bluuebunny/crossref_metadata_2025 huggingface dataset:
Finding functional disease-associated non-coding variation using next-generation sequencing
Authors: Devanna Paolo , Chen Xiaowei Sylvia , Ho Joses , Gajewski Dario , Gialluisi Alessandro , Francks Clyde , Fisher Simon E. , Newbury Dianne , Vernes Sonja C.
Published: June 2016

Next generation sequencing has opened the way for the large scale interrogation of cohorts at the whole exome, or whole genome level. Currently, the field largely focuses on potential disease causing variants that fall within coding sequences and that are predicted to cause protein sequence changes, generally discarding non-coding variants. However non-coding DNA makes up~98% of the genome and contains a range of sequences essential for controlling the expression of protein coding genes. Thus, potentially causative non-coding variation is currently being overlooked. To address this, we have designed an approach to assess variation in one class of non-coding regulatory DNA; the 3′UTRome. Variants in the 3'UTR region of genes are of particular interest because 3'UTRs are responsible for modulating protein expression levels via their interactions with microRNAs. Furthermore they are amenable to large scale analysis as 3′UTR-microRNA interactions are based on complementary base pairing and as such can be predictedin silicoat the genome-wide level. We report a strategy for identifying and functionally testing variants in microRNA binding sites within the 3'UTRome and demonstrate the efficacy of this pipeline in a cohort of language impaired children. Using whole exome sequence data from 43 probands, we extracted variants that lay within 3'UTR microRNA binding sites. We identified a common variant (SNP) in a microRNA binding site and found this SNP to be associated with an endophenotype of language impairment (non-word repetition). We showed that this variant disrupted microRNA regulation in cells and was linked to altered gene expression in the brain, suggesting it may represent a risk factor contributing to SLI. This work demonstrates that biologically relevant variants are currently being under-investigated despite the wealth of next-generation sequencing data available and presents a simple strategy for interrogating non-coding regions of the genome. We propose that this strategy should be routinely applied to whole exome and whole genome sequence data in order to broaden our understanding of how non-coding genetic variation underlies complex phenotypes such as neurodevelopmental disorders.
Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland
Authors: Annunziato Stefano , Kas Sjors M. , Nethe Micha , Yücel Hatice , Del Bravo Jessica , Pritchard Colin , Bin Ali Rahmen , van Gerwen Bas , Siteur Bjørn , Drenth Anne Paulien , Schut Eva , van de Ven Marieke , Boelens Mirjam C. , Klarenbeek Sjoerd , Huijbers Ivo J. , van Miltenburg Martine H. , Jonkers Jos
Published: June 2016

Large-scale sequencing studies are rapidly identifying putative oncogenic mutations in human tumors. However, discrimination between passenger and driver events in tumorigenesis remains challenging and requires in vivo validation studies in reliable animal models of human cancer. In this study, we describe a novel strategy for in vivo validation of candidate tumor suppressors implicated in invasive lobular breast carcinoma (ILC), which is hallmarked by loss of the cell–cell adhesion molecule E-cadherin. We describe an approach to model ILC by intraductal injection of lentiviral vectors encoding Cre recombinase, the CRISPR/Cas9 system, or both in female mice carrying conditional alleles of the Cdh1 gene, encoding for E-cadherin. Using this approach, we were able to target ILC-initiating cells and induce specific gene disruption of Pten by CRISPR/Cas9-mediated somatic gene editing. Whereas intraductal injection of Cas9-encoding lentiviruses induced Cas9-specific immune responses and development of tumors that did not resemble ILC, lentiviral delivery of a Pten targeting single-guide RNA (sgRNA) in mice with mammary gland-specific loss of E-cadherin and expression of Cas9 efficiently induced ILC development. This versatile platform can be used for rapid in vivo testing of putative tumor suppressor genes implicated in ILC, providing new opportunities for modeling invasive lobular breast carcinoma in mice.
Small-angle scattering and scale-dependent heterogeneity
Authors: Gommes Cedric J.
Published: June 2016

