bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing for pollinator recognition in multiple species ofHeliconia
Authors: Gannon Dustin G. , Hadley Adam S. , Kormann Urs G. , Andrew Jones F. , Betts Matthew G. 
Published: April 2021

AbstractMany plants have evolved floral traits that, in effect, filter pollinator communities and promote pollination by efficient pollinators. Most documented pollinator filter traits act to deter or reduce visitation rates by a subsect of the community of floral visitors. However, a recently described pollinator filter termed ‘pollinator recognition’ (PR) acts at a stage after a pollinator visit. PR was first documented experimentally inHeliconia tortuosawhereby pollen tube germination – a proxy for reproduction – was enhanced following visits from morphologically specialized pollinators, but not generalists. This is thought to promote outcrossing among plants by preferentially investing in reproduction following visits by long-ranging hummingbirds with specialized bill shapes. To date, this plant behavior has only been described inH. tortuosa, but, if widespread, could have important ecological implications; given declines in abundances of specialist pollinators, visits by generalists would not buffer the loss of pollination services to plants with PR. We therefore tested for PR in four taxa spread widely across the Heliconiaceae.We corroborated previous results that visits by long-billed, but not short-billed hummingbirds increased pollen tubes inH. tortuosawith aviary experiments that standardized pollen quality and minimized variation in pollen quantity. Across species, we found great variation in pollen tube responses to experimental treatments. For one species (H. rostrata), we found increased numbers of pollen tubes in those visited by hummingbirds compared to hand pollination alone, regardless of the visiting bird’s bill morphology, indicating recognition of hummingbirds in general. In other cases, hummingbird visits decreased pollen tube counts compared to hand pollinations alone. Furthermore, our results could not substantiate any specific mechanism for pollinator recognition and highlight the need for further work on the complexities of and variability in reproductive strategies across plant taxa.
Proteomic insight into soybean response to flooding stress reveals changes in basic energy metabolism and cell wall modifications
Authors: Khan Mudassar Nawaz , Ahmad Iftikhar , Israr-ud-Din  , Ali Essa , Noureldeen Ahmed , Darwish Hadeer , Khan Muhammad Ishfaq , Tayyab Muhammad , Khan Majid 
Published: April 2021

AbstractSoybean is a legume crop enriched with proteins and oil. It is frequently exposed to anthropogenic and natural flooding that limits its growth and yield. Current study applied gel-free proteomic techniques to unravel soybean response mechanism to flooding stress. Two-days-old soybeans were flooded for 4 days continuously and root samples were collected at days 2 to 6 for proteomic and enzymatic analyses. Age-matched untreated soybeans were collected as control. After protein extraction, purification and tryptic digestion, the peptides were analyzed on nano-liquid chromatography-mass spectrometry. A total of 539 and 472 proteins with matched peptides 2 or more were identified in control and flooded seedlings, respectively. Among these 364 proteins were commonly identified in both control and flooded soybeans. Fourty-two protein’s abundances were changed 4-fold after 2-days of flooding stress as compared to starting point. The cluster analysis showed that highly increased proteins included cupin family proteins, enolase, pectin methylesterase inhibitor, glyoxalase II, alcohol dehydrogenase and aldolase. The enzyme assay of enolase and pectin methylesterase inhibitor confirmed protein abundance changes. These findings suggest that soybean adopts the less energy consuming strategies and brings biochemical and structural changes in the cell wall to effectively respond to flooding stress and for the survival.
Microvasculature-on-a-Chip: Bridging the interstitial blood-lymph interface via mechanobiological stimuli
Authors: Bachmann Barbara , Spitz Sarah , Jordan Christian , Schuller Patrick , Wanzenböck Heinz D. , Haddadi Bahram , Harasek Michael , Redl Heinz , Holnthoner Wolfgang , Ertl Peter 
Published: April 2021

