bluuebunny/crossref_metadata_2025 huggingface dataset:
Late Miocene Palaeocarya (Engelhardieae: Juglandaceae) from Southwest China and its biogeographic implications
Authors: Meng Hong‐Hu , Su Tao , Huang Yong‐Jiang , Zhu Hai , Zhou Zhe‐Kun
Published: February 2015

Fossil fruits of Palaeocarya (Juglandaceae) are described from late Miocene sediments of southeastern Yunnan, China. The fruits present a tri‐lobed wing consisting of an intact oblong‐ovate middle lobe and two lateral lobes. The lobes are apically obovate, and have pinnate venation. The middle lobe is thicker at the base and gradually tapers to the apex. The nutlet, located at the base of the winged fruit, is round and hispid, and is subdivided by a septum into two compartments. Based on extensive morphological comparisons to previously documented fossil fruits, we found that the fossil fruits align most closely with members of the genus Palaeocarya, but have a unique combination of characters. Thus, we describe the fossils as a new species, Palaeocarya hispida sp. nov. This species represents an important range expansion for low‐latitude occurrences of Palaeocarya in the late Miocene and therefore substantially improves our understanding of the biogeographic history of the genus. We propose that the wide distribution of Palaeocarya and relatively narrow distributions of close relatives, Engelhardia, Alfaropsis, and Oreomunnea, might be associated with a stepwise cooling and a major ice sheet expansion in the Antarctic and Arctic from the late middle Miocene to early Pliocene. In particular, the climatic oscillations during the Quaternary, such as the last glacial maximum, might have led to a decrease in the geographic distribution of Engelhardieae.
Obesity Alters the Peripheral Circadian Clock in the Aorta and Microcirculation
Authors: Nernpermpisooth Nitirut , Qiu Shuiqing , Mintz James D. , Suvitayavat Wisuda , Thirawarapan Suwan , Rudic Daniel R. , Fulton David J. , Stepp David W.
Published: February 2015

Objective

Perturbation of daily rhythm increases cardiovascular risk. The aim of this study was to determine whether obesity alters circadian gene expression and microvascular function in lean mice and obese (db/db) mice.

Methods

Mice were subjected to normal LD or DD to alter circadian rhythm. Metabolic parameters and microvascular vasoreactivity were evaluated. Array studies were conducted in the am and pm cycles to assess the rhythmicity of the entire genomics. Rhythmic expression of specific clock genes (Bmal1, Clock, Npas2, Per1, Per2, and Cry1), clock output genes (dbp), and vascular relaxation‐related genes (eNOS, GTPCH1) were assessed.

Results

Obesity was associated with metabolic dysfunction and impaired endothelial dilation in the microvasculature. Circadian rhythm of gene expression was suppressed 80% in both macro‐ and microcirculations of obese mice. Circadian disruption with DD increased fasting serum glucose and HbA1c in obese but not lean mice. Endothelium‐dependent dilation was attenuated in obese mice and in lean mice subjected to DD. Rhythmic expression of per1 and dbp was depressed in obesity. Expression of eNOS expression was suppressed and GTPCH1 lost rhythmic expression both in obesity and by constant darkness.

Conclusion

These results suggest that obesity reduces circadian gene expression in concert with impaired endothelial function. The causal relationship remains to be determined.
Programmable bio‐nanochip‐based cytologic testing of oral potentially malignant disorders in Fanconi anemia
Authors: Floriano P. N. , Abram T , Taylor L , Le C , Talavera H , Nguyen M , Raja R , Gillenwater A , McDevitt J , Vigneswaran N
Published: February 2015

Fanconi anemia (FA) is caused by mutations of DNA repair genes. The risk of oral squamous cell carcinoma (OSCC) among FA patients is 800‐folds higher than in the general population. Early detection of OSCC, preferably at it precursor stage, is critical in FA patients to improve their survival. In an ongoing clinical trial, we are evaluating the effectiveness of the programmable bio‐nanochip (p‐BNC)‐based oral cytology test in diagnosing oral potentially malignant disorders (OPMD) in non‐FA patients. We used this test to compare cytomorphometric and molecular biomarkers in OSCC cell lines derived from FA and non‐FA patients to brush biopsy samples of a FA patient with OPMD and normal mucosa of healthy volunteers. Our data showed that expression patterns of molecular biomarkers were not notably different between sporadic and FA‐OSCC cell lines. The p‐BNC assay revealed significant differences in cytometric parameters and biomarker MCM2 expression between cytobrush samples of the FA patient and cytobrush samples of normal oral mucosa obtained from healthy volunteers. Microscopic examination of the FA patient's OPMD confirmed the presence of dysplasia. Our pilot data suggests that the p‐BNC brush biopsy test recognized dysplastic oral epithelial cells in a brush biopsy sample of a FA patient.
Acupuncture for posttonsillectomy pain in children: a randomized, controlled study
Authors: Gilbey Peter , Bretler Shlomi , Avraham Yaniv , Sharabi‐Nov Adi , Ibrgimov Sasha , Luder Anthony
Published: February 2015

Background

Surgeons have searched for the technique or medication that will produce a ‘painless tonsillectomy’; however, this seems to be an impossible goal. Previous studies have shown that perioperative acupuncture may be a useful adjunct for acute postoperative pain and that acupuncture, in addition to nonsteroidal anti‐inflammatory drugs, is effective in adults for the treatment of postoperative swallowing pain after tonsillectomy. Acupuncture has been shown to be safe in children. A retrospective review of acupuncture for posttonsillectomy pain in juvenile patients showed a significantly reduced pain score immediately after treatment.

