ACRIM total solar irradiance satellite composite validation versus TSI proxy models

The satellite total solar irradiance (TSI) database provides a valuable record for investigating models of solar variation used to interpret climate changes. The 35-year ACRIM TSI satellite composite was updated using corrections to ACRIMSAT/ACRIM3 results derived from recent testing at the Laboratory for Atmospheric and Space Physics/Total solar irradiance Radiometer Facility (LASP/TRF). The corrections lower the ACRIM3 scale by ~5000 ppm, in close agreement with the scale of SORCE/TIM results (solar constant ~1361 W/m^2). Relative variations and trends are not changed. Differences between the ACRIM and PMOD TSI composites, e.g. the decadal trending during solar cycles 21-22, are tested against a set of solar proxy models, including analysis of Nimbus7/ERB and ERBS/ERBE results available to bridge the ACRIM Gap (1989-1992). Our findings confirm: (1) The validity of the TSI peak in the originally published ERB results in early 1979 during solar cycle 21; (2) The correctness of originally published ACRIM1 results during the SMM spin mode (1981-1984); (3) The upward trend of originally published ERB results during the ACRIM Gap; (4) The occurrence of a significant upward TSI trend between the minima of solar cycles 21 and 22 and (5) a decreasing trend during solar cycles 22-23. Our findings do not support: (1) The downward corrections to originally published ERB and ACRIM1 results during solar cycle 21; (2) A step function sensitivity change in ERB results at the end-of-September 1989; (3) the validity of ERBE's downward trend during the ACRIM Gap or (4) the use of ERBE results to bridge the ACRIM Gap. Our analysis provides a first order validation of the ACRIM TSI composite approach and its 0.037%/decade upward trend during solar cycles 21-22. Thus, solar forcing of climate change may be a significantly larger factor than represented in the CMIP5 general circulation climate models.Comment: 26 pages, 15 figure

Planetary harmonics in the historical Hungarian aurora record (1523-1960)

The historical Hungarian auroral record extends from 1523 to 1960 and is longer than the sunspot record. Harmonic analysis reveals four major multidecadal secular cycles forming an approximate harmonic set at periods of 42.85, 57.13, 85.7 and 171.4 years. These four frequencies are very close to the four major heliospheric oscillations relative to the center of mass of the solar system caused by Jupiter, Saturn, Uranus and Neptune. Similar frequencies are found in solar radiation models based on long cosmogenic isotope records (Steinhilber et al. 2012) and in long records of naked-eye sunspot observations (Vaquero et al., 2002). Harmonic regression models are used to reconstruct and forecast aurora and solar activity for the period 1956-2050. The model predicts: (1) the multidecadal solar minimum in the 1970s that is also observed in the sunspot record; (2) a solar maximum in 2000-2002 that is observed in the ACRIM total solar irradiance satellite composite; (3) a prolonged solar minimum centered in the 2030s. These findings support a hypothesis that the Sun, the heliosphere and the terrestrial magnetosphere are partially modulated by planetary gravitational and magnetic forces synchronized to planetary oscillations, as also found in other recent publications (Scafetta, 2010, 2012a, 2012c, 2012d; Abreu et al., 2012; Tan & Cheng, 2012).Comment: 29 pages, 6 figures, 2 table

Multi-scale comparative spectral analysis of satellite total solar irradiance measurements from 2003 to 2013 reveals a planetary modulation of solar activity and its non-linear dependence on the 11-year solar cycle

