The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut.

BACKGROUND: The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. RESULTS: The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. CONCLUSIONS: This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.

Astroglial Kir4.1 in the lateral habenula drives neuronal bursts in depression.

Enhanced bursting activity of neurons in the lateral habenula (LHb) is essential in driving depression-like behaviours, but the cause of this increase has been unknown. Here, using a high-throughput quantitative proteomic screen, we show that an astroglial potassium channel (Kir4.1) is upregulated in the LHb in rat models of depression. Kir4.1 in the LHb shows a distinct pattern of expression on astrocytic membrane processes that wrap tightly around the neuronal soma. Electrophysiology and modelling data show that the level of Kir4.1 on astrocytes tightly regulates the degree of membrane hyperpolarization and the amount of bursting activity of LHb neurons. Astrocyte-specific gain and loss of Kir4.1 in the LHb bidirectionally regulates neuronal bursting and depression-like symptoms. Together, these results show that a glia-neuron interaction at the perisomatic space of LHb is involved in setting the neuronal firing mode in models of a major psychiatric disease. Kir4.1 in the LHb might have potential as a target for treating clinical depression.

Single-Crystal Three-Dimensional Covalent Organic Framework Constructed from 6-Connected Triangular Prism Node.

The limited structural diversity of three-dimensional covalent organic frameworks (3D COFs) greatly restricts their application exploration. Therefore, there is an urgent need to expand their library of molecular building blocks, such as the development of highly connected (>4 reaction sites) polyhedral nodes. Herein, by precisely controlling the precursor conformation, we rationally designed a new 6-connected triangular prism node derived from the triphenylbenzene molecule and further used it to construct a novel 3D COF (3D-TMTAPB-COF) via imine condensation reaction. Surprisingly, without the addition of competing reagents, 3D-TMTAPB-COF crystallized directly into single crystals of ∼15 µm in size and was determined to adopt a rare 6-fold interpenetrated (Class IIIa interpenetration) acs topology. In addition, 3D-TMTAPB-COF showed a high SF6 adsorption capacity (60.9 cm3 g-1) and good SF6/N2 selectivity (335) at 298 K and 1 bar, superior to those of most crystalline porous materials. This work not only confirms the possibility of growing large-size single-crystal 3D COFs formed with strong covalent bonds by a solvothermal method in the absence of modulators, but also reports a novel triangular prism node for future construction of 3D COFs with interesting applications.

Taurine Alleviates Chronic Social Defeat Stress-Induced Depression by Protecting Cortical Neurons from Dendritic Spine Loss.

Abnormal amino acid metabolism in neural cells is involved in the occurrence and development of major depressive disorder. Taurine is an important amino acid required for brain development. Here, microdialysis combined with metabonomic analysis revealed that the level of taurine in the extracellular fluid of the cerebral medial prefrontal cortex (mPFC) was significantly reduced in mice with chronic social defeat stress (CSDS)-induced depression. Therefore, taurine supplementation may be usable an intervention for depression. We found that taurine supplementation effectively rescued immobility time during a tail suspension assay and improved social avoidance behaviors in CSDS mice. Moreover, taurine treatment protected CSDS mice from impairments in dendritic complexity, spine density, and the proportions of different types of spines. The expression of N-methyl D-aspartate receptor subunit 2A, an important synaptic receptor, was largely restored in the mPFC of these mice after taurine supplementation. These results demonstrated that taurine exerted an antidepressive effect by protecting cortical neurons from dendritic spine loss and synaptic protein deficits.

First report of Fusarium commune causing root rot of soybean seedlings in Indiana.

