bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trading water for carbon: Sustained photosynthesis at the cost of increased water loss during high temperatures in a temperate forest
Authors: Griebel Anne , Bennett Lauren T. , Metzen Daniel , Pendall Elise , Lane Patrick N.J. , Arndt Stefan K. 
Published: September 2019

AbstractForest carbon and water fluxes are often assumed to be coupled as a result of stomatal regulation during dry conditions. However, recent observations have indicated increased transpiration rates during isolated heat waves across a range of eucalypt species under experimental and natural conditions, with inconsistent effects on photosynthesis (ranging from an increase to a near total decline). To improve the empirical basis for understanding carbon and water fluxes in forests under hotter and drier climates, we measured the water use of dominant trees, and the ecosystem-scale carbon and water exchange in a mature temperate eucalypt forest over three summer seasons. The forest maintained photosynthesis within 16% of peak photosynthesis rates during all conditions, despite up to 70% reductions in canopy conductance during a 5-day heatwave. While carbon and water fluxes both decreased by 16% on exceptionally dry summer days, GPP was sustained at the cost of up to 74% increased water loss on the hottest days and during the heatwave. This led to ∼40% variation in ecosystem water use efficiency over the three summers, and ∼two-fold differences depending on the way water use efficiency is calculated. Furthermore, the forest became a net source of carbon following a 137% increase in ecosystem respiration during the heat wave, highlighting that the potential for temperate eucalypt forests to remain net carbon sinks under future climates will depend not only on their potential to maintain photosynthesis during higher temperatures, but also on responses of ecosystem respiration to changes in climate.Key PointsGPP of temperate eucalypts was sustained at the cost of increased water use during hot periods, but both fluxes decreased during dry periods.WUE estimates for the same period differed up to two-fold depending on the way it was calculated.Doubling of ecosystem respiration turned the forest from a net sink into a net source of carbon during a longer heatwave.
Germline RNA helicases couple RNA binding to P granule assembly at nuclear periphery
Authors: Chen Wenjun , Hu Yabing , Lang Charles , Brown Jordan S , Song Xiaoyan , Munro Ed , Bennett Karen , Zhang Donglei , Lee Heng-Chi 
Published: September 2019

ABSTRACTP granules are phase-separated liquid droplets that play important roles in the maintenance of the germ cell fate in C. elegans. The localization and formation of P granules are highly dynamic, but mechanisms that regulate such processes remain poorly understood. Here we show that germline RNA helicases (GLHs) control the formation and disassembly of germ granules through their binding and release of RNAs, respectively. In addition, the FGG repeats in the GLHs promote the formation of germ granules at the perinucleus. Proteomic analyses of a mutation that traps RNA-bound GLH-1 complex revealed transient interactions of GLH-1 with several Argonautes and RNA binding proteins. Finally, we found that defects in perinuclear P granule formation correlate with the fertility defects observed in various GLH mutants. Together, our results highlight the versatile roles of RNA helicases in controlling the formation of liquid droplets in space and time.
The co-stimulation of anti-CD28 and IL-2 enhances the sensitivity of ELISPOT assays for detection of neoantigen-specific T cells in PBMC
Authors: Tang Yunxia , Zhu Linnan , Xu Qumiao , Zhang Xiuqing , Li Bo , Lee Leo J. 
Published: September 2019

