Objective grading of rib eye traits using the Q-FOM™ camera in Australian beef carcasses.

The objective of this study was to develop calibration models against rib eye traits and independently validate the precision, accuracy, and repeatability of the Frontmatec Q-FOM™ Beef grading camera in Australian carcasses. This study compiled 12 different research datasets acquired from commercial processing facilities and were comprised of a diverse range of carcass phenotypes, graded by industry identified expert Meat Standards Australia (MSA) graders and sampled for chemical intramuscular fat (IMF%). Calibration performance was maintained when the device was independently validated. For continuous traits, the Q-FOM™ demonstrated precise (root mean squared error of prediction, RMSEP) and accurate (coefficient of determination, R2) prediction of eye muscle area (EMA) (R2 = 0.89, RMSEP = 4.3 cm2, slope = 0.96, bias = 0.7), MSA marbling (R2 = 0.95, RMSEP = 47.2, slope = 0.98, bias = -12.8) and chemical IMF% (R2 = 0.94, RMSEP = 1.56%, slope = 0.96, bias = 0.64). For categorical traits, the Q-FOM™ predicted 61%, 64.3% and 60.8% of AUS-MEAT marbling, meat colour and fat colour scores equivalent, and 95% within ±1 classes of expert grader scores. The Q-FOM™ also demonstrated very high repeatability and reproducibility across all traits.

A fluorescence spectroscopic study of light transmission and adaxial-abaxial distribution of emitting compounds in leaves of Christmas star (Euphorbia pulcherrima).

In situ fluorescence measurements have been used to investigate relative amounts of blue-green pigments and their distributions in plant leaves from Euphorbia pulcherrima. Advantage was taken from the fact that this species has white leaves on the top, with low pigment concentrations, and green leaves on the stem with ordinary pigment concentrations. Excitation- and emission spectra below 410 nm from white leaves, where pigment absorption is low, are not distorted by self-absorption. Absorption- and reflection spectra from white and green leaves were measured using a spectrophotometer equipped with an integrating sphere. The absorption spectra were used to correct recorded fluorescence spectra for self-absorption. Self-absorption corrected photosystem fluorescence from green leaves, modeling light transmission in leaf tissue exponentially, matches to the excitation/emission spectra from white leaves, apart from small differences due to the pigment concentrations and selective scattering. The introduced exponentially decaying transmission relation also predicts that the ratio of excitation spectra from a white and green leaf is in proportion to the absorption spectrum of the green leaf, which was validated for Photosystem II particle fluorescence. This relation was also used to find a scaled absorption spectrum responsible for blue-green emission, which was assumed to originate from lignin. Excitation/emission spectra of the blue-green fluorescence were decomposed into five components and their relative amounts from adaxial and abaxial sides of the leaves have been quantified. Fluorescence lifetime measurements of the leaves, upon 403 nm excitation, revealed three decay times corresponding to the lignin fluorophores emitting in blue and green spectral region, and indicated that emissions at 500 and 550 nm may originate from the same fluorophore residing in the two physically different environments.

Carotenoid radical ions: A laser flash photolysis study.

