Purification of plant-derived anti-virus mAb through optimized pH conditions for coupling between protein A and epoxy-activated beads
The main goal of this research was to determine optimum pH conditions for coupling between protein A and epoxy-activated Sepharose beads for purification of monoclonal antibodies (mAbs) expressed in plants. To confirm the effect of pH conditions on purification efficacy, epoxy-activated agarose beads were coupled to protein A under the pH conditions of 8.5, 9.5, 10.5, and 11.5 (8.5R, 9.5R, 10.5R, and 11.5R, respectively). A total of 300 g of fresh leaf tissue of transgenic Arabidopsis expressing human anti-rabies mAb (mAbP) SO57 were harvested to isolate the total soluble protein (TSP). An equal amount of TSP solution was applied to five resin groups including commercial protein A resin (GR) as a positive control. The modified 8.5R, 9.5R, 10.5R, and 11.5R showed delayed elution timing compared to the GR control resin. Nano-drop analysis showed that the total amount of purified mAbPSO57 mAbs from 60 g of fresh leaf mass were not significantly different among 8.5R (400 μg), 9.5R (360 μg), 10.5R (380 μg), and GR (350 μg). The 11.5R (25 μg) had the least mAbPSO57. SDS–PAGE analysis showed that the purity of mAbPSO57 was not significantly different among the five groups. Rapid fluorescent focus inhibition tests revealed that virus-neutralizing efficacies of purified mAbPSO57 from all the five different resins including the positive control resin were similar. Taken together, both pH 8.5 and 10.5 coupling conditions with high recovery rate should be optimized for purification of mAbPSO57 from transgenic Arabidopsis plant, which will eventually reduce down-stream cost required for mAb production using the plant system.
Song et al. (2019) Purification of plant-derived anti-virus mAb through optimized pH conditions for coupling between protein A and epoxy-activated beads. PeerJ 7:e6828 https://doi.org/10.7717/peerj.6828
Dietary supplementation of black soldier fly (Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron (Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets
The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.
Foysal et al. (2019) Dietary supplementation of black soldier fly (Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron (Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets. PeerJ 7:e6891 https://doi.org/10.7717/peerj.6891
Enzyme characterization and biological activities of a resuscitation promoting factor from an oil degrading bacterium Rhodococcus erythropolis KB1
Resuscitation-promoting factors (Rpf) are a class of muralytic enzymes, which participate in recovery of dormant cells and promoting bacteria growth in poor media. In the present study the expression vector of the rpf-1 gene from an oil-degrading bacterium Rhodococcus erythropolis KB1 was constructed and expressed in Escherichia coli. The expressed protein was purified by Ni2+-affinity chromatography, and showed muralytic activity when measured with 4-methylumbelliferyl-β-D-N,N′,N″-triacetyl chitotrioside as substrate. Addition of purified Rpf-1 to R. erythropolis culture efficiently improved bacterial cell growth. The purified protein also increased resuscitation of viable but nonculturable cells of R. erythropolis to culturable state. The conserved amino acid residues including Asp45, Glu51, Cys50, Thr60, Gln69, Thr74, Trp75 and Cys114 of the Rpf-1 were replaced with different amino acids. The mutant proteins were also expressed and purified with Ni2+-affinity chromatography. The muralytic activities of the mutant proteins decreased to different extents when compared with that of the wild type Rpf-1. Gln69 was found to play the most important role in the enzyme activity, substitution of Gln69 with lysine (Q69K) resulted in the greatest decrease of muralytic activity. The other amino acid residues such as Asp45, Glu51, Cys50 and Cys114 were also found to be very important in maintaining muralytic activity and biological function of the Rpf-1. Our results indicated that Rpf-1 from R. erythropolis showed muralytic activities and weak protease activity, but the muralytic activity was responsible for its growth promotion and resuscitation activity.
Luo et al. (2019) Enzyme characterization and biological activities of a resuscitation promoting factor from an oil degrading bacterium Rhodococcus erythropolis KB1. PeerJ 7:e6951 https://doi.org/10.7717/peerj.6951
Genetic variability and structure of the Olive Field Mouse: a sigmodontine rodent in a biodiversity hotspot of southern Chile
The temperate rainforests of southern Chile, a recognized biodiversity hotspot, were significantly affected by Pleistocene glacial cycles in their southern portion and have been severely disrupted mainly due to recent human activities. Additionally, the landscape is characterized by a series of potential barriers to gene flow, such as the Chacao Channel, Cordillera de Piuche in Chiloé and both the Ancud and the Corcovado gulfs. We used mitochondrial DNA sequences and microsatellite data across several populations to evaluate the genetic variability and structure of the sigmodontine rodent Abrothrix olivacea brachiotis, one of the most common species of small mammals and an inhabitant of these biodiverse forests. Sequencing data showed that along with the recovery of high haplotype variation for this species, there was a low nucleotide diversity between haplotypes, showing no genetic differences between the Chiloé Island and continental populations in southern Chile or through any other geographic barrier in the study area. However, microsatellite data exhibited some level of population structuring. The most evident clusterings were those of the Chiloé Island and that of North Patagonia. These findings are corroborated by a barrier analysis that showed a genetic barrier in the latter areas, whereas the Chacao Channel was not a significant barrier for this rodent. Overall, the genetic variability and structure of A. o. brachiotis was concordant with historical factors, such as the Last Glacial Maximum and the presence of geographic elements that isolate populations.
