Comparative Genomics and Gene Pool Analysis Reveal the Decrease of Genome Diversity and Gene Number in Rice Blast Fungi by Stable Adaption with Rice

Magnaporthe oryzae caused huge losses in rice and wheat production worldwide. Comparing to long-term co-evolution history with rice, wheat-infecting isolates were new-emerging. To reveal the genetic differences between rice and wheat blast on global genomic scale, 109 whole-genome sequences of M. oryzae from rice, wheat, and other hosts were reanalyzed in this study. We found that the rice lineage had gone through stronger selective sweep and fewer conserved genes than those of Triticum and Lolium lineages, which indicated that rice blast fungi adapted to rice by gene loss and rapid evolution of specific loci. Furthermore, 228 genes associated with host adaptation of M. oryzae were found by presence/absence variation (PAV) analyses. The functional annotation of these genes found that the fine turning of genes gain/loss involved with transport and transcription factor, thiol metabolism, and nucleotide metabolism respectively are major mechanisms for rice adaption. This result implies that genetic base of specific host plant may lead to gene gain/loss variation of pathogens, so as to enhance their adaptability to host. Further characterization of these specific loci and their roles in adaption and evaluation of the fungi may eventually lead to understanding of interaction mechanism and develop new strategies of the disease management.

Assessment of outcomes associated with a Moodle-based lesson design for a research course in pharmacy education: An experimental pilot process validation study

Background: This study aims to evaluate the effectiveness of an online Moodle-based lesson for pharmacy students developed and designed for a research course focused on different methodologies, study variables, and research process applications. Methods: An experimental research methodology was used to determine the effectiveness of the Moodle-based lesson. All fourth term Pharm.D. students were required to complete and provide self-reflection reports. The outcome variables were cluster-based completion time, earned score, subjective feedback on contents, gender differences, and performance. Mean values were used to conduct statistical analysis, and a logistic regression model was applied to identify the significance of independent variables. Results: A total of 35 students completed the Moodle-based lesson. The mean earned score for the module was 81.0%, with an average completion time of 28.5 (range 26.8-30.1) hours. Females showed completion in less time compared to males. The reported knowledge and understanding showed a significant (p<0.001) pre-post increase in mean percentages in all three clusters. The intragroup pool analysis also reported significant (p<0.001) differences among gender and performance. The general feedback was limited to technical difficulties and self-reflection questions. Conclusions: The findings of this study showed that the online Moodle-based lesson module for a research course is an effective and validated tool to improve the knowledge and understanding of pharmacy students.

Fucosylated human milk oligosaccharide foraging within the species Bifidobacterium pseudocatenulatum is driven by glycosyl hydrolase content and specificity

Human milk enriches members of the genus Bifidobacterium in the infant gut. One species, Bifidobacterium pseudocatenulatum , is found in the gastrointestinal tracts of adults and breastfed infants. In this study, B. pseudocatenulatum strains were isolated and characterized to identify genetic adaptations to the breastfed infant gut. During growth on pooled human milk oligosaccharides (HMOs) we observed two distinct groups of B. pseudocatenulatum , isolates that readily consumed HMOs and those that did not, a difference driven by variable catabolism of fucosylated HMOs. A conserved gene cluster for fucosylated HMO utilization was identified in several sequenced B. pseudocatenulatum strains. One isolate, B. pseudocatenulatum MP80, which uniquely possessed GH95 and GH29 α-fucosidases consumed the majority of fucosylated HMOs tested. Furthermore, B. pseudocatenulatum SC585, which possesses only a single GH95 α-fucosidase, lacked the ability to consume the complete repertoire of linkages within the fucosylated HMO pool. Analysis of the purified GH29 and GH95 fucosidase activities directly on HMOs revealed complementing enzyme specificities with the GH95 enzyme preferring 1-2 fucosyl linkages and the GH29 enzyme favoring 1-3 and 1-4 linkages. The HMO binding specificity of the Family 1 solute binding protein component linked to the fucosylated HMO gene cluster in both SC585 and MP80 are similar, suggesting differential transport of fucosylated HMO is not a driving factor in each strain’s distinct HMO consumption pattern. Taken together, this data indicates the presence or absence of specific α-fucosidases directs the strain-specific fucosylated HMO utilization pattern among bifidobacteria and likely influences competitive behavior for HMO foraging in situ . IMPORTANCE Often isolated from the human gut, microbes from the bacterial family Bifidobacteriaceae commonly possess genes enabling carbohydrate utilization. Isolates from breast fed infants often grow on and possess genes for the catabolism of human milk oligosaccharides (HMOs), glycans found in human breast milk. However, catabolism of structurally diverse HMOs differs between bifidobacterial strains. This study identifies gene differences between Bifidobacterium pseudocatenulatum isolates that may impact whether a microbe successfully colonizes an infant gut. In this case, the presence of complementary α-fucosidases may provide an advantage to microbes seeking residence in the infant gut. Such knowledge furthers our understanding of how diet drives bacterial colonization of the infant gut.

