Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved ...structure, multiple programs were developed for the de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rates. Here, we report LTR_retriever, a multithreading-empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity (91%), specificity (97%), accuracy (96%), and precision (90%) in rice (Oryza sativa). LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.5× genome coverage in Arabidopsis (Arabidopsis thaliana), the constructed LTR library showed excellent sensitivity and specificity. In addition to canonical LTR-RTs with 5'-TG...CA-3' termini, LTR_retriever also identifies noncanonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of noncanonical LTRs from 42 out of 50 plant genomes. The majority of noncanonical LTRs are Copia elements, with which the LTR is four times shorter than that of other Copia elements, which may be a result of their target specificity. Strikingly, non-TGCA Copia elements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and their potential as mutagenesis tools.
A novel signal processing algorithm for the surface electromyogram (EMG) is proposed to extract simultaneous and proportional control information for multiple DOFs. The algorithm is based on a ...generative model for the surface EMG. The model assumes that synergistic muscles share spinal neural drives, which correspond to the intended activations of different DOFs of natural movements and are embedded within the surface EMG. A DOF-wise nonnegative matrix factorization (NMF) is developed to estimate neural control information from the multichannel surface EMG. It is shown, both by simulation and experimental studies, that the proposed algorithm is able to extract the multidimensional control information simultaneously. A direct application of the proposed method would be providing simultaneous and proportional control of multifunction myoelectric prostheses.
Soil stabilization technology based on microbial-induced carbonate precipitation (MICP) has gained widespread interest in geotechnical engineering. MICP has been found to be able to improve soil ...strength, stiffness, liquefaction resistance, erosion resistance, while maintaining a good permeability simultaneously. MICP processes involves a series of biochemical reactions that are affected by many factors, both intrinsically and externally. This paper reviews various influential factors for MICP process, including bacterial species, concentration of bacteria, temperature, pH, composition and concentration of cementation solution, grouting strategies, and soil properties. Through this comprehensive review, we find that: (1) the species and strains of bacteria, concentration of bacteria solution, temperature, pH value, and the cementation solution properties all affect the characteristics of formed calcium carbonate, such as crystal type, appearance and size, which consequently affect the cementation degree and distribution in geomaterials; (2) the condition with temperature between 20 and 40 °C, pH between 7 and 9.5, the concentration of the cementation solution within 1 mol/L, and high bacteria concentration is optimal for applying MICP in soil. Under the optimal condition, relatively low temperature, high pH value, and low concentration of cementation solution could help retain permeability and vice versa; (3) the effective grain size ranging from 10 to 1000 µm. MICP treatment works most effectively for larger size, well-graded sand; (4) the multi-phase, multi-concentration or electroosmotic grouting method can improve the MICP treatment efficiency. The grouting velocity below 0.042 mol/L/h is beneficial for improving the utilization ratio of cementation solution. The recommended grouting pressure is generally between 0.1 and 0.3 bar for MICP applications in sand and should not exceed 1.1 bar for silty and clayey soils.
Microbial induced carbonate precipitation (MICP) is a natural bio-mediated process, which has been explored for soil stabilization and heavy metals immobilization in soil and groundwater. Previous ...studies have shown that MICP is capable of immobilizing various heavy metals including lead (Pb). However, most studies focus merely on the immobilization of heavy metals with relatively low concentration. This study: (1) presents results of an investigation into the toxic effects of Pb on bacterial activity and immobilization efficiency within a wide range of Pb concentrations; and (2) identifies controlling biotic and abiotic factors of Pb immobilization by MICP. In the first series of tests, bacterial strains (Sporosarcina pasteurii) are inoculated into nutrient solutions containing 0–50 mM Pb(NO3)2 and incubated at 30 °C. Biochemical parameters are measured over time, which include pH, electrical conductivity, urease activity, and viable cell number. In the second series of tests, grown bacterial strains are mixed with urea, calcium salts and Pb(NO3)2 in solution. Viable cell number, produced ammonium concentration, aqueous Pb concentration of the mixed solution, and total precipitation mass are measured. The results show that the presence of Pb has marginal effect on bacterial growth and associated urease activity at Pb concentration < 30 mM. The calcium source and initial bacteria concentration are found to remarkably influence Pb immobilization efficiency in terms of Pb removal percentage. Supplementary geochemical simulation results indicate that the Pb immobilization mechanisms includes abiotic precipitation, biotic precipitation and bio-sorption.
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•Pb contaminants are immobilized by microbial induced carbonate precipitation.•Pb has toxic effects on bacterial activity and immobilization efficiency.•Abiotic and biotic precipitation and bio-sorption are immobilization mechanisms.
Annotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for ...the identification of LTR retrotransposons but its application on large genomes is hindered by its single-threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting in up to 8500X faster identification of LTR elements. It takes only 72 min to process the 14.5 Gb bread wheat (
) genome in comparison to 1.16 years required by the original sequential version. LTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.
In response to stressors, individuals adopt different behavioral styles, which are essential for survival and form the basis of differential susceptibility to stress-related disorders. ...Corticotropin-releasing factor (CRF) and the medial prefrontal cortex (mPFC) have predominantly been studied in behavioral response to stress, while the role of mPFC CRF neurons is poorly understood. Using morphology, electrophysiology, and calcium imaging approaches, we characterized mPFC CRF neurons as a unique subtype of GABAergic inhibitory interneurons that were directly engaged in the tail suspension challenge. Genetic ablation or chemogenetic inhibition of dorsal mPFC (dmPFC) CRF neurons increased immobility under the tail-suspension and forced-swimming challenges and induced social avoidance behavior, whereas activation had the opposite effect on the same measures. Furthermore, increasing CRF neuronal activity promoted durable resilience to repeated social defeat stress. These results uncover a critical role of mPFC CRF interneurons in bidirectionally controlling motivated behavioral style selection under stress.
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•Prefrontal CRF GABAergic interneurons are recruited during behavioral challenges•Manipulation of CRF neurons motivates selection of behavioral styles under challenges•Activation of CRF neurons promotes persistent stress-resistant behaviors
Chen et al. identify a population of mPFC CRF neurons that form monosynaptic GABAergic inhibitory connections with pyramidal cells and play a key role in controlling behavioral style selection in the face of various stressful challenges.
Comorbid depressive symptoms (CDS) in chronic pain are a common health problem, but the neural circuit mechanisms underlying these symptoms remain unclear. Here we identify a novel pathway involving ...5-hydroxytryptamine (5-HT) projections from the dorsal raphe nucleus (5-HT
) to somatostatin (SOM)-expressing and non-SOM interneurons in the central nucleus of the amygdala (CeA). The SOM
neurons project directly to the lateral habenula, an area known involved in depression. Inhibition of the 5-HT
→SOM
pathway produced depression-like behavior in a male mouse model of chronic pain. Activation of this pathway using pharmacological or optogenetic approaches reduced depression-like behavior in these mice. Human functional magnetic resonance imaging data showed that compared to healthy controls, functional connectivity between the CeA-containing centromedial amygdala and the DRN was reduced in patients with CDS but not in patients in chronic pain without depression. These findings indicate that a novel 5-HT
→SOM
→lateral habenula pathway may mediate at least some aspects of CDS.
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