bluuebunny/crossref_metadata_2025 huggingface dataset:
The m6A‐epitranscriptomic signature in neurobiology: from neurodevelopment to brain plasticity
Authors: Widagdo Jocelyn , Anggono Victor
Published: June 2018

Research over the past decade has provided strong support for the importance of various epigenetic mechanisms, including DNA and histone modifications in regulating activity‐dependent gene expression in the mammalian central nervous system. More recently, the emerging field of epitranscriptomics revealed an equally important role of post‐transcriptional RNA modifications in shaping the transcriptomic landscape of the brain. This review will focus on the methylation of the adenosine base at the N6 position, termed N6 methyladenosine (m6A), which is the most abundant internal modification that decorates eukaryotic messenger RNAs. Given its prevalence and dynamic regulation in the adult brain, the m6A‐epitranscriptome provides an additional layer of regulation on RNA that can be controlled in a context‐ and stimulus‐dependent manner. Conceptually, m6A serves as a molecular switch that regulates various aspects of RNA function, including splicing, stability, localization, or translational control. The versatility of m6A function is typically determined through interaction or disengagement with specific classes of m6A‐interacting proteins. Here we review recent advances in the field and provide insights into the roles of m6A in regulating brain function, from development to synaptic plasticity, learning, and memory. We also discuss how aberrant m6A signaling may contribute to neurodevelopmental and neuropsychiatric disorders.

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Scales of predator detection behavior and escape in Fissurella limbata: A field and laboratory assessment
Authors: Manzur Tatiana , Gonzalez‐Mendez Avia , Broitman Bernardo R.
Published: June 2018

The consumptive effects of predators are widely acknowledged, but predation can also impact prey populations through non‐consumptive effects (NCEs) such as costly antipredator behavioral responses. The magnitude of antipredator behavioral responses by prey is determined by an assessment of risk using sensory cues, which in turn is modulated by the environmental context. We studied the detection behavior and escape response of the keyhole limpet Fissurella limbata from the predatory sea star Heliaster helianthus. Through laboratory and field experimental trials, we quantified the distance and time of predator detection behavior by the prey, and measured their active escape responses when elicited. We found that predator detection by the limpet was chiefly mediated by distance, with experimental individuals capable of detecting predator presence effectively up to distances of at least 50 cm in the field and 70 cm under laboratory conditions. Our results indicate that this prey species is able to evaluate the proximity of its predator and use it as an indication of predation risk; therefore, predator–prey distance appears to be a primary predictor of the magnitude of the antipredator response. Given the tight relationship between predator distance and prey movement and the important role herbivores can play, particularly in this ecosystem, we expect that NCEs will cascade to the patterns of abundance and composition of rocky shore communities through changes in prey foraging behavior under risk.
Methane flux dynamics in relation to methanogenic and methanotrophic populations in the soil of Indian Sundarban mangroves
Authors: Das Subhajit , Ganguly Dipnarayan , Chakraborty Sabyasachi , Mukherjee Abhishek , Kumar De Tarun
Published: June 2018

The dynamics of methane (CH4) flux in relation to populations of methanogenic and methanotrophic bacteria was studied under the different biophysical conditions of the Indian Sundarban mangrove ecosystem. Soil depth profile analysis (up to 60 cm) in the lower littoral zone (LLZ) revealed that a methanogenic population of 6.45 ± 0.19 × 104 cells/g dry weight (dry wt) of soil accounted for a CH4 production rate of 6.23 ± 3.53 × 103 µmol m−2 day−1, whereas in the surface soil, a methanogenic population of 3.34 ± 0.37 × 104 cells/g dry wt of soil accounted for a CH4 production rate of 31.6 ± 0.57 µmol m−2 day−1. The CH4 oxidation rate at 60 cm depth in the LLZ was 24.42 ± 1.28 µmol m−2 day−1, with an average methanotrophic population of 1.33 ± 0.43 × 104 cells/g dry wt of soil, whereas in the surface soil, the oxidation rate and average population were 3.38 ± 1.43 × 103 µmol m−2 day−1 and 12.80 ± 2.54 × 104 cells/g dry wt of soil, respectively. A similar soil profile in terms of CH4 dynamics and the populations of methanogenic and methanotrophic bacteria was found in the mid‐littoral and upper littoral zones of the studied area. The results demonstrate that most of the produced CH4 (approximately 60%) was oxidized by methanotrophic bacteria present in the soil, thus revealing their principal role in regulating the CH4 flux from this unique ecosystem.
Mechanisms accounting for variations in the proportions of carbonaceous and ordinary chondrites in different mass ranges
Authors: Rubin Alan E.
Published: June 2018

