MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling

Background Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. Results After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. Conclusions MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base

Surface-based molecular self-assembly: Langmuir-Blodgett films of amphiphilic Ln(III) complexes

The unique photophysical properties of the Ln(III) series has led to significant research efforts being directed towards their application in sensors. However, for “real-life” applications, these sensors should ideally be immobilised onto surfaces without loss of function. The Langmuir-Blodgett (LB) technique offers a promising method in which to achieve such immobilisation. This mini-review focuses on synthetic strategies for film formation, the effect that film formation has on the physical properties of the Ln(III) amphiphile, and concludes with examples of Ln(III) LB films being used as sensors

The application of chiroptical spectroscopy (circular dichroism) in quantifying binding events in lanthanide directed synthesis of chiral luminescent self-assembly structures

The binding of asymmetrical and optically pure tridentate ligands (L = 1(S) and 1(R)) containing one carboxylic group and 2-naphthyl as an antenna to lanthanide ions (M = La(III) and Eu(III)) was studied in CH3CN, showing the successive formation of M:L, M:L2 and M:L3 stoichiometric species in solution. The europium complexes EuL3 were also synthesised, structurally characterised and their photophysical properties probed in CH3OH and CH3CN. The changes in the chiroptical properties of both 1(S) and 1(R) were used (by circular dichroism (CD) spectroscopy) to monitor the formation of these chiral selfassemblies in solution. While circularly polarised luminescence (CPL) showed the formation of Eu(1(S))3 and Eu(1(R))3 as enantiomers, with high luminescence dissymmetry factors (glum), fitting the CD changes allowed for binding constants to be determined that were comparable to those seen in the analyses of absorbance and luminescence changes

1-Tetra­decyl­pyridinium bromide monohydrate

In the title compound, C19H34N+·Br−·H2O, the dihedral angle between the trans-planar alkyl side chain and the pyridinium ring is 52.73 (7)°. In the crystal structure, O—H⋯Br, C—H⋯Br and C—H⋯O hydrogen bonds form a network, while the hydro­phobic alkyl chains inter­digitate, forming bilayers

pH-regulated nonelectrogenic anion transport by phenylthiosemicarbazones

Gated ion transport across biological membrane is an intrinsic process regulated by protein channels. Synthetic anion carriers (anionophores) have potential applications in biological research, however, previous reported examples are mostly nonspecific, capable of mediating both electrogenic and electroneutral (non-electrogenic) transport processes. Here, we show the transmembrane Cl? transport studies of synthetic phenylthiosemicarbazones mimicking the function of acid-sensing (proton-gated) ion channels. These anionophores have remarkable pH-switchable transport properties with up to 640-fold increase in transport efficacy on going from pH 7.2 to 4.0. This “gated” process is triggered by protonation of the imino nitrogen and concomitant conformational change of the anion binding thiourea moiety from anti to syn. By using a combination of two cationophore-coupled transport assays, with either monensin or valinomycin, we have elucidated the fundamental transport mechanism of phenylthiosemicarbazones which is shown to be non-electrogenic, inseparable H+/Cl? cotransport. This study demonstrates the first examples of pH-switchable non-electrogenic anion transporter

Real‐time biofeedback integrated into neuromuscular training reduces high‐risk knee biomechanics and increases functional brain connectivity: A preliminary longitudinal investigation

