RNA analysis has shown great value in forensic science, such as body fluids and tissue identification, postmortem interval estimation, biological age prediction, etc. Currently, most RNA follow-up experiments involve reverse transcription (RT) procedures. It has been shown that the RT step is variable and has a greater impact on subsequent data analysis, especially for forensic trace samples. However, the pattern of variation between different RNA template inputs and complementary DNA (cDNA) yield is unclear. In this study, a series of 2-fold gradient dilutions of RNA standards (1 μg/μL - 0.24 ng/μL) and forensic samples (including blood samples, saliva samples, bloodstains, and saliva stains) were reverse-transcribed using EasyQuick RT MasterMix. The obtained cDNA was quantified by droplet digital PCR (ddPCR) to assess the RT yield of the ACTB gene. The results showed that the 125 ng RNA template had the highest RT yield in a 10 μL RT reaction system with the selected kit. For all stain samples, the RT yield improved as the amount of RNA template input increased since RNA quantities were below 125 ng. As many commercialized reverse transcription kits using different kinds of enzymes are available for forensic RNA research, we recommend that systematic experiments should be performed in advance to determine the amount of RNA input at the optimum RT yield when using any kit for reverse transcription experiments.

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.

Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.

Pigment proteins play a vital role in the red colour change of the red swamp crayfish (Procambarus clarkii) shell after cooking. In this study, two red-change-related pigment proteins with molecular weights of approximately 170 and 43 kDa-denoted as F1 and F2, respectively-were purified by ammonium sulphate salting-out and size exclusion chromatography. F1 and F2 entirely comprised homomultimeric protein complexes composed of 21 kDa subunits. LC-MS/MS analysis showed that the 21 kDa protein subunit belonged to the crustacyanin family, named P. clarkii crustacyanin A2 (PcCRA2). The full-length cDNA of PcCRA2 was cloned, which encoded 190 amino acid residues and was highly homologous (91.58%) with Cherax quadricarinatus crustacyanin A. The predicted 3D structure showed that PcCRA2 had a β-barrel structure for pigment encapsulation. The colour change of F1 was first detected at 40 °C, and the red change occurred upon heating above 60 °C. Additionally, with increasing temperature, its β-sheet content increased, and its α-helix content reduced. Correlation analysis showed that the redness value of F1 was significantly related to the heating temperature and the β-sheet content.

It is of interest to document the insights gleaned from the cDNA and EST analysis of Antrodia cinnamomea (a fungal species). Hence a library of sequences was constructed and analysed using standard procedures to gain new insights. Therefore, 65 ESTs, with size ranging from 300-2000 bp, were constructed. This included 46 ESTs with definite annotation, 18 ESTs were hypothetical and 1 new protein derived from BLAST analysis. We assigned 227 Gene Ontology terms linked to cell composition, transport, catalytic activity, and regulation functions in these sequences. Moreover, 56 matching genes were found in 8 Kyoto Encyclopedia of Genes and Genomes pathways. Data also showed 271 SSRs from Antrodia cinnamomea ESTs with an occurrence frequency of 96.82%. The STRING data analysis showed 29 genes encoded enzymes highly involved in protein-to-protein interactions linked to expression of regulation function. Thus, we documented some insights from the cDNA and EST analysis of Antrodia cinnamomea for further data mining.

Gametocyte proteins of Eimeria spp. are essential components of the oocyst wall, and some of these proteins have been analysed to identify targets of transmission-blocking vaccines against avian coccidiosis. In the present study, a cDNA from E. necatrix gametocytes was cloned and sequenced. The cDNA is 1473 bp in length and encodes a 490-amino-acid protein containing a tyrosine-serine (Tyr/Ser)-rich domain and a proline-methionine (Pro/Met)-rich domain. A quantitative real-time PCR (qPCR) analysis showed that the cDNA is expressed only during gametogenesis. A fragment containing the Tyr/Ser-rich domain (rEnGAM59) was expressed in Escherichia coli BL21 (DE3) cells. Immunoblotting showed that rEnGAM59 was recognized by the serum of convalescent chickens after infection with E. necatrix, and that an anti-rEnGAM59 antibody recognized a ∼59 kDa protein and two other proteins (∼35 kDa and ∼33 kDa) in gametocyte extracts. An immunofluorescence assay showed that the anti-rEnGAM59 antibody recognized wall-forming bodies in the macrogametocytes and oocyst walls. An in vivo vaccination and challenge trial was conducted to test the potential utility of rEnGAM59 as a vaccine. Immunized chickens performed better than the unimmunized and challenged (positive control) chickens. The intestinal lesion scores were significantly lower in the immunized groups than in the positive control group (P < 0.05). In contrast, the body weight gains (BWG) were significantly higher in the immunized groups than in the positive control group (P < 0.05). There were no significant differences in the lesion scores and BWG between the groups immunized with rEnGAM59 protein or with live oocysts (P> 0.05). Chickens immunized with rEnGAM59 protein had a significantly higher antigen-specific serum IgY response (P < 0.05). rEnGAM59 protein can be used as candidate antigen to develop a recombinant coccidiosis vaccine.

Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.

