Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information

Circular RNAs (circRNAs) are RNA molecules formed by joining a downstream 3 splice donor site and an upstream 5 splice acceptor site. Several recent studies have identified circRNAs as potential biomarker for different diseases. A number of methods are available for the identification of circRNAs. The circRNA identification methods cannot provide full-length sequences. Reconstruction of the full-length sequences is crucial for the downstream analyses of circRNA research including differential expression analysis, circRNA-miRNA interaction analysis and other functional studies of the circRNAs. However, a limited number of methods are available in the literature for the reconstruction of full-length circRNA sequences. We developed a new method, circRNA-full, for full-length circRNA sequence reconstruction utilizing chimeric alignment information from the STAR aligner. To evaluate our method, we used full-length circRNA sequences produced by isocirc and ciri-long using long-reads RNA-seq data. Our method achieved better reconstruction rate, precision, sensitivity and F1 score than the existing full-length circRNA sequence reconstruction tool ciri-full for both human and mouse data.     

Low loss and low dispersion hybrid core photonic crystal fiber for terahertz propagation

In this paper, a hybrid-core circular cladded photonic crystal fiber is designed and analyzed for application in the terahertz frequency range. We introduce a rectangular structure in addition to a conventional hexagonal structure in the core to reduce the material absorption loss. The modal characteristics of the fiber have been investigated using full vector finite element method. Simulated results exhibit an ultra-low effective material loss of 0.035 cm\(^{-1}\) and ultra-flattened dispersion of 0.07 ps/THz/cm. Some other important fiber characteristics suitable for terahertz signal transmission including confinement loss, core power fraction, effective area and single-mode conditions of the fiber have also been investigated. In order to simplify design and facilitate fabrication, only circular shaped air holes have been employed. Due to its promising characteristics, the proposed waveguide may provide efficient transmission of broadband terahertz signals.     

Uncovering a Hub Signaling Pathway of Antimicrobial-Antifungal-Anticancer Peptides’ Axis on Short Cationic Peptides via Network Pharmacology Study

Short cationic peptides (SCPs) with therapeutic efficacy of antimicrobial peptides (AMPs), antifungal peptides (AFPs), and anticancer peptides (ACPs) are known as an enhancement of the host defense system. Here, we investigated the uppermost peptide(s), hub signaling pathway(s), and their associated target(s) through network pharmacology. Firstly, we selected SCPs with positive amino acid residues on N- and C- terminals under 500 Dalton via RStudio. Secondly, the overlapping targets between the bacteria-responsive targets (TTD and OMIM) and AMPs’ targets were visualized by VENNY 2.1. Thirdly, the overlapping targets between AFPs’ targets and fungal-responsive targets were exhibited by VENNY 2.1. Fourthly, the overlapping targets between cancer-related targets (TTD and OMIM) and fungal-responsive targets were displayed by VENNY 2.1. Finally, a molecular docking study (MDS) was carried out to discover the most potent peptides on a hub signaling pathway. A total of 1833 SCPs were identified, and AMPs’, AFPs’, and ACPs’ filtration suggested that 197 peptides (30 targets), 81 peptides (6 targets), and 59 peptides (4 targets) were connected, respectively. The AMPs―AFPs―ACPs’ axis indicated that 27 peptides (2 targets) were associated. Each hub signaling pathway for the enhancement of the host defense system was “Inactivation of Rap1 signaling pathway on AMPs”, “Activation of Notch signaling pathway on AMPs―AFPs’ axis”, and “Inactivation of HIF-1 signaling pathway on AMPs―AFPs―ACPs’ axis”. The most potent peptides were assessed via MDS; finally, HPIK on STAT3 and HVTK on NOS2 and on HIF-1 signaling pathway were the most stable complexes. Furthermore, the two peptides had better affinity scores than standard inhibitors (Stattic, 1400 W). Overall, the most potent SCPs for the human defense system were HPIK on STAT3 and HVTK on NOS2, which might inactivate the HIF-1 signaling pathway.     

