Inferring DNA sequences from mechanical unzipping: an ideal-case study

We introduce and test a method to predict the sequence of DNA molecules from in silico unzipping experiments. The method is based on Bayesian inference and on the Viterbi decoding algorithm. The probability of misprediction decreases exponentially with the number of unzippings, with a decay rate depending on the applied force and the sequence content.Comment: Source as TeX file with ps figure

Relaxation to Native Conformation of a Bond-Fluctuating Protein Chain With Hydrophobic and Polar Nodes

The conformation and dynamics of a protein chain with hydrophobic and polar nodes are examined by the bond-fluctuation model using Monte Carlo simulations on a cubic lattice. The minimal (nearest neighbor) interaction leads to standard (self-avoiding walk) conformation, i.e., the scaling of the radius of gyration Rg with the molecular weight N Rg ∝ Nγ with γ ≃ 3/5/ Specific interactions with longer range and higher strength are needed to approach the native globular conformations with γ \u3c 3/5. Relaxation into the globular ground state shows a weak power-law decay, i.e., Rg ∝ t-α, α ~ 0.06-0.12

Sedimentary Ce anomalies: Secular change and implications for paleoenvironmental evolution

Although Ce anomalies are commonly used to reconstruct past seawater redox conditions, published interpretations are based on various proxy materials and analytical approaches, while no relatively complete compilation of sedimentary Ce anomaly data has yet been made. Here, we report a new compilation comprising >6000 carbonate, iron formation, phosphorite, and chert samples of all ages, of which 1127 passed screening for near primary Ce anomaly values. The Ce anomalies of 592 mudstones were also investigated and found to contain in some cases unambiguous traces of a primary negative Ce anomaly, which was likely inherited during early diagenetic organic degradation or directly from authigenic phases. Here we show that seawater-like rare earth element (REE) patterns may be retained in siliceous mudstones in cases where the detrital REE signature has been diluted by authigenic silica. Mudstone weathering is shown to have a negligible effect on the magnitude of negative Ce anomalies in moderately weathered samples. A critical appraisal of negative Ce anomalies from the published literature, yet to be confirmed through La-Ce isotopic dating, implies that oxygenic photosynthesis likely evolved during 3.0–2.5 Ga. Although our compilation does not capture the onset of the Great Oxidation Episode, a decreasing trend in mean negative Ce anomalies from 2.5 to 2.1 Ga is in accordance with a rise in oxygen levels during the early Paleoproterozoic. Sporadic Ce anomalies might identify transient oxygenation events during 1.8–1.2 Ga with minimum atmospheric concentrations up to 1–6% present atmospheric level. Statistical analysis of Ce anomaly data is consistent with progressive oxygenation of the surface ocean through the late Tonian-early Cambrian interval. While pronounced negative Ce anomalies indicate that shallow marine settings were broadly well oxygenated during the Ediacaran-Cambrian transition, the deeper marine environment remained largely anoxic, consistent with the persistence of a dissolved organic carbon redox buffer. The Ce anomaly compilation also reveals expanded ocean anoxia in the early Paleozoic, followed by more pervasive oxygenation by middle Devonian times, coincident with the emergence and radiation of secondary woody tissues and forests. The redox evolution and estimated pO2 revealed by Ce anomalies are generally compatible with other proxies and modelling results, and therefore we concur that the marine sedimentary Ce anomaly record responds sensitively to oceanic redox changes and can be a useful additional proxy to track Earth system evolution

Phylogeny and Origin of Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency Mutations in Indonesia

The aim of this study is to analyze the relationship between the types of G6PD mutations found in Indonesia and the relationships of mutations found in Indonesia to those found in other countries. We summarize the distribution of G6PDs in West Indonesia and East Indonesia. Moreover, we use bioinformatics methods to construct phylogenetic trees and compare the sequences containing the regions amplifi ed by the commonly used PCR primer pairs. Previous work has shown that Mediterranean G6PD and Chinese CoimbraG6PDare distributed in West Indonesia, whilst G6PD mutations in East Indonesia are Jammu/ViangchanG6PD and Chinese Gaohe G6PD. G6PD Jammu/Viangchan was mostly distributed in Flores Island, East Indonesia along with G6PDGaohe. We constructed phylogenetic trees using the G6PD sequences from various regions in Indonesia and other countries. It appears from phylogenetic trees and percentages of identity that FloresIndonesian G6PD defi ciency (Jammu/Viangchan G6PD, originating in India) is 92.5% identical to the G6PD defi ciency of Chinese origin (GaoheG6PD). It was interesting to note that the genetic region containing the Javanese Indonesian G6PD defi ciency (MediterraneanG6PD, fi rst found in Italy) located in the western parts of Indonesia is closely related (99% identity) to the Chinese G6PD defi ciency(Coimbra G6PD). We concludethat G6PD mutations in West Indonesia are closely related to G6PD mutations from China. G6PD mutations in East Indonesia are also closely related to G6PD mutations from India and China, but more distantly, and to different types to those in West Indonesia. A prediction of protein structure was carried out which allowed visualization of the locations of mutation on the three dimensional structure of G6PD. Key words: G6PD, phylogeny, origin, genetic mutation