ABSTRACTAfter decades of simply being referred to as the body’s sewage system, the lymphatic system has recently been recognized as a key player in numerous physiological and pathological processes. As an essential site of immune cell interactions, the lymphatic system is a potential target for next-generation drug delivery approaches in treatments for cancer, infections, and inflammatory diseases. However, the lack of cell-based assays capable of recapitulating the required biological complexity combined with unreliablein vivoanimal models currently hamper scientific progress in lymph-targeted drug delivery. To gain more in-depth insight into the blood-lymph interface, we established an advanced chip-based microvascular model to study mechanical stimulation’s importance on lymphatic sprout formation. Our microvascular model’s key feature is the co-cultivation of spatially separated 3D blood and lymphatic vessels under controlled, unidirectional interstitial fluid flow while allowing signaling molecule exchange similar to thein vivosituation. We demonstrate that our microphysiological model recreates biomimetic interstitial fluid flow, mimicking the route of fluidin vivo, where shear stress within blood vessels pushes fluid into the interstitial space, which is subsequently transported to the nearby lymphatic capillaries. Results of our cell culture optimization study clearly show an increased vessel sprouting number, length, and morphological characteristics under dynamic cultivation conditions and physiological relevant mechanobiological stimulation. For the first time, a microvascular on-chip system incorporating microcapillaries of both blood and lymphatic originin vitrorecapitulates the interstitial blood-lymph interface.
Differential roles for DNAJ isoforms in HTT-polyQ and mutant FUS aggregation modulation revealed by chaperone network screens
Authors: Rozales Kinneret , Younis Amal , Kellerman Lior , Heinrich Ronit , Berlin Shai , Shalgi Reut 
Published: April 2021

AbstractProtein aggregation is a hallmark of many neurodegenerative diseases1,2. In order to cope with misfolding and aggregation, cells have evolved an elaborate network of molecular chaperones, composed of different families3. But while chaperoning mechanisms for different families are well established, functional and regulatory diversification within chaperone families is still largely a mystery4,5. Here we decided to explore chaperone functional diversity, through the lens of pathological aggregation. We revealed that different naturally-occurring isoforms of DNAJ chaperones showed differential effects on different types of aggregates. We performed a chaperone screen for modulators of two neurodegeneration-related aggregating proteins, the Huntington’s disease-related HTT-polyQ, and the ALS-related mutant FUS (mutFUS). The screen identified known modulators of HTT-polyQ aggregation6,7, confirming the validity of our approach. Surprisingly, modulators of mutFUS aggregation were completely different than those of HTT-polyQ. Interestingly, different naturally-occurring isoforms of DNAJ chaperones had opposing effects on HTT-polyQ vs. mutFUS aggregation. We identified a complex of the full length (FL) DNAJB14 and DNAJB12 isoforms which substantially alleviated mutFUS aggregation, in an HSP70-dependent manner. Their naturally occurring short isoforms were unable to form the complex, nor to interact with HSP70, and lost their ability to reduce mutFUS aggregation. In contrast, the short isoform of DNAJB12 significantly alleviated HTT-polyQ aggregation, while DNAJB12-FL aggravated HTT-polyQ aggregation. Finally, we demonstrated that full-length DNAJB14 ameliorated mutFUS aggregation compared to DNAJB14-short in primary neurons. Together, our data unraveled distinct molecular properties required for aggregation protection in different neurodegenerative diseases, and revealed a new layer of complexity of the chaperone network elicited by naturally occurring J-protein isoforms, highlighting functional diversity among the DNAJ family.
Transfer RNA-derived non-coding RNAs (tncRNAs): Uncovering hidden regulators of transcriptional regulatory circuits in plants
Authors: Zahra Shafaque , Singh Ajeet , Poddar Nikita , Kumar Shailesh 
Published: April 2021