Although small-angle scattering is often discussed qualitatively in terms of material heterogeneity, when it comes to quantitative data analysis this notion becomes somehow hidden behind the concept of correlation function. In the present contribution, a quantitative measure of heterogeneity is defined, it is shown how it can be calculated from scattering data, and its structural significance for the purpose of material characterization is discussed. Conceptually, the procedure consists of using a finite probe volume to define a local average density at any point of the material; the heterogeneity is then quantitatively defined as the fluctuations of the local average density when the probe volume is moved systematically through the sample. Experimentally, it is shown that the so-defined heterogeneity can be estimated by projecting the small-angle scattering intensity onto the form factor of the chosen probe volume. Choosing probe volumes of various sizes and shapes enables one to comprehensively characterize the heterogeneity of a material over all its relevant length scales. General results are derived for asymptotically small and large probes in relation to the material surface area and integral range. It is also shown that the correlation function is equivalent to a heterogeneity calculated with a probe volume consisting of two points only. The interest of scale-dependent heterogeneity for practical data analysis is illustrated with experimental small-angle X-ray scattering patterns measured on a micro- and mesoporous material, on a gel, and on a semi-crystalline polyethylene sample. Using different types of probes to analyse a given scattering pattern enables one to focus on different structural characteristics of the material, which is particularly useful in the case of hierarchical structures.
Characterization of crystal structure and precipitation crystallography of a new MgxAl2−xGd phase in an Mg97Al1Gd2alloy
Authors: Gu X.-F. , Furuhara T.
Published: June 2016

The composition, crystal structure and precipitation crystallography of a newly found precipitate are characterized by Cs-corrected scanning transmission electron microscopy. The composition of the plate-like precipitate could be expressed as MgxAl2−xGd (x= 0.38), and its crystal structure is the same as the face-centered cubic type Laves phases Mg2Gd and Al2Gd, with a lattice parameter of 7.92 Å (space group No. 227, Fd\overline 3m). The orientation relationship between the matrix and precipitate is found to be (0001)m//(111)pand [10\overline 10]m//[1\overline 10]p, and the habit plane is parallel to the (0001)m//(111)pplane. In addition, this preferred crystallography of phase transformation is well explained on the basis of the atomic matching at the interface.
CFEL–ASG Software Suite(CASS): usage for free-electron laser experiments with biological focus
Authors: Foucar Lutz
Published: June 2016

CASS[Foucaret al.(2012).Comput. Phys. Commun.183, 2207–2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements ofCASSfor use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.
A polymeric silver thiosaccarinate complex with a two-dimensional triply entangled mesh and argentophilic interactions
Authors: Dennehy Mariana , Delgado Fermín , Freire Eleonora , Halac Emilia , Baggio Ricardo
Published: June 2016

Silver(I) complexes with sulfur-donor ligands have a broad range of pharmacological applications. One of the most important factors for tuning the biological activity is the type of donor atom and the ease of ligand replacement. Silver thiosaccharinates display a wide range of structures from mono- to polynuclear complexes. We report the synthesis, crystal structure and vibrational spectroscopic analysis of a two-dimensional AgI–thiosaccharinate coordination polymer, namely poly[tris(μ2-4,4′-bipyridine-κ2N:N′)bis(μ3-1,1-dioxo-1,2-benzisothiazole-3-thiolato-κ3N:S3:S3)bis(μ2-1,1-dioxo-1,2-benzisothiazole-3-thiolato-κ2S3:S3)tetrasilver(I)], [Ag2(C7H4NO2S2)2(C10H8N2)1.5]n, with 4,4′-bipyridine acting as a spacer. A relevant feature of the structure is the presence of an unusually short Ag...Ag separation of 2.8859 (10) Å, well within the range of argentophilic interactions and confirmed as such by Raman analysis of the low-frequency spectrum. From a topological point of view, the structure presents interpenetration in the form of a threefold entangled 2D→2D mesh (2D is two-dimensional).
Angular-split/temporal-delay approach to ultrafast protein dynamics at XFELs
Authors: Ren Zhong , Yang Xiaojing
Published: June 2016

X-ray crystallography promises direct insights into electron-density changes that lead to and arise from structural changes such as electron and proton transfer and the formation, rupture and isomerization of chemical bonds. The ultrashort pulses of hard X-rays produced by free-electron lasers present an exciting opportunity for capturing ultrafast structural events in biological macromolecules within femtoseconds after photoexcitation. However, shot-to-shot fluctuations, which are inherent to the very process of self-amplified spontaneous emission (SASE) that generates the ultrashort X-ray pulses, are a major source of noise that may conceal signals from structural changes. Here, a new approach is proposed to angularly split a single SASE pulse and to produce a temporal delay of picoseconds between the split pulses. These split pulses will allow the probing of two distinct states before and after photoexcitation triggered by a laser pulse between the split X-ray pulses. The split pulses originate from a single SASE pulse and share many common properties; thus, noise arising from shot-to-shot fluctuations is self-canceling. The unambiguous interpretation of ultrafast structural changes would require diffraction data at atomic resolution, as these changes may or may not involve any atomic displacement. This approach, in combination with the strategy of serial crystallography, offers a solution to study ultrafast dynamics of light-initiated biochemical reactions or biological processes at atomic resolution.
Islamic bank vs conventional bank: intermediation, fee based service activity and efficiency
Authors: Hardianto Dimas Satria , Wulandari Permata
Published: June 2016

Purpose

The aim of this research is to compare the differences of intermediation, fee-based service activity and efficiency of conventional banks vs Islamic banks in Indonesia for the 2011-2013 period. Moreover, this study also includes some control variables to find their effect on the dependent variables.

