bluuebunny/crossref_metadata_2025 huggingface dataset:
Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg
Authors: Lee Rachelle R.Q. , Cher Wei Yuan , Chae Eunyoung
Published: March 2022

MINORg is an offline gRNA design tool that generates the smallest possible combination of gRNA capable of covering all desired targets in multiple non-reference genomes. As interest in pangenomic research grows, so does the workload required for large screens in multiple individuals. MINORg aims to lessen this workload by capitalising on sequence homology to favour multi-target gRNA while simultaneously screening multiple genetic backgrounds in order to generate reusable gRNA panels. We demonstrated the practical application of MINORg by knocking out a 11 homologous genes tandemly arrayed in a multigene cluster in two Arabidopsis thaliana lineages using three gRNA output by MINORg. Source code is freely available at https://github.com/rlrq/MINORg.
Field and experimental data together with computational models reveal how cleaner fish adjust decisions in a biological market
Authors: Quiñones Andrés E. , Triki Zegni , Bshary Redouan
Published: March 2022

While it is generally straightforward to quantify individual performance in cognitive experiments, identifying the underlying cognitive processes remains a major challenge. Often, different mechanistic underpinnings yield similar performances, and Lloyd Morgan’s cannon warrants acceptance of the simpler explanation. Alternatively, when the different mechanisms interact with environmental conditions, variation in performance across environments might allow to statistically infer the mechanism responsible. We illustrate this point by fitting computational models to experimental data on performance by wild-caught cleaner fishLabroides dimidiatusin an ephemeral reward task, as well as cleaner and client fish densities from the locations of capture. Using Bayesian statistics to fit the model parameters to performance data revealed that cleaner fish most likely estimate future consequences of an action, while it appears unlikely that the removal of the ephemeral reward acts as psychological punishment (negative reinforcement). Incorporating future consequences also yields performances that can be considered the result of locally optimal decision-rules, in contrast to the negative reinforcement mechanism. We argue that the combination of computational models with data is a powerful tool to infer the mechanistic underpinnings of cognitive performance.

Author summary

Performance in behavioural experiments is often used to assess the cognitive abilities of animals. However, animals can get to the same outcome in alternative ways. Thus, the outcome of the experiments does not tell us how animals achieve their performance. In order to overcome this limitation, we used a set of computational models, which provide predictions on how alternative cognitive mechanisms perform in the face of varying environmental conditions, and compare their predictions to performance data from individuals that experienced different conditions throughout their life. Our study system is the cleaner fishLabroides dimidiatus, a coral reef fish that feeds off ectoparasites and dead tissue from the skin of other reef fishes. Cleaner fish often have to choose among alternative clients seeking their cleaning service, and the optimal choice is often hard to achieve. Our performance experiments mimic the natural choices the cleaner fish make. The combination of experiments and computational models points to cleaner fish abilities to account for the future effect of their choices by estimating the long term expected value of those choices. Estimating long term value is a mechanism involved in human foresight.
Modelling the modulation of cortical Up-Down state switching by astrocytes
Authors: Moyse Lisa Blum , Berry Hugues
Published: March 2022

Converging experimental reports have shown that the firing dynamics of neural networks in several cortical brain areas can exhibit Up-Down synchronization regimes, spontaneously alternating between long periods of high collective firing activity (Up state) and long periods of relative silence (Down state). The molecular or cellular mechanisms that support the emergence of these reversible transitions are still uncertain. In addition to intrinsic mechanisms supported by the local neurons of the network, recent experimental studies have suggested that the astrocytes of the local network can actually control the emergence of Up-Down regimes. Here we propose and study a neural network model to explore the implication of astrocytes in this dynamical phenomenon. We consider three populations of cells: excitatory neurons, inhibitory neurons and astrocytes, interconnected by gliotransmission events, from neurons to astrocytes and back. We derive two models for this three-population system: a rate model and a stochastic spiking neural network with thousands of neurons and astrocytes. In numerical simulations of these three-population models, the presence of astrocytes is indeed observed to promote the emergence of Up-Down regimes with realistic characteristics. Linear stability analysis reveals that astrocytes in these models do not change the bifurcation structure of these systems, but change the localization of the bifurcations in the parameter space. Accordingly, with the addition of astrocytes, the network can enter a bistability region of the dynamics, where the Up-Down dynamical regime emerges. Simulations of the stochastic network model further evidence that astrocytes provide a stationary and stable background of gliotransmission events to the neurons, that triggers spontaneous transitions between synchronized Up and Down phases of neuronal firing. Taken together, our work provides a theoretical framework to test scenarios and hypotheses on the modulation of Up-Down dynamics by gliotransmission from astrocytes.
Domain-general and domain-specific functional networks of Broca’s area underlying language processing
Authors: Bulut Talat
Published: March 2022

