Rapid 20th century warming reverses 900-year cooling in the Gulf of Maine

The Gulf of Maine, located in the western North Atlantic, has undergone recent, rapid ocean warming but the lack of long-term, instrumental records hampers the ability to put these significant hydrographic changes into context. Here we present multiple 300-year long geochemical records (oxygen, nitrogen, and previously published radiocarbon isotopes) measured in absolutely-dated Arctica islandica shells from the western Gulf of Maine. These records, in combination with climate model simulations, suggest that the Gulf of Maine underwent a long-term cooling over most of the last 1000 years, driven primarily by volcanic forcing and North Atlantic ocean dynamics. This cooling trend was reversed by warming beginning in the late 1800s, likely due to increased atmospheric greenhouse gas concentrations and changes in western North Atlantic circulation. The climate model simulations suggest that the warming over the last century was more rapid than almost any other 100-year period in the last 1000 years in the region

Evolution of Fruit Traits in Ficus Subgenus Sycomorus (Moraceae): To What Extent Do Frugivores Determine Seed Dispersal Mode?

Fig trees are a ubiquitous component of tropical rain forests and exhibit an enormous diversity of ecologies. Focusing on Ficus subgenus Sycomorus, a phenotypically diverse and ecologically important Old World lineage, we examined the evolution of fruit traits using a molecular phylogeny constructed using 5 kilobases of DNA sequence data from 63 species (50% of global diversity). In particular, we ask whether patterns of trait correlations are consistent with dispersal agents as the primary selective force shaping morphological diversity or if other ecological factors may provide a better explanation? Fig colour, size and placement (axial, cauliflorous, or geocarpic) were all highly evolutionarily liable, and the same fruit traits have evolved in different biogeographic regions with substantially different dispersal agents. After controlling for phylogenetic autocorrelation, we found that fig colour and size were significantly associated with fig placement and plant-life history traits (maximum plant height and leaf area, respectively). However, contrary to prevailing assumptions, fig placement correlated poorly with known dispersal agents and appears more likely determined by other factors, such as flowering phenology, nutrient economy, and habitat preference. Thus, plant life-history, both directly and through its influence on fig placement, appears to have played a prominent role in determining fruit traits in these figs

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Oxygen isotopes of seawater and oxygen and nitrogen isotopes of dissolved nitrate measured in the Gulf of Maine in October, 2016

