Contributions to the early life histories of alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis): Rearing, identification, ageing, and ecology

Early life histories of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis), collectively known as river herring, are poorly documented for Chesapeake Bay populations. Improved knowledge of these early life histories potentially will aid fisheries, habitat and resource management. Investigations were conducted following two lines. First, alewife and blueback herring larvae reared from eggs were used to investigate methods for species identification and to validate the otolith increment method for age determination. Blueback herring larvae hatched from naturally-spawned eggs were reared to age 24 d. Alewife and blueback herring larvae hatched from artificially-spawned eggs were reared to age 32 d and age 37 d. Alewife larvae exhibited paired melanophores laterally along the notochord starting at about 15 mm SL, contracted xanthophores dorsally on the head, and lacked xanthochrome at the caudal fin base. Blueback herring exhibited one or two melanophores dorsally on the notochord starting at about 11 mm SL, relatively large xanthophores dorsally on the head, and xanthochrome at the caudal fin base. Other pigment variation was found. Estimated deposition of otolith increments was 1.16 and 0.90 increment d&\sp{lcub}-1{rcub}& for blueback herring larvae and 0.90 increment d&\sp{lcub}-1{rcub}& for alewife larvae. Increment enumeration was affected by otolith microstructure appearance, but estimated deposition did not differ statistically from one increment d&\sp{lcub}-1{rcub}&. Second, larval river herring distributions, abundances, growth rates, and hatch dates in the Pamunkey River tidal freshwater reach were analyzed. Distributions and abundances of zooplankton prey for river herring larvae were also analyzed. High abundances in two tidal creeks suggested that larvae occur in these areas from about late April to about mid-May. Larval river herring growth, pooled across seasons, was faster in the tidal creeks, 0.46 mm d&\sp{lcub}-1{rcub}&, than the mainstem river, 0.34 mm d&\sp{lcub}-1{rcub}&. Faster growth in the tidal creeks may increase survival by reducing the larval stage duration. Older larvae, pooled across habitats, grew faster than younger larvae, 0.59 mm d&\sp{lcub}-1{rcub}& and 0.35 mm d&\sp{lcub}-1{rcub}&. Larvae with relatively earlier hatch dates were associated primarily with the mainstem river while larvae with relatively later hatch dates were associated primarily with the tidal creeks. Zooplankton abundances were higher in the tidal creeks than the mainstem river

Ecology and dynamics of river herring larvae in the Pamunkey River. Virginia: : June 1, 1989 - December 31, 1991

The early life histories of anadromous herrings (Alosa species) in tidal freshwater are poorly understood. Knowledge of the ecology of anadromous herring larvae in tidal freshwater ecosystems is important in order to understand factors which cause population fluctuations, to mitigate potential adverse effects of modifications to these systems, and to facilitate restoration of populations. This investigation was undertaken to examine the distribution and relative abundance of larval river herring (alewife, Alosa pseudoharengus, and blueback herring, A. aestivalis) and their potential zooplankton prey in tidal freshwater of the Pamunkey River, Virginia, and to quantify growth of larvae between locations that may differ in prey availability within the study area

Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity

To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1′-β-d-2′-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1′-β-d-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor–donor–acceptor and acceptor–acceptor–donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells

Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern

To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA

Xenobiology: A new form of life as the ultimate biosafety tool

Synthetic biologists try to engineer useful biological systems that do not exist in nature. One of their goals is to design an orthogonal chromosome different from DNA and RNA, termed XNA for xeno nucleic acids. XNA exhibits a variety of structural chemical changes relative to its natural counterparts. These changes make this novel information-storing biopolymer “invisible” to natural biological systems. The lack of cognition to the natural world, however, is seen as an opportunity to implement a genetic firewall that impedes exchange of genetic information with the natural world, which means it could be the ultimate biosafety tool. Here I discuss, why it is necessary to go ahead designing xenobiological systems like XNA and its XNA binding proteins; what the biosafety specifications should look like for this genetic enclave; which steps should be carried out to boot up the first XNA life form; and what it means for the society at large

Highly specific unnatural base pair systems as a third base pair for PCR amplification

Toward the expansion of the genetic alphabet of DNA, we present highly efficient unnatural base pair systems as an artificial third base pair for PCR. Hydrophobic unnatural base pair systems between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) were fine-tuned for efficient PCR, by assessing the amplification efficiency and fidelity using different polymerases and template sequence contexts and modified Px bases. Then, we found that some modifications of the Px base reduced the misincorporation rate of the unnatural base substrates opposite the natural bases in templates without reducing the Ds–Px pairing selectivity. Under optimized conditions using Deep Vent DNA polymerase, the misincorporation rate was extremely low (0.005%/bp/replication), which is close to that of the natural base mispairings by the polymerase. DNA fragments with different sequence contexts were amplified ∼1010-fold by 40 cycles of PCR, and the selectivity of the Ds–Px pairing was >99.9%/replication, except for 99.77%/replication for unfavorable purine-Ds-purine motifs. Furthermore, >97% of the Ds–Px pair in DNA survived in the 1028-fold amplified products after 100-cycle PCR (10 cycles repeated 10 times). This highly specific Ds–Px pair system provides a framework for new biotechnology

An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules

Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into DNA. This system can be applied to conventional PCR protocols employing DNA templates containing unnatural bases, natural and unnatural base triphosphates, and a 3′→5′ exonuclease-proficient DNA polymerase. For highly faithful and efficient PCR amplification involving the unnatural base pairing, we identified the natural-base sequences surrounding the unnatural bases in DNA templates by an in vitro selection technique, using a DNA library containing the unnatural base. The system facilitates the site-specific incorporation of a variety of modified unnatural bases, linked with functional groups of interest, into amplified DNA. DNA fragments (0.15 amol) containing the unnatural base pair can be amplified 107-fold by 30 cycles of PCR, with <1% total mutation rate of the unnatural base pair site. Using the system, we demonstrated efficient PCR amplification and functionalization of DNA fragments for the extremely sensitive detection of zeptomol-scale target DNA molecules from mixtures with excess amounts (pmol scale) of foreign DNA species. This unnatural base pair system will be applicable to a wide range of DNA/RNA-based technologies

The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world

Biotechnology has empirically established that it is easier to construct and evaluate variant genes and proteins than to account for the emergence and function of wild-type macromolecules. Systematizing this constructive approach, synthetic biology now promises to infer and assemble entirely novel genomes, cells and ecosystems. It is argued here that the theoretical and computational tools needed for this endeavor are missing altogether. However, such tools may not be required for diversifying organisms at the basic level of their chemical constitution by adding, substituting or removing elements and molecular components through directed evolution under selection. Most importantly, chemical diversification of life forms could be designed to block metabolic cross-feed and genetic cross-talk between synthetic and wild species and hence protect natural habitats and human health through novel types of containment