Non-marine invertebrate trace fossils from the Tertiary Calatayud-Teruel basin, NE Spain

Relatively diverse trace fossils made by insects, other arthropods and oligochaete worms occur in the Miocene lacustrine and marginal lacustrine deposits of the Calatayud-Teruel basin (NE Spain). They include the ichnospecies Celliforma isp., Celliforma? isp. A and B, Celliforma? aff. habari, Rosellichnus cf. arabicus, Spongeliomorpha isp., Labyrintichnus terrerensis n. igen. et isp., Taenidium barreti, Beaconites filiformis n. isp. and Polykladichnus aragonensis n. isp. Their taxonomic and ethologic interpretations and cross-cutting relationships permit to envisage new lines of evidence for reconstructing transitions from dry-ground terrestrial to moist-ground and subaqueous environments, related to episodic floodings in lacustrine ponds. These environmental transitions (related to external controls) are characterized by benthic community replacements, evinced by vertical successions of Termitichnus, Scoyenia and Mermia-like ichnofacies.

PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity, and Sleep under Entrainment

The problem of entrainment is central to circadian biology. In this regard, Drosophila has been an important model system. Owing to the simplicity of its nervous system and the availability of powerful genetic tools, the system has shed significant light on the molecular and neural underpinnings of entrainment. However, much remains to be learned regarding the molecular and physiological mechanisms underlying this important phenomenon. Under cyclic light/dark conditions, Drosophila melanogaster displays crepuscular patterns of locomotor activity with one peak anticipating dawn and the other anticipating dusk. These peaks are characterized through an estimation of their phase relative to the environmental light cycle and the extent of their anticipation of light transitions. In Drosophila chronobiology, estimations of phases are often subjective, and anticipation indices vary significantly between studies. Though there is increasing interest in building flexible analysis software tools in the field, none incorporates objective measures of Drosophila activity peaks in combination with the analysis of fly activity/sleep in the same program. To this end, we have developed PHASE, a MATLAB-based program that is simple and easy to use and (i) supports the visualization and analysis of activity and sleep under entrainment, (ii) allows analysis of both activity and sleep parameters within user-defined windows within a diurnal cycle, (iii) uses a smoothing filter for the objective identification of peaks of activity (and therefore can be used to quantitatively characterize them), and (iv) offers a series of analyses for the assessment of behavioral anticipation of environmental transitions.

Tackling Early Medieval Dietary Transitions Using a Hierarchical and Multi-isotope Approach

Socio-environmental transitions during the first millennium AD had wide-ranging impacts across Europe which have interesting archaeological and palaeoecological implications. This paper uses published and new multi-tissue, multi-isotope data from across Europe to look at changing resource use from c. 350-1200 AD. It highlights cross-cultural interaction at a broad scale as well as focussing on these patterns with Early Medieval England as a regional case study. By using a hierarchical approach, it teases apart human-environment interactions with significant implications for changing foodways in Early Medieval Europe. It highlights how more integrated methodologies allow for better models of human ecology in the Early Middle Ages.

New, Emerging, Re-Emerging Tropical Infectious and Non-Communicable Diseases Persistent to the Climate, Landscape, and Environmental Changes on the Grounds of the Urbanizations, Industrializations, and Globalisation

Historical records evidenced of urban landscape changes, and environmental transitions brought by the improper growths and urban development’s of the urbanisation and industrialization in the developing countries, especially in India, significantly chaotic urban sprawl and industrial growths, and the development of its allied activities for the recent decades, invites new, emerging, re-emerging, and triggers the tropical infectious diseases including vector borne diseases (VBD) as well non-communicable diseases. Urban sprawl has a multiplier effect of growth of unplanned a crowded housing, and industrialization has an impact on the urban landscape with commercial and market development, and roads over large expanses of urban land while little concern for appropriate urban planning. The union government of India is launching to promote 100 mega smart city projects / metropolitan / urban agglomeration across the nation for betterment of the standard of living infrastructure facilities by 2030. The large scale urban landscape architectural changes, land use / land cover changes, environmental transitions, and micro climatic changes in the heart of the urban landscape, and its fringe areas on the consequence of built-up structures, construction of roads transport networks, drainages, commercial buildings, human dwellings, educational buildings, legal and medical health services, income tax professionals, small scale to large scale industries, etc., The census of India, reports highlighted that people mass movements / migration from rural to the urban, and small towns to mega cities are notably accelerating trends for the recent decades mainly for the purposes of occupation, education, trade and commerce, and professional services, generally reasons for male migration, and marriage is the absolute reason for female adults migration. The spatial and temporal aspects of malaria and dengue has been declining trends in rural settings, however, it has been accelerating trends in the urban settings due to the urban buoyant migrants. Urbanization and industrialization effect on urban landscape environment leads to breakdown of sanitations, water-borne diseases associated with inadequate and unsafe drinking water supply, tendency to use metal, plastic, and mud pots water storage containers, discarded domestic waste misshapen to vector breeding habitats containers, urban heat island, garbage waste disposal, liquid waste from dwellings, and industries, air pollution (dust, pollen and spores suspended as particles, Sulphur Dioxide-SO2, nitrogen oxides-NO, Carbonate-CO3, depletion of Oxygen O2, Ozone-O3, Methane Gas- CH₄, Lead- Pb, Mercury- Hg etc.,), exonerated by the industries and urban transport emissions, modern transport / shipping goods and services, and collectively hazard to human health through erratic infectious diseases and vector borne diseases immediately.