Design/methodology/approach

This research uses two methods, namely, stochastic frontier approach and panel data regression.

Findings

The result indicates that Islamic banks have a higher intermediation ratio, have higher proportion on fee income-to-total operating income and are less efficient. The control variable that has a positively significant effect on intermediation ratio is size; meanwhile, inefficiency and non–loan-earning asset are negatively affecting the intermediation ratio. The control variable that show a positively significant effect on the proportion of fee income-to-total operating income is size; meanwhile, the credit risk variable has no significant effect on the proportion of fee income-to-total operating income. Size and credit risk are the control variables that have a negative relation to efficiency.

Originality/value

This study has significantly contributed to Indonesian Islamic banking based on which the Islamic banking manager should recognize that the intermediation level, fee-based service activity and efficiency are crucially important in establishing competition and maintaining sustainable Islamic banking.
The influence of the UAE context on management practice in UAE business
Authors: de Waal André , Frijns Miriam
Published: June 2016

Purpose

This paper aims to investigate whether the United Arab Emirates (UAE) business context as described in the literature still matches with the UAE business context in practice. In many managerial publications, and even in quite a few academic ones, warnings are given about the different and difficult business environment which exists in Arab countries. This environment is allegedly characterized by a high religious influence, a definitive centralization of power, a strong family and tribal culture and a strong role of wasta, which makes doing business in the Middle East arduous. However, the context of the UAE is not typical Arab, as it is very much multicultural with many expatriates working in both local and foreign companies.

Design/methodology/approach

The theoretical aspects of the UAE business context were derived from a literature study. The aspects of the UAE business context in practice were collected during interviews with 36 Emirati and Western and Eastern expat managers working in the UAE. Subsequently, the theoretical aspects were matched with the practical aspects.

Findings

The matching shows that the typical Arab business setting is still there but that it exists next to the international business setting.

Research limitations/implications

Because of the coexisting cultural business settings, more nuance is needed in describing the typical Arab elements of the UAE business context, to fully understand the way of operating in the UAE.

Originality/value

As during this study a cross section of nationalities working in the UAE, including Emirati, was interviewed, it gives an unique insight into the current state of affairs in the UAE.
The internal challenges facing Islamic finance industry
Authors: Abozaid Abdulazeem
Published: June 2016

Purpose

The paper aims to highlight the challenges facing Islamic finance industry and outline the prospectus of what constitutes a sound Islamic banking product in terms of both its Shariah control and product development methodology.

Design/methodology/approach

The paper analytically addresses the internal challenges facing Islamic finance industry by highlighting, first, the deficiencies in the existing Shariah supervisory work and, then, the deficiencies in the product development methodology followed in Islamic banks.

Findings

Islamic banking and finance is facing some internal challenges which require immediate action. Although facing the external challenges may be beyond the capacity of the industry players, Islamic banks have no excuse to overlook or turn a blind eye to their internal challenges which can be overcome by enacting Shariah governance for both products and Shariah control and reforming the methodology of product development.

Originality/value

This paper highlights an issue that has not received the needed attention, and it proposes the necessary solutions to the problems it identifies.
Service value optimization of cloud hosted systems using particle swarm technique
Authors: Murad Salah Eddin , Dowaji Salah
Published: June 2016

Purpose

– Cloud Computing has become a more promising technology with potential opportunities, through reducing the high cost of running the traditional business applications and by leading to new business models. Nonetheless, this technology is fraught with many challenges. From a Software as a Service (SaaS) provider perspective, deployment choices are one of the major perplexing issues in determining the degree to which the application owners’ objectives are met while considering their customers’ targets. The purpose of this paper is to present a new model that allows the service owner to optimize the resources selection based on defined metrics when responding to many customers’ with various priorities.

Design/methodology/approach

– More than 65 academic papers have been collected, a short list of the most related 35 papers have been reviewed, in addition to assessing the functionality of major cloud systems. A potential set of techniques has been investigated to determine the most appropriate ones. Moreover, a new model has been built and a study of different simulation platforms has been conducted.

Findings

– The findings demonstrate that serving many SaaS customer requests, with different agreements and expected outcomes, would have mutual influence that impact the overall provider objectives. Furthermore, this paper investigates how tagging those customers with various priorities, with reflection of their importance to the provider, permits controlling and aligning the selection of computing resources as per the current objectives and defined priorities.

