Publications by authors named "Andrew T Smith"

87 Publications

Cortical visual area CSv as a cingulate motor area: a sensorimotor interface for the control of locomotion.

Authors:
Andrew T Smith

Brain Struct Funct 2021 Jul 8. Epub 2021 Jul 8.

Department of Psychology, Royal Holloway, University of London, Egham, TW20 0EX, UK.

The response properties, connectivity and function of the cingulate sulcus visual area (CSv) are reviewed. Cortical area CSv has been identified in both human and macaque brains. It has similar response properties and connectivity in the two species. It is situated bilaterally in the cingulate sulcus close to an established group of medial motor/premotor areas. It has strong connectivity with these areas, particularly the cingulate motor areas and the supplementary motor area, suggesting that it is involved in motor control. CSv is active during visual stimulation but only if that stimulation is indicative of self-motion. It is also active during vestibular stimulation and connectivity data suggest that it receives proprioceptive input. Connectivity with topographically organized somatosensory and motor regions strongly emphasizes the legs over the arms. Together these properties suggest that CSv provides a key interface between the sensory and motor systems in the control of locomotion. It is likely that its role involves online control and adjustment of ongoing locomotory movements, including obstacle avoidance and maintaining the intended trajectory. It is proposed that CSv is best seen as part of the cingulate motor complex. In the human case, a modification of the influential scheme of Picard and Strick (Picard and Strick, Cereb Cortex 6:342-353, 1996) is proposed to reflect this.
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http://dx.doi.org/10.1007/s00429-021-02325-5DOI Listing
July 2021

Super Stretchable and Compressible Hydrogels Inspired by Hook-and-Loop Fasteners.

Langmuir 2021 06 15;37(25):7760-7770. Epub 2021 Jun 15.

Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.

Inspired by hook-and-loop fasteners, we designed a hydrogel network containing α-zirconium phosphate (ZrP) two-dimensional nanosheets with a high density of surface hydroxyl groups serving as nanopatches with numerous "hooks," while polymer chains with plentiful amine functional groups serve as "loops." Our multiscale molecular simulations confirm that both the high density of hydroxyl groups on nanosheets and the large number of amine functional groups on polymer chains are essential to achieve reversible interactions at the molecular scale, functioning as nano hook-and-loop fasteners to dissipate energy. As a result, the synthesized hydrogel possesses superior stretchability (>2100% strain), resilience to compression (>90% strain), and durability. Remarkably, the hydrogel can sustain >5000 cycles of compression with torsion in a solution mimicking synovial fluid, thus promising for potential biomedical applications such as artificial articular cartilage. This hook-and-loop model can be adopted and generalized to design a wide range of multifunctional materials with exceptional mechanical properties.
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http://dx.doi.org/10.1021/acs.langmuir.1c00924DOI Listing
June 2021

Biomimetic Boroxine-Based Multifunctional Thermosets via One-Pot Synthesis.

ACS Appl Mater Interfaces 2020 Dec 2;12(50):56445-56453. Epub 2020 Dec 2.

Polymer Program, Institute of Materials Science and Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States.

Boroxine-based thermosets with remarkable mechanical tunability, self-healing ability, recyclability, and adhesive strength are of significant importance in various applications. However, complex multistep reactions are often required to prepare such thermosets. Herein, a facile one-pot approach to synthesize boroxine-based malleable thermosets is proposed. Random copolymers with pendant boronic acid groups were synthesized from alkenyl monomers containing boronic acids [4-vinylphenylboronic acid (4-VPBA), 3-vinylphenylboronic acid, or 3-acrylamidophenylboronic acid] and octadecanoxy polyethylene glycol methacrylate. Then, the as-prepared copolymers were cured to form thermosets with boroxine bonds. The tensile strengths of the thermosets were tailored to range from 9.3 to 27.5 MPa by increasing the concentration of 4-VPBA. Moreover, because of the reversible nature of dynamic boroxine bonds (transformation between boroxines and boronic acids) induced by water, the thermosets exhibit remarkable self-healing efficiency (up to 99%), tunable mechanical properties, and excellent recyclability. Additionally, the thermosets also demonstrate superior adhesive strength (as high as 73.9 MPa) on different substrates.
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http://dx.doi.org/10.1021/acsami.0c16736DOI Listing
December 2020

Ultralong lifetime and efficient room temperature phosphorescent carbon dots through multi-confinement structure design.