Laser excitation of a single precursor, namely 2-hydroxy-4'-(2-hydroxyethoxy)-2-methylpropiophenone (HHEMP), has been used for generating the radical cations and radical anions of various carotenoids in methanol. In the presence of oxygen, laser excitation of HHEMP undergoes an efficient α-cleavage reaction (Norrish type I) to form acyl radicals, which react with O2, in a nearly diffusion-controlled reaction, to form their corresponding strong oxidizing acylperoxyl radicals (RO2•) (E = ~1.1 V (v SHE)), which are capable of oxidizing almost all carotenoids. Under argon-saturated conditions and in the presence of strong base (0.01 M NaOH or tetrabutylammonium hydroxide (TBAOH)), the initially formed 2-hydroxy-2-propyl radical (ACH•), generated after LFP of HHEMP, is deprotonated to form the strong reducing acetone ketyl radical (AC•-) (E {acetone/ AC•-} = -2.1 V (v SHE)), which is capable of reducing all carbonyl-containing carotenoids. To validate this new proposed approach, retinal and ß-apo-8'-carotenal (APO), with known spectroscopic data, were investigated in methanol, acetonitrile and tetrahydrofuran (THF). In addition, the radical ions of newly investigated carotenoids, namely 4-oxo-ß-apo-15'-carotenoic acid (4-oxo-15'), crocetindial, 4-oxo-ß-apo-10'-carotenoic acid ethyl ester (4-oxo-10') and 4-oxo-ß-apo-8'-carotenoic acid ethyl ester (4-oxo-8') have been reported. Moreover, the scope of this approach has been extended to investigate the radical ions of chlorophyll b.

Transient and Persistent Gastric Microbiome: Adherence of Bacteria in Gastric Cancer and Dyspeptic Patient Biopsies after Washing.

Helicobacter pylori is a common colonizer of the human stomach, and long-term colonization has been related to development of atrophic gastritis, peptic ulcers and gastric cancer. The increased gastric pH caused by H. pylori colonization, treatment with antibiotics or proton pump inhibitors (PPI) may allow growth of other bacteria. Previous studies have detected non-Helicobacter bacteria in stomach biopsies, but no conclusion has been made of whether these represent a transient contamination or a persistent microbiota. The aim of this study was to evaluate the transient and persistent bacterial communities of gastric biopsies. The washed or unwashed gastric biopsies were investigated by cultivation and microbiota analysis (16S rRNA gene-targeted amplicon sequencing) for the distribution of H. pylori and other non-Helicobacter bacteria. The number of cultured non-Helicobacter bacteria decreased in the washed biopsies, suggesting that they might be a transient contamination. No significant differences in the bacterial diversity were observed in the microbiome analysis between unwashed and washed biopsies. However, the bacterial diversity in biopsies shown H. pylori-positive and H. pylori-negative were significantly different, implying that H. pylori is the major modulator of the gastric microbiome. Further large-scale studies are required to investigate the transient and persistent gastric microbiota.

Emergence of Enteroaggregative Escherichia coli within the ST131 Lineage as a Cause of Extraintestinal Infections.

Escherichia coli sequence type 131 (ST131) is a major cause of urinary and bloodstream infections. Its association with extended-spectrum ß-lactamases (ESBLs) significantly complicates treatment. Its best-described component is the rapidly expanding H30Rx clade, containing allele 30 of the type 1 fimbrial adhesin gene fimH This lineage appears to have emerged in the United States and spread around the world in part due to the acquisition of the ESBL-encoding blaCTX-M-15 gene and resistance to fluoroquinolones. However, non-H30 ST131 sublineages with other acquired CTX-M-type resistance genes are also emerging. Based on whole-genome analyses, we describe here the presence of an (fimH) H27 E. coli ST131 sublineage that has recently caused an outbreak of community-acquired bacteremia and recurrent urinary tract infections (UTIs) in Denmark. This sublineage has acquired both a virulence plasmid (pAA) that defines the enteroaggregative E. coli (EAEC) diarrheagenic pathotype and multiple genes associated with extraintestinal E. coli (ExPEC); combined, these traits have made this particular ST131 sublineage successful at colonizing its human host and causing recurrent UTI. Moreover, using a historic World Health Organization (WHO) E. coli collection and publicly available genome sequences, we identified a global H27 EAEC ST131 sublineage that dates back as far as 1998. Most H27 EAEC ST131 isolates harbor pAA or pAA-like plasmids, and our analysis strongly implies a single ancestral acquisition among these isolates. These findings illustrate both the profound plasticity of this important pathogenic E. coli ST131 H27 sublineage and genetic acquisitions of EAEC-specific virulence traits that likely confer an enhanced ability to cause intestinal colonization.IMPORTANCEE. coli ST131 is an important extraintestinal pathogenic lineage. A signature characteristic of ST131 is its ability to asymptomatically colonize the gastrointestinal tract and then opportunistically cause extraintestinal infections, such as cystitis, pyelonephritis, and urosepsis. In this study, we identified an ST131 H27 sublineage that has acquired the enteroaggregative diarrheagenic phenotype, spread across multiple continents, and caused multiple outbreaks of community-acquired ESBL-associated bloodstream infections in Denmark. The strain's ability to both cause diarrhea and innocuously colonize the human gastrointestinal tract may facilitate its dissemination and establishment in the community.

