An evaluation of Bradfordizing effects

The purpose of this paper is to apply and evaluate the bibliometric method Bradfordizing for information retrieval (IR) experiments. Bradfordizing is used for generating core document sets for subject-specific questions and to reorder result sets from distributed searches. The method will be applied and tested in a controlled scenario of scientific literature databases from social and political sciences, economics, psychology and medical science (SOLIS, SoLit, USB Köln Opac, CSA Sociological Abstracts, World Affairs Online, Psyndex and Medline) and 164 standardized topics. An evaluation of the method and its effects is carried out in two laboratory-based information retrieval experiments (CLEF and KoMoHe) using a controlled document corpus and human relevance assessments. The results show that Bradfordizing is a very robust method for re-ranking the main document types (journal articles and monographs) in today’s digital libraries (DL). The IR tests show that relevance distributions after re-ranking improve at a significant level if articles in the core are compared with articles in the succeeding zones. The items in the core are significantly more often assessed as relevant, than items in zone 2 (z2) or zone 3 (z3). The improvements between the zones are statistically significant based on the Wilcoxon signed-rank test and the paired T-Test

Subcellular location of Piscirickettsia salmonis heat shock protein 60 (Hsp60) chaperone by using immunogold labeling and proteomic analysis

Indexación: Scopus.Piscirickettsia salmonis is the causative bacterial agent of piscirickettsiosis, a systemic fish disease that significantly impacts the Chilean salmon industry. This bacterium possesses a type IV secretion system (T4SS), several proteins of the type III secretion system (T3SS), and a single heat shock protein 60 (Hsp60/GroEL). It has been suggested that due to its high antigenicity, the P. salmonis Hsp60 could be surface-exposed, translocated across the membrane, and (or) secreted into the extracellular matrix. This study tests the hypothesis that P. salmonis Hsp60 could be located on the bacterial surface. Immunogold electron microscopy and proteomic analyses suggested that although P. salmonis Hsp60 was predominantly associated with the bacterial cell cytoplasm, Hsp60-positive spots also exist on the bacterial cell envelope. IgY antibodies against P. salmonis Hsp60 protected SHK-1 cells against infection. Several bioinformatics approaches were used to assess Hsp60 translocation by the T4SS, T3SS, and T6SS, with negative results. These data support the hypothesis that small amounts of Hsp60 must reach the bacterial cell surface in a manner probably not mediated by currently characterized secretion systems, and that they remain biologically active during P. salmonis infection, possibly mediating adherence and (or) invasion.https://www.mdpi.com/2076-2607/8/1/11

Nutritional Immunity Triggers the Modulation of Iron Metabolism Genes in the Sub-Antarctic Notothenioid Eleginops maclovinus in Response to Piscirickettsia salmonis

Iron deprivation is a nutritional immunity mechanism through which fish can limit the amount of iron available to invading bacteria. The aim of this study was to evaluate the modulation of iron metabolism genes in the liver and brain of sub-Antarctic notothenioid Eleginops maclovinus challenged with Piscirickettsia salmonis. The specimens were inoculated with two P. salmonis strains: LF-89 (ATCC® VR-1361™) and Austral-005 (antibiotic resistant). Hepatic and brain samples were collected at intervals over a period of 35 days. Gene expression (by RT-qPCR) of proteins involved in iron storage, transport, and binding were statistically modulated in infected fish when compared with control counterparts. Specifically, the expression profiles of the transferrin and hemopexin genes in the liver, as well as the expression profiles of ferritin-M, ferritin-L, and transferrin in the brain, were similar for both experimental groups. Nevertheless, the remaining genes such as ferritin-H, ceruloplasmin, hepcidin, and haptoglobin presented tissue-specific expression profiles that varied in relation to the injected bacterial strain and sampling time-point. These results suggest that nutritional immunity could be an important immune defense mechanism for E. maclovinus against P. salmonis injection. This study provides relevant information for understanding iron metabolism of a sub-Antarctic notothenioid fish

Head Kidney Transcriptome Analysis and Characterization for the Sub-Antarctic Notothenioid Fish Eleginops maclovinus

This study describes de novo transcriptome sequencing and annotation analyses for the head kidney of the sub-Antarctic notothenioid fish Eleginops maclovinus, a sister group of the Antarctic notothenioid fish clade. Moreover, E. maclovinus is one of the most eurythermal and euryhaline representatives of the Notothenioidei suborder. RNA-seq data were generated by the 454 GS Junior system, resulting in 11,207 contigs that were then assembled by the Genomic Workbench CLC software. The transcriptome was annotated by BLASTing each sequence against the universal, non-redundant NCBI database (National Center for Biotechnology Information) using the AUSTRAL-omics computer cluster. A significant number of transcripts related to innate and adaptive immunity were found in the sequences, which could be used as references in future immunological studies in E. maclovinus

Long-term effects of temperatures on the physiological response of juveniles of the eurythermal sub-antarctic notothenioid Eleginops maclovinus

