CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking.

Proper left-right symmetry breaking is essential for animal development, and in many cases, this process is actomyosin-dependent. In Caenorhabditis elegans embryos active torque generation in the actomyosin layer promotes left-right symmetry breaking by driving chiral counterrotating cortical flows. While both Formins and Myosins have been implicated in left-right symmetry breaking and both can rotate actin filaments in vitro, it remains unclear whether active torques in the actomyosin cortex are generated by Formins, Myosins, or both. We combined the strength of C. elegans genetics with quantitative imaging and thin film, chiral active fluid theory to show that, while Non-Muscle Myosin II activity drives cortical actomyosin flows, it is permissive for chiral counterrotation and dispensable for chiral symmetry breaking of cortical flows. Instead, we find that CYK-1/Formin activation in RhoA foci is instructive for chiral counterrotation and promotes in-plane, active torque generation in the actomyosin cortex. Notably, we observe that artificially generated large active RhoA patches undergo rotations with consistent handedness in a CYK-1/Formin-dependent manner. Altogether, we conclude that CYK-1/Formin-dependent active torque generation facilitates chiral symmetry breaking of actomyosin flows and drives organismal left-right symmetry breaking in the nematode worm.

Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1.

IgG antibodies increase their apparent affinities by using both of their Fabs to simultaneously attach to antigens. HIV-1 foils this strategy by having few, and highly separated, Envelope (Env) spike targets for antibodies, forcing most IgGs to bind monovalently. Here, we develop a statistical mechanics model of synthetic diFabs joined by DNA linkers of different lengths and flexibilities. This framework enables us to translate the energetic and entropic effects of the linker into the neutralization potency of a diFab. We demonstrate that the strongest neutralization potencies are predicted to require a rigid linker that optimally spans the distance between two Fab binding sites on an Env trimer and that avidity can be further boosted by incorporating more Fabs into these constructs. These results inform the design of multivalent anti-HIV-1 therapeutics that utilize avidity effects to remain potent against HIV-1 in the face of the rapid mutation of Env spikes.

A molecular modeling based screening for potential inhibitors to alpha hemolysin from Staphylococcus aureus.

Staphylococcus aureus, a Gram-positive bacterium is pathogenic in nature. It is known that secreted toxins remain active after antibiotic treatment. The alpha hemolysin or alpha toxin damages cell membrane and induces apoptosis and degradation of DNA. The titer of alphahemolysin increases and causes hemostasis disturbances, thrombocytopenia, and pulmonary lesions during staphylococcal infection. Therefore, it is of interest to inhibit alpha hemolysin using novel compounds. We used the structure of alpha hemolysin(PDB: 7AHL) to screen structures for 100,000 compounds from the ZINC database using molecular docking with AutoDock VINA. Nine (9) successive hits were then subjected for pharmacokinetic and toxicity properties by PROTOX (a webserver for the prediction of oral toxicities of small molecules) and FAFDrugs (a tool for prediction of ADME and Toxicity). This exercise further identified hit #1 ({[3a-(Dihydroxymethyl)-6-hydroxy-2,2-dimethyl-1,3,4-trioxatetrahydro-2H-pentalen-5- yl]methyl}amino(9H-fluoren-9-yl)acetate with binding affinity: -10.3 kcal/mol) and hit #2 (6-(Dihydroxymethyl)-2-{2-[3- (methylamino)propyl]-2-azatricyclo[9.4.0.03,8]pentadeca-1(11),3,5,7,12,14-hexaen-6-yloxy}tetrahydro-2H-pyran-3,4,5-triol with binding affinity: -9.6 kcal/mol) with acceptable toxicity and ADME properties for potential predicted hemolysin inhibition. These compounds should then be evaluated in vitro using inhibitory studies.

Locomotion of microorganisms near a no-slip boundary in a viscoelastic fluid.