Research limitations/implications

– This study provides researchers with a useful literature, which can assist them in relevant subject. Additionally, it uses a value-based approach and particle swarm technique to model and solve the optimization of the computing resource selection, considering different business objectives for both stakeholders, providers and customers. This study derives priority of a number of factors, by which service providers can make strong and adaptive decisions.

Practical implications

– The paper includes implications on how the SaaS service provider can make decisions to select the needed virtual machines type driven by his own preferences.

Originality/value

– This paper rests on the usage of Particle Swarm Optimization technique to optimize the business value of the service provider, as well as the usage of value-based approach. This will help model that value in order to combine the total profit of the provider and the customer satisfaction, based on the agreed budget and processing time requested by the customer. Another additional approach has been charted by using the customer severity factor that allows the provider to reflect the customer importance while making the placement decision.
The value of strategy and flexibility in new product development
Authors: Fantazy Kamel A. , Salem Mohamed
Published: June 2016

Purpose

– The purpose of this paper is to examine the relationship between strategy and flexibility in new product development, and the operational and financial performance in the supply chain context. The motives for conducting this research are to introduce the supply chain strategies and new product development flexibility (NPDF) as constructs that could have the potential to contribute to the success of supply chain performance. Based on the relational view of the firm, the authors propose that supply chain strategy is an antecedent of NPDF and can create value for the buying firm in terms of better financial and non-financial performance.

Design/methodology/approach

– The structural equation modeling approach was used to evaluate the proposed model and analyze hypothesized relationships. The analysis, based on data collected from 175 small- and medium-sized (SME) Canadian manufacturing companies.

Findings

– The analysis shows that there are direct positive effects from strategy on NPDF. The findings indicate also a direct positive association between NPDF and performance and showed that the total effect (direct and indirect) positively influenced performance.

Originality/value

– The literature did not reveal any study which attempted to examine strategy, NPDF, and performance in the supply chain context of SMEs. The current study fills this important gap in the literature.
Perception alignment hypothesis: causality of herding?
Authors: Dalko Viktoria
Published: June 2016

Purpose

The purpose of this paper is to uncover an institutional reason behind herding and the key to successful execution of the accumulation-lift-distribution (ALD) trading strategy.

Design/methodology/approach

The paper proposes the perception alignment hypothesis (PAH), which is based on a large number of empirical episodes. Extensive empirical and theoretical literature of 79 articles is reviewed. These are selected from previously unrelated fields of prosecuted cases in market manipulation, sell-side analysts’ recommendations and internet rumors. These studies are put into a unifying conceptual framework.

Findings

The proposed PAH can explain some herding episodes that were generated for the purpose of executing ALD.

Practical implications

The value of the approach is that while behavioral biases are hard to change, perception alignment can be more responsive to regulation.

Originality/value

This paper is the first to propose the PAH. It provides an explanation for the causality of herding that complements the traditional literature on the psychological weaknesses of investors. This paper opens a debate on whether the stock market is fully competitive because investors have behavioral biases and certain institutions take advantage of those biases.
The effects of monetary policy on the Islamic financial services industry
Authors: Yungucu Burak , Saiti Buerhan
Published: June 2016

Purpose

The purpose of this paper is to investigate the effects of monetary policy on the Islamic financial service industry by studying the findings of the existed literature.

Design/methodology/approach

Because of the unavailability of the empirical models in the existing study, the authors used past studies review and proposed a new theoretical model.

Findings

Majority of these studies have documented the negative effects with the exception of a few. The transmission of the monetary policy has been taken place through interest rate risk, asset-liability mismatch, as well as deposit and financing instability. Furthermore, the examined studies have confirmed the viability of the Islamic monetary policy.

Originality/value

The proposed model may offer some insights to policy makers if it is examined empirically.
A qualitative inquiry into the investment decision behaviour of the Malaysian stock market investors
Authors: Jaiyeoba Haruna Babatunde , Haron Razali
Published: June 2016

Purpose

The main purpose of this study was to examine the investment decision behaviour of retail investors in Malaysia.

Design/methodology/approach

The study adopted semi-structured interviews to solicit an understanding of six retail investors on investment decision behaviour in Malaysia. Content analysis technique was used to analyse the data and verbatim texts were applied in discussing the emergent themes.

Findings

The findings indicate that retail investors in Malaysia are patriotic in nature, and their investment decisions are based on feeling of comfort or convention rather than quantitative analysis. They rely so much on their findings rather than third party’s views for making investment decisions. They were influenced by the psychological biases because they herd on the information. Challenges are solved through experience, and they believe that proper understanding of the financial and economic settings of the country can enhance better investment decision-making.

Research limitations/implications

A more detailed investigation on the investors’ behaviour with more samples may expand our understanding of this issue. Future studies need to examine the investment decision behaviour with more samples.