Despite abundant research on the role of Broca’s area in language processing, there is still no consensus on language specificity of this region and its connectivity network. The present study employed the meta-analytic connectivity modeling procedure to identify and compare domain-specific (language-related) and domain-general (non-language) functional connectivity patterns of three subdivisions within the broadly defined Broca’s area: pars opercularis (IFGop), pars triangularis (IFGtri) and pars orbitalis (IFGorb) of the left inferior frontal gyrus. The findings revealed a left-lateralized frontotemporal network for all regions of interest underlying domain-specific linguistic functions. The domain-general network and its conjunction with the domain-specific network, however, spanned frontoparietal regions that overlap with the multiple-demand network. The findings suggest that language-specificity of Broca’s area emerges within a left-lateralized frontotemporal network, and that domain-general resources are garnered from the frontoparietal network when required by task demands.
Risk of ESKD in related older living kidney donors
Authors: Arking Andrew , Ammary Fawaz Al , Kaddu Gabriella , Massie Allan B. , Segev Dorry L. , Garonzik-Wang Jacqueline , Muzaale Abimereki D.
Published: March 2022

Living kidney donors who are biologically related to the recipient have higher risk for end-stage kidney disease (ESKD) compared with those who are unrelated to the recipient. This risk is greater for first-degree relatives than more distant relatives. To understand if this holds true for older donors, who were cleared for donation and might be past the peak-age for hereditary disease, we used donor data (SRTR) linked to ESKD registry data (CMS) and stratified donors by age (younger vs older [≥50 years]) and race (black, Hispanic, and white). Younger related donors of all racial groups had higher risk of ESKD compared with younger unrelated donors; however, only older related white and Hispanic donors had higher risk of ESRD compared with unrelated older donors (2.3-fold for white full-siblings and 1.9-fold for white parents/offspring; 3.3-fold for Hispanic full-siblings and 2.0-fold for Hispanic parents/offspring). Older related black donors did not have higher risk compared to older unrelated black donors (0.8-fold for black full-siblings and 0.5-fold for black parents/offspring). Our study points to an earlier age of onset of kidney disease in black donors with a family history of ESKD. Our findings call for programs that promote living donation among related older black donor candidates.
Association of left atrial structure and function with cognitive function among adults with metabolic syndrome
Authors: Casanova Ines Gonzalez , M. Alonso-Gómez Ángel , Romaguera Dora , Toledo Estefanía , Fortuny Elena , López Luis , Ramallal Raúl , Salas-Salvadó Jordi , Tojal-Sierra Lucas , Castañer Olga , Alonso Alvaro
Published: March 2022

Background

Atrial fibrillation has been associated with cognitive impairment. Whether subclinical abnormalities in atrial function and substrate predisposing to atrial fibrillation impact cognitive function has received limited attention.

Methods

We tested associations of echocardiographic markers of atrial structure and function with cognitive functioning and decline among 510 participants with overweight/obesity and metabolic syndrome (mean age [standard deviation] of 64.4 [5.2] years in men and 66.5 [3.9] in women). Left atrial markers (volume index, emptying fraction, strain, function index, and stiffness index) were estimated based on transthoracic echocardiography. General cognitive functioning (Mini-mental examination), verbal ability (verbal fluency test), memory and attention (Digit Span Tests), and processing speed and executive function (Trail-Making Tests A and B) were assessed at baseline and at the two-year follow-up. Multiple linear regression was used to test associations of atrial markers (modeled in standard deviation units) with baseline and two-year changes in cognitive scores adjusting for demographic and health covariates.

Results

Left atrial structure and function was not associated with cognitive function at baseline. Larger left atrial volume index (standardized β [95% confidence interval] = -0.13 [-0.22, -0.03]), lower peak longitudinal strain (−0.11 [-0.20, -0.01]), and higher stiffness index (−0.18 [-0.28, -0.08) were associated with 2-year worsening in Trail-Making Test A. Strain measurements were also associated with 2-year change in the Controlled Oral Word Association Test.

Conclusion

Overall, adverse markers of left atrial structure and function were associated with 2-year detrimental executive function-related cognitive changes in a sample of participants at high risk for cardiovascular disease, highlighting left atrial substrate as a potential risk factor for cognitive decline and dementia.
Ion channel model reduction using manifold boundaries
Authors: Whittaker Dominic G. , Wang Jiahui , Shuttleworth Joseph G. , Venkateshappa Ravichandra , Kemp Jacob M. , Claydon Thomas W. , Mirams Gary R.
Published: March 2022

Mathematical models of voltage-gated ion channels are used in basic research, industrial and clinical settings. These models range in complexity, but typically contain numerous variables representing the proportion of channels in a given state, and parameters describing the voltage-dependent rates of transition between states. An open problem is selecting the appropriate degree of complexity and structure for an ion channel model given data availability. Here, we simplify a model of the cardiac human Ether-à-go-go Related Gene (hERG) potassium ion channel, which carries cardiac IKr, using the manifold boundary approximation method (MBAM). The MBAM approximates high-dimensional model-output manifolds by reduced models describing their boundaries, resulting in models with fewer parameters (and often variables). We produced a series of models of reducing complexity starting from an established 5-state hERG model with 15 parameters. Models with up to 3 fewer states and 8 fewer parameters were shown to retain much of the predictive capability of the full model and were validated using experimental hERG1a data collected in HEK293 cells at 37°C. The method provides a way to simplify complex models of ion channels that improves parameter identifiability and will aid in future model development.
Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development
Authors: Imprachim Nergis , Yosaatmadja Yuliana , Newman Joseph A
Published: March 2022