AbstractNeoantigen-based cancer immunotherapies hold the promise of being a truly personalized, effective treatment for diverse cancer types. ELISPOT assays, as a powerful experimental technique, can verify the existence of antigen specific T cells to support basic clinical research and monitor clinical trials. However, despite the high sensitivity of ELISPOT assays, detecting immune responses of neoantigen specific T cells in a patient or healthy donor’s PBMCs is still extremely difficult, since the frequency of these T cells can be very low. We developed a novel experimental method, by co-stimulation of T cells with anti-CD28 and IL-2 at the beginning of ELISPOT, to further increase the sensitivity of ELISPOT and mitigate the challenge introduced by low frequency T cells. Under the optimal concentration of 1μg/mL for anti-CD28 and 1U/ml for IL-2, our new method can increase sensitivity by up to 5 folds comparing to a conventional ELISPOT, and outperforms other cytokine stimulation alternatives. To the best of our knowledge, this is the first report that the co-stimulation of anti-CD28 and IL-2 is able to significantly improve the sensitivity of ELISPOT assays, indicating that anti-CD28 and IL-2 signaling can act in synergy to lower the T cell activation threshold and trigger more neoantigen-specific T cells.
Association between the 4p16 genomic locus and different types of congenital heart disease: results from adult survivors in the UK Biobank
Authors: Córdova-Palomera Aldo , Priest James R. 
Published: September 2019

ABSTRACTCongenital heart disease is the most common birth defect in newborns and the leading cause of death in infancy, affecting nearly 1% of live births. A locus in chromosome 4p16, adjacent to MSX1 and STX18, has been associated with atrial septal defects (ASD) in multiple European and Chinese cohorts. Here, genotyping data from the UK Biobank was used to test for associations between this locus and congenital heart disease in adult survivors of left ventricular outflow tract obstruction (n=164) and ASD (n=223), with a control sample of 332,788 individuals, and a meta-analysis of the new and existing ASD data was performed.The results show an association between the previously reported markers at 4p16 and risk for either ASD or left ventricular outflow tract obstruction, with effect sizes similar to the published data (OR between 1.27-1.45; all p<0.05). Differences in allele frequencies remained constant through the studied age range (40-70 years), indicating that the variants themselves do not drive lethal genetic defects. Meta-analysis shows an OR of 1.35 (95% CI: 1.25-1.46; p<10−4) for the association with ASD.The findings show that the genetic associations with ASD can be generalized to adult survivors of both ASD and left ventricular lesions. Although the 4p16 associations are statistically compelling, the mentioned alleles confer only a small risk for disease and their frequencies in this adult sample are the same as in children, likely limiting their clinical significance. Further epidemiological and functional studies may elicit factors triggering disease in interaction with the risk alleles.
Unsupervised Clusterless Decoding using a Switching Poisson Hidden Markov Model
Authors: Ackermann Etienne , Kemere Caleb T. , Cunningham John P. 
Published: September 2019

AbstractSpike sorting is a standard preprocessing step to obtain ensembles of single unit data from multiunit, multichannel recordings in neuroscience. However, more recently, some researchers have started doing analyses directly on the unsorted data. Here we present a new computational model that is an extension of the standard (unsupervised) switching Poisson hidden Markov model (where observations are time-binned spike counts from each of N neurons), to a clusterless approximation in which we observe only a d-dimensional mark for each spike. Such an unsupervised yet clusterless approach has the potential to incorporate more information than is typically available from spike-sorted approaches, and to uncover temporal structure in neural data without access to behavioral correlates. We show that our approach can recover model parameters from simulated data, and that it can uncover task-relevant structure from real neural data.
Within-Host Diversity and Vertical Transmission of Group B Streptococcus Among Mother-infant Dyads in The Gambia
Authors: Foster-Nyarko Ebenezer , Senghore Madikay , Kwambana-Adams Brenda A. , Alikhan Nabil-Fareed , Ravi Anuradha , Jafali James , Jawneh Kaddijatou , Jah Amara , Jarju Maimuna , Ceesay Fatima , Bojang Sainabou , Worwui Archibald , Odutola Aderonke , Ogundare Ezra , Pallen Mark J. , Ota Martin , Antonio Martin 
Published: September 2019