Practical implications

First, it will prepare hit and run investors to be more ready to remain in the market and improve their skills on how to make sound investment decisions. Second, it helps the investors to know that knowledge of traditional finance theory is not sufficient to excel in stock market, and, hence, they need to know more about behavioural finance. Third, investors are exposed to various reasons as to why investment decisions deviate from expected and different means of solving the challenges faced in making investment decision within the Malaysian context. Fourth, investors are reminded that understanding the financial settings before investing is essential. Finally, policy makers in stock market are able to understand the retail investors’ behaviour.

Originality/value

This study examines the experience and prospect to remain as stock market investors, their priorities in selecting the right company for investment purposes, the kind of information seeking from third parties, the challenges faced by them and other important considerations in investment decisions. These have never been examined together in this way in investigation of retail investors’ investment behaviour.
Pathways to de‐extinction: how close can we get to resurrection of an extinct species?
Authors: Shapiro Beth
Published: June 2016

De‐extinction, the idea that extinct species might soon be resurrected, receives considerable attention in both popular and scientific literature, in particular with regard to its potential ecological and ethical consequences.

Here, I review the three main pathways that are being considered at present for de‐extinction: back‐breeding, cloning via somatic cell nuclear transfer (SCNT) and genetic engineering. I present the state of the art in each pathway and discuss the limitations of each approach as a mechanism to resurrect extinct species.

Back‐breeding aims to concentrate ancestral traits that persist within a population into a single individual using selective breeding. In back‐breeding, ancestral phenotypes may be resurrected after many generations, but the genes that underlie these phenotypes may differ from those that were present in the extinct species.

Cloning aims to create genetically identical copies of an extinct species from preserved somatic cells. These somatic cells are fused with egg cells from a closely related and living donor species, which causes cellular reprogramming and embryogenesis, a scientific process known as SCNT. The developing embryo is then brought to term within a surrogate host. Because biological remains degrade post‐mortem, cloning of long‐dead organisms is not likely to be feasible.

Genetic engineering aims to edit the genome sequence within cells of living species so that these genome sequences closely resemble that of a closely related extinct species. This approach draws on recent advances in both ancient DNA and genome editing technologies and is a particularly promising approach to de‐extinction. After the genome of a living cell is edited, that living cell can then be used for SCNT.

Because the phenotype of an organism is the consequence of the interaction between its genotype and the environment in which it develops and lives, even species with cloned nuclear genomes will not be exact copies of the extinct species on which they are modelled. We should therefore consider de‐extinction as a means to create ecological proxies for extinct species.

A lay summary is available for this article.
Leafing intensity and the fruit size/number trade‐off in woody angiosperms
Authors: Dombroskie Sarah L. , Tracey Amanda J. , Aarssen Lonnie W.
Published: June 2016

A sample of woody angiosperm species was used to test a central prediction of the ‘leafing intensity premium’ hypothesis: higher leafing intensity (number of leaves produced per unit dry mass of shoot vegetative tissue produced in the same growing season) confers a larger bud bank (i.e. number of axillary meristems per unit shoot tissue) that can be deployed for reproduction, and thus confers generally greater fruit numbers, and hence higher potential fecundity allocation (i.e. fecundity per unit size of the supporting shoot tissue that is produced in the same growing season.

Current‐year shoots (i.e. bearing leaves) were collected to record: shoot dry mass, total number of leaves, total number of fruits or fruit clusters (if derived from inflorescences), mean individual leaf dry mass and mean individual fruit dry mass. Sampled individuals (shrubs and trees) were also measured for body size (main stem height and circumference).

Species with larger individual fruit (or fruit cluster) mass have generally larger leaves, but they also have a negative trade‐off relationship with ‘fruiting intensity’ – that is the total number of reproductive meristems producing fruits (or fruit clusters) per unit dry mass of shoot vegetative tissue produced in the same growing season. Variation in fruiting intensity, however, is better predicted by a positive relationship with variation in bud bank size.

Species with smaller leaf size (dry mass) have generally higher leafing intensity; species with higher leafing intensity in turn have generally higher fruiting intensity; and species with higher fruiting intensity in turn have generally higher potential fecundity allocation (based on the typical species maximum number of seeds per fruit, obtained from published floras). Species with smaller body size have generally higher potential fecundity allocation, but body size had no significant relationships with other measured traits when controlling for phylogeny (using phylogenetically independent contrasts).

