bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of instructional method on teaching assistants' classroom discourse
Authors: Current Kelley , Kowalske Megan Grunert
Published: April 2016

There has been increased interest in the transformation of post-secondary level instructional practices in STEM from more traditional to evidence-based practices that are more aligned with how learning occurs. Research has shown that instructional practices are linked to student learning outcomes even when content is unchanged; therefore, incorporating evidence-based practices into the classroom represents an area worthy of focus and resources. Problem-based learning (PBL) is an inquiry-oriented instructional strategy wherein students answer ill-structured real world problems through collaboration, research, experimentation, and trial and error. The success or failure of an inquiry-oriented laboratory session depends in large part on the practices of the instructor. The work presented here focuses on the instructional practices of chemistry graduate teaching assistants (GTAs), who over the course of a semester, taught both expository/demonstration and inquiry laboratory sessions. Upon comparing GTA discourse across inquiry and expository/demonstration settings, three assertions were generated: (a) there was an apparent relationship between the instructional mode (expository/demonstrationversusinquiry) and the structure of the classroom discourse employed by GTAs, (b) patterns in classroom discourse repeated within given instructional modes, even when the nature of content being covered varied widely, and (c) patterns in classroom discourse observed in inquiry labs exemplified a constructivist learning environment and were achieved with minimal intervention.
Symmetric full cells assembled by using self-supporting Na3V2(PO4)3 bipolar electrodes for superior sodium energy storage
Authors: Zhang Yi , Zhao Hongyang , Du Yaping
Published: April 2016

Self-supporting NVP/ECF electrodes are employed as bipolar materials for the fabrication of symmetric full cells.
Graphene quantum dots as selective fluorescence sensor for the detection of ascorbic acid and acid phosphatase via Cr(vi)/Cr(iii)-modulated redox reaction
Authors: Shi Fanping , Zhang Yu , Na Weidan , Zhang Xinyang , Li Yan , Su Xingguang
Published: April 2016

A facile and rapid fluorescence assay based on a redox reaction for successively detecting ascorbic acid and acid phosphatase was developedviaCr(vi)-modulated graphene quantum dots (GQDs).
Dynamic regulation of uncoupling protein 2 expression by microRNA-214 in hepatocellular carcinoma
Authors: Yu Guangsheng , Wang Jianlu , Xu Kesen , Dong Jiahong
Published: April 2016

Gemcitabine (GEM), a commonly used chemotherapeutic agent in hepatocellular carcinoma (HCC) patients, uses oxidative stress induction as a common effector pathway. However, GEM alone or in combination with oxaliplatin hardly renders any survival benefits to HCC patients. We have recently shown that this is part due to the overexpression of the mitochondrial uncoupling protein 2 (UCP2) that in turn mediates resistance to GEM in HCC patients. However, not much is known about regulatory mechanisms underlying UCP2 overexpression in HCC. Differential protein expression in HCC cell lines did not show a concomitant change in UCP2 transcript level, indicating post-transcriptional or post-translational regulatory mechanism. In situ analysis revealed that UCP2 is a putative target of miR-214. miR-214 expression is significantly down-regulated in HCC patient samples as compared with normal adjacent tissues and in cell line, human hepatoblastoma cells (HuH6), with high UCP2 protein expression. We demonstrated using miR-214 mimic and antagomir that the miRNA targeted UCP2 expression by directly targeting the wild-type, but not a miR-214 seed mutant, 3’ UTR of UCP2. Overexpression of miR-214 significantly attenuated cell proliferation. Finally, analysis in 20 HCC patients revealed an inverse correlation in expression of UCP2 and miR-214 (Pearson's correlation coefficient, r=−0.9792). Cumulatively, our data indicate that in the context of HCC, miR-214 acts as a putative tumour suppressor by targeting UCP2 and defines a novel mechanism of regulation of UCP2.
Instability of viscoelastic compound jets
Authors: Ye Han-Yu , Yang Li-Jun , Fu Qing-Fei
Published: April 2016

This paper investigates the axisymmetric instability of a viscoelastic compound jet, for which the constitutive relation is described by the Oldroyd B model. It is found that a viscoelastic compound jet is more unstable than a Newtonian compound jet, regardless of whether the viscoelastic compound jet is inner-Newtonian-outer-viscoelastic, inner-viscoelastic-outer-Newtonian, or fully viscoelastic. It is also found that an increase in the stress relaxation time of the inner or outer fluid renders the jet more unstable, while an increase in the time constant ratio makes the jet less unstable. An analysis of the energy budget of the destabilization process is performed, in which a formulation using the relative rate of change of energy is adopted. The formulation is observed to provide a quantitative analysis of the contribution of each physical factor (e.g., release of surface energy and viscous dissipation) to the temporal growth rate. The energy analysis reveals the mechanisms of various trends in the temporal growth rate, including not only how the growth rate changes with the parameters, but also how the growth rate changes with the wavenumber. The phenomenon of the dispersion relation presenting two local maxima, which occurred in previous research, is explained by the present energy analysis.
Transmission properties of terahertz waves through asymmetric rectangular aperture arrays on carbon nanotube films
Authors: Wang Yue , Tong Yijing , Zhang Xin
Published: April 2016