In the summer of 2020, 127 soybean [Glycine max (L.) Merr] seedlings (V1-V3 stage) with reduced growth vigor were sampled as part of a bulk collection of seedling pathogens from Purdue's Agronomy Center for Research and Education in West Lafayette, Indiana. After rinsing off soil, one plant displayed prominent necrotic lesions on both cotyledons and the hypocotyl and rot of the roots. Root tissue segments measuring roughly 5 mm in length and adjacent to lesions were excised and surface sterilized in 0.6% NaOCl for 10 min, then in 70% ethanol for 2 min, rinsed thrice in sterile distilled H2O, and plated on dichloran-chloramphenicol-peptone agar (Andrews and Pitt 1986). Single-spore cultures were produced and grown on potato dextrose agar. The isolate (AC101) developed white aerial mycelium, rings of magenta coloration in the media, and pale orange sporodochia with age. Microscopic observation of two-week-old cultures grown on synthetic low-nutrient agar (NRRL Medium No. 4) in the dark at 28°C revealed 2-3 septate falcate macroconidia measuring 17.1 - 43.9 × 2.8 - 3.5 µm (avg. 29.4 × 3.1 µm, n=20); 0-1 septate straight to slightly curved microconidia measuring 3.9 - 8.6 × 1.9 - 2.5 µm (avg. 7.0 × 2.2 µm, n=20); and round chlamydospores borne singly or doubly with diameter measuring 6.1 - 14.2 µm (avg. 8.9 µm, n=20). These characteristics were consistent with descriptions of Fusarium commune K. Skovg., O'Donnell & Nirenberg (Skovgaard et al. 2003). DNA was extracted from aerial mycelium and the internal transcribed spacer (ITS) region using ITS1/ITS4 primers (White et al. 1990) (GenBank accession MW463361), the mitochondrial small subunit (mtSSU) rDNA using MS1/MS2 primers (White et al. 1990) (MW466537), and the translation elongation factor 1-alpha (TEF1α) gene using 983F/1567R primers (Rehner and Buckley 2005) (MW475296) were amplified and sequenced. Blast searches in GenBank showed that these sequences had 100% identity with corresponding sequences of F. commune (ITS: MN452698; mtSSU: AF362277; and TEF1α: KU171720). The matching mtSSU sequence was an accession from the original species description (Skovgaard et al. 2003). A pathogenicity test was conducted under greenhouse conditions (20-29°C, avg. 24°C) following the infested soil protocol of Ellis et al. (2013a). Ten seeds (cv. Williams) each were used in inoculated and mock-inoculated control treatments with one seed per foam cup. Root rot symptoms similar to, but more destructive than those observed in the field, were observed 14 days after planting on all inoculated plants but not on controls. Inoculated plants reached VE stage compared to controls which reached VC. Disease symptoms included severe necrotic lesions on the cotyledons, dark brown rot of the developing tap root, and brown hypocotyl lesions similar to field symptoms. F. commune was successfully reisolated from inoculated plants, but not from controls, as described above. F. commune has been reported to cause soybean root rot in China (Chang et al. 2018), Korea (Choi et al. 2020), as well as Iowa (Ellis et al. 2013b). To our knowledge this is the first report of F. commune infecting soybean seedlings in the state of Indiana. The expanded distribution of this soybean pathogen warrants heightened attention for its control.

Astroglial N-myc downstream-regulated gene 2 protects the brain from cerebral edema induced by stroke.

Brain edema is a grave complication of brain ischemia and is the main cause of herniation and death. Although astrocytic swelling is the main contributor to cytotoxic edema, the molecular mechanism involved in this process remains elusive. N-myc downstream-regulated gene 2 (NDRG2), a well-studied tumor suppressor gene, is mainly expressed in astrocytes in mammalian brains. Here, we found that NDRG2 deficiency leads to worsened cerebral edema, imbalanced Na+ transfer, and astrocyte swelling after ischemia. We also found that NDRG2 deletion in astrocytes dramatically changed the expression and distribution of aquaporin-4 and Na+ -K+ -ATPase ß1, which are strongly associated with cell polarity, in the ischemic brain. Brain edema and astrocyte swelling were significantly alleviated by rescuing the expression of astrocytic Na+ -K+ -ATPase ß1 in NDRG2-knockout mouse brains. In addition, the upregulation of astrocytic NDRG2 by lentiviral constructs notably attenuated brain edema, astrocytic swelling, and blood-brain barrier destruction. Our results indicate a particular role of NDRG2 in maintaining astrocytic polarization to facilitate Na+ and water transfer balance and to protect the brain from ischemic edema. These findings provide insight into NDRG2 as a therapeutic target in cerebral edema.

Identification and molecular mapping of Rps14, a gene conferring broad-spectrum resistance to Phytophthora sojae in soybean.

