scholarly journals Cargo Transport Shapes the Spatial Organization of a Microbial Community

2018 ◽  
Author(s):  
Abhishek Shrivastava ◽  
Visha K. Patel ◽  
Yisha Tang ◽  
Susan Connolly Yost ◽  
Floyd E. Dewhirst ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Spatial Organization ◽  
Single Cells ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Human Microbiome ◽  
Genomic Analysis ◽  
Oral Microbiome ◽  
Gliding Bacteria ◽  
Semi Solid

AbstractThe human microbiome is an assemblage of diverse bacteria that interact with one another to form communities. Bacteria in a given community are arranged in a three-dimensional matrix with many degrees of freedom. Snapshots of the community display well-defined structures, but the steps required for their assembly are not understood. Here, we show that this construction is carried out with the help of gliding bacteria. Gliding is defined as the motion of cells over a solid or semi-solid surface without the necessity of growth or the aid of pili or flagella. Genomic analysis suggests that gliding bacteria are present in human microbial communities. We focus on Capnocytophaga gingivalis which is present in abundance in the human oral microbiome. Tracking of fluorescently-labeled single cells and of gas bubbles carried by fluid flow shows that swarms of C. gingivalis are layered, with cells in the upper layers moving more rapidly than those in the lower layers. Thus, cells also glide on top of one another. Cells of non-motile bacterial species attach to the surface of C. gingivalis and are propelled as cargo. The cargo cell moves along the length of a C. gingivalis cell, looping from one pole to the other. Multi-color fluorescent spectral imaging of cells of different live but non-motile bacterial species reveals their long-range transport in a polymicrobial community. A swarm of C. gingivalis transports some non-motile bacterial species more efficiently than others and helps shape the spatial organization of a polymicrobial community.SignificanceWe describe a situation in which bacteria typical of the human oral microbiome are organized spatially by gliding cells, species of Capnocytophaga, that move backwards and forwards over the substratum. The mobile adhesins that pull the cells over the substratum also attach to cells of non-motile bacterial species, which are carried up and down the motile cells as cargo. The synchronized transport of non-motile cargo bacteria helps shape a polymicrobial community.

scholarly journals Cargo transport shapes the spatial organization of a microbial community

2018 ◽  
Vol 115 (34) ◽  
pp. 8633-8638 ◽  
Author(s):  
Abhishek Shrivastava ◽  
Visha K. Patel ◽  
Yisha Tang ◽  
Susan Connolly Yost ◽  
Floyd E. Dewhirst ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Spatial Organization ◽  
Single Cells ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Genomic Analysis ◽  
Oral Microbiome ◽  
Gliding Bacteria ◽  
Range Transport ◽  
3D Matrix

The human microbiome is an assemblage of diverse bacteria that interact with one another to form communities. Bacteria in a given community are arranged in a 3D matrix with many degrees of freedom. Snapshots of the community display well-defined structures, but the steps required for their assembly are not understood. Here, we show that this construction is carried out with the help of gliding bacteria. Gliding is defined as the motion of cells over a solid or semisolid surface without the necessity of growth or the aid of pili or flagella. Genomic analysis suggests that gliding bacteria are present in human microbial communities. We focus on Capnocytophaga gingivalis, which is present in abundance in the human oral microbiome. Tracking of fluorescently labeled single cells and of gas bubbles carried by fluid flow shows that swarms of C. gingivalis are layered, with cells in the upper layers moving more rapidly than those in the lower layers. Thus, cells also glide on top of one another. Cells of nonmotile bacterial species attach to the surface of C. gingivalis and are propelled as cargo. The cargo cell moves along the length of a C. gingivalis cell, looping from one pole to the other. Multicolor fluorescent spectral imaging of cells of different live but nonmotile bacterial species reveals their long-range transport in a polymicrobial community. A swarm of C. gingivalis transports some nonmotile bacterial species more efficiently than others and helps to shape the spatial organization of a polymicrobial community.

