Holo-Transcriptome Sequences from the Tropical Marine Sponge Cinachyrella alloclada

Marine sponge transcriptomes are underrepresented in current databases. Furthermore, only two sponge genomes are available for comparative studies. Here we present the assembled and annotated holo-transcriptome of the common Florida reef sponge from the species Cinachyrella alloclada. After Illumina high throughput sequencing, the data assembled using Trinity v2.5 confirmed a highly symbiotic organism, with the complexity of high microbial abundance (HMA) sponges. This dataset is enriched in poly-A selected eukaryotic, rather than microbial transcripts. Overall, 39,813 transcripts with verified sponge sequence homology coded for 8,496 unique proteins. The average sequence length was found to be 946 bp with an N50 sequence length of 1290 bp. Overall, the sponge assembly resulted in a GC content of 51.04%, which is within the range of GC bases in a eukaryotic transcriptome. BUSCO scored completeness analysis revealed a completeness of 60.3% and 60.1% based on the Eukaryota and Metazoa databases, respectively. Overall, this study points to an overarching goal of developing the Cinachyrella alloclada sponge as a useful new experimental model organism.

An Improved Self-Training Method for Positive Unlabeled Time Series Classification Using DTW Barycenter Averaging

Traditional supervised time series classification (TSC) tasks assume that all training data are labeled. However, in practice, manually labelling all unlabeled data could be very time-consuming and often requires the participation of skilled domain experts. In this paper, we concern with the positive unlabeled time series classification problem (PUTSC), which refers to automatically labelling the large unlabeled set U based on a small positive labeled set PL. The self-training (ST) is the most widely used method for solving the PUTSC problem and has attracted increased attention due to its simplicity and effectiveness. The existing ST methods simply employ the one-nearest-neighbor (1NN) formula to determine which unlabeled time-series should be labeled. Nevertheless, we note that the 1NN formula might not be optimal for PUTSC tasks because it may be sensitive to the initial labeled data located near the boundary between the positive and negative classes. To overcome this issue, in this paper we propose an exploratory methodology called ST-average. Unlike conventional ST-based approaches, ST-average utilizes the average sequence calculated by DTW barycenter averaging technique to label the data. Compared with any individuals in PL set, the average sequence is more representative. Our proposal is insensitive to the initial labeled data and is more reliable than existing ST-based methods. Besides, we demonstrate that ST-average can naturally be implemented along with many existing techniques used in original ST. Experimental results on public datasets show that ST-average performs better than related popular methods.

Photogrammetry of sequence and bioherm morphology in the Paradox Formation, Utah, U.S.A.: A test of the coherence of Pennsylvanian (Moscovian) glacio-eustatic sea-level change

