Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction

Polymerase Chain Reaction: A Toolbox for Molecular Discovery

Polymerase chain reaction (PCR), a revolutionary molecular tool, has transformed genetic studies by facilitating rapid DNA amplification. The PCR process relies on several key components: a DNA template or cDNA, two primers, Taq polymerase, nucleotides, and a buffer. These elements collectively facilitate the amplification process, which comprises three stages: denaturation, annealing, and extension. These stages are repeated in cycles to exponentially amplify the target DNA sequence. Furthermore, the power of PCR lies in its ability to generate exponential copies of target DNA in a remarkably short period. Moreover, various PCR techniques are available, encompassing traditional approaches like quantitative PCR, reverse transcription PCR, and nested PCR, as well as innovative methods such as extreme PCR, inverse PCR, and touchdown PCR. These techniques are extensively utilized in molecular, biological, and medical research laboratories for both research and diagnostic applications. This review explores a comprehensive overview of PCR, covering its history, underlying principles, and diverse applications in diagnostics, research, and drug development.

Combined transcriptome and whole genome sequencing analyses reveal candidate drug-resistance genes of Eimeria tenella

Avian coccidiosis is a widespread intestinal disease found in poultry that causes substantial economic losses. To extensively investigate the molecular mechanism of drug resistance in Eimeria tenella, we analyzed the sporozoites and second-generation merozoites of drug-sensitive (DS), diclazuril-resistant (DZR) strain, and salinomycin-resistant (SMR) strains of E. tenella through transcriptome sequencing. Whole genome sequencing analyses were performed on resistant strains at different concentrations-11 sensitive strains, 16 field diclazuril-resistant strains, and 15 field salinomycin-resistant strains of E. tenella. Co-analysis indicated that the ABC transporter protein showed differential expression and base mutations in the two resistant strains compared with the DS strain. KEGG pathway analysis demonstrated that the expression of pABAS and HPPK-DHPS, which are associated with the folate biosynthetic pathway, showed downregulation only in the DZR strain with respect to the DS strain. Several key enzymes in the glycolytic pathway were differentially expressed between DS and SMR strains.

Unveiling the wheat-rust battleground: A transcriptomic journey

The global wheat production faces significant challenges due to major rust-causing fungi, namely Puccinia striiformis f. sp. tritici, P. triticina, and P. graminis f. sp. tritici, responsible for stripe, leaf, and stem rust diseases, respectively. The evolutionary relationship between wheat (host) and Puccinia (pathogen) renders existing wheat resistance ineffective over time. The most viable solution to this issue lies in the development of new resistant wheat varieties. However, achieving this requires a comprehensive understanding of wheat's defense mechanisms against ever-evolving pathogens. Transcriptomics emerges as a powerful tool for analyzing gene activity at the molecular level. Over the last decade, this technique has transformed our comprehension of the wheat-rust interaction. Transcriptomics has unveiled a compelling "biphasic model" of gene expression in wheat infected with rust fungi, delineating two distinct phases of defense activation. Moreover, it has illuminated the intricate signaling pathways, hormonal interactions, and diverse defense mechanisms employed by wheat. These mechanisms encompass the oxidative burst, reinforcement of cell walls, and controlled cessation of photosynthesis, all aimed at combatting the invading pathogen. However, the utility of transcriptomics extends beyond elucidating defense strategies; it enables the identification of novel genes linked to resistance or susceptibility. By unraveling the functions of these genes, researchers can uncover new avenues for breeding resistant wheat varieties, arming wheat with the molecular arsenal necessary to prevail in the ongoing battle against rust fungi. This review represents a pioneering effort in exploring transcriptomic techniques and accumulated data to present a comprehensive overview of the wheat-Puccinia interaction at the system-wide level.

Supplementation of Saussurea costus root alleviates sodium nitrite-induced hepatorenal toxicity by modulating metabolic profile, inflammation, and apoptosis

Sodium nitrite (NaNO2) is a widely used food ingredient, although excessive concentrations can pose potential health risks. In the present study, we evaluated the deterioration effects of NaNO2 additives on hematology, metabolic profile, liver function, and kidney function of male Wistar rats. We further explored the therapeutic potential of supplementation with S. costus root ethanolic extract (SCREE) to improve NaNO2-induced hepatorenal toxicity. In this regard, 65 adult male rats were divided into eight groups; Group 1: control, Groups 2, 3, and 4 received SCREE in 200, 400, and 600 mg/kg body weight, respectively, Group 5: NaNO2 (6.5 mg/kg body weight), Groups 6, 7 and 8 received NaNO2 (6.5 mg/kg body weight) in combination with SCREE (200, 400, and 600 mg/kg body weight), respectively. Our results revealed that the NaNO2-treated group shows a significant change in deterioration in body and organ weights, hematological parameters, lipid profile, and hepatorenal dysfunction, as well as immunohistochemical and histopathological alterations. Furthermore, the NaNO2-treated group demonstrated a considerable increase in the expression of TNF-α cytokine and tumor suppressor gene P53 in the kidney and liver, while a significant reduction was detected in the anti-inflammatory cytokine IL-4 and the apoptosis suppressor gene BCL-2, compared to the control group. Interestingly, SCREE administration demonstrated the ability to significantly alleviate the toxic effects of NaNO2 and improve liver function in a dose-dependent manner, including hematological parameters, lipid profile, and modulation of histopathological architecture. Additionally, SCREE exhibited the ability to modulate the expression levels of inflammatory cytokines and apoptotic genes in the liver and kidney. The phytochemical analysis revealed a wide set of primary metabolites in SCREE, including phenolics, flavonoids, vitamins, alkaloids, saponins and tannins, while the untargeted UPLC/T-TOF-MS/MS analysis identified 183 metabolites in both positive and negative ionization modes. Together, our findings establish the potential of SCREE in mitigating the toxic effects of NaNO2 by modulating metabolic, inflammatory, and apoptosis. Together, this study underscores the promise of SCREE as a potential natural food detoxifying additive to counteract the harmful impacts of sodium nitrite.