The SARS-CoV-2 non-structural protein 14 (NSP14) is a dual function enzyme containing an N-terminal exonuclease domain (ExoN) and C-terminal Guanine-N7-methyltransferase (N7-MTase) domain. Both enzymatic activities appear to be essential for the viral life cycle and thus may be targeted for anti-viral therapeutics. NSP14 forms a stable complex with the SARS-CoV-2 zinc binding protein NSP10, and this interaction greatly enhances the nuclease but not the methyltransferase activity. In this study, we have determined the crystal structure of SARS-CoV-2 NSP14 in the absence of NSP10 to 1.7 Å resolution. Comparisons of this structure with the structure of NSP14/NSP10 complexes solved to date reveal significant conformational changes that occur within the NSP14 ExoN domain upon binding of NSP10, including significant movements and helix to coil transitions that facilitate the formation of the ExoN active site and provide an explanation of the stimulation of nuclease activity by NSP10. Conformational changes are also seen in the MTase active site within a SAM/SAH interacting loop that plays a key role in viral mRNA capping. We have also determined the structure of NSP14 in complex with cap analogue 7MeGpppG, offering new insights into MTase enzymatic activity. We have used our high resolution crystals to perform X-ray fragment screening of NSP14, revealing 72 hits bound to potential sites of inhibition of the ExoN and MTase domains. These structures serve as excellent starting point tools for structure guided development and optimization of NSP14 inhibitors that may be used to treat COVID-19 and potentially other future viral threats.
Optical photothermal infrared spectroscopy can differentiate equine osteoarthritic plasma extracellular vesicles from healthy controls
Authors: Clarke Emily J , Lima Cassio , Anderson James R , Castanheira Catarina , Beckett Alison , James Victoria , Hyett Jacob , Goodacre Roy , Peffers Mandy J
Published: March 2022

Background

Equine osteoarthritis is a chronic degenerative disease of the articular joint, characterised by cartilage degradation resulting in pain and reduced mobility and thus is a prominent equine welfare concern. Diagnosis is usually at a late stage through radiographic examination, whilst treatment is symptomatic not curative. Extracellular vesicles are small nanoparticles that are involved in intercellular communication. The objective of this study was to investigate the feasibility of Raman and optical photothermal infrared spectroscopy to detect osteoarthritis using plasma-derived extracellular vesicles.

Methods

Plasma samples were derived from thoroughbred racehorses. A total of 14 samples were selected (control; n= 6 and diseased; n=8). Extracellular vesicles were isolated using differential ultracentrifugation and characterised using nanoparticle tracking analysis, transmission electron microscopy, and human tetraspanin chips. Samples were then analysed using Raman and optical photothermal infrared spectroscopy.

Results

Infrared spectra were analysed between 950-1800 cm-1. Raman spectra had bands between the wavelengths of 900-1800 cm-1 analysed. Bands below 900 cm-1. Spectral data for both Raman and optical photothermal infrared spectroscopy was used to obtain a classification model and confusion matrices, characterising the techniques ability to distinguish diseased samples. Optical photothermal infrared spectroscopy could differentiate osteoarthritic extracellular vesicles from healthy with good classification (93.4%) whereas Raman displayed poor classification (64.3%). Plasma-derived extracellular vesicles from osteoarthritic horses contained increased signal for proteins, lipids and nucleic acids.

Discussion/ conclusion

For the first time we demonstrated the ability to use optical photothermal infrared spectroscopy to interrogate extracellular vesicles and osteoarthritis-related samples. Optical photothermal infrared spectroscopy was superior to Raman in this study, and could distinguish osteoarthritis samples, suggestive of its potential use diagnostically to identify osteoarthritis in equine patients. This study demonstrates the potential of Raman and optical photothermal infrared spectroscopy to be used as a diagnostic tool in clinical practice, with the capacity to detect changes in extracellular vesicles from clinically derived samples.
Structure and regulation of the myotonic dystrophy kinase-related Cdc42-binding kinase
Authors: Truebestein Linda , Waltenberger Elisabeth , Gehin Charlotte , Gavin Anne-Claude , Leonard Thomas A.
Published: March 2022

Remodeling of the cytoskeleton underlies myriad processes essential for life. Protein kinases of the DMPK family are critical regulators of actomyosin contractility in cells. In the nematode worm, Caenorhabditis elegans, MRCK1 is required for the activation of myosin, leading to the development of cortical tension, apical constriction and early gastrulation. Here, we present the structure, conformation, and membrane-binding properties of C. elegans MRCK1. MRCK1 forms an obligate homodimer with N-terminal kinase domains, a parallel coiled-coil of 55 nm, and a C-terminal tripartite module of C1, PH and CNH domains. High-throughput liposome binding assays indicate binding to specific phosphoinositides, while the C-terminal Cdc42-binding (CRIB) motif binds specifically to activated Cdc42. The length of the coiled-coil domain of MRCK, as well as those of the related DMPK kinases ROCK, CRIK and DMPK, is remarkably conserved over millions of years of evolution, suggesting that they may function as molecular rulers to precisely position kinase activity at a fixed distance from the membrane.
Optimized high-throughput screening of non-coding variants identified from genome-wide association studies
Authors: Morova Tunc , Ding Yi , Huang Chia-Chi Flora , Sar Funda , Schwarz Tommer , Giambartolomei Claudia , Baca Sylvan C. , Grishin Dennis , Hach Faraz , Gusev Alexander , Freedman Matthew L. , Pasaniuc Bogdan , Lack Nathan A.
Published: March 2022