Nat Commun 2020 Nov 5;11(1):5591. Epub 2020 Nov 5.

Key Laboratory for Biobased Materials and Energy of Ministry of Education/Guangdong Provincial Engineering Technology Research Center for Optical Agriculture, College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China.

Room temperature phosphorescence materials have inspired extensive attention owing to their great potential in optical applications. However, it is hard to achieve a room temperature phosphorescence material with simultaneous long lifetime and high phosphorescence quantum efficiency. Herein, multi-confined carbon dots were designed and fabricated, enabling room temperature phosphorescence material with simultaneous ultralong lifetime, high phosphorescence quantum efficiency, and excellent stability. The multi-confinement by a highly rigid network, stable covalent bonding, and 3D spatial restriction efficiently rigidified the triplet excited states of carbon dots from non-radiative deactivation. The as-designed multi-confined carbon dots exhibit ultralong lifetime of 5.72 s, phosphorescence quantum efficiency of 26.36%, and exceptional stability against strong oxidants, acids and bases, as well as polar solvents. This work provides design principles and a universal strategy to construct metal-free room temperature phosphorescence materials with ultralong lifetime, high phosphorescence quantum efficiency, and high stability for promising applications, especially under harsh conditions.
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http://dx.doi.org/10.1038/s41467-020-19422-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645781PMC
November 2020

Broad spectrum antimicrobial activities from spore-forming bacteria isolated from the Vietnam Sea.

PeerJ 2020 16;8:e10117. Epub 2020 Oct 16.

School of Science, RMIT University, Bundoora, Victoria, Australia.

The widespread occurrence of pathogenic bacteria resistant to last-line antibiotics has resulted in significant challenges in human and veterinary medicine. There is an urgent need for new antimicrobial agents that can be used to control these life threating pathogens. We report the identification of antimicrobial activities, against a broad range of bacterial pathogens, from a collection of marine-derived spore-forming bacteria. Although marine environments have been previously investigated as sources of novel antibiotics, studies on such environments are still limited and there remain opportunities for further discoveries and this study has used resources derived from an under-exploited region, the Vietnam Sea. Antimicrobial activity was assessed against a panel of Gram-positive and Gram-negative bacteria, including several multi-drug resistant pathogens. From a total of 489 isolates, 16.4% had antimicrobial activity. Of 23 shortlisted isolates with the greatest antimicrobial activity, 22 were spp. isolates and one was a isolate. Most of the antimicrobial compounds were sensitive to proteases, indicating that they were proteins rather than secondary metabolites. The study demonstrated that marine bacteria derived from the Vietnam Sea represent a rich resource, producing antimicrobial compounds with activity against a broad range of clinically relevant bacterial pathogens, including important antibiotic resistant pathogens. Several isolates were identified that have particularly broad range activities and produce antimicrobial compounds that may have value for future drug development.
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http://dx.doi.org/10.7717/peerj.10117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571411PMC
October 2020

Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity.

Sci Rep 2020 10 15;10(1):17398. Epub 2020 Oct 15.

Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, QLD, 4111, Australia.

Plantacyclin B21AG is a circular bacteriocin produced by Lactiplantibacillus plantarum B21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens, Listeria monocytogenes and Clostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from a food grade Lactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 18 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed that PheAla and TrpAla mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. The LysAla mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the relative importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.
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http://dx.doi.org/10.1038/s41598-020-74332-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7562740PMC
October 2020

Perovskite oxides as transparent semiconductors: a review.

Nano Converg 2020 Oct 2;7(1):32. Epub 2020 Oct 2.

Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT, 06269, USA.

Traditional transparent conducting oxides (TCOs) have been widely used for various optoelectronic applications, but have the trade-off between conductivity and transmittance. Recently, perovskite oxides, with structural and chemical stability, have exhibited excellent physical properties as new TCOs. We focus on SrVO-based perovskites with a high carrier concentration and BaSnO-based perovskites with a high mobility for n-type TCOs. In addition, p-type perovskites are discussed, which can serve as potential future options to couple with n-type perovskites to design full perovskite based devices.
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http://dx.doi.org/10.1186/s40580-020-00242-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532230PMC
October 2020

Discovery and characterisation of circular bacteriocin plantacyclin B21AG from B21.

Heliyon 2020 Aug 21;6(8):e04715. Epub 2020 Aug 21.

Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.