Algorithms for generalized vertex-rankings of partial k-trees

A c-vertex-ranking of a graph G for a positive integer c is a labeling of the vertices of G with integers such that, for any label i, deletion of all vertices with labels >i leaves connected components, each having at most c vertices with label i. A c-vertex-ranking is optimal if the number of labels used is as small as possible. We present sequential and parallel algorithms to find an optimal c-vertex-ranking of a partial k-tree, that is, a graph of treewidth bounded by a fixed integer k. The sequential algorithm takes polynomial-time for any positive integer c. The parallel algorithm takes O(log n) parallel time using a polynomial number of processors on the common CRCW PRAM, where n is the number of vertices in G.     

Flavonoids as Antidiabetic and Anti-Inflammatory Agents: A Review on Structural Activity Relationship-Based Studies and Meta-Analysis

Flavonoids are a group of naturally occurring polyphenolic secondary metabolites which have been reported to demonstrate a wide range of pharmacological properties, most importantly, antidiabetic and anti-inflammatory effects. The relationship between hyperglycaemia and inflammation and vascular complications in diabetes is now well established. Flavonoids possessing antidiabetic properties may alleviate inflammation by reducing hyperglycaemia through different mechanisms of action. It has been suggested that the flavonoids’ biochemical properties are structure-dependent; however, they are yet to be thoroughly grasped. Hence, the main aim of this review is to understand the antidiabetic and anti-inflammatory properties of various structurally diverse flavonoids and to identify key positions responsible for the effects, their correlation, and the effect of different substitutions on both antidiabetic and anti-inflammatory properties. The general requirement of flavonoids for exerting both anti-inflammatory and antidiabetic effects is found to be the presence of a C2–C3 double bond (C-ring) and hydroxyl groups at the C3’, C4’, C5, and C7 positions of both rings A and B of a flavonoid skeleton. Furthermore, it has been demonstrated that substitution at the C3 position of a C-ring decreases the anti-inflammatory action of flavonoids while enhancing their antidiabetic activity. Correlation is discussed at length to support flavonoids possessing essential pharmacophores to demonstrate equipotent effects. The consideration of these structural features may play an important role in synthesizing better flavonoid-based drugs possessing dual antidiabetic and anti-inflammatory effects. A meta-analysis further established the role of flavonoids as antidiabetic and anti-inflammatory agents.     

Groundwater contamination risks with manure-borne microorganisms under different land-application options

There is a huge potential for recycling animal manure in agricultural farms, but fecal microorganisms from land-applied animal manure can join shallow groundwater through leaching especially in alluvial formations. Thus, this study investigated the leaching rate of total viable count (TVC) below a 1.1-m soil depth in a field lysimeter planted with rice–maize–rice rotation, where the rotation received different treatments, i.e., chemical fertilizer, dry manure, fresh manure, alternate wetting and drying (AWD) irrigation, and traditional irrigation. Leachate samples of six major irrigation/rainfall events were collected and analyzed for TVC concentration. In the Aman rice season, manure application had a significantly higher TVC leaching (5.5 × 10⁶ colony forming units (CFU) per milliliter) than the no-manure treatment (8.2 × 10⁴ CFU/mL). In the maize season, manure application increased more than one log-scale of TVC leaching concentration. A higher concentration of TVC leaching (3 × 10⁵ CFU/mL) was observed even after 93 d of fresh manure application. The fresh manure had a higher TVC load, and it possibly helped microorganisms survive longer by providing a more manure-like environment in the soil. In the Boro rice season, manure application increased the TVC leaching up to 3–4 log-scale compared with the control treatment. The AWD irrigation increased TVC leaching compared with the continuous irrigation because the desiccation fractures developed in the AWD irrigation helped TVC bypass the organic-rich topsoil. The Boro rice fields had higher TVC leaching than the maize fields with higher manure doses. The study suggests that there is scope to improve manure management to protect the groundwater quality.     

Chromium adsorption on surface activated biochar made from tannery liming sludge: A waste-to-wealth approach