The vast majority of disease-associated single nucleotide polymorphisms identified from genome-wide association study (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and number of variants tested per loci. Using this strategy, we interrogated 70 of 140 known prostate cancer (PCa) risk-associated loci and demonstrated that 26 (37%) of them harbor 36 SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.
A connectomics-based taxonomy of mammals
Authors: Suárez Laura E. , Yovel Yossi , van den Heuvel Martijn P. , Sporns Olaf , Assaf Yaniv , Lajoie Guillaume , Misic Bratislav
Published: March 2022

Mammalian taxonomies are conventionally defined by morphological traits and genetics. How species differ in terms of neural circuits and whether inter-species differences in neural circuit organization conform to these taxonomies is unknown. The main obstacle for the comparison of neural architectures have been differences in network reconstruction techniques, yielding species-specific connectomes that are not directly comparable to one another. Here we comprehensively chart connectome organization across the mammalian phylogenetic spectrum using a common reconstruction protocol. We analyze the mammalian MRI (MaMI) data set, a database that encompasses high-resolution ex vivo structural and diffusion magnetic resonance imaging (MRI) scans of 124 species across 12 taxonomic orders and 5 superorders, collected using a single protocol on a single scanner. We assess similarity between species connectomes using two methods: similarity of Laplacian eigenspectra and similarity of multiscale topological features. We find greater inter-species similarities among species within the same taxonomic order, suggesting the connectome organization recapitulates traditional taxonomies defined by morphology and genetics. While all connectomes retain hallmark global features and relative proportions of connection classes, inter-species variation is driven by local regional connectivity profiles. By encoding connectomes into a common frame of reference, these findings establish a foundation for investigating how neural circuits change over phylogeny, forging a link from genes to circuits to behaviour.
Bayesian hierarchical model for dose finding trial incorporating historical data
Authors: Han Linxi , Deng Qiqi , He Zhangyi , Fleischer Frank , Yu Feng
Published: March 2022

The Multiple Comparison Procedure and Modelling (MCPMod) approach has been shown to be a powerful statistical tool that can significantly improve the design and analysis of dose finding studies under model uncertainty. Due to its frequentist nature, however, it is difficult to incorporate into MCPMod information from historical trials on the same drug. Recently, a Bayesian version of MCPMod has been introduced by Fleischer et al. (2022) to resolve this issue, which is particularly tailored to the situation where there is information about the placebo dose group from historical trials. In practice, information may also be available on active dose groups from early phase trials, e.g., a dose escalation trial and a preceding small Proof of Concept trial with only a placebo and a high dose. To address this issue, we introduce a Bayesian hierarchical framework capable of incorporating historical information about both placebo and active dose groups with the flexibility of modelling both prognostic and predictive between-trial heterogeneity. Our method is particularly useful in the situation where the effect sizes of two trials are different. Our goal is to reduce the necessary sample size in the dose finding trial while maintaining its target power.
Unplanned ICU transfer from post-anesthesia care unit following cerebral surgery: A retrospective study
Authors: Cao Qinqin , Fan Chengjuan , Li Wei , Bai Shuling , Dong Hemin , Meng Haihong
Published: March 2022

Background

Unplanned transfer to intensive care unit (ICU) lead to reduced trust of patients and their families in medical staff and challenge medical staff to allocate scarce ICU resources. This study aimed to explore the incidence and risk factors of unplanned transfer to ICU during emergence from general anesthesia after cerebral surgery, and to provide guidelines for preventing unplanned transfer from post-anesthesia care unit (PACU) to ICU following cerebral surgery.

Methods

This was a retrospective case-control study and included patients with unplanned transfer from PACU to ICU following cerebral surgery between January 2016 and December 2020. The control group comprised patients matched (2:1) for age (±5 years), sex, and operation date (±48 hours) as those in the case group. Stata14.0 was used for statistical analysis, and p <0.05 indicated statistical significance.

Results

A total of 11,807 patients following cerebral surgery operations were cared in PACU during the study period. Of the 11,807 operations, 81 unscheduled ICU transfer occurred (0.686%). Finally, 76 patients were included in the case group, and 152 in the control group. The following factors were identified as independent risk factors for unplanned ICU admission after neurosurgery: low mean blood oxygen (OR=1.57, 95%CI: 1.20–2.04), low mean albumin (OR=1.14, 95%CI: 1.03–1.25), slow mean heart rate (OR=1.04, 95%CI: 1.00–1.08), blood transfusion (OR=2.78, 95%CI: 1.02–7.58), emergency surgery (OR=3.08, 95%CI: 1.07–8.87), lung disease (OR=2.64, 95%CI: 1.06–6.60), and high mean blood glucose (OR=1.71, 95%CI: 1.21–2.41).