Application of thermally treated sludge residues on an e-waste contaminated soil: effects on PTE bioavailability, soil physicochemical and biological properties, and L. perenne growth

In the context of sustainable development, potentially toxic element (PTE) contamination of soil and large-scale disposal of sludge are two major environmental issues that need to be addressed urgently. It is of great significance to develop efficient and green technologies to solve these problems simultaneously. This study investigated the effects of a 5% addition of thermally treated sludge residues (fermentation and pyrolysis residues) in synergy with L. perenne on soil organic matter, mineral nutrients, PTE speciation, and PTE uptake and transport by L. perenne in an e-waste-contaminated soil through pot experiments. The results showed that the thermally treated sludge residues significantly increased soil electrical conductivity, cation exchange capacity, organic matter, available phosphorus, and exchangeable potassium contents. New PTE-containing crystalline phases were detected, and dissolved humic substances were found. Sludge fermentation residue significantly increased dissolved organic matter content, whereas sludge pyrolysis residue showed no significant effect. The combination of thermally treated sludge residues and L. perenne increased the residual fractions of Cu, Zn, Pb, and Cd. The thermally treated sludge residues promoted L. perenne growth, increasing fresh weight, plant height, and phosphorus and potassium uptake. The uptake of Cu, Zn, Pb, and Cd by L. perenne was significantly reduced. This approach has the potential for applications in the ecological restoration of e-waste-contaminated soils.

Integrated biochemical and transcriptomic analysis reveals the effects of Burkholderia sp. SRB-1 on cadmium accumulating in Chrysopogon zizanioides L. under Cd stress

Application of plant growth-promoting rhizobacteria plays a vital role in enhancing phytoremediation efficiency. In this study, multiple approaches were employed to investigate the underlying mechanisms of Burkholderia sp. SRB-1 (SRB-1) on elevating Cd uptake and accumulation. Inoculation experiment indicated that SRB-1 could facilitate plant growth and Cd tolerance, as evidenced by the enhanced plant biomass and antioxidative enzymes activities. Cd content in plant shoots and roots increased about 36.56%-39.66% and 25.97%-130.47% assisted with SRB-1 when compared with control. Transcriptomics analysis revealed that SRB-1 upregulated expression of amiE, AAO1-2 and GA2-ox related to auxin and gibberellin biosynthesis in roots. Auxin and gibberellin, as hormone signals, regulated plant Cd tolerance and growth through activating hormone signal transduction pathways, which might also contribute to 67.94% increase of dry weight. The higher expression levels of ATP-binding cassette transporter subfamilies (ABCB, ABCC, ABCD and ABCG) in Chrysopogon zizanioides roots contributed to higher Cd uptake in Cd15 B (323.83 mg kg^-1) than Cd15 (136.28 mg kg^-1). Further, SRB-1 facilitated Cd migration from roots to shoots via upregulating the expression of Nramp, ZIP and HMA families. Our integrative analysis provided a molecular-scale perspective on Burkholderia sp. SRB-1 contributing to C. zizanioides performance.

Spatial Confinement of Single-Drop System to Enhance Aggregation-Induced Emission for Detection of MicroRNAs

Due to high incidence, poor prognosis, and easy transformation into pancreatic cancer (PC) with high mortality, early diagnosis and prevention of acute pancreatitis (AP) have become significant research focuses. In this work, we proposed a magnetic single-drop microextraction (SDME) system with spatial confinement to enhance the aggregation-induced emission (AIE) effect for simultaneous fluorescence detection of miRNA-155 (associated with AP) and miRNA-196a (associated with PC). The target miRNAs were selectively recognized by the hairpin probe and triggered the DNA amplification reaction; then, the DNA strands with two independent probes of G-quadruplex/TAIN and Cy5 were constructed on the surfaces of the magnetic beads. The SDME process, in which a drop containing the fluorescence probes was formed at the tip of the magnetic microextraction rod rapidly within 10 s, was performed by magnetic extraction. In this way, G-quadruplex/TAIN was enriched owing to the spatial confinement of the single-drop system, and the fluorescence signal given off (by G-quadruplex/TAIN) was highly enhanced (AIE effect). This was detected directly by fluorescence spectrophotometry. The approach achieved low limits of detection of 2.1 aM for miRNA-196a and 8.1 aM for miRNA-155 and wide linear ranges from 10 aM to 10 nM for miRNA-196a and from 25 aM to 10 nM for miRNA-155. This novel method was applied to the fluorescence detection of miRNAs in human serum samples. High relative recoveries from 95.6% to 104.8% were obtained.

Roles of Skeletal Muscle in Development: A Bioinformatics and Systems Biology Overview

The ability to assess various cellular events consequent to perturbations, such as genetic mutations, disease states and therapies, has been recently revolutionized by technological advances in multiple "omics" fields. The resulting deluge of information has enabled and necessitated the development of tools required to both process and interpret the data. While of tremendous value to basic researchers, the amount and complexity of the data has made it extremely difficult to manually draw inference and identify factors key to the study objectives. The challenges of data reduction and interpretation are being met by the development of increasingly complex tools that integrate disparate knowledge bases and synthesize coherent models based on current biological understanding. This chapter presents an example of how genomics data can be integrated with biological network analyses to gain further insight into the developmental consequences of genetic perturbations. State of the art methods for conducting similar studies are discussed along with modern methods used to analyze and interpret the data.

Optimized Method for the Identification of Candidate Genes and Molecular Maker Development Related to Drought Tolerance in Oil Palm (Elaeis guineensis Jacq.)