Parasites modulate the gut-microbiome in insects: A proof-of-concept study.

Host-parasite interactions may be modulated by host- or parasite-associated microbes, but the role of these are often overlooked. Particularly for parasites with intestinal stages (either larval or adult), the host gut microbiome may play a key role for parasite establishment; moreover, the microbiome may change in response to invading parasites. Hypothesis testing at the organismal level may be hampered, particularly in mammalian definitive hosts, by ethical, logistical, and economical restrictions. Thus, invertebrates naturally serving as intermediate hosts to parasites with complex life cycles may inform the development of mammalian models as an early-stage host-parasite model. In addition, several important pathogens are vectored by insects, and insect gut microbiome-pathogen interactions may provide essential base-line knowledge, which may be used to control vectorborne pathogens. Here, we used the grain beetle, Tenebrio molitor, a host of the tapeworm Hymenolepis diminuta, to explore interactions between infection status and resident gut microbiota at two pre-determined time points (day two and seven) post infection. Using 16S/18S microbial profiling, we measured key parameters of the composition, relative abundance, and diversity of the host gut bacteriome and mycobiome. In addition, we quantified the systemic beetle immune response to infection by Phenoloxidase activity and hemocyte abundance. We found significant changes in the gut bacteriome and mycobiome in relation to infection status and beetle age. Thus, the relative abundance of Proteobacteria was significantly higher in the gut of infected beetles and driven mostly by an increased abundance of Acinetobacter. In addition, the mycobiome was less abundant in infected beetles but maintained higher Shannon diversity in infected compared with non-infected beetles. Beetles treated with a broad-spectrum antibiotic (Tetracycline) exhibited significantly reduced parasite establishment compared with the untreated control group, indicating that the host microbiome may greatly influence hatching of eggs and subsequent establishment of H. diminuta larvae. Our results suggest that experimental work using invertebrates may provide a platform for explorative studies of host-parasite-microbe interactions and their underlying mechanisms.

Using optical fibers to measure absorption in intact conifer leaves, relative numbers of chloroplasts, and pigment content.

For investigations of ongoing processes in plants, such as photosynthesis in conifer leaves, nondestructive and noninvasive measuring techniques are needed. In this paper, a novel approach has been developed for the measurement of chloroplasts' numbers and pigment contents in conifer leaves based on the measurements of leaf absorption spectra using optical fibers and an array spectrophotometer. To eliminate the effect of scattering on the measured absorption spectra, a strategy has been applied taking advantage of the combined use of thin optical fibers normal to the needle's longitudinal axis and the phenomenon that scattering is largest in the forward direction. The optical path in the leaf is nearly the distance between the fiber tips; thus, we were able to obtain the absorption spectrum of the pigments in situ. A effect of the measured absorption spectra, occurring due to the organization of pigments in the leaf and interaction between light and leaf interior, can be accounted for by using the so-called Duysens transformation. Using this transformation, pigment contents and the relative number of chloroplasts can be obtained from the measured absorption spectra. We applied the method to observe pigment concentrations in different stages of the greening process in the leaves of two conifer species, Taxus baccata and Picea abies. The presented method may be used to estimate changes in chloroplast number and pigment content during various phases of greening of a species and to observe differences among various species.

ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin.

