bluuebunny/crossref_metadata_2025 huggingface dataset:
A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and non-vascular plants
Authors: Chini Andrea , Monte Isabel , Fernández-Barbero Gemma , Boter Marta , Hicks Glenn , Raikhel Natasha , Solano Roberto
Published: February 2021

The phytohormone JA-Ile regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein COI1 (Coronatine Insensitive 1) and a JAZ (Jasmonate ZIM-domain) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signalling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI-JAZ interaction and degradation of JAZ1 and JAZ9in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana)COI1-JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1- JAZ also occurs in the liverwortMarchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signalling, J4 works as an antagonist of the closely-related auxin signalling pathway, preventing TIR1/Aux-IAA interaction and auxin responsesin planta,including hormone-mediated degradation of an auxin repressor, gene expression and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways.

One sentence summary

A chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and non-vascular plants.
Analysis of gastric cancer transcriptome allows the identification of histotype specific molecular signatures with prognostic potential
Authors: Carino Adriana , Graziosi Luigina , Marchianò Silvia , Biagioli Michele , Marino Elisabetta , Sepe Valentina , Zampella Angela , Distrutti Eleonora , Donini Annibale , Fiorucci Stefano
Published: February 2021

Gastric cancer is the fifth most common malignancy but the third leading cause of cancer-associated mortality worldwide. Therapy for gastric cancer remain largely suboptimal making the identification of novel therapeutic targets an urgent medical need. In the present study we have carried out a high-throughput sequencing of transcriptome expression in patients with gastric cancers. Twenty-four patients, among a series of 53, who underwent an attempt of curative surgery for gastric cancers in a single center, were enrolled. Patients were sub-grouped according to their histopathology into diffuse and intestinal types, and the transcriptome of the two subgroups assessed by RNAseq analysis and compared to the normal gastric mucosa. The results of this investigation demonstrated that the two histopathology phenotypes express two different patterns of gene expression. A total of 2064 transcripts were differentially expressed between neoplastic and non neoplastic tissues: 772 were specific for the intestinal type and 407 for the diffuse type. Only 885 transcripts were simultaneously differentially expressed by both tumors. The per pathway analysis demonstrated an enrichment of extracellular matrix and immune dysfunction in the intestinal type including CXCR2, CXCR1, FPR2, CARD14, EFNA2, AQ9, TRIP13, KLK11 and GHRL. At the univariate analysis reduced levels AQP9 was found to be a negative predictor of 4 years survival. In the diffuse type low levels CXCR2 and high levels of CARD14 mRNA were negative predictors of 4 years survival. In summary, we have identified a group of genes differentially regulated in the intestinal and diffuse histo-types of gastric cancers with AQP9, CARD14 and CXCR2 impacting on patients prognosis, although CXCR2 is the only factor independently impacting overall survival.

Simple summary

Gastric cancer is the fifth most common malignancy and the third leading cause of cancer-associated mortality worldwide. Although several new pharmacological approaches are currently developed, surgery remains the unique valid option of treatment but survival remains very poor over the last decades. Therefore, understanding the underlying molecular mechanisms of the gastric carcinogenesis and identifying sensitive biomarkers could be helpful for the prevention and treatment of the disease. Currently, the high-throughput sequencing techniques, in particular the transcriptomic analysis (RNA-seq) represents a validated technique to obtain a molecular characterization of human cancers. Moreover, it has been established that genetic susceptibility and environmental factors, such as microbial infections may contribute to carcinogenesis. We have characterized the different patterns of gene expression, using RNA-seq analysis and correlated these findings with gastric cancer histological subtypes.
Consciously detecting and recognizing a stimulus without knowing what it looks like
Authors: Rimsky-Robert Daphné , Lisi Matteo , Noûs Camille , Sergent Claire
Published: February 2021

Does conscious perception occur during initial sensory processing, or does it arise later in a supra modal fashion? If conscious access truly depends on supra modal processes, we may be able to induce “asensory perception”, where only the semantic features of a meaningful stimulus are accessed, untied to its sensory attributes. Here we tested this prediction by degrading the low-level sensory representations of visual words in the brain using pattern masking, and subsequently presenting audio words that were either semantically related to the masked word or not. We hypothesized these retrospective semantic cues would reactivate the remaining traces of the masked word in the brain, and induce awareness of any information that was not disrupted by masking. In three separate experiments we show that, when presented with retrospective cues that are semantically related to the masked word, participants are better at detecting the presence of the preceding masked word and naming it, while at the same time being unable to report its visual features. In other words, participants could consciously detect and recognize the preceding masked word, without knowing what it looked like. These findings suggest that non-sensory information can be consciously accessed in relative independence from the build-up of sensory representations.
Higher-order effects, continuous species interactions, and trait evolution shape microbial spatial dynamics
Authors: Swain Anshuman , Fussell Levi , Fagan William F
Published: February 2021