KEY MESSAGE: A soybean landrace carries broad-spectrum resistance to Phytophthora sojae, which is conferred by a single gene, designated Rps14, on the short arm of chromosome 3. Phytophthora sojae is the causative agent for Phytophthora root and stem rot in soybean [Glycine max (L.) Merr.] and can be managed by deployment of resistance to P. sojae (Rps) genes. PI 340,029 is a soybean landrace carrying broad-spectrum resistance to the pathogen. Analysis of an F2 population derived from a cross between PI 340,029 and a susceptible cultivar 'Williams' reveals that the resistance to P. sojae race 1 is conferred by a single gene, designated Rps14, which was initially mapped to a 4.5-cM region on the short arm of chromosome 3 by bulked segregant analysis (BSA), and subsequently narrowed to a 1.48 cM region corresponding to 229-kb in the Williams 82 reference genome (Wm82 v2.a1), using F3:4 families derived from the F2 population. Further analysis indicates that the broad-spectrum resistance carried by PI 340,029 is fully attributable to Rps14. The genomic sequences corresponding to the defined Rps14 region from a set of diverse soybean varieties exhibit drastic NBS-LRR gene copy number variation, ranging from 3 to 17 copies. Ultimate isolation of Rps14 would be critical for precise selection and deployment of the gene for soybean protection.

First report of Fusarium fujikuroi causing root rot and seedling elongation of soybean in Indiana.

In summer 2020, 127 soybean (Glycine max (L.) Merr) seedlings (V1-V3 stage) showing reduced vigor or crown lesions were collected at Purdue's Agronomy Center for Research and Education in West Lafayette, Indiana. Root tissues from two seedlings with necrotic cotyledons and root rot were surface-sterilized and plated on dichloran-chloramphenicol-peptone agar (Andrews and Pitt 1986). Emerging hyphal tips were transferred to potato dextrose agar (PDA). Single-spore cultures were obtained and grown on PDA. Both isolates developed floccose white aerial mycelia with reddish-pink coloration in the media in 2 weeks on the benchtop. On carnation leaf agar, macroconidia formed on orange sporodochia within 2 weeks in darkness at 25C. Macroconidia were 3-5 septate, measuring 26 - 41 × 2.5 - 3.7 µm (avg. 34.8 × 3.2 µm, n=40). Microconidia were abundant in chains and false heads forming on both mono- and polyphialides, and measured 2.5 - 8.75 x 2.5 µm (avg. 5.9 × 2.5 µm, n=40). These characteristics were consistent with species descriptions of F. fujikuroi [Sawada] Wollenw. (teleomorph Gibberella fujikuroi) (Leslie and Summerell 2006). DNA was extracted from mycelium and the following genes were amplified and sequenced: the internal transcriber spacer (ITS) region using ITS1/ITS4 primers (White et al. 1990) (GenBank accessions MW463362/MW463363), the mitochondrial small subunit (mtSSU) rDNA using MS1/MS2 primers (White et al. 1990) (MW465310/MW465307), and the partial translation elongation factor 1-alpha (TEF1α) gene using 983F/1567R primers (Rehner and Buckley 205) (MW475297/MW475298). In GenBank BLAST searches, these sequences showed 100% identity to both F. proliferatum and F. fujikuroi. Species-specific forward primers Fuji1F and Proli1F were then used in combination with reverse primer TEF1R to amplify another region in the TEF1α gene (Amatulli et al. 2012). Proli1F/TEF1R primers failed under a variety of annealing temperatures while Fuji1F/TEF1R primers succeeded, and the products were sequenced (MW475299/MW475300). GenBank BLAST searches revealed 100% identity of both isolates to F. fujikuroi (MT448248.1). A pathogenicity test was conducted with isolate AC13 in the greenhouse following the protocol of (Ellis et al. 2013). Ten seeds (cv. Williams) each were used for inoculation and control, respectively, with one seed per cup. Root rot symptoms similar to those observed in the field were observed 14 days after planting on all inoculated plants but not on controls (VC stage). Infected plants showed symptoms of pre-emergence damping off, reddish-brown lesions on the tap and lateral roots, and root necrosis. Three plants also exhibited hyper-elongation of the stem (12.5, 11.1, and 18 cm, vs controls: avg. 6.8 cm, max. 8.5 cm, stdev 0.78 cm). F. fujikuroi was successfully reisolated from inoculated plants but not from controls and identified as described above. F. fujikuroi has been reported causing soybean root rot in China (Zhao et al. 2020), Korea (Choi et al. 2019), and the state of Kansas (Pedrozo et al. 2015). To our knowledge this is the first report of F. fujikuroi infecting soybeans in the state of Indiana. F. fujikuroi is known to cause elongated seedlings in rice (Leslie and Summerell 2006). Pedrozo et al. (2015) reported that F. fujikuroi isolated from soybean caused seedling elongation in rice but not in soybean. The increased distribution and new host symptomology observed here warrants heightened attention for the control of this pathogen.

