bluuebunny/crossref_metadata_2025 huggingface dataset:
An investigation of cytochrome p450 (CYP) and glutathione S‐transferase (GST) isoenzyme protein expression and related interactions with phototherapy in patients with psoriasis vulgaris
Authors: Karadag Ayse S. , Uzunçakmak Tuğba K. , Ozkanli Seyma , Oguztuzun Serpil , Moran Busra , Akbulak Ozge , Ozlu Emin , Zemheri Itir E. , Bilgili Serap G. , Akdeniz Necmettin
Published: September 2016

Oxidative stress may play an important role in the pathogenesis of psoriasis. Glutathione S‐transferases (GSTs) make up a group of antioxidant enzymes. Cytochrome p450 (CYP) enzymes can influence oxidation and reduction reactions. We investigated the potential effects of GST and CYP enzymes in the pathogenesis of psoriasis. The study included 32 psoriasis patients and 22 healthy subjects. Psoriasis patients were administered 20 sessions of narrowband ultraviolet B phototherapy. Expressions of GST and CYP enzymes were assessed by immunohistochemical staining. Expression levels of GSTK1, GSTM1, and GSTT1 were significantly higher in psoriasis than in control tissues (P = 0.022, P = 0.001, and P = 0.006, respectively). Pre‐ and post‐treatment expression was similar. Expression of CYP1A1 and CYP2E1 was significantly higher in pre‐ (P = 0.003 and P = 0.001, respectively) and post‐treatment (P = 0.003 and P = 0.001, respectively) psoriatic tissues than in control tissues. No significant differences in CYP1B1 levels between the study and control groups were detected before treatment (P > 0.05). However, CYP1B1 levels were higher in post‐treatment psoriatic tissue than in control tissue (P = 0.045). The significant increases in expression of GSTK1, GSTM1, and GSTT1 in psoriasis may reflect the increased activation of GST in response to excessive free radical formation from activated neutrophils or ultraviolet exposure to maintain antioxidant capacity in psoriasis. Furthermore, expressions of CYP1A1 and CYP2E1 represent important enzymatic systems in psoriasis. These findings suggest that psoriasis is an oxidative stress condition, although phototherapy does not affect these enzymatic systems. Further investigation is required.
Onychomycosis in children. A review
Authors: Solís‐Arias Martha Patricia , García‐Romero Maria Teresa
Published: September 2016

Onychomycosis is considered an age‐related infection with increasing prevalence in the older age groups. It is rare in the pediatric population, except in children with Down syndrome and with immunodeficiencies, who are more likely to have fungal nail infections. The number of reports about onychomycosis in children is relatively small, and the epidemiologic data vary, but a rise in prevalence has been demonstrated. In this article, we review the most up‐to‐date literature and summarize the epidemiology, etiology, clinical presentation, diagnosis, and treatment of onychomycosis in children, as well as the differences with the disease presenting in adults. Dermatologists must consider onychomycosis in the differential diagnosis of nail alterations in children and always perform a mycological study to confirm the diagnosis.
The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant
Authors: Pitsch Gianna , Adamec Lubomír , Dirren Sebastian , Nitsche Frank , Šimek Karel , Sirová Dagmara , Posch Thomas
Published: September 2016

The genus Tetrahymena (Ciliophora, Oligohymenophorea) probably represents the best studied ciliate genus. At present, more than forty species have been described. All are colorless, i.e. they do not harbor symbiotic algae, and as aerobes they need at least microaerobic habitats. Here, we present the morphological and molecular description of the first green representative, Tetrahymena utriculariae n. sp., living in symbiosis with endosymbiotic algae identified as Micractinium sp. (Chlorophyta). The full life cycle of the ciliate species is documented, including trophonts and theronts, conjugating cells, resting cysts and dividers. This species has been discovered in an exotic habitat, namely in traps of the carnivorous aquatic plant Utricularia reflexa (originating from Okavango Delta, Botswana). Green ciliates live as commensals of the plant in this anoxic habitat. Ciliates are bacterivorous, however, symbiosis with algae is needed to satisfy cell metabolism but also to gain oxygen from symbionts. When ciliates are cultivated outside their natural habitat under aerobic conditions and fed with saturating bacterial food, they gradually become aposymbiotic. Based on phylogenetic analyses of 18S rRNA and mitochondrial cox1 genes T. utriculariae forms a sister group to Tetrahymena thermophila.
PETROPHYSICAL AND SEDIMENTOLOGICAL CHARACTERIZATION OF THE APTIAN SHU'AIBA (LOWER QAMCHUQA) FORMATION RESERVOIR AT THE KHABBAZ OILFIELD, NORTHERN IRAQ
Authors: Qader F. , Al‐Qayim B.
Published: September 2016

