Radiocarbon ages and pollen record of a sediment core from Lake Lyadhej-To

An 1180-cm long core recovered from Lake Lyadhej-To (68°15'N, 65°45'E, 150 m a.s.l.) at the NW rim of the Polar Urals Mountains reflects the Holocene environmental history from ca. 11,000 cal. yr BP. Pollen assemblages from the diamicton (ca. 11,000-10,700 cal. yr BP) are dominated by Pre-Quaternary spores and redeposited Pinaceae pollen, pointing to a high terrestrial input. Turbid and nutrient-poor conditions existed in the lake ca. 10,700-10,550 cal. yr BP. The chironomid-inferred reconstructions suggest that mean July temperature increased rapidly from 10.0 to 11.8 °C during this period. Sparse, treeless vegetation dominated on the disturbed and denuded soils in the catchment area. A distinct dominance of planktonic diatoms ca. 10,500-8800 cal. yr BP points to the lowest lake-ice coverage, the longest growing season and the highest bioproductivity during the lake history. Birch forest with some shrub alder grew around the lake reflecting the warmest climate conditions during the Holocene. Mean July temperature was likely 11-13 °C and annual precipitation-400-500 mm. The period ca. 8800-5500 cal. yr BP is characterized by a gradual deterioration of environmental conditions in the lake and lake catchment. The pollen- and chironomid-inferred temperatures reflect a warm period (ca. 6500-6000 cal. BP) with a mean July temperature at least 1-2 °C higher than today. Birch forests disappeared from the lake vicinity after 6000 cal. yr BP. The vegetation in the Lyadhej-To region became similar to the modern one. Shrub (Betula nana, Salix) and herb tundra have dominated the lake catchment since ca. 5500 cal. yr BP. All proxies suggest rather harsh environmental conditions. Diatom assemblages reflect relatively short growing seasons and a longer persistence of lake-ice ca. 5500-2500 cal. yr BP. Pollen-based climate reconstructions suggest significant cooling between ca. 5500 and 3500 cal. yr BP with a mean July temperature 8-10 °C and annual precipitation-300-400 mm. The bioproductivity in the lake remained low after 2500 cal. yr BP, but biogeochemical proxies reflect a higher terrestrial influx. Changes in the diatom content may indicate warmer water temperatures and a reduced ice cover on the lake. However, chironomid-based reconstructions reflect a period with minimal temperatures during the lake history.

Pollen profile and age determination for sediment core M72/5_619-1 (22-GC3)

Sediments from the Black Sea, a region historically dominated by forests and steppe landscapes, are a valuable source of detailed information on the changes in regional terrestrial and aquatic environments at decadal to millennial scales. Here we present multi-proxy environmental records (pollen, dinoflagellate cysts, Ca, Ti and oxygen isotope data) from the uppermost 305 cm of the core 22-GC3 (42°13.53' N, 36°29.55' E) collected from a water depth of 838 m in the southern part of the Black Sea in 2007. The records span the last ~ 18 kyr (all ages are given in cal kyr BP). The pollen data reveal the dominance of the Artemisia-steppe in the region, suggesting rather dry/cold environments ~ 18-14.5 kyr BP. Warming/humidity increase during melt-water pulses (~ 16.1-14.5 kyr BP), indicated by d18O records from the 22-GC3 core sediment and from the Sofular Cave stalagmite, is expressed in more negative d13C values from the Sofular Cave, usually interpreted as the spreading of C3 plants. The records representing the interstadial complex (~ 14.5-12.9 kyr BP) show an increase in temperature and moisture, indicated by forest development, increased primary productivity and reduced surface run-off, whereas the switch from primary terrigenous to primary authigenic Ca origin occurs ~ 500 yr later. The Younger Dryas cooling is clearly demonstrated by more negative d13C values from the Sofular Cave and a reduction of pines. The early Holocene (11.7-8.5 kyr BP) interval reveals relatively dry conditions compared to the mostly moist and warm middle Holocene (8.5-5 kyr BP), which is characterized by the establishment of the species-rich warm mixed and temperate deciduous forests in the low elevation belt, temperate deciduous beech-hornbeam forests in the middle and cool conifer forest in upper mountain belt. The border between the early and middle Holocene in the vegetation records coincides with the opening of the Mediterranean corridor at ~ 8.3 kyr BP, as indicated by a marked change in the dinocyst assemblages and in the sediment lithology. Changes in the pollen assemblages indicate a reduction in forest cover after ~ 5 kyr BP, which was likely caused by increased anthropogenic pressure on the regional vegetation.