Aim

To examine whether acupuncture, in addition to conventional analgesic treatment, will be effective in the treatment of posttonsillectomy pain in children.

Methods

We conducted a randomized, controlled, single‐blinded study comparing conventional postoperative analgesic treatment with the same regime plus acupuncture to assess whether postoperative treatment of children aged 3–12 years undergoing tonsillectomy with acupuncture will reduce pain and to examine possible unwanted effects of this treatment.

Results

Sixty children were recruited and randomly divided into a study group and a control group. The results indicate that in the study group, there was less pain, less analgesic drug consumption, and higher patient/parent satisfaction with analgesic treatment scores. No adverse effects were recorded.

Conclusions

Acupuncture, in addition to conventional analgesic treatment, is an effective treatment for posttonsillectomy pain. Acupuncture is safe and well received by children and their parents.
Infantile Granular Parakeratosis: Cytologic Examination of Superficial Scrapings as an Aid to Diagnosis
Authors: Akkaya A. Deniz , Oram Yasemin , Aydın Özlem
Published: February 2015

Granular parakeratosis (GP) is a benign disorder of keratinization presenting with unilateral or bilateral red to brown hyperkeratotic plaques and papules at the intertriginous areas. The first pediatric case of GP was reported in 2002, and only a few cases have been reported since. Although the exact etiology of GP is unknown, it is thought that certain environmental factors compromise the epidermal barrier and lead to proliferation and altered maturation of the epidermis in predisposed individuals. The histopathology is diagnostic and reveals parakeratosis together with retention of keratohyalin granules within a disproportionately thickened stratum corneum and usually the preservation of stratum granulosum. Herein we report seven cases of infantile GP, six of which also had atopic dermatitis. Cytologic examination confirmed our clinical diagnosis by demonstrating the retention of keratohyalin granules and preservation of the nuclei from the superficial scrapings of the lesions, which we propose as a novel diagnostic technique. In all seven cases the lesions developed after the overuse of topical products and resolved with avoidance of their excessive use. We propose that atopic skin may be more prone to develop GP because the epidermal barrier is disrupted, resulting in the enhanced transepidermal penetration of topical products. In conclusion, GP should be included in the differential diagnosis of diaper area eruptions, especially in atopic children. Cytologic examination of superficial scrapings of the lesions can easily confirm the diagnosis of GP.
Congenital Lupus with Multiorgan Involvement: A Case Report and Review of Literature
Authors: Padilla‐España Laura , Díaz Cabrera Rocio , Del Boz Javier , Lozano Calero Carmen
Published: February 2015

Neonatal lupus erythematosus (NLE) is an autoimmune disease caused by transplacental antibodies that can damage fetal tissue and cause various findings. With the exception of congenital heart block, which can be easily recognized at birth because of neonatal cardiac monitoring during the delivery and immediately after birth, most cases of NLE are recognized within days to weeks of life, but fewer than 10 cases with findings present at birth have been reported. We report the case of a newborn with extensive cutaneous eruption at the time of birth and multisystemic involvement, including hematologic, respiratory, hepatic, and neurologic involvement.
Fibrous Hamartoma of Infancy: A Firm Plaque Presenting with Hypertrichosis and Hyperhidrosis
Authors: Melnick Laura , Berger Emily M. , Elenitsas Rosalie , Chachkin Samuel , Treat James R.
Published: February 2015

Fibrous hamartoma of infancy (FHI) is a rare, benign, soft tissue tumor. The lesion's clinical resemblance to more aggressive soft tissue tumors of childhood makes histologic diagnosis paramount. We report a unique presentation of a FHI associated with localized hypertrichosis and hyperhidrosis.
IgA nephropathy in a girl with mitochondrial disease
Authors: Nishida Masashi , Morimoto Masafumi , Ohno Kunihiko , Hamaoka Kenji
Published: February 2015

Mitochondrial renal disease is one of the important causes of end‐stage renal disease in children and its incidence may be underestimated. We here describe the case of a 13‐year‐old girl who was diagnosed with mitochondrial disease (MD) accompanied by IgA nephropathy (IgAN). She presented with persistent proteinuria, short stature, and hearing defect, and her younger sister had the same symptoms. Renal biopsy indicated mild focal segmental mesangial proliferation with dominant mesangial IgA deposition on immunofluorescence. Electron microscopy showed marked proliferation of abnormal mitochondria in the proximal tubular cells. Enzyme activity of the mitochondrial respiratory chain complex I and IV in cultured skin fibroblasts was significantly decreased. This case indicated the possible co‐occurrence of IgAN and MD. Underlying MD should be considered in patients with urine abnormalities, especially in those with multiple organ involvement.
Combined effects of girdling and leaf removal on fluorescence characteristic of Alhagi sparsifolia leaf senescence
Authors: Tang G. , Li X. , Lin L. , Guo H. , Li L.
Published: February 2015