The number ratio of carbonaceous to ordinary chondrites (the CC/OC ratio) varies with mass. It is very high (≳90) in small mass ranges (10−8 to 10−12 kg) among interplanetary dust particles and micrometeorites; it is moderately high (~5 to 30) for 1 to 10 m size fireball meteoroids (with estimated masses between ~103 and ~106 kg). In the range of most normal‐sized meteorite falls (0.01–20 kg), the ratio is low (0.04–0.05); the ratio increases at greater mass ranges: at ≥200 kg, the ratio is 0.09; at ≥500 kg, the ratio is 0.20. The CC/OC ratio also increases from 0.05 to 0.16 for small meteorite finds (10−3 to 10−4 kg). High CC/OC ratios at low and high mass ranges are due to the predominance of CC material in the outer solar system. Small particles from this region spiral into the inner solar system typically in ≤106 years due to Poynting–Robertson drag. Meter‐sized meteoroids in this region are affected by Yarkovsky forces, pushing them into resonances where they are efficiently transferred to the inner solar system. Normal‐sized meteorites are derived from centimeter‐to‐decimeter‐sized meteoroids that have sluggish drift rates (i.e., they are less affected by the seasonal Yarkovsky effect) compared to larger bodies. Consequently, the centimeter‐to‐decimeter‐sized meteoroids spend more time in interplanetary space (where they are subject to collisions) than larger objects. The greater friability of carbonaceous chondrites relative to ordinary chondrites tends to winnow the carbonaceous chondrites out in this size/mass range during their long interplanetary sojourn, thereby decreasing the CC/OC ratio.
The second messenger cyclic di‐AMP negatively regulates the expression of Mycobacterium smegmatis recA and attenuates DNA strand exchange through binding to the C‐terminal motif of mycobacterial RecA proteins
Authors: Manikandan Kasi , Prasad Deepika , Srivastava Ankita , Singh Nirpendra , Dabeer Sadaf , Krishnan Anuja , Muniyappa K. , Sinha Krishna Murari
Published: June 2018

Cyclic di‐GMP and cyclic di‐AMP are second messengers produced by a wide variety of bacteria. They influence bacterial cell survival, biofilm formation, virulence and bacteria–host interactions. However, many of their cellular targets and biological effects are yet to be determined. A chemical proteomics approach revealed that Mycobacterium smegmatis RecA (MsRecA) possesses a high‐affinity cyclic di‐AMP binding activity. We further demonstrate that both cyclic di‐AMP and cyclic di‐GMP bind specifically to the C‐terminal motif of MsRecA and Mycobacterium tuberculosis RecA (MtRecA). Escherichia coli RecA (EcRecA) was devoid of cyclic di‐AMP binding but have cyclic di‐GMP binding activity. Notably, cyclic di‐AMP attenuates the DNA strand exchange promoted by MsRecA as well as MtRecA through the disassembly of RecA nucleoprotein filaments. However, the structure and DNA strand exchange activity of EcRecA nucleoprotein filaments remain largely unaffected. Furthermore, M. smegmatis ΔdisA cells were found to have undetectable RecA levels due to the translational repression of recA mRNA. Consequently, the ΔdisA mutant exhibited enhanced sensitivity to DNA‐damaging agents. Altogether, this study points out the importance of sequence diversity among recA genes, the role(s) of cyclic di‐AMP and reveals a new mode of negative regulation of recA gene expression, DNA repair and homologous recombination in mycobacteria.
Performance regulation in a networked healthcare system: From cosmetic to institutionalized compliance
Authors: van Erp Judith , Wallenburg Iris , Bal Roland
Published: June 2018

This article studies the role of a public regulator in managing the performance of healthcare professionals. It combines a networked governance perspective with responsive regulation theory to show the mechanisms that have added to significant changes in medical cost management in the Netherlands. In a five‐year period, hospital practices transitioned from cosmetic compliance with performance regulation and strategic upcoding to institutionalized compliance more in line with regulatory goals. The article demonstrates how policy changes transformed incentive structures, introduced new forms of accountability, and added actors to the network with technocratic disciplining tasks. The networked character of performance regulation offered opportunities for a responsive, non‐coercive regulatory strategy that engaged various actors in a regulatory conversation about strategic coding. Responsive regulation can reduce strategic responses to performance regulation and manage the gap between administrative and clinical logics. The case study contributes to our understanding of the effectiveness of responsive, non‐punitive regulation in networked settings.
Biased, not blind: An experimental test of self‐serving biases in service users’ evaluations of performance information
Authors: Christensen Julian
Published: June 2018

Based on literature about motivated reasoning, this article proposes that choosing a public service provider from among competing options may bias service users in a positive direction when evaluating the performance of their chosen provider. Users are expected to defend their choice through processes of goal reprioritization, meaning that they will alter the weight they assign to given pieces of information depending on the (in)convenience of that information. This article uses nine experimental studies to test this expectation on students who had recently chosen to study at one university instead of competing universities. As expected, findings show signs of biases in students’ evaluations, but the biases are small and not consistently significant. Thus, prior research may have been too pessimistic regarding the general potential of performance information in the public sector.
Systems Integration and the Dynamics of Partial Outsourcing
Authors: Anderson Edward G. , Jiang Xiaoyue , Parker Geoffrey G. , Tan Burcu
Published: June 2018