Transmission spectra of terahertz waves through a two-dimensional array of asymmetric rectangular apertures on super-aligned multi-walled carbon nanotube films were obtained experimentally. In this way, the anisotropic transmission phenomena of carbon nanotube films were observed. For a terahertz wave polarization parallel to the orientation of the carbon nanotubes and along the aperture short axis, sharp resonances were observed and the resonance frequencies coincided well with the surface plasmon polariton theory. In addition, the minima of the transmission spectra were in agreement with the location predicted by the theory of Wood’s anomalies. Furthermore, it was found that the resonance profiles through the carbon nanotube films could be well described by the Fano model.
A guinea pig's tale: learning to review end-to-end marine ecosystem models for management applications
Authors: Kaplan Isaac C. , Marshall Kristin N.
Published: April 2016

A shift towards ecosystem-based management in recent decades has led to new analytical tools such as end-to-end marine ecosystem models. End-to-end models are complex and typically simulate full ecosystems from oceanography to foodwebs and fisheries, operate on a spatial framework, and link to physical oceanographic models. Most end-to-end approaches allow multiple ways to implement human behaviours involving fishery catch, fleet movement, or other impacts such as nutrient loading or climate change effects. Though end-to-end ecosystem models were designed specifically for marine management, their novelty makes them unfamiliar to most decision makers. Before such models can be applied within the context of marine management decisions, additional levels of vetting will be required, and a dialogue with decision makers must be initiated. Here we summarize a review of an Atlantis end-to-end model, which involved a multi-day, expert review panel with local and international experts, convened to challenge models and data used in the management context. We propose nine credibility and quality control standards for end-to-end models intended to inform management, and suggest two best practice guidelines for any end-to-end modelling application. We offer our perspectives (as recent test subjects or “guinea pigs”) on how a review could be motivated and structured and on the evaluation criteria that should be used, in the most specific terms possible.
Classification of Southern Ocean krill and icefish echoes using random forests
Authors: Fallon Niall G. , Fielding Sophie , Fernandes Paul G.
Published: April 2016

Target identification remains a challenge for acoustic surveys of marine fauna. Antarctic krill, Euphausia superba, are typically identified through a combination of expert scrutiny of echograms and analysis of differences in mean volume backscattering strengths (SV; dB re 1 m−1) measured at two or more echosounder frequencies. For commonly used frequencies, however, the differences for krill are similar to those for many co-occurring fish species that do not possess swimbladders. At South Georgia, South Atlantic, one species in particular, mackerel icefish, Champsocephalus gunnari, forms pelagic aggregations, which can be difficult to distinguish acoustically from large krill layers. Mackerel icefish are currently surveyed using bottom-trawls, but the resultant estimates of abundance may be biased because of the species' semi-pelagic distribution. An acoustic estimate of the pelagic component of the population could indicate the magnitude of this bias, but first a reliable target identification method is required. To address this, random forests (RFs) were generated using acoustic and net sample data collected during surveys. The final RF classified as krill, icefish, and mixed aggregations of weak scattering fish species with an overall estimated accuracy of 95%. Minimum SV, mean aggregation depth (m), mean distance from the seabed (m), and geographic positional data were most important to the accuracy of the RF. Time-of-day and the difference between SV at 120 kHz (SV 120) and that at 38 kHz (SV 38) were also important. The RF classification resulted in significantly higher estimates of backscatter apportioned to krill when compared with widely applied identification methods based on fixed and variable ranges of SV 120–SV 38. These results suggest that krill density is underestimated when those SV-differencing methods are used for target identification. RFs are an objective means for target identification and could enhance the utility of incidentally collected acoustic data.
Assembly and Activation of Dynein-Dynactin by the Cargo Adaptor Protein Hook3
Authors: Schroeder Courtney M. , Vale Ronald D.
Published: April 2016

Metazoan cytoplasmic dynein moves processively along microtubules with the aid of dynactin and an adaptor protein that joins dynein and dynactin into a stable ternary complex. Here, we have examined how Hook3, a cargo adaptor involved in Golgi and endosome transport, forms a motile dynein-dynactin complex. We show that the conserved Hook domain interacts directly with the dynein light intermediate chain 1 (LIC1). By solving the crystal structure of the Hook domain and using structure-based mutagenesis, we identify two conserved surface residues that are each critical for LIC1 binding. Hook proteins with mutations in these residues fail to form a stable dynein-dynactin complex, revealing a crucial role for LIC1 in this interaction. We also identify a region of Hook3 specifically required for an allosteric activation of processive motility. Our work reveals the structural details of Hook3’s interaction with dynein and offers insight into how cargo adaptors form processive dynein-dynactin motor complexes.
Workplace conflict and willingness to cooperate
Authors: Ayoko Oluremi Bolanle
Published: April 2016

Purpose

This paper aims to clarify the relationship between conflict, apologies, forgiveness and willingness to cooperate after a conflict event.