The Aptian Shu'aiba Formation is a shallow‐marine carbonate which occurs in the subsurface of central and southern Iraq and in other parts of the Arabian Plate including Oman, the UAE and Saudi Arabia. An equivalent unit is exposed at outcrop in northern Iraq where it is known as the lower part of the Qamchuqa Formation. For this study, core, cuttings and well log data from six wells in the Khabbaz oilfield (20 km SW of Kirkuk) were used to investigate the reservoir properties of the Shu'aiba Formation. The formation is 180–195 m thick at Khabbaz field and the reservoir section can be divided into three lithological units: an upper unit (A, 8–15 m thick) consisting of partly dolomitized marly limestones; a middle unit (B, 52–56 m thick) which is composed of vuggy dolomitic limestone and dolostone; and a lower unit (C, >110 m thick) which consists of shale‐rich and dolomitic limestones. Limestone microfacies include shelfal bioclastic wackestones, Orbitolina bioclastic packstones, Orbitolina grainstones, and pelagic bioclastic wackestones. Dolomite fabrics show little variation and are dominated by coarse crystalline planar‐e types. Most matrix porosity is associated with intercrystalline pores in medium‐crystalline (100–50 µm) planar‐e dolostone. Fracturing of variable intensity has resulted in a flow type which is dominated by fracture flow superimposed on matrix flow.
Nonalcoholic steatohepatitis is associated with a state of betaine‐insufficiency
Authors: Sookoian Silvia , Puri Puneet , Castaño Gustavo O. , Scian Romina , Mirshahi Faridodin , Sanyal Arun J. , Pirola Carlos J.
Published: September 2016

Background and Aims

Nonalcoholic fatty liver disease (NAFLD) develops from a complex process, which includes changes in the liver methylome. Betaine plays a pivotal role in the regulation of methylogenesis. We performed a two‐stage case–control study, which included patients with biopsy‐proven NAFLD to explore circulating levels of betaine and its association with the histological spectrum. We also explored the association between a missense rs1805074, p.Ser646Pro variant in DMGDH (dimethylglycine dehydrogenase mitochondrial) and NAFLD severity (n=390).

Results

In the discovery phase (n=48), betaine levels were associated with the disease severity (P=.0030), including liver inflammation (Spearman R:−0.51, P=.001), ballooning degeneration (R: −0.50, P=.01) and fibrosis (R: −0.54, P=.0008). Betaine levels were significantly decreased in nonalcoholic steatohepatitis (NASH) in comparison with nonalcoholic fatty liver (NAFL). Further replication (n=51) showed that betaine levels were associated with advanced NAFLD (P=.0085), and patients with NASH had a 1.26‐fold decrease in betaine levels compared with those with NAFL. The rs1805074 was significantly associated with the disease severity (P=.011).

Conclusion

NAFLD severity is associated with a state of betaine‐insufficiency.
Midodrine and tolvaptan in patients with cirrhosis and refractory or recurrent ascites: a randomised pilot study
Authors: Rai Nitish , Singh Baljinder , Singh Akash , Vijayvergiya Rajesh , Sharma Navneet , Bhalla Ashish , Singh Virendra
Published: September 2016

Background

Splanchnic arterial vasodilatation and subsequent sodium and water retention play an important role in cirrhotic ascites. Midodrine and tolvaptan have been used separately in these patients. However, there are no reports on the use of combination of midodrine and tolvaptan in the control of ascites. The aim of this study was to evaluate the safety and efficacy of midodrine, tolvaptan and their combination in control of refractory or recurrent ascites in cirrhotics.

Methods

Fifty cirrhotic patients with refractory or recurrent ascites were randomised to receive midodrine (n=13), tolvaptan (n=12) or both (n=13) plus standard medical therapy (SMT) or SMT alone (n=12).

Results

A significant increase in urinary volume and urinary sodium at 1 and 3 months (P<.05) was observed in all groups except SMT. There was no worsening of renal or hepatic function in any group. There was deterioration of model for end‐stage liver disease (MELD) in SMT. Midodrine as well as combination of midodrine and tolvaptan but not tolvaptan alone was superior to SMT in control of ascites at 3 months (P<.05). The combination therapy was also superior to midodrine in the control of ascites at 1 month. The morbidity and mortality were similar in all the groups except SMT.