First report of Mycoleptodiscus terrestris causing root rot of soybean in Indiana.

During the summers in 2019 and 2020, 137 soybean (Glycine max (L.) Merr) seedlings (V1-V3 stage) showing stunting, delayed emergence, and/or crown lesions were collected at Purdue's Agronomy Center for Research and Education in West Lafayette, Indiana. Four seedlings were stunted with reddish-brown girdled lesions along the hypocotyl and crown, rotted tap and lateral roots, and brown discoloration of the cortex and vascular tissues. Four fungal isolates (AC4, AC58, AC96, and AC127) were recovered by plating surface-sterilized symptomatic root tissue onto water agar plates and incubating on the benchtop until mycelia emerged. The growing hyphal tips were transferred to the semi-selective medium DCPA (Andrews and Pitt 1986). On potato dextrose agar, the fungal colonies developed olivaceous green mycelia which melanized into a mat of black microsclerotia with time and no conidia were observed. On 1.5% water agar plates amended with twice autoclaved soybean leaf and root tissue collected from flowering soybean plants, conidia were formed in sporodochia in darkness at 28 οC within one week. Conidia were 1-2 septate, cylindrical with two setae on either end, and measured 20.8 to 26.4 x 4 to 5.6 µm (average 23.9 x 4.7 µm, n=20). The morphological characters matched with the description of Mycoleptodiscus terrestris (Gerd.) Ostaz (Gerdemann 1953). Species identification was further confirmed by sequencing the internal transcribed spacers (ITS) region of rDNA amplified by ITS1 and ITS4 primers (White et al. 1990) and the translation elongation factor 1 alpha (TEF1-α) gene using 983F and 1567R primers with annealing temperature at 53 ○C (Rehner and Buckley 2005). The sequences were deposited in GenBank under the following accession numbers: ITS: MW002684, MT998441, MW010258, and MW010260; and TEF1-α: MW015941-MW015944. The GenBank BLAST searches revealed 100% identity in the ITS region (accession NR_145373.1) and 99.75% identity in the TEF1-α region (MK495977.1) to M. terrestris. Pathogenicity test was conducted on soybean seedlings (cv. Williams) at V1 growth stage using a root dip assay. Isolate AC58 was grown in a modified cotton seed meal broth (CSMB) to produce microsclerotia as inoculum (Gray 1978; Shearer and Jackson 2006). Microsclerotia concentration was measured using a hemocytometer and adjusted to 1.5 x 104 per ml. Five soybean seedlings each were dipped into inoculum or sterile CSMB for 30 minutes then planted individually in vermiculite-filled Styrofoam cups placed on flooded trays in 16-hr photoperiod light racks at room temperature. Seven days after inoculation, all inoculated plants were visibly stunted with root and crown symptoms identical to field symptoms while all controls were healthy. M. terrestris was successfully re-isolated from inoculated plants, but not from the controls, and identified by morphology and sequencing as above. M. terrestris has been previously reported causing root rot of soybean in Illinois (Gray 1978) and Wisconsin (Smith et al. 1998). To our knowledge, this is the first report of M. terrestris infecting soybean in Indiana. Increased geographic distribution of this pathogen warrants more attention for its control. M. terrestris has been proposed as a biological control agent against multiple aquatic weeds (Verma and Charudattan 1993; Shearer and Jackson 2006). Introduction of this fungus into soybean production regions should be avoided.

Phytophthora infestans RNA virus 2, a novel RNA virus from Phytophthora infestans, does not belong to any known virus group.

Phytophthora infestans is the causal agent of potato and tomato late blight. In this study, we obtained the complete genome sequence of a novel RNA virus from this plant pathogen, tentatively named "Phytophthora infestans RNA virus 2" (PiRV-2). The PiRV-2 genome is 11,170 nt in length and lacks a polyA tail. It contains a single large open reading frame (ORF) with short 5' and 3' untranslated regions. The ORF is predicted to encode a polyprotein of 3710 aa (calculated molecular weight, 410.94 kDa). This virus lacks significant similarity to any other known viruses, even in the conserved RNA-dependent RNA polymerase region. Phylogenetic analysis demonstrated that it did not cluster with any known virus group. We conclude that PiRV-2 belongs to a new virus family yet to be described. This virus was found to be faithfully transmitted through asexual reproduction.