B21 isolated from Vietnamese sausage () has previously displayed broad antimicrobial activity against Gram-positive bacteria including foodborne pathogens and . This study successfully identified the antimicrobial agent as plantacyclin B21AG, a 5668 Da circular bacteriocin demonstrating high thermostability, resistance to a wide range of pH, proteolytic resistance and temporal stability. We report a reverse genetics approach to identify and characterise plantacyclin B21AG from first principles. The bacteriocin was purified from culture supernatant by a three-step process consisting of concentration, n-butanol extraction and cation exchange chromatography. A peptide sequencing using LC-MS/MS techniques identified two putative peptide fragments which were mapped to the genome sequence of B21. This revealed an ORF corresponding to a putative circular bacteriocin with a 33-amino acid leader peptide and a 58-amino acid mature peptide encoded on a native plasmid pB21AG01. The bacteriocin is shown to be a small cationic predominantly α-helical protein (69%). The corresponding gene cluster, consisted of seven genes associated with post-translational circularisation, immunity and secretion. Whilst plantacyclin B21AG is 86% identical to the newly published plantaricyclin A it is more highly cationic having a net charge of +3 due to an additional basic residue in the putative membrane interaction region. This and other substitutions may well go some way to explaining functional differences. The robust nature of plantacyclin B21AG, its antimicrobial activity and associated machinery for cyclisation make it an interesting biotechnological target for development, both as a food-safe antimicrobial or potentially a platform technology for recombinant protein circularisation.
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http://dx.doi.org/10.1016/j.heliyon.2020.e04715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7452424PMC
August 2020

Cloning and functional expression of a food-grade circular bacteriocin, plantacyclin B21AG, in probiotic Lactobacillus plantarum WCFS1.

PLoS One 2020 12;15(8):e0232806. Epub 2020 Aug 12.

School of Science, RMIT University, Bundoora, Victoria, Australia.

There is an increasing consumer demand for minimally processed, preservative free and microbiologically safe food. These factors, combined with risks of antibiotic resistance, have led to interest in bacteriocins produced by lactic acid bacteria (LAB) as natural food preservatives and as potential protein therapeutics. We previously reported the discovery of plantacyclin B21AG, a circular bacteriocin produced by Lactobacillus plantarum B21. Here, we describe the cloning and functional expression of the bacteriocin gene cluster in the probiotic Lactobacillus plantarum WCFS1. Genome sequencing demonstrated that the bacteriocin is encoded on a 20 kb native plasmid, designated as pB21AG01. Seven open reading frames (ORFs) putatively involved in bacteriocin production, secretion and immunity were cloned into an E. coli/Lactobacillus shuttle vector, pTRKH2. The resulting plasmid, pCycB21, was transformed into L. plantarum WCFS1. The cell free supernatants (CFS) of both B21 and WCFS1 (pCycB21) showed an antimicrobial activity of 800 AU/mL when tested against WCFS1 (pTRKH2) as the indicator strain, showing that functional expression of plantacyclin B21AG had been achieved. Real-time PCR analysis revealed that the relative copy number of pB21AG01 was 7.60 ± 0.79 in L. plantarum B21 whilst pCycB21 and pTRKH2 was 0.51 ± 0.05 and 25.19 ± 2.68 copies respectively in WCFS1. This indicates that the bacteriocin gene cluster is located on a highly stable low copy number plasmid pB21AG01 in L. plantarum B21. Inclusion of the native promoter for the bacteriocin operon from pB21AG01 results in similar killing activity being observed in both the wild type and recombinant hosts despite the lower copy number of pCycB21.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232806PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7423119PMC
October 2020

Bioinformatic prospecting and phylogenetic analysis reveals 94 undescribed circular bacteriocins and key motifs.

BMC Microbiol 2020 04 6;20(1):77. Epub 2020 Apr 6.

Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia.

Background: Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are twenty experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence.

Results: Through bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 119. They were grouped into two families within class I modified bacteriocins (i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes.

Conclusions: Sequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.
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http://dx.doi.org/10.1186/s12866-020-01772-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7132975PMC
April 2020

Multisite Evaluation of Next-Generation Methods for Small RNA Quantification.

J Biomol Tech 2020 07;31(2):47-56

Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA.

Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs . Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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http://dx.doi.org/10.7171/jbt.20-3102-001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953595PMC
July 2020

Dry hydrated potassium carbonate for effective CO capture.

