionary history and adaptation to climate shape plant traits. Some include leaf traits that influence litter quality. Thus, evolutionary history should affect litter decomposition, a crucial ecosystem process. In addition, litter decomposition is directly influenced by climate. We consequently expect plant phylogeny, adaptation and climate to jointly influence litter decomposition. These effects and their interactions have yet to be untangled at a global scale.

Here we present an analysis of variation in litter decomposition rates in rivers and streams across 285 published studies for 239 species (from ferns to angiosperms) distributed at 494 locations world‐wide. We estimated the relative contributions of climatic conditions and phylogenetic heritage on litter decomposition rates, partitioning phylogenetic from climatic effects at the site and species levels using phylogenetic eigenvector analysis and phylogenetic linear mixed models. In addition, we modelled transitions in decomposition rates under a suite of multiple adaptive‐regime Ornstein–Uhlenbeck models to test the hypothesis that natural selection has shaped clade‐level litter decomposition rates.

Leaf litter decomposition rate exhibited a significant phylogenetic signal. Modelling decomposition rate as a function of location, climatic niche and phylogeny consistently recovered phylogeny alone as one of the top models in species‐level analyses. Since many previous studies have focused on the same species across many locations, we also conducted analyses at the species × site level. Both phylogenetic and climatic factors were favoured in models of this analysis, but the single most important predictor for angiosperms and for all taxa analysed together was phylogeny alone.

Synthesis.For plant species distributed globally at nearly 500 locations we found that plant phylogenetic history is a critically important predictor of litter decomposition rate in rivers and streams, explaining more of the variance in decomposition than site or climatic regime. Thus, our study demonstrates the influence of evolutionary history on suites of plant traits that shape a key ecosystem process.