Conclusions

The results of this pilot study suggest that midodrine and combination with tolvaptan better controls ascites without any renal or hepatic dysfunction. The combination therapy rapidly controls ascites as compared to midodrine or tolvaptan alone.
Demographic modelling with whole‐genome data reveals parallel origin of similarPundamiliacichlid species after hybridization
Authors: Meier Joana I. , Sousa Vitor C. , Marques David A. , Selz Oliver M. , Wagner Catherine E. , Excoffier Laurent , Seehausen Ole
Published: September 2016

Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genusPundamiliaencompass a complex of young species and polymorphic populations. OnePundamiliaspecies pair,P. pundamiliaandP. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation intoP. nyerereiandP. pundamiliaoccurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin ofP. pundamiliaandP. nyerereipopulation pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatricP. nyerereipopulation that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
How far did feedback between biodiversity and early diagenesis affect the nature of Early Palaeozoic sea floors?
Authors: Wright V. Paul , Cherns Lesley
Published: September 2016

Latest Precambrian to Early Palaeozoic biosphere evolution triggered changes in early diagenesis and carbonate precipitation which fed back to biodiversity through colonization of hard substrates. Progressive increase in the depth and intensity of bioturbation and bio‐irrigation lowered the zone of early carbonate cementation in the uppermost sediment column. This firstly led to a decline in the abundance of the flat‐pebble conglomerates which had been a common feature of Cambrian and Early Ordovician successions, replaced by the peak and subsequent decline in the Palaeozoic abundance of submarine hardgrounds. The availability of very widespread lithified sea floors in shallow subtidal settings during the Ordovician promoted a rapid expansion in sclerobiont diversity and contributed to the Great Ordovician Biodiversification Event.
Targeted mutagenesis of a conserved anther‐expressed P450 gene confers male sterility in monocots
Authors: Cigan A. Mark , Singh Manjit , Benn Geoffrey , Feigenbutz Lanie , Kumar Manish , Cho Myeong‐Je , Svitashev Sergei , Young Joshua
Published: September 2016

Targeted mutagenesis using programmable DNA endonucleases has broad applications for studying gene function in planta and developing approaches to improve crop yields. Recently, a genetic method that eliminates the need to emasculate the female inbred during hybrid seed production, referred to as Seed Production Technology, has been described. The foundation of this genetic system relied on classical methods to identify genes critical to anther and pollen development. One of these genes is a P450 gene which is expressed in the tapetum of anthers. Homozygous recessive mutants in this gene render maize and rice plants male sterile. While this P450 in maize corresponds to the male fertility gene Ms26, male fertility mutants have not been isolated in other monocots such as sorghum and wheat. In this report, a custom designed homing endonuclease, Ems26+, was used to generate in planta mutations in the rice, sorghum and wheat orthologs of maize Ms26. Similar to maize, homozygous mutations in this P450 gene in rice and sorghum prevent pollen formation resulting in male sterile plants and fertility was restored in sorghum using a transformed copy of maize Ms26. In contrast, allohexaploid wheat plants that carry similar homozygous nuclear mutations in only one, but not all three, of their single genomes were male fertile. Targeted mutagenesis and subsequent characterization of male fertility genes in sorghum and wheat is an important step for capturing heterosis and improving crop yields through hybrid seed.
Patterns of CRISPR/Cas9 activity in plants, animals and microbes
Authors: Bortesi Luisa , Zhu Changfu , Zischewski Julia , Perez Lucia , Bassié Ludovic , Nadi Riad , Forni Giobbe , Lade Sarah Boyd , Soto Erika , Jin Xin , Medina Vicente , Villorbina Gemma , Muñoz Pilar , Farré Gemma , Fischer Rainer , Twyman Richard M. , Capell Teresa , Christou Paul , Schillberg Stefan
Published: September 2016

The CRISPR/Cas9 system and related RNA‐guided endonucleases can introduce double‐strand breaks (DSBs) at specific sites in the genome, allowing the generation of targeted mutations in one or more genes as well as more complex genomic rearrangements. Modifications of the canonical CRISPR/Cas9 system from Streptococcus pyogenes and the introduction of related systems from other bacteria have increased the diversity of genomic sites that can be targeted, providing greater control over the resolution of DSBs, the targeting efficiency (frequency of on‐target mutations), the targeting accuracy (likelihood of off‐target mutations) and the type of mutations that are induced. Although much is now known about the principles of CRISPR/Cas9 genome editing, the likelihood of different outcomes is species‐dependent and there have been few comparative studies looking at the basis of such diversity. Here we critically analyse the activity of CRISPR/Cas9 and related systems in different plant species and compare the outcomes in animals and microbes to draw broad conclusions about the design principles required for effective genome editing in different organisms. These principles will be important for the commercial development of crops, farm animals, animal disease models and novel microbial strains using CRISPR/Cas9 and other genome‐editing tools.
Citrulline for urea cycle disorders in Japan
Authors: Tanaka Kenichi , Nakamura Kimitoshi , Matsumoto Shirou , Kido Jun , Mitsubuchi Hiroshi , Ohura Toshihiro , Endo Fumio
Published: September 2016

Background

The amino acid l‐citrulline is used as a therapeutic agent for urea cycle disorders (UCD) including ornithine transcarbamylase deficiency (OTCD), carbamoyl phosphate synthetase I deficiency (CPSD), and N‐acetylglutamate synthase deficiency. There are few reports, however, on the use of l‐citrulline in Japan and little consensus regarding the effects of l‐citrulline.