Drought is a major constraint in oil palm (Elaeis guineensis Jacq.) production. As oil palm breeding takes a long time, molecular markers of genes related to drought tolerance characteristics were developed for effective selection. Two methods of gene identification associated with drought, differential display reverse transcription polymerase chain reaction (DDRT-PCR) and pyrosequencing platform, were conducted before developing the EST-SSR marker. By DDRT-PCR, fourteen out of twenty-four primer combinations yielded the polymorphism in leaf as 77.66% and root as 96.09%, respectively. BLASTN and BLASTX revealed nucleotides from 8 out of 236 different banding similarities to genes associated with drought stress. Five out of eight genes gave a similarity with our pyrosequencing sequencing database. Furthermore, pyrosequencing analysis of two oil palm libraries, drought-tolerant, and drought sensitive, found 117 proteins associated with drought tolerance. Thirteen out of sixty EST-SSR primers could be distinguished in 119 oil palm parents in our breeding program. All of our found genes revealed an ability to develop as a molecular marker for drought tolerance. However, the function of the validated genes on drought response in oil palm must be evaluated.

Molecular Evaluation of the Impact of Nd:YAG Laser and Static Magnetic Field on Genomic DNA of Some Bacterial Isolates using RAPD-PCR

Antimicrobial therapy is frequently associated with the emergence of resistant bacteria with a high rate of morbidity and mortality worldwide. The present study was aimed at investigating the impact of a neodymium-doped yttrium aluminum (Nd:YAG) laser, and a static magnetic field (SMF) on cellular growth and DNA alteration in some clinical bacterial isolates. Samples from cutaneous wounds were collected by sterile cotton swabs from three elderly women admitted to Tikrit Teaching Hospital, Tikrit City, Iraq. Isolation and identification of Streptococcus agalactiae, Staphylococcus aureus, and Pseudomonas aeruginosa were carried out using cultural characteristics, microscopy, and biochemical tests. Three broth cultures were prepared for each of the test isolates. The first broth culture served as untreated control, the second was exposed to an Nd:YAG laser and the third was exposed to SMF. Colony counting was done on all the samples. DNA was extracted from the test bacteria and used to perform the RAPD-PCR assay. In contrast to the untreated control, the results showed that Nd:YAG laser radiation was more effective than SMF at inhibiting the cellular growth of the test isolates. Also, the radiation caused DNA alteration, which was established by decreased microbial growth, as well as the development of new bands and the loss of original bands. According to the findings of this study, the Nd:YAG laser is a promising technique for influencing the healing of infected cutaneous wounds. RAPD-PCR is also a useful biomarker assay for assessing the biological impact of laser radiation and SMF on bacteria.

Glyphosate-induced GhAG2 is involved in resistance to salt stress in cotton

KEY MESSAGE

The transcription of GhAG2 was strongly enhanced by glyphosate treatment. Overexpression of GhAG2 could improve plant tolerance to salt and salicylic acid stress. Although glyphosate has been widely used as an herbicide over the past decade owing to its high efficacy on weed controls and worldwide commercialization of glyphosate-resistant crops, little is known about the glyphosate-induced responses and transcriptional changes in cotton plants. Here, we report the identification of 26 differentially expressed genes after glyphosate treatment, among which, six highly up-regulated sequences share homology to cotton expressed sequence tags (ESTs) responsive to abiotic stresses. In addition, we cloned GhAG2, a gene whose transcription was strongly enhanced by glyphosate treatment and other abiotic stresses. Transgenic GhAG2 plants showed improved tolerance to salt, and salicylic acid (SA) stress. The results could open the door to exploring the function of the GhAG2 proteins, the glyphosate-induced transcriptional profiles, and the physiological biochemical responses in cotton and other crops. GhAG2 could also be used to improve salt stress tolerance through breeding and biotechnology in crops. Furthermore, these results could provide guidelines to develop a glyphosate-inducible system for controlled expression of targeted genes in plants.

Efficient gene editing through an intronic selection marker in cells

BACKGROUND

Gene editing technology has provided researchers with the ability to modify genome sequences in almost all eukaryotes. Gene-edited cell lines are being used with increasing frequency in both bench research and targeted therapy. However, despite the great importance and universality of gene editing, the efficiency of homology-directed DNA repair (HDR) is too low, and base editors (BEs) cannot accomplish desired indel editing tasks.

RESULTS AND DISCUSSION

Our group has improved HDR gene editing technology to indicate DNA variation with an independent selection marker using an HDR strategy, which we named Gene Editing through an Intronic Selection marker (GEIS). GEIS uses a simple process to avoid nonhomologous end joining (NHEJ)-mediated false-positive effects and achieves a DsRed positive rate as high as 87.5% after two rounds of fluorescence-activated cell sorter (FACS) selection without disturbing endogenous gene splicing and expression. We re-examined the correlation of the conversion tract and efficiency, and our data suggest that GEIS has the potential to edit approximately 97% of gene editing targets in human and mouse cells. The results of further comprehensive analysis suggest that the strategy may be useful for introducing multiple DNA variations in cells.

The transcriptomic revolution and radiation biology

PURPOSE

This article will briefly review the origins and evolution of functional genomics, first describing the experimental technology, and then some of the approaches applied to data analysis and visualization. It will emphasize application of functional genomics to radiation biology, using examples from the author's work to illustrate several key types of analysis. It concludes with a look at non-coding RNA, alternative reading of the genome, and single-cell transcriptomics, some of the innovative areas that may help to shape future research in radiation biology and oncology.

CONCLUSIONS

Transcriptomic approaches have provided insight into many areas of radiation biology and medicine, and innovations in technology and data analysis approaches promise continued contributions to radiation science in the future.

In Vitro Florigenesis with Special Reference to Orchids- A Review

BACKGROUND

Orchids are widely used in floriculture as attractive cut flowers all over the world. The current paper reviews factors affecting the in vitro flowering in orchid species.

METHODS

The phenomenon of in vitro flowering is advantageous as it shortens the breeding cycle, which is prolonged in the in vivo grown orchid species of commercial value. Certain genetic and biochemical mechanisms are involved at the time of onset of flowering in orchid plants. In the present endeavour, efforts have been made to initiate in vitro flowering in terrestrial and epiphytic orchid species. Various phenomenon involved during transition of vegetative shoot apex into floral axis is also reviewed.