AbstractThe lateral emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic regulatory networks. Among them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands their exploration in the plant kingdom. Here, we have designed a methodology to uncover the bigger picture of tncRNAome in plants. Using this, we have identified diverse tncRNAs of length 14-50 nt in ~2500 small RNA sequencing (sRNA-seq) samples of six major angiosperms, and further studied their various features including length, codon-usage, cleavage pattern, and modified tRNA nucleosides. Codon-dependent generation of tncRNAs indicates that the process is highly specific rather than being mere random tRNA degradation. Analysis for nucleotide composition of tncRNA cleavage positions indicates that they are generated through precise endoribonucleolytic machinery. Certain tRNA nucleoside modifications on tncRNAs were found to be conserved across the plants, and hence may influence tRNA cleavage, as well as tncRNA functions. Pathway enrichment analysis revealed that common tncRNA targets were majorly involved in the metabolic and developmental processes of plants. Also, many tRFs were found to be associated with transposable elements. Distinct tissue-specific tncRNA clusters indicate their role in plant development under normal physiological conditions. Furthermore, the identification of a significant number of differentially expressed tncRNAs under several abiotic and biotic stresses highlights their probable role as gene expression modulators during various stress conditions. Thus, this study will be beneficial to investigate the emerging role of tncRNAs as prospective biomarkers in plant development and stress.HighlightsComputational pipeline for accurate identification of genuine transfer RNA-derived non-coding RNAs (tncRNAs) using small RNA sequencing (sRNA-seq) datasets.Six major tncRNA classes of length ranging from 14 to 50 nt were identified in ~2,500 sRNA-seq datasets in six different angiosperms.tRNA nucleoside modifications may affect tncRNA cleavage in plants.Conserved tncRNAs target transcripts are involved in plant growth, development, and metabolism.tncRNAs are expressed in a tissue-dependent, and stress-specific manner in plants.
Motor unit recruitment patterns of the quadriceps differ between continuous high- and low-torque isometric knee extension to momentary failure
Authors: Murphy Jonathan , Hodson-Tole Emma , Vigotsky Andrew D. , Potvin Jim R. , Fisher James P. , Steele James 
Published: April 2021

AbstractThe size principle is a theory of motor unit (MU) recruitment that suggests MUs are recruited in an orderly manner from the smallest (lower threshold) to the largest (higher threshold) MUs. A consequence of this biophysical theory is that, for isometric contractions, recruitment is dependent on the intensity of actual effort required to meet task demands. This concept has been supported by modelling work demonstrating that, in tasks performed to momentary failure, full MU recruitment will have occurred upon reaching failure irrespective of the force requirements of the task. However,in vivostudies examining this are limited. Therefore, the aim of the current study was to examine MU recruitment of the quadriceps under both higher- and lower-torque (70% and 30% of MVC, respectively) isometric knee extension, performed to momentary failure. Specifically, we compared surface electromyography (sEMG) frequency characteristics, determined by wavelet analysis, across the two continuous isometric knee extension tasks to identify potential differences in recruitment patterns. A convenience sample of 10 recreationally active adult males (height: 179.6±6.0 cm; mass: 76.8±7.3 kg; age: 26±7 years) with previous resistance training experience (6±3 years) were recruited. Using a within-session, repeated-measures, randomised crossover design participants performed the knee extension tasks whilst sEMG was collected from the vastus medialis (VM), rectus femoris (RF) and vastus lateralis (VL). Myoelectric signals were decomposed into intensities as a function of time and frequency using an EMG-specific wavelet transformation. Our first analysis compared the mean frequency at momentary failure; second, we investigated the effects of load on relative changes in wavelet intensities; finally, we quantified the degree of wavelet similarity over time. Wavelet-based calculation of the mean signal frequency appeared to show similar mean frequency characteristics occurring when reaching momentary failure. However, individual wavelets revealed that different changes in frequency components occurred between the two tasks, suggesting that patterns of recruitment differed. Low-torque conditions resulted in an increase in intensity of all frequency components across the trials for each muscle whereas high-torque conditions resulted in a wider range of frequency components contained within the myoelectric signals at the beginning of the trials. However, as the low-torque trial neared momentary failure there was an increased agreement between conditions across wavelets. Our results corroborate modelling studies as well as recent biopsy evidence, suggesting overall MU recruitment may largely be similar for isometric tasks performed to momentary failure with the highest threshold MUs likely recruited, despite being achieved with differences in the pattern of recruitment over time utilised.
Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities
Authors: Song Yun Min , Hong Hyukpyo , Kim Jae Kyoung 
Published: April 2021