Dalton Trans 2020 Apr 10;49(13):3965-3969. Epub 2019 Jul 10.

Key Laboratory of Enhanced Heat Transfer and Energy Conservation of the Ministry of Education, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China.

Dry hydrated potassium carbonate (DHPC) is a free-flowing powder prepared by uniformly mixing hydrated KCO and hydrophobic nanosilica. We demonstrated that DHPCs can absorb CO rapidly because of their high surface-to-volume ratio. Their CO capture performance is superior to that of 30 wt% monoethanolamine (MEA), an industry standard. DHPC-75 (containing 75 wt% KCO) has a CO uptake capacity of 233 mg g (90% saturation uptake within 13 min), higher than the widely used 30 wt% MEA aqueous solution (111 mg g, 90% saturation uptake within 25 min). DHPC-75 also exhibits an excellent cycling performance, thus becoming a promising candidate for practical application.
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http://dx.doi.org/10.1039/c9dt01909jDOI Listing
April 2020

The role of spatial structure in the collapse of regional metapopulations.

Ecology 2018 12 19;99(12):2815-2822. Epub 2018 Nov 19.

School of Life Sciences, Arizona State University, Tempe, Arizona, 85287-4501, USA.

Many wildlife populations are either naturally, or as a result of human land use, patchily distributed in space. The degree of fragmentation-specifically the remaining patch sizes and habitat configuration-is an important part of population dynamics. Demographic stochasticity is also likely to play an important role in patchy habitats that host small local populations. We develop a simulation model to evaluate the significance of demographic stochasticity and the role fragmentation plays in the determination of population dynamics and the risk of extinction of populations on habitat patches. Our model is formulated as a Markov-chain stochastic process on a finite, spatially explicit array of patches in which probability of successful dispersal is a function of interpatch distance. Unlike past work, we explicitly model local population dynamics and examine how these scale up to the entire population. As a test case, we apply the model to the American pika (Ochotona princeps) population living on the ore dumps in the ghost mining town of Bodie, California. This population has been studied nearly continuously for over four decades and has been of conservation concern as the southern half of the population declined precipitously beginning in 1989. Our model suggests that both the specific configuration of habitat and landscape heterogeneity are necessary and sufficient predictors of the eventual extinction of the southern constellation of patches. This example has important implications, as it suggests that fragmentation alone can lead to regional extinctions within metapopulations.
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http://dx.doi.org/10.1002/ecy.2546DOI Listing
December 2018

Versatile Nanostructures from Rice Husk Biomass for Energy Applications.

Angew Chem Int Ed Engl 2018 10 19;57(42):13722-13734. Epub 2018 Sep 19.

Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut, 06269, USA.

Converting biomass into valuable products has great benefits in terms of both economic and environmental considerations, and has attracted considerable attention in recent years. Rice husk biomass was initially utilized to produce bulk materials for conventional applications while a variety of advanced nanostructures (NSs) have been fabricated over the past few years. In addition to their low cost and environmental friendliness, RH-derived NSs (RH-NSs) exhibit versatile properties, which are promising for broad applications in various fields. In this Review, we summarize the latest research on RH-NSs, covering their design, fabrication, properties, and applications in the modern energy field. Based on the unique structure and components of RHs, a series of carbon/silicon-based novel NSs with outstanding performances have been exploited, which are difficult to be synthesized using conventional chemical reagents. We also discuss perspective uses of RH-NSs on the basis of the current research progress.
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http://dx.doi.org/10.1002/anie.201802050DOI Listing
October 2018

Functional-trait ecology of the plateau pika Ochotona curzoniae in the Qinghai-Tibetan Plateau ecosystem.

Integr Zool 2019 Jan;14(1):87-103

School of Life Sciences, Arizona State University, Tempe, Arizona, USA.