Chronic Inflammatory Pain Impairs mGluR5-Mediated Depolarization-Induced Suppression of Excitation in the Anterior Cingulate Cortex.

The anterior cingulate cortex (ACC) is a critical hub for nociceptive perception and pain-related anxiety. Long-term synaptic plasticity in ACC was found to be important for chronic inflammatory pain and pain-related anxiety. As short-term synaptic plasticity, depolarization-induced suppression of excitation (DSE) is involved in several conditions, such as chronic stress, epilepsy, and autism. However, it is still unknown whether DSE in the ACC is involved in the central sensitization of pain and anxiety. Using a whole-cell patch clamp, calcium imaging, western blot, and behavioral testing, we found that DSE was induced by a 2 s depolarization in postsynaptic pyramidal cells in ACC. DSE was mediated by endocannabinoid signaling and modulated by metabotropic glutamate receptor 5 (mGluR5). DSE was impaired by decreasing expression and dysfunction of mGluR5 in a mouse model of inflammatory pain induced by complete Freund's adjuvant. CDPPB, an mGluR5-positive allosteric modulator, could rescue hypersensitivity and anxiety-like behavior in this pain model. Our results demonstrated that mGluR5-mediated short-term plasticity in ACC may be a critical mechanism for chronic pain, and mGluR5 may potentially serve as a target of pain therapy, including treatments for hyperalgesia and anxiety.

Chronic inflammatory pain decreases the glutamate vesicles in presynaptic terminals of the nucleus accumbens.

Reward system has been proved to be important to nociceptive behavior, and the nucleus accumbens (NAc) is a key node in reward circuitry. It has been further revealed that dopamine system modulates the NAc to influence the pain sensation, whereas the role of glutamatergic projection in the NAc in the modulation of chronic pain is still elusive. In this study, we used a complete Freund's adjuvant-induced chronic inflammatory pain model to explore the changes of the glutamatergic terminals in the NAc, and we found that following the chronic inflammation, the protein level of vesicular glutamate transporter1 (VGLUT1) was significantly decreased in the NAc. Immunofluorescence staining further showed a reduced expression of VGLUT1-positive terminals in the dopamine receptor 2 (D2R) spiny projection neurons of NAc after chronic inflammatory pain. Furthermore, using a whole-cell recording in double transgenic mice, in which dopamine receptor 1- and D2R-expressing neurons can be visualized, we found that the frequency of spontaneous excitatory postsynaptic currents was significantly decreased and paired-pulse ratio of evoked excitatory postsynaptic currents was increased in D2R neurons, but not in dopamine receptor 1 neurons in NAc of complete Freund's adjuvant group. Moreover, the abnormal expression of soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex contributed to the reduced formation of glutamate vesicles. Hence, our results demonstrated that decreased glutamate release in the indirect pathway of the NAc may be a critical mechanism for chronic pain and provided a novel evidence for the presynaptic mechanisms in chronic pain regulation.

Association of Circulating Transfer RNA fragments with antibody response to Mycoplasma bovis in beef cattle.

BACKGROUND: High throughput sequencing allows identification of small non-coding RNAs. Transfer RNA Fragments are a class of small non-coding RNAs, and have been identified as being involved in inhibition of gene expression. Given their role, it is possible they may be involved in mediating the infection-induced defense response in the host. Therefore, the objective of this study was to identify 5' transfer RNA fragments (tRF5s) associated with a serum antibody response to M. bovis in beef cattle. RESULTS: The tRF5s encoding alanine, glutamic acid, glycine, lysine, proline, selenocysteine, threonine, and valine were associated (P < 0.05) with antibody response against M. bovis. tRF5s encoding alanine, glutamine, glutamic acid, glycine, histidine, lysine, proline, selenocysteine, threonine, and valine were associated (P < 0.05) with season, which could be attributed to calf growth. There were interactions (P < 0.05) between antibody response to M. bovis and season for tRF5 encoding selenocysteine (anticodon UGA), proline (anticodon CGG), and glutamine (anticodon TTG). Selenocysteine is a rarely used amino acid that is incorporated into proteins by the opal stop codon (UGA), and its function is not well understood. CONCLUSIONS: Differential expression of tRF5s was identified between ELISA-positive and negative animals. Production of tRF5s may be associated with a host defense mechanism triggered by bacterial infection, or it may provide some advantage to a pathogen during infection of a host. Further studies are needed to establish if tRF5s could be used as a diagnostic marker of chronic exposure.