Methods

We conducted a questionnaire survey of patients undergoing l‐citrulline treatment for a UCD to evaluate the current status of this therapy. The survey included patient background, details of l‐citrulline treatment, clinical examination data, treatment, frequency of vomiting, and liver transplantation.

Results

We retrospectively investigated 43 questionnaire respondents (OTCD, n = 33; CPSD, n = 10). The weight of male OTCD patients improved by +0.79 SD, and the ammonia level decreased by a mean of 44.3 μmol/L in all patients. The protein intake of all patients and of male OTCD patients increased by 0.14 g/kg/day and 0.17 g/kg/day, respectively.

Conclusions

l‐Citrulline effectively reduced ammonia level, increased protein intake, and improved weight gain in UCD patients. l‐Citrulline should be considered a standard therapy in OTCD and CPSD patients.
Amelioration by glycine of brain damage in neonatal rat brain following hypoxia–ischemia
Authors: Mori Hiroko , Momosaki Ken , Kido Jun , Naramura Tetsuo , Tanaka Kenichi , Matsumoto Shirou , Nakamura Kimitoshi , Mitsubuchi Hiroshi , Endo Fumio , Iwai Masanori
Published: September 2016

Background

Glycine protected adult brains against injury in an experimental model of stroke, but, because the ischemic response of neonatal brains differs from that of adult brains, we examined the neuroprotective efficacy of glycine and associated mechanisms in an experimental model of neonatal hypoxic–ischemic (HI) encephalopathy.

Methods

Neonatal (postnatal day 7) Wistar rats were randomly divided into an untreated group (non‐HI) and two HI groups that were treated with left common carotid artery ligation and saline control or glycine. After recovery, pups that received surgery were injected i.p. with saline or glycine (800 mg/kg; optimal dose determined in pilot experiments) and were placed in a controlled 8% O2 chamber for 120 min. Brains were harvested at various times after return to normoxia (several hours–days after HI) for analysis of infarct area, glial activation, cell apoptosis, and tumor necrosis factor‐α (TNF‐α) expression on histology and reverse transcription–polymerase chain reaction.

Results

Glycine injections induced large (approx. 15‐fold) but brief (approx. 2 h) increases in cerebrospinal fluid concentrations. In particular, the glycine group had a >70% decrease in infarct areas compared with controls at 7 days after HI. Glycine also significantly reduced astrocyte reactive transformation, microglia activation, and terminal deoxynucleotidyl transferase dUTP nick end labeling‐positive (apoptotic) cell numbers in peri‐lesional areas at 3 days after HI, and TNF‐α mRNA expression in the injured hemisphere at 12 and 24 h after HI.

Conclusion

Glycine protected neonatal rat brains against HI, in part by inhibiting TNF‐α‐induced inflammation and gliosis. Hence, systemic glycine infusions may have clinical utility for the treatment of HI injury in human newborns.
Dehydration rate determines the degree of membrane damage and desiccation tolerance in bryophytes
Authors: Cruz de Carvalho Ricardo , Catalá Myriam , Branquinho Cristina , Marques da Silva Jorge , Barreno Eva
Published: September 2016

Desiccation tolerant (DT) organisms are able to withstand an extended loss of body water and rapidly resume metabolism upon rehydration. This ability, however, is strongly dependent on a slow dehydration rate. Fast dehydration affects membrane integrity leading to intracellular solute leakage upon rehydration and thereby impairs metabolism recovery. We test the hypothesis that the increased cell membrane damage and membrane permeability observed under fast dehydration, compared with slow dehydration, is related to an increase in lipid peroxidation. Our results reject this hypothesis because following rehydration lipid peroxidation remains unaltered, a fact that could be due to the high increase of NO upon rehydration. However, in fast‐dried samples we found a strong signal of red autofluorescence upon rehydration, which correlates with an increase in ROS production and with membrane leakage, particularly the case of phenolics. This could be used as a bioindicator of oxidative stress and membrane damage.
Identification and characterization of a plastidial phosphatidylglycerophosphate phosphatase in Arabidopsis thaliana
Authors: Zhou Yonghong , Hölzl Georg , vom Dorp Katharina , Peisker Helga , Melzer Michael , Frentzen Margrit , Dörmann Peter
Published: September 2016

