Drivers of distance‐decay in bryophyte assemblages at multiple spatial scales: Dispersal limitations or environmental control?

Questions: Despite the increasing scientific interest in distance decay of compositional similarity in ecology, the scale dependence of geographical versus environmental control on distance decay of biological communities has not been properly addressed so far. The present work highlights the relative importance of niche-based processes versus dispersal limitations on distance decay patterns of epilithic bryophyte assemblages at different spatial scales. Location: Serra de Sintra, central Portugal. Methods: We adopted a nested sampling design with 32 selected sampling sites in each of which two clusters, each with five rocks, were surveyed. Each cluster was characterized by a set of 15 macroscale variables, which were divided into environmental and anthropogenic. For each rock eight microscale variables were recorded. Partial Mantel tests were used to assess the relative importance of geographical and environmental distance on community dissimilarity for each grain size (site, cluster, rock). Quantile regressions were used to describe the decay patterns of community similarity with respect to geographical and environmental distances. Ordination analyses and variation partitioning techniques were applied to assess the pure and shared effects of measured variables on bryophyte community composition. Results: Environmental distance based upon macroscale predictors was significantly correlated to community similarity, while no significant correlation was found for ecological distance calculated for microscale predictors, except at the largest grain size. The decrease of community similarity with geographical and environmental distance was thus consistently strengthened with increasing sample grain. Compositional variation was best explained by anthropogenic variables. Conclusions: The relative importance of environmental versus geographical distance on compositional similarity in epilithic bryophyte communities varies with the spatial scale of the predictors and with the sample grain. The decrease of similarity with increasing distance is related to changes in habitat features, especially those driven by human disturbance, while it is weakly affected by variations in substrate features.info:eu-repo/semantics/publishedVersio

Drivers of distance-decay in bryophyte assemblages at multiple spatial scales: Dispersal limitations or environmental control?

Questions: Despite the increasing scientific interest in distance decay of compositional similarity in ecology, the scale dependence of geographical versus environmental control on distance decay of biological communities has not been properly addressed so far. The present work highlights the relative importance of niche-based processes versus dispersal limitations on distance decay patterns of epilithic bryophyte assemblages at different spatial scales. Location: Serra de Sintra, central Portugal. Methods: We adopted a nested sampling design with 32 selected sampling sites in each of which two clusters, each with five rocks, were surveyed. Each cluster was characterized by a set of 15 macroscale variables, which were divided into environmental and anthropogenic. For each rock eight microscale variables were recorded. Partial Mantel tests were used to assess the relative importance of geographical and environmental distance on community dissimilarity for each grain size (site, cluster, rock). Quantile regressions were used to describe the decay patterns of community similarity with respect to geographical and environmental distances. Ordination analyses and variation partitioning techniques were applied to assess the pure and shared effects of measured variables on bryophyte community composition. Results: Environmental distance based upon macroscale predictors was significantly correlated to community similarity, while no significant correlation was found for ecological distance calculated for microscale predictors, except at the largest grain size. The decrease of community similarity with geographical and environmental distance was thus consistently strengthened with increasing sample grain. Compositional variation was best explained by anthropogenic variables. Conclusions: The relative importance of environmental versus geographical distance on compositional similarity in epilithic bryophyte communities varies with the spatial scale of the predictors and with the sample grain. The decrease of similarity with increasing distance is related to changes in habitat features, especially those driven by human disturbance, while it is weakly affected by variations in substrate features

Adversarial attacks on crowdsourcing quality control

Crowdsourcing is a popular methodology to collect manual labels at scale. Such labels are often used to train AI models and, thus, quality control is a key aspect in the process. One of the most popular quality assurance mechanisms in paid micro-task crowdsourcing is based on gold questions: the use of a small set of tasks of which the requester knows the correct answer and, thus, is able to directly assess crowd work quality. In this paper, we show that such mechanism is prone to an attack carried out by a group of colluding crowd workers that is easy to implement and deploy: the inherent size limit of the gold set can be exploited by building an inferential system to detect which parts of the job are more likely to be gold questions. The described attack is robust to various forms of randomisation and programmatic generation of gold questions. We present the architecture of the proposed system, composed of a browser plug-in and an external server used to share information, and briefly introduce its potential evolution to a decentralised implementation. We implement and experimentally validate the gold detection system, using real-world data from a popular crowdsourcing platform. Our experimental results show that crowd workers using the proposed system spend more time on signalled gold questions but do not neglect the others thus achieving an increased overall work quality. Finally, we discuss the economic and sociological implications of this kind of attack