Zepeda et al. (2019) Genetic variability and structure of the Olive Field Mouse: a sigmodontine rodent in a biodiversity hotspot of southern Chile. PeerJ 7:e6955 https://doi.org/10.7717/peerj.6955
Actuopaleoichnology of a modern Bay of Fundy macro-tidal flat: analogy with a Mississippian tidal flat deposit (Hartselle Sandstone) from Alabama
Trace fossil zonation in the Hartselle Sandstone of Mississippian age (Chesterian: Visean-Serpukhovian) exposed on Fielder Ridge, Alabama is compared with modern macro-tidal flat ichnocoenoses on the Bay of Fundy at Lubec, Maine, and demonstrated to be analogous by sedimentologic and ichnotaxonomic criteria. The modern flat has minimal influence from either waves or freshwater influx, and can be divided into five distinct ichnocoenoses, characterized by surface traces (epichnia) and four sedimentologic facies defined by gross grain texture or hydrodynamic characteristics, but lacking significant surface traces. Several characteristics of tidal flat deposits in a fetch-limited, marine (i.e., non-estuarine), meso- to macro-tidal regime can be used to recognize similar environments as old as the late Paleozoic. These criteria include (1) limited influence of wind and waves on the depositional environment, (2) lack of significant freshwater influence and therefore any persistent brackish environments, (3) a distinct spatial distribution of microenvironments defined by substrate and exposure period, (4) high diversity of epichnial traces directly associated with microenvironments across the tidal flat, (5) generally low degree of reworking of traces by bioturbation but high degree of reworking by tidal currents, and (6) preservation of traces of predation and scavenging behavior on an exposed surface. These features, together with the regional depositional pattern of the Hartselle Sandstone interpreted as tide-influenced bars and shoals, support a meso- to macro-tidal interpretation of the depositional environment.
Zachos et al. (2019) Actuopaleoichnology of a modern Bay of Fundy macro-tidal flat: analogy with a Mississippian tidal flat deposit (Hartselle Sandstone) from Alabama. PeerJ 7:e6975 https://doi.org/10.7717/peerj.6975
Evidence for low prevalence of ranaviruses in Ontario, Canada’s freshwater turtle population
Background Ontario, Canada is home to eight native species of turtles; all eight are federally listed as Species At Risk, due to anthropogenic threats. However, until recently, reports of infectious disease have been lacking. Ranavirus is seen as an emerging threat for ectotherms globally, with mass die-offs most often reported in amphibians. Ranavirus has been detected in Ontario’s amphibian populations, can be transmitted via water, and can be transmitted from amphibians to turtles. However, no studies on the prevalence of this virus in Ontario’s turtles have previously been carried out. With recent reports of two confirmed positive case of ranavirus in turtles in Ontario, a knowledge of the ecology of ranavirus in Ontario’s turtles has become even more important. This study estimates the prevalence of ranavirus in Ontario’s turtles, and investigates the hypothesis that this is a newly emergent disease. Methods Sixty-three samples were tested for ranavirus via PCR. These included a variety of turtle species, across their home range in Southern Ontario. Fifty-two of the samples originated from the liver and kidney of turtles who had succumbed to traumatic injuries after being admitted to the Ontario Turtle Conservation Centre; ten of the samples were taken from cloacal swabs, lesion swabs, or tail clips collected from live turtles showing signs of clinical disease. One of the live turtles was later euthanized for humane reasons and PCR was also carried out on the liver/kidney. Results None of the 63 samples were found to be positive for ranavirus via PCR. The zero prevalence found in this study translates into a population prevalence estimate of less than 5%, with no change in prevalence from 2014–2018. Discussion This is the first report on the prevalence of ranavirus in Ontario’s turtles, and will help build an understanding of the ecology of this virus in Ontario. Ranavirus has historically been underreported in reptiles, but there has been an increase in global reports recently, most likely due to increased awareness. A carrier state is thought to exist in reptiles which makes surveillance in the population via random sampling a viable method of detection of prevalence. The first report of ranavirus in Ontario turtles occurred in 2018. This study suggests a continued low population prevalence for the years 2014–2018, however. Ongoing surveillance is necessary, as well as investigation of the eDNA presence in waterways as compared to the PCR of resident turtles, to further understand the sensitivity of these species to ranavirus infection. The utilization of qPCR would be helpful, to better quantify any positives encountered.