The assembly and maintenance of microbial diversity in natural communities, despite the abundance of toxin-based antagonistic interactions, presents major challenges for biological understanding. A common framework for investigating such antagonistic interactions involve cyclic dominance games with pairwise interactions. The incorporation of higher-order interactions in such models permits increased levels of microbial diversity, especially in communities where antibiotic producing, sensitive, and resistant strains co-exist. However, most such models involve a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which well represents the highly interlinked, quickly evolving, and continuous nature of microbial phenotypic space. Here, we present an alternative vision of spatial dynamics for microbial communities based on antagonistic interactions—one in which a large number of species interact in continuous phenotypic space, are capable of rapid mutation, and engage in both direct and higher-order interactions mediated by production of and resistance to antibiotics. Focusing on toxin production, vulnerability, and inhibition among species, we observe highly divergent patterns of diversity and spatial community dynamics. We find that species interaction constraints (rather than mobility) best predict spatiotemporal disturbance regimes, whereas community formation time, mobility, and mutation size best explain patterns of diversity. We also report an intriguing relationship among community formation time, spatial disturbance regimes, and diversity dynamics. This relationship, which suggests that both higher-order interactions and rapid evolution are critical for the origin and maintenance of microbial diversity, has broad-ranging links to the maintenance of diversity in other systems.

Significance Statement

Persistently diverse microbial communities are one of biology’s great puzzles. Using a novel continuous trait space modeling framework that accommodates high mutation rates, elevated species richness, and direct and higher-order antagonistic species interactions, we find that two parameters characterizing mutation size and mobility best explain patterns of microbial diversity. Moreover, community formation time (the duration of the transient phase in community assembly) provides an unexpectedly clear guide to the diversity profiles of the resulting communities. These discoveries showcase how complex, antagonistic interactions mediated by the production of, inhibition of, and vulnerability to toxins (antibiotics) can shape microbial communities, allowing for extraordinarily high levels of diversity and temporal persistence.
A development guide for evaluating the maximum yield potential stage in barley
Authors: Thirulogachandar Venkatasubbu , Schnurbusch Thorsten
Published: February 2021

Determining the grain yield potential contributed by grain number is a step towards advancing cereal crops’ yield. To achieve this aim, it is pivotal to recognize the maximum yield potential (MYP) of the crop. In barley (Hordeum vulgareL.), the MYP is defined as the maximum spikelet primordia number of a spike. Previous barley studies often assumed the awn primordium (AP) stage as the MYP stage regardless of genotypes and growth conditions. From our spikelet-tracking experiments using the two-rowed cultivar Bowman, we found that the MYP stage can be different from the AP stage. Importantly, we find that the occurrence of inflorescence meristem (IM) deformation and its loss of activity coincided with the MYP stage, indicating the end of further spikelet initiation. Thus, we recommend validating the barley MYP stage with the IM’s shape and propose this approach (named Spikelet Stop) for MYP staging. Following this approach, we compared the MYP stage and the MYP in 27 two- and six-rowed barley accessions grown in the greenhouse and field. Our results reveal that the MYP stage can be reached at various developmental stages, which majorly depend on the genotype and growth conditions. Furthermore, we found that two-rowed barleys’ MYP and the duration reaching the MYP stage may determine their yield potential. Based on our findings, we suggest key steps for the identification of the MYP in barley that can also be applied in a related crop such as wheat.

Highlight

We show that the maximum yield potential stage in barley can be different from the awn primordium stage as proposed in earlier studies and it varies depending on the genotype and growth conditions. We suggest key steps to identify maximum yield potential in barley that might apply to related cereals.
A model of the appearance of the moving human eye
Authors: Aguirre Geoffrey K
Published: February 2021

The entrance pupil and first Purkinje reflection (“glint”) in an image of the human eye serve as important features in 3D, model-based eye tracking applications. Here I present a physically and biologically accurate, ray-traced model that supplies the appearance of the pupil and glint of a moving eye. Once biometrically calibrated for a subject under study, simultaneous fitting of the pupil and glint features by the model supplies eye rotation, radius of the aperture stop, and the translation of the eye relative to the initial camera position. The biometric parameters of the model, including corneal curvature and the depth of the centers of rotation, are obtained by model-based fitting of images of the eye posed at known gaze angles. This approach was applied to eye recordings from 30 people obtained during gaze calibration, and while head position was recorded simultaneously using echoplanar magnetic resonance imaging. The refractive and reflective effects of spectacle and contact lenses worn by some subjects were incorporated into the model. The fitted parameters reveal that the center of rotation for horizontal eye movements is deeper (13.8 mm) than that for vertical eye movements (12.1) mm, consistent with prior studies. Individual differences in the depth of the rotation centers, and in corneal curvature, were well related to biometric measures obtained from these subjects using clinical ophthalmologic instruments. Once biometrically calibrated for each subject, gaze position was modeled with a cross-validated, median (across subject) absolute error of 0.58°, and image-plane translation of the head was estimated with sub-millimeter accuracy. The open-source model described here produces biologically accurate simulations of the appearance of the eye in motion, and may be used in model-based search to derive eye pose and biometric properties from empirical data.
Balanced Input from the tRNA Prenyltransferase MiaA Controls the Stress Resistance and Virulence Potential of Extraintestinal PathogenicEscherichia coli
Authors: Blango Matthew G. , Fleming Brittany A. , Kincannon William M. , Tran Alex , Lewis Adam J. , Russell Colin W. , Zhou Qin , Baird Lisa M. , Brannon John R. , Beebout Connor J. , Bandarian Vahe , Hadjifraniskou Maria , Howard Michael T. , Mulvey Matthew A.
Published: February 2021