SMALL RNA EXPRESSION DURING PROGRAMMED REARRAGEMENT OF A VERTEBRATE GENOME

The sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangements (PGRs) during embryogenesis that results in the deletion of ~0.5 Gb of germline DNA from the somatic lineage. The underlying mechanism of these rearrangements remains largely unknown. miRNAs (microRNAs) and piRNAs (PIWI interacting RNAs) are two classes of small noncoding RNAs that play important roles in early vertebrate development, including differentiation of cell lineages, modulation of signaling pathways, and clearing of maternal transcripts. Here, I utilized next generation sequencing to determine the temporal expression of miRNAs, piRNAs, and other small noncoding RNAs during the first five days of lamprey embryogenesis, a time series that spans the 24-32 cell stage to the formation of the neural crest. I obtained expression patterns for thousands of miRNA and piRNA species. These studies identified several thousand small RNAs that are expressed immediately before, during, and immediately after PGR. Significant sequence variation was observed at the 3’ end of miRNAs, representing template-independent covalent modifications. Patterns observed in lamprey are consistent with expectations that the addition of adenosine and uracil residues plays a role in regulation of miRNA stability during the maternal-zygotic transition. We also identified a conserved motif present in sequences without any known annotation that is expressed exclusively during PGR. This motif is similar to binding motifs of known DNA binding and nuclear export factors, and our data could represent a novel class of small noncoding RNAs operating in lamprey

Selective Release of MicroRNA Species from Normal and Malignant Mammary Epithelial Cells

MicroRNAs (miRNAs) in body fluids are candidate diagnostics for a variety of conditions and diseases, including breast cancer. One premise for using extracellular miRNAs to diagnose disease is the notion that the abundance of the miRNAs in body fluids reflects their abundance in the abnormal cells causing the disease. As a result, the search for such diagnostics in body fluids has focused on miRNAs that are abundant in the cells of origin. Here we report that released miRNAs do not necessarily reflect the abundance of miRNA in the cell of origin. We find that release of miRNAs from cells into blood, milk and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. In particular, the bulk of miR-451 and miR-1246 produced by malignant mammary epithelial cells was released, but the majority of these miRNAs produced by non-malignant mammary epithelial cells was retained. Our findings suggest the existence of a cellular selection mechanism for miRNA release and indicate that the extracellular and cellular miRNA profiles differ. This selective release of miRNAs is an important consideration for the identification of circulating miRNAs as biomarkers of disease

How to make public works work : a review of the experiences

This paper reviews the experience with public works programs (PWPs) in several countries over the past 20 years to delineate use patterns and to determine the factors contributing to its use as a successful safety net program. The analysis shows that PWP have been used extensively in response to either a one-time large covariate shock, or repeated shocks. In low income countries, PWPs also have an antipoverty or poverty reduction objective. Our review shows that well designed and implemented PWPs can help mitigating income shocks; the program can also be used as an effective anti-poverty instrument. The paper examines the factors behind the observed wide variation in the effectiveness of the program in accomplishing its goals and identifies prerequisites for making PWPs successful safety net interventions capable of protecting the poor from income shocks, thus reducing both temporal and seasonal poverty, while creating useful public goods or services for the communities. For public works programs to be successful, it is important firstly to: a) have clear objectives; b) select projects that can create valuable public goods; and c) ensure predictable funding. Secondly, the success of the program depends critically on careful design and incorporation of all the key design features. Finally, a credible monitoring and evaluation system designed right upfront, prior to launching of theprogram can allow for mid course corrections and to respond to sudden changes which can inhibit effective implementation. The potential of the PWP program is enormous both in countries that have experiences with these programs and especially in countries that never used them. However, more research is needed investigation is needed to better understand the impact of PWPs, such as second round effects from the created assets, the impacts on the labor market, and their cost-effectiveness after factoring in both the immediate and second round benefits from its program.Safety Nets and Transfers,Rural Poverty Reduction,Labor Markets,Labor Policies,Public Sector Economics

Holocene sea level and climate interactions on wet dune slack evolution in SW Portugal: a model for future scenarios?

We examine the Holocene environmental changes in a wet dune slack of the Portuguese coast, Poco do Barbarroxa de Baixo. Lithology, organic matter, biological proxies and high-resolution chronology provide estimations of sediment accumulation rates and changes in environmental conditions in relation to sea-level change and climate variability during the Holocene. Results show that the wet dune slack was formed 7.5 cal. ka BP, contemporaneous with the last stages of the rapid sea-level rise. This depositional environment formed under frequent freshwater flooding and water ponding that allowed the development and post-mortem accumulation of abundant plant remains. The wetland evolved into mostly palustrine conditions over the next 2000 years, until a phase of stabilization in relative sea-level rise, when sedimentation rates slowed down to 0.04 mm yr(-1), between 5.3 and 2.5 cal. ka BP. Later, about 0.8 cal. ka BP, high-energy events, likely due to enhanced storminess and more frequent onshore winds, caused the collapse of the foredune above the wetlands' seaward margin. The delicate balance between hydrology (controlled by sea-level rise and climate change), sediment supply and storminess modulates the habitat's resilience and ecological stability. This underpins the relevance of integrating past records in coastal wet dune slacks management in a scenario of constant adaptation processes.Faculdade de Ciencias da Universidade de Lisboa [FCT UID/GEO/50019/2013