RESULTS

In vitro flowering was induced in Dendrobium nobile and Zeuxine strateumatica in Mitra medium supplemented with BAP at 0.5 in mgl^-1.

CONCLUSION

In vitro flowering can be initiated by manipulating physical and chemical stimulus in the nutrient regime. The study would be helpful in better understanding the complex process of flowering in vitro as well as ex vitro.

Gene expression analysis of human prostate cell lines with and without tumor metastasis suppressor CD82

BACKGROUND

Tetraspanin CD82 is a tumor metastasis suppressor that is known to down regulate in various metastatic cancers. However, the exact mechanism by which CD82 prevents cancer metastasis is unclear. This study aims to identify genes that are regulated by CD82 in human prostate cell lines.

METHODS

We used whole human genome microarray to obtain gene expression profiles in a normal prostate epithelial cell line that expressed CD82 (PrEC-31) and a metastatic prostate cell line that does not express CD82 (PC3). Then, siRNA silencing was used to knock down CD82 expression in PrEC-31 while CD82 was re-expressed in PC3 to acquire differentially-expressed genes in the respective cell line.

RESULTS

Differentially-expressed genes with a P < 0.05 were identified in 3 data sets: PrEC-31 (+CD82) vs PrEC-31(-CD82), PC3-57 (+CD82) vs. PC3-5 V (-CD82), and PC3-29 (+CD82) vs. PC3-5 V (-CD82). Top 25 gene lists did not show overlap within the data sets, except (CALB1) the calcium binding protein calbindin 1 which was significantly up-regulated (2.8 log fold change) in PrEC-31 and PC3-29 cells that expressed CD82. Other most significantly up-regulated genes included serine peptidase inhibitor kazal type 1 (SPINK1) and polypeptide N-acetyl galactosaminyl transferase 14 (GALNT14) and most down-regulated genes included C-X-C motif chemokine ligand 14 (CXCL14), urotensin 2 (UTS2D), and fibroblast growth factor 13 (FGF13). Pathways related with cell proliferation and angiogenesis, migration and invasion, cell death, cell cycle, signal transduction, and metabolism were highly enriched in cells that lack CD82 expression. Expression of two mutually inclusive genes in top 100 gene lists of all data sets, runt-related transcription factor (RUNX3) and trefoil factor 3 (TFF3), could be validated with qRT-PCR.

CONCLUSION

Identification of genes and pathways regulated by CD82 in this study may provide additional insights into the role that CD82 plays in prostate tumor progression and metastasis, as well as identify potential targets for therapeutic intervention.

Differential Gene Expression Responding to Low Phosphate Stress in Leaves and Roots of Maize by cDNA-SRAP

Phosphate (Pi) deficiency in soil can have severe impacts on the growth, development, and production of maize worldwide. In this study, a cDNA-sequence-related amplified polymorphism (cDNA-SRAP) transcript profiling technique was used to evaluate the gene expression in leaves and roots of maize under Pi stress for seven days. A total of 2494 differentially expressed fragments (DEFs) were identified in response to Pi starvation with 1202 and 1292 DEFs in leaves and roots, respectively, using a total of 60 primer pairs in the cDNA-SRAP analysis. These DEFs were categorized into 13 differential gene expression patterns. Results of sequencing and functional analysis showed that 63 DEFs (33 in leaves and 30 in roots) were annotated to a total of 54 genes involved in diverse groups of biological pathways, including metabolism, photosynthesis, signal transduction, transcription, transport, cellular processes, genetic information, and organismal system. This study demonstrated that (1) the cDNA-SRAP transcriptomic profiling technique is a powerful method to analyze differential gene expression in maize showing advantageous features among several transcriptomic methods; (2) maize undergoes a complex adaptive process in response to low Pi stress; and (3) a total of seven differentially expressed genes were identified in response to low Pi stress in leaves or roots of maize and could be used in the genetic modification of maize.

Petal abscission in roses is associated with the activation of a truncated version of the animal PDCD4 homologue, RbPCD1

Abscission is a developmental process that leads to shedding of organs not needed by the plant. Apart from wall hydrolysis, the cells of the abscission zone (AZ) are also believed to undergo programmed cell death (PCD). We show that ethylene-induced petal abscission in Rosa bourboniana is accompanied with the activation of RbPCD1 (PROGRAMMED CELL DEATH LIKE 1) encoding a protein of 78 amino acids. Its expression increases during natural and ethylene-induced petal abscission. Its transcription in most tissues is up-regulated by ethylene. RbPCD1 shows similarity to the N-terminal domain of animal PDCD4 (PROGRAMMED CELL DEATH PROTEIN 4) proteins that are activated during apoptosis and function as transcriptional and translational repressors. RbPCD1 resides in the nucleus and cytoplasm and acts as a transcriptional repressor. Constitutive expression of RbPCD1 in transgenic Arabidopsis is seedling lethal. Heat-induced expression of RbPCD1 under the soybean heat-shock promoter affects leaf function, inflorescence development, silique formation, seed yield and reduces survival. Nuclear localization of RbPCD1 is necessary for manifestation of its effects. RbPCD1 may be necessary to mediate some of the ethylene-induced changes during abscission and senescence in specific tissues.