An ability to adapt to rapidly changing and often hostile environments is key to the success of many bacterial pathogens. InEscherichia coli, the highly conserved enzymes MiaA and MiaB mediate the sequential prenylation and methylthiolation of adenosine-37 within tRNAs that decode UNN codons. Here, we show that MiaA, but not MiaB, is critical to the fitness and virulence of extraintestinal pathogenicE. coli(ExPEC), a major cause of urinary tract and bloodstream infections. Deletion ofmiaAhas pleiotropic effects, rendering ExPEC especially sensitive to stressors like nitrogen and oxygen radicals and osmotic shock. We find that stress can stimulate striking changes inmiaAexpression, which in turn can increase translational frameshifting and markedly alter the bacterial proteome. Cumulatively, these data indicate that ExPEC, and likely other organisms, can vary MiaA levels as a means to fine-tune translation and the spectrum of expressed proteins in response to changing environmental challenges.
The structural and electrophysiological properties of progesterone receptor expressing neurons vary along the anterior-posterior axis of the ventromedial hypothalamus and undergo local changes across the reproductive cycle
Authors: Dias Inês C. , Gutierrez-Castellanos Nicolas , Ferreira Liliana , Lima Susana Q.
Published: February 2021

Sex hormone levels continuously fluctuate across the reproductive cycle, changing the activity of neuronal circuits to coordinate female behavior and reproductive capacity. The ventrolateral division of the ventromedial hypothalamus (VMHvl) contains neurons expressing receptors for sex hormones and its function is intimately linked to female sexual receptivity. However, recent findings suggest that the VMHvl is functionally heterogeneous. Here, we used whole cell recordings and intracellular labeling to characterize the electrophysiological and morphological properties of individual VMHvl neurons in naturally cycling females. We found that the properties of progesterone receptor expressing (PR+) neurons, but not PR- neurons, depended systematically on the neuron’s location along the anterior-posterior axis of the VMHvl and the phase within the reproductive cycle. Prominent amongst this, the resting membrane potential of anterior PR+ neurons decreased during the receptive phase, while the excitability of medial PR+ neurons increased during the non-receptive phase. During the receptive phase of the cycle, posterior PR+ neurons simultaneously showed an increase in dendritic complexity and a decrease in spine density. These findings reveal an extensive diversity of local rules driving structural and physiological changes in response to fluctuating levels of sex hormones, supporting the anatomical and functional subdivision of the VMHvl and its possible role in the orchestration of different aspects of female socio-sexual behavior.
A novel vascular endothelial growth factor-trap KP-VR2 with enhanced ligand blocking
Authors: Kim Mi-Ra , kim Bongkyu , Na Yunsu , Yoo Jingon , Kim Se-Ho , Seo In-Ra
Published: February 2021

Antiangiogenic therapies targeting vascular endothelial growth factor (VEGF)-A have been commonly used in clinics to treat cancers over the past decade. However, their clinical efficacy has been limited, with drawbacks including the acquisition of resistance and activation of compensatory pathways resulting from elevated circulating VEGF-B and placental growth factor (PlGF) levels. Thus, we developed a novel VEGF-Trap, KP-VR2, which can neutralize VEGF-A, VEGF-B, and PlGF to mediate these problems. KP-VR2 consists of two consecutive second Ig-like domains (D2s) of VEGF receptor 1 (VEGFR-1) fused to human IgG1 Fc. KP-VR2 showed more potent decoy activity than the current VEGF-Trap against VEGF and PlGF. Most importantly, two consecutive D2s of VEGFR-1 can generate two putative binding sites, resulting in a significant improvement in binding capacity. These advances resulted in stronger antitumor efficacy in implanted tumor models than aflibercept and bevacizumab. Overall, the results of this study highlight KP-VR2 as a promising therapeutic candidate for further clinical drug development.
Alpha oscillations shape sensory representation and perceptual sensitivity
Authors: Zhou Ying Joey , Iemi Luca , Schoffelen Jan-Mathijs , de Lange Floris P. , Haegens Saskia
Published: February 2021