Struktur Komunitas Fitoplankton di Kolam Bekas Pertambangan Batubara Desa Kampung Baru Kecamatan Cempaka

This study aims to determine the structure of phytoplankton communities in the pool are former coal mining Desa Kampung Baru Kecamatan Cempaka which include abundance, diversity, uniformity and dominance. Phytoplankton samples taken in two pools with a purposive sampling method with a three-point shooting at each pond. Sampling was performed three times. Phylum of phytoplankton were identified in both pools as much as 2 phylum (Chloropyta and Chrysopita) with 17 genera. Average abundance of phytoplankton in the first pool of 7174 ind / liter and 6873 ind / liter in the second pool. The average diversity index of phytoplankton in the first pool of 1.540 and 1.621 in the second pool. Average uniformity index of phytoplankton in the first pool of 0622 and 0.623 in the second pool. The average index of phytoplankton dominance in the first pool of 0271 and 0250 in the second pool. Analysis of community structure (abundance, diversity, uniformity and dominance) shows the condition of the two ponds in the state is quite stable and capable of supporting life inside the phytoplankton. Where the pool in the fertility rate is the level of contamination is, the conditions included in the category of individuals spread more evenly and there are no species that dominate other species in the extreme.

Additive Role of Immune System Infiltration and Angiogenesis in Uveal Melanoma Progression

Uveal melanoma (UM) is a malignant tumor that arises in the melanocytes of the uveal tract. It is the most frequent eye cancer, and despite new therapeutic approaches, prognosis is still poor, with up to 50% of patients developing metastasis with no efficient treatment options available. In contrast to cutaneous melanoma, UM is considered an “immune-cold” tumor due to the low mutational burden and the unique immunosuppressive microenvironment. To gain insight into the role of the UM microenvironment in regard to prognosis and metastatic progression, we have performed a pool analysis characterizing the UM microenvironment by using a bioinformatic approach. A variety of scores based on gene expression measuring stromal infiltration were calculated and used to assess association with prognosis. As a result, the highest immune and stromal scores were associated with poor prognosis. Specifically, stromal cells (fibroblasts and endothelial cells), T cells CD8+, natural killer (NK) cells, and macrophages M1 and M2 infiltration were associated with poor prognosis. Contrary to other tumors, lymphocytic infiltration is related to poor prognosis. Only B cells were associated with more favorable prognosis. UM samples scoring high in both angiogenesis (Angio) and antigen presentation (AP) pathways showed a poor prognosis suggesting an additive role of both functions. Almost all these tumors exhibited a chromosome 3 monosomy. Finally, an enrichment analysis showed that tumors classified as high Angio-high AP also activated metabolic pathways such as glycolysis or PI3K-AKT-MTOR. In summary, our pool analysis identified a cluster of samples with angiogenic and inflammatory phenotypes exhibiting poor prognosis and metabolic activation. Our analysis showed robust results replicated in a pool analysis merging different datasets from different analytic platforms.

