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Renibacterium salmoninarum (Rs) is the etiological agent of bacterial kidney disease (BKD), which significantly affects farmed and wild salmonids worldwide. Although the whole genome of Rs (~3.1 million nucleotides) is highly conserved, genomic epidemiology analyses have identified four sub‐lineages from Chilean isolates. A total of 94 Rs genomes from the BIGSdb aquaculture database were aligned and compared using bioinformatics tools, identifying 2199 independent single‐nucleotide polymorphisms (SNPs) spread along the genome. A detailed analysis of the distribution of the SNPs showed five local zones of a length in the range of 10–15 kbp that should be used to unambiguously identify a specific sub‐lineage. Based on the Rs type strain DSM 20767T, we designed multiplex PCR primers that produce specific amplification products which were further sequenced by the Sanger method to obtain the genotype of the sub‐lineage. For the genetic typing, we evaluated 27 Rs isolates recovered from BKD outbreaks from different fish species and regions of Chile. Based on the findings reported here, we propose the PCR approach as a valuable tool for the rapid and reliable studying of the relationships between Rs isolates and the different sub‐lineages without requiring the sequencing of the entire genome. [ABSTRACT FROM AUTHOR]

Renibacterium salmoninarum, a Gram‐positive intracellular pathogen, is the causative agent of bacterial kidney disease (BKD), the impacts of which are high mortalities and economic losses for the salmon industry. This study provides novel analyses for the whole‐genome sequences of 50 R. salmoninarum isolates and the reference strain ATCC 33209 using a pan‐genomic approach to elucidate phylogenomic relationships and identify unique and shared genes associated with pathogenicity and infection mechanisms. Genome size varied from 3,061,638 to 3,155,332 bp; gene count from 3452 to 3580; and predicted coding sequences from 3402 to 3527. Comparative analyses revealed an open, but approaching closed, pan‐genome. The pan‐genome analysis recovered 4064 genes, with a core genome containing 3306 genes. Phylogenetic analysis of R. salmoninarum showed high genomic homogeneity, apart from one isolate obtained from Salmo trutta in Norway. All genomes presented the 57‐kDa protein (p57). Strain ATCC 33209 and the Chilean isolates H‐2 and DJ2R presented two copies of the msa gene, while the remaining isolates had one copy. The pan‐genome analysis further identified differences in the number of copies and length of the signalling peptide for p57, the principal virulence factor reported for this bacterium. This heterogeneity could be associated with the secretion levels of p57, potentially influencing virulence. Additionally identified were numerous common genes related to iron uptake, the stress response and regulation, and cell signalling—all of which constitute the pathogenic repertoire of R. salmoninarum. This investigation provides information that is applicable in future studies for identifying therapeutic targets and/or for designing new strategies (e.g., vaccines) to prevent BKD infections in salmon farming. [ABSTRACT FROM AUTHOR]

Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum (Rs), can be transmitted both horizontally and vertically and there is no available cure or prophylaxis. The control of BKD requires continuous surveillance, which is challenging in aquaculture as well as in programs for conservation and restoration of salmonid fish strains. BKD is a notifiable disease in Sweden and is monitored through the mandatory health control program using a polyclonal ELISA for detection of the Rs p57 protein in kidney. Fish must be killed for sampling, an obvious disadvantage especially regarding valuable broodfish. The present study shows that gill‐/cloacal swabs collected in vivo for real‐time PCR (qPCRgc), allow a sensitive and specific detection of Rs. The sensitivity of qPCRgc was estimated to 97.8% (credible interval (ci) 93.8%–100%) compared to 98.3% (ci 92.7%–100%) and 48.8% (ci 38.8%–58.8%) of kidney samples for qPCR (qPCRk) and ELISA (ELISAk) respectively, by use of the Bayesian Latent Class Analysis (BLCA). Since the goal of the program is eradication of BKD the most sensitive test is preferrable. Using qPCRgc instead of ELISAk will result in a lower false negative rate and can be useful for surveillance in aquaculture and in breeding programs with valuable fish. However, a higher false positive rate warrants confirmatory lethal testing before a previously Rs negative farm is subject to restrictions. [ABSTRACT FROM AUTHOR]