Firms in advanced economies are increasingly outsourcing software and technology development as well as other knowledge work to a worldwide supply base. Standard economic and learning models predict that focal firms should outsource either all or none of a particular activity unless extra resources are required during cyclical demand peaks or access is needed to some tightly appropriable intellectual property. However, recent evidence shows that, even when these exceptions do not apply, many firms pursue a partial outsourcing strategy. We develop a dynamic optimization model to provide a rational explanation for this observation. In our model, learning from prior projects occurs at both the subsystem level and the overall systems level (e.g., systems integration and architecture). Learning at the two levels interacts such that integration capabilities can dynamically build and decay. The model generates conditions where partial outsourcing is rational and dominates the extreme conditions of complete insourcing or complete outsourcing. Our model also specifies the conditions for regime change between insourcing and outsourcing and cycling between insourcing and outsourcing, and overshooting or undershooting the long‐run outsourcing target. Furthermore, we show that these results are highly path‐dependent under short horizons. The model also provides explanation for interesting questions such as why the rate of outsourcing might be U‐shaped in the rate of technological change and why startups so often insource in contrast to more established counterparts in similar industries.
A Manufacturer's New Product Preannouncement Decision and the Supplier's Response
Authors: Sun Haoying , Kumar Subodha
Published: June 2018

We study a manufacturer's product preannouncement decision in a setting where there is uncertainty about when an innovative new product design will be finalized for production, and a key component supplier needs to reserve the capacity before the realization of the final product design. The marketing literature has shown that product preannouncement changes the product demand: it may create buzz about the new product so the demand increases; or it may induce stronger competition from rivals so the demand decreases. We characterize the supplier's optimal response in reserving capacity given the uncertainty in the product design timing and the changing demand. Furthermore, we characterize the conditions under which the manufacturer may benefit from preannouncing her product release date. We show that even when preannouncement leads to a shorter sales window of the product, the manufacturer may still be better off in preannouncing her new product release date because the supplier's response of reserving the capacity earlier improves the manufacturer's profit. For a similar reason, we find that the manufacturer's expected profit may increase in the wholesale price that she pays to the supplier for the key component. In addition, we show that the supplier trusts the manufacturer's preannounced product release date only when this date is sufficiently late; otherwise, he ignores the preannounced product release date. Finally, we demonstrate that the supplier reserves less capacity, but reserves earlier when the competitive response is stronger, the market potential is smaller, and the sales window is shorter.
Exposure to tobacco smoke prenatally and during infancy and risk of hearing impairment among children in Japan: A retrospective cohort study
Authors: Wilunda Calistus , Yoshida Satomi , Tanaka Shiro , Kanazawa Yuji , Kimura Takeshi , Kawakami Koji
Published: June 2018

Background

Previous studies of the association between tobacco smoke and hearing loss in children are limited, involve small samples and are cross‐sectional. We investigated the association of maternal smoking during pregnancy and exposure to tobacco smoke at age 4 months with hearing impairment at age 3 years in children.

Methods

This population‐based retrospective cohort study included 50 734 children born between 2004 and 2010 in Kobe City, Japan. Smoking during pregnancy and exposure to tobacco smoke at 4 months was measured using parent‐reported questionnaires. Hearing impairment was determined by the whispered voice test.

Results

Of the included children, 3.8% were exposed to smoking only during pregnancy; 3.9% were exposed only to second‐hand smoke at 4 months; and 0.9% were exposed to tobacco smoke during pregnancy and at 4 months. The prevalence of hearing impairment at age 3 years was 4.6%. Compared with children not exposed to tobacco smoke prenatally and at 4 months, the risk of hearing impairment was elevated in children exposed to only maternal past smoking during pregnancy (RR 1.26, 95% CI 1.13, 1.40), only second‐hand smoke at 4 months (RR 1.30, 95% CI 1.07, 1.56), only smoking during pregnancy (RR 1.68, 95% CI 1.42, 2.00) and smoking during pregnancy and second‐hand smoke at 4 months (RR 2.35, 95% CI 1.79, 3.10).

Conclusions

Exposure to tobacco smoke prenatally and postnatally was associated with hearing impairment in children. A prevention of smoking before and during pregnancy and exposure to second‐hand smoke postnatally may reduce hearing impairment risk in children.
Oral manifestations and rehabilitation in Fraser syndrome: A case report
Authors: Gallottini Marina , Llanos Alexandre Hugo , Romito Giuseppe Alexandre , Romano Marcelo Munhóes , de Oliveira Felipe Beraldo , de Rezende Nathalie Pepe Medeiros
Published: June 2018

Fraser syndrome (FS) is a rare recessive autosomal genetic disorder characterized by multisystemic malformations typically comprising cryptophthalmos, syndactyly, and renal defects. We report the case of a 16‐year‐old patient who exhibited facial asymmetry, short roots, hypodontia, and malocclusion. Oral rehabilitation included orthodontics, exodontia, and osseointegrated dental implants to improve the patient's self‐esteem and eating function. We suggest short roots and hypodontia assessment in patients with FS.
Lockean Essentialism and the Possibility of Miracles
Authors: Rockwood Nathan
Published: June 2018

If the laws of nature are metaphysically necessary, then it appears that miracles are metaphysically impossible. Yet Locke accepts both essentialism, which takes the laws to be metaphysically necessary, and the possibility of miracles. I argue that the apparent conflict here can be resolved if the laws are by themselves insufficient for guaranteeing the outcome of a particular event. This suggests that, on Locke's view, the laws of nature entail how an object would behave absent divine intervention. While other views of laws also make miracles counterfactually dependent on God's will, I show how this view is consistent with the essentialist commitment to the view that the laws are metaphysically necessary. Further, I argue that Locke's view is a relatively attractive version of essentialism, in part, because it allows for the possibility of miracles.
Egyptian blue pigment in East Mediterranean wall paintings: A study of the lifetime of its optical infrared emission
Authors: Linn R. , Comelli D. , Valentini G. , Mosca S. , Nevin A.
Published: June 2018

