Biology subjects

Duff, A.

Publications and source records attributed to Duff, A..

5 recordsLinked to original sources

bioRxiv2025

Tumbleweed: an artificial motor protein that walks along a DNA track

Summary ParagraphMolecular motors are fundamental to life1-6 because of their ability to convert chemical energy into mechanical work, an ability that is conferred by the chemical and structural complexity of their constituent proteins. Scientists have long sought to create artificial protein motors that may reveal insights into how biological motors function. While artificial molecular motors based on small molecules7 and DNA8,9 have been developed, creating an artificial motor protein has remained an elusive goal in synthetic biology10. Here we demonstrate the realization of an artificial protein motor called Tumbleweed (TW) that walks directionally along a DNA track under external control. TW consists of three legs, each with a ligand-gated DNA-binding domain that enables selective interaction with specific sites along a DNA track11. Using single-molecule fluorescence assays and a programmable microfluidic device, we show that TW steps directionally along a designed DNA track in response to a defined sequence of ligand inputs. We built our TW molecular walker using a modular approach, combining existing proteins with known properties to achieve emergent motor function, similar to how Nature evolves new proteins. Our design strategy thus offers a a platform for engineering advanced and dynamic protein functionality. Our demonstration of TW walking represents a step toward developing fully autonomous protein motors and opens new avenues for uncovering and leveraging the principles by which biological motors transduce chemical energy into motion.

biophysics↗

bioRxiv2019

Comparative of probiotics reveals cecal microbial component associated with performance parameters in broilers

Probiotics have become increasingly popular in poultry industry as a promising nutritional intervention to promote modulation of intestinal microbiota as a means of improving health and performance. This study aimed to determine the effects of different probiotic formulations on the cecal microbial communities and performance in 21 and 42 day-old-broilers, as well as to define associations between ceca microbial profile and growth parameters. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-forming Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Dietary inclusion of SYNBIO, YEAST, and SINGLE2 increased body weight (BW) by 7, 14, and 21d (p<0.05) compared to a basal diet without probiotics (CON). The treatments SYNBIO, and YEAST decreased mortality by 21d, while SYNBIO reduced the overall mortality rate by 42d (p<0.05). Bifidobacteriales had the highest (p<0.05) population in SINGLE2, whereas Clostridiales was reduced compared to CON, SINGLE1, and SINGLE3. The addition of SYNBIO into diet mainly stimulated (p<0.05) the cecal relative abundance of Lactobacillales by 21d. Besides, Spearmans correlation analyses revealed that population of Lactobacillales was associated with lower Enterobacteriales, higher BW, and lower mortality of growing broilers. These results suggest that the modulation of ceca microbiota and the greatest productive parameters were achieved by supplementation of specific probiotic mixture. The selection of probiotics by their ability to drive cecal microbiota towards lactic acid bacteria colonization may be a strategic approach to improve the indicators of performance in broilers.

microbiology↗

bioRxiv2019

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers

The potential of probiotics to manipulate the intestinal microbial ecosystem toward commensal bacteria growth offers great hope for enhancing health and performance in poultry. This study aimed to evaluate the efficacy of five probiotic-based formulations in modulating cecal microbiota in broilers at 21 and 42 days of age. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-forming Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Metagenomics analyses showed that the cecal microbiota of SINGLE, YEAST, and MULTI supplemented birds had low diversity compared to the control diet without probiotics (CON) at 21d. At the same age, birds fed SYNBIO had a high population of Lactobacillus salivarus and Lachnospiraceae, which was reflected in a singular microbial community illustrated by beta-diversity analyses. By 42d, there were no differences in alpha or beta-diversity in the microbiota of probiotic-treated broilers compared to CON. Birds treated with SINGLE2 had a lower abundance of lactic acid bacteria, while a higher (p<0.05) population of unidentified Lachnospiraceae and Ruminococcaceae. Although the investigated probiotic formulations shared similar taxonomy, modulation of microbiota was not a core outcome for all probiotic-treated broilers indicating the success of microbiota-based intervention may ultimately be dependent on probiotic mixture and broilers age.

microbiology↗

bioRxiv2018

Comparison of microbiome and culture techniques for determination of gastrointestinal microbial communities in ceca of chickens

The use of 16S next generation sequencing (NGS) technology to identify the relative abundance of microbial communities have become the standard when studying the intestinal microbiome. The increased use is due to the ability to identify a proportion of bacteria that cannot be observed with culture-based methods. However, culture-based techniques are acceptable to identify key bacterial groups, yet may grossly underestimate the microbial community in question. Since there is limited research comparing NGS results to colony forming units (CFU), the objective of this study was to compare total Enterobacteriaceae and lactic acid bacteria (LAB) recovery with culture techniques (CFU/g ceca) to total number of reads from operational taxonomic units (OTU) categorized as Enterobacteriaceae or LAB from Illumina MiSeq platform from matched chick cecal samples at three and 10 days of age. Both CFU recovery (1.09x109 {+/-} 2.42x108; 1.37x108 {+/-} 5.57x107) and reads (5460 {+/-} 1164; 282 {+/-} 163) belonging to Enterobacteriaceae decreased by 10 days of age (p < 0.001). Similarly, LAB reads decreased over time (21,128 {+/-} 2262; 6220 {+/-} 817, respectively p < 0.0001). However, LAB CFU recovery increased by 10 days (1.18x108 {+/-} 1.91x107; 1.62x109 {+/-} 5.00x108, respectively p < 0.01). At three days the Pearsons correlation was -0.082 between CFU of culturable Enterobacteriaceae to reads and culturable LAB CFU to reads at 0.097, showing no correlation (p = 0.606, 0.551; respectively). By 10 days, no correlation of reads and CFU occurred with Enterobacteriaceae (r=-0.049; p-value = 0.769) while with LAB the correlation was 0.290 (p = 0.066) at 10 days. The CFU may be appropriate to identify a few families that change due to treatment or product. Without identifying viable cells to DNA recovered from NGS, there will always be the question whether the reads within the binned OTU in the intestinal tract is accurate.

microbiology↗

bioRxiv2018

Revealing an extended critical window of recovery post-stroke

The impact of rehabilitation on post-stroke motor recovery and its dependency on the patients chronicity remain unclear. The existence and regularity of a, so called, proportional recovery rule across a range of functional deficits and therapies supports the notion that functional interventions have little or no impact beyond spontaneous recovery rates in a critical window of recovery which lasts from 3 to 6 months post-stroke. In this meta-analysis, we apply a bootstrap analysis method to assess the overall impact of a specific VR-based rehabilitation protocol for the upper extremities on a homogeneous sample of 219 individuals with hemiparesis at various stages post stroke. Our analysis uncovers a precise gradient of sensitivity to treatment that expands more than one year beyond the limits of the so-called critical window of recovery. These findings redefine the limits of the so-called critical window of recovery and suggest that stroke-derived plasticity mechanisms do facilitate functional recovery even at the chronic and late chronic stage.

neuroscience↗