Two-factor ANOVA of SSH and RNA-seq analysis reveal development-associated Pi-starvation genes in oilseed rape

The 5-leaf-stage rape seedlings were more insensitive to Pi starvation than that of the 3-leaf-stage plants, which may be attributed to the higher expression levels of ethylene signaling and sugar-metabolism genes in more mature seedlings. Traditional suppression subtractive hybridization (SSH) and RNA-Seq usually screen out thousands of differentially expressed genes. However, identification of the most important regulators has not been performed to date. Here, we employed two methods, namely, a two-round SSH and two-factor transcriptome analysis derived from the two-factor ANOVA that is commonly used in the statistics, to identify development-associated inorganic phosphate (Pi) starvation-induced genes in Brassica napus. Several of these genes are related to ethylene signaling (such as EIN3, ACO3, ACS8, ERF1A, and ERF2) or sugar metabolism (such as ACC2, GH3, LHCB1.4, XTH4, and SUS2). Although sucrose and ethylene may counteract each other at the biosynthetic level, they may also work synergistically on Pi-starvation-induced gene expression (such as PT1, PT2, RNS1, ACP5, AT4, and IPS1) and root acid phosphatase activation. Furthermore, three new transcription factors that are responsive to Pi starvation were identified: the zinc-finger MYND domain-containing protein 15 (MYND), a Magonashi family protein (MAGO), and a B-box zinc-finger family salt-tolerance protein. This study indicates that the two methods are highly efficient for functional gene screening in non-model organisms.

Transcript profiling of chickpea pod wall revealed the expression of floral homeotic gene AGAMOUS-like X2 (CaAGLX2)

The differentially expressed genes in the chickpea pod wall have been identified for the first time using a forward suppression subtractive hybridization (SSH) library. In all, 226 clones of SSH library were sequenced and analyzed. A total of 179 high-quality expressed sequence tags (ESTs) were generated and based on the CAP3 assembly of these ESTs, 126 genes (97 singletons and 29 contigs) were computationally annotated. The mapping of 88.26% ESTs by gene ontology (GO) annotation distributed them into 751 GO terms of three categories, cellular location, molecular function, and biological process. The KEGG pathway analysis revealed 45 ESTs are involved in 49 different biological pathways. Also, 67 ESTs encodes four different classes of enzymes such as oxidoreductases (29), transferase (20), hydrolases (16) and isomerase (2). Six genes were selected and subjected to qPCR analysis, of these, two genes (FHG Floral homeotic AGAMOUS-like isoform X2, MADS1 MADS-box transcription factor) showed significant up-regulation in the pod wall compared to leaves. Surprisingly, one of the MADS1 box gene, FHG (CaAGLX2), responsible for flower development expressed in the pod wall. Therefore, understanding its specific role in the pod wall could be interesting. Thus, the transcript dynamics of the chickpea pod wall revealed differentially expressed genes in the pod wall, which may be participating in the metabolic build-up of both pod wall and seeds.

Surface Charge-Reversible Tubular Micromotors for Extraction of Nucleic Acids in Microsystems

Extraction of nucleic acids in microsystems is of significance for biomedical applications, but the current extraction methods generally require sophisticated microchannels and external equipment, hindering their practical applications. In this work, we have demonstrated a simple, versatile and efficient approach to extract nucleic acids in microsystems by developing cationic branched polyethyleneimine (PEI)-functionalized tubular micromotors. The as-developed tubular micromotors are fabricated by a two-step process combining the template-assisted electrodeposition and carbodiimide chemistry, and contain an inner catalytic Pt layer, a middle magnetic Ni layer and an outer cationic PEI layer. They exhibit autonomous bubble-propelled motion in aqueous hydrogen peroxide solutions, which can be guided by an external magnetic field, and the surface charges can be reversibly modulated by changing the pH value of the solution. Consequently, the as-developed tubular micromotors can selectively absorb nucleic acids from acidic solutions and desorb them into alkaline solutions, leading to the extraction of nucleic acids with high efficiency without external stirring. Furthermore, they can be operated in a microchannel chip without the aid of a pumping system. Our results indicate that this PEI-functionalized tubular micromotor platform provides a novel, simple and versatile microsystem nucleic acid extraction technology, holding considerable promise for important practical applications.

Identification of Differentially Expressed Genes of Rice Under Cadmium Stress Using DDRT-PCR Approach

Cadmium (Cd) is one of the hazardous environmental pollutants, and it can be harmful to human health through consumption of food-plants capable of bioaccumulating Cd. Therefore, lowering cadmium accumulation in plants is highly desirable. Here, a rice cultivar 'Qisanzhan' was studied using differential display reverse transcription-polymerase chain reaction (DDRT-PCR). Fifty-six differentially expressed genes were found in the root tips of 4-leaf stage rice seedlings exposed to 4 and 12 h of 50 µmol/L Cd(NO₃)₂ in a nutrient solution using DDRT-PCR. Further validation using semi-quantitative RT-PCR showed that the expression patterns of 16 genes were consistent with those found in DDRT-PCR. These genes encode receptor-like protein kinase, pleiotropic drug resistance protein, aquaporin protein, plasma membrane ATPase, etc. The differentially genes identified here can be used to obtain a better understanding of the molecular mechanisms of Cd absorption and accumulation in plants.

Functional diversifications of GhERF1 duplicate genes after the formation of allotetraploid cotton

Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood, both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors (GhERF1s), anchored on Chr-A07 and Chr-D07, were isolated from a high-yielding cotton hybrid (XZM2) and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress. Nucleotide sequence analysis of 524 diverse accessions, together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de- and neo-functionalization occurred in one of the duplicate genes, thus providing new genomic insight into the evolution of allotetraploid cotton species.

Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate

MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level via a complex regulatory network that requires genome-wide miRNA profiling to dissect. The patterns of miRNA expression at the genome scale are rich in diagnostic and prognostic information for human diseases such as cancers. This analysis, however, requires multi-step purification of RNAs from large quantities of cells, which is not only time consuming and costly but also challenging in situations where cell numbers are limited. In this study, we report direct capture, amplification, and library preparation of miRNAs from whole cell lysate without the need of pre-purification. As a result, it enables genome-wide miRNA profiling reproducibly with low quantity of cell samples (∼500 hematopoietic cells). Specifically, we conducted a systematic investigation of two key steps - cell lysis for miRNA release and 3' adaptor ligation required for direct miRNA capture and amplification. The obtained expression profile not only distinguishes cell types but also detects individual miRNA alterations in closely related isogenic cell lines. This approach, which is substantially simple as compared to the standard methods because of elimination of the need for RNA purification, is advantageous for the measurement of low quantity samples.