OBJECTIVES: This study compares the genome of an ST131 CMY-2-producing Escherichia coli isolate from a Danish patient with other ST131 CMY-2-producing E. coli isolates of both human and animal origin. METHODS: In 2016, an ST131 CMY-2-producing E. coli isolate (ESBL20160056) was obtained from a patient with a bloodstream infection. The genome of the ESBL20160056 isolate was compared with genomes from six ST131 CMY-2-producing E. coli isolates obtained from broiler meat imported to Denmark, 15 ST131 CMY-2-producing E. coli isolates obtained from Enterobase (http://enterobase.warwick.ac.uk) and two ST131 CMY-2-producing E. coli from European collaborators. The plasmid from ESBL20160056 was sequenced using a MinION Mk1B (Oxford Nanopore Technologies). RESULTS: The E. coli isolate from the Danish patient clustered together with 13 other fimH22 ST131 CMY-2-producing E. coli isolates in a distinct clade. The clade consisted of genomes from six E. coli isolates from humans collected in Denmark, Spain, Cambodia and the USA, six E. coli isolates obtained from broiler meat samples imported to Denmark from France, the Netherlands and Germany, and two E. coli isolates obtained from broilers in Belgium and Luxembourg. The 101.5 kb plasmid with blaCMY-2 from ESBL20160056 had an IncI1 replicon and belonged to ST12 using the plasmid MLST scheme. In total, 10 of the 14 ST131 E. coli isolates belonging to the fimH22 clade carried an IncI1 ST12 plasmid with blaCMY-2. CONCLUSIONS: From our data, it seems plausible that the ST131 fimH22 CMY-2-producing E. coli isolate obtained from the Danish patient could have a zoonotic broiler origin.

Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones.

Escherichia coli sequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410 E. coli isolates from Danish patients. Furthermore, E. coli ST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genes blaOXA-181 and blaNDM-5 of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework of E. coli ST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades in E. coli ST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum ß-lactamase (ESBL)-encoding gene blaCTX-M-15 and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying a blaOXA-181 carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene, blaNDM-5, on a conserved IncFII plasmid. From an epidemiological investigation of 49 E. coli ST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients with blaOXA-181- and blaNDM-5-carrying B4/H24RxC isolates. The accumulated multidrug resistance in E. coli ST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus, E. coli ST410 should be considered a lineage with emerging "high-risk" clones, which should be monitored closely in the future.IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a "high-risk" clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of the E. coli ST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively.

Exploring the reactivity of retinol radical cation toward organic and biological molecules: A laser flash photolysis study.

Vitamin A (retinol) and various natural retinoids are essential for life. Under oxidative conditions, vitamin A radical cation (RET+) can be formed. Many deleterious effects were reported about the formation of carotenoid radical cations in biological environments, on the other hand, little is known about the consequences of the RET+ formation in these environments. Therefore, it is important to explore the reactivity of RET+ toward various biological substrates. Here, we employed nanosecond laser flash photolysis (LFP) to generate RET+ (λmax=580nm in methanol) and examine its reactivity toward a wide range of biological molecules including amino acids, vitamins, carotenoids, naturally-occurring phenols, neurotransmitters such as catecholamines, wide range of phenol derivatives and some selected electron-donors. The results show that the reactivity of RET+ toward various substrates is strongly dependent on the polarity of solvent. In addition, RET+ is able to oxidize amino acids, which subsequently can lead to protein damage. However, the presence of vitamins (vitamins E and C), carotenoids and naturally-occurring phenols (e.g. resveratrol, vanillin, dopamine hydrochloride and l-Dopa) can inhibit the damaging effect of retinol+ by reducing it back to retinol. Vitamin E and carotenoids are the most efficient quenchers for the RET+ (diffusion-controlled reactions). Importantly, our results clearly indicate that the reactivity of RET+ is as strong as that of the powerful trichloromethylperoxyl radical (CCl3O2). Thereby, formation of RET+ in biological media is expected to induce bio-damage.