Detection of Large Holocene Earthquakes in the Sedimentary Record of Wellington, New Zealand, Using Diatom Analysis

<p>New Zealand is situated on the boundary between the Pacific and Australian tectonic plates. The Wellington region lies near the southern end of the Hikurangi subduction zone and within a zone of major, active strike-slip faults. Wellington's paleoseismic and historic records indicate that large surface rupture earthquakes have occurred on these faults in the past. Development of a complete record of past large earthquakes is a high priority for the region because of the risk posed by occurrence of large earthquakes in the future. The existing paleoseismic record has been derived predominantly from studies of fault trench stratigraphy, raised beach ridges and offset river terraces. The sedimentary record of lakes and coastal waterbodies is a source of information that has not been used specifically for paleoseismic purposes in the region. Therefore investigation of Wellington's sedimentary record is used in this thesis to make a contribution to the paleoseismic record. Holocene sedimentary sequences are studied from three small, low elevation, coastal waterbodies: Taupo Swamp, Okupe Lagoon and Lake Kohangapiripiri. Sequences of between 200 and 650 cm depth were collected using a hand-operated coring device. Sedimentology and diatom microfossil content were analysed and interpreted to enable reconstruction of paleoenvironment at each site. Radiocarbon dating was used to provide chronologies for the sequences that are aged between 5000 and 7500 calibrated years before present (cal. years BP). Diatom analysis is the main tool used to reconstruct paleoenvironment and detect evidence for occurrence of past large earthquakes. To aid reconstruction of sedimentary sequences used in this project, as well as coastal sequences in New Zealand in general, a coastal diatom calibration set was constructed using 50 sites around New Zealand. Modern diatom distribution and abundance, and associated environmental variables are analysed using ordination and weighted averaging techniques. Detrended correspondence analysis arranges species according to salinity preferences and divides sites clearly into waterbody types along a coastal gradient. This analysis enables reconstruction of waterbody type from fossil samples by passive placement onto ordination diagrams. Weighted averaging regression of calibration set samples results in a high correlation (r2jack=0.84) between observed and diatom inferred salinity, and enables salinity preferences and tolerances to be derived for 100 species. This confirms for the first time that species' preferences derived in the Northern Hemisphere are generally applicable to diatoms living in the coastal zone of New Zealand. Weighted averaging calibration and the modern analogue technique are used to generate quantitative estimates of paleosalinity for fossil samples. Paleoenvironmental reconstructions of Taupo Swamp, Okupe Lagoon and Lake Kohangapiripiri indicate that each waterbody has been isolated from the sea during the late Holocene. Isolation has been achieved through interplay of sediment accumulation causing growth of barrier beaches, and coseismic uplift. Ten distinct transitions between different paleoenvironments are recognised from the three sequences. These transitions involve changes in relative sea level or water table level often in association with catchment disturbance or marine influx events. All transitions occur suddenly and are laterally extensive and synchronous within each waterbody. Quantitative estimates of paleosalinity and waterbody type are used to differentiate between large and small magnitude changes in paleoenvironment. Five transitions involve large amounts of paleoenvironmental change and provide evidence for earthquakes occurring at approximately 5200, approximately 3200, and approximately 2300 cal. years BP. Five other transitions are consistent with the effects of large earthquakes occurring at approximately 6800, 2200, approximately 1000, approximately 500 cal. years BP and 1855 AD but do not provide independent evidence of the events. Environmental transitions at Lake Kohangapiripiri clarify the timing of rupture of the Wairarapa Fault by bracketing incompatible age estimates derived from two different sites on the fault. The oldest environmental transitions recognised at Taupo Swamp and Okupe Lagoon both occur at approximately 3200 cal. years BP indicating that western Wellington was uplifted at this time. Environmental transitions are recorded at all three study sites at approximately 2300 cal. years BP indicating that the entire western and central Wellington region experienced coseismic uplift at this time. Because of the distance between sites this apparent synchroneity implies that several faults in the region ruptured at a similar time. Investigation of sedimentary sequences contributes to the existing paleoseismic record by providing additional estimates of timing for past large earthquakes, enabling estimation of the areal extent of the effects of past earthquakes, and by highlighting periods of fault rupture activity in the late Holocene.</p>

