Entropy subspace separation-based clustering for noise reduction (ENCORE) of scRNA-seq data

Single-cell RNA sequencing enables us to characterize the cellular heterogeneity in single cell resolution with the help of cell type identification algorithms. However, the noise inherent in single-cell RNA-sequencing data severely disturbs the accuracy of cell clustering, marker identification and visualization. We propose that clustering based on feature density profiles can distinguish informative features from noise. We named such strategy as ‘entropy subspace’ separation and designed a cell clustering algorithm called ENtropy subspace separation-based Clustering for nOise REduction (ENCORE) by integrating the ‘entropy subspace’ separation strategy with a consensus clustering method. We demonstrate that ENCORE performs superiorly on cell clustering and generates high-resolution visualization across 12 standard datasets. More importantly, ENCORE enables identification of group markers with biological significance from a hard-to-separate dataset. With the advantages of effective feature selection, improved clustering, accurate marker identification and high-resolution visualization, we present ENCORE to the community as an important tool for scRNA-seq data analysis to study cellular heterogeneity and discover group markers.     

Comparative Transcriptomic Analysis of Storage Roots in Cassava During Postharvest Physiological Deterioration

Plant Molecular Biology Reporter - Cassava is an important starchy and food crop; however, the commercial value of cassava is seriously constrained by postharvest physiological deterioration (PPD)....     

Inhibiting roles of FOXA2 in liver cancer cell migration and invasion by transcriptionally suppressing microRNA-103a-3p and activating the GREM2/LATS2/YAP axis

Cytotechnology - Forkhead box A2 (FOXA2) has emerged as a tumor inhibitor in several human malignancies. This work focused on the effect of FOXA2 on liver cancer (LC) cell invasion and migration...     

A new biological method to control Anobium punctatum,by using the parasitoid wasp Spathius exarator

Biological pest control by means of beneficial organisms is for long part of agriculture and Integrated Pest Management (IPM). A new and efficient strategy to control the most common timber pest species in churches and museums, the furniture beetle Anobium punctatum (De Geer) (Coleoptera: Anobiidae), is based on the parasitoid wasp species Spathius exarator (Linnaeus) (Hymenoptera: Braconidae). Once this braconid wasp detects its host species beneath the surface, it pierces the wood with its ovipositor to lay one single egg onto the beetle larva. After hatching, the wasp larva feeds on the beetle larva thereby killing it. Afterwards, it pupates and emerges through a self-gnawed hole as an adult wasp. The tiny, 0.5-mm-wide exit hole can easily be distinguished from the 1- to 2-mm-wide exit hole of A. punctatum. Laboratory tests revealed that female wasps have an average life span of 85 days and produce a total of 24 offspring, when nutrition is provided. Between 2012 and 2019, braconid wasps were introduced into 54 different A. punctatum infested buildings. Treatment success was monitored by examining exit holes of new beetles and wasps thereby calculating corresponding parasitism rates. After the first year of treatment, parasitism rates were significantly higher with a mean value of 0.15 when compared to untreated objects with a natural parasitism and a mean value of 0.08 (n = 54). Following treatment of three objects over a period of eight years, parasitism rates continuously increased from 0.02 up to 0.31. In a church organ, which was treated during this period, the monitoring revealed a complete suppression of pest activity. These data prove that this biological method of pest control is an efficient, sustainable and non-toxic option to manage the common furniture beetle.     

The optimum dietary methionine requirement of juvenile humpback grouper (Cromileptes altivelis): effects on growth,micromorphology, protein and lipid metabolism

An 8-week feeding trial was conducted to evaluate optimum dietary methionine (Met) requirement of juvenile humpback grouper (Cromileptes altivelis) and the influence of dietary methionine (Met) supplementations on growth, gut micromorphology, protein and lipid metabolism. Seven isoproteic (48.91%) and isolipidic diets (10%) were made to contain 0.70, 0.88, 1.04, 1.27 1.46, 1.61 and 1.76% of dry matter Met levels. Results showed that lower survival, weight gain (WG%), protein efficiency ratio (PER), protein productive value (PPV) but higher daily feed intake (DFI) and feed conversion ratio (FCR) were observed in the Met deficient groups (0.70 and 0.88%). Optimum dietary Met requirement for humpback grouper was found to be 1.07% through the straight-broken line analysis of WG% against Met. Fish fed Met deficient diets (0.70, 0.88%) exhibited lower mRNA levels of growth hormone (GH), growth hormone receptor (GHR), insulin-like growth factor-I (IGF-1), target of rapamycin (TOR) as well as S6 kinase 1 (S6K1) than other dietary groups. Whereas, expression of genes related to general control nonderepressible (GCN2) kinase i.e., GCN2 and C/EBPβ enhancer-binding protein β was upregulated in fish fed low Met diets (P < 0.05). The mRNA expression of hepatic fatty acid synthase (FAS) and sterol regulatory element-binding protein-1 (SREBP-1) were higher in fish fed 0.70 and 0.88% dietary Met group and the lipolytic genes, hepatic peroxisome proliferator-activated receptor α (PPARα) and carnitine palmitoyl transferase-1 (CPT-1) showed an opposite variation tendency as FAS or SREBP1. Generally, the optimum Met requirement for humpback grouper was predicted to be 1.07% of dry matter.