AbstractBiochemical systems consist of numerous elementary reactions governed by the law of mass action. However, experimentally characterizing all the elementary reactions is nearly impossible. Thus, over a century, their deterministic models that typically contain rapid reversible bindings have been simplified with non-elementary reaction functions (e.g., Michaelis-Menten and Morrison equations). Although the non-elementary reaction functions are derived by applying the quasi-steady-state approximation (QSSA) to deterministic systems, they have also been widely used to derive propensities for stochastic simulations due to computational efficiency and simplicity. However, the validity condition for this heuristic approach has not been identified even for the reversible binding between molecules, such as protein-DNA, enzyme-substrate, and receptor-ligand, which is the basis for living cells. Here, we find that the non-elementary propensities based on the deterministic total QSSA can accurately capture the stochastic dynamics of the reversible binding in general. However, serious errors occur when reactant molecules with similar levels tightly bind, unlike deterministic systems. In that case, the non-elementary propensities distort the stochastic dynamics of a bistable switch in the cell cycle and an oscillator in the circadian clock. Accordingly, we derive alternative non-elementary propensities with the stochastic low-state QSSA, developed in this study. This provides a universally valid framework for simplifying multiscale stochastic biochemical systems with rapid reversible bindings, critical for efficient stochastic simulations of cell signaling and gene regulation. To facilitate the framework, we provide a user-friendly open-source computational package, ASSISTER, that automatically performs the present framework.
DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia
Authors: Liu Wei , Sun Yaoting , Ge Weigang , Zhang Fangfei , Gan Lin , Zhu Yi , Guo Tiannan , Liu Kexin 
Published: April 2021

AbstractDrug resistance is a critical obstacle to effective treatment in patients with chronic myeloid leukemia (CML). To understand the underlying resistance mechanisms in response to imatinib (IMA) and adriamycin (ADR), the parental K562 cells were treated with low doses of IMA or ADR for two months to generate derivative cells with mild, intermediate and severe resistance to the drugs as defined by their increasing resistance index (RI). PulseDIA-based quantitative proteomics was then employed to reveal the proteome changes in these resistant cells. In total, 7,082 proteotypic proteins from 98,232 peptides were identified and quantified from the dataset using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. Sirtuin Signaling Pathway was found to be significantly enriched in both ADR- and IMA-resistant K562 cells. In particular, IDH2 was identified as a potential drug target correlated with the drug resistance phenotype, and its inhibition by the antagonist AGI-6780 reversed the acquired resistance in K562 cells to either ADR or IMA. Together, our study has implicated IDH2 as a potential target that can be therapeutically leveraged to alleviate the drug resistance in K562 cells when treated with IMA and ADR.
Multiplexed electrokinetic sensor for detection and therapy monitoring of extracellular vesicles from liquid biopsies of non-small-cell lung cancer patients
Authors: Cavallaro Sara , Hååg Petra , Sahu Siddharth S. , Berisha Lorenca , Kaminsky Vitaliy O. , Ekman Simon , Lewensohn Rolf , Linnros Jan , Viktorsson Kristina , Dev Apurba 
Published: April 2021

AbstractLiquid biopsies based on extracellular vesicle (EV) protein profiles represent a promising tool for treatment monitoring of tumors, including non-small-cell lung cancers (NSCLC). In this study, we present the development of an electrokinetic sensor for multiplexed surface protein profiling of EVs and analysis of clinical samples. The method detects the difference in the streaming current obtained as a result of EV binding to the inner surface of a functionalized microcapillary, thereby estimating the expression level of a surface marker. Using multiple microchannels functionalized with different antibodies in a parallel fluidic connection, we first demonstrate the capacity for simultaneous detection of multiple surface markers in small EVs (sEVs) from NSCLC cells. To investigate the prospects of liquid biopsies based on EVs, we then apply the method to profile sEVs isolated from the pleural effusion (PE) fluids of three NSCLC adenocarcinoma patients with different genomic alterations (ALK-fusion, KRAS and EGFR) and applied treatments (chemotherapy, EGFR or ALK tyrosine kinase inhibitors). These vesicles were targeted against CD9 tetraspanin, as well as EGFR and PD-L1, two markers of interest in NSCLC. The electrokinetic signals showed detection of these markers on sEVs yet highlighting distinct interpatient differences, e.g., increased EGFR levels in sEVs from a patient with EGFR mutation as compared to an ALK-mutant one. The sensors also detected differences in PD-L1 expressions, in line with those measured by complementary methods. The analysis of sEVs from a patient prior and post crizotinib treatment also revealed a significant increase in the expression of some markers, e.g. EGFR and PD-L1. The obtained results hold promise for the application of the method for tumor treatment monitoring based on sEVs from liquid biopsies.
Redundancy-selection trade-off in phenotype-structured populations
Authors: Miele Leonardo , Evans R M L , Azaele Sandro 
Published: April 2021