Design/methodology/approach

The paper used scenarios and quantitative measures to examine the connection between conflict, perceived apology sincerity, forgiveness and willingness to cooperate in 358 business undergraduates.

Findings

Data revealed that relationship conflict was significantly but negatively associated with forgiveness and willingness to cooperate. Additionally, attitudes toward forgiveness were directly and positively related not only to forgiveness but also to willingness to cooperate. Finally, forgiveness mediated the link between both perceived apology sincerity attitudes to forgiveness and willingness to cooperate.

Research limitations/implications

Data were cross-sectional and may be subject to bias. Longitudinal studies are needed to further tease out the connection between the variables in the current study. Similarly, future research should explore the role of climate and individuals’ disposition and readiness to apologize, forgive and their willingness to cooperate at work.

Practical implications

The paper includes practical implications for managers interested in eliciting cooperation after a workplace conflict. Specifically, apology and forgiveness should be included in managers’ conflict management training programs.

Social implications

Our findings indicated that apology and forgiveness are social skills that are important for conflict management and cooperation after a workplace conflict.

Originality/value

Beyond reconciliation, the current study provides new insights into the important role of actual forgiveness in whether employees are willing to cooperate after conflict at work. Practical assistance is offered to managers who are interested in fostering cooperation and increased performance after conflict episodes.
Towards an understanding of the role of anticipatory justice in the employment dispute-resolution process
Authors: Goldman Barry , Shapiro Debra L. , Pearsall Matthew
Published: April 2016

Purpose

The paper aims to investigate why organizations often opt to reject Equal Employment Opportunity Commission (EEOC)-sponsored mediation of employment disputes (in contrast to employees who tend to readily agree to it). It is guided by recent research associated with Shapiro and Kirkman’s (1999, 2001) theory of “anticipatory justice”, whereby (in)justice is anticipated, or expected, when people think about an event they have not yet experienced whose likely fairness they are questioning. In contrast, “organizational justice” reflects people’s retrospective assessments of how fair they have been treated to date.

Design/methodology/approach

The paper relied upon data made available by the mediation program administered by the US EEOC. The EEOC provided the names and contact information for the officially designated EEOC contacts for each dispute. The authors distributed surveys to each of these organizational representatives and received completed surveys from 492 organizations (a response rate of 85.8 per cent).

Findings

The authors tested the extent to which organizational representatives’ decision to accept or reject mediation as a means of settling discrimination claims is influenced by representatives’ expectation of more versus less fair treatments – by the opposing party as well as by the third-party mediator – during the mediation procedure. The pattern of findings in the study support all hypotheses and, thus, also the expectation-oriented theories that have guided them.

Research limitations/implications

The study relies on self-reports. However, this concern is somewhat lessened because of the salience and recency of events to the time of surveying.

Practical implications

The paper provides new insights on the need for organizations to implement rules, policies and procedures to constrain decision-maker choices consistent with organizational goals. The authors offer specific procedural proposals to reduce this organizational tendency to reject mediation.

Social implications

Employee grievances are costly to organizations in terms of finances, reputation and to the emotional climate of the organization. Moreover, it is similarly costly to employees. This study provides new insights to better understand why employees (as opposed to organizations) are almost three times more likely to elect mediation of employment disputes. As such, it offers some promising ideas to narrow that gap.

Originality/value

The paper investigates a little-studied phenomenon – the differential participation rate of employees versus organizations in EEOC-sponsored mediation.
The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone
Authors: Lee Kevin C. , Stott Matthew B. , Dunfield Peter F. , Huttenhower Curtis , McDonald Ian R. , Morgan Xochitl C.
Published: April 2016

Chthonomonas calidirosea
T49
T
is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the
C. calidirosea
genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four
C. calidirosea
isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in
C. calidirosea
relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the
C. calidirosea
isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of
C. calidirosea
distribution. This dispersal and extinction mechanism is likely not limited to
C. calidirosea
but may shape the populations and genomes of many other low-abundance free-living taxa.