Improvement of Drought Tolerance in Rice (Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family

Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.

Intrinsic Survival Mechanisms for Retinal Ganglion Cells

Retinal ganglion cells (RGCs) undergo programmed cell death (apoptosis) after axonal injury. This cell death is mediated by several mechanisms, including deprivation of neurotrophic factors, alterations in gene expression, and production of reactive oxygen species. However, death of RGCs is delayed after axonal injury, and a significant number survive even after several days. This suggests that RGC death is not an immediate result of axonal injury, and that other pro-survival factors may play a role. While we and other researchers have focused on the mechanisms of cell death after axonal injury, it may be that determining the regulation of cell survival mechanisms may lead to innovative methods for neuroprotection. The final common pathway of glaucomatous optic neuropathy is RGC death, probably via damage to their axons occurring at or near the lamina cribrosa. Axonal injury leads directly (1) or indirectly (2) to the death of retinal ganglion cells. We and others have demonstrated that axotomy is associated with RGC apoptosis (3-7) as well as specific changes in expression of certain genes at the mRNA and protein level (8, 9). Reactive oxygen species may also be part of the pathway for RGC death (10, 11). We therefore hypothesize that axotomy leads to molecular events that are potentially destructive to RGCs, but also induces changes that are potentially protective against cellular injury. If this is the case, then RGC death from axonal injury would result not only from initiation of apoptosis, but also from failure of intrinsic neuroprotective mechanisms. It should therefore be theoretically possible to modulate these two classes of responses, and thus improve RGC cell survival after axotomy.

An ultrafast one-step assay for the visual detection of RNA virus

A one-step, rapid, and visual method was developed for the detection of RNA viruses and a few copies of the Zika RNA virus were directly detected within 25 min by naked-eye observation. This method will prove to be promising for point-of-care testing in out-of-lab and inconvenient settings.

Analysis of Reverse Transcribed mRNA Using PCR and Polyacrylamide Gel Electrophoresis

The patterns of gene expression in the fission yeast Schizosaccharomyces pombe under various experimental conditions form the basis of any transcriptomic study. We describe a method involving reverse transcription of the mRNA, Polymerase Chain Reaction (PCR), and the subsequent separation of the products onto Urea-Polyacrylamide gel that can be used to study the gene expression patterns in the fission yeast. The method described is cost effective and reproducible with satisfactory resolution of expressed transcripts in the gel. The method has the following essential steps: total RNA isolation and purification, cDNA synthesis from mRNAs, PCR amplification of cDNAs, visualization of PCR products, re-amplification and cloning of the differentially expressed PCR products, sequencing the confirmed clones, and finally cDNA library screening to isolate the genes of interest. The technique is also popularly known as Differential Display Reverse Transcription (DDRT-PCR). After its invention in 1992, a number of modifications have been introduced to optimize the technique and specifically to reduce the major problem of "false positives." Since understanding of specific gene expression patterns that regulate developmental and stress responses is a major concern of biology, DDRT-PCR has become a very popular molecular technique during the past two decades.

The interactive effects of diclofop-methyl and silver nanoparticles on Arabidopsis thaliana: Growth, photosynthesis and antioxidant system

Diclofop-methyl (DM), a common post-emergence herbicide, is frequently used in agricultural production. Silver nanoparticles (AgNPs) are one of the most widely used nanoparticles, and as such, have been detected and monitored in several environmental systems. Here we investigated the interactive effects of DM and AgNPs on the physiological morphology, photosynthesis and antioxidant system of Arabidopsis thaliana. Our results demonstrated that a 1.0 mg/L DM treatment had no significant effect on the fresh weight of plant shoots and the content of total chlorophyll and anthocyanin. However, a 0.5 mg/L AgNPs treatment was found to significantly inhibit plant growth and chlorophyll synthesis, and was found to cause more severe oxidative damage in plants compared to the effects observed in a hydroponic suspension in which DM and AgNPs were jointly present. Meanwhile, the relative transcript levels of photosynthesis related genes (psbA, rbcL, pgrl1A and pgrl1B) in the combined group were found to be slightly increased compared to transcript levels in the AgNPs group, in order to maintain ATP generation at relatively normal levels in order to repair light damage. One explanation for these observed antagonistic effects was that the existence of DM affects the stability of AgNPs and reduced Ag⁺ release from AgNPs in the mixed solution. Thereupon, the Ag⁺-content was found to decrease in shoots and roots in the combined group by 15.2% and 9.4% respectively, compared to the AgNPs group. The coexistence of herbicides and nanomaterials in aquatic environments or soil systems will continue to exist due to their wide usages. Our current study highlights that the antagonistic effects between DM and AgNPs exerted a positive impact on A. thaliana growth.

From Classical Toxicology to Tox21: Some Critical Conceptual and Technological Advances in the Molecular Understanding of the Toxic Response Beginning From the Last Quarter of the 20th Century

Toxicology has made steady advances over the last 60+ years in understanding the mechanisms of toxicity at an increasingly finer level of cellular organization. Traditionally, toxicological studies have used animal models. However, the general adoption of the principles of 3R (Replace, Reduce, Refine) provided the impetus for the development of in vitro models in toxicity testing. The present commentary is an attempt to briefly discuss the transformation in toxicology that began around 1980. Many genes important in cellular protection and metabolism of toxicants were cloned and characterized in the 80s, and gene expression studies became feasible, too. The development of transgenic and knockout mice provided valuable animal models to investigate the role of specific genes in producing toxic effects of chemicals or protecting the organism from the toxic effects of chemicals. Further developments in toxicology came from the incorporation of the tools of "omics" (genomics, proteomics, metabolomics, interactomics), epigenetics, systems biology, computational biology, and in vitro biology. Collectively, the advances in toxicology made during the last 30-40 years are expected to provide more innovative and efficient approaches to risk assessment. A goal of experimental toxicology going forward is to reduce animal use and yet be able to conduct appropriate risk assessments and make sound regulatory decisions using alternative methods of toxicity testing. In that respect, Tox21 has provided a big picture framework for the future. Currently, regulatory decisions involving drugs, biologics, food additives, and similar compounds still utilize data from animal testing and human clinical trials. In contrast, the prioritization of environmental chemicals for further study can be made using in vitro screening and computational tools.