Plant senescence is largely influenced by carbohydrate content. In order to investigate the impact of carbohydrate content on leaf senescence and photosystem II (PSII) during the senescence process, phloem girdling (PG), leaf removal (LR) and a combination of phloem girdling and leaf removal (GR) were performed on Alhagi sparsifolia (Fabaceae) at the end of the growing season. The results showed that during senescence, leaf soluble sugar content, starch content, the energy absorbed by the unit reaction centre (ABS/RC) increased; whereas, leaf photosynthetic rate, photosynthetic pigment content, maximum photochemical efficiency (φPo) and energy used by the acceptor site in electron transfer (ETo/RC) decreased. The degree of change was PG> GR> CK (control)> LR. The results of the present work implied that phloem girdling (PG) significantly accelerated leaf senescence, and that single leaf removal (LR) slightly delayed leaf senescence; although leaf removal significantly delayed the senescence process on the girdled leaf (GR). Natural or delayed senescence only slightly inhibited the acceptor site of PSII and did not damage the donor site of PSII. On the other hand, induced senescence not only damaged the donor site of PSII (e.g. oxygen‐evolving complex), but also significantly inhibited the acceptor site of PSII. In addition, leaf senescence led to an increase in the energy absorbed by the unit reaction centre (ABS/RC), which subsequently resulted in increasing excitation pressure in the reaction centre (DIo/RC), as well as additional saved Car for absorbing residual light energy and quenching reactive oxygen species during senescence.
Local climate explains degree of seed dormancy in Hypericum elodes L. (Hypericaceae)
Authors: Carta A. , Probert R. , Puglia G. , Peruzzi L. , Bedini G.
Published: February 2015

Seed dormancy and germination characteristics may vary within species in response to several factors. Knowledge of such variation is crucial to understand plant evolution and adaptation to environmental changes. We examined the correlation of climate and population genetic differentiation (ISSR) with primary seed dormancy and germination behaviour in populations of the Atlantic–European soft‐water pool specialist Hypericum elodes. Primary dormancy was measured by analysing seed germination response of fresh seeds and after various periods of cold stratification. Laboratory germination experiments revealed that the single most important factor for promoting germination was cold stratification prior to placing at the germination temperature. However, in agreement with their weaker primary dormancy, the seeds germinated well when fresh, and the benefit of cold stratification was more relaxed for the southern populations. Seeds of all populations demonstrated a near absolute requirement for a light and alternating temperature regime in order to germinate. The promoting effect of alternating temperatures was particularly effective at warm temperatures (mean 20 °C) but not at cool temperatures. Whilst seed germination requirements were similar among populations, the degree of primary dormancy varied considerably and was not associated with population genetic differentiation. Primary dormancy degree was instead associated with local climate: higher temperature in summer and rainfall in winter predicted weak and rapid loss of dormancy. These results suggest that seed maturation environment may play a substantial role in explaining the degree of dormancy in H. elodes, highlighting that physiological dormancy can be modulated by local climate.
Congenital Abnormality of the Vagina Complicated by Haemato‐Pyocolpos in a 1‐Year Labrador Retriever
Authors: Alonge S , Romussi S , Grieco V , Luvoni GC
Published: February 2015

Contents

A 1‐year‐old female Labrador retriever was referred with a few days history of haematic‐like vulvar discharge. Physical examination, vaginal inspection and palpation did not reveal any remarkable finding. Transabdominal ultrasound showed echogenic fluid accumulation in the vagina suggesting haemato‐pyocolpos. An exploratory laparotomy was performed: a well‐delimited ectasic vagina was identified. Ovariohysterectomy and partial vaginectomy and vaginoplasty were performed to spay the bitch and to remove the ectasic vagina. Post‐operative recovery and 12‐month follow‐up were uneventful. Clinical, morphological and histological findings were consistent with a congenital abnormality of the muscular layer of the vagina complicated by haemato‐pyocolpos. The disorganization of the vaginaltunica muscularismay have acted aslocus minoris resistentiaein the vaginal wall. The organ was dilated and atonic due to the gradual accumulation of physiological fluids complicated by an overgrowth of genital bacteria. This congenital disorder has to be taken into account as differential diagnosis of haemato‐pyocolpos with vaginal discharge in young bitches.
Determination of Appropriate Cryopreservation Protocols for Epididymal Cat Spermatozoa
Authors: Buranaamnuay K
Published: February 2015