Extensive horizontal gene transfers between plant pathogenic fungi.

BACKGROUND: Horizontal gene transfer (HGT) plays an important role in the adaptation of lineages to changing environments. The extent of this process in eukaryotes, however, remains controversial. The most well-known and dramatic form of HGT represents intracellular gene transfer from endosymbionts to the host nuclear genome. Such episodes of transfer typically involve hundreds of genes and are thought to be possible only in the case of endosymbiosis. RESULTS: Using a conservative phylogenomic approach, we analyzed genomic data from the fungal pathogen Magnaporthiopsis incrustans in the order Magnaporthales and identified two instances of exclusive sharing of HGT-derived gene markers between Magnaporthales and another lineage of plant-pathogenic fungi in the genus Colletotrichum. Surprisingly, inspection of these data demonstrated that HGT is far more widespread than anticipated, with more than 90 genes (including 33 highly supported candidates) being putatively transferred between Magnaporthales and Colletotrichum. These gene transfers are often physically linked in the genome and show more than two-fold functional enrichment in carbohydrate activating enzymes associated with plant cell wall degradation. CONCLUSIONS: Our work provides a novel perspective on the scale of HGT between eukaryotes. These results challenge the notion that recognized HGT plays a minor role in the evolution of fungal lineages, and in the case we describe, is likely implicated in the evolution of plant pathogenesis. More generally, we suggest that the expanding database of closely related eukaryotic genomes and the application of novel analytic methods will further underline the significant impact of foreign gene acquisition across the tree of life. Major lifestyle transitions such as those accompanying the origin of extremophily or pathogenesis are expected to be ideal candidates for studying the mode and tempo of HGT.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

Fungicide Resistance in Cercospora kikuchii, a Soybean Pathogen.

Isolates of Cercospora kikuchii, a soybean (Glycine max) pathogen causing Cercospora leaf blight and purple seed stain, were tested to determine baseline sensitivities (n = 50) to selected quinone outside inhibitor (QoI) fungicides by conducting radial growth assays on fungicide-amended media. Baseline effective fungicide concentration to inhibit 50% of fungal radial growth (EC50) values were compared with EC50 values for isolates collected in 2011 (n = 50), 2012 (n = 50), and 2013 (n = 36) throughout soybean-producing areas in Louisiana. Median EC50 values for isolates subjected to QoI fungicides were significantly (P = 0.05) higher across all 3 years. Cross-resistance to QoI fungicides was observed in resistant isolates collected in 2011 to 2013. Discriminatory doses were developed for QoI fungicides to distinguish between sensitive and resistant isolates. On average, 89% of all isolates screened in 2011 to 2013 were resistant to QoI fungicides. At a discriminatory dose of thiophanate methyl (TM), a methyl benzimidazole carbamate (MBC) fungicide, at 5 µg/ml, resistance was detected in the 2000, 2011, 2012, and 2013 collections at 23, 38, 29, and 36%, respectively. Isolates exhibiting multiple resistance to QoI fungicides and TM also were detected in 2011, 2012, and 2013 at frequencies of 34, 26, and 31%, respectively. Based on these results, Cercospora leaf blight management strategies in Louisiana using solo applications of QoI or MBC fungicides in soybean should be reconsidered.

Transjugular intrahepatic portosystemic shunt for symptomatic portal hypertension in hepatocellular carcinoma with portal vein tumor thrombosis.