This study presents advances in the application of laser‐based methods to image and measure the luminescence lifetime of historical wall paintings containing Egyptian blue. Samples from Tel Kabri, a major Canaanite palace dated to 18th C. BCE, from the Roman city of Caesarea Maritima, from the 4–5th C. Byzantine tomb in Lohamei HaGeta'ot, and from a 6th C. Byzantine church of Shivta have been studied using time‐resolved photoluminescence spectroscopy and imaging. Taking into account the high sensitivity of the emission lifetime to the microenvironment surrounding the emitting species, here, we show for the first time that the optical emission from historical samples containing Egyptian blue particles exhibits meaningful lifetime variations. Indeed, the wall paintings from Tel Kabri, Lohamei HaGeta'ot, and Shivta present the shortest emission lifetime, close to 115–120 μs. However, samples from Caesarea Maritima wall paintings exhibit a different optical emission, which dumps more slowly with an average lifetime of 130 μs. Egyptian blue pigment particles, synthetised with modern methods, are associated with the longest emission lifetime of 147 μs. This study suggests that there is a possible link between the lifetime of the pigment's emission and its synthesis method.
Birthing experience and quality of life after vacuum delivery and second‐stage caesarean section: a prospective cohort study in Uganda
Authors: Nolens Barbara , van den Akker Thomas , Lule John , Twinomuhangi Sulphine , van Roosmalen Jos , Byamugisha Josaphat
Published: June 2018

Objective

To assess perceptions of women undergoing vacuum extraction or second‐stage caesarean section (SSCS) in a tertiary referral hospital in sub‐Saharan Africa.

Methods

Prospective cohort study, with six‐month follow‐up, of women who gave birth to a term singleton in cephalic presentation by vacuum extraction (n = 289) or SSCS (n = 357) between 25 November 2014, to 8 July 2015, in Mulago Hospital, Uganda. Excluded were women who had failed vacuum extraction, severe birth complications and those whose babies had died. Outcome measures were birthing experience satisfaction, physical component summary (PCS) and mental component summary (MCS) of the SF‐12 quality‐of‐life questionnaire, pain scores and dyspareunia.

Results

One day after vacuum extraction, 63.7% (181/284) of women were feeling well vs. 48.1% (167/347) after SSCS (OR 1.89; 95%CI 1.37–2.61) and mean pain sores were 2.70 vs. 3.87 (P < 0.001). In both groups, >90% of women were satisfied with their birthing experience. At six weeks, in vacuum extraction vs. SSCS, mean pain sores were 0.40 vs. 0.89 (P < 0.001); mean PCS was 48.67 vs. 44.03 (P < 0.001); mean MCS was 52.80 vs. 51.23 (P = 0.203); 40% (70/175) vs. 28.3% (70/247) of women had resumed sexual intercourse (OR 1.69; 95%CI 1.12–2.54) and 21.4% (15/70) vs. 28.6% (20/70) had dyspareunia (OR 0.68; 95%CI 0.32–1.47). No differences were found at six months after birth.

Conclusion

One day and six weeks after birth, outcomes were better in women who had vacuum extraction. At six months, outcomes were similar. To promote quick recovery, vacuum extraction should be the first intervention considered in the second stage of labour.
Secretory vesicle trafficking in awake and anaesthetized mice: differential speeds in axons versus synapses
Authors: Knabbe Johannes , Nassal Joris Paul , Verhage Matthijs , Kuner Thomas
Published: June 2018

Key points

Despite their immense physiological and pathophysiological importance, we know very little about the biology of dense core vesicle (DCV) trafficking in the intact mammalian brain.

DCVs are transported at similar average speeds in the anaesthetized and awake mouse brain compared to neurons in culture, yet maximal speed and pausing fraction of transport were higher.

Microtubule plus (+)‐end extension imaging visualized microtubular growth at 0.12 μm/s and revealed that DCVs were transported faster in the anterograde direction.

DCV transport slowed down upon presynaptic bouton approach, possibly promoting synaptic localization and cargo release.

Our work provides a basis to extrapolate DCV transport properties determined in cultured neurons to the intact mouse brain and reveals novel features such as slowing upon bouton approach and brain state‐dependent trafficking directionality.