Contents

Effects of Equex and glycerol additions and sample dilution step on frozen–thawed epididymal cat spermatozoa were investigated. The epididymal sperm pellets were resuspended in extenders using one‐ (groups III and IV) or two‐ (groups I, II, V and VI) step dilution. For one‐step dilution, the pellets were resuspended in plain egg yolk‐Tris medium (EYT) + 5% glycerol with (IV)/without (III) 0.5% Equex and cooled (4°C, 1 h). For two‐step dilution, the pellets were resuspended in EYT (I and V) and in EYT + 3% glycerol (II and VI), cooled and further diluted with EYT + 10% glycerol with (I)/without (V) 1% Equex and with EYT + 7% glycerol with (II)/without (VI) 1% Equex. Immediately after freeze–thawing, no differences (p > 0.05) were found in the motility, viability and membrane integrity (HOST) among the groups except the lowest HOST in IV (p = 0.005 to p = 0.04). The acrosome integrity (FITC) in group I was comparable to that in group II (p > 0.05) and was higher than the rest (p < 0.001 to p = 0.02). At 2 h after thawing, the motility, viability and HOST were comparable among the groups (p > 0.05) except the lower percentages of viability in III (p = 0.008 to p = 0.3) and of HOST in IV (p = 0.005 to p = 0.2). Two‐step dilutions with Equex (I, II) were more beneficial for the FITC at 2 h than without Equex (V) (p = 0.005 and p = 0.02) and than one‐step dilutions (III, IV) (p < 0.001 to p = 0.02). In conclusion, epididymal cat sperm quality after freeze–thawing could be improved when Equex was added and two‐step dilution was performed during freezing. The extenders prepared for the first step of dilution could be with (3%) or without (0%) glycerol.
Forced regressive deposits of a deglaciation sequence: Example from the Late Quaternary succession in the Lake Saint‐Jean basin (Québec, Canada)
Authors: Nutz Alexis , Ghienne Jean‐François , Schuster Mathieu , Dietrich Pierre , Roquin Claude , Hay Murray B. , Bouchette Frédéric , Cousineau Pierre A.
Published: February 2015

Differentiating between forced regressive deposits from deglacial periods in high latitude domains and forced regressive deposits from the onset of glacial periods in low latitude domains is fundamental for the accurate interpretation of glacial cycles within the geological record and then for the reconstruction of palaeogeography and palaeo‐climate. A forced regressive deglacial sequence is documented from the Lake Saint‐Jean basin (Québec, Canada). In this area, the Late Pleistocene to Holocene sediments have recorded the Laurentide ice sheet retreat accompanied by the invasion of marine waters (Laflamme Gulf) from ca 12·9 cal kyr bp. Subsequently, fluvio‐deltaic and coastal prograding wedges were deposited; they followed the base‐level fall due to glacio‐isostatic rebound. This succession, representing a transition from glacial to post‐glacial periods within a previously glaciated area, was investigated through recent mapping, preserved landforms, facies analysis, and new optical stimulated luminescence and radiocarbon dates. Three basin‐scale geological sections share a common lower part made of isolated ice‐contact fan deposits overlying bedrock. Throughout the entire basin, ice‐contact fans are capped by glacimarine muds. Above, fluvial and coastal prograding systems were deposited and evolved through four steps: (i) deltaic systems progressively increased in width; (ii) coastal influence on sedimentation increased; (iii) hydrographic drainage systems became more organised; and (iv) deltas graded from steep (Gilbert delta) to low‐angle foresets (mouth‐bar delta). Deposited during the base‐level fall from glacio‐isostatic rebound, the complete succession has been designated as a single falling stage system tract referred to as a deglacial falling stage system tract. It is representative of a deglaciation sequence in areas previously covered by ice during glacial periods (i.e. medium to high latitude domains). Diagnostic criteria are provided to identify such a deglacial falling stage system tract in the geological record, which may aid identification of previously unknown glacial cycles.
Extension of the Optimised Virtual Fields Method to Estimate Viscoelastic Material Parameters from 3D Dynamic Displacement Fields
Authors: Connesson N. , Clayton E. H. , Bayly P. V. , Pierron F.
Published: February 2015

In vivo measurement of the mechanical properties of soft tissues is essential to provide necessary data in biomechanics and medicine (early cancer diagnosis, study of traumatic brain injuries, etc.). Imaging techniques such as magnetic resonance elastography can provide 3D displacement maps in the bulk and in vivo, from which, using inverse methods, it is then possible to identify some mechanical parameters of the tissues (stiffness, damping, etc.). The main difficulties in these inverse identification procedures consist in dealing with the pressure waves contained in the data and with the experimental noise perturbing the spatial derivatives required during the processing. The optimised virtual fields method (OVFM) (Comput. Mech. 34, 2004, 439), designed to be robust to noise, presents natural and rigorous solution to deal with these problems. The OVFM has been adapted to identify material parameter maps from magnetic resonance elastography data consisting of 3D displacement fields in harmonically loaded soft materials. In this work, the method has been developed to identify elastic and viscoelastic models.