Phosphatidylglycerol (PG) is the only phospholipid in the thylakoid membranes of chloroplasts of plants, and it is also found in extraplastidial membranes including mitochondria and the endoplasmic reticulum. Previous studies showed that lack of PG in the pgp1‐2 mutant of Arabidopsis deficient in phosphatidylglycerophosphate (PGP) synthase strongly affects thylakoid biogenesis and photosynthetic activity. In the present study, the gene encoding the enzyme for the second step of PG synthesis, PGP phosphatase, was isolated based on sequence similarity to the yeast GEP4 and Chlamydomonas PGPP1 genes. The Arabidopsis AtPGPP1 protein localizes to chloroplasts and harbors PGP phosphatase activity with alkaline pH optimum and divalent cation requirement. Arabidopsis pgpp1‐1 mutant plants contain reduced amounts of chlorophyll, but photosynthetic quantum yield remains unchanged. The absolute content of plastidial PG (34:4; total number of acyl carbons:number of double bonds) is reduced by about 1/3, demonstrating that AtPGPP1 is involved in the synthesis of plastidial PG. PGP 34:3, PGP 34:2 and PGP 34:1 lacking 16:1 accumulate in pgpp1‐1, indicating that the desaturation of 16:0 to 16:1 by the FAD4 desaturase in the chloroplasts only occurs after PGP dephosphorylation.
Inhibition of B‐cell activation and antibody production by triggering inhibitory signals via the PD‐1/PD‐ligand pathway
Authors: Buermann Anna , Römermann Dorothee , Baars Wiebke , Hundrieser Joachim , Klempnauer Jürgen , Schwinzer Reinhard
Published: September 2016

Background

The development of donor‐reactive antibodies is regarded to be an important barrier limiting long‐term outcome of allo‐ and xenografts. We asked whether enhanced signaling via the co‐inhibitory receptor programmed cell death‐1 (PD‐1; CD279) can downregulate human B‐cell activation.

Methods

Proliferation of human purified CD19+ B cells was induced by in vitro stimulation with CpG oligodeoxynucleotides (CpG‐B). To induce antibody production, peripheral blood mononuclear cells were co‐cultured with the porcine B‐cell line L23. Triggering of inhibitory signals via the PD‐1 receptor was obtained either using a recombinant agonistic soluble ligand (PD‐L1.Ig) or L23 transfectants overexpressing membrane‐bound human PD‐L1 (CD274; L23‐PD‐L1 cells).

Results

Stimulation of purified CD19+ B cells with CpG‐B resulted in upregulation of PD‐1 and strong proliferation. Addition of PD‐L1.Ig significantly reduced B‐cell proliferation in a dose‐dependent manner. A great proportion (~1%) of human circulating B cells recognizes the epitope galactose‐α1,3‐galactose‐β1,4‐N‐acetylglucosamine‐R (α‐gal). Thus, when B cells—in the presence of T cell help—were cocultured with α‐gal‐expressing L23 cells, anti‐gal and anti‐L23 antibodies could readily be detected in the culture supernatant. The level of induced antibodies was significantly reduced when stimulation was performed by L23‐PD‐L1 cells.

Conclusions

Enhancing inhibitory signals may be part of future protocols to better control humoral immunity to allo‐ and xenografts.
Evaluation of an Arm Support With Trunk Motion Capability
Authors: Dunning A. G. , Janssen M. M. H. P. , Kooren P. N. , Herder J. L.
Published: September 2016

Due to progressive muscle weakness, the arm function in boys with Duchenne muscular dystrophy (DMD) reduces. An arm support can compensate for this loss of function. Existing arm supports are wheelchair bound, which restricts the ability to perform trunk movements. To evaluate the function of a body-bound arm support, a prototype (based on the Wilmington robotic exoskeleton (WREX) arm support) that allows trunk movements was built. In order to examine the effect of this device and to compare it with an existing wheelchair-bound device, three healthy subjects performed single joint movements (SJMs) and activities of daily living (ADL) with and without the devices. The range of motion (RoM) of the arm and the surface electromyography (sEMG) signal of five different arm muscles were measured. The range of motion increased when compared to the wheelchair-bound device, and the trunk motion was perceived as important to make specific movements easier and more natural, especially the more extreme movements like reaching for a far object and reaching to the top of the head. The sEMG signal was comparable to that of the wheelchair-bound device. This means that an arm support with trunk motion capability can increase the range of motion of the user, while the amount of support to the arm is equal.
Computationally designed peptides for self-assembly of nanostructured lattices
Authors: Zhang Huixi Violet , Polzer Frank , Haider Michael J. , Tian Yu , Villegas Jose A. , Kiick Kristi L. , Pochan Darrin J. , Saven Jeffery G.
Published: September 2016

Peptide lattices were designed using computational methods and controlled by tuning self-assembly solution conditions.
Optomechanical measurement of photon spin angular momentum and optical torque in integrated photonic devices
Authors: He Li , Li Huan , Li Mo
Published: September 2016

Photon spin angular momentum in integrated waveguides.
Super-heavy electron material as metallic refrigerant for adiabatic demagnetization cooling
Authors: Tokiwa Yoshifumi , Piening Boy , Jeevan Hirale S. , Bud’ko Sergey L. , Canfield Paul C. , Gegenwart Philipp
Published: September 2016