IMPORTANCE
This study compares the genomic sequence variations and metabolisms of four strains of
Chthonomonas calidirosea
, a rare thermophilic bacterium from the phylum
Armatimonadetes
. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four
C. calidirosea
strains were isolated.
C. calidirosea
was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the
C. calidirosea
genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that
C. calidirosea
genotypes are not primarily determined by adaptive evolution. Instead, the presence of
C. calidirosea
may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.
A Structurally Novel Chitinase from the Chitin-Degrading Hyperthermophilic Archaeon Thermococcus chitonophagus
Authors: Horiuchi Ayumi , Aslam Mehwish , Kanai Tamotsu , Atomi Haruyuki
Published: April 2016

A structurally novel chitinase,
Tc
-ChiD, was identified from the hyperthermophilic archaeon
Thermococcus chitonophagus
, which can grow on chitin as the sole organic carbon source. The gene encoding
Tc
-ChiD contains regions corresponding to a signal sequence, two chitin-binding domains, and a putative catalytic domain. This catalytic domain shows no similarity with previously characterized chitinases but resembles an uncharacterized protein found in the mesophilic anaerobic bacterium
Clostridium botulinum
. Two recombinant
Tc
-ChiD proteins were produced in
Escherichia coli
, one without the signal sequence [
Tc
-ChiD(ΔS)] and the other corresponding only to the putative catalytic domain [
Tc
-ChiD(ΔBD)]. Enzyme assays using
N
-acetylglucosamine (GlcNAc) oligomers indicated that both proteins hydrolyze GlcNAc oligomers longer than (GlcNAc)
4
. Chitinase assays using colloidal chitin suggested that
Tc
-ChiD is an exo-type chitinase that releases (GlcNAc)
2
or (GlcNAc)
3
. Analysis with GlcNAc oligomers modified with
p
-nitrophenol suggested that
Tc
-ChiD recognizes the reducing end of chitin chains. While
Tc
-ChiD(ΔBD) displayed a higher initial velocity than that of
Tc
-ChiD(ΔS), we found that the presence of the two chitin-binding domains significantly enhanced the thermostability of the catalytic domain. In
T. chitonophagus
, another chitinase ortholog that is similar to the
Thermococcus kodakarensis
chitinase ChiA is present and can degrade chitin from the nonreducing ends. Therefore, the presence of multiple chitinases in
T. chitonophagus
with different modes of cleavage may contribute to its unique ability to efficiently degrade chitin.

IMPORTANCE
A structurally novel chitinase,
Tc
-ChiD, was identified from
Thermococcus chitonophagus
, a hyperthermophilic archaeon. The protein contains a signal peptide for secretion, two chitin-binding domains, and a catalytic domain that shows no similarity with previously characterized chitinases.
Tc
-ChiD thus represents a new family of chitinases.
Tc
-ChiD is an exo-type chitinase that recognizes the reducing end of chitin chains and releases (GlcNAc)
2
or (GlcNAc)
3
. As a thermostable chitinase that recognizes the reducing end of chitin chains was not previously known,
Tc
-ChiD may be useful in a wide range of enzyme-based technologies to degrade and utilize chitin.
Population- and Individual-Level Dynamics of the Intestinal Microbiota of a Small Primate
Authors: Aivelo Tuomas , Laakkonen Juha , Jernvall Jukka
Published: April 2016

Longitudinal sampling for intestinal microbiota in wild animals is difficult, leading to a lack of information on bacterial dynamics occurring in nature. We studied how the composition of microbiota communities changed temporally in free-ranging small primates, rufous mouse lemurs (
Microcebus rufus
). We marked and recaptured mouse lemurs during their mating season in Ranomafana National Park in southeastern mountainous rainforests of Madagascar for 2 years and determined the fecal microbiota compositions of these mouse lemurs with MiSeq sequencing. We collected 160 fecal samples from 71 animals and had two or more samples from 39 individuals. We found small, but statistically significant, effects of site and age on microbiota richness and diversity and effects of sex, year, and site on microbiota composition, while the within-year temporal trends were less clear. Within-host microbiota showed pervasive variation in intestinal bacterial community composition, especially during the second study year. We hypothesize that the biological properties of mouse lemurs, including their small body size and fast metabolism, may contribute to the temporal intraindividual-level variation, something that should be testable with more-extensive sampling regimes.