Bacterial kidney disease (BKD) can be a devastating bacterial infection in salmonids, and it is present in aquaculture throughout the world. BKD is caused by the Gram‐positive facultative intracellular bacterium Renibacterium salmoninarum (R. salmoninarum) that is spread both horizontally and vertically. Disease signs include external ulcerations and blisters and internal signs such as organ swelling, granulomas, petechiae and ascites. In Sweden, BKD accounts for a significant income loss in aquacultures due to expensive decontamination of the facility and increased disease susceptibility for the immunocompromised fish leading to higher mortality rates. In addition, uncontrolled spread in aquaculture may threaten the survival of wild fish populations. The aim of our study was to investigate the prevalence of R. salmoninarum in wild salmonids caught in Swedish waters where net pen farms with a recent history of BKD are present. Four rivers with at least one BKD‐positive or recently BKD‐positive farm were selected. In addition, we evaluated the use of environmental DNA (eDNA) for surveillance and monitoring of ongoing infections at these locations. In total, 1058 fish were sampled from four different river systems, and of them 52 (4.9%) were positive for R. salmoninarum by antigen ELISA. Surprisingly, these fish were not evenly distributed between the four river systems, but 50 were caught in the same river (Ljungan). This accounts for an alarmingly high rate of 17% R. salmoninarum‐positive samples in wild salmonids in this area. This number is far above what was expected and clearly shows the risk with an open farming system as well as the importance of effective health monitoring programmes to avoid an uncontrolled spread of the disease. The use of eDNA for monitoring BKD is somewhat difficult to evaluate. Few of the water samples analysed were PCR positive for R. salmoninarum (2 of 38) and those were collected where no ELISA positive fish were identified. In addition to water, sediment samples were collected under a net pen farm that had recently slaughtered all fish due to ongoing R. salmoninarum infections. Sediment samples are more promising than water as 4 of 5 samples at one farming facility where positive for R. salmoninarum. Thus, sediment samples may be valuable for monitoring potential ongoing BKD in farms, without the need to sacrifice valuable fish. [ABSTRACT FROM AUTHOR]

Teknologi informasi menjadi salah satu bagian terpenting dalam suatu instansi, salah satu instansi yang memerlukan teknologi informasi yaitu Lembaga Layanan Pendidikan Tinggi (LLDikti) Wilayah II. LLDikti Wilayah II merupakan suatu instansi Pemerintah yang berada di bawah Kementerian Riset, Teknologi, dan Pendidikan Tinggi yang tugasnya memberikan pengawasan, pengendalian dan pembinaan terhadap Perguruan Tinggi Swasta yang ada dalam lingkungannya. Salah satu teknologi informasi yang telah digunakan adalah aplikasi teknologi informasi Beban Kerja Dosen (BKD), maka diperlukan suatu metode untuk melihat layanan teknologi informasi tersebut dengan menggunakan salah satu framework. Framework UTAUT dapat menunjukkan bagaimana pengaruh perbedaan dari setiap responden dalam menggunakan teknologi informasi. Lebih khusus lagi, hubungan antara persepsi suatu pemanfaatan, kemudahan penggunaan, dan niat penggunaan dapat dimoderatori oleh usia, jenis kelamin, golongan/pangakat, dan pengalaman dalam penggunan aplikasi teknologi informasi BKD. Dengan menggunakan variabel-variabel yang ada pada framework UTAUT tersebut diharapkan memberikan kualitas layanan teknologi informasi di LLDikti Wilayah II lebih jelas dan bisa diukur sejauh mana pengadopsian teknologi informasi BKD selama ini bagi dosen di lingkungannya dalam melakukan aktifitas kependidikan.