Synthesis. Our results indicate that bud bank size is an important functional trait for defining adaptive strategy in woody angiosperms. A larger bud bank is generated by higher leafing intensity, which in turn generates higher fruiting intensity, thus generating greater potential fecundity allocation. These traits will be important for maximizing reproductive economy – that is capacity to produce offspring despite growth or body size limitation (e.g. due to crowding/competition, or because of limited time available for growth, flowering, pollination or fruit/seed maturation).
Unravelling the natural dynamics and resilience patterns of underwater Mediterranean forests: insights from the demography of the brown alga Cystoseira zosteroides
Authors: Capdevila Pol , Hereu Bernat , Riera Juan Lluís , Linares Cristina
Published: June 2016

Despite being among the most important habitat‐forming organisms in temperate seas almost nothing is known about the demography of many algal species. This limits our ability to understand the effects of global and local stressors and to predict future trends under ongoing environmental change, which in turn hinders conservation actions.

Cystoseira species develop important forest‐like assemblages along the sublittoral zone in the Mediterranean Sea. In this study we investigated the natural population dynamics and resilience patterns of a deep‐water brown and canopy‐forming macroalga, Cystoseira zosteroides. We used density‐dependent and stochastic matrix models to estimate its basic life‐history and compare it with other relevant habitat‐forming marine (brown algae) and terrestrial (plants) species. We also evaluated the consequences of increasing the disturbances caused by storms and the impact of lost fishing gear, and their interaction, on C. zosteroides population dynamics.

The population dynamics of C. zosteroides showed similar patterns to terrestrial long‐lived species such as shrubs and trees, with high survival due to their investment in structural biomass. Our data and models suggest that this species is able to buffer mortality pulses by increasing the number of recruits (and probably recruit survival) due to the new space liberated and, therefore, lower intraspecific competition. Nevertheless, when storm disturbances were more frequent than once every 50 years, their populations collapsed, and this effect worsened when several stressors acted simultaneously.

Our results improve our understanding about the demography of algal forests, and highlight the fact that increases in local and global stressors may erode the resilience of macroalgae, resulting in a loss of structural complexity in the benthic communities of temperate seas.

Synthesis. Our findings reveal that deep‐water C. zosteroides forests display slow population dynamics, similar to terrestrial perennials and trees. The increase in disturbance frequencies due to global and local stressors and their interaction will cause the decline of underwater macroalgal forests and may induce profound changes in their population and community dynamics.
Evidence of local adaptation to fine‐ and coarse‐grained environmental variability inPoa alpinain the Swiss Alps
Authors: Hamann Elena , Kesselring Halil , Armbruster Georg F. J. , Scheepens J. F. , Stöcklin Jürg
Published: June 2016

In the alpine landscape, characterized by high spatiotemporal heterogeneity and barriers, divergent selection is likely to lead to local adaptation of plant populations either through adaptive genetic differentiation or through phenotypic plasticity. The relative importance of these processes has rarely been investigated in relation to the spatial scale of environmental heterogeneity. In this study, we used reciprocal transplantation experiments of populations across nearby and distant field sites to shed light on these complementary processes.

We reciprocally transplanted populations of the widespread alpine grass,Poa alpina, within and across regions in the Swiss Alps. We inferred local adaptation at the metapopulation level by comparing fitness of plants transplanted to their site of origin and to nearby or distant novel sites. Additionally, we measured specific leaf area (SLA) and performed selection analyses to investigate directional selection on mean trait value at each field site and on the degree of plasticity of this trait to assess whether plastic responses were adaptive. In parallel, all populations were genotyped with microsatellite markers to assess neutral molecular differentiation.

Molecular differentiation was high among populations within and among regions, indicating restricted gene flow amongP. alpinapopulations. Reproductive biomass was highest in individuals grown in their region of origin, revealing local adaptation to coarse‐grained environmental variability. Similarly, inflorescence height, associated with reproductive biomass, reflected adaptation to fine‐ and coarse‐grained environmental variability. Furthermore, we found evidence that plasticity inSLAacross coarse‐grained habitats was correlated with plant fitness, suggesting that plasticity in this trait is adaptive.

Synthesis. Our results revealed adaptive genetic differentiation betweenP. alpinapopulations in the Swiss Alps reflecting local adaptation. Furthermore, high phenotypic plasticity inSLAcontributed to the maintenance of fitness homoeostasis across habitats. Hence, adaptive genetic differentiation and phenotypic plasticity play a complementary role for adaption ofP. alpinato environmental heterogeneity in the Swiss Alps and both may be critical to mitigate local extinction risk under rapid climate change.
Regeneration processes on coarse woody debris in mixed forests: do tree germinants and seedlings have species‐specific responses when grown on coarse woody debris?
Authors: Orman Olga , Adamus Michał , Szewczyk Janusz
Published: June 2016

Tree regeneration on coarse woody debris (CWD) is considered to be one the most ecologically valuable aspects of CWD in forest systems. However, most studies have focused solely on uncovering the differences in establishment and growth on CWD (regarded as a homogeneous substrate) in comparison with the forest floor. Our study concentrates on the underlying mechanisms of germinant and seedling colonization patterns and demographic responses relative to various properties of CWD.