Herein we adopt a multi-scale dynamical spectral analysis technique to compare and study the dynamical evolution of the harmonic components of the overlapping ACRIMSAT/ACRIM3, SOHO/VIRGO and SORCE/TIM total solar irradiance (TSI) records during 2003.15 to 2013.16 in solar cycles 23 and 24. The three TSI time series present highly correlated patterns. Significant power spectral peaks are common to these records and are observed at the following periods: 0.070 year, 0.097 year, 0.20 year, 0.25 year, 0.30-0.34 year, 0.39 year. Less certain spectral peaks occur at about 0.55 year, 0.60-0.65 year and 0.7-0.9 year. Four main frequency periods at 24.8 days (0.068 year), 27.3 days (0.075 year), at 34-35 days (0.093-0.096 year) and 36-38 days (0.099-0.104 year) characterize the solar rotation cycle. The amplitude of these oscillations, in particular of those with periods larger than 0.5 year, appears to be modulated by the 11-year solar cycle. Similar harmonics have been found in other solar indices. The observed periodicities are found highly coherent with the spring, orbital and synodic periods of Mercury, Venus, Earth and Jupiter. We conclude that solar activity is likely modulated by planetary gravitational and electromagnetic forces acting on the sun. The strength of the sun's response to planetary forcing depends non-linearly on the state of internal solar dynamics: planetary-sun coupling effects are enhanced during solar activity maxima and attenuated during minima.Comment: 18 pages, 10 figures, 3 table

Comparison of Decadal Trends among Total Solar Irradiance Composites of Satellite Observations

We present a new analysis of the two-decade-old controversy over interpretation of satellite observations of total solar irradiance (TSI) since 1978 and the implications of our findings for TSI as a driver of climate change. Our approach compares the methods of constructing the two most commonly referenced TSI composites (ACRIM and PMOD) that relate successive observational databases and two others recently constructed using a novel statistical approach. Our primary focus is on the disparate decadal trending results of the ACRIM and PMOD TSI composite time series, namely, whether they indicate an increasing trend from 1980 to 2000 and a decreasing trend thereafter (ACRIM) or a continuously decreasing trend since 1980 (PMOD). Construction of the four-decade observational TSI composites from 1978 to the present requires the use of results from two less precise Earth Radiation Budget experiments (Nimbus7/ERB and ERBS/ERBE) during the so-called ACRIM-Gap (1989.5–1991.8), between the end of the ACRIM1 and the beginning of the ACRIM2 experiments. The ACRIM and PMOD composites used the ERB and ERBE results, respectively, to bridge the gap. The well-established paradigm of positive correlation between Solar Magnetic Field Strength (SMFS) and TSI supports the validity of the upward trend in the ERB results and the corresponding decadal upward trend of the ACRIM composite during solar cycles 21 and 22. The ERBE results have a sensor degradation caused downward gap trend, contrary to the SMFS/TSI paradigm, that biased the PMOD composite decadal trend downward during solar cycles 21 and 22. The different choice of gap bridging data is clearly the cause of the ACRIM and PMOD TSI trending difference, agreeing closely in both magnitude and direction. We also analyze two recently proposed statistical TSI composites. Unfortunately their methodology cannot account for the gap degradation of the ERBE experiment and their resulting uncertainties are too large to uniquely distinguish between the trending of the ACRIM and PMOD composites. Our analysis supports the ACRIM TSI increasing trend during the 1980 to 2000 period, followed by a long-term decreasing trend since

Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay

Changes in the population levels of specific bacterial species within the gut microbiome have been linked to a variety of illnesses. Most assays that determine the relative abundance of specific taxa are based on amplification and sequencing of stable phylogenetic gene regions. Such lab-based analysis requires pre-analytical sample preservation and storage that have been shown to introduce biases in the characterization of microbial profiles. Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification method that employs commercially available, easy-to-use freeze-dried enzyme pellets that can be used to analyze specimens rapidly in the field or clinic, using a portable fluorometer. Immediate analysis of diverse bacterial communities can lead to a more accurate quantification of relative bacterial abundance. In this study, we discovered that universal bacterial 16S ribosomal DNA primers give false-positive signals in RPA analysis because manufacturing host Escherichia coli DNA is present in the RPA reagents. The manufacturer of RPA reagents advises against developing an RPA assay that detects the presence of E. coli due to the presence of contaminating E. coli DNA in the reaction buffer (www.twistdx.co.uk/). We, therefore, explored four strategies to deplete or fragment extraneous DNA in RPA reagents while preserving enzyme activity: metal-chelate affinity chromatography, sonication, DNA cleavage using methylation-dependent restriction endonucleases, and DNA depletion using anti-DNA antibodies. Removing DNA with anti-DNA antibodies enabled the development of a quantitative RPA microbiome assay capable of determining the relative abundance of the physiologically-important bacterium Akkermansia muciniphila in human feces

