Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.     

An electrogenetic toggle switch model

Synthetic biology uses molecular biology to implement genetic circuits that perform computations. These circuits can process inputs and deliver outputs according to predefined rules that are encoded, often entirely, into genetic parts. However, the field has recently begun to focus on using mechanisms beyond the realm of genetic parts for engineering biological circuits. We analyse the use of electrogenic processes for circuit design and present a model for a merged genetic and electrogenetic toggle switch operating in a biofilm attached to an electrode. Computational simulations explore conditions under which bistability emerges in order to identify the circuit design principles for best switch performance. The results provide a basis for the rational design and implementation of hybrid devices that can be measured and controlled both genetically and electronically.     

THE FINE STRUCTURE OF THE DNP COMPONENT OF THE NUCLEUS : An Electron Microscopic Study Utilizing Autoradiography to Localize DNA Synthesis

In the present investigation, the sites of deoxyribonucleic acid (DNA) synthesis and the fate of labeled deoxyribonucleoprotein (DNP) were studied in autoradiographs of ultrathin sections viewed with the electron microscope. Tritiated thymidine was employed as a label for DNA in the nuclei of proliferating cells of regenerating salamander limbs. In the autoradiographic method reported here, dilute NaOH was used to remove the gelatin of the emulsion after exposure and development. The exposed silver grains are not displaced by this treatment and the resolution of fine structure in the underlying section is greatly improved. Our observations suggest that the DNP component is a meshwork of interconnected filaments 50 to 75 A in diameter, which may be cross-linked to form what Frey-Wyssling would term a "reticular gel." The filamentous DNP meshwork is dispersed throughout the interphase nucleus during DNA synthesis, whereas in chromosomes, which are relatively inert metabolically, the meshwork is denser and is aggregated into compact masses. Dense chromatin centers in interphase nuclei are similar in fine structure to chromosomes and are also inert with respect to DNA synthesis. In the Discussion, the structure of the filamentous meshwork in chromatin is compared with that in chromosomes, and speculations are made as to the functional significance of the variations in DNP fine structure observed.     

Morphological and Chemical Studies of the Spores and Parasporal Bodies of Bacillus laterosporus

Spores of Bacillus laterosporus were studied to determine the chemical and morphological nature of their basophilic canoe-shaped parasporal bodies. An unusually high phosphorus content of these spores compared to other Bacillus species appeared to be associated with the parasporal body. Preparations of these "canoes" still attached to the spore coats were indeed high in phosphorus, but also in nitrogen. They were free of lipide-soluble and nucleic acid phosphorus and stained for protein. Some 50 per cent of the total nitrogen, but only 6 to 10 per cent of the total P were liberated by extraction with alkali-thioglycollate (pH 11.5) or alkali alone (pH 12.2–12.5). Proteinaceous material was recovered from these alkaline extracts and electron microscopy indicated that there had been a marked loss of "canoe" substance. Extraction with acid, removed some 80 per cent of the phosphorus associated with the "canoes" as orthophosphate. Chromatographic analyses for amino acids indicated some 14 ninhydrin-positive spots in the canoe-coat preparations whereas the whole spores contained at least 16.     

Radiolabelling Studies of Lipids in the Marine Cryptomonad Chroomonas salina in Relation to Fatty Acid Desaturation

Cells of Chroomonas salina were exposed to [¹⁴C]acetate, [^l4C]16:0,[¹⁴C]18:0, [¹⁴C]18:1(n-9), [¹⁴C]18:2(n–6) or [¹⁴C]18:3(n–3)for 1 h and then incubated for 24 h in non-radioactive medium.At the end of the pulse period, non-glycolipid polar lipidscontained the highest proportions of radioactivity incorporatedfrom [¹⁴C]acetate and [¹⁴C]18:3(n–3) whereas with [¹⁴C]16:0,[¹⁴C]18:1 and [¹⁴C]18:2(n–6), triacylglycerols were mosthighly labelled. ¹⁴C-18:0 was recovered mainly as non-esterifiedfatty acid. Monogalactosyldiacylglycerol initially contained17% of label incorporated from [¹⁴C]acetate but less than 3%of that from [¹⁴C]fatty acids. With all substrates, excluding[¹⁴C]18:0, a gradual transfer of label from polar lipids totriacylglycerols was observed during the chase period. Saturatesand monoenes synthesised from [¹⁴C]acetate were mostly transferedfrom phospholipids and glycolipids to neutral lipid withoutfurther desaturation. Most of the incorporated ¹⁴C-fatty acidsremained unchanged and only with [¹⁴C]18:3(n–3) was substantialamounts of label recovered in penta- and hexaenoic fatty acids.The results indicate that, under the conditions of the study,lipid synthesis in the algae was heavily dominated by triacylglycerolformation and that the mechanisms of fatty acid desaturationin this species may differ from those in higher plants. (Received December 10, 1991; Accepted March 6, 1992)     