The OVFM sensitivity to spatial resolution and to noise has been studied by analysing 3D analytically simulated displacement data. This study evaluates and describes the OVFM identification performances: Different biases on the identified parameters are induced by the spatial resolution and experimental noise. The well‐known identification problems in the case of quasi‐incompressible materials also find a natural solution in the OVFM. Moreover, an a posteriori criterion to estimate the local identification quality is proposed. The identification results obtained on actual experiments are briefly presented.
A Bee Swarm Algorithm for Optimising Sensor Distributions for Impact Detection on a Composite Panel
Authors: Scott M. , Worden K.
Published: February 2015

This paper describes the development of a bee swarm algorithm for optimising the distribution of impact detection sensors on a composite plate. The algorithm was initially developed and tested on a travelling salesman problem, it was then adapted to solve the sensor placement problem using an artificial neural network to assess the fitness of sensor distributions. It performed well, managing to quickly find optimum distributions within a constrained set of neural network parameters. The algorithm was modified further, to optimise the neural network parameters alongside the sensor distributions and the range that the network parameters could take was substantially increased. This led to significant increases in accuracy. The algorithm showed itself to be a very effective tool in the sensor optimisation problem as well as demonstrating the benefits of thoroughly optimising the neural network parameters.
Exploring lava‐flow hazards at Pico Island, Azores Archipelago (Portugal)
Authors: Cappello Annalisa , Zanon Vittorio , Del Negro Ciro , Ferreira Teresa J. L. , Queiroz Maria G. P. S.
Published: February 2015

Pico, the youngest island of the Azores Archipelago (Portugal), is characterized by a central volcano and a 30‐km‐long fissure zone. Its eruption rate is the highest of the Azores islands, with more than 35 eruptions in the last 2000 years. Here, we estimate the lava‐flow hazard for Pico Island by combining the vent opening probability derived from the spatial distribution of eruptive fissures, the classes of expected eruptions inferred from the physical and chemical characteristics of historical eruptions, and the lava‐flow paths simulated by the MAGFLOW model. The most likely area to host new eruptions is along a WNW–ESE trend centred on the central volcano, with the highest hazard affecting the two main residential zones of Lajes do Pico and Madalena. Our analysis is the first attempt to assess the lava‐flow hazard for Pico Island, and may have important implications for decision‐making in territorial management and future land‐use planning.
Immunization after renal transplantation: current clinical practice
Authors: Struijk G.H. , Lammers A.J.J. , Brinkman R.J. , Lombarts M.J.M.H. , van Vugt M. , van der Pant K.A.M.I. , ten Berge I.J.M. , Bemelman F.J.
Published: February 2015

Background

The use of potent immunosuppressive drugs and increased travel by renal transplant recipients (RTR) has augmented the risk for infectious complications. Immunizations and changes in lifestyle are protective. The Kidney Disease: Improving Global Outcomes (KDIGO) Transplant Work Group has developed guidelines on vaccination following solid organ transplantation. The degree of adherence to these guidelines is unknown, as is which barriers must be overcome to improve adherence.

Methods

We performed a cross‐sectional national survey among Dutch nephrologists to assess vaccination policy and adherence to the KDIGO guidelines. In addition, to investigate awareness and attitude of RTR regarding their risk of infection, we performed a cross‐sectional survey of RTR in our outpatient clinic.

Results

A total of 132 (63%) nephrologists completed the survey. Reported immunization rates were 90.8% for influenza and 27.3% for hepatitis B. However, pneumococcal, tetanus toxoid, and meningococcal immunization rates were low. Twenty‐seven percent of respondents were familiar with the guideline contents. The most frequent perceived barrier to guideline adherence was expectation of low effectiveness. A total of 403 RTR (62%) completed the survey. Sixty‐eight percent perceived more risk for complicated infection. A significant correlation was found between education level and variables concerning awareness and attitude toward risk of infection.

Conclusions

Our results show that nephrologists' knowledge of and adherence to the recommendations regarding immunization after renal transplantation is suboptimal. Most Dutch RTR are aware of their increased risk and the possible seriousness of infectious complications. However, their behavior does not match their awareness. This disparity points to an important role for nephrologists in providing adequate counseling.
A cross‐intersection theorem for subsets of a set
Authors: Borg Peter
Published: February 2015

A set of sets is called a family. Two families and are said to be cross-intersecting if each set in intersects each set in . For any two integers and with , let denote the family of all subsets of that have at most elements. We show that if is a subfamily of , is a subfamily of , and and are cross‐intersecting, then and equality holds if and .
Subfactors of index exactly 5
Authors: Izumi Masaki , Morrison Scott , Penneys David , Peters Emily , Snyder Noah
Published: February 2015

We give the classification of subfactor planar algebras at index exactly 5. All the examples arise as standard invariants of subgroup subfactors. Some of the requisite uniqueness results come from work of Izumi in preparation. The non‐existence results build upon the classification of subfactor planar algebras with index less than 5, with some additional analysis of special cases.
Vanishing of l2‐cohomology as a computational problem
Authors: Grabowski Łukasz
Published: February 2015

We show that it is impossible to algorithmically decide if the ‐cohomology of the universal cover of a finite CW‐complex is trivial, even if we only consider complexes whose fundamental group is equal to the elementary amenable group . A corollary of the proof is that there is no algorithm which decides if an element of the integral group ring of the group is a zero‐divisor. On the other hand, we show, assuming some standard conjectures, that such an algorithm exists for the integral group ring of any group with a decidable word problem and a bound on the sizes of finite subgroups.
Methicillin-Resistant Staphylococcus aureus in Commercial Swine Herds Is Associated with Disinfectant and Zinc Usage
Authors: Slifierz Mackenzie Jonathan , Friendship Robert M. , Weese J. Scott
Published: February 2015