scholarly journals A Linear Plasmid-Like Prophage of Actinomyces odontolyticus Promotes Biofilm Assembly

2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Mengyu Shen ◽  
Yuhui Yang ◽  
Wei Shen ◽  
Lujia Cen ◽  
Jeffrey S. McLean ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Human Microbiome ◽  
Genomic Analysis ◽  
Electron Microscopic Examination ◽  
Oral Microbiome ◽  
Extracellular Dna ◽  
Linear Plasmid ◽  
Electron Microscopic ◽  
Content Type ◽  
Human Oral Cavity

ABSTRACT The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated Actinomyces odontolyticus subsp. actinosynbacter strain XH001 from the human oral cavity, and genomic analysis revealed the presence of an intact prophage named xhp1. Here, we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus. The prophage xhp1 genome is a 35-kb linear double-stranded DNA with 10-bp single-stranded, 3’ cohesive ends. xhp1 exists extrachromosomally, with an estimated copy number of 5. Annotation of xhp1 revealed 54 open reading frames, while phylogenetic analysis suggests that it has limited similarity with other phages. xhp1 phage particles can be induced by mitomycin C and belong to the Siphoviridae family, according to transmission electron microscopic examination. The released xhp1 particles can reinfect the xhp1-cured XH001 strain and result in tiny blurry plaques. Moreover, xhp1 promotes XH001 biofilm formation through spontaneous induction and the release of host extracellular DNA (eDNA). In conclusion, we identified a linear plasmid-like prophage of A. odontolyticus, which enhances bacterial host biofilm assembly and could be beneficial to the host for its persistence in the oral cavity. IMPORTANCE The biology of phages as members of the human oral microbiome is understudied. Here, we report the characterization of xhp1, a novel linear plasmid-like prophage identified from a human oral isolate, Actinomyces odontolyticus subsp. actinosynbacter strain XH001. xhp1 can be induced and reinfect xhp1-cured XH001. The spontaneous induction of xhp1 leads to the lysis of a subpopulation of bacterial hosts and the release of eDNA that promotes biofilm assembly, thus potentially contributing to the persistence of A. odontolyticus within the oral cavity.

scholarly journals Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology

2015 ◽  
Vol 112 (24) ◽  
pp. 7569-7574 ◽  
Author(s):  
Lihong Guo ◽  
Jeffrey S. McLean ◽  
Youngik Yang ◽  
Randal Eckert ◽  
Christopher W. Kaplan ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Therapeutic Potential ◽  
Bacterial Species ◽  
Recovery Period ◽  
Human Microbiome ◽  
Human Saliva ◽  
Oral Microbiome ◽  
Individual Species ◽  
Significant Shift

One major challenge to studying human microbiome and its associated diseases is the lack of effective tools to achieve targeted modulation of individual species and study its ecological function within multispecies communities. Here, we show that C16G2, a specifically targeted antimicrobial peptide, was able to selectively kill cariogenic pathogenStreptococcus mutanswith high efficacy within a human saliva-derived in vitro oral multispecies community. Importantly, a significant shift in the overall microbial structure of the C16G2-treated community was revealed after a 24-h recovery period: several bacterial species with metabolic dependency or physical interactions withS. mutanssuffered drastic reduction in their abundance, whereasS. mutans’ natural competitors, including health-associated Streptococci, became dominant. This study demonstrates the use of targeted antimicrobials to modulate the microbiome structure allowing insights into the key community role of specific bacterial species and also indicates the therapeutic potential of C16G2 to achieve a healthy oral microbiome.

scholarly journals Principal curve approaches for inferring 3D chromatin architecture

Biostatistics ◽  
2020 ◽  
Author(s):  
Elena Tuzhilina ◽  
Trevor J Hastie ◽  
Mark R Segal
Keyword(s):  
Degrees Of Freedom ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Direct Analysis ◽  
Added Value ◽  
Imaging Data ◽  
Proximity Data ◽  
Single Chromosome ◽  
Genome Spatial Organization ◽  
Principal Curve