In a beamhouse, liming plays a key role in the removal of hair/wool and epidermis, but problems are created when waste liming sludge is discharged to the environment. The treatment of tannery wastewater is another major challenge to the industry. In this study, thermally-activated biochars derived from liming sludge were studied for their effective adsorption of chromium (Cr) from the tannery wastewater. The thermally activated biochars (B500, B550, B600, and B650) were prepared at different temperatures from the liming sludge. Their characteristics before and after the treatment were investigated using Fourier transform infrared spectroscopy, energy dispersive X-ray spectroscopy, Brunauer–Emmett–Teller, and scanning electron microscopy analyses. The related functional groups (C–H, O–H, C–N, and =C–O) and chromium adsorption capacity were determined according to the surface morphology, element contents (C, O, Ca, Na, Al, Mg, and Si), surface area (5.8–9.2 m²/g), pore size (5.22–5.53 nm), and particle size (652–1 034 nm) of the experimental biochars. The biochar originated at 600°C from the tannery liming sludge (B600) had a greater surface area with a chromium adsorption capacity of 99.8% in comparison to B500, B550, and B650 biochars. This study developed an innovative way of utilizing liming sludge waste to minimize the pollution load and wastewater treatment cost in the tannery industry.     

Transmission of vibration through gloves: effects of material thickness

It might be assumed that increasing the thickness of a glove would reduce the vibration transmitted to the hand. Three material samples from an anti-vibration glove were stacked to produce three thicknesses: 6.4, 12.8 and 19.2 mm. The dynamic stiffnesses of all three thicknesses, the apparent mass at the palm and the finger and the transmission of vibration to the palm and finger were measured. At frequencies from 20 to 350 Hz, the material reduced vibration at the palm but increased vibration at the finger. Increased thickness reduced vibration at the palm but increased vibration at the finger. The measured transmissibilities could be predicted from the material dynamic stiffness and the apparent mass of the palm and finger. Reducing the dynamic stiffness of glove material may increase or decrease the transmission of vibration, depending on the material, the frequency of vibration and the location of measurement (palm or finger).

Practitioner Summary: Transmission of vibration through gloves depends on the dynamic response of the hand and the dynamic stiffness of glove material, which depends on material thickness. Measuring the transmission of vibration through gloves to the palm of the hand gives a misleading indication of the transmission of vibration to the fingers.     

Receptor for Activated C Kinase1B (OsRACK1B) Impairs Fertility in Rice through NADPH-Dependent H2O2 Signaling Pathway

The scaffold protein receptor for Activated C Kinase1 (RACK1) regulates multiple aspects of plants, including seed germination, growth, environmental stress responses, and flowering. Recent studies have revealed that RACK1 is associated with NADPH-dependent reactive oxygen species (ROS) signaling in plants. ROS, as a double-edged sword, can modulate several developmental pathways in plants. Thus, the resulting physiological consequences of perturbing the RACK1 expression-induced ROS balance remain to be explored. Herein, we combined molecular, pharmacological, and ultrastructure analysis approaches to investigate the hypothesized connection using T-DNA-mediated activation-tagged RACK1B overexpressed (OX) transgenic rice plants. In this study, we find that OsRACK1B-OX plants display reduced pollen viability, defective anther dehiscence, and abnormal spikelet morphology, leading to partial spikelet sterility. Microscopic observation of the mature pollen grains from the OX plants revealed abnormalities in the exine and intine structures and decreased starch granules in the pollen, resulting in a reduced number of grains per locule from the OX rice plants as compared to that of the wild-type (WT). Histochemical staining revealed a global increase in hydrogen peroxide (H₂O₂) in the leaves and roots of the transgenic lines overexpressing OsRACK1B compared to that of the WT. However, the elevated H₂O₂ in tissues from the OX plants can be reversed by pre-treatment with diphenylidonium (DPI), an NADPH oxidase inhibitor, indicating that the source of H₂O₂ could be, in part, NADPH oxidase. Expression analysis showed a differential expression of the NADPH/respiratory burst oxidase homolog D (RbohD) and antioxidant enzyme-related genes, suggesting a homeostatic mechanism of H₂O₂ production and antioxidant enzyme activity. BiFC analysis demonstrated that OsRACK1B interacts with the N-terminal region of RbohD in vivo. Taken together, these data indicate that elevated OsRACK1B accumulates a threshold level of ROS, in this case H₂O₂, which negatively regulates pollen development and fertility. In conclusion, we hypothesized that an optimal expression of RACK1 is critical for fertility in rice plants.     

Significant enhancement of electrical conductivity by incorporating carbon fiber into CoSb3 thermoelectric skutterudite fabricated by spark plasma sintering method

Journal of Materials Science - The effects of carbon fiber additions on the electrical and thermoelectric performance in p-type CoSb3-based skutterudite are reported. A threefold enhancement in...