Neuronal dense core vesicles (DCVs) transport many cargo molecules like neuropeptides and neurotrophins to their release sites in dendrites or axons. The transport properties of DCVs in axons of the intact mammalian brain are unknown. We used viral expression of a DCV cargo reporter (NPY‐Venus/Cherry) in the thalamus and two‐photon in vivo imaging to visualize axonal DCV trafficking in thalamocortical projections of anaesthetized and awake mice. We found an average speed of 1 μm/s, maximal speeds of up to 5 μm/s and a pausing fraction of ∼11%. Directionality of transport differed between anaesthetized and awake mice. In vivo microtubule +‐end extension imaging using MACF18‐GFP revealed microtubular growth at 0.12 μm/s and provided positive identification of antero‐ and retrograde axonal transport. Consistent with previous reports, anterograde transport was faster (∼2.1 μm/s) than retrograde transport (∼1.4 μm/s). In summary, DCVs are transported with faster maximal speeds and lower pausing fraction in vivo compared to previous results obtained in vitro. Finally, we found that DCVs slowed down upon presynaptic bouton approach. We propose that this mechanism promotes synaptic localization and cargo release.
Two new Diptacus species (Acari: Trombidiformes: Diptilomiopidae) from Iran
Authors: Gol Ali , Sadeghi Namaghi Hussein , De Lillo Enrico
Published: June 2018

Two new Diptacus species (Diptilomiopidae: Diptilomiopinae) including D. genusetosus sp. nov. and D. longiscatuber sp. nov. were collected from Alnus subcordata C. A. Meyer (Betulaceae) and Cornus sanguinea L. (Cornaceae), respectively, in Aliabad-e-Katul, Iran. They are described and illustrated. The new species appear to be vagrants on the leaf underside, they are white wax producers and no damage was observed on the infested plants. This is the first record of an eriophyoid mite on Cornaceae in Iran.
Genus Agistemus Summers (Acari: Trombidiformes: Stigmaeidae) from Saudi Arabia and a key to the world species
Authors: Rehman Muneeb Ur , Kamran Muhammad , Alatawi Fahad Jaber
Published: June 2018

Five stigmaeid species belonging to the genus Agistemus Summers (Acari: Trombidiformes: Stigmaeidae) are recorded from different regions of Saudi Arabia. Among these, Agistemus jawadi sp. nov., inhabiting on Ziziphus spina-christi (L.) Desf. is described and illustrated based on female. Two species, A. fleschneri Summers and A. aimogastaensis Leiva et al. are recorded as new to the fauna of Saudi Arabia. Two species A. fleschneri and A. exsertus Gonzalez-Rodriguez are re-described based on adult females. Moreover, Agistemus species are categorized in two species groups; fleschneri and terminalis based on one and two pairs of aggenital setae respectively. A key to the world species of the genus Agistemus is provided. Three species, Agistemus rafiqi Khan et al., A. rawalpindiensis Khan et al. and A. layyahensis Khan et al. are considered as junior synonyms of Agistemus garrulus Chaudhri et al. 1974.
Late Ediacaran trackways produced by bilaterian animals with paired appendages
Authors: Chen Zhe , Chen Xiang , Zhou Chuanming , Yuan Xunlai , Xiao Shuhai
Published: June 2018

Ediacaran trackways suggest the evolution of early legged bilaterian animals 551 to 541 million years ago.
Nucleolar integrity during interphase supports faithful Cdk1 activation and mitotic entry
Authors: Hayashi Yuki , Fujimura Akiko , Kato Kazashi , Udagawa Rina , Hirota Toru , Kimura Keiji
Published: June 2018

The maintenance of nucleolar integrity during interphase is essential for proper cell cycle progression to mitosis.
Self-organized stress patterns drive state transitions in actin cortices
Authors: Tan Tzer Han , Malik-Garbi Maya , Abu-Shah Enas , Li Junang , Sharma Abhinav , MacKintosh Fred C. , Keren Kinneret , Schmidt Christoph F. , Fakhri Nikta
Published: June 2018

The interplay between network percolation and myosin-generated stress propagation leads to dynamically distinct steady states in cortices.
Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral
Authors: Liew Yi Jin , Zoccola Didier , Li Yong , Tambutté Eric , Venn Alexander A. , Michell Craig T. , Cui Guoxin , Deutekom Eva S. , Kaandorp Jaap A. , Voolstra Christian R. , Forêt Sylvain , Allemand Denis , Tambutté Sylvie , Aranda Manuel
Published: June 2018

Changes in gene body methylation predict phenotypic acclimatization of the coral
Stylophora pistillata
to ocean acidification.
Effect of the Novel Antifungal Drug F901318 (Olorofim) on Growth and Viability of Aspergillus fumigatus
Authors: du Pré Saskia , Beckmann Nicola , Almeida Mariana Cruz , Sibley Graham E. M. , Law Derek , Brand Alexandra C. , Birch Mike , Read Nick D. , Oliver Jason D.
Published: June 2018

F901318 (olorofim) is a novel antifungal drug that is highly active against
Aspergillus
species. Belonging to a new class of antifungals called the orotomides, F901318 targets dihydroorotate dehydrogenase (DHODH) in the
de novo
pyrimidine biosynthesis pathway.
Multilocus Variable-Number Tandem-Repeat Analysis of Yersinia ruckeri Confirms the Existence of Host Specificity, Geographic Endemism, and Anthropogenic Dissemination of Virulent Clones
Authors: Gulla Snorre , Barnes Andrew C. , Welch Timothy J. , Romalde Jesús L. , Ryder David , Ormsby Michael J. , Carson Jeremy , Lagesen Karin , Verner-Jeffreys David W. , Davies Robert L. , Colquhoun Duncan J.
Published: June 2018