Listeria monocytogenes is a foodborne bacterial pathogen that causes listeriosis. Positive regulatory factor A (PrfA) is a pleiotropic master activator of virulence genes of L. monocytogenes that becomes active upon the entry of the bacterium into the cytosol of infected cells. L. monocytogenes can survive and multiply at low temperatures; this is accomplished through the maintenance of appropriate membrane fluidity via branched-chain fatty acid (BCFA) synthesis. Branched-chain α-keto acid dehydrogenase (BKD), which is composed of four polypeptides encoded by lpd , bkdA1 , bkdA2 , and bkdB , is known to play a vital role in BCFA biosynthesis. Here, we constructed BKD-deficient Listeria strains by in-frame deletion of lpd , bkdA1 , bkdA2 , and bkdB genes. To determine the role in in vivo and in vitro , mouse model challenges, plaque assay in murine L2 fibroblast, and intracellular replication in J744A.1 macrophage were conducted. BKD-deficient strains exhibited defects in BCFA composition, virulence, and PrfA-regulon function within the host cells. Transcriptomics analysis revealed that the transcript level of the PrfA-regulon was lower in Δ bkdA1 strain than those in the wild-type. This study demonstrates that L. monocytogenes strains lacking BKD complex components were defective in PrfA-regulon function, and full activation of wild-type prfA may not occur within host cells in the absence of BKD. Further study will investigate the consequences of BKD deletion on PrfA function through altering BCFA catabolism.IMPORTANCE Listeria monocytogenes is the causative agent of listeriosis, a disease with a high mortality rate. In this study, we have shown that the deletion of BKD can impact the function of PrfA and the PrfA-regulon. The production of virulence proteins within host cells is necessary for L. monocytogenes to promote its intracellular survival and is likely dependent on membrane integrity. We thus report a link between L. monocytogenes membrane integrity and the function of PrfA. This knowledge will increase our understanding of L. monocytogenes pathogenesis, which may provide insight into the development of antimicrobial agents., Competing Interests: The authors declare no conflict of interest.

Bacterial kidney disease (BKD) is widespread in many areas of the world and can cause substantial economic losses for the salmon aquaculture industry. The objective of this study was to investigate the pathophysiological response and gene expression profiles related to the immune response at different water temperatures and to identify the best immunopathological biomarkers to define a phenotype of resistance to BKD. The abundance of msa transcripts of R. salmoninarum in the head kidney was significantly higher in infected fish at 11°C. R. salmoninarum induced significantly more severe kidney lesions, anemia and impaired renal function at 11°C. In addition, the expression pattern of the genes related to humoral and cell-mediated immune responses in infected fish at 11 and 15°C was very similar, although R. salmoninarum induced a significantly greater downregulation of the adaptive immune response genes at the lower water temperature. These results could be due to a suppressed host response directly related to the lowest water temperature and/or associated with a delayed host response related to the lowest water temperature. Although no significant differences in survival rate were observed, fish infected at the lowest temperature showed a higher probability of death and delayed the mortality curve during the late stage of infection (35 days after infection). Thirty-three immunopathological biomarkers were identified for potential use in the search for a resistance phenotype for BKD, and eight were genes related specifically to the adaptive cell-mediated immune response.

Surveillance of antibiotic resistance is of paramount importance for animal welfare and production. Despite aquaculture being a main source of animal protein, studies on antibiotic susceptibility in fish pathogens are scarce. Renibacterium salmoninarum, the aetiological agent of bacterial kidney disease (BKD), is one of the most common bacterial pathogens affecting salmon farming. In this work, we present an analysis of susceptibility patterns using determinations of minimum inhibitory concentration (MIC) for 65 field isolates, which were collected over seven years (2013–2019) from Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch) farms across southern Chile. The MIC protocol described by the Clinical Laboratory Standards Institute (CLSI) was used, but with microdilution instead of macrodilution and eight instead of four days of incubation. Two laboratories independently conducted analyses to provide data on the epidemiological cut‐off values for R. salmoninarum to florfenicol, oxytetracycline and erythromycin. By using two calculation methods, our results provide evidence for an evolving subpopulation of non‐wild‐type isolates for the macrolide erythromycin, which is consistent with the respective treatment frequencies prescribed against BKD. Contrasting with what was expected, R. salmoninarum isolates were most susceptible to florfenicol and oxytetracycline, both of which are widely used antibiotics currently used in the Chilean salmon industry. The presented findings can serve as a reference for national or international antibiotic surveillance programmes, for both MIC interpretation and to identify emerging resistance to the conventional drugs used in BKD management. Finally, our results indicate that an 8‐day incubation period for establishing MIC values of R. salmoninarum should be considered in a future revision of the CLSI guidelines. [ABSTRACT FROM AUTHOR]