Oceanic redox conditions across the Cambrian-Ordovician boundary

Trace element and isotope geochemistry is used to evaluate paleoenvironments. Uranium and molybdenum geochemistry in particular have been used as reliable paleoredox indicators, leading to valuable developments. Here, these proxies are applied to the transgressive sedimentary succession spanning the Cambrian ‒ Ordovician GSSP boundary section of the Cow Head Group exposed at Green Point, western Newfoundland (Canada). In Chapter 2, the distal slope environment of deposition is evaluated based on the green to black shales’ geochemistry. It underwent significant changes during the transgression occurring around the Cambrian-Ordovician boundary. As the platform became increasingly flooded and more carbonate-dominated, the cratonic siliciclastic supply decreased, lowering the proportion of Al (6.2±1.1 wt% to 5.2±1.0 wt%), Cr (64±12 ppm to 55±10 ppm), Sc (9.1±1.8 ppm to 7.5±1.6 ppm), Th (7.4±1.2 ppm to 5.9±1.4 ppm) and Cs (3.7±1.0 ppm to 2.6±0.8 ppm) and increasing the proportion of Ca (3.8±3.0 wt% to 4.8±2.8 wt%) in the shales. Conditions became more reducing as relative sea level rose, becoming more strongly suboxic, with more frequent anoxic intervals. Due to short-term fluctuations (reflected in the highly variable lithology), this is reflected most accurately by the higher proportion of shales demonstrating significant U and Mo authigenic enrichment above the anomaly level, and their relationship to higher TOC values. Bioproductivity was low throughout the section, based on low P (494±141 ppm), Ni (32.8±10.5 ppm) and Cu (36.1±16.8 ppm). Bioproductivity variation across the anomaly level could not be ascertained however. The geochemical patterns observed correlate well with the carbonate carbon isotope stratigraphy, clearly defining trends and systems tract. In Chapter 3, we focus on Mo and U elemental and isotopic geochemistry. We first evaluate the relationship of U/Mo ratio vs U and Mo (both concentrations and EFs) in the Green Point shales and compare the results to several modern and Phanerozoic-aged siliciclastic environments to evaluate repeatability and predictability. Secondly, this method is applied to the Green Point carbonates and modern Bahamas carbonates. In the third part of this chapter, we focus on the δ⁹⁸Mo ratios from the Green Point carbonates and their reliability as a predictive paleoredox tool. Uranium and Molybdenum were found to have divergent relationships to the U/Mo ratios. In the Green Point shales, the relationship between U/Moauth vs MoEF or UEF enrichment factors were found to be reliable redox indicators, particularly U/Moauth vs MoEF. When applied to other siliciclastic datasets, plotting U/Moauth to MoEF or UEF yielded a different yet consistent pattern relative to the UEF vs MoEF plot of Algeo and Tribovillard (2009), differentiating oxygen levels, most notably within the suboxic range, and marine basin restriction. Within the carbonates, the main factor controlling the low U concentrations was calcite being the carbonate species present. The decrease across the anomaly is likely due to the TOC decrease; enhanced by low dissolved porewater sulfide levels and the presence of carbonate material. The positive U/Mo vs U trend supports the conclusion that authigenic enrichment was not tot the main control on observed variations. The Mo values were within the range of previously carbonates, indicating pH and carbonate species present may not affect Mo enrichment. The U/Mo vs Mo plot behaved like in the shales, showing potential as a redox indicator. When applied to the Bahamas carbonates, both relationships consistently differentiated low and high pore-water sulfide levels, and shows potential to differentiate paleoenvironments. The Mo isotope ratios were interpreted as being a mixed detrital-authigenic signature, and so are minimum values. The increase across the anomaly level suggests increasingly reducing conditions during the deposition of the Green Point carbonates. This agrees with previous interpretations, indicating δ⁹⁸Mo ratios are reliable at Green Point

Poboljšanje proizvodnje fruktanohidrolaze dodatkom estera šečera pri uzgoju Aspergillus niger SL-09