Understanding a species' functional traits allows for a directed and productive perspective on the role a species plays in nature, and thus its relative importance to conservation planning. The functional-trait ecology of the plateau pika Ochotona curzoniae is examined to better understand the resilience and sustainability of the high alpine grasslands of the Qinghai-Tibetan Plateau (QTP). The key functional traits of plateau pikas are their abundance and behavior of digging extensive burrow systems. Plateau pikas have been poisoned over a significant part of their original geographic distribution across the QTP, allowing comparison of ecological communities with and without pikas. Nearly all mammalian and avian carnivores, most of which are obligate predators on pikas, have been lost in regions where pikas have been poisoned. Most endemic birds on the QTP nest in pika burrows; when pikas are poisoned, burrows collapse, and these birds are greatly reduced in number. Due to the biopedturbation resulting from their burrows, regional plant species richness is higher in areas with pikas than without. The presence of pika burrows allows higher rates of infiltration during heavy monsoon rains compared to poisoned areas, possibly mitigating runoff and the potential for serious downslope erosion and flooding. Thus, the functional traits of plateau pikas enhance native biodiversity and other important ecosystem functions; these traits are irreplaceable. As plateau pikas are not natural colonizers, active re-introduction programs are needed to restore pikas to areas from which they have been poisoned to restore the important functional ecological traits of pikas.
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http://dx.doi.org/10.1111/1749-4877.12300DOI Listing
January 2019

Draft Genome Sequence of Strain A6, a Strong Acid Producer Isolated from a Vietnamese Fermented Sausage (Nem Chua).

Genome Announc 2017 Oct 12;5(41). Epub 2017 Oct 12.

Griffith Sciences, Griffith University, Brisbane, Queensland, Australia.

strain A6, a strong acid producer, was isolated from a Vietnamese fermented sausage (nem chua). Here, we report the genome sequence of this strain (3,368,579 bp).
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http://dx.doi.org/10.1128/genomeA.00987-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637488PMC
October 2017

Linc-ing Circulating Long Non-coding RNAs to the Diagnosis and Malignant Prediction of Intraductal Papillary Mucinous Neoplasms of the Pancreas.

Sci Rep 2017 09 5;7(1):10484. Epub 2017 Sep 5.

Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective biomarkers for early detection. We hypothesized that circulating long non-coding RNAs (lncRNAs) may act as diagnostic markers of incidentally-detected cystic PDAC precursors known as intraductal papillary mucinous neoplasms (IPMNs) and predictors of their pathology/histological classification. Using NanoString nCounter® technology, we measured the abundance of 28 candidate lncRNAs in pre-operative plasma from a cohort of pathologically-confirmed IPMN cases of various grades of severity and non-diseased controls. Results showed that two lncRNAs (GAS5 and SRA) aided in differentiating IPMNs from controls. An 8-lncRNA signature (including ADARB2-AS1, ANRIL, GLIS3-AS1, LINC00472, MEG3, PANDA, PVT1, and UCA1) had greater accuracy than standard clinical and radiologic features in distinguishing 'aggressive/malignant' IPMNs that warrant surgical removal from 'indolent/benign' IPMNs that can be observed. When the 8-lncRNA signature was combined with plasma miRNA data and quantitative 'radiomic' imaging features, the accuracy of predicting IPMN pathological classification improved. Our findings provide novel information on the ability to detect lncRNAs in plasma from patients with IPMNs and suggest that an lncRNA-based blood test may have utility as a diagnostic adjunct for identifying IPMNs and their pathology, especially when incorporated with biomarkers such as miRNAs, quantitative imaging features, and clinical data.
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http://dx.doi.org/10.1038/s41598-017-09754-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585319PMC
September 2017

Moisture-Responsive Wrinkling Surfaces with Tunable Dynamics.

Adv Mater 2017 Jun 21;29(24). Epub 2017 Apr 21.

Department of Chemical and Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT, 06269, USA.

The wrinkle dynamics (such as reversibility and stability) of human skin are affected by the external stimuli, as well as the skin's structure and mechanical properties. Inspired by these tunable responses, three types of moisture-responsive wrinkle dynamics are achieved, for the first time, through a single film-substrate system. These dynamics include: (1) completely reversible wrinkles formation; (2) irreversible wrinkles formation I: the initially formed wrinkles can be permanently erased and never reappear; and (3) irreversible wrinkles formation II: once the wrinkles form, they can no longer be erased. The key to success is to control the stiffness and thickness ratios of the film and the substrate, and tailor the crosslink degree/gradient of the film to allow for moisture-dependent changes of modulus and swelling degree. These unique responsive dynamics motivate the invention of a series of optical devices triggered by moisture, including anticounterfeit tabs, encryption devices, water indicators, light diffusors, and antiglare films. This study also paves the road for further understanding of the skin wrinkling dynamics and manipulation.
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http://dx.doi.org/10.1002/adma.201700828DOI Listing
June 2017

Connectivity of the Cingulate Sulcus Visual Area (CSv) in the Human Cerebral Cortex.