Bacterial kidney disease (BKD) is widespread in many areas of the world and can cause substantial economic losses for the salmon aquaculture industry. The objective of this study was to investigate the pathophysiological response and gene expression profiles related to the immune response at different water temperatures and to identify the best immunopathological biomarkers to define a phenotype of resistance to BKD. The abundance of msa transcripts of R. salmoninarum in the head kidney was significantly higher in infected fish at 11°C. R. salmoninarum induced significantly more severe kidney lesions, anemia and impaired renal function at 11°C. In addition, the expression pattern of the genes related to humoral and cell-mediated immune responses in infected fish at 11 and 15°C was very similar, although R. salmoninarum induced a significantly greater downregulation of the adaptive immune response genes at the lower water temperature. These results could be due to a suppressed host response directly related to the lowest water temperature and/or associated with a delayed host response related to the lowest water temperature. Although no significant differences in survival rate were observed, fish infected at the lowest temperature showed a higher probability of death and delayed the mortality curve during the late stage of infection (35 days after infection). Thirty-three immunopathological biomarkers were identified for potential use in the search for a resistance phenotype for BKD, and eight were genes related specifically to the adaptive cell-mediated immune response. [ABSTRACT FROM AUTHOR]

Renibacterium salmoninarum is the aetiological agent of bacterial kidney disease (BKD) in salmonid farms. This pathogen possesses at least three iron‐acquisition mechanisms, but the link between these mechanisms and virulence is unclear. Therefore, this study used RT‐qPCR to assess the effects of normal and iron‐limited conditions on iron‐uptake genes controlled by IdeR and related to iron acquisition in Chilean R. salmoninarum strain H‐2 and the type strain DSM20767T. Further evaluated was the in vitro immune‐related response of the Atlantic Salmon Kidney (ASK) cell line, derived from the primary organ affected by BKD. R. salmoninarum grown under iron‐limited conditions overexpressed genes involved in haemin uptake and siderophore transport, with overexpression significantly higher in H‐2 than DSM20767T. These overexpressed genes resulted in higher cytotoxicity and an increased immune response (i.e., TNF‐α, IL‐1β, TLR1 and INF‐γ) in the ASK cell line. This response was significantly higher against bacteria grown under iron‐limited conditions, especially H‐2. These observations indicate that iron‐acquisition mechanisms are possibly highly related to the virulence and pathogenic capacity of R. salmoninarum. In conclusion, treatments that block iron‐uptake mechanisms or siderophore synthesis are attractive therapeutic approaches for treating R. salmoninarum, which causes significant aquaculture losses. [ABSTRACT FROM AUTHOR]

Jumlah difabel daksa di kabupaten Bantul termasuk dalam kategori tinggi dibandingkan daerah lain, terutama pascagempa tahun 2006. Meskipun pemerintah telah memperhatikan keberlanjutan hidup yang layak bagi difabel, namun sampai saat ini, program pemberdayaan yang dilakukan pemerintah belum memberikan dampak yang signifikan bagi kemandirian dan life skills bagi para difabel daksa. Salah satu lembaga difabel yang berperan dalam program pemberdayaan ini adalah Paguyuban Bangkit Bersama (PBB). Forum ini merupakan wadah dari perwakilan DPO seluruh (17) kecamatan di Kabupaten Bantul. FPDB sudah memiliki berbagai macam kegiatan pemberdayaan, diantaranya pembuatan dan reparasi sepatu roda, kerajinan anyaman bambu, dan pembuatan meja kursi untuk cafe. Sayangnya, FPDB belum memiliki manajemen SDM yang bagus dan tertata rapi, di samping hasil produk dari program pemberdayaan yang sebenarnya sudah layak jual, namun proses pemasaran yang kurang dapat menarik pasar. Oleh karenaitu, melalui Kegiatan Pengabdian kepada Masyarakat ini akan diusulkan PRODADISA (Program Pemberdayaan Difabel Daksa) yang meliputi kegiatan assessment, kelanjutan program yang diselenggarakan PBB, dan evaluasi program pemberdayaan difabel yang selama ini telah dilakukan oleh PBB bersama pemda kabupaten Bantul. Tujuan PRODADISA adalah untuk: meningkatkan kemampuan difabel daksa anggota PBB dalam hal manajemen SDM; membentuk masyarakat difabel yang mandiri dalam berwirausaha; memberikan pelatihan teknologi informasi kepada anggota FPDB dalam mendukung usahanya; memberikan pelatihan menjahit dan pengembangan produk jahit yang marketable. Tujuan akhir dari kegiatan ini adalah FPDB menjadi percontohan Balai Kerja Difabel (BKD), sehingga sustainability kegiatan dapat terus terjaga.