Metallic super-heavy fermion compounds can be used for adiabatic demagnetization cooling to temperatures well below 0.1 K.
Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features
Authors: Speranzini Valentina , Rotili Dante , Ciossani Giuseppe , Pilotto Simona , Marrocco Biagina , Forgione Mariantonietta , Lucidi Alessia , Forneris Federico , Mehdipour Parinaz , Velankar Sameer , Mai Antonello , Mattevi Andrea
Published: September 2016

The binding mode of newly discovered histone demethylase inhibitors could have applications in the design and repurposing of drugs.
X-ray laser–induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene
Authors: Abbey Brian , Dilanian Ruben A. , Darmanin Connie , Ryan Rebecca A. , Putkunz Corey T. , Martin Andrew V. , Wood David , Streltsov Victor , Jones Michael W. M. , Gaffney Naylyn , Hofmann Felix , Williams Garth J. , Boutet Sébastien , Messerschmidt Marc , Seibert M. Marvin , Williams Sophie , Curwood Evan , Balaur Eugeniu , Peele Andrew G. , Nugent Keith A. , Quiney Harry M.
Published: September 2016

Coherent electron dynamics in a periodic array of C
60
molecular targets driven by intense x-ray pulses of femtosecond duration.
The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes
Authors: Hu Yongfei , Yang Xi , Li Jing , Lv Na , Liu Fei , Wu Jun , Lin Ivan Y. C. , Wu Na , Weimer Bart C. , Gao George F. , Liu Yulan , Zhu Baoli
Published: September 2016

Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in
Proteobacteria
. The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens.

IMPORTANCE
The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found that dozens of ARGs are transferred between the human and animal gut and human pathogens. This work demonstrates the whole profile of mobile ARGs and their transfer network in bacteria and provides further insight into the evolution and spread of antibiotic resistance in nature.
Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution
Authors: Peabody George , Winkler James , Fountain Weston , Castro David A. , Leiva-Aravena Enzo , Kao Katy C.
Published: September 2016

Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of
Escherichia coli
engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load.

IMPORTANCE
Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual
Escherichia coli
and determine if a sexual strain of
E. coli
can become an effective tool for strain development.
Expression of Surface Protein LapB by a Wide Spectrum of Listeria monocytogenes Serotypes as Demonstrated with Anti-LapB Monoclonal Antibodies
Authors: Boivin Teela , Elmgren Cathie , Brooks Brian W. , Huang Hongsheng , Pagotto Franco , Lin Min
Published: September 2016

Protein antigens expressed on the surface of all strains of
Listeria monocytogenes
and absent from nonpathogenic
Listeria
spp. are presumably useful targets for pathogen identification, detection, and isolation using specific antibodies (Abs). To seek such surface proteins expressed in various strains of
L. monocytogenes
for diagnostic applications, we focused on a set of surface proteins known to be involved or putatively involved in
L. monocytogenes
virulence and identified
Listeria
adhesion protein B (LapB) as a candidate based on the bioinformatics analysis of whole-genome sequences showing that the gene coding for LapB was present in
L. monocytogenes
strains and absent from strains of other
Listeria
spp. Immunofluorescence microscopy (IFM), performed with rabbit polyclonal antibodies against the recombinant LapB protein (rLapB) of
L. monocytogenes
serotype 4b strain L10521, confirmed expression of LapB on the surface. A panel of 48 mouse monoclonal antibodies (MAbs) to rLaB was generated, and 7 of them bound strongly to the surface of
L. monocytogenes
cells as demonstrated using IFM. Further characterization of these 7 anti-LapB MAbs, using an enzyme-linked immunosorbent assay (ELISA), revealed that 6 anti-LapB MAbs (M3484, M3495, M3500, M3509, M3517, and M3519) reacted strongly with 46 (86.8%) of 53 strains representing 10 of the 12 serotypes tested (1/2a, 1/2b, 1/2c, 3a, 3b, 3c, 4ab, 4b, 4d, and 4e). These results indicate that LapB, together with companion anti-LapB MAbs, can be targeted as a biomarker for the detection and isolation of various
L. monocytogenes
strains from contaminated foods.

