Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants.

High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). Based on this analysis, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nucleotide periodicity in the position of free 5' RNA ends and a bias toward the translational frame. By examining conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice, we found a predominance of 5' termini of RNA degradation intermediates that were separated by a length equal to a ribosome-protected mRNA fragment. Through the analysis of RNA degradome data, we discovered uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, our analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a noncleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.

Subcellular-Scale Drug Transport via Ultrasound-Degradable Mesoporous Nanosilicon to Bypass Cancer Drug Resistance.

Delivering and releasing anticancer agents directly to their subcellular targets of action in a controlled manner are almost the ultimate goal of pharmacology, but it is challenging. In recent decades, plenty of efforts have been made to send drugs to tumor tissue or even specifically to cancer cells; however, at the subcellular scale, cancer cells have multiple cunning ways to hinder drugs from reaching their final action targets. Here, we demonstrate a strategy to bypass the last defense of cancer drug resistance by contolling the drug transportation and release at subcellular scale. We developed a platform based on ultrasound-degradable mesoporous nanosilicon, which allows drug delivery towards, ultrasound controlled drug release into the cell nucleus. This strategy altered the drug distribution within cells and remarkably enhanced the drug accumulation ratio at the action target, i.e. nucleus. In vitro and in vivo studies proved that this strategy reduced the drug dosage by an order of magnitude, prolonged drug retention and amplified therapeutic efficacy in tumor-bearing mice. These results offer new insights into bypassing cancer drug resistance through transport and release drugs directly to their action targets in a controlled manner.

Black Tungsten Nitride as a Metallic Photocatalyst for Overall Water Splitting Operable at up to 765†nm.

Semiconductor photocatalysts are hardly employed for overall water splitting beyond 700 nm, which is due to both thermodynamic aspects and activation barriers. Metallic materials as photocatalysts are known to overcome this limitation through interband transitions for creating electron-hole pairs; however, the application of metallic photocatalysts for overall water splitting has never been fulfilled. Black tungsten nitride is now employed as a metallic photocatalyst for overall water splitting at wavelengths of up to 765 nm. Experimental and theoretical results together confirm that metallic properties play a substantial role in exhibiting photocatalytic activity under red-light irradiation for tungsten nitride. This work represents the first red-light responsive photocatalyst for overall water splitting, and may open a promising venue in searching of metallic materials as efficient photocatalysts for solar energy utilization.

Investigating the Effect of Tissue Size on Mycelial Growth of Seven Mushroom Species by Using a Novel Device for Precise Tissue Isolation.

Tissue isolation from mushrooms is frequently practiced by both researchers and growers to isolate new and improved strains. In the present study, we designed a simple and convenient device for precise tissue isolation and therefore investigated the effect of tissue size on mycelial growth of seven mushroom species. The developed device consists of a cutting needle and a transfer needle. The cutting needle was used to obtain circular tissue plugs having a height up to 3 mm and variable diameters (2-5 mm) from mushroom fruit bodies. The transfer needle was a stainless steel round rod (1.5 mm in diameter) with a blade-like end. It can be used for collecting mushroom tissue when the cutting needle fails to extract it. With the aid of these devices, precise tissue isolation was achieved. Plate cultures demonstrated that tissue size had little effect on mycelium extension for Lentinula edodes (the winter shiitake), Hypsizygus marmoreus, and Agrocybe aegerita, but influenced the aerobic mycelium density. For Pleurotus ostreatus, Pleurotus eryngii, and Volvariella volvacea, large tissue plugs produced faster mycelial growth and higher aerobic mycelium density compared with small ones. On the contrary, small plugs from the tissue of the flower shiitake and Agaricus bisporus favored mycelial growth. The present study revealed that the preferable tissue size for mycelial growth varies among mushroom species, and the developed device is expected to greatly facilitate the isolation of new and improved mushroom strains.

Orange Zinc Germanate with Metallic Ge-Ge Bonds as a Chromophore-Like Center for Visible-Light-Driven Water Splitting.

The efficiency of solar-energy-conversion devices depends on the absorption region and intensity of the photon collectors. Organic chromophores, which have been widely stabilized on inorganic semiconductors for light trapping, are limited by the interface between the chromophore and semiconductor. Herein we report a novel orange zinc germanate (Zn-Ge-O) with a chromophore-like structure, by which the absorption region can be dramatically expanded. Structural characterizations and theoretical calculations together reveal that the origin of visible-light response can be attributed to the unusual metallic Ge-Ge bonds which act in a similar way to organic chromophores. Benefiting from the enhanced light harvest, the orange Zn-Ge-O demonstrates superior capacity for solar-driven hydrogen production.