Methicillin-resistant
Staphylococcus aureus
(MRSA) originating from swine is concerning for public health, but an understanding of the emergence and persistence of MRSA in nursery herds is lacking. The aim of this study was to determine whether MRSA in nursery pigs is associated with particular herd-level parameters, including the use of antimicrobials, disinfectants, and heavy metals, which may be driving the selection and persistence of antimicrobial resistance. Nasal cultures for MRSA were completed for 390 pigs from 26 farms at the end of the suckling phase and again at 3 weeks postweaning. Herd-level information was collected, and a random subset of MRSA isolates was screened for resistance to zinc and quaternary ammonium compounds (QACs). Multivariate analysis revealed that in-feed concentrations of zinc (
P
< 0.001) and frequent disinfection of nursery pens (
P
< 0.001) are associated with MRSA shedding in nursery pigs. Furthermore, 62.5% (25/40) of MRSA isolates carried the zinc resistance gene
czrC
and demonstrated decreased susceptibility to zinc. All MRSA isolates carried at least 1 QAC resistance gene. The most common genotype was
qacG qacH smr
, which occurred in 32.5% (13/40) of isolates. Seven isolates (17.5%) demonstrated a significant tolerance to benzalkonium chloride, indicating a potential to survive commercial QAC exposure in the presence of organic matter. Overall, these findings indicate that high levels of in-feed zinc and QAC-based disinfectants are important drivers in the selection and persistence of MRSA in commercial swine herds, and these agents may be coselecting for other antimicrobial resistance genes.
The
fur
Gene as a New Phylogenetic Marker for Vibrionaceae Species Identification
Authors: Machado Henrique , Gram Lone
Published: February 2015

Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family
Vibrionaceae
, where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of
Vibrio
species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an
in silico
approach based on genomes from 103
Vibrionaceae
strains, we demonstrate here the high resolution of the
fur
gene in the identification of
Vibrionaceae
species and its usefulness as a phylogenetic marker. The
fur
gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermore, we developed a
fur
PCR sequencing-based method that allowed identification of
Vibrio
species. The discovery of the phylogenetic power of the
fur
gene and the development of a PCR method that can be used in amplification and sequencing of the gene are of general interest whether for use alone or together with the previously suggested loci in an MLSA.
Efficacies of Nisin A and Nisin V Semipurified Preparations Alone and in Combination with Plant Essential Oils for Controlling Listeria monocytogenes
Authors: Field Des , Daly Karen , O'Connor Paula M. , Cotter Paul D. , Hill Colin , Ross R. Paul
Published: February 2015

The food-borne pathogenic bacterium
Listeria
is known for relatively low morbidity and high mortality rates, reaching up to 25 to 30%.
Listeria
is a hardy organism, and its control in foods represents a significant challenge. Many naturally occurring compounds, including the bacteriocin nisin and a number of plant essential oils, have been widely studied and are reported to be effective as antimicrobial agents against spoilage and pathogenic microorganisms. The aim of this study was to investigate the ability of semipurified preparations (SPP) containing either nisin A or an enhanced bioengineered derivative, nisin V, alone and in combination with low concentrations of the essential oils thymol, carvacrol, and
trans
-cinnamaldehyde, to control
Listeria monocytogenes
in both laboratory media and model food systems. Combinations of nisin V-containing SPP (25 μg/ml) with thymol (0.02%), carvacrol (0.02%), or cinnamaldehyde (0.02%) produced a significantly longer lag phase than any of the essential oil-nisin A combinations. In addition, the log reduction in cell counts achieved by the nisin V-carvacrol or nisin V-cinnamaldehyde combinations was twice that of the equivalent nisin A-essential oil treatment. Significantly, this enhanced activity was validated in model food systems against
L. monocytogenes
strains of food origin. We conclude that the fermentate form of nisin V in combination with carvacrol and cinnamaldehyde offers significant advantages as a novel, natural, and effective means to enhance food safety by inhibiting food-borne pathogens such as
L. monocytogenes
.
Targeting Enterococcus faecalis Biofilms with Phage Therapy
Authors: Khalifa Leron , Brosh Yair , Gelman Daniel , Coppenhagen-Glazer Shunit , Beyth Shaul , Poradosu-Cohen Ronit , Que Yok-Ai , Beyth Nurit , Hazan Ronen
Published: February 2015