Competitive ligand exchange of crosslinking ions for ionotropic hydrogel formation.

Currently there are limitations to gelation strategies to form ionically crosslinked hydrogels, derived in particular from a lack of control over the release kinetics of crosslinking ions, which severely restrict applications. To address this challenge, we describe a new approach to form hydrogels of ionotropic polymers using competitive displacement of chelated ions, thus making specific ions available to induce interactions between polymer chains and form a hydrogel. This strategy enables control of ion release kinetics within an aqueous polymer solution and thus control over gelation kinetics across a wide range of pH. The described technique simplifies or facilitates the use of ionotropic hydrogels in a range of applications, such as 3D printing, microfluidic-based cell encapsulation, injectable preparations and large scale bubble and solid free mouldable gels. We investigate a range of chelator-ion combinations and demonstrate this powerful method to form hydrogels across a wide range of pH and µm-cm length scales. We highlight our findings by applying this gelation strategy to some of the more challenging hydrogel application areas using alginate and polygalacturonate as model polymer systems.

Hexanol-induced order-disorder transitions in lamellar self-assembling aggregates of bacteriochlorophyll c in Chlorobium tepidum chlorosomes.

Chlorosomes are light-harvesting complexes of green photosynthetic bacteria. Chlorosomes contain bacteriochlorophyll (BChl) c, d, or e aggregates that exhibit strong excitonic coupling. The short-range order, which is responsible for the coupling, has been proposed to be augmented by pigment arrangement into undulated lamellar structures with spacing between 2 and 3 nm. Treatment of chlorosomes with hexanol reversibly converts the aggregated chlorosome chlorophylls into a form with spectral properties very similar to that of the monomer. Although this transition has been extensively studied, the structural basis remains unclear due to variability in the obtained morphologies. Here we investigated hexanol-induced structural changes in the lamellar organization of BChl c in chlorosomes from Chlorobium tepidum by a combination of X-ray scattering, electron cryomicroscopy, and optical spectroscopy. At a low hexanol/pigment ratio, the lamellae persisted in the presence of hexanol while the short-range order and exciton interactions between chlorin rings were effectively eliminated, producing a monomer-like absorption. The result suggested that hexanol hydroxyls solvated the chlorin rings while the aliphatic tail partitioned into the hydrophobic part of the lamellar structure. This partitioning extended the chlorosome along its long axis. Further increase of the hexanol/pigment ratio produced round pigment-hexanol droplets, which lost all lamellar order. After hexanol removal the spectral properties were restored. In the samples treated under the high hexanol/pigment ratio, lamellae reassembled in small domains after hexanol removal while the shape and long-range order were irreversibly lost. Thus, all the interactions required for establishing the short-range order by self-assembly are provided by BChl c molecules alone. However, the long-range order and overall shape are imposed by an external structure, e.g., the proteinaceous chlorosome baseplate.

Epidemiology and control of an outbreak of classical swine fever in wild boar in Switzerland.

An outbreak of classical swine fever in wild boar in the southern part of Switzerland (Canton of Ticino) was investigated after the implementation of control measures in a defined infected area (the risk zone), and in a surrounding surveillance zone (the non-risk zone). After the disease had been detected, hunting was not allowed in the risk zone for over six months, during which the disease was left to run its course, but hunting was continued in the non-risk zone for one month. After seven months, a hunting strategy targeted at young animals was implemented in both zones. Between May 1998 and January 2000,1294 wild boar were shot or found dead, and diagnostic and biological data were collected and analysed. Only one animal from the non-risk zone was found to be seropositive for antibodies to the virus, whereas 179 of 528 wild boar from the risk zone were virus positive and 162 were seropositive. The proportion of virus-positive animals decreased from 62.7 per cent to zero over one year. During the first hunting season, seropositive animals were found in all age groups, but 12 months later only animals more than one year old had antibodies against the virus.