Inflammation and Connexin 43 profiles in the prefrontal cortex are relevant to stress susceptibility and resilience in mice.

Depression is a major chronic mental illness worldwide, characterized by anhedonia and pessimism. Exposed to the same stressful stimuli, some people behave normally, while others exhibit negative behaviors and psychology. The exact molecular mechanisms linking stress-induced depressive susceptibility and resilience remain unclear. Connexin 43 (Cx43) forms gap junction channels between the astrocytes, acting as a crucial role in the pathogenesis of depression. Cx43 dysfunction could lead to depressive behaviors, and depression down-regulates the expression of Cx43 in the prefrontal cortex (PFC). Besides, accumulating evidence indicates that inflammation is one of the most common pathological features of the central nervous system dysfunction. However, the roles of Cx43 and peripheral inflammation in stress-susceptible and stress-resilient individuals have rarely been investigated. Thus, animals were classified into the chronic unpredictable stress (CUS)-susceptible group and the CUS-resilient group based on the performance of behavioral tests following the CUS protocol in this study. The protein expression of Cx43 in the PFC, the Cx43 functional changes in the PFC, and the expression levels including interleukin (IL)-1ß, tumor necrosis factor-α, IL-6, IL-2, IL-10, and IL-18 in the peripheral serum were detected. Here, we found that stress exposure triggered a significant reduction in Cx43 protein expression in the CUS-susceptible mice but not in the CUS-resilient mice accompanied by various Cx43 phosphorylation expression and the changes of inflammatory signals. Stress resilience is associated with Cx43 in the PFC and fluctuation in inflammatory signaling, showing that therapeutic targeting of these pathways might promote stress resilience.

Complete genome sequence of "Candidatus Phytoplasma pruni" PR2021, an uncultivated bacterium associated with poinsettia (Euphorbia pulcherrima).

The complete genome sequence of "Candidatus Phytoplasma pruni" strain PR2021, which consists of one 705,138 bp circular chromosome and one 4,757 bp circular plasmid, is presented in this work. This bacterium is associated with poinsettia (Euphorbia pulcherrima) cultivar "Princettia Pink."

Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome.

The type VI secretion system (T6SS) is deployed by many proteobacteria to secrete effector proteins into bacterial competitors for competition or eukaryotic cells for pathogenesis. Agrobacteria, a group of soilborne phytopathogens causing crown gall disease on various plant species, deploy the T6SS to attack closely and distantly related bacterial species in vitro and in planta. Current evidence suggests that the T6SS is not essential for pathogenesis under direct inoculation, but it remains unknown whether the T6SS influences natural disease incidence or the microbial community within crown galls (i.e., the gallobiome). To address these two key questions, we established a soil inoculation method on wounded tomato seedlings that mimics natural infections and developed a bacterial 16S rRNA gene amplicon enrichment sequencing platform. By comparing the Agrobacterium wild-type strain C58 with two T6SS mutants, we demonstrate that the T6SS influences both disease occurrence and gallobiome composition. Based on multiple inoculation trials across seasons, all three strains induced tumors, but the mutants had significantly lower disease incidences. The season of inoculation played a more important role than the T6SS in shaping the gallobiome. The influence of the T6SS was evident in summer, during which two Sphingomonadaceae species and the family Burkholderiaceae were enriched in the gallobiome induced by the mutants. Further in vitro competition and colonization assays demonstrated the T6SS-mediated antagonism to a Sphingomonas sp. R1 strain isolated from tomato rhizosphere in this study. In conclusion, this work demonstrates that the Agrobacterium T6SS promotes tumorigenesis in infection processes and provides competitive advantages in gall-associated microbiota. IMPORTANCE The T6SS is widespread among proteobacteria and used for interbacterial competition by agrobacteria, which are soil inhabitants and opportunistic bacterial pathogens causing crown gall disease in a wide range of plants. Current evidence indicates that the T6SS is not required for gall formation when agrobacteria are inoculated directly on plant wounding sites. However, in natural settings, agrobacteria may need to compete with other bacteria in bulk soil to gain access to plant wounds and influence the microbial community inside crown galls. The role of the T6SS in these critical aspects of disease ecology have remained largely unknown. In this study, we successfully developed a soil inoculation method coupled with blocker-mediated enrichment of bacterial 16S rRNA gene amplicon sequencing, named SI-BBacSeq, to address these two important questions. We provided evidence that the T6SS promotes disease occurrence and influences crown gall microbiota composition by interbacterial competition.

Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq.

Ribosome profiling (Ribo-seq) measures ribosome density along messenger RNA (mRNA) transcripts and is used to estimate the "translational fitness" of a given mRNA in response to environmental or developmental cues with high resolution. Here, we describe a protocol for Ribo-seq in plants adapted for the model plant Arabidopsis thaliana. We describe steps for lysis and nucleolytic digestion and ribosome footprinting. We then detail library construction, sequencing, and data analysis.

Complete genome sequence of "Candidatus Phytoplasma cynodontis" GY2015, a plant pathogen associated with Bermuda grass white leaf disease in Taiwan.

The complete genome sequence of "Candidatus Phytoplasma cynodontis" strain GY2015, which consists of one 498,922-bp circular chromosome, is presented in this work. This uncultivated plant-pathogenic bacterium is associated with Bermuda grass white leaf disease in Taoyuan, Taiwan.

Ciliated Cells Express a Novel Pattern of Brain-Derived Neurotrophic Factor in Allergic Rhinitis.

Background: Mounting research indicates that brain-derived neurotrophic factor (BDNF), has great potential to increase neuro-hyperresponsiveness and airway resistance in airway allergic disease. The expression level of BDNF has been found to be notably elevated in lung/nasal lavage (NAL) fluid. However, the expression and position of BDNF in ciliated cells with allergic rhinitis remains unclear. Methods: Nasal mucosal cells were collected from patients with allergic rhinitis (AR) and mice which were performed under different allergen challenge time, then observed the expression and position of BDNF located in ciliated cells through the immunofluorescence staining. Nasal mucosa, serum and NAL fluid were collected also. The expression level of BDNF and IL-4/5/13 were detected by RT-PCR. The expressions of BDNF (in serum and NAL fluid), and total-IgE, ovalbumin sIgE (in serum) were detected by ELISA. Results: We found that MFI of BDNF in AR group's ciliated cells was obviously lower than that in the control group, and a negative correlation was discovered between MFI and VAS score. It can be roughly divided into 5 patterns according to its location in the cytoplasm of ciliated cells. In the mouse model, the expressions of BDNF in serum and NAL fluid increased temporarily after allergen stimulation. The MFI of BDNF in ciliated cells displayed an initial increase followed by a subsequent decrease. Conclusion: Our study shows for the first time that, the expression and localization of BNDF were observed in the human nasal ciliated epithelial cells of allergic rhinitis, and the expression of level was less than the control group under the persistent state of allergy. BDNF expression in ciliated cells was transient increased after allergen stimulation and decreased to normal level after 24h in mouse model of allergic rhinitis. This might be the possible source of the transient increase of BNDF in serum and NAL fluid.

ESE1/AGR2 axis antagonizes TGF-ß-induced epithelial-mesenchymal transition in low-grade pancreatic cancer.

Epithelium-specific ETS transcription factor 1 (ESE1) has been implicated in epithelial homeostasis, inflammation, as well as tumorigenesis, and cancer progression. However, numerous studies have reported contradictory roles-as an oncogene or a tumor suppressor of ESE1 in different cancers, and its function in the development and progression of pancreatic ductal adenocarcinoma (PDAC) has remained largely unexplored. Herein, we report that ESE1 was found upregulated in primary PDAC compared to normal pancreatic tissue, but high expression of ESE1 correlated to better relapse-free survival in patients with PDAC. Interestingly, ESE1 was found to exhibit dual roles in regulation of malignant properties of PDAC cells in that its overexpression promoted cell proliferation, whereas its downregulation enhanced epithelial-mesenchymal transition (EMT) phenotype. In the context of TGF-ß-induced EMT, ESE1 is markedly downregulated at post-transcriptional level, and reconstituted ESE1 expression partially reversed TGF-ß-induced EMT marker expression. Furthermore, we identify AGR2 as a novel transcriptional target of ESE1 that participates in TGF-ß-induced EMT in PDAC. Collectively, our findings reveal an ESE1/AGR2 axis that interacts with TGF-ß signaling to modulate EMT phenotype in PDAC.