Renibacterium salmoninarum , a slow-growing facultative intracellular pathogen belonging to the high C + G content Actinobacteria phylum, is the causative agent of bacterial kidney disease, a progressive granulomatous infection affecting salmonids worldwide. This Gram-positive bacterium has existed in the Chilean salmonid industry for >30 years, but little or no information is available regarding the virulence mechanisms and genomic characteristics of Chilean isolates. In this study, the genomes of two Chilean isolates (H-2 and DJ2R) were sequenced, and a search was conducted for genes and proteins involved in virulence and pathogenicity, and we compare with the type strain ATCC 33209 T genome. The genome sizes of H-2 and DJ2R are 3,155,332 bp and 3,155,228 bp, respectively. They genomes presented six ribosomal RNA, 46 transcription RNA, and 25 noncodingRNA, and both had the same 56.27% G + C content described for the type strain ATCC 33209 T. A total of 3,522 and 3,527 coding sequences were found for H-2 and DJ2R, respectively. Meanwhile, the ATCC 33209 T type strain had 3,519 coding sequences. The in silico genome analysis revealed a genes related to tricarboxylic acid cycle, glycolysis, iron transport and others metabolic pathway. Also, the data indicated that R salmoninarum may have a variety of possible virulence-factor and antibiotic-resistance strategies. Interestingly, many of genes had high identities with Mycobacterium species, a known pathogenic Actinobacteria bacterium. In summary, this study provides the first insights into and initial steps towards understanding the molecular basis of antibiotic resistance, virulence mechanisms and host/environment adaptation in two Chilean R. salmoninarum isolates that contain proteins of which were similar to those of Mycobacterium. Furthermore, important information is presented that could facilitate the development of preventive and treatment measures against R. salmoninarum in Chile and worldwide. [ABSTRACT FROM AUTHOR]

Bacterial kidney disease (BKD) diagnosis is often carried out by IFAT, ELISA, and PCR because these tests yield rapid results compared with bacterial culture for the causative agent, Renibacterium salmoninarum . However, the diagnostic sensitivity (DSe) and specificity (DSp) of these tests is generally unknown, particularly in subclinically infected Atlantic salmon. Bayesian models were used to analyse test results from 454 field samples sourced from salmon populations with different infection status and submitted to independent laboratories. Results showed that DSe was highly dependent on the presentation of infection. When applied to fish with BKD-associated gross lesions, the highest to lowest posterior medians for DSe were: PCR2 (0.98), PCR1 (0.97), bacterial culture (0.86), ELISA (0.82) and IFAT (0.75). When applied to fish without lesions, the posterior medians for DSe were: PCR1 (0.82), PCR2 (0.82), bacterial culture (0.29), IFAT (0.29) and ELISA (0.21). The posterior medians for DSp were similar in populations with and without lesions. ELISA had the highest DSp (0.99), followed by culture (0.98–0.99), IFAT (0.96), PCR1 (0.94–0.96) and PCR2 (0.83–0.84), where different numbers reflect the estimates for populations with or without lesions respectively. Among tests that were evaluated for intra-laboratory repeatability (ELISA, PCR1 and IFAT), ELISA had the highest repeatability (kappa = 0.82). We concluded that PCR tests were the fittest of the evaluated tests for the purpose of screening subclinically-infected adult Atlantic salmon. [ABSTRACT FROM AUTHOR]