Alpha activity (8–14 Hz) is the dominant rhythm in the awake brain, and thought to play an important role in setting the brain’s internal state. Previous work has associated states of decreased alpha power with enhanced neural excitability. However, evidence is mixed on whether and how such excitability enhancement modulates sensory signals of interest versus noise differently, and what, if any, the consequences are for subsequent perception. Here, human subjects (male and female) performed a visual detection task in which we manipulated their decision criteria in a block-wise manner. While our manipulation led to substantial criterion shifts, these shifts were not reflected in pre-stimulus alpha-band changes. Rather, lower pre-stimulus alpha power in occipital-parietal areas improved perceptual sensitivity and enhanced information content decodable from neural activity patterns. Additionally, oscillatory alpha phase immediately before stimulus presentation modulated accuracy. Together, our results suggest that alpha-band dynamics modulate sensory signals of interest more strongly than noise.

Significance statement

The internal state of our brain fluctuates, giving rise to variability in perception and action. Neural oscillations, most prominently in the alpha-band, have been suggested to play a role in setting this internal state. Here, we show that ongoing alpha-band activity in occipital-parietal regions predicts the quality of visual information decodable in neural activity patterns, and subsequently human observer’s sensitivity in a visual detection task. Our results provide comprehensive evidence that visual representation is modulated by ongoing alpha-band activity, and advance our understanding on how, when faced with unchanging external stimuli, internal neural fluctuations influence perception and behavior.
Paradoxical hyperexcitability from NaV1.2 sodium channel loss in neocortical pyramidal cells
Authors: Spratt Perry W.E. , Ben-Shalom Roy , Sahagun Atehsa , Keeshen Caroline M. , Sanders Stephan J. , Bender Kevin J.
Published: February 2021

Loss-of-function variants in the geneSCN2A, which encodes the sodium channel NaV1.2, are strongly associated with autism spectrum disorder and intellectual disability. An estimated 20-30% of children with these variants are co-morbid for epilepsy, with altered neuronal activity originating in neocortex, a region where NaV1.2 channels are expressed predominantly in excitatory pyramidal cells. This is paradoxical, as sodium channel loss in excitatory cells would be expected to dampen neocortical activity rather than promote seizure. Here, we examined pyramidal neurons lacking NaV1.2 channels and found that they were intrinsically hyperexcitable, firing high-frequency bursts of action potentials (APs) despite decrements in AP size and speed. Compartmental modeling and dynamic clamp recordings revealed that NaV1.2 loss prevented potassium channels from properly repolarizing neurons between APs, increasing overall excitability by allowing neurons to reach threshold for subsequent APs more rapidly. This cell-intrinsic mechanism may therefore account for whySCN2Aloss-of-function can paradoxically promote seizure.
Norepinephrine and glucocorticoids modulate chronic unpredictable stress-induced increase in the type 2 CRF and glucocorticoid receptors in brain structures related to the HPA axis activation
Authors: Malta Marilia B , Martins Joelcimar , Novaes Leonardo S , dos Santos Nilton B , Sita Luciane , Camarini Rosana , Scavone Cristoforo , Bittencourt Jackson , Munhoz Carolina D.
Published: February 2021

The stress response is multifactorial and enrolls circuitries to build a coordinated reaction, leading to behavioral, endocrine, and autonomic changes. These changes are mainly related to the hypothalamus-pituitary-adrenal (HPA) axis activation and the organism’s integrity. However, when self-regulation is ineffective, stress becomes harmful and predisposes the organism to pathologies. The chronic unpredictable stress (CUS) is a widely used experimental model since it induces physiological and behavioral changes and better mimics the stressors variability encountered in daily life. Corticotropin-releasing factor (CRF) and glucocorticoid (GCs) are deeply implicated in the CUS-induced physiological and behavioral changes. Nonetheless, the CUS modulation of CRF receptors and GR and the norepinephrine role in extra-hypothalamic brain areas were not well explored. Here, we show that 14-days of CUS induced a long-lasting HPA axis hyperactivity evidenced by plasmatic corticosterone increase and adrenal gland hypertrophy, which was dependent on both GCs and NE release induced by each stress session. CUS also increased CRF2mRNA expression and GR protein levels in fundamental brain structures related to HPA regulation and behavior, such as the lateral septal nucleus intermedia part (LSI), ventromedial hypothalamic nucleus (VMH), and central nucleus of the amygdala (CeA). We also showed that NE participates in the CUS-induced increase in CRF2and GR levels in the LSI, reinforcing thelocus coeruleus(LC) involvement in the HPA axis modulation. Despite the CUS-induced molecular changes in essential areas related to anxiety-like behavior, this phenotype was not observed in CUS animals 24 h after the last stress session.

Highlights

CUS persistently increased plasma CORT levels via GCs and NE signaling.