Is It Time to Remove Radiotherapy in the Management of Primary Central Nervous System Lymphoma? Population-based Study, Pool-Analysis and Retrospective Study of Recurrence Pattern.

BackgroundBefore the introduction of the chemotherapeutic agent methotrexate, radiotherapy (RT) and steroids have been the sole, first-line treatment of primary central nervous system lymphoma (PCNSL). With the application of methotrexate, the role of RT in the treatment of PCNSL has been challenged. MethodsWe performed observation analysis on 2,486 PCNSL patients between 1988 and 2016 from the Surveillance, Epidemiology and End Results (SEER) database. Propensity score matching (PSM) was employed to ensure well-balanced characteristics of two groups of patients who received RT and those who did not receive it. Two randomized controlled trials (RCTs) were pooled to further evaluate the role of consolidation whole-brain radiotherapy (WBRT) in PCNSL. To clarify whether WBRT is necessary for PCNSL, 27 relapsed patients who attained complete response (CR), partial response (PR) or stable disease (SD) during or after first-line treatment without WBRT for newly diagnosed PCNSL in our institution was retrospectively analyzed; the pattern and location of relapse was identified. ResultsAfter matching, there was no statistical difference on survival between the two groups. In patients did not received chemotherapy, RT significantly improved the survival of patients who undergone biopsy (All P < .0001) or subtotal resection (All P < .0001). In particular, RT helped improve survival for patients with other infectious and parasitic diseases including HIV (OIPDH). Pool-analysis shown the better progression free survival (PFS) of patients with WBRT arm compared with no WBRT arm in per-protocol (PP) population (HR 0.71, 95% CI 0.52 to 0.98). In the 27 relapse patients, 17 (63%) had new measurable enhancing lesions at relapse at a spatially distinct site, the remote recurrence after CR was 9/11 (82%), and after PR was 8/15 (53%). Single lesion occurred remote recurrence was 11/13 (85%), while multiple lesions were 7/14 (50%). We also established a novel prediction model with excellent performance to estimate the potential benefit from RT with respect to the end point of overall survival. ConclusionsRT is still an important method in the treatment of PCNSL, which cannot be removed. More precise studies should be carried out to perfect the treatment strategies of the disease.

Systematic review and meta-analysis of surgical drain management after the diagnosis of postoperative pancreatic fistula after pancreaticoduodenectomy: draining-tract-targeted works better than standard management

Purpose Drains’ role after pancreaticoduodenectomy (PD) is debated by proponents of no drain, draining selected cases, and early drain removal. The aim of the study was to assess the effect of “standard” and “draining-tract-targeted” management of abdominal drains still in situ after diagnosing a postoperative pancreatic fistula (POPF). Methods PubMed and Scopus were searched for “pancreaticoduodenectomy or pancreatoduodenectomy or duodenopancreatectomy,” “Whipple,” “proximal pancreatectomy,” “pylorus-preserving pancreatectomy,” and “postoperative pancreatic fistula or POPF.”. Main outcomes included clinically relevant (CR) POPF, grade-C POPF, overall mortality, POPF-related mortality, and CR-POPF-related mortality. Secondary outcomes were incidence of radiological and/or endoscopic interventions, reoperations, and completion pancreatectomies. Results Overall, 12,089 studies were retrieved by the search of the English literature (01/01/1990–31/12/2018). Three hundred and twenty-six studies (90,321 patients) reporting ≥ 100 PDs and ≥ 10 PD/year were finally included into the study. Average incidences were obtained by averaging the incidence rates reported in the single articles. Pooled incidences were calculated by combining the number of events and the total number of patients considered in the various studies. These were then meta-analyzed using DerSimonian and Laird’s (1986) method. Pearson’s chi-squared test was used to compare pooled incidences between groups. Post hoc testing was used to see which groups differed. The meta-analyzed incidences were compared using a fixed effect for moderators. “Draining-tract-targeted” management showed a significant advantage over “standard” management in four clinically relevant outcomes out of eight according to pool analysis and in one of them according to meta-analysis. Conclusion Clinically, “draining-targeted” management of POPF should be preferred to “standard” management.