IMPORTANCE
While microbiome research has blossomed in recent years, there is a lack of longitudinal studies on microbiome dynamics on free-ranging hosts. To fill this gap, we followed mouse lemurs, which are small heterothermic primates, for 2 years. Most studied animals have shown microbiota to be stable over the life span of host individuals, but some previous research also found ample within-host variation in microbiota composition. Our study used a larger sample size than previous studies and a study setting well suited to track within-host variation in free-ranging mammals. Despite the overall microbiota stability at the population level, the microbiota of individual mouse lemurs can show large-scale changes in composition in time periods as short as 2 days, suggesting caution in inferring individual-level patterns from population-level data.
The Type VI Secretion System inEscherichia coliand Related Species
Authors: Journet Laure , Cascales Eric
Published: April 2016

The type VI secretion system (T6SS) is a multiprotein complex widespread inProteobacteriaand dedicated to the delivery of toxins into both prokaryotic and eukaryotic cells. It thus participates in interbacterial competition as well as pathogenesis. The T6SS is a contractile weapon, related to the injection apparatus of contractile tailed bacteriophages. Basically, it assembles an inner tube wrapped by a sheath-like structure and anchored to the cell envelope via a membrane complex. The energy released by the contraction of the sheath propels the inner tube through the membrane channel and toward the target cell. Although the assembly and the mechanism of action are conserved across species, the repertoire of secreted toxins and the diversity of the regulatory mechanisms and of target cells make the T6SS a highly versatile secretion system. The T6SS is particularly represented inEscherichia colipathotypes andSalmonellaserotypes. In this review we summarize the current knowledge regarding the prevalence, the assembly, the regulation, and the roles of the T6SS inE. coli,Salmonella, and related species.
Systems Metabolic Engineering of
Escherichia coli
Authors: Choi Kyeong Rok , Shin Jae Ho , Cho Jae Sung , Yang Dongsoo , Lee Sang Yup
Published: April 2016

Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in
Escherichia coli
. First, we cover the various tools developed for genetic manipulation in
E. coli
to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in
E. coli
, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in
E. coli
strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered
E. coli
listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including
E. coli
that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
Bordetella holmesii
: Still Emerging and Elusive 20 Years On
Authors: Pittet Laure F. , Posfay-Barbe Klara M.
Published: April 2016

Since the first description of
Bordetella holmesii
in 1995, almost 100 publications have contributed to the increasing knowledge of this emerging bacterium. Although first reported to induce bacteremia mainly in immunocompromised patients, it has also been isolated in healthy persons and has shown the capacity to induce pertussis-like symptoms and other clinical entities, such as meningitis, arthritis, or endocarditis. Respiratory diseases are generally less severe than those induced by
Bordetella pertussis
. However,
B. holmesii
was found to have a higher capacity of invasiveness given the various infection sites in which it was isolated. The diagnosis is difficult, particularly as it is a slow-growing organism but also because respiratory infections are systematically misdiagnosed as
B. pertussis
. Treatment is delicate, as its susceptibility to macrolides (prescribed in respiratory infections) and ceftriaxone (used in invasive disease) is challenged. Regarding prevention, there is no consensus on prophylactic treatment following index cases and no vaccine is available. Epidemiological data are also sparse, with few prevalence studies available. In this chapter, we provide an overview of the current state of knowledge on
B. holmesii
.
The Phylogeny of
Bacillus cereus sensu lato
Authors: Okinaka Richard T. , Keim Paul
Published: April 2016

The three main species of the
Bacillus cereus sensu lato
,
B. cereus
,
B. thuringiensis
, and
B. anthracis
, were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits.
B. thuringiensis
isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen.
B. anthracis
, the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease, and
B. cereus
, a common soil organism, is also an occasional opportunistic pathogen of humans. In addition to these three historical species designations, are three less-recognized and -understood species:
B. mycoides
,
B. weihenstephanensis
, and
B. pseudomycoides
. All of these “species” combined comprise the
Bacillus cereus sensu lato
group. Despite these apparently clear phenotypic definitions, early molecular approaches to separate the first three by various DNA hybridization and 16S/23S ribosomal sequence analyses led to some “confusion” because there were limited differences to differentiate between these species. These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species. But the pathogenic properties of
B. anthracis
and the biopesticide applications of
B. thuringiensis
appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained.
B. cereus sensu lato
represents a classic example of a now common bacterial species taxonomic quandary.
Stress Responses, Adaptation, and Virulence of Bacterial Pathogens During Host Gastrointestinal Colonization
Authors: Flint Annika , Butcher James , Stintzi Alain
Published: April 2016

Invading pathogens are exposed to a multitude of harmful conditions imposed by the host gastrointestinal tract and immune system. Bacterial defenses against these physical and chemical stresses are pivotal for successful host colonization and pathogenesis. Enteric pathogens, which are encountered due to the ingestion of or contact with contaminated foods or materials, are highly successful at surviving harsh conditions to colonize and cause the onset of host illness and disease. Pathogens such as
Campylobacter
,
Helicobacter
,
Salmonella
,
Listeria
, and virulent strains of
Escherichia
have evolved elaborate defense mechanisms to adapt to the diverse range of stresses present along the gastrointestinal tract. Furthermore, these pathogens contain a multitude of defenses to help survive and escape from immune cells such as neutrophils and macrophages. This chapter focuses on characterized bacterial defenses against pH, osmotic, oxidative, and nitrosative stresses with emphasis on both the direct and indirect mechanisms that contribute to the survival of each respective stress response.
The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for
Mycobacterium tuberculosis
Authors: Salaemae Wanisa , Booker Grant W. , Polyak Steven W.
Published: April 2016

Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized
de novo
in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the
Mycobacterium tuberculosis
life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.
Iron Acquisition Strategies of Bacterial Pathogens
Authors: Sheldon Jessica R. , Laakso Holly A. , Heinrichs David E.
Published: April 2016

Iron is an essential micronutrient for both microbes and humans alike. For well over half a century we have known that this element, in particular, plays a pivotal role in health and disease and, most especially, in shaping host-pathogen interactions. Intracellular iron concentrations serve as a critical signal in regulating the expression not only of high-affinity iron acquisition systems in bacteria, but also of toxins and other noted virulence factors produced by some major human pathogens. While we now are aware of many strategies that the host has devised to sequester iron from invading microbes, there are as many if not more sophisticated mechanisms by which successful pathogens overcome nutritional immunity imposed by the host. This review discusses some of the essential components of iron sequestration and scavenging mechanisms of the host, as well as representative Gram-negative and Gram-positive pathogens, and highlights recent advances in the field. Last, we address how the iron acquisition strategies of pathogenic bacteria may be exploited for the development of novel prophylactics or antimicrobials.
Mechanisms of Antibiotic Resistance
Authors: Munita Jose M. , Arias Cesar A.
Published: April 2016

Emergence of resistance among the most important bacterial pathogens is recognized as a major public health threat affecting humans worldwide. Multidrug-resistant organisms have not only emerged in the hospital environment but are now often identified in community settings, suggesting that reservoirs of antibiotic-resistant bacteria are present outside the hospital. The bacterial response to the antibiotic “attack” is the prime example of bacterial adaptation and the pinnacle of evolution. “Survival of the fittest” is a consequence of an immense genetic plasticity of bacterial pathogens that trigger specific responses that result in mutational adaptations, acquisition of genetic material, or alteration of gene expression producing resistance to virtually all antibiotics currently available in clinical practice. Therefore, understanding the biochemical and genetic basis of resistance is of paramount importance to design strategies to curtail the emergence and spread of resistance and to devise innovative therapeutic approaches against multidrug-resistant organisms. In this chapter, we will describe in detail the major mechanisms of antibiotic resistance encountered in clinical practice, providing specific examples in relevant bacterial pathogens.
Recent Advances and Understanding of Using Probiotic-Based Interventions to Restore Homeostasis of the Microbiome for the Prevention/Therapy of Bacterial Diseases
Authors: Suchodolski Jan S. , Jergens Albert E.
Published: April 2016

The importance of the microbiome in health and disease has galvanized interest in using manipulations of the gastrointestinal ecosystem to prevent and/or combat gut bacterial infections and to restore mucosal homeostasis in patients with generalized microbial imbalances (i.e., dysbiosis), including the human inflammatory bowel diseases, Crohn’s disease, and ulcerative colitis. Probiotics, prebiotics, or their combination use (i.e., synbiotics) are one mechanism for modifying the microbiota and exerting direct and indirect effects on the host immune responses and metabolomics profiles. These beneficial effects are transferred through various pathways, including the production of antimicrobial peptides, promoting the growth of beneficial microbes and enhancing immunomodulatory functions via various metabolites. While probiotic therapy has been used empirically for decades with mixed success, the recent advances in molecular and mass spectrophotometric techniques for the characterization of the complexity and diversity of the intestinal microbiome has aided in better understanding of host-microbe interactions. It is important to better understand the functional properties of the microbiome, because it is now clear that the microbiota secretes many metabolites that have a direct impact on host immune responses. This information will improve selection of the most appropriate probiotic strains that selectively target intestinal disease processes.
Exploring the experience of sleep and fatigue in male and female adults over the 2 years following traumatic brain injury: a qualitative descriptive study
Authors: Theadom Alice , Rowland Vickie , Levack William , Starkey Nicola , Wilkinson-Meyers Laura , McPherson Kathryn
Published: April 2016

Objectives

To explore the experience of fatigue and sleep difficulties over the first 2 years after traumatic brain injury (TBI).

Design

Longitudinal qualitative descriptive analysis of interviews completed as part of a larger longitudinal study of recovery following TBI. Data relating to the experience of fatigue and/or sleep were extracted and coded by two independent researchers.

Setting

Community-based study in the Hamilton and Auckland regions of New Zealand.

