Flooding and dam operations facilitate rapid upstream migrations of native and invasive fish species on a regulated large river.

Dams commonly restrict fish movements in large rivers but can also help curtail the spread of invasive species, such as invasive bigheaded carps (Hypophthalmichthys spp). To determine how dams in the upper Mississippi River (UMR) affect large-scale invasive and native fish migrations, we tracked American paddlefish (Polyodon spathula) and bigheaded carp across > 600 river km (rkm) and 16 navigation locks and dams (LD) of the UMR during 2 years with contrasting water levels. In 2022, a low-water year, both native paddlefish and invasive bigheaded carp had low passage rates (4% and 0.

Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy.

Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers.

Comparison of K- and N- Mutagenic Hot Spots for UVC Damage.

It has been well established that mutations in K- and N- proto-oncogenes can convert them into active oncogenes. Current molecular cancer research has been focused on determining the key steps by which cellular genes become oncogenes and not on the underlying and fundamental chemical damage mechanism and susceptibility to damage. In this study, we investigate the damage hot spots present in the N- and K- genes upon exposure to UVC radiation.

Probing DNA damage induced by common antiviral agents using multiple analytical techniques.

Hepatocellular carcinoma is one of the most common malignant tumors in the world. Chronic hepatitis B and C infections are the most common etiologies of hepatocellular carcinoma worldwide. In this study, we explore the potential DNA damaging effect of some FDA-approved antiviral drugs which may be able to serve as anticancer agents for hepatocellular carcinoma, in order to better elucidate their mode of action.

Characterization of the binding interactions between EvaGreen dye and dsDNA.

Understanding the dsDNA·EG binding interaction is important because the EvaGreen (EG) dye is increasingly used in real-time quantitative polymerase chain reaction, high resolution melting analysis, and routine quantification of DNA. In this work, a binding isotherm for the interactions of EG with duplex DNA (poly-dA·poly-dT) has been determined from the absorption and fluorescence spectra of the EG and dsDNA·EG complex. The isotherm has a sigmoidal shape and can be modeled with the Hill equation, indicating positive cooperativity for the binding interaction.

A luminescent probe of mismatched DNA hybridization: Location and number of mismatches.

The human genome is susceptible to change; base mismatches can arise from damaged DNA, replication errors, and spontaneous mutation, and have the potential to cause apoptosis, carcinogenesis, and mutagenesis. Many techniques have been developed for DNA mismatch detection, but many of these methods have complex, time-consuming procedures and are limited to the detection of specific types of DNA mismatches. In this work, we present a general method for the simple and sensitive nucleobase-sensitized luminescent detection of mismatches in double-stranded DNA (dsDNA) using terbium ions.

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited-State Structural Dynamics of Uracil More than C6 Substituents.

Resonance Raman derived initial excited-state structural dynamics provide insight into the photochemical mechanisms of pyrimidine nucleobases, in which the photochemistry appears to be dictated by the C5 and C6 substituents. The absorption and resonance Raman spectra and excitation profiles of 5,6-dideuterouracil were measured to further test this photochemical dependence on the C5 and C6 substituents. The resulting set of excited-state reorganization energies of the observed internal coordinates were calculated and compared to those of other 5- and 6-substituted uracils.

Effects of ethanol on systemic hemodynamics in a porcine model of accidental hypothermia.

Objectives: Accidental hypothermia is frequently associated with ethanol intoxication. Each has independent effects on systemic hemodynamics, but their combined effects are poorly understood. We aimed to describe the hemodynamic effects of ethanol intoxication in a model of severe hypothermia and rewarming.

Initial excited-state structural dynamics of 6-substituted uracil derivatives: femtosecond angle and bond lengthening dynamics in pyrimidine nucleobase photochemistry.

Substituents on the pyrimidine ring of nucleobases appear to play a major role in determining their initial excited-state structural dynamics and resulting photochemistry. To better understand the determinants of nucleobase initial excited-state structural dynamics, we have measured the absorption and resonance Raman excitation profiles of 6-deuterouracil (6-d-U) and 6-methyluracil (6-MeU). Simulation of the resonance Raman excitation profiles and absorption spectrum with a self-consistent, time-dependent formalism shows the effect of the deuterium and methyl group on the photochemically active internal coordinates, i.