Summary Three-dimensional (3D) genome spatial organization is critical for numerous cellular processes, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome architecture had been notoriously difficult to elucidate, but the advent of the suite of chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin structure and provided downstream biological insights. Although many findings have flowed from direct analysis of the pairwise proximity data produced by these assays, there is added value in generating corresponding 3D reconstructions deriving from superposing genomic features on the reconstruction. Accordingly, many methods for inferring 3D architecture from proximity data have been advanced. However, none of these approaches exploit the fact that single chromosome solutions constitute a one-dimensional (1D) curve in 3D. Rather, this aspect has either been addressed by imposition of constraints, which is both computationally burdensome and cell type specific, or ignored with contiguity imposed after the fact. Here, we target finding a 1D curve by extending principal curve methodology to the metric scaling problem. We illustrate how this approach yields a sequence of candidate solutions, indexed by an underlying smoothness or degrees-of-freedom parameter, and propose methods for selection from this sequence. We apply the methodology to Hi-C data obtained on IMR90 cells and so are positioned to evaluate reconstruction accuracy by referencing orthogonal imaging data. The results indicate the utility and reproducibility of our principal curve approach in the face of underlying structural variation.

scholarly journals Principal curve approaches for inferring 3D chromatin architecture

2020 ◽  
Author(s):  
Elena Tuzhilina ◽  
Trevor J. Hastie ◽  
Mark R. Segal
Keyword(s):  
Degrees Of Freedom ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Direct Analysis ◽  
Added Value ◽  
Imaging Data ◽  
Proximity Data ◽  
Single Chromosome ◽  
Genome Spatial Organization ◽  
Principal Curve

AbstractThree dimensional (3D) genome spatial organization is critical for numerous cellular processes, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome architecture had been notoriously difficult to elucidate, but the advent of the suite of chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin structure and provided downstream biological insights. Although many findings have flowed from direct analysis of the pairwise proximity data produced by these assays, there is added value in generating corresponding 3D reconstructions deriving from superposing genomic features on the reconstruction. Accordingly, many methods for inferring 3D architecture from proximity d hyperrefata have been advanced. However, none of these approaches exploit the fact that single chromosome solutions constitute a one dimensional (1D) curve in 3D. Rather, this aspect has either been addressed by imposition of constraints, which is both computationally burdensome and cell type specific, or ignored with contiguity imposed after the fact. Here we target finding a 1D curve by extending principal curve methodology to the metric scaling problem. We illustrate how this approach yields a sequence of candidate solutions, indexed by an underlying smoothness or degrees-of-freedom parameter, and propose methods for selection from this sequence. We apply the methodology to Hi-C data obtained on IMR90 cells and so are positioned to evaluate reconstruction accuracy by referencing orthogonal imaging data. The results indicate the utility and reproducibility of our principal curve approach in the face of underlying structural variation.

scholarly journals Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany

2021 ◽  
Vol 9 (7) ◽  
pp. 1345
Author(s):  
Stefan E. Heiden ◽  
Katharina Sydow ◽  
Stephan Schaefer ◽  
Ingo Klempien ◽  
Veronika Balau ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Public Health Problem ◽  
Multidrug Resistant ◽  
Mercury Resistance ◽  
Major Public Health Problem ◽  
Eastern Germany ◽  
North Eastern ◽  
Resistance Plasmids