Participants

30 adult participants who had experienced mild, moderate or severe brain injury within the past 6 months (>16 years of age). 15 participants also nominated significant others to take part. Interviews were completed at 6, 12 and 24 months postinjury.

Results

Participants described feeling unprepared for the intensity, impact and persistent nature of fatigue and sleep difficulties after injury. They struggled to learn how to manage their difficulties by themselves and to adapt strategies in response to changing circumstances over time. Four themes were identified: (1) Making sense of fatigue and sleep after TBI; (2) accepting the need for rest; (3) learning how to rest and; (4) need for rest impacts on ability to engage in life.

Conclusions

Targeted support to understand, accept and manage the sleep and fatigue difficulties experienced may be crucial to improve recovery and facilitate engagement in everyday life. Advice needs to be timely and revised for relevance over the course of recovery.
CYCLE pilot: a protocol for a pilot randomised study of early cycle ergometry versus routine physiotherapy in mechanically ventilated patients
Authors: Kho Michelle E , Molloy Alexander J , Clarke France , Herridge Margaret S , Koo Karen K Y , Rudkowski Jill , Seely Andrew J E , Pellizzari Joseph R , Tarride Jean-Eric , Mourtzakis Marina , Karachi Timothy , Cook Deborah J ,   the Canadian Critical Care Trials Group
Published: April 2016

Introduction

Early exercise with in-bed cycling as part of an intensive care unit (ICU) rehabilitation programme has the potential to improve physical and functional outcomes following critical illness. The objective of this study is to determine the feasibility of enrolling adults in a multicentre pilot randomised clinical trial (RCT) of early in-bed cycling versus routine physiotherapy to inform a larger RCT.

Methods and analysis

60-patient parallel group pilot RCT in 7 Canadian medical-surgical ICUs. We will include all previously ambulatory adult patients within the first 0–4 days of mechanical ventilation, without exclusion criteria. After informed consent, patients will be randomised using a web-based, centralised electronic system, to 30 min of in-bed leg cycling in addition to routine physiotherapy, 5 days per week, for the duration of their ICU stay (28 days maximum) or routine physiotherapy alone. We will measure patients' muscle strength (Medical Research Council Sum Score, quadriceps force) and function (Physical Function in ICU Test (scored), 30 s sit-to-stand, 2 min walk test) at ICU awakening, ICU discharge and hospital discharge. Our 4 feasibility outcomes are: (1) patient accrual of 1–2 patients per month per centre, (2) protocol violation rate <20%, (3) outcome measure ascertainment >80% at the 3 time points and (4) blinded outcomes ascertainment >80% at hospital discharge. Hospital outcome assessors are blinded to group assignment, whereas participants, ICU physiotherapists, ICU caregivers, research coordinators and ICU outcome assessors are not blinded to group assignment. We will analyse feasibility outcomes with descriptive statistics.

Ethics and dissemination

Each participating centre will obtain local ethics approval, and results of the study will be published to inform the design and conduct of a future multicentre RCT of in-bed cycling to improve physical outcomes in ICU survivors.

Trial registration number

NCT02377830; Pre-results.
Dysregulation of the intrinsic apoptotic pathway mediates megakaryocytic hyperplasia in myeloproliferative neoplasms
Authors: Malherbe Jacques A J , Fuller Kathryn A , Mirzai Bob , Kavanagh Simon , So Chi-Chiu , Ip Ho-Wan , Guo Belinda B , Forsyth Cecily , Howman Rebecca , Erber Wendy N
Published: April 2016

Aims

Megakaryocyte expansion in myeloproliferative neoplasms (MPNs) is due to uncontrolled proliferation accompanied by dysregulation of proapoptotic and antiapoptotic mechanisms. Here we have investigated the intrinsic and extrinsic apoptotic pathways of megakaryocytes in human MPNs to further define the mechanisms involved.

Methods

The megakaryocytic expression of proapoptotic caspase-8, caspase-9, Diablo, p53 and antiapoptotic survivin proteins was investigated in bone marrow specimens of the MPNs (n=145) and controls (n=15) using immunohistochemistry. The megakaryocyte percentage positivity was assessed by light microscopy and correlated with the MPN entity,JAK2V617F/CALRmutation status and platelet count.

Results

The proportion of megakaryocytes in the MPNs expressing caspase-8, caspase-9, Diablo, survivin and p53 was significantly greater than controls. A greater proportion of myeloproliferative megakaryocytes expressed survivin relative to its reciprocal inhibitor, Diablo. Differences were seen between myelofibrosis, polycythaemia vera and essential thrombocythaemia for caspase-9 and p53.CALR-mutated cases had greater megakaryocyte p53 positivity compared to those with theJAK2V617Fmutation. Proapoptotic caspase-9 expression showed a positive correlation with platelet count, which was most marked in myelofibrosis andCALR-mutated cases.