Conclusion

We identified independent risk factors for unplanned transfer from PACU to ICU after cerebral surgery based on electronic medical records. Early identification of patients who may undergo unplanned ICU transfer after cerebral surgery is important to provide guidance for accurately implementing a patient’s level of care.
Humans prioritize walking efficiency or walking stability based on environmental risk
Authors: Kulkarni Ashwini , Cui Chuyi , Rietdyk Shirley , Ambike Satyajit
Published: March 2022

In human gait, the body’s mechanical energy at the end of one step is reused to achieve forward progression during the subsequent step, thereby reducing the required muscle work. During the single stance phase, humans rely on the largely uncontrolled passive inverted pendular motion of the body to perpetuate forward motion. These passive body dynamics, while improving walking efficiency, also indicate that lower passive dynamic stability in the anterior direction since the individual will be less able to withstand a forward external perturbation. Here we test the novel hypothesis that humans manipulate passive anterior-posterior (AP) stability via active selection of step length to either achieve energy-efficient gait or to improve stability when it is threatened. We computed the AP margin of stability, which quantifies the passive dynamic stability of gait, for multiple steps as healthy young adults (N=20) walked on a clear and on an obstructed walkway. Participants used passive dynamics to achieve energy-efficient gait for all but one step; when crossing the obstacle with the leading limb, AP margin of stability was increased. This increase indicated caution to offset the greater risk of falling after a potential trip. Furthermore, AP margin of stability increased while approaching the obstacle, indicating that humans proactively manipulate the passive dynamics to meet the demands of the locomotor task. Finally, the step length and the center of mass motion co-varied to maintain the AP margin of stability for all steps in both tasks at the specific values for each step. We conclude that humans actively regulate step length to maintain specific levels of passive dynamic stability for each step during unobstructed and obstructed gait.
Muscle calcium stress cleaves junctophilin1, unleashing a gene regulatory program predicted to correct glucose dysregulation
Authors: Tammineni Eshwar R. , Figueroa Lourdes , Manno Carlo , Varma Disha , Kraeva Natalia , Ibarra Carlos A , Klip Amira , Riazi Sheila , Ríos Eduardo
Published: March 2022

Calcium ion movements between cellular stores and the cytosol govern muscle contraction, the most energy-consuming function in mammals, which confers skeletal myofibers a pivotal role in glycemia regulation. Chronic myoplasmic calcium elevation, found in malignant hyperthermia-susceptible (MHS) patients and multiple myopathies, has been suggested to underlie the progression from hyperglycemia to insulin resistance. What drives such progression remains elusive. We find that muscle cells derived from MHS patients have increased an activated fragment of GSK3β — a specialized kinase that inhibits glycogen synthase, impairing glucose utilization and delineating a path to hyperglycemia. We also find decreased content of junctophilin1, an essential structural protein that colocalizes in the couplon with the voltage-sensing CaV1.1, the calcium channel RyR1 and calpain1, accompanied by an increase in a 44-kDa junctophilin1 fragment (JPh44) that moves into nuclei. We trace these changes to activated proteolysis by calpain1, secondary to increased myoplasmic calcium. We demonstrate that a JPh44-like construct induces transcriptional changes predictive of increased glucose utilization in myoblasts, including less transcription and translation of GSK3β and decreased transcription of proteins that reduce utilization of glucose. These effects reveal a stress-adaptive response, mediated by the novel regulator of transcription JPh44.
The sunflower WRINKLED1 transcription factor regulates fatty acid biosynthesis genes through an AW box binding sequence with a particular base bias
Authors: Sánchez R , González-Thuillier I , Venegas-Calerón M , Garcés R , Salas JJ , Martínez-Force E
Published: March 2022

Sunflower (Helianthus annuus L.) is an important oilseed crop in which the biochemical pathways leading to seed oil synthesis and accumulation have been widely studied. However, how these pathways are regulated is less well understood. The WRINKLED1 (WRI1) transcription factor is considered a master regulator in the transcriptional control of triacylglycerol biosynthesis, acting through the AW box binding element (CNTNG(N)7CG) that resides in the promoter of target genes. Here, we identified the sunflower WRI1 gene and characterized its activity in electrophoretic mobility shift assays. We studied its role as a co-regulator of sunflower genes involved in plastidial fatty acid synthesis, identifying genes bound by this transcription factor. Sunflower WRI1-targets included genes encoding all subunits of the pyruvate dehydrogenase complex, the α-CT and BCCP genes of the acetyl-CoA carboxylase complex, genes encoding acyl carrier proteins and key genes of the fatty acid synthase complex (KASIII, KASI and KAR), together with the FATA1 gene. As such, sunflower WRI1 regulates seed plastid fatty acid biosynthesis in a coordinated manner, establishing a WRI1 push and pull strategy that drives oleic acid synthesis for its export into the cytosol. We also analyzed the sequence of the functional sunflower AW box, determining the base bias at the N positions in the active sunflower AW box motif. Accordingly, we conclude that the sunflower AW box is sequence-sensitive at the non-conserved positions, enabling WRI1-binding. Moreover, we found that sunflower WRI1 could bind to a non-canonical AW-box motif, opening the possibility of searching for new target genes.
kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase
Authors: Shaffer Michael , Borton Mikayla A , Bolduc Ben , Ghadermazi Parsa , Edirisinghe Janaka N , Faria José P , Miller Christopher S , Chan Siu Hung Joshua , Sullivan Matt B , Henry Christopher S , Wrighton Kelly C.
Published: March 2022