Initial excited-state dynamics of an N-alkylated indanylidene-pyrroline (NAIP) rhodopsin analog.

N-Alkylated indanylidene-pyrroline-based molecular switches mimic different aspects of the light-induced retinal chromophore isomerization in rhodopsin: the vertebrate dim-light visual pigment. In particular, they display a similar ultrashort excited-state lifetime, subpicosecond photoproduct appearance time, and photoproduct vibrational coherence. To better understand the early light-induced dynamics of such systems, we measured and modeled the resonance Raman spectra of the Z-isomer of the N-methyl-4-(5'-methoxy-2',2'-dimethyl-indan-1'-ylidene)-5-methyl-2,3-dihydro-2H-pyrrolium (NAIP) switch in methanol solution.

Identifying correlates of success and failure of native freshwater fish reintroductions.

Reintroduction of imperiled native freshwater fish is becoming an increasingly important conservation tool amidst persistent anthropogenic pressures and new threats related to climate change. We summarized trends in native fish reintroductions in the current literature, identified predictors of reintroduction outcome, and devised recommendations for managers attempting future native fish reintroductions. We constructed random forest classifications using data from 260 published case studies of native fish reintroductions to estimate the effectiveness of variables in predicting reintroduction outcome.

Initial excited-state structural dynamics of 5,6-dimethyluracil from resonance Raman spectroscopy.

In order to understand the effect of methyl substitution patterns on the initial excited-state structural dynamics of uracil derivatives, we measured the resonance Raman spectra of 5,6-dimethyluracil (5,6-DMU). The results show that the resonance Raman spectrum is a combination of that of 5-methyl- and 6-methyluracil. The resonance Raman excitation profiles (RREPs) and absorption spectrum are simulated with a self-consistent, time-dependent formalism to yield the excited-state slopes and broadening parameters.

Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids.

Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)).

Chimeric RNA-DNA molecular beacons for quantification of nucleic acids, single nucleotide polymophisms, and nucleic acid damage.

Single nucleotide polymorphisms (SNPs) are the main cause for variations in the human genome. DNA lesions, such as cyclobutane pyrimidine dimers (CPDs), [6-4] pyrimidine-pyrimidinones, dewar pyrimidinones, and photohydrates, can subsequently lead to mutagenesis, carcinogenesis, and cell death. Much effort has focused on methods for detecting DNA, SNPs, or damaged nucleic acids.

Multiplexed, UVC-induced, sequence-dependent DNA damage detection.

The exposure of DNA to ultraviolet (UV) radiation causes sequence-dependent damage. Thus, there is a need for an analytical technique that can detect damage in large numbers of DNA sequences simultaneously. In this study, we have designed an assay for UVC-induced DNA damage in multiple oligonucleotides simultaneously by using a 96-well plate and a novel automated sample mover.

Initial excited-state structural dynamics of thymine derivatives.

Thymine is one of the pyrimidine nucleobases found in DNA. Upon absorption of UV light, thymine forms a number of photoproducts, including the cyclobutyl photodimer, the pyrimidine pyrimidinone [6-4] photoproduct and the photohydrate. Here, we use UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of the N(1)-substituted thymine derivatives N(1)-methylthymine, thymidine, and thymidine 5'-monophosphate in an effort to understand the role of the N1 substituent in determining the excited-state structural dynamics and the subsequent photochemistry.

2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage.

Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage.

Molecular beacon probes for the detection of cisplatin-induced DNA damage.

Cisplatin (cis-diamminedichloroplatinum(II)) causes crosslinking of DNA at AG and GG sites in cellular DNA, inhibiting replication, and making it a useful anti-cancer drug. Several techniques have been used previously to detect nucleic acid damage but most of these tools are labour-intensive, time-consuming, and/or expensive. Here, we describe a sensitive, robust, and quantitative tool for detecting cisplatin-induced DNA damage by using fluorescent molecular beacon probes (MB).