Methods for determining the genetic affinity of microorganisms and viruses

Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism

Microbial identification by mass cataloging

BACKGROUND: The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample. Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms. RESULTS: Ribonuclease T(1 )and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T(1 )of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T(1)-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described. CONCLUSION: The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T(1 )is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine

Recovery of Small DNA Fragments from Serum Using Compaction Precipitation

Background: While most nucleic acids are intracellular, trace amounts of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), including micro RNAs, can also be found in peripheral blood. Many studies have suggested the potential utility of these circulating nucleic acids in prenatal diagnosis, early cancer detection, and the diagnosis of infectious diseases. However, DNA circulating in blood is usually present at very low concentrations (ng/ml), and is in the form of relatively small fragments (,1,000 bp), making its isolation challenging. Methods: Here we report an improved method for the isolation of small DNA fragments from serum using selective precipitation by quaternary ammonium compaction agents. A 151 bp fragment of double-stranded DNA from the Escherichia coli bacteriophage lambda served as the model DNA in our experiments. DNA was serially diluted in serum until undetectable by conventional polymerase chain reaction (PCR), before being enriched by compaction precipitation. Results: Starting with concentrations two to three orders of magnitude lower than the PCR-detectable level (0.01 ng/ml), we were able to enrich the DNA to a detectable level using a novel compaction precipitation protocol. The isolated DNA product after compaction precipitation was largely free of serum contaminants and was suitable for downstream applications. Conclusions: Using compaction precipitation, we were able to isolate and concentrate small DNA from serum, and increase the sensitivity of detection by more than four orders of magnitude. We were able to recover and detect very low levels (0.01 ng/ml) of a small DNA fragment in serum. In addition to being very sensitive, the method is fast, simple, inexpensive, and avoids the use of toxic chemicals

Bacterial genotyping by 16S rRNA mass cataloging

BACKGROUND: It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. Because mass spectrometry is extremely rapid and widely available such techniques offer significant advantages in some applications. A key element in favor of mass spectrometric analysis of RNA fragmentation patterns is that a reference database for analysis of the results can be generated from sequence information. In contrast to hybridization approaches, the genetic affinity of any unknown isolate can in principle be determined within the context of all previously sequenced 16S rRNAs without prior knowledge of what the organism is. In contrast to the original RNase T(1 )cataloging method, when digestion products are analyzed by mass spectrometry, products with the same base composition cannot be distinguished. Hence, it is possible that organisms that are not closely related (having different underlying sequences) might be falsely identified by mass spectral coincidence. We present a convenient spectral coincidence function for expressing the degree of similarity (or distance) between any two mass-spectra. Trees constructed using this function are consistent with those produced by direct comparison of primary sequences, demonstrating that the inherent degeneracy in mass spectrometric analysis of RNA fragments does not preclude correct organism identification. RESULTS: Neighbor-joining trees for important bacterial pathogens were generated using distances based on mass spectrometric observables and the spectral coincidence function. These trees demonstrate that most pathogens will be readily distinguished using mass spectrometric analyses of RNA digestion products. A more detailed, genus-level analysis of pathogens and near relatives was also performed, and it was found that assignments of genetic affinity were consistent with those obtained by direct sequence comparisons. Finally, typical values of the coincidence between organisms were also examined with regard to phylogenetic level and sequence variability. CONCLUSION: Cluster analysis based on comparison of mass spectrometric observables using the spectral coincidence function is an extremely useful tool for determining the genetic affinity of an unknown bacterium. Additionally, fragmentation patterns can determine within hours if an unknown isolate is potentially a known pathogen among thousands of possible organisms, and if so, which one