Cereb Cortex 2018 02;28(2):713-725

Department of Experimental Psychology and Centre for Functional fMRI of the Brain (FMRIB), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.

The human cingulate sulcus visual area (CSv) responds selectively to visual and vestibular cues to self-motion. Although it is more selective for visual self-motion cues than any other brain region studied, it is not known whether CSv mediates perception of self-motion. An alternative hypothesis, based on its location, is that it provides sensory information to the motor system for use in guiding locomotion. To evaluate this hypothesis we studied the connectivity pattern of CSv, which is completely unknown, with a combination of diffusion MRI and resting-state functional MRI. Converging results from the 2 approaches suggest that visual drive is provided primarily by areas hV6, pVIP (putative intraparietal cortex) and PIC (posterior insular cortex). A strong connection with the medial portion of the somatosensory cortex, which represents the legs and feet, suggests that CSv may receive locomotion-relevant proprioceptive information as well as visual and vestibular signals. However, the dominant connections of CSv are with specific components of the motor system, in particular the cingulate motor areas and the supplementary motor area. We propose that CSv may provide a previously unknown link between perception and action that serves the online control of locomotion.
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http://dx.doi.org/10.1093/cercor/bhx002DOI Listing
February 2018

Processing of Egomotion-Consistent Optic Flow in the Rhesus Macaque Cortex.

Cereb Cortex 2017 01;27(1):330-343

Université de Toulouse, Centre de Recherche Cerveau et Cognition, Toulouse, France.

The cortical network that processes visual cues to self-motion was characterized with functional magnetic resonance imaging in 3 awake behaving macaques. The experimental protocol was similar to previous human studies in which the responses to a single large optic flow patch were contrasted with responses to an array of 9 similar flow patches. This distinguishes cortical regions where neurons respond to flow in their receptive fields regardless of surrounding motion from those that are sensitive to whether the overall image arises from self-motion. In all 3 animals, significant selectivity for egomotion-consistent flow was found in several areas previously associated with optic flow processing, and notably dorsal middle superior temporal area, ventral intra-parietal area, and VPS. It was also seen in areas 7a (Opt), STPm, FEFsem, FEFsac and in a region of the cingulate sulcus that may be homologous with human area CSv. Selectivity for egomotion-compatible flow was never total but was particularly strong in VPS and putative macaque CSv. Direct comparison of results with the equivalent human studies reveals several commonalities but also some differences.
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http://dx.doi.org/10.1093/cercor/bhw412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939222PMC
January 2017

Macrolactam analogues of macrolide natural products.

Org Biomol Chem 2016 Dec;14(48):11301-11316

School of Chemistry, the Bio21 Institute, The University of Melbourne, VIC 3010, Australia.

The chemical modification of macrolide natural products into aza- or lactam analogues is a strategy employed to improve their metabolic stability and biological activity. The methods for the synthesis of several lactam analogues of macrolide natural products are highlighted and aspects of their biological properties presented.
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http://dx.doi.org/10.1039/c6ob02149bDOI Listing
December 2016

An fMRI Investigation of Preparatory Set in the Human Cerebral Cortex and Superior Colliculus for Pro- and Anti-Saccades.

PLoS One 2016 8;11(7):e0158337. Epub 2016 Jul 8.

Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, United Kingdom.

Previous studies have identified several cortical regions that show larger BOLD responses during preparation and execution of anti-saccades than pro-saccades. We confirmed this finding with a greater BOLD response for anti-saccades than pro-saccades during the preparation phase in the FEF, IPS and DLPFC and in the FEF and IPS in the execution phase. We then applied multi-voxel pattern analysis (MVPA) to establish whether different neural populations are involved in the two types of saccade. Pro-saccades and anti-saccades were reliably decoded during saccade execution in all three cortical regions (FEF, DLPFC and IPS) and in IPS during saccade preparation. This indicates neural specialization, for programming the desired response depending on the task rule, in these regions. In a further study tailored for imaging the superior colliculus in the midbrain a similar magnitude BOLD response was observed for pro-saccades and anti-saccades and the two saccade types could not be decoded with MVPA. This was the case both for activity related to the preparation phase and also for that elicited during the execution phase. We conclude that separate cortical neural populations are involved in the task-specific programming of a saccade while in contrast, the SC has a role in response preparation but may be less involved in high-level, task-specific aspects of the control of saccades.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158337PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938211PMC
July 2017

Bio-inspired sensitive and reversible mechanochromisms via strain-dependent cracks and folds.