Desempenho reprodutivo de varrões e matrizes suínas de diferentes linhagens durante as estações do ano

The industrial Brazilian pig farming despite of the constant advance in the genetic improvement, nutrition, and in handling, seasonality problems occur in the production of weaned piglet, mainly due to the stations of the year that can impact directly in the profitability. These problems can be deepen due to breed and line of decent used in Brazil are all source from tempered weather countries. To the pig farmer it's difficult to determine the relations between indoor temperature of the barns, relative humidity of the air and top thermal amplitude which can provide good reproductive rates for the boars and arrays lodged in conventional barns. The lack research to production of environmental indices of easy interpretation to pigs, which are not dependent of complicated handling machines and also which are not expensive is considered as a negative factor from the producers. the objective os this experiment is evaluate the effects of the stations of the year over the reproductive performance of the boars Agroceres PIC 425, Agroceres PIC 337 and D.B. Dambred LM 6200, and of arrays Agroceres Canborough 22, Penarlan Naima e DB90 Danbred, in addition develop an environmental index with easy interpretation and use to the pig farmers of the region of Uberlândia - MG, using the maxim temperatures, rainfall monthly accumulated and of the thermal amplitude of the barn. The features rated during the stations of the years 2013 and 2014 were the volume and spermatic quality of the boars and the mainly reproductive indexes of the arrays as the total number of piglets born alive and total number of weaned piglets/ array/ parturition. The station of the year which had the worst results in the reproductive feature of the boars and arrays was the spring. Boars from different line of decent are sensitive to the effects of stress of the heat of spring causing lowest volume, concentration and problems in the spermatic morphology (p<0,05). The spring prejudice the reproductive indexes of arrays from different line of decent (p<0,05) and the pig farmers of Uberlândia are subjected to operating losses and income evasion due to the thermal stress in the reproduction that added can reach $150.000,00 annual for each 1000 arrays lodged/year.

Predicting Transcript Production Rates in Yeast With Sparse Linear Models

To provide biological insights into transcriptional regulation, a couple of groups have recently presented models relating the promoter DNA-bound transcription factors (TFs) to downstream gene’s mean transcript level or transcript production rates over time. However, transcript production is dynamic in response to changes of TF concentrations over time. Also, TFs are not the only factors binding to promoters; other DNA binding factors (DBFs) bind as well, especially nucleosomes, resulting in competition between DBFs for binding at same genomic location. Additionally, not only TFs, but also some other elements regulate transcription. Within core promoter, various regulatory elements influence RNAPII recruitment, PIC formation, RNAPII searching for TSS, and RNAPII initiating transcription. Moreover, it is proposed that downstream from TSS, nucleosomes resist RNAPII elongation.

Here, we provide a machine learning framework to predict transcript production rates from DNA sequences. We applied this framework in the S. cerevisiae yeast for two scenarios: a) to predict the dynamic transcript production rate during the cell cycle for native promoters; b) to predict the mean transcript production rate over time for synthetic promoters. As far as we know, our framework is the first successful attempt to have a model that can predict dynamic transcript production rates from DNA sequences only: with cell cycle data set, we got Pearson correlation coefficient Cp = 0.751 and coefficient of determination r2 = 0.564 on test set for predicting dynamic transcript production rate over time. Also, for DREAM6 Gene Promoter Expression Prediction challenge, our fitted model outperformed all participant teams, best of all teams, and a model combining best team’s k-mer based sequence features and another paper’s biologically mechanistic features, in terms of all scoring metrics.