IMPORTANCE
Strains of
L. monocytogenes
are traditionally grouped into serotypes. Identification of a surface protein expressed in all or the majority of at least 12 serotypes would aid in the development of surface-binding monoclonal antibodies (MAbs) for detection and isolation of
L. monocytogenes
from foods. Bioinformatics analysis revealed that the gene coding for
Listeria
adhesion protein B (LapB), a surface protein involved in
L. monocytogenes
virulence, was present in
L. monocytogenes
strains and absent from other
Listeria
spp. Polyclonal antibodies against recombinant LapB (rLapB) detected the exposed epitopes on the surface of
L. monocytogenes
. Production and extensive assessment of 48 MAbs to rLapB showed that 6 anti-LapB MAbs (M3484, M3495, M3500, M3509, M3517, and M3519) detected the expression of LapB in a wide range of
L. monocytogenes
isolates representing 10 of 12 serotypes tested, suggesting that LapB, together with specific MAbs, can be targeted as a biomarker for pathogen detection and isolation.
Epithelial Coculture and
l
-Lactate Promote Growth of Helicobacter cinaedi under H
2
-Free Aerobic Conditions
Authors: Schmitz Jonathan E. , Taniguchi Takako , Misawa Naoaki , Cover Timothy L.
Published: September 2016

Helicobacter cinaedi
is an emerging opportunistic pathogen associated with infections of diverse anatomic sites. Nevertheless, the species demonstrates fastidious axenic growth; it has been described as requiring a microaerobic atmosphere, along with a strong preference for supplemental H
2
gas. In this context, we examined the hypothesis that
in vitro
growth of
H. cinaedi
could be enhanced by coculture with human epithelial cells. When inoculated (in Ham's F12 medium) over Caco-2 monolayers, the type strain (ATCC BAA-847) gained the ability to proliferate under H
2
-free aerobic conditions. Identical results were observed during coculture with several other monolayer types (LS-174T, AGS, and HeLa). Under chemically defined conditions, 40 amino acids and carboxylates were screened for their effect on the organism's atmospheric requirements. Several molecules promoted H
2
-free aerobic proliferation, although it occurred most prominently with millimolar concentrations of
l
-lactate. The growth response of
H. cinaedi
to Caco-2 cells and
l
-lactate was confirmed with a collection of 12 human-derived clinical strains. mRNA sequencing was next performed on the type strain under various growth conditions. In addition to providing a whole-transcriptome profile of
H. cinaedi
, this analysis demonstrated strong constitutive expression of the
l
-lactate utilization locus, as well as differential transcription of terminal respiratory proteins as a function of Caco-2 coculture and
l
-lactate supplementation. Overall, these findings challenge traditional views of
H. cinaedi
as an obligate microaerophile.

IMPORTANCE
H. cinaedi
is an increasingly recognized pathogen in people with compromised immune systems. Atypical among other members of its bacterial class,
H. cinaedi
has been associated with infections of diverse anatomic sites. Growing
H. cineadi
in the laboratory is quite difficult, due in large part to the need for a specialized atmosphere. The suboptimal growth of
H. cinaedi
is an obstacle to clinical diagnosis, and it also limits investigation into the organism's biology. The current work shows that
H. cinaedi
has more flexible atmospheric requirements in the presence of host cells and a common host-derived molecule. This nutritional interplay raises new questions about how the organism behaves during human infections and provides insights for how to optimize its laboratory cultivation.
Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii
Authors: Kirs Marek , Caffaro-Filho Roberto A. , Wong Mayee , Harwood Valerie J. , Moravcik Philip , Fujioka Roger S.
Published: September 2016

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated
Bacteroides
spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [
n
= 11], 30% of mongoose [
n
= 10], and 10% of feline [
n
= 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii.

IMPORTANCE
This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and
Escherichia coli
). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers.
Aerosol and Surface Deposition Characteristics of Two Surrogates for Bacillus anthracis Spores
Authors: Bishop Alistair H. , Stapleton Helen L.
Published: September 2016

Spores of an acrystalliferous derivative of
Bacillus thuringiensis
subsp.
kurstaki
, termed
Btcry
−, are morphologically, aerodynamically, and structurally indistinguishable from
Bacillus anthracis
spores.
Btcry
− spores were dispersed in a large, open-ended barn together with spores of
Bacillus atrophaeus
subsp.
globigii
, a historically used surrogate for
Bacillus anthracis
. Spore suspensions (2 × 10
12
CFU each of
B. atrophaeus
subsp.
globigii
and
Btcry
−) were aerosolized in each of five spray events using a backpack misting device incorporating an air blower; a wind of 4.9 to 7.6 m s
−1
was also flowing through the barn in the same direction. Filter air samplers were situated throughout the barn to assess the aerosol density of the spores during each release. Trays filled with a surfactant in aqueous buffer were placed on the floor near the filter samplers to assess spore deposition. Spores were also recovered from arrays of solid surfaces (concrete, aluminum, and plywood) that had been laid on the floor and set up as a wall at the end of the barn.
B. atrophaeus
subsp.
globigii
spores were found to remain airborne for significantly longer periods, and to be deposited on horizontal surfaces at lower densities, than
Btcry
− spores, particularly near the spray source. There was a 6-fold-higher deposition of
Btcry
− spores than of
B. atrophaeus
subsp.
globigii
spores on vertical surfaces relative to the surrounding airborne density. This work is relevant for selecting the best
B. anthracis
surrogate for the prediction of human exposure, hazard assessment, and hazard management following a malicious release of
B. anthracis
.