Two Different Aspects of Genomics: the Construction of a High-Density Radiation Hybrid Map and the Study of the Involvement of Mirnas in the Mammary Gland

In questa tesi vengono affrontati due diversi tipi di studio. Il primo tratta della costruzione di una mappa di ibridi bovino-criceto di radiazione di seconda generazione tramite la tipizzazione di un pannello RH, fornito dal Roslin Institut, con un set di Est non ridondanti provenienti da una libreria di cloni a cDNA di cervello bovino. Il secondo soggetto è il coinvolgimento dei microRNA, una nuova classe di piccoli RNA regolatori non codificanti, nello sviluppo della ghiandola mammaria. E' stata analizzata l'espressione di un set di microRNA noti in letteratura nei diversi stadi dello sviluppo dell'organo e sono state costruite librerie di cloni a cDNA di potenziali microRNA a partire da diversi stadi del ciclo dell'organo.In this thesis two different subjects have been studied. The first is the construction of a second generation high-density RH map of the bovine using the RH panel of the Roslin Institute. The panel have been characterized by PCR with a set of non-redundant EST chosen from a cDNA library of bovine brain. The second work treats about the involvement of miRNAs in the development of mammary gland. A set of 25 known miRNAs have been chosen and their expression have been examined in the different stages of mammary gland development. Libraries of potential miRNAs have been constructed from different stages of mammary gland development and some miRNAs have been validated

Stage-specific histone modification profiles are shaped by mitotic activity during Xenopus development

Vertebrate embryogenesis is a complex process, in which multiple regulatory layers have to cooperate in time and space. Epigenetic information, specifically the unfolding pattern of covalent posttranslational histone modifications, represents a major mechanism for gene regulation, whose impact on development is underinvestigated. The general antagonism of cell proliferation and differentiation illustrates the importance of another regulatory layer, i.e. the proper control of the cell cycle. In this work I have investigated a possible interplay between these two regulatory layers during Xenopus embryogenesis. To address this hypothesis, I have applied a systemic cell cycle block to Xenopus gastrula embryos and followed their development until the tadpole stage. Developmental consequences of the cell cycle arrest were analysed morphologically and molecularly. To obtain information on consequential changes in the embryonic epigenome, a mass spectrometry pipeline was successfully established and used to quantify histone post-translational modifications extracted from bulk chromatin at four key developmental stages. The results of this work indicate that a systemic G1/S-phase arrest from the gastrula stage on is principally compatible with embryonic survival and morphological differentiation, although some organs and tissues cannot be formed under the cell cycle block. The arrested embryos develop a perturbed chromatin landscape, whose features are illustrated in abnormal stage-specific histone modification profiles. Transcriptionally repressive histone modifications are overrepresented in the chromatin of arrested embryos, compared to controls. Embryos released from the cell cycle block during neurulation revert towards normal-like on morphological, molecular and epigenetic levels. Altogether the results indicate that the cell cycle plays a role in establishment and maintenance of stage-specific histone modification profiles during Xenopus development.Die Embryonalentwicklung von Wirbeltieren ist ein komplexer Prozess, bei dem mehrere Regulationsebenen zeitlich und räumlich zusammenarbeiten müssen. Epigenetische Merkmale wie die kovalenten Modifikationen von Histonproteinen auf dem chromosomalen Chromatin liefern dabei einen wichtigen Beitrag zur Genregulation, deren Dynamik und Bedeutung für das Entwicklungsgeschehen wir gegenwärtig nur ansatzweise verstehen. Der allgemeine Antagonismus von Zellproliferation und Zelldifferenzierung veranschaulicht die Bedeutung einer zweiten regulatorischen Ebene - der entwicklungsspezifischen Kontrolle des Zellzyklusgeschehens. In dieser Arbeit habe ich ein mögliches Zusammenspiel dieser beiden Regulationsebenen während der Embryonalentwicklung von X. laevis untersucht. Dazu wurden Embryonen im Gastrulastadium einem systemischen Zellzyklusblock unterworfen und ihre Entwicklung bis zum Kaulquappenstadium verfolgt. Die Auswirkungen des Zellzyklus-Arrests wurden sowohl morphologisch als auch hinsichtlich regionaler Genexpressions-muster analysiert. Um Informationen über die mit der Behandlung einhergehenden Veränderungen im embryonalen Chromatin zu erhalten, wurde eine Massenspektrometrie-Pipeline erfolgreich etabliert und zur Quantifizierung der Histonmodifikationen verwendet, die zu vier wichtigen Entwicklungsstadien aus embryonalem Chromatin extrahiert wurden. Die Ergebnisse dieser Arbeit zeigen, dass ein systemischer Zellzyklusblock am G1/S-Phasenübergang ab dem Stadium der Gastrula grundsätzlich mit dem Überleben des Embryos und der morphologischen Differenzierung vereinbar ist, obwohl unter diesen Bedingungen einige Organe und Gewebe nicht gebildet werden können. Die nichtproliferierenden Embryonen weisen zudem eine epigenetische Fehlentwicklung auf, deren Merkmale sich in selektiven Veränderungen der stadienspezifischen Histonmodifikationsprofile widerspiegeln. Insbesondere sind transkriptionell repressiv wirkende Histonmodifikationen im Zellzyklus-arretierten Chromatin gegenüber Kontrollembryonen überrepräsentiert. Wie Embryonen belegen, die zum Zeitpunkt der Neurulation aus dem Zellzyklusblock wieder entlassen wurden, sind die auf morphologischer, molekularer und epigenetischer Ebene beobachteten Veränderungen prinzipiell revertierbar. Insgesamt zeigen diese Ergebnisse, dass die Etablierung und Aufrechterhaltung der stadienspezifischen Histonmodifikationsprofile vom Zellzyklus beeinflusst wird