Locomotion of microorganisms plays a vital role in most of their biological processes. In many of these processes, microorganisms are exposed to complex fluids while swimming in confined domains, such as spermatozoa in mucus of mammalian reproduction tracts or bacteria in extracellular polymeric matrices during biofilm formation. Thus, it is important to understand the kinematics of propulsion in a viscoelastic fluid near a no-slip boundary. We use a squirmer model with a time-reversible body motion to analytically investigate the swimming kinematics in an Oldroyd-B fluid near a wall. Analysis of the time-averaged motion of the swimmer shows that both pullers and pushers in a viscoelastic fluid swim towards the no-slip boundary if they are initially located within a small domain of "attraction" in the vicinity of the wall. In contrast, neutral swimmers always move towards the wall regardless of their initial distance from the wall. Outside the domain of attraction, pullers and pushers are both repelled from the no-slip boundary. Time-averaged locomotion is most pronounced at a Deborah number of unity. We examine the swimming trajectories of different types of swimmers as a function of their initial orientation and distance from the no-slip boundary.

Tunable patterning of microparticles and cells using standing surface acoustic waves.

We have developed an acoustic-based tunable patterning technique by which microparticles or cells can be arranged into reconfigurable patterns in microfluidic channels. In our approach, we use pairs of slanted-finger interdigital transducers (SFITs) to generate a tunable standing surface acoustic wave field, which in turn patterns microparticles or cells in one- or two-dimensional arrays inside the microfluidic channels--all without the assistance of fluidic flow. By tuning the frequency of the input signal applied to the SFITs, we have shown that the cell pattern can be controlled with tunability of up to 72%. This acoustic-based tunable patterning technique has the advantages of wide tunability, non-invasiveness, and ease of integration to lab-on-a-chip systems, and shall be valuable in many biological and colloidal studies.

Bacterial aggregation and biofilm formation in a vortical flow.

Bacterial aggregation and patchiness play an important role in a variety of ecological processes such as competition, adaptation, epidemics, and succession. Here, we demonstrate that hydrodynamics of their environment can lead to their aggregation. This is specially important since microbial habitats are rarely at rest (e.g., ocean, blood stream, flow in porous media, and flow through membrane filtration processes). In order to study the dynamics of bacterial collection in a vortical flow, we utilize a microfluidic system to mimic some of the important microbial conditions at ecologically relevant spatiotemporal scales. We experimentally demonstrate the formation of "ring"-shaped bacterial collection patterns and subsequently the formation of biofilm streamers in a microfluidic system. Acoustic streaming of a microbubble is used to generate a vortical flow in a microchannel. Due to bacteria's finite-size, the microorganisms are directed to closed streamlines and trapped in the vortical flow. The collection of bacteria in the vortices occurs in a matter of seconds, and unexpectedly, triggers the formation of biofilm streamers within minutes. Swimming bacteria have a competitive advantage to respond to their environmental conditions. In order to investigate the role of bacterial motility on the rate of collection, two strains of Escherichia coli bacteria with different motilities are used. We show that the bacterial collection in a vortical flow is strongly pronounced for high motile bacteria.

Three-dimensional continuous particle focusing in a microfluidic channel via standing surface acoustic waves (SSAW).

Three-dimensional (3D) continuous microparticle focusing has been achieved in a single-layer polydimethylsiloxane (PDMS) microfluidic channel using a standing surface acoustic wave (SSAW). The SSAW was generated by the interference of two identical surface acoustic waves (SAWs) created by two parallel interdigital transducers (IDTs) on a piezoelectric substrate with a microchannel precisely bonded between them. To understand the working principle of the SSAW-based 3D focusing and investigate the position of the focal point, we computed longitudinal waves, generated by the SAWs and radiated into the fluid media from opposite sides of the microchannel, and the resultant pressure and velocity fields due to the interference and reflection of the longitudinal waves. Simulation results predict the existence of a focusing point which is in good agreement with our experimental observations. Compared with other 3D focusing techniques, this method is non-invasive, robust, energy-efficient, easy to implement, and applicable to nearly all types of microparticles.