Detection of Large Holocene Earthquakes in the Sedimentary Record of Wellington, New Zealand, Using Diatom Analysis

<p>New Zealand is situated on the boundary between the Pacific and Australian tectonic plates. The Wellington region lies near the southern end of the Hikurangi subduction zone and within a zone of major, active strike-slip faults. Wellington's paleoseismic and historic records indicate that large surface rupture earthquakes have occurred on these faults in the past. Development of a complete record of past large earthquakes is a high priority for the region because of the risk posed by occurrence of large earthquakes in the future. The existing paleoseismic record has been derived predominantly from studies of fault trench stratigraphy, raised beach ridges and offset river terraces. The sedimentary record of lakes and coastal waterbodies is a source of information that has not been used specifically for paleoseismic purposes in the region. Therefore investigation of Wellington's sedimentary record is used in this thesis to make a contribution to the paleoseismic record. Holocene sedimentary sequences are studied from three small, low elevation, coastal waterbodies: Taupo Swamp, Okupe Lagoon and Lake Kohangapiripiri. Sequences of between 200 and 650 cm depth were collected using a hand-operated coring device. Sedimentology and diatom microfossil content were analysed and interpreted to enable reconstruction of paleoenvironment at each site. Radiocarbon dating was used to provide chronologies for the sequences that are aged between 5000 and 7500 calibrated years before present (cal. years BP). Diatom analysis is the main tool used to reconstruct paleoenvironment and detect evidence for occurrence of past large earthquakes. To aid reconstruction of sedimentary sequences used in this project, as well as coastal sequences in New Zealand in general, a coastal diatom calibration set was constructed using 50 sites around New Zealand. Modern diatom distribution and abundance, and associated environmental variables are analysed using ordination and weighted averaging techniques. Detrended correspondence analysis arranges species according to salinity preferences and divides sites clearly into waterbody types along a coastal gradient. This analysis enables reconstruction of waterbody type from fossil samples by passive placement onto ordination diagrams. Weighted averaging regression of calibration set samples results in a high correlation (r2jack=0.84) between observed and diatom inferred salinity, and enables salinity preferences and tolerances to be derived for 100 species. This confirms for the first time that species' preferences derived in the Northern Hemisphere are generally applicable to diatoms living in the coastal zone of New Zealand. Weighted averaging calibration and the modern analogue technique are used to generate quantitative estimates of paleosalinity for fossil samples. Paleoenvironmental reconstructions of Taupo Swamp, Okupe Lagoon and Lake Kohangapiripiri indicate that each waterbody has been isolated from the sea during the late Holocene. Isolation has been achieved through interplay of sediment accumulation causing growth of barrier beaches, and coseismic uplift. Ten distinct transitions between different paleoenvironments are recognised from the three sequences. These transitions involve changes in relative sea level or water table level often in association with catchment disturbance or marine influx events. All transitions occur suddenly and are laterally extensive and synchronous within each waterbody. Quantitative estimates of paleosalinity and waterbody type are used to differentiate between large and small magnitude changes in paleoenvironment. Five transitions involve large amounts of paleoenvironmental change and provide evidence for earthquakes occurring at approximately 5200, approximately 3200, and approximately 2300 cal. years BP. Five other transitions are consistent with the effects of large earthquakes occurring at approximately 6800, 2200, approximately 1000, approximately 500 cal. years BP and 1855 AD but do not provide independent evidence of the events. Environmental transitions at Lake Kohangapiripiri clarify the timing of rupture of the Wairarapa Fault by bracketing incompatible age estimates derived from two different sites on the fault. The oldest environmental transitions recognised at Taupo Swamp and Okupe Lagoon both occur at approximately 3200 cal. years BP indicating that western Wellington was uplifted at this time. Environmental transitions are recorded at all three study sites at approximately 2300 cal. years BP indicating that the entire western and central Wellington region experienced coseismic uplift at this time. Because of the distance between sites this apparent synchroneity implies that several faults in the region ruptured at a similar time. Investigation of sedimentary sequences contributes to the existing paleoseismic record by providing additional estimates of timing for past large earthquakes, enabling estimation of the areal extent of the effects of past earthquakes, and by highlighting periods of fault rupture activity in the late Holocene.</p>