This dataset contains salinity and stable isotope measurements taken of water samples collected during an October 2016 research cruise in the Gulf of Maine aboard the NOAA ship Pisces. Water samples were collected at 44 different stations throughout the Gulf of Maine at various depths from the surface to the seafloor using a carousel sampler with 12 different Niskin bottles and attached to a SeaBIRD 911 CTD. Salinity was measured in situ using the SeaBird 911 CTD with auxiliary sensors. Water samples were collected from depth in Niskin bottles and transferred to triple rinsed Thermo Scientific Nalgene 4 Oz natural hdpe plastic wide mouth leakproof bottles. Parafilm was secured around the cap of each bottle to help prevent evaporation. Samples designated for δ18O(water) analyses were stored in containers in the wet lab of the boat. Samples designated for δ15N(NO3-) and δ18O(NO3-) analyses were immediately placed in a walk-in freezer set at − 8°C. Once back at port, samples were overnight shipped to the Stable Isotope Lab at Iowa State University. Frozen samples were shipped in coolers with additional ice added and, upon arrival, immediately placed back in a freezer. This dataset also contains two freshwater samples collected from the Kennebec River in November and December 2016. Samples were hand collected and stored in Thermo Scientific Nalgene 4 Oz natural hdpe plastic wide mouth leakproof bottles. Samples were shipped on dry ice to Iowa State University and processed in the same way as the other saltwater samples as detailed below. Once at Iowa State University, samples designated for δ18O(water) were stored in the temperature controlled laboratory and then analyzed using a Picarro L2130-I Isotopic Liquid Water Analyzer with attached autosampler. Three different isotopic reference standards, VSMOW, USGS 48, and USGS 47, were used. At least one reference standard sample was used per 5 samples. The average combined uncertainty (analytical and average correction factor) was ±0.20‰ (2σ). Samples designated for isotopic analyses (δ15N and δ18O) of dissolved NO3- were first unfrozen at Iowa State University and filtered using 0.2 μm pore filters (Sartorius Minisart high flow syringe sterile PES membrane). Subsequently, water samples were treated with sulfamic acid (ACS grade, 99.3-100.3%) to remove any NO2- following the procedures outlined in Granger and Sigman (2009; doi:10.1002/rcm.4307). Briefly, glassware was acid washed and baked at 500°C. 60 ml of sample were treated with 600 μL 0.4M sulfamic acid (made using 10% v/v HCl) to reduce the pH to between 1.6 and 1.8, which is necessary to reduce NO2- to N2 and therefore remove it from the sample. After the reaction was allowed to occur for at least 5 min, samples were neutralized by adding 2M NaOH to the sample to return the sample to a pH of 7 (±0.5). Approximately 310 μL of NaOH were added to each sample but the exact amount of NaOH varied by sample and was determined using a pH meter. Samples were then refrozen, put on dry ice and shipped overnight to the University of California Davis Stable Isotope Facility. Samples were analyzed for δ15N(NO3-) and δ18O(NO3-) using the bacterial denitrification assay method as outlined by Sigman et al., (2001; doi:10.1021/ac010088e) and Casciotti et al., (2002; doi:10.1021/ac020113w), respectively. Isotopes were measured using a Thermoscientific Delta V Plus isotope ratio mass spectrometer coupled to a ThermoFinnigan GasBench + PreCon trace gas concentration system. Seven different reference standards were used to correct samples and report values on the international scale, Air: USGS34 KNO3, USGS35 NaNO3, Acros KNO3, Fisher KNO3, Strem KNO3, New Acros KNO3, and IAEA-NO-3 KNO3 (not used on all samples). Average analytical uncertainty (2σ) was ±0.5‰ for δ15N(NO3-) and ±0.3‰ for δ18O(NO3-). In order to assess the extent to which nitrification is occurring in the Gulf of Maine, we used the following equation for Δ(15, 18), first proposed by Sigman et al., (2005; doi:10.1029/2005GB002458): Δ(15, 18) = (δ15N(NO3-) - δ15Nm)-(15ε/18ε)x(δ18O(NO3-)-δ18Om) δ15Nm and δ18Om are mean δ15N and δ18O of dissolved NO3- in deep source waters, respectively. In this case, we use average values for samples taken at and below 100 m, where δ15N(NO3-) and δ18O(NO3-) remain relatively constant with depth. 15ε/18ε is the ratio of isotope fractionation factors for nitrogen and oxygen, respectively, for assimilation, which is taken to be 1 here. The propagated ([a2+b2]1/2) uncertainty for Δ(15, 18), calculated using the uncertainty associated with δ15N(NO3-) and δ18O(NO3-), is ±0.6‰ (2σ)

Oxygen isotope and salinity measurements of coastal surface waters in the Gulf of Maine

These data include salinity and oxygen isotope measurements of water samples collected from coastal sites along the Gulf of Maine between 2003 and 2015. In particular, a suite of samples were collected along the coast of Maine, east of Penobscot Bay, on a monthly basis between April 2014 and March 2015. These data also include several freshwater samples collected from the Kennebec and Penobscot Rivers on a semi-monthly basis in 2014 and 2015. For the water samples with sample IDs starting with DSW, JSW, NSW, or OSW: The water samples were collected by hand from shore or boat using French square glass bottles with phenolic polycone lined caps. Salinity was measured using a Oakton SALT 6+ handheld salinity meter. Oxygen isotopes were measured using a Picarro L2130-i Isotopic Liquid Water Analyzer with an attached autosampler. Water samples with sample IDs starting with ASW were collected from shore. Samples with sample IDs starting with DMC 2010 were collected at the flowing seawater laboratory at the Darling Marine Center. Samples with sample IDs starting with Summer 2011 were collected from a boat. For these last 3 sample types (ASW, DMC 2010, Summer 2011): Salinity was measured with YSI Professional Plus salinity meter and oxygen isotopes were measured using a Picarro L1102-i Isotopic Liquid Water Analyzer with an attached autosampler. Data from Owen et al., 2008 and Wanamaker et al. (2006, 2007) was collected from the flowing seawater laboratory at the Darling marine center. Salinity was measured using a YSI model 85 oxygen, conductivity, salinity, and temperature system and oxygen isotopes were measured using a dual-inlet VG/Micromass SIRA (CO2–H2O equilibration method at 30 °C for 12 h)