The influence of carbon sources, nitrogen sources, and the addition of sucrose ester on fructanohydrolase production was investigated. The enzyme production varied depending on the carbon source. Apart from that, it was found that the enzyme activities formed by Aspergillus niger SL-09 were enhanced dramatically by the addition of sucrose ester S-770 to the medium. The effect of sucrose ester on enzyme production was also studied on molecular level, and it was confirmed that the transcription was activated by the addition of sucrose ester to the medium. The response surface methodology (RSM) was used to optimize the composition for the production of fructanohydrolase, and the enzyme activities were enhanced more than 7-fold than those obtained in the basal medium.Ispitan je utjecaj izvora ugljika i dušika te dodatak estera šećera na proizvodnju fruktanohidrolaze s pomoću Aspergillus niger SL-09. Proizvodnja enzima mijenjala se ovisno o izvoru ugljika, ali se enzimska aktivnost dramatično povećala dodavanjem estera šečera S-770 (ester masne kiseline) u podlogu. Učinak estera šećera na proizvodnju enzima ispitan je na molekularnoj razini, pa je utvrđeno da on aktivira transkripciju. Sastav podloge za proizvodnju fruktanohidrolaze optimiran je metodom odzivnih površina, a enzimska se aktivnost povećala više od 7 puta u usporedbi s proizvodnjom na osnovnoj podlozi

Author index transactions of the Royal Society of Canada. Table des noms d\u27auteurs : comptes rendus de la Société royale du Canada : sections I-V, troisième série, tomes I-XXXV, 1907-1941.

https://digitalrepository.trincoll.edu/eastbooks/1070/thumbnail.jp

Phylogeny and Origin of Glucose-6-Phosphate Dehydrogenase (G6PD) Defi ciency Mutations in Indonesia

The aim of this study is to analyze the relationship between the types of G6PD mutations found in Indonesia and the relationships of mutations found in Indonesia to those found in other countries. We summarize the distribution of G6PDs in West Indonesia and East Indonesia. Moreover, we use bioinformatics methods to construct phylogenetic trees and compare the sequences containing the regions amplifi ed by the commonly used PCR primer pairs. Previous work has shown that Mediterranean G6PD and Chinese CoimbraG6PDare distributed in West Indonesia, whilst G6PD mutations in East Indonesia are Jammu/ViangchanG6PD and Chinese Gaohe G6PD. G6PD Jammu/Viangchan was mostly distributed in Flores Island, East Indonesia along with G6PDGaohe. We constructed phylogenetic trees using the G6PD sequences from various regions in Indonesia and other countries. It appears from phylogenetic trees and percentages of identity that FloresIndonesian G6PD defi ciency (Jammu/Viangchan G6PD, originating in India) is 92.5% identical to the G6PD defi ciency of Chinese origin (GaoheG6PD). It was interesting to note that the genetic region containing the Javanese Indonesian G6PD defi ciency (MediterraneanG6PD, fi rst found in Italy) located in the western parts of Indonesia is closely related (99% identity) to the Chinese G6PD defi ciency(Coimbra G6PD). We concludethat G6PD mutations in West Indonesia are closely related to G6PD mutations from China. G6PD mutations in East Indonesia are also closely related to G6PD mutations from India and China, but more distantly, and to different types to those in West Indonesia. A prediction of protein structure was carried out which allowed visualization of the locations of mutation on the three dimensional structure of G6PD.Key words: G6PD, phylogeny, origin, genetic mutations</div

An Investigation into the Perceptions of Veterinarians towards Perioperative Pain Management in Calves

While veterinarians are instrumental to the welfare of calves (Bos taurus), limited knowledge exists concerning veterinary perceptions towards perioperative pain management in calves. As a part of a larger, nationwide study investigating the perceptions of veterinarians towards calf welfare, the current work sought to quantify veterinary perceptions towards perioperative pain management, including barriers to its use, and investigate demographic influences affecting those perceptions. An electronic mixed-methods survey was completed by 104 veterinarians registered with the Veterinary Council of New Zealand. The current work revealed that most veterinarians considered a multimodal approach as the most effective method for ameliorating perioperative pain in calves, rejected the practice of differential treatment based on developmental age, and perceived that postprocedural pain persists beyond 24 h for the majority of procedures included in the survey. Despite this, veterinarians identified certain barriers that may inhibit the provision of pain mitigation on-farm, including costs, inadequate recognition of pain, and ingrained farming practices. Certain demographic effects were found to influence perceptions towards perioperative pain management, including gender, the number of years since graduation, and species emphasis. Nevertheless, the current work demonstrated considerable support among veterinarians to improve pain management protocols during routine husbandry procedures. The asymmetries that exist between the current minimum provisions of perioperative pain management and veterinary perspectives suggest that substantive improvements are necessary in order to reconcile New Zealand’s existing regulatory regime with developments in scientific knowledge