A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

Background: The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes. Results: We assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters. Conclusions: These assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies

Female bone physiology resilience in 750-300 BP ‘Polynesian Outlier’ community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in n = 69 individuals from 750 – 300 BP Taumako in Solomon Islands, a remote ‘Polynesian Outlier’ island in Melanesia. We tested whether bone remodelling indicators differed between age-at-death groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-to-osteon (~10%) did not differ between the sexes. Compared to males, the femora of Taumako females experienced higher frequencies of remodelling events, which mirrors bone health paradigms through the life-course today. However, contrary to modern populations, female femoral bone tissue did not decline with age. This matches findings in other archaeological samples, and is testament to ancient female bone physiology resilience also in the Pacific region.Introduction - The importance of bone remodelling through human life-course - Bone remodelling in archaeological humans Results - Trends in bone remodelling at Taumako Discussion - Sex-specific trends in cortical bone remodelling - Bone remodelling with age at Taumako Limitations and remarks on temporal and spatial data Conslusions Materials and Method

Female bone physiology resilience in a past Polynesian Outlier community

Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440–150 BP Taumako in Solomon Islands, a remote ‘Polynesian Outlier’ island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples—a testament to past female bone physiology resilience, also now observed in the Pacific region.Introduction - Bone remodelling through human life‑course. - Bone remodelling in archaeological humans. Results - Femoral vascular porosity and bone remodelling indicators at Taumako. Discussion - Sex and cortical bone histology at Taumako. - The effect of age on bone histology at Taumako. Remarks on temporal and spatial bone histology data Limitations Conclusions Materials and method

Small sinking particles control anammox rates in the Peruvian oxygen minimum zone

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas

Complete results for five years of GNO solar neutrino observations

We report the complete GNO solar neutrino results for the measuring periods GNO III, GNO II, and GNO I. The result for GNO III (last 15 solar runs) is [54.3 + 9.9 - 9.3 (stat.)+- 2.3 (syst.)] SNU (1 sigma) or [54.3 + 10.2 - 9.6 (incl. syst.)] SNU (1 sigma) with errors combined. The GNO experiment is now terminated after altogether 58 solar exposure runs that were performed between May 20, 1998 and April 9, 2003. The combined result for GNO (I+II+III) is [62.9 + 5.5 - 5.3 (stat.) +- 2.5 (syst.)] SNU (1 sigma) or [62.9 + 6.0 - 5.9] SNU (1 sigma) with errors combined in quadrature. Overall, gallium based solar observations at LNGS (first in GALLEX, later in GNO) lasted from May 14, 1991 through April 9, 2003. The joint result from 123 runs in GNO and GALLEX is [69.3 +- 5.5 (incl. syst.)] SNU (1 sigma). The distribution of the individual run results is consistent with the hypothesis of a neutrino flux that is constant in time. Implications from the data in particle- and astrophysics are reiterated.Comment: 22 pages incl. 9 Figures and 8 Tables. to appear in: Physics Letters B (accepted April 13, 2005) PACS: 26.65.+t ; 14.60.P

GNO Solar Neutrino Observations: Results for GNOI

We report the first GNO solar neutrino results for the measuring period GNOI, solar exposure time May 20, 1998 till January 12, 2000. In the present analysis, counting results for solar runs SR1 - SR19 were used till April 4, 2000. With counting completed for all but the last 3 runs (SR17 - SR19), the GNO I result is [65.8 +10.2 -9.6 (stat.) +3.4 -3.6 (syst.)]SNU (1sigma) or [65.8 + 10.7 -10.2 (incl. syst.)]SNU (1sigma) with errors combined. This may be compared to the result for Gallex(I-IV), which is [77.5 +7.6 -7.8 (incl. syst.)] SNU (1sigma). A combined result from both GNOI and Gallex(I-IV) together is [74.1 + 6.7 -6.8 (incl. syst.)] SNU (1sigma).Comment: submitted to Physics Letters B, June 2000. PACS: 26.65. +t ; 14.60 Pq. Corresponding author: [email protected] ; [email protected]

A New 76Ge Double Beta Decay Experiment at LNGS

This Letter of Intent has been submitted to the Scientific Committee of the INFN Laboratori Nazionali del Gran Sasso (LNGS) in March 2004. It describes a novel facility at the LNGS to study the double beta decay of 76Ge using an (optionally active) cryogenic fluid shield. The setup will allow to scrutinize with high significance on a short time scale the current evidence for neutrinoless double beta decay of 76Ge using the existing 76Ge diodes from the previous Heidelberg-Moscow and IGEX experiments. An increase in the lifetime limit can be achieved by adding more enriched detectors, remaining thereby background-free up to a few 100 kg-years of exposure.Comment: 67 pages, 19 eps figures, 17 tables, gzipped tar fil

New results on solar neutrino fluxes from 192 days of Borexino data

We report the direct measurement of the ^7Be solar neutrino signal rate performed with the Borexino detector at the Laboratori Nazionali del Gran Sasso. The interaction rate of the 0.862 MeV ^7Be neutrinos is 49+-3(stat)+-4(syst) counts/(day * 100ton). The hypothesis of no oscillation for ^7Be solar neutrinos is inconsistent with our measurement at the 4sigma level. Our result is the first direct measurement of the survival probability for solar nu_e in the transition region between matter-enhanced and vacuum-driven oscillations. The measurement improves the experimental determination of the flux of ^7Be, pp, and CNO solar nu_e, and the limit on the magnetic moment of neutrinos

Sinking Organic Particles in the Ocean—Flux Estimates From in situ Optical Devices

Optical particle measurements are emerging as an important technique for understanding the ocean carbon cycle, including contributions to estimates of their downward flux, which sequesters carbon dioxide (CO2) in the deep sea. Optical instruments can be used from ships or installed on autonomous platforms, delivering much greater spatial and temporal coverage of particles in the mesopelagic zone of the ocean than traditional techniques, such as sediment traps. Technologies to image particles have advanced greatly over the last two decades, but the quantitative translation of these immense datasets into biogeochemical properties remains a challenge. In particular, advances are needed to enable the optimal translation of imaged objects into carbon content and sinking velocities. In addition, different devices often measure different optical properties, leading to difficulties in comparing results. Here we provide a practical overview of the challenges and potential of using these instruments, as a step toward improvement and expansion of their applications