AIM: Transjugular intrahepatic portosystemic shunt (TIPS) represents a major advance in the treatment of complications of portal hypertension. However, this procedure is contraindicated in hepatocellular carcinoma (HCC) patients with portal vein tumor thrombosis (PVTT). This study aims to evaluate the safety and efficacy of TIPS in these patients with portal hypertension and determine the predictors of survival after TIPS creation. METHODS: Between 2005 and 2011, 58 consecutive HCC patients with symptomatic portal hypertension and concomitant PVTT underwent TIPS placement. Procedure-related complications, treatment efficacy of portal hypertension complications and survival were evaluated. RESULTS: After TIPS, no patient experienced major procedure-related complications such as hemorrhage or contrast extravasation. Portosystemic pressure gradient was decreased by 14 mmHg on average. Refractory ascites was partially or completely resolved in 19 of 20 patients. Hydrothorax was decreased in all of eight patients. Acute variceal bleeding was successfully controlled in all of five patients. Severe diarrhea was controlled successfully in all of nine patients. During the follow-up period (mean, 78.5 days; range, 11-1713), 56 patients died and two patients remained alive. The median survival period after TIPS was 77 days. Multivariate Cox regression analysis showed that ascites (P = 0.026), white blood cell (P = 0.007) and degree of PVTT (P < 0.001) were independent predictors for survival. CONCLUSION: TIPS may be effective for the palliative treatment of portal hypertension in HCC patients with PVTT. Major procedure-related complications were rarely observed. Ascites, white blood cell and degree of PVTT were independently associated with survival.

MicroRNAs and liver disease: viral hepatitis, liver fibrosis and hepatocellular carcinoma.

MicroRNAs (miRNAs), a type of highly conserved small non-coding RNAs with an average length of 22 nucleotides, may serve as major regulators of gene expression and indispensable components of cellular gene expression networks. They have critical roles in normal biological processes and have been linked to many tumours, including hepatocellular carcinoma (HCC). HCC is the fifth most common malignancy and the third leading cause of cancer-related death worldwide. Viral hepatitis, caused by infection with hepatitis B or C viruses (HBV or HCV), can increase the risk of HCC and contributes to a significant disease burden around the world. Because of the variety of molecular alterations that may arise during the development and progression of HCC, standard of care and treatment for patients with HCC remains unsatisfactory. MiRNAs have been shown to participate in the pathogenesis of both HBV and HCV. In addition to a role in pathogenesis, miRNAs have significant clinical value in the early diagnosis of HCC since they are present in the blood and can be used as diagnostic markers and potential targets for specific systemic treatment.

The factors influencing the accuracy of pre-operative endoscopic ultrasonography assessment in endoscopic treatments for gastrointestinal tumors.

BACKGROUND: This retrospective study aimed to evaluate the factors influencing the accuracy of Endoscopic Ultrasonography (EUS) as a preoperative assessment for gastrointestinal tumors. METHODS: A total of 261 patients with 264 gastrointestinal tumors were enrolled in the study. The parameters of the gastrointestinal lesions examined under EUS and their pathology were recorded and analyzed. RESULTS: The accuracy of EUS for detecting intramucosal lesions and subepithelial lesions (SELs) were 83.6% and 91.4%, respectively. One hundred and ninety-four (73.5%) lesions originated from the mucous layer, as determined by pre-operation EUS examinations. The accuracy of EUS in predicting the correct T stage for intramucosal lesions in the gastric region, esophagus, and colorectum was 77%, 71.8%, and 84.6%, respectively. According to the Paris endoscopic classification, the distribution of macroscopic patterns was different between the EUS-pathology conformity and nonconformity groups (p = 0.018). In the nonconformity group, 48.6% of erosive lesions were classified as 0-IIc, 0-IIa + IIc, 0-IIc + IIa or 0-III macroscopic patterns compared with 26% patients in the conformity group (p = 0.025). Univariate analyses demonstrated that ulcerative lesions (OR = 7.516, 95% Confidence Interval [CI] 2.574-21.952, p < 0.001), location at the cardia of the stomach (OR = 3.619, 95%CI 1.076-12.168, p = 0.038), malignant tumor (OR = 2.920, 95%CI 1.339-6.368, p = 0.007) were significantly associated with EUS inaccuracy. Multivariate logistic regression analyses showed that ulcer was an independent risk factor associated with EUS inaccuracy, with odds ratios of 5.094 (95% CI: 1.641-15.807, p = 0.005). CONCLUSIONS: Our findings suggested that EUS is a reliable and easy-to-use diagnostic tool in decision-making regarding appropriate endoscopic treatment for gastrointestinal tumors. However, the diagnostic accuracy of EUS appeared questionable in the presence of ulceration.