AbstractIntroductionUnderstanding mother-to-infant transmission of Group B Streptococcus (GBS) is vital to the prevention and control of GBS disease. We investigated the transmission and phylogenetic relationships of mothers colonised by GBS and their infants in a peri-urban setting in The Gambia.MethodsWe collected nasopharyngeal swabs from 35 mother-infant dyads at weekly intervals from birth until six weeks post-partum. GBS was isolated by conventional microbiology techniques. Whole-genome sequencing was performed on GBS isolates from one mother-infant dyad (dyad 17).ResultsWe recovered 85 GBS isolates from the 245 nasopharyngeal swabs. GBS was isolated from 16.33% and 18.37% of sampled mothers and infants, respectively. In 87% of cultured swabs, the culture status of an infant agreed with that of the mother (Kappa p-value <0.001). In dyad 17, phylogenetic analysis revealed within-host strain diversity in the mother and clone to her infant.ConclusionGBS colonisation in mothers presents a significant risk of colonisation in their infants. We confirm vertical transmission from mother to child in dyad 17, accompanied by within-host diversity.
Predicting the impacts of sea level rise in sea turtle nesting habitat on Bioko Island, Equatorial Guinea
Authors: Veelenturf Callie A. , Sinclair Elizabeth M. , Paladino Frank V. , Honarvar Shaya 
Published: September 2019

AbstractSea level is expected to rise 44 to 74 cm by the year 2100, which may have critical, previously un-investigated implications for sea turtle nesting habitat on Bioko Island, Equatorial Guinea. This study investigates how nesting habitat will likely be lost and altered with various increases in sea level, using global sea level rise (SLR) predictions from the Intergovernmental Panel on Climate Change. Beach profiling datasets from Bioko’s five southern nesting beaches were used in GIS to create models to estimate habitat loss with predicted increases in sea level by years 2046-2065 and 2081-2100. The models indicate that an average of 62% of Bioko’s current nesting habitat could be lost by 2046-2065 and 87% by the years 2081-2100. Beach D is predicted to be the least vulnerable to increases in sea level. Erosion and tall vegetation berms have been documented on Beaches A and B, causing green turtles to nest uncharacteristically in front of the vegetation line. Development plans are currently underway for Beach D. With Beach D being the least susceptible to future increases in sea level, development and anthropogenic encroachment here would be especially detrimental to nesting turtle populations. Identified habitat sensitivities to SLR will be used to inform the government of Equatorial Guinea to consider the vulnerability of their resident turtle populations and projected climate change implications when planning for future development. To our knowledge this is the first study to predict the impacts of SLR on sea turtle nesting habitat in Africa.
Proprioceptive accuracy in immersive virtual reality: A developmental perspective
Authors: Valori Irene , McKenna-Plumley Phoebe E. , Bayramova Rena , Callegher Claudio Zandonella , Altoè Gianmarco , Farroni Teresa 
Published: September 2019

AbstractProprioceptive development relies on a variety of sensory inputs, among which vision is hugely dominant. Focusing on the developmental trajectory underpinning the integration of vision and proprioception, the present research explores how this integration is involved in interactions with Immersive Virtual Reality (IVR) by examining how proprioceptive accuracy is affected byage, perception, andenvironment. Individuals from 4 to 43 years old completed a self-turning task which asked them to manually return to a previous location with different sensory modalities available in both IVR and reality. Results were interpreted from an exploratory perspective using Bayesian model comparison analysis, which allows the phenomena to be described using probabilistic statements rather than simplified reject/not-reject decisions. The most plausible model showed that 4–8-year-old children can generally be expected to make more proprioceptive errors than older children and adults. Across age groups, proprioceptive accuracy is higher when vision is available, and is disrupted in the visual environment provided by the IVR headset. We can conclude that proprioceptive accuracy mostly develops during the first eight years of life and that it relies largely on vision. Moreover, our findings indicate that this proprioceptive accuracy can be disrupted by the use of an IVR headset.
Carbendazim-resistance associated β2-tubulin substitutions increase deoxynivalenol biosynthesis by reducing the interaction between β2-tubulin and IDH3 in Fusarium graminearum
Authors: Zhou Zehua , Duan Yabing , Zhou Mingguo 
Published: September 2019