ABSTRACT Despite long-standing recognition of high-amplitude, high-frequency sea-level variation resulting from repeated glaciations of Gondwanaland, recorded as “cyclothems” in late Paleozoic strata worldwide, major questions remain concerning their precise timing and expression in the stratigraphic record. A deep meandering canyon in southern Utah cut by the San Juan River exposes cyclic Pennsylvanian (Moscovian) carbonate strata of the Paradox Formation of the Hermosa Group in three dimensions. These peritidally to subtidally deposited strata archive a long record of Pennsylvanian sea-level change that was important to the early development of sequence stratigraphy. Their interpretation with respect to sea level is complicated by lateral variations in sequence thickness and a lack, until recently, of precise geochronologic control. In this study, we use Structure from Motion photogrammetry (SfM) to quantify lateral stratigraphic variation in three dimensions (3D) in the inner gorge of the canyon, then integrate these data with published U-Pb geochronology and conodont biostratigraphy to assess magnitude and temporal significance of depositional cyclicity. 3D SfM models were used to precisely measure the thickness of sixteen depositional sequences in the Barker Creek and Akah intervals, which constitute the lower Paradox Formation. Bioherms ranging from 2–18 m in relief occur within five sequences, and are typically constructed by either microbialites, the sponge Chaetetes, or a mixture of both. On average, bioherms containing Chaetetes are steeper and thicker than those without them. Bioherm-generated bathymetric highs can influence overlying strata in several characteristic ways: 1) by serving as a nucleation site for bioherms in overlying sequences, 2) sequences often onlap bioherms, leading to local stratal truncations, and in some cases, 3) progradational geometries extend laterally outward from preexisting highs in underlying units. Sequence thickness can vary laterally by up to four times in areas with no obvious bioherms; sequences tend to be thickest in the vicinity of bioherms. To better understand the potential orbital significance and correlation of Paradox Formation cyclicity to an increasingly precise global record, we projected photogrammetry-generated average sequence thicknesses onto an age framework using conodont and fusulinid biostratigraphy and CA-TIMS U-Pb zircon ages for correlative strata in Eastern Europe. To mitigate the influence of local variability of accumulation rate, SfM-based average sequence thicknesses in the study area were used to construct a relative-sea-level history that can be compared to global records. While regional averaging cannot correct for the unknown durations of sequence-bounding unconformities, underfilled accommodation, or autocyclicity due to shoal migration, it does provide a more quantitative means to consider timescales of deposition and mechanisms responsible for cyclicity than is possible with a one-dimensional section or core. Paradox Formation cyclicity shares a broad similarity with the global record, suggesting coherent glacio-eustatic sea-level variation across several different tectonic regimes. If one explores a thickness to duration relationship in these sequences, it is plausible that eight thin (2–4 m) sequences in the investigated strata (S2.6–11; S3.5–6) have apparent durations ranging from 100 to 350 kyr, within the plausible range of short and long eccentricity. In contrast, four thicker (6–12 m) sequences in the middle Akah interval (S3.1–S3.4) contain deeper-water lithofacies and have apparent durations ranging from 500 to 1000 kyr, implying that they may be down-dip composites of multiple documented cyclothems in the North American Midcontinent, Urals–Donets, and South China Block successions.

Synthesis, Characterization, and Aqueous Properties of an Amphiphilic Terpolymer with a Novel Nonionic Surfmer

A series of surfactive amphiphilic polymer PAADs were prepared from the copolymerization of sodium acrylate, dodecyl polyoxyethylene acrylate (DPA, a surfmer), and acrylamide under the action of a mixed initiating agent consisting of ammonium persulfate-sodium bisulfite/2,2′-azobis[2-(2-imidazolin-2-yl) propane] dihydrochloride. The aggregative behaviors of PAADs were explored by 13C nuclear magnetic resonance, a viscometer, and a surface tension instrument. It was found that the apparent viscosity and surface activity of PAADs were significantly improved by the increase of average sequence length of hydrophobic micro blocks, strong intermolecular hydrophobic association, or the formation of mixed micelles between hydrophobic micro blocks and micromolecular surface-active agent. The introduction of long-chain alkyls on molecular chains prolonged the average sequence length of hydrophobic micro blocks in molecular chains and enhanced the hydrophobic association between molecular chains and the tight arrangement of molecular chains on water surfaces, thereby increasing the surface activity. Moreover, the anionic monomer sodium acrylate on molecular chains, via electrostatic repulsion, promoted the conversion from intrachain association to intermolecular association and thereby facilitated the formation of dense interfacial films, enhancing the surface activity of water solutions. Then, the anion surfmer sodium dodecylbenzenesulfonate interacted with the hydrophobic micro blocks on the molecular chains to form mixed micelles, which accelerated the interchain association and enhanced the polymer surface activity. The novel polymeric micelle with higher viscosifying ability and surface activity was expected to be a promising oil drive agent for tertiary oil recovery.

Poly(ethylene glycol-co-1,4-cyclohexanedimethanol terephthalate) random copolymers: effect of copolymer composition and microstructure on the thermal properties and crystallization behavior

The glass transition temperature of the statistically random PETG copolymers increased linearly with the increasing CT content. An increase in the average sequence length resulted in a higher melting temperature.