This comprehensive population study substantially improves our understanding of the epizootiological history and nature of an internationally important fish-pathogenic bacterium. The MLVA assay developed and presented represents a high-resolution typing tool particularly well suited for
Yersinia ruckeri
infection tracing, selection of strains for vaccine inclusion, and risk assessment. The ability of the assay to separate isolates into geographically linked and/or possibly host-specific clusters reflects its potential utility for maintenance of national biosecurity. The MLVA is internationally applicable and robust, and it provides clear, unambiguous, and easily interpreted results. Typing is reasonably inexpensive, with a moderate technological requirement, and may be completed from a harvested colony within a single working day. As the resulting MLVA profiles are readily portable, any
Y. ruckeri
strain may rapidly be placed in a global epizootiological context.
Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut
Authors: Lugli Gabriele Andrea , Mancino Walter , Milani Christian , Duranti Sabrina , Turroni Francesca , van Sinderen Douwe , Ventura Marco
Published: June 2018

The ecological success of bifidobacteria relies on the activity of extracellular proteins that are involved in the metabolism of nutrients and the interaction with the environment. To date, information on secreted proteins encoded by bifidobacteria is incomplete and just related to few species. In this study, we reconstructed the bifidobacterial pan-secretome, revealing extracellular proteins that modulate the interaction of bifidobacteria with their natural environment. Furthermore, a survey of the secretion systems between bifidobacterial genomes allowed the identification of a conserved Sec-dependent secretion machinery in all the analyzed genomes and the Tat protein translocation system in the chromosomes of 23 strains belonging to
Bifidobacterium longum
subsp.
longum
and
Bifidobacterium aesculapii
.
Genome Sequence of Lactobacillus plantarum JMCC0013, Isolated from Traditional Chinese Fermented Milk
Authors: Wang Shijie , Feng Lili , Zhang Dong , Xue Yuling , Xun Yiping , Ke Yuehua , Zhu Hong
Published: June 2018

Fermented food products have been consumed for thousands of years in China, so fermented Chinese foods may contain huge lactic acid bacterial resources. Here, we report the draft genome sequence of a
Lactobacillus plantarum
isolate, JMCC0013, collected from traditional Chinese fermented milk, which provides a precious resource for the genomic analysis of
Lactobacillus
strains.
Complete Genome Sequence of Melissococcus plutonius DAT561, a Strain That Shows an Unusual Growth Profile, Obtained by PacBio Sequencing
Authors: Okumura Kayo , Takamatsu Daisuke , Okura Masatoshi
Published: June 2018

Melissococcus plutonius
is the causative agent of European foulbrood, and its isolates were believed to be remarkably genetically homogeneous. However, recent epidemiological and pathogenic studies have shown this pathogen to be more heterogeneous than expected. Herein, we present the whole-genome sequence of
M. plutonius
DAT561, a representative atypical strain.
Draft Genome Sequence of the Lichen-Forming Fungus Ramalina intermedia Strain YAF0013
Authors: Wang Yi , Yuan Xiaolong , Chen Li , Wang Xinyu , Li Changtian
Published: June 2018

Here, we report a draft genome sequence of
Ramalina intermedia
strain YAF0013. The functional annotation of
R. intermedia
provides important information related to its ability to produce secondary metabolites. The genome sequence reported here builds the basis for further genome mining.
Draft Genome Sequence of Brazilian Leptospira interrogans Serovar Pomona Strain GR5, Isolated from Apparently Healthy Gilt
Authors: Moreno Luisa Zanolli , Miraglia Fabiana , de Oliveira Carolina Helena , Vasconcellos Silvio Arruda , Heinemann Marcos Bryan , Moreno Andrea Micke
Published: June 2018

Leptospira interrogans
serovar Pomona is one of the most important serovars associated with worldwide porcine leptospirosis, and its infection is characterized by high antibody titers and the establishment of a renal carrier state. Here, we present the draft genome sequence of
Leptospira interrogans
serovar Pomona strain GR5 isolated from apparently healthy gilt in Brazil.
Reproducing Clinically Significant Multi-Organism Cultures to Improve Clinical Microbiology Education and Practice
Authors: Barr Rebecca , Davis Mary Feller
Published: June 2018

Medical microbiology courses focus on clinically relevant organisms, but designing laboratory experiments that mimic clinical specimens can be challenging. Many clinical specimens produce multi-organism cultures, which are difficult to reproducibly create in the academic laboratory. With experience with only single organism cultures, students may find it challenging to transition to the clinical laboratory where they must identify pathogens and normal flora from mixed cultures. Here, we present protocols for the creation of multi-organism cultures for mock wound, stool, urine, and throat cultures with medically relevant bacteria that allow these principles to be taught in an academic laboratory prior to clinical experiences.
Creating Successful Campus Partnerships for Teaching Communication in Biology Courses and Labs
Authors: Hall Susanne E. , Birch Christina
Published: June 2018