Nat Commun 2016 07 8;7:11802. Epub 2016 Jul 8.

Department of Chemical and Biomolecular Engineering and Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, USA.

A number of marine organisms use muscle-controlled surface structures to achieve rapid changes in colour and transparency with outstanding reversibility. Inspired by these display tactics, we develop analogous deformation-controlled surface-engineering approaches via strain-dependent cracks and folds to realize the following four mechanochromic devices: (1) transparency change mechanochromism (TCM), (2) luminescent mechanochromism (LM), (3) colour alteration mechanochromism (CAM) and (4) encryption mechanochromism (EM). These devices are based on a simple bilayer system that exhibits a broad range of mechanochromic behaviours with high sensitivity and reversibility. The TCM device can reversibly switch between transparent and opaque states. The LM can emit intensive fluorescence as stretched with very high strain sensitivity. The CAM can turn fluorescence from green to yellow to orange as stretched within 20% strain. The EM device can reversibly reveal and conceal any desirable patterns.
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http://dx.doi.org/10.1038/ncomms11802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941047PMC
July 2016

Global Motion Processing in Human Visual Cortical Areas V2 and V3.

J Neurosci 2016 07;36(27):7314-24

Department of Psychology, Royal Holloway, University of London, Egham TW20 0EX, United Kingdom

Unlabelled: Global motion perception entails the ability to extract the central direction tendency from an extended area of visual space containing widely disparate local directions. A substantial body of evidence suggests that local motion signals generated in primary visual cortex (V1) are spatially integrated to provide perception of global motion, beginning in the middle temporal area (MT) in macaques and its counterpart in humans, hMT. However, V2 and V3 also contain motion-sensitive neurons that have larger receptive fields than those found in V1, giving the potential for spatial integration of motion signals. Despite this, V2 and V3 have been overlooked as sites of global motion processing. To test, free of local-global confounds, whether human V2 and V3 are important for encoding global motion, we developed a visual stimulus that yields a global direction yet includes all possible local directions and is perfectly balanced at the local motion level. We then attempted to decode global motion direction in such stimuli with multivariate pattern classification of fMRI data. We found strong sensitivity to global motion in hMT, as expected, and also in several higher visual areas known to encode optic flow. Crucially, we found that global motion direction could be decoded in human V2 and, particularly, in V3. The results suggest the surprising conclusion that global motion processing is a key function of cortical visual areas V2 and V3. A possible purpose is to provide global motion signals to V6.

Significance Statement: Humans can readily detect the overall direction of movement in a flock of birds despite large differences in the directions of individual birds at a given moment. This ability to combine disparate motion signals across space underlies many aspects of visual motion perception and has therefore received considerable research attention. The received wisdom is that spatial integration of motion signals occurs in the cortical motion complex MT+ in both human and nonhuman primates. We show here that areas V2 and V3 in humans are also able to perform this function. We suggest that different cortical areas integrate motion signals in different ways for different purposes.
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http://dx.doi.org/10.1523/JNEUROSCI.0025-16.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705536PMC
July 2016

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

J Hered 2016 07 26;107(4):295-308. Epub 2016 Feb 26.

From the Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy (Fontanesi); Vertebrate and Health Genomics, The Genome Analysis Centre (TGAC), Norwich, UK (Di Palma); Broad Institute of MIT and Harvard, Cambridge, MA (Di Palma); European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (Flicek); School of Life Sciences, Arizona State University, Tempe, AZ (Smith); Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Thulin); CIBIO, Centro de Investigação em Biodiversidade e Recursos Geneticos, Universidade do Porto, Campus Agrario de Vairao, Vairao, Portugal (Alves); and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal (Alves).

The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.
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http://dx.doi.org/10.1093/jhered/esw010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888434PMC
July 2016

Binocular vision: joining up the eyes.

Authors:
Andrew T Smith

Curr Biol 2015 Aug;25(15):R661-3

Department of Psychology, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. Electronic address:

To provide a unitary view of the external world, signals from the two eyes must be combined: a new study pinpoints the location in the human brain where the requisite combination occurs.
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http://dx.doi.org/10.1016/j.cub.2015.06.013DOI Listing
August 2015

Herbivory and Competition of Tibetan Steppe Vegetation in Winter Pasture: Effects of Livestock Exclosure and Plateau Pika Reduction.