A Colorimetric Method for Monitoring Tryptic Digestion Prior to Shotgun Proteomics

Tryptic digestion is an important preanalytical step in shotgun proteomics because inadequate or excessive digestion can result in a failed or incomplete experiment. Unfortunately, this step is not routinely monitored before mass spectrometry because methods available for protein digestion monitoring either are time/sample consuming or require expensive equipment. To determine if a colorimetric method (ProDM Kit) can be used to identify the extent of tryptic digestion that yields the best proteomics outcome, plasma and serum digested for 8 h and 24 h were screened with ProDM, Bioanalyzer, and LC/MS/MS, and the effect of digestion on the number of proteins identified and sequence coverage was compared. About 6% and 16% less proteins were identified when >50% of proteins were digested in plasma and serum, respectively, compared to when ~46% of proteins were digested. Average sequence coverage for albumin, haptoglobin, and serotransferrin after 2 h, 8 h, and 24 h digestion was 52%, 45%, and 45% for serum and 54%, 47%, and 42% for plasma, respectively. This paper reiterates the importance of optimizing the tryptic digestion step and demonstrates the extent to which ProDM can be used to monitor and standardize protein digestion to achieve better proteomics outcomes.

Relationship between Sequence Length and Thermal Properties of Poly(ethylene Terephthalate-Co-4, 4’-Bibenzoate) (PETBB)

Poly(ethylene terephthalate-co-4,4’-bibenzoate)s (PETBBs) with 0-25mol% bibenzoate unit were prepared from terephthalic acid (PTA), 4,4'- bibenzoic acid (BBA) and ethylene glycol (EG). The chemical composition and number-average sequence length of the resultant PETBBs were investigated by 13C-NMR. It was improved that the chemical composition of PETBBs is identical with the feed ratio, and the number-average sequence length of PET segment (LPET) becomes reduced with increasing BBA unit. The molecular weights of PETBBs reaches the high level for practical use. DSC analysis explains that the glass transition temperature (Tg) increases almost linearly and the crystallization becomes difficulty with increasing content of BBA unit. X-ray diffraction also illustrates that both crystallinity and crystal size reduced as more BBA unit is incorporated. Moreover, the relationship between the number-average sequence length and the melting temperature was investigated. The linear correlation between the number-average sequence length (LPET) and the melting temperature was observed.

A central limit theorem for randomly indexed m-dependent random variables

In this note, we prove a central limit theorem for the sum of a random number Nn of m-dependent random variables. The sequence Nn and the terms in the sum are not assumed to be independent. Moreover, the conditions of the theorem are not stringent in the sense that a simple moving average sequence serves as an example.

Nesting biology and DNA barcode analysis of Ceratina dupla and C. mikmaqi, and comparisons with C. calcarata (Hymenoptera: Apidae: Xylocopinae)

Using DNA barcode analysis, nest collections, and pan-trapping we compared molecular differences, nesting behaviour, and phenology of three of the four species of Ceratina Latreille present in the Niagara Region of southern Ontario, Canada: C. dupla Say, C. calcarata Robertson, and C. mikmaqi Rehan and Sheffield. Ceratina dupla and C. mikmaqi were separated by five fixed nucleotide differences and an average sequence divergence of 1.86%. In our population, C. mikmaqi and C. calcarata were common and C. dupla was rare. Ceratina dupla nested earlier than C. mikmaqi and C. calcarata, and sometimes produced a second brood in late July – early August. Each species constructed linear nests in the pith of dead twigs, C. mikmaqi and C. dupla usually in Fuller's teasel (Dipsacus fullonum L.; Dipsacaceae) and C. calcarata usually in raspberry (Rubus L.; Rosaceae). Genetically distinct, each species occupies a slightly different niche in the Niagara bee assemblage.