Creating and teaching successful writing and communication assignments for biology undergraduate students can be challenging for faculty trying to balance the teaching of technical content. The growing body of published research and scholarship on effective teaching of writing and communication in biology can help inform such work, but there are also local resources available to support writing within biology courses that may be unfamiliar to science faculty and instructors. In this article, we discuss common on-campus resources biology faculty can make use of when incorporating writing and communication into their teaching. We present the missions, histories, and potential collaboration outcomes of three major on-campus writing resources: writing across the curriculum and writing in the disciplines initiatives (WAC/WID), writing programs, and writing centers. We explain some of the common misconceptions about these resources in order to help biology faculty understand their uses and limits, and we offer guiding questions faculty might ask the directors of these resources to start productive conversations. Collaboration with these resources will likely save faculty time and effort on curriculum development and, more importantly, will help biology students develop and improve their critical reading, writing, and communication skills.
Changing the Culture of Science Communication Training for Junior Scientists
Authors: Bankston Adriana , McDowell Gary S.
Published: June 2018

Being successful in an academic environment places many demands on junior scientists. Science communication currently may not be adequately valued and rewarded, and yet communication to multiple audiences is critical for ensuring that it remains a priority in today’s society. Due to the potential for science communication to produce better scientists, facilitate scientific progress, and influence decision-making at multiple levels, training junior scientists in both effective and ethical science communication practices is imperative, and can benefit scientists regardless of their chosen career path. However, many challenges exist in addressing specific aspects of this training. Principally, science communication training and resources should be made readily available to junior scientists at institutions, and there is a need to scale up existing science communication training programs and standardize core aspects of these programs across universities, while also allowing for experimentation with training. We propose a comprehensive core training program be adopted by universities, utilizing a centralized online resource with science communication information from multiple stakeholders. In addition, the culture of science must shift toward greater acceptance of science communication as an essential part of training. For this purpose, the science communication field itself needs to be developed, researched and better understood at multiple levels. Ultimately, this may result in a larger cultural change toward acceptance of professional development activities as valuable for training scientists.
Communication Ambassadors—an Australian Social Media Initiative to Develop Communication Skills in Early Career Scientists
Authors: Wang Jack T. H. , Power Cheryl J. , Kahler Charlene M. , Lyras Dena , Young Paul R. , Iredell Jonathan , Robins-Browne Roy
Published: June 2018

Science communication is a skill set to be developed through ongoing interactions with different stakeholders across a variety of platforms. Opportunities to engage the general public are typically reserved for senior scientists, but the use of social media in science communication allows all scientists to instantaneously disseminate their findings and interact with online users. The Communication Ambassador program is a social media initiative launched by the Australian Society for Microbiology to expand the online presence and science communication portfolios of early-career scientists. Through their participation in the program, a rotating roster of Australian microbiologists have broadened the online reach of the Society’s social media channels as well as their own professional networks by attending and live-tweeting microbiology events throughout the year. We present the Communication Ambassador program as a case study of coordinated social media activity in science communication to the general public, and describe the potential for its applications in science education and training.
Learning Science Communication Skills Using Improvisation, Video Recordings, and Practice, Practice, Practice
Authors: Ponzio Nicholas M. , Alder Janet , Nucci Mary , Dannenfelser David , Hilton Holly , Linardopoulos Nikolaos , Lutz Carol
Published: June 2018

Doctoral students in science disciplines spend countless hours learning how to conduct cutting-edge research but very little time learning to communicate the nature and significance of their science to people outside their field. To narrow this disparity, we created an unusual course titled Communicating Science for doctoral science trainees at Rutgers University. Our goal was to help students develop an advanced ability to communicate their research clearly and accurately and to emphasize its value and significance to diverse audiences. Course design included classroom instruction supplemented with improvisation, video recordings, and ample opportunity for students to practice and receive immediate, constructive feedback in a supportive environment. A multidisciplinary faculty with expertise in science, education, communication, and theater arts taught this course. PhD students came from diverse scientific disciplines, ranging from biology and chemistry to civil engineering. Students also completed a capstone project in which they worked with a professional in the academic or private sector to explore a possible career aspiration. Assessment was in the form of feedback on students’ oral and poster presentations, and written abstracts about their research. Student evaluations and comments about course format and content were mostly positive and also provided input for ways to improve the course. We discovered that the diversity of scientific backgrounds among our students enhanced their ability to learn how to communicate their science to others outside their disciplines. We are leveraging the success of our initial course offering to reach other student and faculty groups at Rutgers.
CLIPS (Communication Learning in Practice for Scientists): A New Online Resource Leverages Assessment to Help Students and Academics Improve Science Communication
Authors: Rowland Susan , Hardy James , Colthorpe Kay , Pedwell Rhianna , Kuchel Louise
Published: June 2018

The ability to communicate is a crucial graduate outcome for science students; however, crowded curricula and large class sizes make it difficult to find time to explicitly teach foundational communication skills. In response to these challenges, we developed an online resource called Communication Learning in Practice for Scientists, or CLIPS. CLIPS provides a multi-point mentoring model that has allowed us to successfully integrate the teaching and learning of a complex set of tacitly-understood skills across multiple scientific disciplines. It also provides a flexible way for industry experts, academics, and students to learn from one another’s experiences of, and expertise in, science communication. CLIPS leverages the student focus on assessment; students access CLIPS for pragmatic, detailed, and consistent advice when undertaking assessment tasks. In creating CLIPS, our philosophy was that communication is the core business of any scientific practice, not an add-on after the event. Extensive, repeated use of CLIPS by both students and academics indicates that the resource and its delivery model are considered useful, respected, and impactful for, and by, the intended audiences. We have provided CLIPS to the science education community through
www.clips.edu.au
.
On the Problem and Promise of Metaphor Use in Science and Science Communication
Authors: Taylor Cynthia , Dewsbury Bryan M.
Published: June 2018