Carstairs (2019) Evidence for low prevalence of ranaviruses in Ontario, Canada’s freshwater turtle population. PeerJ 7:e6987 https://doi.org/10.7717/peerj.6987
Candiduria in hospitalized patients: an investigation with the Sysmex UF-1000i urine analyzer
Background Candiduria is common in hospitalized patients. Its management is limited because of inadequate understanding. Previous epidemiological studies based on culture assay have been limited to small study populations. Therefore, data collected by automated systems from a large target population are necessary for more comprehensive understanding of candiduria in hospitalized patients. Methods To determine the performance of the Sysmex UF-1000i in detecting candiduria, a cross-sectional study was designed and conducted. A total of 203 yeast-like cell (YLC)-positive and 127 negative samples were randomly chosen and subjected to microbiologic analysis. The receiver operating characteristic curve (ROC) was used to evaluate the ability of YLC counts as measured by the Sysmex UF1000i to predict candiduria. Urinalysis data from 31,648 hospitalized patients were retrospectively investigated, and statistical analysis was applied to the data collected. Results Using a cutoff value of 84.6 YLCs/µL, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the yeast like cell (YLC) counts to predict candiduria were 61.7%, 84.1%, 88.6% and 66.3%, respectively. C. glabrata (33.6%) and C. tropicalis (31.4%) were more prevalent than C. albicans (24.3%) in the present study. Of the investigated hospitalized patients, 509 (1.61%) were considered candiduria-positive. Age, gender and basic condition were associated with candiduria in hospitalized patients. In the ICU setting, urinary catheterization appeared to be the only independent risk factor contributing to candiduria according to our investigation. Although antibiotic therapy has been reported to be a very important risk factor, we could not confirm its significance in ICU candiduria patients because of excessive antibiotic usage in our hospital. Conclusions The YLC measured by Sysmex UF-1000i is a practical and convenient tool for clinical candiduria screening prior to microbiologic culture. Candiduria is common in hospitalized patients, and its incidence varies according to age, gender and the wards where it is isolated. Candiduria had no direct connection with mortality but might be considered a marker of seriously ill patients who need particular attention in the clinic.
He et al. (2019) Candiduria in hospitalized patients: an investigation with the Sysmex UF-1000i urine analyzer. PeerJ 7:e6935 https://doi.org/10.7717/peerj.6935
Clinicopathological characteristics and prognosis of pulmonary large cell neuroendocrine carcinoma aged ≥65 years
Objective The present study was designed to better characterize the clinicopathological features and prognosis in patients aged ≥65 years with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods Eligible patients with pulmonary LCNEC were retrieved from the Surveillance, Epidemiology, and End Results database between January 2004 and December 2013. The primary endpoints included cancer-specific survival (CSS) and overall survival (OS). Results Data of 1,619 eligible patients with pulmonary LCNEC were collected. These patients were subsequently categorized into two groups: 890 patients in the older group (age ≥65 years), and 729 in the younger group (age <65 years). More patients were of white ethnicity, stage I, married, and with tumor size <5 cm in the older group in comparison to the younger group. However, there were a significantly lower proportion of patients undergoing surgery, chemotherapy, and radiotherapy in the older group. The 5-year CSS rates of the younger group and older group were 23.94% and 17.94% (P = 0.00031), respectively, and the 5-year OS rates were 20.51% and 13.47% (P < 0.0001), respectively. Multivariate analyses indicated that older age (CSS: HR 1.20, 95% CI [1.07–1.36], P = 0.0024; OS: HR 1.26, 95% CI [1.12–1.41], P < 0.0001) was an independent risk factor for poor prognosis. The mortality risk of the elderly increased in almost every subgroup, especially in OS. Finally, significant predictors for better OS and CSS in patients over age 65 included tumor size <5 cm, lower stage, and receiving surgery, chemotherapy, or radiotherapy. Conclusion The prognosis of patients aged ≥65 years with pulmonary LCNEC was worse than that of younger patients. However, active and effective therapy could significantly improve the survival of older patients with pulmonary LCNEC.