Molecular beacon probes of oligonucleotides photodamaged by psoralen.

Ultraviolet A (UVA)-irradiated 4'-hydroxymethyl-4,5',8-trimethyl psoralen (HMT) in the presence of a poly-dT(17) and dA(7) TTA(8) oligonucleotides produces HMT-dT(17) and HMT-dA(7) TTA(8) adducts in aqueous solution. In this article, we determine whether these HMT-dT(17) and HMT-dA(7) TTA(8) adducts can be detected with a molecular beacon (MB) probe. We measure the degree of damage in dT(17) and dA(7) TTA(8) solutions containing UVA-activated HMT via monitoring the decrease in MB fluorescence.

Initial excited-state structural dynamics of 2'-deoxyguanosine determined via UV resonance Raman spectroscopy.

The resonance Raman spectra of 2'-deoxyguanosine, a DNA nucleoside, were measured in aqueous solution at wavelengths throughout its 260 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism with two electronic states yielded the initial excited-state structural dynamics in both states. The vibrational modes containing the N(7)═C(8) stretching and C(8)-H bending internal coordinates were found to exhibit significant initial structural dynamics upon photoexcitation to either state and are coincident with the photochemical reaction coordinate involving the formation of the 2'-deoxyguanosine cation radical.

Initial excited-state structural dynamics of 9-methyladenine from UV resonance Raman spectroscopy.

The photophysics and photochemistry of nucleobases are the factors governing the photostability of DNA and RNA, since they are the UV chromophores in nucleic acids. Because the formation of photoproducts involves structural changes in the excited electronic state, we study here the initial excited-state structural dynamics of 9-methyladenine (9-MeA) by using UV resonance Raman (UVRR) spectroscopy. UV resonance Raman intensities are sensitive to the initial excited-state structural dynamics of molecules.

Self-quenching smart probes as a platform for the detection of sequence-specific UV-induced DNA photodamage.

Molecular beacons (MBs) are sensitive probes for many DNA sequence-specific applications, such as DNA damage detection, but suffer from technical and cost limitations. We have designed smart probes with self-quenching properties as an alternative to molecular beacons to monitor sequence-specific UV-induced photodamage of oligonucleotides. These probes have similar stem-loop structural characteristics as molecular beacons, but quenching is achieved instead via photoinduced intramolecular electron transfer by neighboring guanosine residues.

The effect of tryptophan on UV-induced DNA photodamage.

Trp-DNA adducts resulting from UV irradiation of pyrimidine bases and nucleotides in the presence of tryptophan (Trp) have been the subject of previous research. However, the relative yield of the adducts compared with the UV screening effect of Trp has not been previously considered. To determine whether Trp-DNA adduct formation or absorption "screening" by Trp is the predominant process when DNA solutions are irradiated with UV light in the presence of Trp, we irradiated Trp-containing DNA oligonucleotide solutions with UVC light and incubated aliquots of those solutions with molecular beacons (MBs) to detect the damage.

Initial excited-state structural dynamics of uracil from resonance Raman spectroscopy are different from those of thymine (5-methyluracil).

To explore the origin of the differences in UV photochemistry of uracil (RNA) and thymine (DNA) nucleobases, we have measured the UV resonance Raman spectra of uracil in aqueous solution at wavelengths throughout the lowest-energy absorption band and analyzed the resulting resonance Raman excitation profiles and absorption spectra using a time-dependent wave-packet formalism to obtain the initial excited-state structural changes. In contrast to thymine, which differs from uracil only by the presence of a methyl group at C(5), most of the resonance Raman intensity and resulting initial excited-state structural dynamics for uracil occur along in-plane hydrogen-bond angle deformation, ring stretching, and carbonyl vibrational modes. Weaker intensities and less significant structural dynamics are observed along the C=C stretching mode.

pH-dependent UV resonance Raman spectra of cytosine and uracil.

Cytosine is a nucleobase found in both DNA and RNA, while uracil is found only in RNA. Uracil has abstractable protons at N3 and N1. Cytosine has only one abstractable proton at N1 but can also accept a proton at N3.