Moreover, our framework shows its capability of identifying generalizable fea- tures by interpreting the highly predictive models, and thereby provide support for associated hypothesized mechanisms about transcriptional regulation. With the learned sparse linear models, we got results supporting the following biological insights: a) TFs govern the probability of RNAPII recruitment and initiation possibly through interactions with PIC components and transcription cofactors; b) the core promoter amplifies the transcript production probably by influencing PIC formation, RNAPII recruitment, DNA melting, RNAPII searching for and selecting TSS, releasing RNAPII from general transcription factors, and thereby initiation; c) there is strong transcriptional synergy between TFs and core promoter elements; d) the regulatory elements within core promoter region are more than TATA box and nucleosome free region, suggesting the existence of still unidentified TAF-dependent and cofactor-dependent core promoter elements in yeast S. cerevisiae; e) nucleosome occupancy is helpful for representing +1 and -1 nucleosomes’ regulatory roles on transcription.

Dentofacial parameters associated with the unilateral palatally impacted canine

Aims To investigate the relationship between unilateral PIC and specific dentofacial parameters. Materials and methods A sample of 216 subjects, with 108 subjects in the retrospective and prospective samples respectively. Dental parameters: The following dental parameters were assessed: Inter-canine and intermolar width; palatal depth and palatal area; anterior Bolton tooth-size discrepancy (TSD); maxillary arch shape and ratio and maxillary central and lateral incisor shape and ratio. Facial parameters: Three-dimensional (3D) images were taken for subjects in the prospective sample only, and were used to assess the following facial parameters: Face shape; face ratio and 3D distances and angles. Results Dental parameters: Inter-canine width was significantly smaller in the test group compared to the control group in the retrospective (p= 0.0002) and prospective (p= 0.0018) samples respectively. Anterior Bolton TSD was significantly higher in the prospective test group compared to controls (p= 0.0070). Arch ratio was significantly smaller in the test group than the control group for the retrospective sample (p= 0.0029), whereas no significant difference was recorded in the prospective sample (p= 0.1017). Arch shape distribution was significantly different in the retrospective sample (p= 0.009). Tooth shape distribution was significantly different for the maxillary right central incisor in the retrospective sample (p= 0.030). Tooth ratio showed no significant difference for both samples. Facial parameters: Basal width was significantly smaller in the test compared to the control group (p= 0.0001). No significant difference was found in all other 3D distances and angles measured. Conclusion Inter-canine width was significantly smaller in unilateral PIC subjects compared to controls. Anterior Bolton TSD was significantly higher in prospective unilateral PIC compared to controls. Maxillary arch ratio was significantly smaller in retrospective subjects. Square/tapered tooth shape was significantly more common in the retrospective group. Basal width was significantly smaller in subjects with unilateral PIC than controls.

Pollen record and age determination of profile CS98-10 at Cape Shpindler, Yugorski Peninsula, northwest Russia

New pollen and radiocarbon data from an 8.6-m coastal section, Cape Shpindler (69°43' N; 62°48' E), Yugorski Peninsula, document the latest Pleistocene and Holocene environmental history of this low Arctic region. Twelve AMS 14C dates indicate that the deposits accumulated since about 13,000 until 2000 radiocarbon years BP. A thermokarst lake formed ca. 13,000-12,800 years BP, when scarce arctic tundra vegetation dominated the area. By 12,500 years BP, a shallow lake existed at the site, and Arctic tundra with Poaceae, Cyperaceae, Salix, Saxifraga, and Artemisia dominated nearby vegetation. Climate was colder than today. Betula nana became dominant during the Early Preboreal period about 9500 years BP, responding to a warm event, which was one of the warmest during the Holocene. Decline in B. nana and Salix after 9500 years BP reflects a brief event of Preboreal cooling. A subsequent increase in Betula and Alnus fruticosa pollen percentages reflects amelioration of environmental conditions at the end of Preboreal period (ca. 9300 years BP). A decline in arboreal taxa later, with a dramatic increase in herb taxa, reflects a short cold event at about 9200 years BP. The pollen data reflect a northward movement of tree birch, peaking at the middle Boreal period, around 8500 years BP. Open Betula forest existed on the Kara Sea coast of the Yugorski Peninsula during the Atlantic period (8000-4500 years BP), indicating that climate was significantly warmer than today. Deteriorating climate around the Atlantic-Subboreal boundary (ca. 4500 years BP) is recorded by a decline in Betula percentages. Sedimentation slowed at the site, and processes of denudation and/or soil formation started at the beginning of the Subatlantic period, when vegetation cover on Yugorski Peninsula shifted to near-modern assemblages.