AbstractRealistic fitness landscapes generally display a redundancy-fitness trade-off: highly fit trait configurations are inevitably rare, while less fit trait configurations are expected to be more redundant. The resulting sub-optimal patterns in the fitness distribution are typically described by means of effective formulations. However, the extent to which effective formulations are compatible with explicitly redundant landscapes is yet to be understood, as well as the consequences of a potential miss-match. Here we investigate the effects of such trade-off on the evolution of phenotype-structured populations, characterised by continuous quantitative traits. We consider a typical replication-mutation dynamics, and we model redundancy by means of two dimensional landscapes displaying both selective and neutral traits. We show that asymmetries of the landscapes will generate neutral contributions to the marginalised fitness-level description, that cannot be described by effective formulations, nor disentangled by the full trait distribution. Rather, they appear as effective sources, whose magnitude depends on the geometry of the landscape. Our results highlight new important aspects on the nature of sub-optimality. We discuss practical implications for rapidly mutant populations such as pathogens and cancer cells, where the qualitative knowledge of their trait and fitness distributions can drive disease management and intervention policies.
Intranasal HD-Ad Vaccine Protects the Upper and Lower Respiratory Tracts of hACE2 Mice against SARS-CoV-2
Authors: Cao Huibi , Mai Juntao , Zhou Zhichang , Li Zhijie , Duan Rongqi , Watt Jacqueline , Chen Ziyan , Bandara Ranmal Avinash , Li Ming , Ahn Sang Kyun , Boon Betty , Christie Natasha , Gray-Owen Scott , Kozak Rob , Mubareka Samira , Rini James M. , Hu Jim , Liu Jun 
Published: April 2021

AbstractThe COVID-19 pandemic has affected more than 120 million people and resulted in over 2.8 million deaths worldwide. Several COVID-19 vaccines have been approved for emergency use in humans and are being used in many countries. However, all of the approved vaccines are administered by intramuscular injection and this may not prevent upper airway infection or viral transmission. Here, we describe intranasal immunization of a COVID-19 vaccine delivered by a novel platform, the helper-dependent adenoviral (HD-Ad) vector. Since HD-Ad vectors are devoid of adenoviral coding sequences, they have a superior safety profile and a large cloning capacity for transgenes. The vaccine (HD-Ad_RBD) codes for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and intranasal immunization induced robust mucosal and systemic immunity. Moreover, intranasal immunization of K18-hACE2 mice with HD-Ad_RBD using a prime-boost regimen, resulted in complete protection of the upper respiratory tract against SARS-CoV-2 infection. As such, intranasal immunization based on the HD-Ad vector promises to provide a powerful platform for constructing highly effective vaccines targeting SARS-CoV-2 and its emerging variants.
Rapid adaptation of a complex trait during experimental evolution ofMycobacterium tuberculosis
Authors: Smith Tracy M. , Youngblom Madison A. , Kernien John F. , Mohamed Mohamed A. , Fry Sydney S. , Bohr Lindsey L. , Mortimer Tatum D. , O’Neill Mary B. , Pepperell Caitlin S. 
Published: April 2021

AbstractTuberculosis (TB), caused byMycobacterium tuberculosis(M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, butM. tbbiofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here we usedM. tbexperimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlyingM. tbbiofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important inM. tbadaptation to changing environments.