We analysed the effects of CWD properties (decay class, form, species and diameter) on: (i) germinant and seedling annual counts; (ii) annual germinant and seedling survival; and (iii) seedling growth and height. Our study comprised three species (beech, fir and spruce) over 7‐year span in two old‐growth stands in the Western Carpathians, and employed generalized linear models and mixed models to test for differences between species.

CWD properties affected regeneration at the germination stage. There were some demographic differences between species relative to CWD properties. Decay class had the most pronounced effect on beech, not only on its establishment but also survival and growth. Beech and spruce established and survived in higher densities on beech CWD, while their height growth was enhanced on conifer‐derived CWD, particularly on spruce CWD. Stumps enhanced establishment of all species and survival of conifer seedlings.

Synthesis. Our study shows that CWD properties do influence seedling establishment, growth, height distribution and survival. Moreover, there may be trade‐offs between seedling growth and survival among tree species growing on different species of CWD. This highlights the need to include CWD heterogeneity as a factor that can affect the role of CWD in regeneration in forest ecosystems.
Mechanisms of resilience: empirically quantified positive feedbacks produce alternate stable states dynamics in a model of a tropical reef
Authors: Muthukrishnan Ranjan , Lloyd‐Smith James O. , Fong Peggy
Published: June 2016

Alternate stable states (ASS) theory is a dominant conceptual framework for understanding processes that support resilience of ecological communities in the face of multiple anthropogenic disturbances. For decades, coral reefs have been cited as a classic example of ASS, yet this position remains highly controversial, largely because convincing empirical evaluations have been elusive.

Using a combination of empirical measurements of positive feedback processes and simulation modelling, we assessed ASS in coral reefs of the Eastern Tropical Pacific (ETP) by identifying the potential for multiple basins of attraction from a mechanistic perspective.

Using bioassays of algal growth and consumption, we quantified two spatially localized positive feedback mechanisms on coral reefs: increasing herbivore activity associated with higher coral abundances and amelioration of nutrient limitation leading to higher algal growth in areas with higher algal abundance.

Analysis of a model of benthic community dynamics incorporating these feedbacks showed they were central to producing hysteresis and bistability in the model, two hallmarks of ASS. Further, reefs simulated with conditions matching those measured at Isla Contadora, Panamá, displayed ASS dynamics while producing spatial patterns matching field observations. This provides model‐derived support, based on empirically measured conditions of ETP reefs, for the presence of ASS.

Synthesis. The combination of experimental bioassays to measure feedback strengths and simulation models to evaluate the influence of those feedbacks provides a novel, non‐destructive approach to evaluating ASS dynamics that can be applied in threatened ecosystems where classic approaches are not viable.
The role of habitat filtering in the leaf economics spectrum and plant susceptibility to pathogen infection
Authors: Welsh Miranda E. , Cronin James Patrick , Mitchell Charles E.
Published: June 2016

The leaf economics spectrum (LES) describes global covariation in the traits of plant leaves. TheLESis thought to arise from biophysical constraints and habitat filtering (ecological selection against unfit trait combinations along environmental gradients). However, the role of habitat filtering in generating theLEShas not been tested experimentally.

If the process of habitat filtering plays a role in generating theLES, theLEScould weaken in communities that have yet to be filtered by the current environment, for example after abiotic environmental change.LEStraits are commonly used to predict community and ecosystem processes, and if theLESweakens in unfiltered communities,LES‐based models may no longer apply.

In the glasshouse, we experimentally simulated three stages of habitat filtering in response to abiotic change: from unfiltered, to semi‐filtered, to completely filtered communities. In each stage, we quantified the strength of theLESand assessed the accuracy of trait‐based models of an important ecological process, pathogen infection.

The strength of theLESincreased with the completeness of habitat filtering, as did the accuracy of trait‐based models of plant susceptibility to pathogen infection.