Cardamonin, the chalcone class, is one of the natural components from the spicy herbaceous plant (Alpinia conchigera Griff) and has anticancer activities in many human cancer cell lines. There is, however, no information to show that cardamonin induces cell apoptosis and alters apoptosis associated gene expressions in mouse leukemia cells. Thus, we investigated the effects of cardamonin on the apoptotic cell death and associated gene expression in mouse leukemia WEHI-3 cells in vitro. Results indicated that cardamonin decreased total viable cell number via induced cell morphological changes and apoptotic cell death in WEHI-3 cells that were assay by contrast-phase microscopy and flow cytometry examinations, respectively. The flow cytometry assay indicated that cardamonin increased reactive oxygen species (ROS) and Ca 2+ production, decreased the levels of mitochondrial membrane potential ( ΔΨm) and increased caspase-3, -8 and -9 activities in WEHI-3 cells. Western blotting was performed to analyze expression of relevant pro- and anti-apoptotic proteins and results showed that cardamonin decreased anti-apoptotic protein of Bcl-2 but increased pro-apoptotic protein of Bax in WEHI-3 cells. Furthermore, cardamonin increased cytochrome c, AIF and Endo G release, increased GRP78, caspase-12 that were associated with ER stress and increased Fas, Fas-Ligand and FADD expression. Furthermore, cardamonin increased the gene expressions of DAP (death-associated protein), TMBIM4 transmembrane (BAX inhibitor motif containing 4), ATG5 (autophagy related 5) but decreased the gene expression of DDIT3 (DNA-damage inducible transcript 3), DDIT4 (DNA-damage-inducible transcript 4), BAG6 (BCL2-associated athanogene 6), BCL2L13 [BCL2-like 13 (apoptosis facilitator)] and BRAT1 (BRCA1-associated ATM activator 1) that are associated with apoptosis pathways. Based on those findings, we may suggest cardamonin induced apoptotic cell death through Fas and Fas-Ligand-, caspase- and mitochondria-dependently pathways and also affects the apoptotic gene expression in WEHI-3 cells in vitro.

Quercetin is one of the natural components from natural plant and it induces cell apoptosis in many human cancer cell lines. However, no available reports show that quercetin induces apoptosis and altered associated gene expressions in human gastric cancer cells, thus, we investigated the effect of quercetin on the apoptotic cell death and associated gene expression in human gastric cancer AGS cells. Results indicated that quercetin induced cell morphological changes and reduced total viability via apoptotic cell death in AGS cells. Furthermore, results from flow cytometric assay indicated that quercetin increased reactive oxygen species (ROS) production, decreased the levels of mitochondrial membrane potential (ΔΨm ), and increased the apoptotic cell number in AGS cells. Results from western blotting showed that quercetin decreased anti-apoptotic protein of Mcl-1, Bcl-2, and Bcl-x but increased pro-apoptotic protein of Bad, Bax, and Bid. Furthermore, quercetin increased the gene expressions of TNFRSF10D (Tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain), TP53INP1 (tumor protein p53 inducible nuclear protein 1), and JUNB (jun B proto-oncogene) but decreased the gene expression of VEGFB (vascular endothelial growth factor B), CDK10 (cyclin-dependent kinase 10), and KDELC2 (KDEL [Lys-Asp-Glu-Leu] containing 2) that are associated with apoptosis pathways. Thus, those findings may offer more information regarding the molecular, gene expression, and signaling pathway for quercetin induced apoptotic cell death in human gastric cancer cells.

Fertilizer applications have important effects on soil microbial abundance and community structure. In this study, total soil microbial DNA and RNA were directly extracted from paddy soils of N0 (control treatment, no nitrogen fertilizer), NPK (balanced fertilization), NPK+LS (balanced fertilization with additional 3.0 t·hm-2 rice straw incorporation) and NPK+HS (balanced fertilization with additional 6.0 t·hm-2 rice straw incorporation) treatments in a long-term fertilization experiment of double rice cropping system in Changsha County, Hunan Province. Soil bacteria community structures were evaluated by analyzing the 16S rRNA gene fragments at DNA and cDNA levels with Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR techniques. Balancing fertilization with chemical fertilizers and rice straw incorporation significantly changed the composition of bulk (DNA-based) and potentially active (mRNA-based) soil bacterial community as shown in T-RFLP profiles, and also reduced the bulk soil microbial diversity, but not the potentially active ones, as compared with the control treatment. The DNA-based abundance of 16S rRNA gene was on average 377 times as many as the m-RNA based population size. Compared to N0,balanced fertilization with rice straw incorporation (NPK+LS and NPK+HS) increased the bulk and active copy numbers of 16S rRNA gene, but not for balanced fertilization (NPK). The abundance and microbial community structure were not significantly different between the NPK+LS and NPK+HS treatments. Redundancy analysis (RDA) showed that soil ammonium was the key environmental factor determining the bulk and active soil microbial community structure among the treatments. In conclusion, the effect of fertilization on soil microbial abundance and community structure could be indicated at both DNA and cDNA levels; the cDNA information could better reflect the adaptability of bacterial community to the environmental stress.