The emergence of carbapenemase-producing Enterobacteriaceae limits therapeutic options and presents a major public health problem. Resistances to carbapenems are mostly conveyed by metallo-beta-lactamases (MBL) including VIM, which are often encoded on resistance plasmids. We characterized four VIM-positive isolates that were obtained as part of a routine diagnostic screening from two laboratories in north-eastern Germany between June and August 2020. Whole-genome sequencing was performed to address (a) phylogenetic properties, (b) plasmid content, and (c) resistance gene carriage. In addition, we performed phenotypic antibiotic and mercury resistance analyses. The genomic analysis revealed three different bacterial species including C. freundii, E. coli and K. oxytoca with four different sequence types. All isolates were geno- and phenotypically multidrug-resistant (MDR) and the phenotypic profile was explained by the underlying resistance gene content. Three isolates of four carried nearly identical VIM-1-resistance plasmids, which in addition encoded a mercury resistance operon and showed some similarity to two publicly available plasmid sequences from sources other than the two laboratories above. Our results highlight the circulation of a nearly identical IncN-type VIM-1-resistance plasmid in different Enterobacteriaceae in north-eastern Germany.

scholarly journals Design, Fabrication, and Testing of a Novel 3D 3-Fingered Electrothermal Microgripper with Multiple Degrees of Freedom

Micromachines ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 444
Author(s):  
Guoning Si ◽  
Liangying Sun ◽  
Zhuo Zhang ◽  
Xuping Zhang
Keyword(s):  
Degrees Of Freedom ◽  
Dynamic Properties ◽  
Three Dimensional ◽  
Polyimide Film ◽  
Zebrafish Embryos ◽  
Multiple Degrees Of Freedom ◽  
Electrothermal Actuator ◽  
3D Space ◽  
Pick And Place

This paper presents the design, fabrication, and testing of a novel three-dimensional (3D) three-fingered electrothermal microgripper with multiple degrees of freedom (multi DOFs). Each finger of the microgripper is composed of a V-shaped electrothermal actuator providing one DOF, and a 3D U-shaped electrothermal actuator offering two DOFs in the plane perpendicular to the movement of the V-shaped actuator. As a result, each finger possesses 3D mobilities with three DOFs. Each beam of the actuators is heated externally with the polyimide film. The durability of the polyimide film is tested under different voltages. The static and dynamic properties of the finger are also tested. Experiments show that not only can the microgripper pick and place microobjects, such as micro balls and even highly deformable zebrafish embryos, but can also rotate them in 3D space.

scholarly journals Asymmetry in Three-Dimensional Sprinting with and without Running-Specific Prostheses

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 580
Author(s):  
Anna Lena Emonds ◽  
Katja Mombaur
Keyword(s):  
Degrees Of Freedom ◽  
Body Position ◽  
Three Dimensional ◽  
Problem Formulation ◽  
Contact Phase ◽  
Individual Level ◽  
Lower Trunk ◽  
Floating Base ◽  
The Asymmetry ◽  
Limb Asymmetry

As a whole, human sprinting seems to be a completely periodic and symmetrical motion. This view is changed when a person runs with a running-specific prosthesis after a unilateral amputation. The aim of our study is to investigate differences and similarities between unilateral below-knee amputee and non-amputee sprinters—especially with regard to whether asymmetry is a distracting factor for sprint performance. We established three-dimensional rigid multibody models of one unilateral transtibial amputee athlete and for reference purposes of three non-amputee athletes. They consist of 16 bodies (head, ipper, middle and lower trunk, upper and lower arms, hands, thighs, shanks and feet/running specific prosthesis) with 30 or 31 degrees of freedom (DOFs) for the amputee and the non-amputee athletes, respectively. Six DOFs are associated with the floating base, the remaining ones are rotational DOFs. The internal joints are equipped with torque actuators except for the prosthetic ankle joint. To model the spring-like properties of the prosthesis, the actuator is replaced by a linear spring-damper system. We consider a pair of steps which is modeled as a multiphase problem with each step consisting of a flight, touchdown and single-leg contact phase. Each phase is described by its own set of differential equations. By combining motion capture recordings with a least squares optimal control problem formulation including constraints, we reconstructed the dynamics of one sprinting trial for each athlete. The results show that even the non-amputee athletes showed less symmetrical sprinting than expected when examined on an individual level. Nevertheless, the asymmetry is much more pronounced in the amputee athlete. The amputee athlete applies larger torques in the arm and trunk joints to compensate the asymmetry and experiences a destabilizing influence of the trunk movement. Hence, the inter-limb asymmetry of the amputee has a significant effect on the control of the sprint movement and the maintenance of an upright body position.