IMPORTANCE
There is concern that pathogenic bacteria could be maliciously disseminated in the air to cause human infection and disruption of normal life. The threat from spore-forming organisms, such as the causative agent of anthrax, is particularly serious. In order to assess the extent of this risk, it is important to have a surrogate organism that can be used to replicate the dispersal characteristics of the threat agent accurately. This work compares the aerosol dispersal and deposition behaviors of the surrogates
Btcry
− and
B. atrophaeus
subsp.
globigii
.
Btcry
− spores remained in the air for a shorter time, and were markedly more likely to adhere to vertical surfaces, than
B. atrophaeus
subsp.
globigii
spores.
Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine
Authors: Trachsel Julian , Bayles Darrell O. , Looft Torey , Levine Uri Y. , Allen Heather K.
Published: September 2016

Studying the host-associated butyrate-producing bacterial community is important, because butyrate is essential for colonic homeostasis and gut health. Previous research has identified the butyryl coenzyme A (CoA):acetate-CoA transferase (EC 2.3.8.3) as a gene of primary importance for butyrate production in intestinal ecosystems; however, this gene family (
but
) remains poorly defined. We developed tools for the analysis of butyrate-producing bacteria based on 12 putative
but
genes identified in the genomes of nine butyrate-producing bacteria obtained from the swine intestinal tract. Functional analyses revealed that eight of these genes had strong But enzyme activity. When
but
paralogues were found within a genome, only one gene per genome encoded strong activity, with the exception of one strain in which no gene encoded strong But activity. Degenerate primers were designed to amplify the functional
but
genes and were tested by amplifying environmental
but
sequences from DNA and RNA extracted from swine colonic contents. The results show diverse
but
sequences from swine-associated butyrate-producing bacteria, most of which clustered near functionally confirmed sequences. Here, we describe tools and a framework that allow the bacterial butyrate-producing community to be profiled in the context of animal health and disease.

IMPORTANCE
Butyrate is a compound produced by the microbiota in the intestinal tracts of animals. This compound is of critical importance for intestinal health, and yet studying its production by diverse intestinal bacteria is technically challenging. Here, we present an additional way to study the butyrate-producing community of bacteria using one degenerate primer set that selectively targets genes experimentally demonstrated to encode butyrate production. This work will enable researchers to more easily study this very important bacterial function that has implications for host health and resistance to disease.
Laser Acupuncture Attenuates Oxaliplatin-Induced Peripheral Neuropathy in Patients with Gastrointestinal Cancer: A Pilot Prospective Cohort Study
Authors: Hsieh Yueh-Ling , Chou Li-Wei , Hong Shao-Fu , Chang Fei-Chi , Tseng Szu-Wen , Huang Chi-Chou , Yang Ching-Hsiang , Yang Chen-Chia , Chiu Wei-Feng
Published: September 2016

Background

Oxaliplatin is a platinum compound that is widely used in the treatment of some solid tumours. Oxaliplatin-induced peripheral neuropathy (OIPN) in the upper and lower extremities is the major adverse side effect and represents the main dose-limiting factor of this drug. The aim of this single-arm study was to evaluate the feasibility and effects of laser acupuncture (LA) in the treatment of OIPN in patients with advanced gastrointestinal cancers.

Methods

17 gastrointestinal cancer survivors (14 colorectal and 3 gastric cancers), who had been treated with oxaliplatin-based chemotherapies, were recruited. Low-level laser stimulation (50 mW) bilaterally at PC6, PC7, PC8, P9, LU11, SP6, KI3, BL60, KI1, and KI2 was administered for 20 min/point for 12 sessions over 4 weeks. The pain quality assessment scale (PQAS), chemotherapy-induced neurotoxicity questionnaire (CINQ), oxaliplatin-specific neurotoxicity scale (OSNS), quantitative touch-detection threshold (using von Frey filaments), and cold-triggered pain withdrawal latency (using the cold-water immersion test) were measured before and after completion of the 12 treatment sessions.

Results

PQAS, CINQ, and OSNS scores, as well as touch-detection threshold and cold-trigger pain withdrawal latency all improved significantly after LA in the cancer patients with OIPN (p<0.05). LA significantly relieved both oxaliplatin-induced cold and mechanical allodynia and also decreased the incidence and severity of neurotoxicity symptoms in the patients’ upper and lower extremities and impact on their daily activities (all p<0.05).

Conclusions

Following treatment with LA, neurotoxicity symptoms were significantly improved in cancer patients with OIPN. Further randomised controlled trials are needed to evaluate the role of LA as a therapeutic option in the management of OIPN.