City climate and landscape structure shape pollinators, nectar and transported pollen along a gradient of urbanization

Urbanization gradients influence both landscape and climate and provide opportunity for understanding how species, especially plants and pollinators, respond to artificially driven environmental transitions. Here, we investigated several aspects of pollination along an urbanization gradient in landscape and climate. We quantified wild hoverfly and bee abundances with trapping, standing crop of nectar with spectrophotometer, and the pollen transported by flower-visitors with DNA-metabarcoding, in 40 independent sites from seminatural to built-up areas in Northern Italy. Linear and nonlinear relationships were detected along the urbanization gradient. Pollinator abundances increased until 22% of impervious surface, dropping by 34% after that, and it also decreased with green patch distance and urban park size. Thus, suburban landscapes host more pollinators than highly cemented or seminatural areas. Moreover, pollinators diminished by up to 45% in areas with low temperature seasonality: urbanized areas likely posing thermic stress. Furthermore, the sugar mass available in nectar increased by 91% with impervious cover, indicating that city nectars were less consumed or flowers more productive. Furthermore, the species richness of pollen decreased by 32% in highly urbanized areas, and with a high incidence of exotic plants, hinting for anthropized plant communities. Synthesis and applications: Urbanization influences pollinator abundances, nectar resources and transported pollen. Pollinators are negatively affected by a thermally harsh climate in highly urbanized areas with isolated green areas and large parks. Suburban landscapes demonstrated the highest pollinator presence. In the city core, flowers contained more nectary sugar, while pollinators collected pollen from a small number of plants, mainly exotic. These findings highlight the influence of urban landscape structure and climate on pollinators and plants, showing that cities are heterogenous realities. Patterns from this study will serve as basis for pollinator-friendly planning and management of urban landscapes.

Transition of Vibrio cholerae through a natural host induces resistance to environmental changes

The pandemic related strains of Vibrio cholerae are known to cause diarrheal disease in animal hosts. These bacteria must overcome rapid changes in their environment, such as the transition from fresh water to the gastrointestinal system of their host. To study the morphological adjustments during environmental transitions, we used zebrafish as a natural host. Using a combination of fluorescent light microscopy, cryogenic electron tomography and serial block face scanning electron microscopy, we studied the structural changes that occur during the infection cycle. We show that the transition from an artificial nutrient rich environment to a nutrient poor environment has a dramatic impact on the cell shape, most notably membrane dehiscence. In contrast, excreted bacteria from the host retain a uniform distance between the membranes as well as their vibrioid shape. Inside the intestine, V. cholerae cells predominantly colonized the anterior to midgut, forming microcolonies associated with the microvilli as well as within the lumen. The cells retained their vibrioid shape but changed their cell length depending on their localization. Our results demonstrate dynamic changes in morphological characteristics of V. cholerae during the transition between the different environments, and we propose that these structural changes are critical for the pathogens ability to colonize host tissues.

Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen

The family Flavobacteriaceae (phylum Bacteroidetes) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum is a freshwater pathogen that infects salmonid fish worldwide, with critical environmental and economic impact. Here, we report an extensive transcriptome analysis that established the genome map of transcription start sites and transcribed regions, predicted alternative sigma factor regulons and regulatory RNAs, and documented gene expression profiles across 32 biological conditions mimicking the pathogen life cycle. The results link genes to environmental conditions and phenotypic traits and provide insights into gene regulation, highlighting similarities with better known bacteria and original characteristics linked to the phylogenetic position and the ecological niche of the bacterium. In particular, osmolarity appears as a signal for transition between free-living and within-host programs and expression patterns of secreted proteins shed light on probable virulence factors. Further investigations showed that a newly discovered sRNA widely conserved in the genus, Rfp18, is required for precise expression of proteases. By pointing proteins and regulatory elements probably involved in host–pathogen interactions, metabolic pathways, and molecular machineries, the results suggest many directions for future research; a website is made available to facilitate their use to fill knowledge gaps on flavobacteria.