Annotation is predicting the location of and assigning function to genes in a genome. DRAM is a tool developed to annotate bacterial, archaeal and viral genomes derived from pure cultures or metagenomes. DRAM distills multiple gene annotations to summaries of functional potential. Despite these benefits, a downside of DRAM is processing requires large computation resources, which limits its accessibility, and it did not integrate with downstream metabolic modelling tools. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated in the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point and click interface, as well as generate genome scale metabolic models from these DRAM annotations.

Availability and Implementation

The kb_DRAM software is available at https://github.com/shafferm/kb_DRAM. The kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. A narrative with examples of running all KBase apps is available at https://kbase.us/n/88325/84/.

Contact

Michael Shaffer, michael.t.shaffer@colostate.edu; Kelly Wrighton, kelly.wrighton@colostate.edu

Supplementary Information

Supplementary data are available at Bioinformatics online.
Novel tuberculosis combination regimens of two and three-months therapy duration
Authors: Gumbo Tawanda , Chapagain Moti , Magombedze Gesham , Srivastava Shashikant , Deshpande Devyani , Pasipanodya Jotam G. , Gumbo Ruramai , Dheda Keertan , Diacon Andreas , Hermann David , Hanna Debra
Published: March 2022

The tuberculosis treatment duration is 4-6 months, but can be 18–20 months with multidrug resistance. Ultrashort regimens that cure regardless of resistance status [“pan-tuberculosis regimens”] would be a major step towards global tuberculosis control. Starting with seven drugs [bedaquiline, delamanid, pretomanid, OPC-167832, sutezolid, moxifloxacin, and pyrazinamide] in clinical testing, we calculated that there were thousands of possible novel combinations to evaluate. We used mathematical and pharmacokinetics/pharmacodynamic-based hollow fiber modeling to reduce this complexity to nine combinations, which we tested. Each regimen’s fast and slow growth bacteria kill-slope trajectories and times-to-extinction were estimated and translated to minimum required therapy duration in patients. Sputum microbial kill trajectories of two combination regimens that have undergone clinical testing were correctly predicted by this approach. Four pan-tuberculosis regimens were predicted to achieve relapse-free cure after 2-3 months therapy in patients. The kill-slopes were used to design expedited clinical trials that minimize patients’ risks.
Virgin Birth: A genetic basis for facultative parthenogenesis
Authors: Braun A. L. , Fabian D. K. , Garrison E. , Glover D. M.
Published: March 2022

Sexual reproduction evolved 1-2 billion years ago and underlies the biodiversity of our planet. Nevertheless, devolution of sexual into asexual reproduction can occur across all phyla of the animal kingdom. The genetic basis for how parthenogenesis can arise is completely unknown. To understand the mechanism and benefits of parthenogenesis, we have sequenced the genome of the facultative parthenogen, Drosophila mercatorum, and compared its organisation and expression pattern during parthenogenetic or sexual reproduction. We identified three genes, desat2, Myc, and polo in parthenogenetic D. mercatorum that when mis-regulated in a non-parthenogenetic species, D. melanogaster, enable facultative parthenogenetic reproduction. This simple genetic switch leads us to propose that sporadic facultative parthenogenesis could evolve as an ‘escape route’ preserving the genetic lineage in the face of sexual isolation.
EPI-589, a redox-active neuroprotectant, potently protects cultured cells from oxidative stress and alleviates symptomatic and pathological progression of motor neuron disease in the wobbler mouse
Authors: Matsumoto Yuji , Sampei Kazuaki , Nashida Tetsuaki , Fujii Yuta , Tani Naoko , Ishibashi Fumiaki , Yamanaka Mitsugu , Ishiyama Takeo
Published: March 2022

Oxidative stress is believed to play a significant role in the pathophysiology of amyotrophic lateral sclerosis (ALS), the most common form of motor neuron disease. The present study aims to firstly investigate the antioxidant activities of EPI-589, a small-molecule quinone derivative, under cell-free or cell culture conditions, and explore the in vivo efficacy of EPI-589 in the wobbler mouse model of human motor neuron disease. The reduced form of EPI-589 showed hydroxyl radical scavenging activities, whereas the oxidized form i.e. EPI-589 did not. In cellular models utilizing ALS patient-derived fibroblasts carrying mutations in the fused in sarcoma (FUS) gene or superoxide dismutase 1 (SOD1) gene, EPI-589 potently protected cells from oxidative stress induced by buthionine sulfoximine and ferric citrate. Protective effect of EPI-589 was also observed in culture of mouse immortalized striatal STHdHQ7/Q7 cells with cystine deprivation. In wobbler mice, oral administration of dietary EPI-589 provided long-lasting amelioration of both of deterioration of the rotarod walking performance and progression of forelimb deformity in wobbler mice throughout the treatment. In separate studies, we found that EPI-589 significantly suppressed changes of pathophysiological markers such as plasma phosphorylated neurofilament heavy chain, urinary 8-hydroxy-2’-deoxyguanosine, and cervical N-acetylaspartate in untreated wobbler mice. Thus, the present study firstly demonstrates that EPI-589 is a highly potent, redox-active neuroprotectant and robustly delays the symptomatic and pathophysiological progression of motor neuron disease in the wobbler mouse, and these findings strongly encourage further exploration of the therapeutic potential of EPI-589 for the treatment of ALS.
Molecular docking between human TMPRSS2 and the serine protease Kunitz-type inhibitor rBmTI-A
Authors: Bomediano Camillo Lívia de Moraes , Sasaki Sergio Daishi
Published: March 2022

