Water Quality of Boko-boko Peat Swamp Based on Physical-chemical Parameters Langgam Village, Pelalawan Regency, Riau Province

The area around the Boko-Boko peat swamp has been used for palm plantation. Remains of fertilizer and pestiside used in the plantation may enter the water and decrease the water quality of the swamp. To understand the water quality of the Boko-Boko peat swamp\u27s waters, a research was conducted in March 2016. There were three sampling stations namely Station 1, Station 2, and Station 3 and in each station there were three sampling points, in the surface, 1.5 secchi and in the bottom. Samplings were conducted 3 times, once/week. Water quality parameters measured were depths, temperature, transparency, pH, DO, CO2, nitrate and phosphate. Results shown that depths was 70-250 cm, temperature: 30-31 oC, pH : 4-5, DO :0.35-3.28 mg/L, CO2: 4-21,97 mg/L, nitrate : 0.14-1.24 mg/L, and phosphate 0.01-0.17 mg/L. Nitrate concentration indicate that the Boko-Boko peat swamp was categorized as eutrophic, and phosphate concentration indicate that the Boko-Boko peat swamp is eutrophic

Analysis of genetic diversity in chickpea (Cicer arietinum L.) cultivars using random amplified polymorphic DNA (RAPD) markers

Genetic diversity of seven chickpea (Cicer arietinum L.) cultivars of Pakistani origin was analyzed by using random amplified polymorphic DNA (RAPD) markers, an extremely effective method to determine the variations among the chickpea cultivars. Polymerase chain reaction (PCR) conditions were optimized for RAPD and the conditions which gave the optimized results were selected for further amplifications. Using nine random decamers for seven genotypes of chickpea, 63 bands were amplified. Out of 63 bands, 50 were polymorphic in all the seven chickpea cultivars. The numbers of RAPD fragments generated per primer ranged from 3 to 11. However, majority of the primers amplified 7 to 11 fragments. The Jaccard’s similarity coefficients ranged from 0.333 to 0.651. Maximum similarity (65.1%) was observed between PK G-3 and PK G-4 and the lowest similarity (33.3%) was observed between PK G-3 and PK G-7. A dendrogram was constructed by using the unweighted pair group arithmetic mean arrangement (UPGMA) that was based on similarity coefficients. Seven chickpea cultivars were clustered in two distinct groups of which two cultivars (PK G-6 and PK G-7) stood separately in the dendrogram. The results from this study may be useful to maximize the selection of diverse parent cultivars and to broaden the germplasm base in the future for chickpea breeding programs. The information generated from this study can also be used in identifying efficient strategies for the sustainable management of the genetic resources of chickpea crop.Keywords: Random amplified polymorphic DNA (RAPD), polymerase chain reaction (PCR), chickpea cultivars, genetic diversit

Consistent association of fungus Fusarium mangiferae Britz with mango malformation disease in Pakistan

Mango malformation disease (MMD) deforms the natural shape of panicles and shoots. The disease incitant is of great concern due to its complexity and mode of infection. Recently, a new species Fusarium mangiferae Britz was confirmed as the etiological agent of MMD in African and Asian clade. There was a need to confirm the fungus in other Asian countries. We investigated the association of F. mangiferae with malformed branches of five exotic and five indigenous cultivars of Mangifera indica L. in Pakistan. F. mangiferae proved to be the dominant fungus hosting majority of the malformed tissues. Among the indigenous cultivars, maximum tissue infection of 96.66% was found in cultivar Anwar Rataul and minimum was found in cultivar Late Chaunsa (48.33%). In exotic ones, maximum and minimum infections of 97.33 and 70.67% were noted in the cultivars Sensation and Pop, respectively. Light and transmission electron microscopy proved helpful in investigating the morphological matrix and ultrastructure of the propagules of fungus F. mangiferae.Key words: Mangifera indica, microconidium, Pakistan, tissue assay, transmission electron microscopy

Government policy failure in public support for research and development

peer-reviewedPromoting Research and Development (R&D) and innovative activity is a key element of the EU Lisbon Agenda and is seen as playing a central part in stimulating economic development. In this paper we argue that, even allowing for benevolent policy-makers, informational asymmetries can lead to a misallocation of public support for R&D, hence government policy failure, with the potential to exacerbate preexisting market failures. Initially, we explore alternative allocation mechanisms for public support, which can help to minimize the scale of these government policy failures. Of these mechanisms (grants, tax credits, or allocation rules based on past performance), our results suggest that none is universally most efficient. Rather, the effectiveness of each allocation rule depends on the severity of financial constraints and on the level of innovative capabilities of the firms themselves.ACCEPTEDpeer-reviewe

The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation

The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap complex, consisting of an oligomer of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex, which reveals that FliD is pentameric, with the N-terminal region of the protomer forming an extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded, contrary to a previously published cryo-EM structure, and propose a molecular model for the filament-cap interaction