Long-term biogenic particle fluxes in the Bering Sea and the central subarctic Pacific Ocean

Time-series sediment traps were deployed for five consecutive years in two distinctively different subarctic marine environments. The centrally located subarctic pelagic Station SA (49°N, 174°W; water depth 5406 m) was simultaneously studied along with the marginal sea Station AB (53.5°N, 177°W; water depth 3788 m) in the Aleutian Basin of the Bering Sea. A mooring system was tethered to the sea-floor with a PARFLUX type trap with 13 sample bottles, which was placed at 600 m above the sea-floor at each of the two stations. Sampling intervals were synchronized at the stations, and they were generally set for 20 days during highly productive seasons, spring through fall, and 56 days during winter months of low productivity. Total mass fluxes, which consisted of mainly biogenic phases, were significantly greater at the marginal sea Station AB than at the pelagic Station SA for the first four years and moderately greater for the last year of the observations. This reflects the generally recognized higher productivity in the Bering Sea. Temporal excursion patterns of the mass fluxes at the two stations generally were in parallel, implying that temporal changes in their biological productivity are strongly governed by a large-scale seasonal climatic variability over the region rather than local phenomena. The primary reason for the difference in total mass flux at the two stations stems mainly from varying contributions of siliceous and calcareous planktonic assemblages. A significantly higher opal contribution at Station AB than at Station SA was mainly due to diatoms. Diatom fluxes at the marginal sea station were about twice those observed at the pelagic station, resulting in a very high opal contribution at Station AB. In contrast to the opal fluxes, CaCO3 fluxes at Station AB were slightly lower than at Station SA. The ratios of Corg/Cinorg were usually significantly greater than one in both regions, suggesting that preferentially greater organic carbon from cytoplasm than skeletal inorganic carbon was exported from the surface layers. Such a process, known as the biological pump, leads to a carbon sink which effectively lowers p CO2 in the surface layers and then allows a net flux of atmospheric CO2 into the surface layer. The efficiency of the biological pump is greater in the Bering Sea than at the open-ocean station.

A 2.8 Ma sedimentological, geochemical and palynological record of sediment core ICDP5011-1 in Lake Elgygytgyn, NE Russia

The reliability of Arctic climate predictions is currently hampered by insufficient knowledge of natural climate variability in the past. A sediment core from Lake El'gygytgyn (NE Russia) provides a continuous high-resolution record from the Arctic spaning the past 2.8 Ma. The core reveals numerous "super interglacials" during the Quaternary, with maximum summer temperatures and annual precipitation during marine benthic isotope stages (MIS) 11c and 31 ~4-5 °C and ~300 mm higher than those of MIS 1 and 5e. Climate simulations show these extreme warm conditions are difficult to explain with greenhouse gas and astronomical forcing alone, implying the importance of amplifying feedbacks and far field influences. The timing of Arctic warming relative to West Antarctic Ice Sheet retreats implies strong interhemispheric climate connectivity.

Pollen record from a swamp in Ukraine

(1967): In 1956-1962 investigations of swamps from the forest-steppe and steppe of Ukraine were carried out. They were followed by spore-pollen studies of swamp deposits. These materials are partially published in papers devoted to the history of vegetation in the south of Ukraine and re-vegetation of landscape in different phases of Holocene (Artyushenko, Bachurina, 1958; Artyushenko, 1959, 1960; Artyushenko, Kucheryava, 1964). Peat area in the investigated region is very small. In the forest-steppe peat occupies 1.1%, and in the steppe - 0.03% of the whole area (Peat Reserve of the Ukrainian SSR, 1959).