Eleginops maclovinus is a subantartic notothenic with eurythermal characteristics and potential for Chilean aquaculture. However, the information regarding their physiological response to long-term temperatures and optimum temperature range for physiological process is unknown. In the present study, we evaluated under experimental conditions, the long-term effects (60 days) of temperatures of 15 degrees C and high temperatures of 20 and 25 degrees C, (10 degrees C as control) on the physiology of E. maclovinus juveniles. At the end of the experimental period, survival was 36% at 25 degrees C and mortality started after 30 days, while at the other temperatures the survival was 100%. The growth and food intake did not present significant differences at 10, 15 and 20 degrees C, while at 25 degrees C growth decreased at day 15, to subsequently present a compensatory growth at day 30 and finally a decrease in growth and food intake at day 60. In general, the energy substrates in liver, gills, serum, and spleen showed a significant decrease at 25 degrees C, with a marked decrease in triglycerides, while white muscle presented an opposite pattern with an increase in total lipids and glycogen at 25 degrees C. Serum cortisol and ammonium increased at the higher temperature suggesting an increased metabolism. In the brain, high temperatures had a marked effect on monoamine neurotransmitters, with increased levels of serotonin (5-HT) and norepinephrine (NAd). Fatty acids in white muscle were modulated by high temperatures. In general, saturated fatty acids were significantly decreased at higher temperatures, while for monounsaturated fatty acids only C20:1n9 showed a decrease at 25 degrees C. The most abundant polyunsaturated fatty acids in white muscle were C22:6n3 (DHA) and C20:5n3 (EPA), which did not change at a higher temperature, while C20:4n6 (ARA) and C18:3n3 (ALA) showed an increase and a decrease at 25 degrees C, respectively. In conclusion, we suggest that E. maclovinus juveniles tolerate up to 20 degrees C, increasing their metabolism without negatively affecting their physiology, while a temperature of 25 degrees C or higher could be lethal in a long-term scenario

Expression analysis and functional characterization of two PHT1 family phosphate transporters in ryegrass

Main conclusion: The phosphate transporters LpPHT1;1 and LpPHT1;4 have different roles in phosphate uptake and translocation in ryegrass under P stress condition. Abstract: The phosphate transporter 1 (PHT1) family are integral membrane proteins that operate in phosphate uptake, distribution and remobilization within plants. In this study, we report on the functional characterization and expression of two PHT1 family members from ryegrass plants (Lolium perenne L.) and determine their roles in the specificity of Pi transport. The expression level of LpPHT1;4 was strongly influenced by phosphorus (P) status, being higher under P-starvation condition. In contrast, the expression level of LpPHT1;1 was not correlated with P supply. Yeast mutant complementation assays showed that LpPHT1;4 can complement the growth defect of the yeast mutant Δpho84 under Pi-deficient conditions, whereas the yeast mutant expressing LpPHT1;1 was not able to restore growth. Phylogenetic and molecular analyses indicated high sequence similarity to previously identified PHT1s from other species in the Poaceae. These results suggest that LpPHT1;1 may function as a low-affinity Pi transporter, whereas LpPHT1;4 could acts as a high-affinity Pi transporter to maintain Pi homeostasis under stress conditions in ryegrass plants. This study will form the basis for the long-term goal of improving the phosphate use efficiency of ryegrass plants.We would like to thank the Scientific and Technological Bioresource Nucleus of Universidad de La Frontera (BIORENUFRO) for providing access to specialized equipment. This work was supported by Project (FONDECYT 1181050), CONICYT Doctoral scholarship (No. 21151320) and the Spanish Ministry of Economy, Industry and Competitivity Project (AGL2015-67098-R)

Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from Genetically Resistant Farmed Atlantic Salmon (<i>Salmo salar</i>) during 2021–2022

Infectious pancreatic necrosis (IPN), caused by IPNV, affects several species of farmed fish, particularly Atlantic salmon, and is responsible for significant economic losses in salmon aquaculture globally. Despite the introduction of genetically resistant farmed Atlantic salmon and vaccination strategies in the Chilean salmon industry since 2019, the number of IPN outbreaks has been increasing in farmed Atlantic salmon in the freshwater phase. This study examined gross and histopathological lesions of IPNV-affected fish, as well as the IPNV nucleotide sequence encoding the VP2 protein in clinical cases. The mortality reached 0.4% per day, and the cumulative mortality was from 0.4 to 3.5%. IPNV was isolated in the CHSE-214 cell line and was confirmed by RT-PCR, and VP2 sequence analysis. The analyzed viruses belong to IPNV genotype 5 and have 11 mutations in their VP2 protein. This is the first report of IPN outbreaks in farmed Atlantic salmon genetically resistant to IPNV in Chile. Similar outbreaks were previously reported in Scotland and Norway during 2018 and 2019, respectively. This study highlights the importance of maintaining a comprehensive surveillance program in conjunction with the use of farmed Atlantic salmon genetically resistant to IPNV