Conclusions

Disruptions targeting the intrinsic apoptotic cascade promote megakaryocyte hyperplasia and thrombocytosis in the MPNs. There is progressive dysfunction of apoptosis as evidenced by the marked reduction in proapoptotic caspase-9 and accumulation of p53 in myelofibrosis. The dysfunction of caspase-9, which is necessary for proplatelet formation, may be the mechanism for the excess thrombocytosis associated withCALRmutations. Survivin seems to be the key protein mediating the megakaryocyte survival signature in the MPNs and is a potential therapeutic target.
An overview of Chinese Silurian acritarch research
Authors: Yan Kui , Li Jun , Servais Thomas
Published: April 2016

The present paper reviews all investigations of Silurian acritarchs in China. Since Silurian acritarchs were first reported in China in 1978, significant progress has been made in Chinese Silurian acritarch research. A total of 30 scientific articles and theses have been published on Silurian acritarchs from China. The majority of these papers recorded acritarchs from South China, and most Silurian acritarch studies concentrated on the Llandovery. Two papers describing material thought to be Silurian have since been shown to be Ordovician acritarch assemblages. We have updated the systematics of the taxa in these reported assemblages and documented their biostratigraphic distribution within China. Investigations of Silurian acritarchs, however, are still very limited, and more research is needed for systematic, biostratigraphic, and palaeoecological interpretations.
Structural and lithostratigraphic controls of earth-flow evolution, Montaguto earth flow, Southern Italy
Authors: Pinto Felice , Guerriero Luigi , Revellino Paola , Grelle Gerardo , Senatore Maria Rosaria , Guadagno Francesco M.
Published: April 2016

This paper aims to define the control exerted by geological setting on the evolution and segmentation of the Montaguto earth flow in Southern Italy. A detailed geological survey and multi-temporal maps were used to reconstruct the geological model of La Montagna Mt. and to quantify the evolution of the flow in terms of sediment pulse formation, movement direction and spatial change in earth-flow area. The spatial distribution of structural fabric of the mountainside was compared with (1) planar geometry of earth-flow source area, (2) orientation of strike-slip faults bounding the earth-flow moving core (i.e. movement direction) and (3) kinematic-zone position and extent. We infer that the evolution of the earth flow is controlled by geological structures and lithology. Moreover, the entire basal-slip surface is composed of newly formed basal-slip surface in the source area, and corresponds to pre-earth-flow topography downslope from the neck. Implications of our work are that (1) a detailed geological model of an unstable mountainside, combined with information about earth-flow spatial evolution, might be considered as a tool that allows the localization of areas of possible earth-flow enlargement and (2) geological structures constrain earth-flow movement, inducing a predictable seasonal behaviour in terms of movement direction.
A short-term, post-Lomagundi positive C isotope excursion at
c.
2.03 Ga recorded by the Wooly Dolomite, Western Australia
Authors: Bekker Andrey , Krapež Bryan , Müller Stefan G. , Karhu Juha A.
Published: April 2016

It is generally accepted that carbon isotope variations in seawater were muted between
c.
2.06 Ga, after the end of the Lomagundi carbon isotope excursion (LCIE), and
c.
1.3 Ga. Evidence is presented here that
c.
30 myr after the end of the LCIE, the biogeochemical cycle of carbon experienced a short-term (
c.
2 myr), high-amplitude (up to +8.4‰ V-PDB) perturbation, recorded in the Horseshoe rift basin, Western Australia. The basin was initiated at
c.
2.03 Ga with deposition of fluvial and shallow-marine sandstones, followed by the eruption of flood basalt, and culminated with the deposition of platform carbonates, and accompanying volcaniclastic and siliciclastic sediments (Wooly Dolomite). The Horseshoe rift basin during deposition of the Wooly Dolomite was fault-compartmentalized but connected to an ocean. Six depositional sequences make up the Wooly Dolomite. Sequence 1 records establishment of a carbonate platform conformably on basalt and coevally with volcaniclastic sedimentation. All other sequences have dominant carbonate-platform deposits and are unconformity-bounded. Sequence 3 contains a
c.
57 m thick section with
13
C-enriched carbonates bracketed between carbonates with close to 0‰ carbon isotope values. Further high-resolution chemostratigraphic studies may reveal a more complex pattern of carbon isotope variations during the ‘boring billion years’, but without precise geochronology similar short-term carbon isotope excursions in carbonate successions could be incorrectly correlated to the LCIE.

Supplementary material:
Table 2 including chemical and isotopic data, sample locations and their position in Figure 8 is available at
https://doi.org/10.6084/m9.figshare.c.2868055
.