Intestinal Microbiota Shifts towards Elevated Commensal Escherichia coli Loads Abrogate Colonization Resistance against Campylobacter jejuni in Mice

Background: The zoonotic pathogen Campylobacter jejuni is a leading cause of bacterial foodborne enterocolitis in humans worldwide. The understanding of immunopathology underlying human campylobacteriosis is hampered by the fact that mice display strong colonization resistance against the pathogen due to their host specific gut microbiota composition. Methodology/Principal Findings: Since the microbiota composition changes significantly during intestinal inflammation we dissected factors contributing to colonization resistance against C. jejuni in murine ileitis, colitis and in infant mice. In contrast to healthy animals C. jejuni could stably colonize mice suffering from intestinal inflammation. Strikingly, in mice with Toxoplasma gondii-induced acute ileitis, C. jejuni disseminated to mesenteric lymphnodes, spleen, liver, kidney, and blood. In infant mice C. jejuni infection induced enterocolitis. Mice suffering from intestinal inflammation and C. jejuni susceptible infant mice displayed characteristical microbiota shifts dominated by increased numbers of commensal Escherichia coli. To further dissect the pivotal role of those distinct microbiota shifts in abrogating colonization resistance, we investigated C. jejuni infection in healthy adult mice in which the microbiota was artificially modified by feeding live commensal E. coli. Strikingly, in animals harboring supra-physiological intestinal E. coli loads, colonization resistance was significantly diminished and C. jejuni infection induced enterocolitis mimicking key features of human campylobacteriosis. Conclusion/Significance: Murine colonization resistance against C. jejuni is abrogated by changes in the microbiot

Novel Murine Infection Models Provide Deep Insights into the “Ménage à Trois” of Campylobacter jejuni, Microbiota and Host Innate Immunity

BACKGROUND: Although Campylobacter jejuni-infections have a high prevalence worldwide and represent a significant socioeconomic burden, it is still not well understood how C. jejuni causes intestinal inflammation. Detailed investigation of C. jejuni-mediated intestinal immunopathology is hampered by the lack of appropriate vertebrate models. In particular, mice display colonization resistance against this pathogen. METHODOLOGY/PRINCIPAL FINDINGS: To overcome these limitations we developed a novel C. jejuni-infection model using gnotobiotic mice in which the intestinal flora was eradicated by antibiotic treatment. These animals could then be permanently associated with a complete human (hfa) or murine (mfa) microbiota. After peroral infection C. jejuni colonized the gastrointestinal tract of gnotobiotic and hfa mice for six weeks, whereas mfa mice cleared the pathogen within two days. Strikingly, stable C. jejuni colonization was accompanied by a pro-inflammatory immune response indicated by increased numbers of T- and B-lymphocytes, regulatory T-cells, neutrophils and apoptotic cells, as well as increased concentrations of TNF-α, IL-6, and MCP-1 in the colon mucosa of hfa mice. Analysis of MyD88(-/-), TRIF(-/-), TLR4(-/-), and TLR9(-/-) mice revealed that TLR4- and TLR9-signaling was essential for immunopathology following C. jejuni-infection. Interestingly, C. jejuni-mutant strains deficient in formic acid metabolism and perception induced less intestinal immunopathology compared to the parental strain infection. In summary, the murine gut flora is essential for colonization resistance against C. jejuni and can be overcome by reconstitution of gnotobiotic mice with human flora. Detection of C. jejuni-LPS and -CpG-DNA by host TLR4 and TLR9, respectively, plays a key role in immunopathology. Finally, the host immune response is tightly coupled to bacterial formic acid metabolism and invasion fitness. CONCLUSION/SIGNIFICANCE: We conclude that gnotobiotic and "humanized" mice represent excellent novel C. jejuni-infection and -inflammation models and provide deep insights into the immunological and molecular interplays between C. jejuni, microbiota and innate immunity in human campylobacteriosis

RNA-centric approaches to study RNA-protein interactions in vitro and in silico

Given their central role in translation, splicing, localization and stability of transcripts, RNA binding proteins (RBPs) are key regulators of several cellular processes. While experimental efforts have been put to study how RBPs bind to transcripts, very little is known about the RNA contributions to the interaction. Here, we review the most common RNA-centric methods to reveal interactions with RBPs: both in vitro (SELEX, SEQR, RNA-compete and RBNS) and in silico (MEME, SeAMotE, GLAM2, iDeep, MEMERIS, RNA context, RCK, RNApromo and GraphProt). We emphasize the main advantages and disadvantages of each technique and highlight the key physico-chemical features contributing to the identification of RNA motifs involved in RBP recognition. We discuss extrinsic determinants influencing protein-RNA binding, such as post-transcriptional and post-translational modifications as well as expression and location of transcripts