Endoscopic nasal surgery for mucocele and pyogenic mucocele of turbinate: Three case reports.

BACKGROUND: Cases of turbinate mucocele or pyogenic mucocele are extremely rare. During nasal endoscopy, turbinate hypertrophy can be detected in patients with turbinate or pyogenic mucocele. However, in many instances, differentiating between turbinate hypertrophy and turbinate mucocele is difficult. Radiological examinations, such as computed tomography (CT) or magnetic resonance imaging (MRI), are essential for the accurate diagnosis of turbinate mucocele. Herein, we report three cases of mucocele or pyogenic mucocele of turbinate, including their clinical presentation, imaging findings, and treatments, to help rhinologists understand this condition better. CASE SUMMARY: Three cases of turbinate and pyogenic mucocele were encountered in our hospital. In all patients, nasal obstruction and headache were the most common symptoms, and physical examination revealed hypertrophic turbinates. On CT scan, mucocele appeared as non-enhancing, homogeneous, hypodense, well-defined, rounded, and expansile lesions. Meanwhile, MRI clearly illustrated the cystic nature of the lesion on T2 sequences. Two patients with inferior turbinate mucocele underwent mucocele lining removal, while the patient with pyogenic mucocele underwent endoscopic middle turbinate marsupialization. The patients were followed up on the first, third, sixth month, and 1 year after discharge, and no complaints of headache and nasal congestion were reported during this period. CONCLUSION: In conclusion, both CT and MRI are helpful in the diagnosis of turbinate or pyogenic mucocele. Additionally, endoscopic nasal surgery is considered to be the most effective treatment method.

Complete Genome Sequence of Xylella taiwanensis and Comparative Analysis of Virulence Gene Content With Xylella fastidiosa.

The bacterial genus Xylella contains plant pathogens that are major threats to agriculture in America and Europe. Although extensive research was conducted to characterize different subspecies of Xylella fastidiosa (Xf), comparative analysis at above-species levels was lacking due to the unavailability of appropriate data sets. Recently, a bacterium that causes pear leaf scorch (PLS) in Taiwan was described as the second Xylella species (i.e., Xylella taiwanensis; Xt). In this work, we report the complete genome sequence of Xt type strain PLS229T. The genome-scale phylogeny provided strong support that Xf subspecies pauca (Xfp) is the basal lineage of this species and Xylella was derived from the paraphyletic genus Xanthomonas. Quantification of genomic divergence indicated that different Xf subspecies share ∼87-95% of their chromosomal segments, while the two Xylella species share only ∼66-70%. Analysis of overall gene content suggested that Xt is most similar to Xf subspecies sandyi (Xfs). Based on the existing knowledge of Xf virulence genes, the homolog distribution among 28 Xylella representatives was examined. Among the 11 functional categories, those involved in secretion and metabolism are the most conserved ones with no copy number variation. In contrast, several genes related to adhesins, hydrolytic enzymes, and toxin-antitoxin systems are highly variable in their copy numbers. Those virulence genes with high levels of conservation or variation may be promising candidates for future studies. In summary, the new genome sequence and analysis reported in this work contributed to the study of several important pathogens in the family Xanthomonadaceae.

[Clinical observation of "experienced ten acupoints" for functional dyspepsia of liver stagnation and spleen deficiency].

OBJECTIVE: To verify the clinical effect of acupuncture at "experienced ten acupoints" for functional dyspepsia (FD) of liver stagnation and spleen deficiency. METHODS: A total of 96 patients with FD of liver stagnation and spleen deficiency were randomly divided into an observation group and a control group, 48 cases in each group. In the observation group, "experienced ten acupoint" prescription was applied，acupoints included Shangwan (CV 13), Zhongwan (CV 12), Xiawan (CV 10), Qihai (CV 6), Tianshu (ST 25), Zusanli (ST 36) and Neiguan (PC 6). In the control group, irrelevant acupoint prescription was applied, acupoints included Feiyang (BL 58), Heding (EX-LE 2), Yingu (KI 10), Tianfu (LU 3), Xiabai (LU 4). The needles were retained for 30 min in both groups, 5 times a week for 2 weeks. Before and after treatment, the symptom score was compared in the two groups, and the clinical effect was evaluated. RESULTS: Compared before treatment, the symptom score after treatment was decreased in the observation group (P<0.05), and was lower than the control group (P<0.05). The total effective rate was 95.8% (46/48) in the observation group, which was higher than 33.3% (16/48) in the control group (P<0.05). CONCLUSION: Acupuncture at "experienced ten acupoints" can improve symptoms in patients with FD of liver stagnation and spleen deficiency, has the better clinical effect.