SARS-CoV-2 entrance into host cells is dependent of ACE2 receptor and viral protein S initiation by serine protease TMPRSS2. Cleavage of coronavirus protein S at the junctions Arg685/Ser686 and Arg815/Ser816 leads to the production of the S1/S2 and S2’ fragments needed for the fusion of viral and cell membranes. Studying and identifying serine protease inhibitors is an important step towards the development of candidate drugs to prevent SARS-CoV-2 infection. It has already been stablished that camostat mesylate, a serine protease inhibitor, is capable of blocking TMPRSS2 activity and prevent SARS-CoV-2 entrance into host cells. In this work, the interaction between the two domains of Kunitz-type serine protease inhibitor rBmTI-A and TMPRSS2 was studied through molecular docking. rBmTI-A domain 2 (P1 site Leu84) had the best complex results with predicted binding affinity of -12 Kcal.mol-1 and predicted dissociation constant at 25°C of 1.6 nM. The results suggest that rBmTI-A is capable of binding TMPRSS2 cleavage site at the junction Arg815/Ser816 using essentially the same residues that camostat mesylate.
Mid-term subclinical myocardial injury detection in patients recovered from COVID-19 according pulmonary lesion severity
Authors: Chamtouri Ikram , Kaddoussi Rania , Abroug Hela , Hafsa Mariem , Abdeleli Mabrouk , Fahem Nessrine , Lassoued Taha , Abdallah Asma Ben , Achour Asma , Migaou Asma , Cheikhm’hamed Sawssen , Jomaa Walid , Sriha Asma , Hamda Khaldoun Ben , Maatouk Faouzi
Published: March 2022

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2) may cause damage of the cardiovascular system during the acute phase of infection. However, Recent studies described a mid and long-term subtle cardiac injuries after recovery from acute Coronavirus disease 19 (COVID-19).The aim of this study was to determine the relationship between the severity of chest computed tomography (CT) lesions and the persistence of subtle myocardial injuries at mid-term follow-up of patients recovered from COVID-19 infection.

Methods

All COVID-19 patients were enrolled prospectively in this study. Sensitive troponin T (hsTnT) and chest CT scan was performed in all patients at the acute phase of Covid-19 infection. At the mid-term follow up, conventional transthoracic echocardiograph and global longitudinal strain (GLS) of left and right ventricles (LV and RV) were determined and compared between patients with chest CT scan lesions less than 50% (Group 1) and those with severe chest CT scan greater or equal to 50% (Group 2).

Results

The mean age was 55 more or less than 14 years. Both LV GLS and RV GLS were significantly decreased in the group 2 (p=0.013 and p=0.011, respectively). LV GLS value more than -18% was noted in 43% of all the patients and RV GLS value more than -20% was observed in 48% of them. The group with severe chest CT scan lesions included more patients with reduced LV GLS and reduced RV GLS than the group with mild chest CT scan lesions (G1:29% vs. G2:57%, p=0.002) and (G1:36% vs. G2:60 %, p=0.009) respectively).

Conclusion

Patients with severe chest CT scan lesions are more likely to develop subclinical myocardial damage. TTE could be recommended in patients recovering from COVID-19 to detect subtle LV and RV lesions.

Trial registration

The cohort of patients is a part of the research protocol (IORG 00093738 N°102/OMB 0990-0279) approved by the Hospital Ethics Committee.
Glucose and lipid profiles in men with non-obstructive azoospermia
Authors: Birowo Ponco , Prasetyo Dimas Tri , Pujianto Dwi Ari , Atmoko Widi , Rasyid Nur
Published: March 2022