Kikuchi diffraction patterns can provide fundamental information about the lattice metric of a crystalline phase. In order to improve the possible precision and accuracy of lattice parameter determination from the features observed in Kikuchi patterns, some useful fundamental relationships of geometric crystallography are reviewed, which hold true independently of the actual crystal symmetry. The Kikuchi band positions and intersections and the Kikuchi band widths are highly interrelated, which is illustrated by the fact that all lattice plane trace positions of the crystal are predetermined by the definition of only four traces. If, additionally, the projection centre of the gnomonic projection is known, the lattice parameter ratios and the angles between the basis vectors are fixed. A further definition of one specific Kikuchi band width is sufficient to set the absolute sizes of all lattice parameters and to predict the widths of all Kikuchi bands. The mathematical properties of the gnomonic projection turn out to be central to an improved interpretation of Kikuchi pattern data, emphasizing the importance of the exact knowledge of the projection centre. [ABSTRACT FROM AUTHOR]

ABSTRACT Branched-chain fatty acids (BCFAs) are important precursors for the production of advanced biofuels with improved cold-flow properties. Previous efforts in engineering type II fatty acid synthase (FAS) for BCFA production suffered from low titers and/or the co-production of a large amount of straight-chain fatty acids (SCFAs), making it nearly impossible for further conversion of BCFAs to branched biofuels. Synthesis of both SCFAs and BCFAs requires FabH, the only β-ketoacyl-(acyl-carrier-protein) synthase in Escherichia coli that catalyzes the initial condensation reaction between malonyl-ACP and a short-chain acyl-CoA. In this study, we demonstrated that replacement of the acetyl-CoA-specific E. coli FabH with a branched-chain-acyl-CoA-specific FabH directed the flux to the synthesis of BCFAs, resulting in a significant enhancement in BCFA titer compared to a strain containing both acetyl-CoA- and branched-chain-acyl-CoA-specific FabHs. We further demonstrated that the composition of BCFAs can be tuned by engineering the upstream pathway to control the supply of different branched-chain acyl-CoAs, leading to the production either even-chain-iso-, odd-chain-iso-, or odd-chain-anteiso-BCFAs separately. Overall, the top-performing strain from this study produced BCFAs at 126 mg/L, comprising 52% of the total free fatty acids. Biotechnol. Bioeng. 2015;112: 1613-1622. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: The movement of live fish between fish farms has been identified as a critical risk factor in the spread of disease yet these movements are an essential part of fish farm production cycles. Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, is a disease which affects farmed salmon and trout production, although the impact on trout is considered less serious than on salmon. It is therefore desirable to minimise the exposure of salmon to R. salmoninarum. The approach presented here shows the potential for the salmon and trout industries to be split into two separately managed compartments in terms of control of spread of BKD by live fish movements. This compartmentalisation system is supported by the low number of cross compartment movements with only six out of 207 active farms in compartment S (mainly salmon) receiving fish from a farm located in compartment T (mainly trout). [Copyright &y& Elsevier]

Abstract: Bacterial kidney disease (BKD) (caused by Renibacterium salmoninarum) can result in significant mortality in Scottish salmon farms, but is considered to be a minor issue on trout farms. Controlling R. salmoninarum infection in trout to protect farmed salmon would be effective only if the risk posed from trout is significant both in absolute terms and relative to other potential sources of R. salmoninarum. To assess this, three complementary reviews are undertaken: review of data quality on BKD in Scotland and the national level prevalence and dynamics these data imply; case studies of recent BKD outbreaks in Scotland; and an assessment of the epidemiological and management factors that maintain and spread R. salmoninarum within and between the trout and salmon industries. These are then synthesised into a conclusion on the factors required for control of BKD in salmon. Most observed spread of R. salmoninarum occurred within single species or even companies, so the majority of cases in farmed salmon are linked to other salmon (and not to trout) farms. There is substantive geographical separation of areas of production for trout and salmon and transmission between salmon and trout networks is limited. The bacterium does not survive long in water so hydrodynamic transmission is likely to be localised. Currently R. salmoninarum is extremely rare in Scottish wild fish; this has not always been the case. Wild fish therefore probably play a limited role, but might act as reservoirs or vectors. The general conclusion is that to a large extent the transmission of R. salmoninarum in salmon and trout production can be separated and so there is potential to compartmentalise BKD controls, either by host species or geographical area. [Copyright &y& Elsevier]

The article discusses research on the changes in the histopathology and immune responses of 2 Chinook salmon stocks from Lake Michigan, Wisconsin and from Green River in Washington, which are related to their differential survival after Renibacterium salmoninarum infection challenge. It compares the onset of death and mean day to death (MDD) in both stocks. It is said that the improved capability of a stock from Wisconsin to resist such infection serves as a possible mechanism for its survival. The research revealed increased levels of mortality in Green River stock upon reaching the 44 d post-infection (dpi). Also noted is the link between greater survival of the WI stock and reduced case of immune-mediated pathology.