PLoS One 2015 24;10(7):e0132897. Epub 2015 Jul 24.

Department of Forest Management, University of Montana, Missoula, Montana, United States of America.

Rangeland degradation has been identified as a serious concern in alpine regions of western China on the Qinghai-Tibetan plateau (QTP). Numerous government-sponsored programs have been initiated, including many that feature long-term grazing prohibitions and some that call for eliminating pastoralism altogether. As well, government programs have long favored eliminating plateau pikas (Ochotona curzoniae), assumed to contribute to degraded conditions. However, vegetation on the QTP evolved in the presence of herbivory, suggesting that deleterious effects from grazing are, to some extent, compensated for by reduced plant-plant competition. We examined the dynamics of common steppe ecosystem species as well as physical indicators of rangeland stress by excluding livestock and reducing pika abundance on experimental plots, and following responses for 4 years. We established 12 fenced livestock exclosures within pastures grazed during winter by local pastoralists, and removed pikas on half of these. We established paired, permanent vegetation plots within and outside exclosures and measured indices of erosion and biomass of common plant species. We observed modest restoration of physical site conditions (reduced bare soil, erosion, greater vegetation cover) with both livestock exclusion and pika reduction. As expected in areas protected from grazing, we observed a reduction in annual productivity of plant species avoided by livestock and assumed to compete poorly when protected from grazing. Contrary to expectation, we observed similar reductions in annual productivity among palatable, perennial graminoids under livestock exclusion. The dominant grass, Stipa purpurea, displayed evidence of density-dependent growth, suggesting that intra-specific competition exerted a regulatory effect on annual production in the absence of grazing. Complete grazing bans on winter pastures in steppe habitats on the QTP may assist in the recovery of highly eroded pastures, but may not increase annual vegetative production.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132897PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514881PMC
May 2016

Activity in the human superior colliculus relating to endogenous saccade preparation and execution.

J Neurophysiol 2015 Aug 3;114(2):1048-58. Epub 2015 Jun 3.

Royal Holloway, University of London, Egham, Surrey, United Kingdom.

In recent years a small number of studies have applied functional imaging techniques to investigate visual responses in the human superior colliculus (SC), but few have investigated its oculomotor functions. Here, in two experiments, we examined activity associated with endogenous saccade preparation. We used 3-T fMRI to record the hemodynamic activity in the SC while participants were either preparing or executing saccadic eye movements. Our results showed that not only executing a saccade (as previously shown) but also preparing a saccade produced an increase in the SC hemodynamic activity. The saccade-related activity was observed in the contralateral and to a lesser extent the ipsilateral SC. A second experiment further examined the contralateral mapping of saccade-related activity with a larger range of saccade amplitudes. Increased activity was again observed in both the contralateral and ipsilateral SC that was evident for large as well as small saccades. This suggests that the ipsilateral component of the increase in BOLD is not due simply to small-amplitude saccades producing bilateral activity in the foveal fixation zone. These studies provide the first evidence of presaccadic preparatory activity in the human SC and reveal that fMRI can detect activity consistent with that of buildup neurons found in the deeper layers of the SC in studies of nonhuman primates.
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http://dx.doi.org/10.1152/jn.00825.2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725108PMC
August 2015

Self-Assembly of Amyloid Fibrils That Display Active Enzymes.

ChemCatChem 2014 Jul 4;6(7):1961-1968. Epub 2014 Jun 4.

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chaoyang District, Beijing 100101 (China) ; Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW (UK).

Enzyme immobilization is an important strategy to enhance the stability and recoverability of enzymes and to facilitate the separation of enzymes from reaction products. However, enzyme purification followed by separate chemical steps to allow immobilization on a solid support reduces the efficiency and yield of the active enzyme. Here we describe polypeptide constructs that self-assemble spontaneously into nanofibrils with fused active enzyme subunits displayed on the amyloid fibril surface. We measured the steady-state kinetic parameters for the appended enzymes in situ within fibrils and compare these with the identical protein constructs in solution. Finally, we demonstrated that the fibrils can be recycled and reused in functional assays both in conventional batch processes and in a continuous-flow microreactor.
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http://dx.doi.org/10.1002/cctc.201402125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413355PMC
July 2014
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