Cao et al. (2019) Clinicopathological characteristics and prognosis of pulmonary large cell neuroendocrine carcinoma aged ≥65 years. PeerJ 7:e6824 https://doi.org/10.7717/peerj.6824
Retrospective study on the impact of ulnar nerve dislocation on the pathophysiology of ulnar neuropathy at the elbow
Introduction High resolution ultrasonography (US) has been used for diagnosis and evaluation of entrapment peripheral neuropathy. Ulnar neuropathy at the elbow (UNE) is the second most common focal entrapment neuropathy. The ulnar nerve tends to move to the anteromedial side and sometimes subluxates or dislocates over the medial epicondyle as the elbow is flexed. Dislocation of the ulnar nerve during elbow flexion may contribute to friction injury. We aimed to investigate the effects which the dislocation of ulnar nerve at the elbow could have on the electrophysiologic pathology of UNE. Materials We retrospectively reviewed 71 arms of UNE. The demographic data, electrodiagnosis findings and US findings of ulnar nerve were analyzed. We classified the electrodiagnosis findings of UNE into three pathologic types; demyelinating, sensory axonal loss, and mixed sensorimotor axonal loss. The arms were grouped into non-dislocation, partial dislocation, and complete dislocation groups according to the findings of nerve dislocation in US examination. We compared the electrodiagnosis findings, ulnar nerve cross sectional areas in US and electrodiagnosis pathology types among the groups. Results A total of 18 (25.3%) arms showed partial dislocation, and 15 (21.1%) arms showed complete dislocation of ulnar nerve in US. In the comparison of electrodiagnosis findings, the partial and complete dislocation groups showed significantly slower conduction velocities and lower amplitudes than non-dislocation group in motor conduction study. In the sensory conduction study, the conduction velocity was significantly slower in partial dislocation group and the amplitude was significantly lower in complete dislocation group than non-dislocation group. In the comparison of US findings, patients in partial and complete dislocation groups showed significantly larger cross sectional areas of the ulnar nerve. The comparison of electrodiagnosis pathologic types among the groups revealed that there were significantly larger proportions of the axonal loss (sensory axonal loss or mixed sensorimotor axonal loss) in partial and complete dislocation groups than non-dislocation group. Conclusion The ulnar nerve dislocation could influence on the more severe damage of the ulnar nerve in patients with UNE. It might be important to evaluate the dislocation of the ulnar nerve using US in diagnosing ulnar neuropathy for predicting the prognosis and determining the treatment direction of UNE.
Kang et al. (2019) Retrospective study on the impact of ulnar nerve dislocation on the pathophysiology of ulnar neuropathy at the elbow. PeerJ 7:e6972 https://doi.org/10.7717/peerj.6972
Lateralization (handedness) in Magellanic penguins
Lateralization, or asymmetry in form and/or function, is found in many animal species. Brain lateralization is considered adaptive for an individual, and often results in “handedness,” “footedness,” or a side preference, manifest in behavior and morphology. We tested for lateralization in several behaviors in a wild population of Magellanic penguins Spheniscus magellanicus breeding at Punta Tombo, Argentina. We found no preferred foot in the population (each penguin observed once) in stepping up onto an obstacle: 53% stepped up with the right foot, 47% with the left foot (n = 300, binomial test p = 0.27). We found mixed evidence for a dominant foot when a penguin extended a foot for thermoregulation, possibly depending on the ambient temperature (each penguin observed once). Penguins extended the right foot twice as often as the left foot (n = 121, p < 0.0005) in 2 years when we concentrated our effort during the heat of the day. In a third year when we observed penguins early and late in the day, there was no preference (n = 232, p = 0.59). Penguins use their flippers for swimming, including searching for and chasing prey. We found morphological evidence of a dominant flipper in individual adults: 60.5% of sternum keels curved one direction or the other (n = 76 sterna from carcasses), and 11% of penguins had more feather wear on one flipper than the other (n = 1217). Right-flippered and left-flippered penguins were equally likely in both samples (keels: p = 0.88, feather wear: p = 0.26), indicating individual but not population lateralization. In fights, aggressive penguins used their left eyes preferentially, consistent with the right side of the brain controlling aggression. Penguins that recently fought (each penguin observed once) were twice as likely to have blood only on the right side of the face (69%) as only on the left side (31%, n = 175, p < 0.001). The proportion of penguins with blood only on the right side increased with the amount of blood. In most fights, the more aggressive penguin used its left eye and attacked the other penguin’s right side. Lateralization depended on the behavior tested and, in thermoregulation, likely on the temperature. We found no lateralization or mixed results in the population of Magellanic penguins in three individual behaviors, stepping up, swimming, and thermoregulation. We found lateralization in the population in the social behavior fighting.
Stor et al. (2019) Lateralization (handedness) in Magellanic penguins. PeerJ 7:e6936 https://doi.org/10.7717/peerj.6936