CUS persistently increased CRF2mRNA in extra-hypothalamic brain areas.

CUS increased GR protein levels in brain regions related to GCs release control.

NE and GCs participate in the CUS-induced increase in CRF2and GR levels.

LSI could be the brain nucleus that dictates the fine-tuned response of CUS.

CUS animals did not present anxiety-like behavior.
Privacy-Preserving Genotype Imputation in a Trusted Execution Environment
Authors: Dokmai Natnatee , Kockan Can , Zhu Kaiyuan , Wang XiaoFeng , Sahinalp S. Cenk , Cho Hyunghoon
Published: February 2021

Genotype imputation is an essential tool in genetics research, whereby missing genotypes are inferred based on a panel of reference genomes to enhance the power of downstream analyses. Recently, public imputation servers have been developed to allow researchers to leverage increasingly large-scale and diverse genetic data repositories for imputation. However, privacy concerns associated with uploading one’s genetic data to a third-party server greatly limit the utility of these services. In this paper, we introduce a practical, secure hardware-based solution for a privacy-preserving imputation service, which keeps the input genomes private from the service provider by processing the data only within a Trusted Execution Environment (TEE) offered by the Intel SGX technology. Our solution features SMac, an efficient, side-channel-resilient imputation algorithm designed for Intel SGX, which employs the hidden Markov model (HMM)-based imputation strategy also utilized by a state-of-the-art imputation software Minimac. SMac achieves imputation accuracies virtually identical to those of Minimac and provides protection against known attacks on SGX while maintaining scalability to large datasets. We additionally show the necessity of our strategies for mitigating side-channel risks by identifying vulnerabilities in existing imputation software and controlling their information exposure. Overall, our work provides a guideline for practical and secure implementation of genetic analysis tools in SGX, representing a step toward privacy-preserving analysis services that can facilitate data sharing and accelerate genetics research.†

Availability

Our software is available athttps://github.com/ndokmai/sgx-genotype-imputation.
Potential global impact of the N501Y mutation on MHC-II presentation and immune escape
Authors: Castro Andrea , Carter Hannah , Zanetti Maurizio
Published: February 2021

The B.1.1.7 SARS-CoV-2 variant, characterized by the N501Y mutation, is rapidly emerging, raising concerns about its effectiveness on natural as well as vaccine-induced adaptive viral immunity at the population level. Since CD4 T cell responses are of critical importance to the antibody response, we examined the global effects of N501Y mutation on MHC-II presentation compared to the N501 wildtype and found poorer presentation across the majority of MHC-II alleles. This suggests that the N501Y mutation may not only diminish binding of antibodies to the RBD but also interfere with their production by weakening the cooperation between T and B cells, facilitating immune escape.
Characterization of novel regulatory modules controlling leaf angle in maize
Authors: Wang Xianglan , Wang Xiaokun , Sun Shilei , Tu Xiaoyu , Lin Kande , Qin Lei , Wang Xingyun , Li Gang , Zhong Silin , Li Pinghua
Published: February 2021

Leaf angle is an important agronomic trait determining maize planting density and light penetration into the canopy, and contributes significantly to the yield gain in modern maize hybrids. However, little is known about its molecular mechanism beyond theLiguless1(LG1) andLiguless2(LG2) genes. In this study, we found that transcription factorZmBEH1is targeted by ZmLG2 and regulates the leaf angle formation by influencing the sclerenchyma cells layers on the adaxial side. ZmBEH1 can interact with transcription factor ZmBZR1, whose expression is directly activated by ZmLG1. Both ZmBEH1 and ZmBZR1 bind to the promoter ofZmSCL28, the third transcription factors that influences the leaf angle. Our study demonstrates novel regulatory modules controlling leaf angle, and provides new gene editing targets for creating optimal maize architecture suitable for dense-planting.
DAZL regulates mRNA deadenylation independently of translation in germ cells
Authors: Smith Richard W. P. , Gorgoni Barbara , Johnston Zoë C. , Richardson William A. , Grieve Kelsey M. , Anderson Ross C. , Gray Nicola K.
Published: February 2021