Pollen and macrofossil profiles from six cores in Illinois, U.S.A

Pollen analysis of Wisconsinan sediments from eleven localities in northern and central Illinois, combined with the results of older studies, allows a first general survey of the vegetational changes in Illinois during the last glaciation. In the late Altonian (after 40,000 B.P.), pine was already the most prevalent tree type in northern Illinois. Probably because of the influence of the last Altonian ice advance to northern Illinois, pine migrated to the south and reached south-central Illinois, which was at that time a region of prairie, with oak and hickory trees in favorable sites. Likewise in the late Altonian, spruce appeared in northern Illinois. Spruce also expanded its area to the south during the Wisconsinan, reaching south-central Illinois only after 21,000 B.P., in the early Woodfordian. Deciduous trees (predominantly oak) were present in south-central Illinois throughout the Wisconsinan. Their prevalence decreased to the north. The vegetation during the different subdivisions of the last glacial period in Illinois was approximately as follows: Late Altonian: Pine/spruce forest with some deciduous trees in northern and central Illinois; prairie and oak/hickory stands in south-central Illinois; immigration of pine. Farmdalian: Pine/spruce forest in central Illinois; deciduous trees and pine in south-central Illinois, with areas of open vegetation, perhaps similar to the present-day transition of prairie to forest in the northern Great Plains. Woodfordian: Northern and central Illinois ice covered; in south central Illinois, spruce and oak as dominant tree types, but also pine and grassland. During the Woodfordian, pine and spruce disappeared again from south-central Illinois, and oak/hickory forest and prairie again prevailed. The ice-free areas of northern Illinois become populated temporarily with spruce, but later there is proof of deciduous forest in this region. Pollen investigations in south-central Illinois have shown convincingly that deciduous trees could survive relatively close (less than 60 km) to the ice margin. Therefore the frequently presented view that arctic climatic conditions prevailed in North America during the last glaciation far south of the ice margin can be refuted for the Illinois area, confirming the opinion of other authors resulting from investigations of fossil mollusks and frost-soil features. The small number of localities investigated still permits no complete reconstruction of the vegetation zones and their possible movements in Illinois. During the Altonian and Farmdalian in Illinois, a vegetational zonation probably existed similar to that of today in North America. As the ice pushed southward as far as 39° 20' N. lat in the early Woodfordian, this zonation was apparently broken up under the influence of a relatively moderate climate. In any case, the Vandalia area, which was only about 60 km south of the ice, was at that time neither in a tundra zone nor in a zone of boreal coniferous forest.

Chlorophyll-a, primary production rates, carbon concentrations and cell counts of coccolithophores, diatoms and microzooplankton measured in water samples from the North Atlantic during the M87/1 cruise in April 2012

The Deep Convection cruise repeatedly sampled two locations in the North Atlantic, sited in the Iceland and Norwegian Basins, onboard the RV Meteor (19 March - 2 May 2012). Samples were collected from multiple casts of a conductivity-temperature-depth (CTD) - Niskin rosette at each station. Water samples for primary production rates, community structure, chlorophyll a [Chl a], calcite [PIC], particulate organic carbon [POC] and biogenic silicic acid [BSi] were collected from predawn casts from six light depths (55%, 20%, 14%, 7%, 5% and 1% of incident PAR). Additional samples for community structure and ancillary parameters were collected from a second cast. Carbon fixation rates were determined using the 13C stable isotope method. Water samples for diatom and micro zooplankton counts, collected from the predawn casts, were preserved with acidic Lugol's solution (2% final solution) and counted using an inverted light microscope. Water samples for coccolithophore counts were collected onto cellulose nitrate filters and counted using polarising light microscopy. Water samples for Chl a analysis were filtered onto MF300 and polycarbonate filters and extracted in 90% acetone. PIC and BSi samples were filtered onto polycarbonate filters and analysed using an inductively coupled plasma emission optical spectrometer and a SEAL QuAAtro autoanalyser respectively.

Seawater carbonate chemistry, nutrients, and Calcidiscus leptoporus (strain RCC1135) growth rate and calcification rate during experiments, 2012

The coccolithophore Calcidiscus leptoporus was grown in batch culture under nitrogen (N) as well as phosphorus (P) limitation. Growth rate, particulate inorganic carbon (PIC), particulate organic carbon (POC), particulate organic nitrogen (PON), and particulate organic phosphorus (POP) production were determined and coccolith morphology was analysed. While PON production decreased by 70% under N-limitation and POP production decreased by 65% under P-limitation, growth rate decreased by 33% under N- as well as P-limitation. POC as well as PIC production (calcification rate) increased by 27% relative to the control under P-limitation, and did not change under N-limitation. Coccolith morphology did not change in response to either P or N limitation. While these findings, supported by a literature survey, suggest that coccolith morphogenesis is not hampered by either P or N limitation, calcification rate might be. The latter conclusion is in apparent contradiction to our data. We discuss the reasons for this inference.