Phage therapy has been proven to be more effective, in some cases, than conventional antibiotics, especially regarding multidrug-resistant biofilm infections. The objective here was to isolate an anti-
Enterococcus faecalis
bacteriophage and to evaluate its efficacy against planktonic and biofilm cultures.
E. faecalis
is an important pathogen found in many infections, including endocarditis and persistent infections associated with root canal treatment failure. The difficulty in
E. faecalis
treatment has been attributed to the lack of anti-infective strategies to eradicate its biofilm and to the frequent emergence of multidrug-resistant strains. To this end, an anti-
E. faecalis
and
E. faecium
phage, termed EFDG1, was isolated from sewage effluents. The phage was visualized by electron microscopy. EFDG1 coding sequences and phylogeny were determined by whole genome sequencing (GenBank accession number
KP339049
), revealing it belongs to the
Spounavirinae
subfamily of the
Myoviridae
phages, which includes promising candidates for therapy against Gram-positive pathogens. This analysis also showed that the EFDG1 genome does not contain apparent harmful genes. EFDG1 antibacterial efficacy was evaluated
in vitro
against planktonic and biofilm cultures, showing effective lytic activity against various
E. faecalis
and
E. faecium
isolates, regardless of their antibiotic resistance profile. In addition, EFDG1 efficiently prevented
ex vivo
E. faecalis
root canal infection. These findings suggest that phage therapy using EFDG1 might be efficacious to prevent
E. faecalis
infection after root canal treatment.
Sulfur Isotope Fractionation during the Evolutionary Adaptation of a Sulfate-Reducing Bacterium
Authors: Pellerin André , Anderson-Trocmé Luke , Whyte Lyle G. , Zane Grant M. , Wall Judy D. , Wing Boswell A.
Published: February 2015

Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in
Desulfovibrio vulgaris
Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm.
PeBL1, a Novel Protein Elicitor from Brevibacillus laterosporus Strain A60, Activates Defense Responses and Systemic Resistance in Nicotiana benthamiana
Authors: Wang Haoqian , Yang Xiufen , Guo Lihua , Zeng Hongmei , Qiu Dewen
Published: February 2015

We report the identification, characterization, and gene cloning of a novel protein elicitor (PeBL1) secreted from
Brevibacillus laterosporus
strain A60. Through a purification process consisting of ion-exchange chromatography and high-performance liquid chromatography (HPLC), we isolated a protein that was identified by electrospray ionization quadrupole time of flight tandem mass spectrometry (ESI–Q-TOF–MS-MS). The 351-bp PeBL1 gene produces a 12,833-Da protein with 116 amino acids that contains a 30-residue signal peptide. The PeBL1 protein was expressed in
Escherichia coli
. The recombinant protein can induce a typical hypersensitive response (HR) and systemic resistance in
Nicotiana benthamiana
, like the endogenous protein. PeBL1-treated
N. benthamiana
exhibited strong resistance to the infection of tobacco mosaic virus-green fluorescent protein (TMV-GFP) and
Pseudomonas syringae
pv. tabaci compared to control
N. benthamiana
. In addition, PeBL1 triggered a cascade of events that resulted in defense responses in plants, including reactive oxygen species (ROS) production, extracellular-medium alkalization, phenolic-compound deposition, and expression of several defense-related genes. Real-time quantitative-PCR analysis indicated that the known defense-related genes
PR-1
,
PR-5
,
PDF1.2
,
NPR1
, and
PAL
were upregulated to varying degrees by PeBL1. This research not only provides insights into the mechanism by which beneficial bacteria activate plant systemic resistance, but also sheds new light on a novel strategy for biocontrol using strain A60.
Diverse Nitrogen Sources in Seminal Fluid Act in Synergy To Induce Filamentous Growth of Candida albicans
Authors: Alvarez Francisco J. , Ryman Kicki , Hooijmaijers Cornelis , Bulone Vincent , Ljungdahl Per O.
Published: February 2015

The pathogenic fungus
Candida albicans
is the leading cause of vulvovaginal candidiasis (VVC). VVC represents a major quality-of-life issue for women during their reproductive years, a stage of life where the vaginal epithelium is subject to periodic hormonally induced changes associated with menstruation and concomitant exposure to serum as well as potential intermittent contact with seminal fluid. Seminal fluid potently triggers
Candida albicans
to switch from yeastlike to filamentous modes of growth, a developmental response tightly linked to virulence. Conversely, vaginal fluid inhibits filamentation. Here, we used artificial formulations of seminal and vaginal fluids that faithfully mimic genuine fluids to assess the contribution of individual components within these fluids to filamentation. The high levels of albumin, amino acids, and
N
-acetylglucosamine in seminal fluid act synergistically as potent inducers of filamentous growth, even at atmospheric levels of CO
2
and reduced temperatures (30°C). Using a simplified
in vitro
model that mimics the natural introduction of seminal fluid into the vulvovaginal environment, a pulse of artificial seminal fluid (ASF) was found to exert an enduring potential to overcome the inhibitory efficacy of artificial vaginal fluid (AVF) on filamentation. These findings suggest that a transient but substantial change in the nutrient levels within the vulvovaginal environment during unprotected coitus can induce resident
C. albicans
cells to engage developmental programs associated with virulent growth.
Phenotypic and Genotypic Description of Sedimenticola selenatireducens Strain CUZ, a Marine (Per)Chlorate-Respiring Gammaproteobacterium, and Its Close Relative the Chlorate-Respiring Sedimenticola Strain NSS
Authors: Carlström Charlotte I. , Loutey Dana E. , Wang Ouwei , Engelbrektson Anna , Clark Iain , Lucas Lauren N. , Somasekhar Pranav Y. , Coates John D.
Published: February 2015