Loop-mediated isothermal amplification (LAMP) is a novel technique for nucleic acid amplification with high specificity, sensitivity and rapidity and does not require expensive equipment or reagents. In the present study, we developed and evaluated a LAMP method for the rapid detection of Renibacterium salmoninarum causing the bacterial kidney disease in salmonids. This method was more sensitive than quantitative real-time polymerase chain reaction (qPCR). Using DNA template extracted from cultured R. salmoninarum, the LAMP method gave an amplification signal from template diluted to 10−8 while the limit of detection of qPCR was10−7. The LAMP method was also highly specific and did not amplify DNA purified from five other Gram-positive and -negative bacterial fish pathogens. The method also worked well using extracts of macrophages infected with R. salmoninarum and kidney material from rainbow trout, which were positive for R. salmoninarum by qPCR and crude R. salmoninarum culture. There was some evidence for inhibitors of the LAMP reaction in the kidney samples, which was overcome by diluting the sample. [ABSTRACT FROM AUTHOR]

The objective of this study was to obtain diagnostic performance estimates for immunofluorescence antibody test (IFAT) and quantitative polymerase chain reaction (qPCR) tests, for Bacterial Kidney Disease (BKD) surveillance in farmed Atlantic salmon (Salmo salar.) broodstock without clinical signs compatible with the disease in Chile. To obtain diagnostic sensitivity (DSe) and specificity (DSp) estimates of those tests, an expert elicitation process was conducted using the trial roulette method during a workshop with 18 national experts on BKD diagnostics and control. A questionnaire was given to the experts to gather information on their previous experience with BKD, and 12 experts who received an introduction to the expert-elicitation process and graphical representation of statistical distributions. Experts were divided into three groups and requested to draw distributions of DSe and DSp parameters using an online tool. Then figures where projected and discussed among participants. After the discussion round, experts were requested to redraw their distributions (if considered necessary). The agreement between groups was assessed by calculating the overlapping areas between the three distributions for each parameter. Finally, a consensus distribution was generated. In general, groups had moderate to high agreement with overlapping areas between 53% to 93% for DSp IFAT , DSe qPCR , and DSp qPCR. Conversely, no agreement was reached for the DSe IFAT distribution. Specifically, median estimates of 89.5%, 90.5%, and 95.9%, were obtained for DSp IFAT , DSe qPCR , & DSp qPCR , respectively. In the case of DSe IFAT , the first group provided a median estimate of 28%, whereas groups 2 and 3 reached a consensus value of approximately 62%. This study provides information that is not available in the country, and will help to adjust current BKD control programs, which mainly rely on the use of qPCR assays. • This research estimates diagnostic performance of IFAT and qPCR tests for BKD surveillance in Atlantic salmon broodstock. • To obtain diagnostic sensitivity (DSe) and specificity (DSp) estimates of those tests, an expert elicitation process was conducted using the trial roulette method. • Expert agreed in DSp IFAT , DSe qPCR , & DSp qPCR parameters with median estimates of 89.5%, 90.5%, and 95.9%, respectively. • No agreement was reached on DSe IFAT test performance among experts. [ABSTRACT FROM AUTHOR]