Pollen record from Eifel maar

A new interglacial pollen sequence from the Döttinger dry maar in the Eifel region of the Rheinish Schield is presented. Palynology is used to correlated to several classical north German Holsteinian sites. The lake sediments reveal the complete interglacial and also 60 m of laminated sediments from the glacial preceding the Holsteinian. The interglacial section indicates limnic conditions in its lower part and telmatic conditions in its upper part with an intermediate episode of peat formation. Ash layers document internsive volcansim during the interglacial in the Eifel region. Some of the north German Holsteinian sites reval spikes of high abundance of Pinus, Beutal and Poaceae and/or setbacks of more demanding taxa during the interglacial, often interpreted as cold events. The Döttingen profile shows similar pattern, but with little response from the thermophilous pollen taxa. In the Döttingen sequence these vegetation 'anomalies' are preceded, or accompanied by phases of active volcanism. The role/interaction of climate and/or volcanism as a likely cause for these vegetation 'anomalies' ist still to be quantified.

Seawater carbonate chemistry and biological processes of Emiliania huxleyi (strains RCC1256 and NZEH) during experiments, 2011

With respect to their sensitivity to ocean acidification, calcifiers such as the coccolithophore Emiliania huxleyi have received special attention, as the process of calcification seems to be particularly sensitive to changes in the marine carbonate system. For E. huxleyi, apparently conflicting results regarding its sensitivity to ocean acidification have been published (Iglesias-Rodriguez et al., 2008a; Riebesell et al., 2000). As possible causes for discrepancies, intra-specific variability and different effects of CO2 manipulation methods, i.e. the manipulation of total alkalinity (TA) or total dissolved inorganic carbon (DIC), have been discussed. While Langer et al. (2009) demonstrate a high degree of intra-specific variability between strains of E. huxleyi, the question whether different CO2 manipulation methods influence the cellular responses has not been resolved yet. In this study, closed TA as well as open and closed DIC manipulation methods were compared with respect to E. huxleyi's CO2-dependence in growth rate, POC- and PIC-production. The differences in the carbonate chemistry between TA and DIC manipulations were shown not to cause any differences in response patterns, while the latter differed between open and closed DIC manipulation. The two strains investigated showed different sensitivities to acidification of seawater, RCC1256 being more negatively affected in growth rates and PIC production than NZEH.

The effect of nitrate and phosphate availability on Emiliania huxleyi(NZEH) physiology under different CO2 scenarios

Growth and calcification of the marine coccolithophorid Emiliania huxleyi is affected by ocean acidification and macronutrients limitation and its response varies between strains. Here we investigated the physiological performance of a highly calcified E. huxleyi strain, NZEH, in a multiparametric experiment. Cells were exposed to different CO2 levels (ranging from 250 to 1314 µatm) under three nutrient conditions [nutrient replete (R), nitrate limited (-N), and phosphate limited (-P)]. We focused on calcite and organic carbon quotas and on nitrate and phosphate utilization by analyzing the activity of nitrate reductase (NRase) and alkaline phosphatase (APase), respectively. Particulate inorganic (PIC) and organic (POC) carbon quotas increased with increasing CO2 under R conditions but a different pattern was observed under nutrient limitation. The PIC:POC ratio decreased with increasing CO2 in nutrient limited cultures. Coccolith length increased with CO2 under all nutrient conditions but the coccosphere volume varied depending on the nutrient treatment. Maximum APase activity was found at 561 ?atm of CO2 (pH 7.92) in -P cultures and in R conditions, NRase activity increased linearly with CO2. These results suggest that E. huxleyi's competitive ability for nutrient uptake might be altered in future high-CO2 oceans. The combined dataset will be useful in model parameterizations of the carbon cycle and ocean acidification.