AbstractMicrotubule is a well-known structural protein participating in cell division, motility and vesicle traffic. In this study, we found that β2-tubulin, one of the microtubule components, plays an important role in regulating secondary metabolite deoxynivalenol (DON) biosynthesis in Fusarium graminearum by interacting with isocitrate dehydrogenase subunit 3 (IDH3). We found IDH3 negatively regulate DON biosynthesis by reducing acetyl-CoA accumulation in F. graminearum and DON biosynthesis was stimulated by exogenous acetyl-CoA. In addition, the expression of IDH3 significantly decreased in the carbendazim-resistant mutant nt167 (Fgβ F167Y). Furthermore, we found that carbendazim-resistance associated β2-tubulin substitutions reducing the interaction intensity between β2-tubulin and IDH3. Interestingly, we demonstrated that β2-tubulin inhibitor carbendazim can disrupt the interaction between β2-tubulin and IDH3. The decreased interaction intensity between β2-tubulin and IDH3 resulted in the decreased expression of IDH3, which can cause the accumulation of acetyl-CoA, precursor of DON biosynthesis in F. graminearum. Thus, we revealed that carbendazim-resistance associated β2-tubulin substitutions or carbendazim treatment increases DON biosynthesis by reducing the interaction between β2-tubulin and IDH3 in F. graminearum. Taken together, the novel findings give the new perspectives of β2-tubulin in regulating secondary metabolism in phytopathogenic fungi.Author SummaryThe deoxynivalenol (DON) biosynthesis is increased in carbendazim-resistant strains in Fusarium graminearum. To date, the molecular mechanism between the carbendazim-resistant substitution and the increased DON production remained elusive. Here we found that acetyl-CoA-associated enzyme IDH3 negatively regulates acetyl-CoA and DON biosynthesis. Moreover, β2 tubulin interacted with IDH3 physically and increase its expression. We further found that carbendazim-resistant substitution in β2 tubulin reducing the interaction between β2 tubulin and IDH3, which resulted in the decreased expression of IDH3. In addition, we demonstrated that carbendazim disrupting the binding between β2 tubulin and IDH3, which also decreases the expression of IDH3. Taken together, our results give a newly insights into the mechanism of β2 tubulin and its carbendazim-resistant substitution in regulating DON biosynthesis.
Loss of pyrethroid resistance in newly established laboratory colonies of Aedes aegypti
Authors: Vera-Maloof Farah Z. , Saavedra-Rodriguez Karla , Penilla-Navarro Rosa P. , Rodriguez-Ramirez Americo D. , Dzul Felipe , Manrique Pablo , Black William C. 
Published: September 2019

AbstractBackgroundResistance to pyrethroid insecticides in Aedes aegypti has become widespread after almost two decades of their frequent use to reduce arbovirus transmission. Despite this, use of pyrethroids continues because they are relatively inexpensive and because of their low human toxicity. Resistance management has been proposed as a means to retain the use of pyrethroids in natural populations. A key component of resistance management assumes that there is a negative fitness associated with resistance alleles so that when insecticides are removed, resistance alleles will decline in frequency. At least three studies in Ae. aegypti have demonstrated a decrease in pyrethroid resistance once the insecticide is removed.Methods/Principal FindingsThe present study aims to evaluate variation in the loss of pyrethroid resistance among newly established laboratory populations of Ae. aegypti from Mexico. Eight field collections were maintained for up to eight generations and we recorded changes in the frequencies of mutations at the V1,016I locus and at the F1,534C locus in the voltage gated sodium channel (VGSC) gene. I1,016 and C1,534 confer resistance. We also examined resistance ratios (RR) with type 1 and 2 pyrethroids.Conclusions/SignificanceWe demonstrate that, in general, the frequency of the Ae. aegypti pyrethroid resistance alleles I1,016 and C1,534 decline when they are freed from pyrethroid pressure in the laboratory. However, the pattern of decline is strain dependent. In agreement with earlier studies, RR was positively correlated with I1,016 resistant allele frequencies and showed significant protection against permethrin, and deltamethrin whereas F1534C showed protection against permethrin but not against deltamethrin.Author SummaryThe author is interested in the evolution of genes that confer resistance to insecticides, especially when this evolution affects binding of insecticides to their target site. The Voltage Gated Sodium Channel gene represents an excellent opportunity to understand how mutations at the target site(s) affect the evolution of resistance in many different pest insect species including Aedes aegypti, the primary vector of Dengue Virus, Yellow Fever, Zika and Chikungunya arboviruses.
Mapping the S1 and S1’ subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents
Authors: Cianni Lorenzo , Lemke Carina , Gilberg Erik , Feldmann Christian , Rosini Fabiana , dos Reis Rocho Fernanda , Ribeiro Jean F.R. , Tezuka Daiane Y. , Lopes Carla D. , de Albuquerque Sérgio , Bajorath Jürgen , Laufer Stefan , Leitão Andrei , Gütschow Michael , Montanari Carlos A. 
Published: September 2019