Microplastics in the Rhine River – from the Swiss catchment towards the North Sea

The threat of plastic waste in the environment has evoked rising concern over the past decades. While these versatile and incredibly popular polymer materials undoubtedly fulfil unprecedented services, their extreme durability and alleged toxicity represent major downsides, once in the environment. As plastics break down into smaller microplastics (MP) they evidently pollute almost every thinkable habitat on the globe today. While an estimated 5–12 million tons of plastic end up in the oceans every year, rivers are important pathways, carrying an annual freight of 0.41–4 million tons downstream. The Rhine River, one of Europe’s main streams and one of the World’s busiest waterways, reportedly holds substantial amounts of MP in its near-surface waters and sediments. However, little is known about potential MP sources, seasonal dynamics and the MP pollution of benthic sediments of this major river. In my dissertation I address three pivotal knowledge gaps about MP in the Rhine River and investigate a new type of method to safely and efficiently separate MP from surrounding environmental sample matrices. The surface water MP pollution of the Rhine River was earlier characterised by the distinct appearance of vast amounts (~60%) of rigid polystyrene microbeads of unknown origin and former purpose. In a sustained investigation of a defined river stretch in the Lower Rhine downstream Cologne, we managed to narrow down the entry region of these pollutants and close-to-certainly unveil the particle’s former purpose as ion-exchange resin beads used in diverse fluid purification applications. As more data on MP in rivers emerges, an interesting gap opens: empirical field studies tend to generate temporally restricted snapshot data while modellers, laudably seeking the bigger picture, are confronted with enormous uncertainties in their results. In a bid to reduce this void we embarked on a quadruplicate surface water MP observation in the Rhine catchment during 2016–2017. The investigation included three nival discharge regime tributaries and the Rhine in Switzerland as well as a pluvial Rhine River section towards the German-Dutch border. It became evident that despite a coherent increasing MP concentration gradient downstream, reflecting average discharge and catchment size, overall variability in environmental MP data was large. This hampers clear-cut estimations about concentration fluctuations but at the same time reinforces the theory of high MP seasonal pollution fluxes in the European winter months, when Rhine discharge is highest. Seeking to contribute to the very scarce knowledge of MP and benthic sediment interaction in large dynamic rivers, we took a diving bell and a dredging vessel to the riverbed at two previously identified surface MP hotspots at the German Middle and Lower Rhine. Due to expected water turbulence and flow velocity, substantial settling of MP in such stretches is not necessarily anticipated. Interestingly, it showed that even the Rhine riverbed is not spared from vast MP pollution. The applied research technology allowed for reliable detection of MP down to particle sizes of 11 μm and yielded strongly varying concentrations of 260–11,000 MP kg^–1, with a strongly skewed size class distribution towards the smallest MP particles. Experience showed us that environmental sample preparation for MP research can be a tedious and resource-intensive enterprise – including health and environmental hazards. Instead of attacking the unwanted portions in a sample (e.g. biogenic residue to isolate MP), a more efficient approach is to select the MP specifically. We refined a proposed lipophilicity-based separation technique and broadened its scope by successfully testing it to four different types of environmental matrices. This one-for-all approach may present a promising means for quicker, cheap, safe and efficient MP data compilation. The method was successfully applied for the seasonal surface MP investigation presented in this dissertation