Prospective evidence indicates that functional biomechanics and brain connectivity may predispose an athlete to an anterior cruciate ligament injury, revealing novel neural linkages for targeted neuromuscular training interventions. The purpose of this study was to determine the efficacy of a real‐time biofeedback system for altering knee biomechanics and brain functional connectivity. Seventeen healthy, young, physically active female athletes completed 6 weeks of augmented neuromuscular training (aNMT) utilizing real‐time, interactive visual biofeedback and 13 served as untrained controls. A drop vertical jump and resting state functional magnetic resonance imaging were separately completed at pre‐ and posttest time points to assess sensorimotor adaptation. The aNMT group had a significant reduction in peak knee abduction moment (pKAM) compared to controls (p = .03, d = 0.71). The aNMT group also exhibited a significant increase in functional connectivity between the right supplementary motor area and the left thalamus (p = .0473 after false discovery rate correction). Greater percent change in pKAM was also related to increased connectivity between the right cerebellum and right thalamus for the aNMT group (p = .0292 after false discovery rate correction, r2 = .62). No significant changes were observed for the controls (ps > .05). Our data provide preliminary evidence of potential neural mechanisms for aNMT‐induced motor adaptations that reduce injury risk. Future research is warranted to understand the role of neuromuscular training alone and how each component of aNMT influences biomechanics and functional connectivity.Emergent evidence indicates that the risk of anterior cruciate ligament (ACL) injury is, in part, due to central nervous system alterations that could be targeted using neural mechanistic sensorimotor‐based treatments. Young female athletes completed 6 weeks of neuromuscular training while interacting with a real‐time, visual biofeedback stimulus. Our training was designed to reduce the risk of by (a) promoting injury‐resistant movement and (b) strengthening brain functional connectivity. Our data not only indicated that athletes’ biomechanics and brain connectivity were improved following training, but the observed biomechanical improvements were related to distinct, strengthened connectivity within regions important for sensorimotor control. This study supports the use of real‐time biofeedback systems to reduce the risk of ACL injury by leveraging neuroplasticity.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154933/1/psyp13545_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154933/2/psyp13545.pd

WASP family members and formin proteins coordinate regulation of cell protrusions in carcinoma cells

We examined the role of the actin nucleation promoters neural Wiskott-Aldrich syndrome protein (N-WASP) and WAVE2 in cell protrusion in response to epidermal growth factor (EGF), a key regulator in carcinoma cell invasion. We found that WAVE2 knockdown (KD) suppresses lamellipod formation and increases filopod formation, whereas N-WASP KD has no effect. However, simultaneous KD of both proteins results in the formation of large jagged protrusions with lamellar properties and increased filopod formation. This suggests that another actin nucleation activity is at work in carcinoma cells in response to EGF. A mammalian Diaphanous–related formin, mDia1, localizes at the jagged protrusions in double KD cells. Constitutively active mDia1 recapitulated the phenotype, whereas inhibition of mDia1 blocked the formation of these protrusions. Increased RhoA activity, which stimulates mDia1 nucleation, was observed in the N-WASP/WAVE2 KD cells and was shown to be required for the N-WASP/WAVE2 KD phenotype. These data show that coordinate regulation between the WASP family and mDia proteins controls the balance between lamellar and lamellipodial protrusion activity

Long-cavity [Pd2L4]4+ cages and designer 1,8-naphthalimide sulfonate guests: rich variation in affinity and differentiated binding stoichiometry

One of the most appealing features of [Pd2L4]4+ cages is their well-defined cavities, giving binding affinity for specific guests. If seeking to bind larger and more complex guests, an attractive strategy is to lengthen the ligand backbone and therefore the inter-palladium(II) distance and cavity length. In comparison to large hollow [PdnL2n]2n+ polyhedra, this approach retains a well-ordered cavity environment. We report here a novel ligand, 1,3-bis(4-(4-ethynylpyridine)-phenyl)-adamantane, that has a hydrophobic bis(phenyl)adamantane core and forms [Pd2L4]4+ cages with a large 19 Å inter-palladium(II) cavity length. This cage binds long designer anions: naphthalimide sulfonates at ≥15 Å in length, which consist of two distinct domains: a naphthalimide and a phenyl sulfonate. This binding derives from hydrogen bonding between the endohedral pyridyl protons of the cage and the phenyl sulfonate group, and π–hydrophobic interactions between the adamantane core and the naphthalimide unit. The strength of binding depends on the degree of electron deficiency of the naphthalimide, brought about by the nature of substituents on this moiety, with binding constants for monoanionic guests ranging from 400 to 1800 M−1. The host/guest stoichiometry was found to be 1 : 2, unless the guest possessed a second sulfonate group, and was small enough to fit end-to-end within the cavity, in which case the stoichiometry was 1 : 1, and resulted in a high binding constant (for DMSO solvent) of 6100 M−1. This work demonstrates the subtle interplay and potential between cages and guests that are both large and that both have distinct dual zones able to interact with each other, and offers a pathway to specific and tunable binding of large guests.The authors would like to thank the University of Canterbury, the Australian National University, Massey University Albany and the University of Otago for funding. DP, KP and PK would like to thank the MacDiarmid Institute for funding. DP would like to thank the Royal Society of New Zealand for a Rutherford Postdoctoral Fellowship, and the Australian Research Council for a DECRA Fellowship