AbstractThe cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. A series of 26 new compounds waswere designed, synthesized, and tested against the recombinant cruzain (Cz) to map its S1/S1′ subsites. The same series was evaluated on a panel of four human cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which is a potential target for the treatment of cutaneous leishmaniasis. The synthesized compounds are dipeptidyl nitriles designed based on the most promising combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building blocks). Eight compounds exhibited a Ki smaller than 20.0 nM for Cz, whereas three compounds met these criteria for LmCPB. The three inhibitors had an EC50 value of ca. 4 μM, thus being equipotent to benznidazole according to the anti-trypanosomal effects. Our mapping approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cysteine proteases.Author SummaryDespite many achievements in identifying novel agents for the treatment of tropical and neglected diseases, further research continues to be of fundamental importance. Our research groups have been using the cruzipain cysteine protease in its recombinant form, cruzain (Cz), to identify new trypanocidal agents. Considering the possible interchangeability with other cysteine proteases, the same series of dipeptidyl nitriles was tested in Leishmania mexicana LmCPB. Other potential targets for such inhibitors are human cysteine cathepsins, which are involved in different disease states. Thus, the inhibitors were also tested against cathepsins B, L, K, and S. Our results demonstrate that inhibition of these cysteine proteases can be achieved by appropriate structural modifications of dipeptidyl nitriles. It was also possible to identify trypanocidal agents, equipotent to benznidazole, the current drug of choice used for the treatment of Chagas disease.
Bioinformatics analysis of endophytic bacteria related to berberine in the Chinese medicinal plant Coptis teeta Wall
Authors: Liu Tian-hao , Zhang Xiao-mei , Tian Shou-zheng , Chen Li-guo , Yuan Jia-li 
Published: September 2019

AbstractPlant endophytic microorganisms absorb nutrients and prevent pathogen damage, supporting healthy plant growth. However, relationships between endophytic bacteria of the medicinal plant Coptis teeta Wall. and berberine production remain unclear. Herein, we explored the microbial composition of wild-type (WT) and cultivated Coptis teeta Wall. root, stem and leaf, and endophytic bacteria related to berberine. Microbial characteristics of were analyzed by 16S rDNA sequencing, and berberine in roots was analyzed by high-performance liquid chromatography (HPLC). Proteobacteria, Actinobacteria and Bacteroidetes were the major phyla, and Mycobacterium, Salmonella, Nocardioides, Burkholderia-Paraburkholderia and Rhizobium were the dominant genera. Berberine was positively correlated with total P (TP), total N (TN), total K (TK) and available K (AK) in rhizosphere soil, and with Microbacterium and norank_f_7B-8, whereas TK was positively correlated with Microbacterium, TN, AK and Burkholderia-Paraburkholderia. The findings will support further studies on endophytic bacteria and berberine in Coptis teeta Wall., and may promote berberine production.