Aberrant gene expression during gametogenesis is one of the factors underlying infertility, which affects roughly 15% of couples worldwide.Deleted-in-Azoospermia-Like (DAZL),a member of theDAZ-genefamily, encodes an mRNA-specific regulator of translation which is essential for gametogenesis in both sexes. In this study we show that DAZL controls gene expression in oocytes by regulating the length of the mRNA poly(A) tail, a major determinant of temporal and amplitudinal gene regulation in germ cells, in which gene expression is regulated entirely post-transcriptionally. We show that DAZL does not induce polyadenylation but that binding of DAZL efficiently inhibits mRNA deadenylation induced by oocyte maturation. We reveal that this activity depends on DAZL-mediated recruitment of poly(A)-binding protein, PABP, to the mRNA. Although DAZL also activates mRNA translation via PABP recruitment, mechanistic analysis revealed that neither translation nor translational activation are required for DAZL to stabilise the poly(A) tail, suggesting two mutually independent posttranscriptional roles for the DAZL-PABP complex. We show that recruited PABP must maintain its ability to bind RNA, leading to a model in which DAZL recruits PABP and/or stabilises PABP binding to poly(A) thereby preventing access of deadenylases. These results indicate that the role of DAZL in regulating germ-cell mRNA fate is more complex than previously thought and inform on the poorly understood links between mRNA translation and deadenylation, showing that they can be mechanistically separable.
High Throughput Fitness Profiling Reveals Loss Of GacS-GacA Regulation Improves Indigoidine Production InPseudomonas putida
Authors: Eng Thomas , Banerjee Deepanwita , Lau Andrew K. , Bowden Emily , Herbert Robin A. , Trinh Jessica , Prahl Jan-Philip , Deutschbauer Adam , Tanjore Deepti , Mukhopadhyay Aindrila
Published: February 2021

Pseudomonas putidaKT2440 is an emerging industrial microbe amenable for use with renewable carbon streams including aromatics such aspara-coumarate (pCA). We examined this microbe under common stirred-tank bioreactor parameters with quantitative fitness assays using a pooled transposon library containing nearly all (4,778) non-essential genes. Assessing differential fitness values by monitoring changes in mutant strain abundance over time identified 31 genes with improved fitness in multiple bioreactor-relevant parameters. Twenty-one genes from this subset were reconstructed, including GacA, a signaling protein, TtgB, an ABC transporter, and PP_0063, a lipid A acyltransferase. Twelve deletion strains with roles in varying cellular functions were evaluated for conversion ofpCA, to a heterologous bioproduct, indigoidine. Several mutants, such as the ΔgacAstrain improved both fitness in a bioreactor and showed an 8-fold improvement in indigoidine production (4.5 g/L, 0.29 g/gpCA, 23% MTY) frompCA as the carbon source.
The effect of mentee and mentor gender on scientific productivity of applicants for NIH training fellowships
Authors: Yu Hao , Willis Kristine A. , Litovitz Aviva , Harriman Robert M. , Davis Matthew T. , Meyer Payam , Busse Brad , Meseroll Rebecca A. , Wijayatilake Hashanthi D. , Perkins Matthew J. , Anderson James M. , Santangelo George M.
Published: February 2021

Several studies have suggested that women in science are less productive than men, and that this gap contributes to their under-representation in the ranks of senior researchers. However, few studies have examined the role of mentoring, and in particular mentor gender, on the productivity of female scientists early in their careers. Such efforts are limited by the difficulties of unambiguously linking mentees to their mentors and measuring the research productivity resulting from those relationships. Here we use our novel author disambiguation solution to investigate the role of self-identified gender in mentorship of 12,932 trainees who either successfully or unsuccessfully applied to the National Institutes of Health for research fellowships between fiscal years 2011 and 2017, applying a multi-dimensional framework to assess productivity. We found that, after normalizing for the funding level of mentors, the productivity of female and male mentees is indistinguishable; it is also independent of the gender of the mentor, other than in measures of clinical impact, where women mentored by women outperform other mentee-mentor dyads.
Effect of air pockets in drug delivery in jet injections
Authors: Rohilla Pankaj , Khusnatdinov Emil , Marston Jeremy
Published: February 2021

Needle-free jet injections are actuated by a pressure impulse that can be delivered by different mechanisms, and the resultant jets are(102) m/s. Here, we report on the effect of entrapped air bubbles since filling procedures for pre-filled ampoules can induce bubbles, especially for viscous fluids. We use spring-piston devices as the principal actuation mechanism and vary both the location and size of the initial bubble. We find that the bubble location does have a statistically significant (p< 0.05) effect on the jet exit speed, based upon the volumetric flow rate. However, we reveal subtle features such as intermittent atomization when the gas pockets pass through the orifice and de-pressurize, which leads to spray formation and a temporary increase in jet dispersion, both of which can lead to product loss during an injection. These results have implications for the development of prefilled ampoules for jet injection applications.
Drug delivery via tattooing: Effect of needle and fluid properties
Authors: Lawal Idera , Rohilla Pankaj , Marston Jeremy
Published: February 2021