Two (per)chlorate-reducing bacteria, strains CUZ and NSS, were isolated from marine sediments in Berkeley and San Diego, CA, respectively. Strain CUZ respired both perchlorate and chlorate [collectively designated (per)chlorate], while strain NSS respired only chlorate. Phylogenetic analysis classified both strains as close relatives of the gammaproteobacterium
Sedimenticola selenatireducens
. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations showed the presence of rod-shaped, motile cells containing one polar flagellum. Optimum growth for strain CUZ was observed at 25 to 30°C, pH 7, and 4% NaCl, while strain NSS grew optimally at 37 to 42°C, pH 7.5 to 8, and 1.5 to 2.5% NaCl. Both strains oxidized hydrogen, sulfide, various organic acids, and aromatics, such as benzoate and phenylacetate, as electron donors coupled to oxygen, nitrate, and (per)chlorate or chlorate as electron acceptors. The draft genome of strain CUZ carried the requisite (per)chlorate reduction island (PRI) for (per)chlorate respiration, while that of strain NSS carried the composite chlorate reduction transposon responsible for chlorate metabolism. The PRI of strain CUZ encoded a perchlorate reductase (Pcr), which reduced both perchlorate and chlorate, while the genome of strain NSS included a gene for a distinct chlorate reductase (Clr) that reduced only chlorate. When both (per)chlorate and nitrate were present, (per)chlorate was preferentially utilized if the inoculum was pregrown on (per)chlorate. Historically, (per)chlorate-reducing bacteria (PRB) and chlorate-reducing bacteria (CRB) have been isolated primarily from freshwater, mesophilic environments. This study describes the isolation and characterization of two highly related marine halophiles, one a PRB and the other a CRB, and thus broadens the known phylogenetic and physiological diversity of these unusual metabolisms.
Cyanobacterial Blue Color Formation during Lysis under Natural Conditions
Authors: Arii Suzue , Tsuji Kiyomi , Tomita Koji , Hasegawa Masateru , Bober Beata , Harada Ken-Ichi
Published: February 2015

Cyanobacteria produce numerous volatile organic compounds (VOCs), such as β-cyclocitral, geosmin, and 2-methylisoborneol, which show lytic activity against cyanobacteria. Among these compounds, only β-cyclocitral causes a characteristic color change from green to blue (blue color formation) in the culture broth during the lysis process. In August 2008 and September 2010, the lysis of cyanobacteria involving blue color formation was observed at Lake Tsukui in northern Kanagawa Prefecture, Japan. We collected lake water containing the cyanobacteria and investigated the VOCs, such as β-cyclocitral, β-ionone, 1-propanol, 3-methyl-1-butanol, and 2-phenylethanol, as well as the number of cyanobacterial cells and their damage and pH changes. As a result, the following results were confirmed: the detection of several VOCs, including β-cyclocitral and its oxidation product, 2,2,6-trimethylcyclohexene-1-carboxylic acid; the identification of phycocyanin based on its visible spectrum; the lower pH (6.7 and 5.4) of the lysed samples; and characteristic morphological change in the damaged cyanobacterial cells. We also encountered the same phenomenon on 6 September 2013 in Lake Sagami in northern Kanagawa Prefecture and obtained almost the same results, such as blue color formation, decreasing pH, damaged cells, and detection of VOCs, including the oxidation products of β-cyclocitral. β-Cyclocitral derived from
Microcystis
has lytic activity against
Microcystis
itself but has stronger inhibitory activity against other cyanobacteria and algae, suggesting that the VOCs play an important role in the ecology of aquatic environments.
Evidence of the Internalization of Animal Caliciviruses via the Roots of Growing Strawberry Plants and Dissemination to the Fruit
Authors: DiCaprio Erin , Culbertson Doug , Li Jianrong
Published: February 2015

Human norovirus (NoV) is the leading cause of foodborne disease in the United States, and epidemiological studies have shown that fresh produce is one of the major vehicles for the transmission of human NoV. However, the mechanisms of norovirus contamination and persistence in fresh produce are poorly understood. The objective of this study is to determine whether human NoV surrogates, murine norovirus (MNV-1) and Tulane virus (TV), can attach and become internalized and disseminated in strawberries grown in soil. The soil of growing strawberry plants was inoculated with MNV-1 and TV at a level of 10
8
PFU/plant. Leaves and berries were harvested over a 14-day period, and the viral titer was determined by plaque assay. Over the course of the study, 31.6% of the strawberries contained internalized MNV-1, with an average titer of 0.81 ± 0.33 log
10
PFU/g. In comparison, 37.5% of strawberries were positive for infectious TV, with an average titer of 1.83 ± 0.22 log
10
PFU/g. A higher percentage (78.7%) of strawberries were positive for TV RNA, with an average titer of 3.15 ± 0.51 log
10
RNA copies/g as determined by real-time reverse transcriptase quantitative PCR (RT-qPCR). In contrast, no or little virus internalization and dissemination were detected when TV was inoculated into bell peppers grown in soil. Collectively, these data demonstrate (i) virally contaminated soils can lead to the internalization of virus via plant roots and subsequent dissemination to the leaf and fruit portions of growing strawberry plants and (ii) the magnitude of internalization is dependent on the type of virus and plant.