Using a single abdominal computed tomography image to differentiate five contrast-enhancement phases: A machine-learning algorithm for radiomics-based precision medicine.

PURPOSE: The clinical adoption of quantitative imaging biomarkers (radiomics) has established the need for high quality contrast-enhancement in medical images. We aimed to develop a machine-learning algorithm for Quality Control of Contrast-Enhancement on CT-scan (CECT-QC). METHOD: Multicenter data from four independent cohorts [A, B, C, D] of patients with measurable liver lesions were analyzed retrospectively (patients:time-points; 503:3397): [A] dynamic CTs from primary liver cancer (60:2359); [B] triphasic CTs from primary liver cancer (31:93); [C] triphasic CTs from hepatocellular carcinoma (121:363); [D] portal venous phase CTs of liver metastasis from colorectal cancer (291:582). Patients from cohort A were randomized to training-set (48:1884) and test-set (12:475). A random forest classifier was trained and tested to identify five contrast-enhancement phases. The input was the mean intensity of the abdominal aorta and the portal vein measured on a single abdominal CT scan image at a single time-point. The output to be predicted was: non-contrast [NCP], early-arterial [E-AP], optimal-arterial [O-AP], optimal-portal [O-PVP], and late-portal [L-PVP]. Clinical utility was assessed in cohorts B, C, and D. RESULTS: The CECT-QC algorithm showed performances of 98 %, 90 %, and 84 % for predicting NCP, O-AP, and O-PVP, respectively. O-PVP was reached in half of patients and was associated with a peak in liver malignancy density. Contrast-enhancement quality significantly influenced radiomics features deciphering the phenotype of liver neoplasms. CONCLUSIONS: A single CT-image can be used to differentiate five contrast-enhancement phases for radiomics-based precision medicine in the most common liver neoplasms occurring in patients with or without liver cirrhosis.

[Association of EGFR expression with angiogenesis and chemoresistance in ovarian carcinoma].

OBJECTIVE: To clarify the association of EGFR expression with angiogenesis and chemoresistance in ovarian cancer. METHODS: Immunohistochemical PV-6000 staining was used to detect the expression of EGFR, LRP protein and MVD in 102 ovarian tumor specimens. RESULTS: EGFR, LRP positive rates and MVD in borderline and malignant ovarian specimens were significantly higher than those in the normal and benign ones (P < 0.01). EGFR positive expression rate in stage III-IV carcinoma tissues, poor differentiation and with ascites was higher than that in stage I-II carcinomas of well differentiation and without ascites (P < 0.05). MVD was related to histological grade, residual tumor and ascites, LRP positive expression had no correlation with the clinicopathologic parameters (P > 0.05). The effective rate of chemotherapy in patients with EGFR and LRP-positive expression were 57.1% and 53.7%, respectively, significantly lower than that in cases with EGFR and LRP-negative expression (85.0% and 90.9%, P < 0.05). In the 64 cases with complete data, the three-year survival rate was 53.0%. The survival time was shorter in the cases with EGFR and LRP-positive expression, poor differentiation, ascites and chemoresistance (P < 0.01), and only LRP-positive expression and chemotherapeutic effect were independently related to survival time (P < 0.05). There was a correlation between EGFR and MVD (r = 0.548, P < 0.01), EGFR and LRP positive expression (P = 0.020). CONCLUSION: The expression of EGFR in ovarian cancer is related to angiogenesis and chemoresistance. EGFR and LRP-positive expression are related to chemoresistance, and detection of the two proteins may be helpful in guiding chemotherapy choice for ovarian cancer. LRP-positive expression and chemotherapeutic effect may be independent prognostic factors.

[A duplex nested PCR assay detecting of Vibrio cholerae and its application on environmental specimens].

