Genotype But Not Body Shape Predicts River Migration Success in Atlantic Salmon.

Migratory species typically undertake demanding long-distance journeys, across different habitat types during which they are exposed to multiple natural and anthropogenic stressors. Mortality during migration is typically high and may be human induced. Understanding individual responses to these selection pressures is rarely attempted because of the challenges of relating individual phenotypic and genetic data to migration success.

Lake shape and the characteristics of migration behavior modify Atlantic salmon smolt migration success through lakes.

Migration is a high-risk behavior. For the Atlantic salmon, Salmo salar, migrating from its river nursery area to marine feeding grounds, the magnitude of risk varies with habitat type. Passage through lakes, in particular, is associated with low rates of migration success.

HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability.

G-quadruplexes (G4s) form throughout the genome and influence important cellular processes. Their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected role for the double-stranded DNA (dsDNA) translocase helicase-like transcription factor (HLTF) in responding to G4s.

Negative DNA supercoiling induces genome-wide Cas9 off-target activity.

CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an important consideration for therapeutic applications. We have previously shown that force-stretching DNA induces off-target activity and hypothesized that distortions of the DNA topology in vivo, such as negative DNA supercoiling, could reduce Cas9 specificity. Using single-molecule optical-tweezers, we demonstrate that negative supercoiling λ-DNA induces sequence-specific Cas9 off-target binding at multiple sites, even at low forces.

Is shape in the eye of the beholder? Assessing landmarking error in geometric morphometric analyses on live fish.

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon ( L.) from two rivers.

Search and processing of Holliday junctions within long DNA by junction-resolving enzymes.

Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction.

CRISPR/Cas9 On- and Off-Target Activity Using Correlative Force and Fluorescence Single-Molecule Microscopy.

The discovery of CRISPR/Cas9 as an easily programmable endonuclease heralds a new era of genetic manipulation. With this comes the prospect of novel gene therapy approaches, and the potential to cure previously untreatable genetic diseases. However, reports of spurious off-target editing by CRISPR/Cas9 pose a significant hurdle to realizing this potential.

An opinion piece: the evolutionary and ecological consequences of changing selection pressures on marine migration in Atlantic salmon.

There are strong signals that the selection forces favouring the expression of long-distance sea migration by Atlantic salmon (Salmo salar) are changing. Unlike many other behavioural traits, the costs of migration are incurred before any fitness benefits become apparent to the migrant. The expression of this behaviour has thus been shaped by selection forces over multiple generations and cannot respond to short interval (within a single generation) environmental change as many other behavioural traits can.

HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51.

DNA double-stranded breaks (DSBs) are deleterious lesions, and their incorrect repair can drive cancer development. HELQ is a superfamily 2 helicase with 3' to 5' polarity, and its disruption in mice confers germ cells loss, infertility and increased predisposition to ovarian and pituitary tumours. At the cellular level, defects in HELQ result in hypersensitivity to cisplatin and mitomycin C, and persistence of RAD51 foci after DNA damage.

Cas12a target search and cleavage on force-stretched DNA.

Using optical tweezers, we investigate target search and cleavage by CRISPR-Cas12a on force-stretched λ-DNA. Cas12a uses fast, one-dimensional hopping to locate its target. Binding and cleavage occur rapidly and specifically at low forces (≤5 pN), with a 1.

A Minimal Load-and-Lock Ru Luminescent DNA Probe.

Threading intercalators bind DNA with high affinities. Here, we describe single-molecule studies on a cell-permeant luminescent dinuclear ruthenium(II) complex that has been previously shown to thread only into short, unstable duplex structures. Using optical tweezers and confocal microscopy, we show that this complex threads and locks into force-extended duplex DNA in a two-step mechanism.

Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis.

Here, we describe a rapid and versatile protocol to generate gapped DNA substrates for single-molecule (SM) analysis using optical tweezers via site-specific Cas9 nicking and force-induced melting. We provide examples of single-stranded (ss) DNA gaps of different length and position. We outline protocols to visualize these substrates by replication protein A-enhanced Green Fluorescent Protein (RPA-eGFP) and SYTOX Orange staining using commercially available optical tweezers (C-TRAP).

Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins.

Homologous recombination (HR) is an essential DNA double-strand break (DSB) repair mechanism, which is frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated, resected DNA and catalyzes strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain.