Tattooing is a commonplace practice among the general populace in which ink is deposited within dermal tissue. Typically, an array of needles punctures the skin which facilitates the delivery of a fluid within the dermis. Although, a few studies in the past have investigated the potential of tattooing as an intradermal (ID) drug injection technique, an understanding of the fluid dynamics involved in the delivery of fluid into skin is still lacking. Herein, we sought to provide insight into the process via an in vitro study. We utilize a five needle flat array (5F) with a tattoo machine to inject fluids into gelatin gels. High-speed imaging was used to visualize the injection process and estimate the amount of fluid delive red after each injection upto the 50thinjection. We investigate the role of reciprocating frequency (f) of the needle array and the physical properties of the fluids on the volume (Vo) and the percentage delivery (η) after injection. In addition, we illustrate the physical mechanism of fluid infusion during tattooing, which has not been reported. An understanding of the injection process via tattooing can be useful in the development of ID tattoo injectors as drug delivery devices.
Mitochondrial ATP Synthase Subunit d, a Component of the Peripheral Stalk, is Essential for Growth and Heat Stress Tolerance inArabidopsis thaliana
Authors: Liu Tianxiang , Arsenault Jesse , Vierling Elizabeth , Kim Minsoo
Published: February 2021

As rapid changes in climate threaten global crop yields, an understanding of plant heat stress tolerance is increasingly relevant. Heat stress tolerance involves the coordinated action of many cellular processes and is particularly energy demanding. We acquired a knockout mutant and generated knockdown lines inArabidopsis thalianaof the d subunit of mitochondrial ATP synthase (gene name:ATPQ, AT3G52300, referred to hereafter asATPd), a subunit of the peripheral stalk, and used these to investigate the phenotypic significance of this subunit in normal growth and heat stress tolerance. Homozygous knockout mutants forATPdcould not be obtained due to gametophytic defects, while heterozygotes possess no visible phenotype. Therefore, we used RNAi to create knockdown plant lines for further studies. Proteomic analysis and blue native gels revealed thatATPddownregulation impairs only subunits of the mitochondrial ATP synthase (complex V of the electron transport chain). Knockdown plants were more sensitive to heat stress, had abnormal leaf morphology, and were severely slow growing compared to wild type. These results indicate thatATPdplays a crucial role in proper function of the mitochondrial ATP synthase holoenzyme, which, when reduced, leads to wide-ranging defects in energy-demanding cellular processes. In knockdown plants, more hydrogen peroxide accumulated and mitochondrial dysfunction stimulon (MDS) genes were activated. These data establish the essential structural role ofATPdand provide new information about complex V assembly and quality control, as well as support the importance of mitochondrial respiration in normal plant growth and heat stress tolerance.

SIGNIFICANCE STATEMENT

The energy converter, mitochondrial ATP synthase, is critical for all organisms, but the functional importance of ATP synthase subunit d remains largely unknown in plants. We demonstrate the contributions of subunit d to plant growth, development, and heat stress tolerance, as well as to ATP synthase stability, ROS signaling and mitochondrial dysfunction regulation.
Autophagy as a mechanism for adaptive prediction-mediated emergence of drug resistance
Authors: Nivedita Nivedita , Aitchison John D. , Baliga Nitin S.
Published: February 2021

Drug resistance is a major problem in treatment of microbial infections and cancers. There is growing evidence that a transient drug tolerant state may precede and potentiate the emergence of drug resistance. Therefore, understanding the mechanisms leading to tolerance is critical for combating drug resistance and for the development of effective therapeutic strategy. Through laboratory evolution of yeast, we recently demonstrated that adaptive prediction (AP), a strategy employed by organisms to anticipate and prepare for a future stressful environment, can emerge within 100 generations by linking the response triggered by a neutral cue (caffeine) to a mechanism of protection against a lethal agent (5-FOA). Here, we demonstrate that mutations selected across multiple laboratory evolved lines had linked the neutral cue response to core genes of autophagy. Across these evolved lines, conditional activation of autophagy through AP conferred tolerance, and potentiated subsequent selection of mutations in genes specific to overcoming the toxicity of 5-FOA. We propose a model to explain how extensive genome-wide genetic interactions of autophagy facilitates emergence of AP over short evolutionary timescales to potentiate selection of resistance-conferring mutations.
Improving deep learning-based protein distance prediction in CASP14
Authors: Guo Zhiye , Wu Tianqi , Liu Jian , Hou Jie , Cheng Jianlin
Published: February 2021

Accurate prediction of residue-residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions (i.e. classifying distances between two residues into two categories: in contact (< 8 Angstrom) and not in contact otherwise) and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the F1 measure. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps.
Integration of APSIM and PROSAIL models to develop more precise radiometric estimation of crop traits using deep learning
Authors: Chen Qiaomin , Zheng Bangyou , Chen Tong , Chapman Scott
Published: February 2021