COMPONENTS OF PHENOTYPIC SELECTION: POLLEN EXPORT AND FLOWER COROLLA WIDTH IN IPOMOPSIS AGGREGATA

In the hummingbird-pollinated herb Ipomopsis aggregata, selection through male function during pollination favors wide corolla tubes. We explored the mechanisms behind this selection, using phenotypic selection analysis to compare effects of corolla width on two components of male pollination success, pollinator visit rate and pollen exported per visit. During single visits by captive hummingbirds, flowers with wider corollas exported more pollen, and more dye used as a pollen analogue, to stigmas of recipient flowers. Corolla width was less strongly related to visit rate in the field, and had no direct effect on visit rate after nectar production and corolla length were controlled for. Moreover, the phenotypic selection differential was 80% higher for the effect on pollen exported per visit, suggesting that this is the more important mechanism of selection.     

FLORAL INITIATION AND EARLY DEVELOPMENT IN ERIGERON PHILADELPHICUS (ASTERACEAE)

The order of floral initiation and subsequent organogeny of Erigeron philadelphicus L. (Asteraceae: Astereae) was found to deviate from the acropetal pattern generally reported for the Asteraceae. Light micrographs show periclinal divisions in the first, second, and deeper subsurface layers of cells on the flanks of the inflorescence apex as the earliest evidence of floral initiation. Scanning electron microscope micrographs indicate that the disk flowers appear first and arise as small protuberances approximately one-third of the way up the previously and undifferentiated highly convex inflorescence apex. A succession of disk flowers arises acropetally in a complex anthotaxy characterized by about 21 dextrorse and 12–15 sinistrorse parastichies (although this pattern is obscured at the apex). After one to three disk flowers have been initiated in each parastichy, the first ray flower initials can be seen to initiate in sites proximal to the oldest and largest disk flowers. Additional ray flowers then initiate basipetally following the dextrorse parastichies established by the disk flowers. Overall floral initiation on the inflorescence apex proceeds acropetally for the disk flowers and basipetally for the ray flowers until the available space is filled. Floral development adheres to the same plan—proceeding bidirectionally on the inflorescence meristem with the oldest and most complete flowers of both types located on the equator established at initiation.     

PHYLOGENY OF THE ULVOPHYCEAE (CHLOROPHYTA): CLADISTIC ANALYSIS OF NUCLEAR-ENCODED rRNA SEQUENCE DATA1

Cladistic analysis of nuclear-encoded rRNA sequence data provided us with the basis for some new hypotheses of relationships within the green algal class Ulvophyceae. The orders Ulotrichales and Ulvales are separated from the clade formed by the remaining orders of siphonous and siphonocladous Ulvophyceae (Caulerpales, Siphonocladales /Cladophorales [S/C] complex, and the Dasycladales), by the Chlorophyceae and Pleurastrophyceae. Our results suggest that the Ulvophyceae is not a monophyletic group. Examination of inter- and intra-ordinal relationships within the siphonous and siphonocladous ulvophycean algae revealed that Cladophora, Chaetomorpha, Anadyomene, Microdictyon, Cladophoropsis and Dictyosphaeria form a clade. Thus the hypothesis, based on ultrastructural features, that the Siphonocladales and Cladophorales are closely related is supported. Also, the Caulerpales is a monophyletic group with two lineages; Caulerpa, Halimeda, and Udotea comprise one, and Bryopsis and Codium comprise the other. The Dasycladales (Cymopolia and Batophora) also forms a clade, but this clade is not inferred to be the sister group to the S/C complex as has been proposed. Instead, it is either the sister taxon to the Caulerpales or basal to the Caulerpales and S/C clade The Trentepohliales is also included at the base of the siphonous and siphonocladous ulvophycean clade. The Pleurastrophyceae, which, like the Ulvophyceae, posses a counter-clockwise arrangement of flagellar basal bodies, are more closely related to the Chlorophyceae than to the Ulvophyceae based on rRNA sequences. Thus, the arrangement of basal bodies does not diagnose a monophyletic group. Previously reported hypotheses of phylogenetic relationships of ulvophycean algae were tested. In each case, additional evolutionary steps were required to obtain the proposed relationships. Relationships of ulvophycean algae to other classes of green algae are discussed.