The language of science is largely metaphorical. Scientists rely on metaphor and analogy to make sense of scientific phenomena and communicate their findings to each other and to the public. Yet, despite their utility, metaphors can also constrain scientific reasoning, contribute to public misunderstandings, and, at times, inadvertently reinforce stereotypes and messages that undermine the goals of inclusive science. This paper 1) examines the generative potential of metaphors to the advancement of scientific knowledge and science communication, 2) highlights the ways in which outdated metaphors may limit scientific inquiry and contribute to public misunderstandings, and 3) critically analyzes the implications of cryptic social and political messages embedded in common metaphors in the life sciences.
The Surface-Exposed PA
51-72
-Loop of the Influenza A Virus Polymerase Is Required for Viral Genome Replication
Authors: Nilsson-Payant Benjamin E. , Sharps Jane , Hengrung Narin , Fodor Ervin
Published: June 2018

Influenza A viruses are a major global health threat, not only causing significant morbidity and mortality every year but also having the potential to cause severe pandemic outbreaks like the 1918 influenza pandemic. The viral polymerase is a protein complex which is responsible for transcription and replication of the viral genome and therefore is an attractive target for antiviral drug development. For that purpose it is important to understand the mechanisms of how the virus replicates its genome and how the viral polymerase works on a molecular level. In this report, we characterize the role of the flexible surface-exposed PA
51-72
-loop in polymerase function and offer new insights into the replication mechanism of influenza A viruses.
Intravitreal chemotherapy in retinoblastoma: expanded use beyond intravitreal seeds
Authors: Abramson David H , Ji Xunda , Francis Jasmine H , Catalanotti Federica , Brodie Scott E , Habib Larissa
Published: June 2018

Background/aims

Ophthalmic artery chemosurgery (OAC) has changed the face of retinoblastoma treatment and led to a higher rate of globe salvage. The introduction of intravitreal chemotherapy (IVitC) has further enhanced globe salvage with increased success in treatment of intravitreal seeds. Our group has seen success at treating non-vitreous disease that is refractory to OAC using IVitC. This study was undertaken to quantify and report on this success.

Methods

A retrospective review was used to identify patients treated with IVitC for indications other than vitreous seeds from two centres. The indication, prior and concurrent treatment, response time and duration of treatment were documented. Kaplan-Meier estimates were used to evaluate ocular and recurrence-free survival. Ocular toxicity was evaluated using the 30 Hz flicker electroretinogram (ERG). Continuous and categorical variables were compared with Student’s t-test and χ2 test, respectively.

Results

Fifty-six eyes from 52 retinoblastoma patients were identified. There were no disease-related or treatment-related deaths. One patient developed a second primary malignancy (pinealoblastoma) and subsequent leptomeningeal spread. Ninety-eight per cent of the eyes showed clinical regression. Recurrence was seen in 14.3%. Of the recurrences, five occurred in retinal tumours and three in subretinal seeds. The Kaplan-Meier estimated risk of recurrence in all patients treated was 83.5% (95% CI 7.9 to 14.1) at 10 months. The mean change in ERG over treatment course was −17.7 μV.

Conclusions

Intravitreal chemotherapy is successful for the treatment of subretinal seeds and recurrent retinal tumours and could be considered as adjunctive therapy in globe-sparing treatment of retinoblastoma.
Iris anomalies and the incidence ofACTA2mutation
Authors: Taubenslag Kenneth J , Scanga Hannah L , Huey Jennifer , Lee Jennifer , Medsinge Anagha , Sylvester Christin L , Cheng Kenneth P , Nischal Ken K
Published: June 2018

Background

Central cysts of the iris pigment epithelium, or iris flocculi, are frequently reported in the literature in association with thoracic aortic aneurysm and dissection due to smooth muscle alpha-actin 2 (ACTA2) mutations. Children withACTA2mutations may also present with congenital mydriasis. We report our experience regarding the frequency ofACTA2mutation in children with the above iris anomalies.

Methods

This is a retrospective, consecutive case series of all children presenting for iris flocculi or congenital mydriasis at a single tertiary centre from October 2012 to December 2016.

Results

13 children with iris flocculi and 3 with congenital mydriasis presented during the study period. 10 children with iris flocculi completed genetic testing, and none were positive forACTA2mutation. All children with congenital mydriasis presented with a multisystem smooth muscle dysfunction syndrome; two of these three children tested positive for missense R179ACTA2mutations.

Conclusions

In this series,ACTA2mutation or copy number variation was not detected in children presenting for iris flocculi, whereas congenital mydriasis was associated with R179 mutation in both cases that tested positive forACTA2mutation. The case of congenital mydriasis without typical cardiac features of the R179ACTA2phenotype or intracranial vasculopathy was negative forACTA2mutation. While all children presenting with these iris anomalies should be offered a genetic evaluation, incidence data should inform genetic counselling, particularly in the absence of a family history of aneurysm or sudden death, or systemic signs of smooth muscle dysfunction.