Are we designing fishways for diversity? Potential selection on alternative phenotypes resulting from differential passage in brown trout.

Fishways are commonly employed to improve river connectivity for fishes, but the extent to which they cater for natural phenotypic diversity has been insufficiently addressed. We measured differential upstream passage success of three wild brown trout (Salmo trutta) phenotypes (anadromous, freshwater-resident adult and parr-marked), encompassing a range of sizes and both sexes, at a Larinier superactive baffle fishway adjacent to a flow-gauging weir, using PIT telemetry (n = 160) and radio telemetry (n = 53, double tagged with PIT tags). Fish were captured and tagged downstream of the weir in the autumn pre-spawning period, 2017, in a tributary of the River Wear, England, where over 95% of tributary spawning habitat was available upstream of the weir.

The Use of Small-Sided Games as an Aerobic Fitness Assessment Supplement Within Elite Level Professional Soccer.

The purpose of this investigation was to quantify the association between 5 vs. 5 small sided games (SSG) running performance and physiological performance during the Yo-YoIR1 test to ascertain the utility of SSGs as a potential fitness test modality within elite professional soccer players. Twenty-three (n = 23) elite male professional soccer players (mean ± SD age 25.

A conserved ATP- and Scc2/4-dependent activity for cohesin in tethering DNA molecules.

Sister chromatid cohesion requires cohesin to act as a protein linker to hold chromatids together. How cohesin tethers chromatids remains poorly understood. We have used optical tweezers to visualize cohesin as it holds DNA molecules.

Comparative genomics of 10 new species.

The nematode has been central to the understanding of metazoan biology. However, is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus , many of which await formal species description.

DNA stretching induces Cas9 off-target activity.

CRISPR/Cas9 is a powerful genome-editing tool, but spurious off-target edits present a barrier to therapeutic applications. To understand how CRISPR/Cas9 discriminates between on-targets and off-targets, we have developed a single-molecule assay combining optical tweezers with fluorescence to monitor binding to λ-DNA. At low forces, the Streptococcus pyogenes Cas9 complex binds and cleaves DNA specifically.

Field testing a novel high residence positioning system for monitoring the fine-scale movements of aquatic organisms.

Acoustic telemetry is an important tool for studying the behaviour of aquatic organisms in the wild.VEMCO high residence (HR) tags and receivers are a recent introduction in the field of acoustic telemetry and can be paired with existing algorithms (e.g.

Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease.

The CRISPR-Cas9 RNA-guided endonuclease system allows precise and efficient modification of complex genomes and is continuously developed to enhance specificity, alter targeting and add new functional moieties. However, one area yet to be explored is the base chemistry of the associated RNA molecules. Here we show the design and optimisation of hybrid DNA-RNA CRISPR and tracr molecules based on structure-guided approaches.

Paper #43: A Multi-Center Assessment of Neurological Changes in Distraction-Based Surgery for Early-Onset Scoliosis.

In a series of 748 traditional growing rod patients the overall rate of post-op neurological deficit was 0.45%, and the rate of permanent deficit was 0.05%.

Analyzing Change in Nursing Home Information Technology Sophistication: A 2-Year Survey.

Nursing home (NH) health information technology (IT) is becoming more prevalent across the country. Currently, a national sample of NHs is being surveyed for 3 consecutive years to determine trends in NH IT sophistication (e.g.

Unloading of homologous recombination factors is required for restoring double-stranded DNA at damage repair loci.

Cells use homology-dependent DNA repair to mend chromosome breaks and restore broken replication forks, thereby ensuring genome stability and cell survival. DNA break repair via homology-based mechanisms involves nuclease-dependent DNA end resection, which generates long tracts of single-stranded DNA required for checkpoint activation and loading of homologous recombination proteins Rad52/51/55/57. While recruitment of the homologous recombination machinery is well characterized, it is not known how its presence at repair loci is coordinated with downstream re-synthesis of resected DNA We show that Rad51 inhibits recruitment of proliferating cell nuclear antigen (PCNA), the platform for assembly of the DNA replication machinery, and that unloading of Rad51 by Srs2 helicase is required for efficient PCNA loading and restoration of resected DNA As a result, srs2Δ mutants are deficient in DNA repair correlating with extensive DNA processing, but this defect in srs2Δ mutants can be suppressed by inactivation of the resection nuclease Exo1.