Increased postpartum anxiety symptoms after perinatal SARS-CoV-2 infection in a large, prospective pregnancy cohort in New York City

Numerous studies reported an increase of postpartum mood symptoms during the COVID-19 pandemic. Yet, the link between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and perinatal mental health is less well understood. We investigated the associations between prenatal SARS-CoV-2 infection and postpartum depressive and anxiety symptoms, including examinations of infection timing and pandemic timeline. We included 595 participants from Generation C, a prospective pregnancy cohort in New York City (2020–2022). Prenatal SARS-CoV-2 infection was determined via laboratory or medical diagnosis. Depression and anxiety symptoms were measured 4–12 weeks postpartum using the Edinburgh Postnatal Depression Scale (EPDS) and Generalized Anxiety Disorder questionnaire (GAD), respectively. Quantile regressions were conducted with prenatal SARS-CoV-2 infection as exposure and continuously measured EPDS and GAD scores as outcomes. We reran the analyses in those with COVID-19-like symptoms in the trimester during which infection occurred. 120 (20.1%) participants had prenatal SARS-CoV-2 infection. After adjusting for socio-demographic, obstetric and other maternal health factors, prenatal SARS-CoV-2 infection was associated with higher median postpartum anxiety scores (b = 0.55, 95% CI = 0.15; 0.96). Late gestation infection (b = 1.15, 95% CI = 0.22; 2.09) and symptomatic infection (b = 1.15, 95% CI = 0.12; 2.18) were also associated with higher median postpartum anxiety scores. No associations were found with depressive symptoms. The associations were not moderated by time since the start of the pandemic. This study suggests that prenatal SARS-CoV-2 infection increases the risk of postpartum anxiety symptoms among participants reporting median anxiety symptoms. Given that this association was not affected by pandemic timing and that SARS-CoV-2 transmission continues, individuals infected with SARS-CoV-2 during pregnancy should be monitored for postpartum anxiety symptoms.</p

Caryospora-like Coccidia infecting green turtles (Chelonia mydas): an emerging disease with evidence of interoceanic dissemination

Protozoa morphologically consistent with Caryospora sp. are one of the few pathogens associated with episodic mass mortality events involving free-ranging sea turtles. Parasitism of green turtles (Chelonia mydas) by these coccidia and associated mortality was first reported in maricultured turtles in the Caribbean during the 1970s. Years later, epizootics affecting wild green turtles in Australia occurred in 1991 and 2014. The first clinical cases of Caryospora-like infections reported elsewhere in free-ranging turtles were from the southeastern US in 2012. Following these initial individual cases in this region, we documented an epizootic and mass mortality of green turtles along the Atlantic coast of southern Florida from November 2014 through April 2015 and continued to detect additional, sporadic cases in the southeastern US in subsequent years. No cases of coccidial disease were recorded in the southeastern US prior to 2012 despite clinical evaluation and necropsy of stranded sea turtles in this region since the 1980s, suggesting that the frequency of clinical coccidiosis has increased here. Moreover, we also recorded the first stranding associated with infection by a Caryospora-like organism in Hawai'i in 2018. To further characterize the coccidia, we sequenced part of the 18S ribosomal and mitochondrial cytochrome oxidase I genes of coccidia collected from 62 green turtles found in the southeastern US and from one green turtle found in Hawai'i. We also sequenced the ribosomal internal transcribed spacer regions from selected cases and compared all results with those obtained from Caryospora-like coccidia collected from green turtles found in Australia. Eight distinct genotypes were represented in green turtles from the southeastern US. One genotype predominated and was identical to that of coccidia collected from the green turtle found in Hawai'i. We also found a coccidian genotype in green turtles from Florida and Australia with identical 18S and mitochondrial sequences, and only slight inter-regional differences in the internal transcribed spacer 2. We found no evidence of geographical structuring based on phylogenetic analysis. Low genetic variability among the coccidia found in green turtle populations with minimal natural connectivity suggests recent interoceanic dissemination of these parasites, which could pose a risk to sea turtle populations