The impact of a low testosterone level among men with non-obstructive azoospermia with various testicular histopathological patterns on the regulation of glucose and lipid metabolism is less well known than among the general population. The aim of this retrospective study was to examine the association between testicular histopathology and components of the metabolic profile among men with non-obstructive azoospermia. Participants were divided into two groups: men with non-obstructive azoospermia and men with obstructive azoospermia. Testicular biopsies were performed among those with non-obstructive azoospermia. We included 115 patients in this study: 83 (72.2%) had non-obstructive azoospermia and 32 (27.8%) had obstructive azoospermia. The plasma glucose concentration, glycated hemoglobin level, and lipid profile were similar between patients with non-obstructive azoospermia and those with obstructive azoospermia. Upon subgroup analysis of patients with non-obstructive azoospermia, those with Sertoli-cell-only syndrome had the lowest testosterone (431 ± 238 ng/dL;P=0.039) and highest follicle-stimulating hormone (23.4 ± 18.2 mIU/mL;P=0.002) concentrations. They also had the highest triglyceride concentration (163 ± 114 mg/dL;P=0.001). Interestingly, patients with Sertoli-cell-only syndrome had a lower fasting plasma glucose concentration (92 ± 11 mg/dL;P<0.001) and glycated hemoglobin level (5.9 ± 0.8%;P=0.022) than those with histopathological patterns of maturation arrest and hypospermatogenesis. In conclusion, differences in glucose and lipid metabolism are evident between men with non-obstructive azoospermia with different spermatogenesis patterns.
Genetic mapping of multiple metabolic traits identifies novel genes for adiposity, lipids and insulin secretory capacity in outbred rats
Authors: Le Thu H , Crouse Wesley L , Keele Gregory R , Holl Katie , Seshie Osborne , Tschannen Michael , Craddock Ann , Das Swapan K. , McDonald Bailey , Sharma Neeraj K , Key Chia-Chi Chuang , Hawkins Gregory , Valdar William , Mott Richard , Woods Leah C Solberg
Published: March 2022

Despite the successes of human genome-wide association studies, the causal genes underlying most metabolic traits remain unclear. We used outbred heterogeneous stock (HS) rats, coupled with expression data and mediation analysis, to identify quantitative trait loci (QTLs) and candidate gene mediators for adiposity, glucose tolerance, serum lipids and other metabolic traits. Physiological traits were measured in 1519 male HS rats, with liver and adipose transcriptomes measured in over 410 rats. Genotypes were imputed from low coverage whole genome sequence. Linear mixed models were used to detect physiological and expression QTLs (pQTLs and eQTLs, respectively), employing both SNP- and haplotype-based models for pQTL mapping. Genes with cis-eQTLs that overlapped pQTLs were assessed as causal candidates through mediation analysis. We identified 15 SNP-based pQTLs and 19 haplotype-based pQTLs, of which 11 were in common. Using mediation, we identified the following genes as candidate mediators of pQTLs: Grk5 for a fat pad weight pQTL on Chr1, Krtcap3 for fat pad weight and serum lipids pQTLs on Chr6, Ilrun for a fat pad weight pQTL on Chr20 and Rfx6 for a whole pancreatic insulin content pQTL on Chr20. Furthermore, we verified Grk5 and Ktrcap3 using gene knock-down/out models, thereby shedding light on novel regulators of obesity.
Intratumor Childhood Vaccine-Specific CD4+T cell Recall Coordinates Antitumor CD8+T cells and Eosinophils
Authors: Brown Michael C. , McKay Zachary P. , Yang Yuanfan , Beasley Georgia M. , Ashley David M. , Bigner Darell D. , Nair Smita K. , Gromeier Matthias
Published: March 2022

Background

CD4+T cells are key contributors to cancer immune surveillance. However, means to effectively harness CD4+T cell help for cancer immunotherapy are lacking, and antitumor mechanisms of CD4+T cells remain crudely defined.

Methods

The impact of polio immunization on polio virotherapy was tested in syngeneic murine melanoma and breast cancer models. Antitumor effects of polio and tetanus toxoid antigens were assessed in polio and tetanus immunized mice. T and B cell knockout mice, CD4+T cell adoptive transfer, and eosinophil depletion demonstrated cell-type specific contributions to the antitumor efficacy of polio recall. Phenotyping of adoptively transferred OT-I (OVA-specific) T cells in B16-OVA tumor bearing mice, as well as adoptive transfer of T cells to naïve tumor-bearing recipients, measured the impact of intratumor polio/tetanus recall on antitumor T cell immunity. Pan-cancer human transcriptome data sets were queried to test associations between eosinophils and Tregs; cytokine profiles of polio and tetanus recall were defined in human peripheral blood of healthy donors and cancer patients; CD40L blockade was used to determine dependency of recall antigen therapy on CD40:CD40L signaling.

Results

Prior vaccination against poliovirus substantially bolstered the antitumor efficacy of polio virotherapy in mice, and intratumor recall of poliovirus or tetanus immunity delayed tumor growth in a manner complemented by pattern recognition receptor agonist therapy and PD1 blockade. Intratumor recall antigens augmented antitumor T cell function, and caused marked tumor infiltration of type 2 innate lymphoid cells (ILC2s) and eosinophils, coinciding with decreased proportions of intratumor Tregs. Antitumor effects of recall antigens were mediated by CD4+T cells, independent of CD40L signaling, and were dependent on both eosinophils and CD8+T cells. Human PBMCs mounted diverse cytokine/chemokine responses, which were not impaired in patients with advanced cancer, and an inverse relationship between eosinophil and Treg signatures was observed across TCGA cancer types.

Conclusion

This work defines cancer immunotherapy potential of childhood vaccines, reveals their utility to engage CD4+T cell help for antitumor CD8+T cells, and implicates eosinophils as antitumor effectors of CD4+T cells.