OBJECTIVE: To establish a duplex nested PCR assay system which is capable for detecting O1 and O139 groups of Vibrio cholerae simultaneously, and is applicable to environmental specimens from routine cholera surveillance. METHODS: Based on nucleic acid sequences available in GenBank, six sets of primers were designed by PrimerSelect program of DNAStar, targeting the rfb gene that encodes the O antigens of O1 and O139 V. cholerae, respectively. The specificity of several primer combinations was tested. A duplex nested PCR assay system for simultaneously detecting O1 and O139 V. cholerae was established, subsequently, its sensitivity, specificity, reproducibility and field evaluation were tested. The sensitivity of this assay was evaluated by comparing detection limits of nested PCR and conventional PCR. Its reproducibility was tested by 32 positive samples (11 samples positive for O1, 21 samples positive for O139) from environmental surveillance. In addition, the selected amplicons from positive samples were sequenced and analyzed with relevant sequences. RESULTS: This newly-established duplex nested PCR assay might distinguish O1 V. cholerae from O139 V. cholerae, based on fragment lengths of amplicons, with reliable reproducibility, and no specific amplification was observed as compared with other vibrio species. The sensitivity of this nested PCR was (15 000) higher than conventional PCR, and there was no interference observed with multiple primers and complicated templates in the same vial. In its field evaluation, 32 positive DNA samples were detected and be further confirmed with double or triple tests, implying reliable reproducibility and consistency of this system. These results indicated that this assay had reliable reproducibility. No amplification was observed in all negative specimens and also suggested the acceptable specificity of this assay. Sequence analysis of the selected amplification products revealed 100% homogeneous with relevant genes from V.cholerae, indicating that these amplicons were originated from V. cholerae. CONCLUSION: This duplex nested PCR assay system should be rapid, sensitive and especially applicable to small laboratories, and be suitable for dynamic environmental surveillance.

[Quantitative retrieval of soil salinity using hyperspectral data in the region of inner Mongolia hetao irrigation district].

In the present paper, to investigate the spectral property of salinized soil and the relationship between the soil salinity and the hyperspectral data, the field soil samples were collected in the region of Hetao irrigation, Neimeng in the northwest China from the end of July to the beginning of August. The partial least squares regression (PLSR) model was established based on the statistical analysis of the soil ions and the reflectance of hyperspectra. The independent validation using data which are not included in the calibration model reveals that the proposed model can predicate the main soil components such as the content of total ions (S%), SO4(2+), PH and K+ + Na+ with higher determination coefficients (R2) Of 0.728, 0.801, 0.715 and 0.734 respectively. And the ratio of prediction to deviation (RPD) of the above predicted value is larger than 1.6, which indicates that the calibrated PLSR model can be used as a tool to retrieve soil salinity with accurate results. When the PLSR model's regression coefficients were aggregated according to the wavelength of visual (blue, green and red) and near infrared bands of LandSat Thematic Mapper(TM) sensor, some significant response values were observed, which indicates that the proposed method in this paper can be used to analyse the remotely sensed data from the space-boarded platform.

Differentiations in Gene Content and Expression Response to Virulence Induction Between Two Agrobacterium Strains.

Agrobacterium tumefaciens is important in biotechnology due to its ability to transform eukaryotic cells. Although the molecular mechanisms have been studied extensively, previous studies were focused on the model strain C58. Consequently, nearly all of the commonly used strains for biotechnology application were derived from C58 and share similar host ranges. To overcome this limitation, better understanding of the natural genetic variation could provide valuable insights. In this study, we conducted comparative analysis between C58 and 1D1609. These two strains belong to different genomospecies within the species complex and have distinct infectivity profiles. Genome comparisons revealed that each strain has >1,000 unique genes in addition to the 4,115 shared genes. Furthermore, the divergence in gene content and sequences vary among replicons. The circular chromosome is much more conserved compared to the linear chromosome. To identify the genes that may contribute to their differentiation in virulence, we compared the transcriptomes to screen for genes differentially expressed in response to the inducer acetosyringone. Based on the RNA-Seq results with three biological replicates, ∼100 differentially expressed genes were identified in each strain. Intriguingly, homologous genes with the same expression pattern account for <50% of these differentially expressed genes. This finding indicated that phenotypic variation may be partially explained by divergence in expression regulation. In summary, this study characterized the genomic and transcriptomic differences between two representative Agrobacterium strains. Moreover, the short list of differentially expressed genes are promising candidates for future characterization, which could improve our understanding of the genetic mechanisms for phenotypic divergence.