Purpose: Membrane fluidity to a large extent is governed by the presence of branched-chain fatty acids (BCFAs). Branched-chain α-keto acid dehydrogenase (BKD) is the key enzyme in BCFA synthesis. A Staphylococcus aureus BKD-deficient strain still produced substantial levels of BCFAs. Pyruvate dehydrogenase (PDH) with structural similarity to BKD has been speculated to contribute to BCFAs in S. aureus., Methodology: This study was carried out using BKD-, PDH- and BKD : PDH-deficient derivatives of methicillin-resistant S. aureus strain JE2. Differences in growth kinetics were evaluated spectrophotometrically, membrane BCFAs using gas chromatography and membrane fluidity by fluorescence polarization. Carotenoid levels were estimated by measuring A465 of methanol extracts from 48 h cultures. MIC values were determined by broth microdilution.Results/Key findings. BCFAs made up 50 % of membrane fatty acids in wild-type but only 31 % in the BKD-deficient mutant. BCFA level was ~80 % in the PDH-deficient strain and 38 % in the BKD : PDH-deficient strain. BKD-deficient mutant showed decreased membrane fluidity, the PDH-deficient mutant showed increased membrane fluidity. The BKD- and PDH-deficient strains grew slower and the BKD : PDH-deficient strain grew slowest at 37 °C. However at 20 °C, the BKD- and BKD : PDH-deficient strains grew only a little followed by autolysis of these cells. The BKD-deficient strain produced higher levels of staphyloxanthin. The PDH-deficient and BKD : PDH-deficient strains produced very little staphyloxanthin. The BKD-deficient strain showed increased susceptibility to daptomycin., Conclusion: The BCFA composition of the cell membrane in S. aureus seems to significantly impact cell growth, membrane fluidity and resistance to daptomycin.

During infection, macrophage lineage cells eliminate infiltrating pathogens through a battery of antimicrobial responses, where the efficacy of these innate immune responses is pivotal to immunological outcomes. Not surprisingly, many intracellular pathogens have evolved mechanisms to overcome macrophage defenses, using these immune cells as residences and dissemination strategies. With pathogenic infections causing increasing detriments to both aquacultural and wild fish populations, it is imperative to garner greater understanding of fish phagocyte antimicrobial responses and the mechanisms by which aquatic pathogens are able to overcome these teleost macrophage barriers. Insights into the regulation of macrophage immunity of bony fish species will lend to the development of more effective aquacultural prophylaxis as well as broadening our understanding of the evolution of these immune processes. Accordingly, this review focuses on recent advances in the understanding of teleost macrophage antimicrobial responses and the strategies by which intracellular fish pathogens are able to avoid being killed by phagocytes, with a focus on Mycobacterium marinum., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The errors associated with calculating misorientation axes from electron backscatter diffraction (EBSD) data have been assessed experimentally. EBSD measurements were made on the same grains after imposed rotations of 2°, 5°, 7°, 10°, 12°, 17°, 27° and 180° around the normal to the specimen surface. The misorientation magnitudes and the misorientation axes associated with the imposed rotations have been calculated from the EBSD data. Individual measurements of misorientation axes are precise for misorientation magnitudes greater than ≈ 20°. The errors must be appreciated when assessing misorientation data at lower misorientation magnitudes and particularly at magnitudes less than 5°. Where misorientation axes can be characterized by the distribution of axes from a number of individual measurements, current EBSD techniques are satisfactory, for data sets of 30 measurements, as long as misorientation magnitudes are 10° or more. With larger data sets it may be possible to extend this approach to smaller misorientation magnitudes. For characterization of individual misorientations less than 5°, new EBSD techniques need to be developed. [ABSTRACT FROM AUTHOR]

Two waxy rice (TNW1 and TCSW1, exhibiting high and low amylase activity, respectively), were stored at 4 and 17 °C (polished rice) and at room temperature (paddy rice) for 15 months. The fine structure of starch isolated from the aged rice and the pasting properties of starch and rice flour were studied. After storage, the percentage of short amylopectin (AP) chains increased in TNW1, and no uniform changing pattern was observed in the chain-length (CL) distribution of TCSW1. The viscosity of starch isolated from the aged rice increased as the storage temperature and duration increased. We hypothesised that this increase was due to the hydrolysis of AP by endogenous amylase and the generation of small clusters during storage, which caused the simple dissociation of AP and a high swelling degree of starch granules during gelatinisation. Factor analysis of the first two factors associated with the characteristics of viscograms and the CL of AP explained 72% of the total variation., (Copyright © 2013 Elsevier Ltd. All rights reserved.)