scholarly journals EPCO-31. EPIGENOMIC INTRATUMORAL HETEROGENEITY OF GLIOBLASTOMA IN THREE-DIMENSIONAL SPACE

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii76-ii76
Author(s):  
Radhika Mathur ◽  
Sriranga Iyyanki ◽  
Stephanie Hilz ◽  
Chibo Hong ◽  
Joanna Phillips ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Spatial Location ◽  
Therapy Resistance ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Intratumoral Heterogeneity ◽  
Tumor Evolution ◽  
Open Chromatin

Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and generation of therapy-resistant clones. While ITH in glioblastoma has been well-characterized at the genomic and transcriptomic levels, the extent of ITH at the epigenomic level and its biological and clinical significance are not well understood. In collaboration with neurosurgeons, neuropathologists, and biomedical imaging experts, we have established a novel topographical approach towards characterizing epigenomic ITH in three-dimensional (3-D) space. We utilize pre-operative MRI scans to define tumor volume and then utilize 3-D surgical neuro-navigation to intra-operatively acquire 10+ samples representing maximal anatomical diversity. The precise spatial location of each sample is mapped by 3-D coordinates, enabling tumors to be visualized in 360-degrees and providing unprecedented insight into their spatial organization and patterning. For each sample, we conduct assay for transposase-accessible chromatin using sequencing (ATAC-Seq), which provides information on the genomic locations of open chromatin, DNA-binding proteins, and individual nucleosomes at nucleotide resolution. We additionally conduct whole-exome sequencing and RNA sequencing for each spatially mapped sample. Integrative analysis of these datasets reveals distinct patterns of chromatin accessibility within glioblastoma tumors, as well as their associations with genetically defined clonal expansions. Our analysis further reveals how differences in chromatin accessibility within tumors reflect underlying transcription factor activity at gene regulatory elements, including both promoters and enhancers, and drive expression of particular gene expression sets, including neuronal and immune programs. Collectively, this work provides the most comprehensive characterization of epigenomic ITH to date, establishing its importance for driving tumor evolution and therapy resistance in glioblastoma. As a resource for further investigation, we have provided our datasets on an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

Three-dimensional asymmetric maximum weight lifting prediction considering dynamic joint strength

2021 ◽  
pp. 095441192098703
Author(s):  
Rahid Zaman ◽  
Yujiang Xiang ◽  
Jazmin Cruz ◽  
James Yang
Keyword(s):  
Experimental Data ◽  
Degrees Of Freedom ◽  
Inverse Dynamics ◽  
Three Dimensional ◽  
Optimization Method ◽  
Weight Lifting ◽  
Joint Torque ◽  
Maximum Weight ◽  
Angular Velocities ◽  
Asymmetric Lifting

In this study, the three-dimensional (3D) asymmetric maximum weight lifting is predicted using an inverse-dynamics-based optimization method considering dynamic joint torque limits. The dynamic joint torque limits are functions of joint angles and angular velocities, and imposed on the hip, knee, ankle, wrist, elbow, shoulder, and lumbar spine joints. The 3D model has 40 degrees of freedom (DOFs) including 34 physical revolute joints and 6 global joints. A multi-objective optimization (MOO) problem is solved by simultaneously maximizing box weight and minimizing the sum of joint torque squares. A total of 12 male subjects were recruited to conduct maximum weight box lifting using squat-lifting strategy. Finally, the predicted lifting motion, ground reaction forces, and maximum lifting weight are validated with the experimental data. The prediction results agree well with the experimental data and the model’s predictive capability is demonstrated. This is the first study that uses MOO to predict maximum lifting weight and 3D asymmetric lifting motion while considering dynamic joint torque limits. The proposed method has the potential to prevent individuals’ risk of injury for lifting.

Sign in / Sign up

Export Citation Format

Share Document