Synthesis. Our results suggest that habitat filtering plays a fundamental role in strengthening the trait correlations of theLESand that trait‐based models may be less accurate when communities have not been filtered by the current environment, for example, following rapid environmental change.
INCENTIVES FOR COLLECTIVE DEVIANCE: GROUP SIZE AND CHANGES IN PERCEIVED RISK, COST, AND REWARD*
Authors: MCGLOIN JEAN MARIE , THOMAS KYLE J.
Published: June 2016

Research has demonstrated that the presence of others shifts decision‐making about risky/deviant behavior. One reason for this shift could be changes in the anticipated experience of formal sanctions, informal costs, and rewards. To investigate this possibility, this study conducted two randomized controlled trials with hypothetical vignettes, in which a range of how many other people were also involved in the criminal act defined the treatment conditions. Across two samples of university students (Ns = 396 and 263), the results revealed that as the size of the involved group increased, the anticipated experience of sanction risk and several informal social costs associated with engaging in the act decreased, and the anticipated experience of two rewards increased. Additional analyses suggest that, with one exception in each data set, these changes are not only tied to the solo/group distinction.
Microbial Diversity of Type I Sourdoughs Prepared and Back‐Slopped with Wholemeal and Refined Soft (Triticum aestivum) Wheat Flours
Authors: Taccari Manuela , Aquilanti Lucia , Polverigiani Serena , Osimani Andrea , Garofalo Cristiana , Milanović Vesna , Clementi Francesca
Published: June 2016

The fermentation of type I sourdough was studied for 20 d with daily back‐slopping under laboratory and artisan bakery conditions using 1 wholemeal and 2 refined soft wheat (Triticum aestivum) flours. The sourdough bacterial and yeast diversity and dynamics were investigated by plate counting and a combination of culture‐dependent and culture‐independent PCR‐DGGE approach. The pH, total titrable acidity, and concentration of key organic acids (phytic, lactic, and acetic) were measured. Three flours differed for both chemical and rheological properties. A microbial succession was observed, with the atypical sourdough species detected at day 0 (i.e. Lactococcus lactis and Leuconostoc holzapfelii/citreum group for bacteria and Candida silvae and Wickerhamomyces anomalus for yeasts) being progressively replaced by taxa more adapted to the sourdough ecosystem (Lactobacillus brevis, Lactobacillus alimentarius/paralimentarius, Saccharomyces cerevisiae). In mature sourdoughs, a notably different species composition was observed. As sourdoughs propagated with the same flour at laboratory and artisan bakery level were compared, the influence of both the substrate and the propagation environment on microbial diversity was assumed.
Measuring the biodiversity of microbial communities by flow cytometry
Authors: Props Ruben , Monsieurs Pieter , Mysara Mohamed , Clement Lieven , Boon Nico
Published: June 2016

Measuring the microbial diversity in natural and engineered environments is important for ecosystem characterization, ecosystem monitoring and hypothesis testing. Although the conventional assessment through single marker gene surveys has resulted in major advances, the complete procedure remains slow (i.e. weeks to months), labour‐intensive and susceptible to multiple sources of laboratory and data processing bias. Growing interest, in highly resolved, temporal surveys of microbial diversity, necessitates rapid, inexpensive and robust analytical platforms that require limited computational effort.

Here, we demonstrate that sensitive single‐cell measurements of phenotypic attributes, obtained via flow cytometry, can provide fast (i.e. within minutes) first‐line assessments of microbial diversity dynamics, without demanding extensive sample preparation and downstream data processing. We developed a data processing pipeline that fits bivariate kernel density functions to phenotypic parameter combinations of an entire microbial community and concatenates them to a single one‐dimensional phenotypic fingerprint. By calculating established diversity metrics from such phenotypic fingerprints, we construct an alternative interpretation of the microbial diversity that incorporates distinct phenotypic traits underlying cell‐to‐cell heterogeneity (i.e. morphology and nucleic acid content).

Based on a detailed longitudinal study of a highly dynamic microbial ecosystem, our approach delivered temporal alpha diversity profiles that strongly correlated with the reference diversity, as estimated by 16S rRNA amplicon sequencing. This strongly suggests that the distribution of a limited amount of phenotypic features within a microbial community already provides sufficient resolving power for the measurement of diversity dynamics at the species level.

We present a fast, robust analysis method for monitoring the microbial biodiversity of natural and engineered ecosystems that correlates well with the conventional marker gene surveys. Our work has both applied and fundamental implications that stretch from ecosystem monitoring and studies on microbial community dynamics, to supervised sampling strategies. Furthermore, our approach offers perspectives for the development of online and in situ monitoring systems for microbial ecosystems.
CDMetaPOP: an individual‐based, eco‐evolutionary model for spatially explicit simulation of landscape demogenetics
Authors: Landguth Erin L. , Bearlin Andrew , Day Casey C. , Dunham Jason
Published: June 2016

Combining landscape demographic and genetics models offers powerful methods for addressing questions for eco‐evolutionary applications.

Using two illustrative examples, we present Cost–Distance Meta‐POPulation, a program to simulate changes in neutral and/or selection‐driven genotypes through time as a function of individual‐based movement, complex spatial population dynamics, and multiple and changing landscape drivers.

Cost–Distance Meta‐POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.