Differential gene expression analysis in ageing muscle and drug discovery perspectives

Identifying therapeutic target genes represents the key step in functional genomics-based therapies. Within this context, the disease heterogeneity, the exogenous factors and the complexity of genomic structure and function represent important challenges. The functional genomics aims to overcome such obstacles via identifying the gene functions and therefore highlight disease-causing genes as therapeutic targets. Genomic technologies promise to reshape the research on ageing muscle, exercise response and drug discovery. Herein, we describe the functional genomics strategies, mainly differential gene expression methods microarray, serial analysis of gene expression (SAGE), massively parallel signature sequence (MPSS), RNA sequencing (RNA seq), representational difference analysis (RDA), and suppression subtractive hybridization (SSH). Furthermore, we review these illustrative approaches that have been used to discover new therapeutic targets for some complex diseases along with the application of these tools to study the modulation of the skeletal muscle transcriptome.

Quantum dots for a high-throughput Pfu polymerase based multi-round polymerase chain reaction (PCR)

We developed a Pfu polymerase based multi-round PCR technique assisted by quantum dots (QDs).

Identification and Characterization of the Diverse Stress-Responsive R2R3-RMYB Transcription Factor from Hibiscus sabdariffa L

Various regulatory proteins play a fundamental role to manage the healthy plant growth under stress conditions. Differential display reverse transcriptase PCR and random amplification of cDNA ends (RACE) was used to explore the osmotic stress-responsive transcripts. We identified and characterized the salt stress-responsive R2R3 type RMYB transcription factor from Hibiscus sabdariffa which has an open reading frame of 690 bp, encoding 229 long chain amino acids. In silico analysis confirmed the conserved R2 and R3 domain as well as an NLS-1 localization site. The deduced amino acids of RMYB shared 83, 81, 80, 79, 72, 71, and 66% homology with Arabidopsis thaliana, Glycine max, Oryza sativa, Zea maize, Malus domestica, Populus tremula × Populus alba, and Medicago sativa specific MYB family, respectively. We observed the gene upregulation in stem, leaf, and root tissue in response to abiotic stress. Furthermore, RMYB gene was cloned into plant expression vector under CaMV35S promoter and transformed to Gossypium hirsutum: a local cotton cultivar. Overexpression of RMYB was observed in transgenic plants under abiotic stresses which further suggests its regulatory role in response to stressful conditions. The RMYB transcription factor-overexpressing in transgenic cotton plants may be used as potential agent for the development of stress tolerant crop cultivars.

Introduction: How We Encountered TCTP and Our Purpose in Studying It

In this brief introduction, we describe our encounter with TCTP. Back in 2000, we discovered TCTP in two quite different ways: first, we looked at protein partners of TSAP6 and one of them was TCTP. Then, in collaboration with Sidney Brenner, we performed a high-throughput differential screening comparing the parental cancer cells with revertants. The results indicated that TCTP was of the most differentially expressed genes. These two approaches were carried out only months apart. They guided our research and led to the discoveries of drugs that inhibit the function of TCTP. Much of the preclinical data on sertraline as an inhibitor of TCTP in cancer were obtained with Judith Karp at Johns Hopkins. This drug is now given in combination with Ara-C to patients in a phase I clinical trial for Acute Myeloid Leukemia. We will here detail how all this happened in our lab while working around one central project: tumor reversion.

Role of TCTP for Cellular Differentiation and Cancer Therapy

The translationally controlled tumor protein (TCTP) is a highly conserved protein that is regulated due to a high number of extracellular stimuli. TCTP has an important role for cell cycle and normal development. On the other side, tumor reversion and malignant transformation have been associated with TCTP. TCTP has been found among the 12 genes that are differentially expressed during mouse oocyte maturation, and an overexpression of this gene was reported in a wide variety of different cancer types. Its antiapoptotic effect is indicated by the interaction with several proapoptotic proteins of the Bcl-2 family and the p53 tumor suppressor protein. In this article, we draw attention to the role of TCTP in cancer, especially, focusing on cell differentiation and tumor reversion, a biological process by which highly tumorigenic cells lose their malignant phenotype. This protein has been shown to be the most strongly downregulated protein in revertant cells compared to the parental cancer cells. Decreased expression of TCTP results either in the reprogramming of cancer cells into reversion or apoptosis. As conventional chemotherapy is frequently associated with the development of drug resistance and high toxicity, the urge for the development of new or additional scientific approaches falls into place. Differentiation therapy aims at reinducing differentiation backward to the nonmalignant cellular state. Here, different approaches have been reported such as the induction of retinoid pathways and the use of histone deacetylase inhibitors. Also, PPARγ agonists and the activation of the vitamin D receptor have been reported as potential targets in differentiation therapy. As TCTP is known as the histamine-releasing factor, antihistaminic drugs have been shown to target this protein. Antihistaminic compounds, hydroxyzine and promethazine, inhibited cell growth of cancer cells and decreased TCTP expression of breast cancer and leukemia cells. Recently, we found that two antihistaminics, levomepromazine and buclizine, inhibited cancer cell growth by direct binding to TCTP and induction of cell differentiation. These data confirmed that TCTP is an exquisite target for anticancer differentiation therapy and antihistaminics have potential to be lead compounds for the direct interaction with TCTP as new inhibitors of human TCTP and tumor growth.