A major challenge for the estimation of crop traits (biophysical variables) from canopy reflectance is the creation of a high-quality training dataset. This can be addressed by using radiative transfer models (RTMs) to generate training dataset representing ‘real-world’ data in situations with varying crop types and growth status as well as various observation configurations. However, this approach can lead to “ill-posed” problems related to assumptions in the sampling strategy and due to uncertainty in the model, resulting in unsatisfactory inversion results for retrieval of target variables. In order to address this problem, this research investigates a practical way to generate higher quality ‘synthetic’ training data by integrating a crop growth model (CGM, in this case APSIM) with an RTM (in this case PROSAIL). This allows control of uncertainties of the RTM by imposing biological constraints on distribution and co-distribution of related variables. Subsequently, the method was theoretically validated on two types of synthetic dataset generated by PROSAIL or the coupling of APSIM and PROSAIL through comparing estimation precision for leaf area index (LAI), leaf chlorophyll content (Cab), leaf dry matter (Cm) and leaf water content (Cw). Additionally, the capabilities of current deep learning techniques using high spectral resolution hyperspectral data were investigated. The main findings include: (1) Feedforward neural network (FFNN) provided with appropriate configuration is a promising technique to retrieve crop traits from input features consisting of 1 nm-wide hyperspectral bands across 400-2500 nm range and observation configuration (solar and viewing angles), leading to a precise joint estimation forLAI(RMSE=0.061 m2m-2),Cab(RMSE=1.42 µg cm-2),Cm(RMSE=0.000176 g cm-2) andCw(RMSE=0.000319 g cm-2); (2) For the aim of model simplification, a narrower range in 400-1100 nm without observation configuration in input of FFNN model provided less precise estimation forLAI(RMSE=0.087 m2m-2),Cab(RMSE=1.92 µg cm-2),Cm(RMSE=0.000299 g cm-2) andCw(RMSE=0.001271 g cm-2); (3) The introduction of biological constraints in training datasets improved FFNN model performance in both average precision and stability, resulting in a much accurate estimation forLAI(RMSE=0.006 m2m-2),Cab(RMSE=0.45 µg cm-2),Cm(RMSE=0.000039 g cm-2) andCw(RMSE=0.000072 g cm-2), and this improvement could be further increased by enriching sample diversity in training dataset.
Year-round dynamics of amplicon sequence variant communities differ among eukaryotes,Mimiviridae, and prokaryotes in a coastal ecosystem
Authors: Prodinger Florian , Endo Hisashi , Takano Yoshihito , Li Yanze , Tominaga Kento , Isozaki Tatsuhiro , Blanc-Mathieu Romain , Gotoh Yasuhiro , Tetsuya Hayashi , Taniguchi Etsunori , Nagasaki Keizo , Yoshida Takashi , Ogata Hiroyuki
Published: February 2021

Coastal seawater is the habitat of different microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. In this work, we investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses infecting eukaryotes (i.e.Mimiviridae),as well as prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and theMimiviridae polBgene as marker genes in 43 seawater samples collected during 20 months. Communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles for eukaryotes,Mimiviridae,and prokaryotes. However, the community dynamics showed intriguing differences in several aspects such as the recovery rate after a year. We further show that the differences in the community dynamics can be explained by differences in the recurrence/persistence levels of individual ASVs among eukaryotes,Mimiviridae,and prokaryotes.MimiviridaeASVs were less persistent than eukaryotic ASVs, and prokaryotic ASVs were the most persistent. We argue that the differences in the specificity of interactions (i.e. virus-eukaryotevsprokaryote-eukaryote) as well as the survival strategies are at the origin of the distinct community dynamics among eukaryotes,Mimiviridae,and prokaryotes.

One sentence summary

A one year observation of coastal microbial communities revealed similar but different community dynamics for eukaryotes, a group of large viruses, and prokaryotes.
Central inhibition of P2Y12R differentially regulates survival and neuronal loss in MPTP-induced Parkinsonism in mice
Authors: Iring András , Tóth Adrián , Baranyi Mária , Otrokocsi Lilla , Módis László V. , Gölöncsér Flóra , Varga Bernadett , Hortobágyi Tibor , Bereczki Dániel , Dénes Ádám , Sperlágh Beáta
Published: February 2021

Parkinson’s disease (PD) is a chronic, progressive neurodegenerative condition; characterized with the degeneration of the nigrostriatal dopaminergic pathway and neuroinflammation. During PD progression, microglia, the resident immune cells in the central nervous system (CNS) display altered activity, but their role in maintaining PD development has remained unclear to date. The purinergic P2Y12 receptor (P2Y12R), which is exclusively expressed on the microglia in the CNS has been shown to regulate microglial activity and responses; however, the function of the P2Y12R in PD is unknown. Here we show that while pharmacological or genetic targeting of P2Y12R previous to disease onset augments acute mortality, these interventions protect against neurodegenerative cell loss and the development of neuroinflammation in vivo. Pharmacological inhibition of receptors during disease development reverses the symptoms of PD and halts disease progression. We found that P2Y12R regulate ROCK and p38 MAPK activity and control cytokine production. Understanding protective and detrimental P2Y12 receptor-mediated actions in the CNS may reveal novel approaches to control neuroinflammation and modify disease progression in PD.