Pulmonary TNFα is a critical mediator in Adult Respiratory Distress Syndrome

The development of effective pharmacotherapies to combat the Adult Respiratory Distress Syndrome (ARDS) is critically dependent upon: (1) the development of clinically-relevant animal models; (2) identification of inflammatory mediators centrally involved in eliciting lung injury; (3) understanding the inter-relationships or 'cross-talk' between pro and anti-inflammatory mediators which modulate the lung inflammation; and (4) the application of molecular techniques to isolate potentially novel genes involved in the development of ARDS. In this paper, we will present evidence from a rat model of microvascular lung injury produced by interleukin-2 (IL-2), that pulmonary TNFα is a primary and pivotal mediator of lung injury and that different modes of TNFα inhibition may represent feasible strategies to prevent ARDS. Furthermore, we will describe how the application of Differential Display Reverse Transcriptase Polymerase Chain Reaction (DDRT-PCR) can allow the rapid isolation of partial fragments of potentially new genes involved in ARDS. The products of such genes could represent future target sites for pharmacotherapeutic intervention.

Review : Single-Cell mRNA Amplification: Implications for Basic and Clinical Neuroscience

The application of molecular biological techniques to the study of single cells has provided a unique window for exploring the mechanisms that underlie integrated cellular function. Analysis of gene expression in indi vidual cells of the central nervous system is critical to understanding how distinct cell populations with differing chemical and anatomic phenotypes respond to pharmacological agents or are altered in disease states. Quantification of mRNA by single-cell analysis gives a high-resolution picture of changes in gene expression within individual cells, whereas more conventional types of mRNA analysis may obscure subtle changes in gene expression because of a lack of change in surrounding cells that are included in the mRNA sample. In addition, the sensitivity for detecting low levels of mRNA is enhanced when individual versus groups of cells are analyzed. With the advent of various mRNA amplification strategies, it is now possible to determine the mRNA composition or "expression profile" of individual cells. Information about relative levels of different mRNAs, the subcellular localization of mRNAs, and insight into cell-specific RNA splicing and RNA editing can be obtained. When these molecular data are combined with electrophysiological, morpho logical, immunohistochemical, and anatomical analyses, a detailed portrait of neuronal functioning can be obtained. Moreover, alterations in cellular functioning induced by physiological manipulation, drug adminis tration, or disease state can be monitored by combining these approaches. This precise cellular information may be useful in developing pharmaceuticals designed to alter mRNA levels or protein levels in a predictable manner (transcript-aided drug design) to elicit specific physiological states. The Neuroscientist 1:200-211, 1995

Gene Chips: Applications to Neuroscience

A convergence between molecular biological technique and the technology of miniaturization has produced the "gene chip" or microhybridization array. This device multiplies by several thousand fold the power of the northern blot for studying gene expression. Now, it is possible to survey simultaneously a large fraction of all genes in an experimental organism, and within a few years all of the approximately 140,000 human genes will be within reach of the technique. This capability is not only accelerating the rate of research into gene expression and function, it is changing the perspective of inquiry from single genes in isolation to networks of genes operating as a system. Many neurological diseases, from hydrocephalus to schizophrenia, have a genetic component, and individual responses to therapeutic drugs can vary with the genetic background of patients. In neurology and neurobiology, the ability to obtain "gene expression profiles" from nervous tissue promises to illuminate interactions between neuronal genes and the environment, development, disease, aging, and response to drugs and injury.

Identification of differentially expressed genes between high and low marbling score grades of the longissimus lumborum muscle in Hanwoo (Korean cattle)

We conducted DD-RT-PCR analysis to identify differentially expressed genes between high and low marbling score groups with extremely different IMF content of the longissimus lumborum muscles in Hanwoo. We detected 137 DEGs between two marbling score groups. Of these DEGs, 41 DEGs were highly expressed in the high marbling score group, whereas 96 DEGs showed a higher expression in the low marbling score group. Among them, we selected eight DEGs exhibiting the greatest differential expression levels between two marbling score groups. These genes could be classified as five candidate genes according to homology to known genes and biological functions. The expression of four DEGs except for ATP6 gene was confirmed by qRT-PCR. The TPI1 gene was significantly higher expressed at the high marbling group, whereas ACTA1, TNNT1 and MDH2 genes were significantly higher expressed at the low marbling group. Therefore, the TPI1 gene was up-regulated, suggesting that this gene may have an important function related to IMF deposition.

Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview

The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term “Next-Generation Sequencing (NGS)” with another less confusing synonym such as “RNA-seq”, “high throughput sequencing”, or “massively parallel sequencing” to avoid confusion with any future sequencing technologies.

60 YEARS OF POMC: N-terminal POMC peptides and adrenal growth

The peptide hormones contained within the sequence of proopiomelanocortin (POMC) have diverse roles ranging from pigmentation to regulation of adrenal function to control of our appetite. It is generally acknowledged to be the archetypal hormone precursor, and as its biology has been unravelled, so too have many of the basic principles of hormone biosynthesis and processing. This short review focuses on one group of its peptide products, namely, those derived from the N-terminal of POMC and their role in the regulation of adrenal growth. From a historical and a personal perspective, it describes how their role in regulating proliferation of the adrenal cortex was identified and also highlights the key questions that remain to be answered.

Use of Metatranscriptomics in Microbiome Research

The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes. As most commensal species are difficult or impossible to culture, genomic characterization of microbiome composition and function, under various environmental conditions, comprises a central tool in understanding its roles in health and disease. The first decade of microbiome research was mainly characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome sequencing, allowing for the elucidation of microbial composition and genome structure. Technological advances in RNA-seq have recently provided us with an ability to gain insight into the genes that are actively expressed in complex bacterial communities, enabling the elucidation of the functional changes that dictate the microbiome functions at given contexts, its interactions with the host, and functional alterations that accompany the conversion of a healthy microbiome toward a disease-driving configuration. Here, we highlight some of the key metatranscriptomics strategies that are implemented to determine microbiota gene expression and its regulation and discuss the advantages and potential challenges associated with these approaches.