Effects of fuel cetane number on the structure of diesel spray combustion: An accelerated Eulerian stochastic fields method

An Eulerian stochastic fields (ESF) method accelerated with the chemistry coordinate mapping (CCM) approach for modelling spray combustion is formulated, and applied to model diesel combustion in a constant volume vessel. In ESF-CCM, the thermodynamic states of the discretised stochastic fields are mapped into a low-dimensional phase space. Integration of the chemical stiff ODEs is performed in the phase space and the results are mapped back to the physical domain. After validating the ESF-CCM, the method is used to investigate the effects of fuel cetane number on the structure of diesel spray combustion. It is shown that, depending of the fuel cetane number, liftoff length is varied, which can lead to a change in combustion mode from classical diesel spray combustion to fuel-lean premixed burned combustion. Spray combustion with a shorter liftoff length exhibits the characteristics of the classical conceptual diesel combustion model proposed by Dec in 1997 (http://dx.doi.org/10.4271/970873), whereas in a case with a lower cetane number the liftoff length is much larger and the spray combustion probably occurs in a fuel-lean-premixed mode of combustion. Nevertheless, the transport budget at the liftoff location shows that stabilisation at all cetane numbers is governed primarily by the auto-ignition process

Numerical and experimental investigations of interdigital transducer configurations for efficient droplet streaming and jetting induced by surface acoustic waves

Surface acoustic wave (SAW) based technologies have recently been explored for various sensing and microfluidic applications, and numerous experimental studies and numerical modelling of SAW streaming and liquid-solid interactions have been performed. However, the large deformation of droplet interface actuated by SAWs has not been widely explored, mainly due to the complex physics of SAW-droplet interactions and interfacial phenomena. In this paper, a computational interface tracking method is developed based on the couple level set the volume of fluid (CLSVOF) approach to simulate the interactions between liquid and acoustic waves and deformation of the liquid-air surface. A dynamic contact angle boundary condition is developed and validated by experimental results to simulate the three-phase contact line dynamics. The modified CLSVOF method is then used to study the droplet jetting and internal streaming behaviours by analyzing the energy terms within the liquid medium. Furthermore, by applying the numerical model, effects of configurations and positions of two interdigital transducers (IDTs) on droplet actuation have been investigated to achieve efficient mixing, separation, and jetting. Results show that two perfectly aligned IDTs are optimal for mixing applications. In contrast, two offset IDTs are optimal for concentration and separation applications. The maximum jetting velocity and minimum jetting time are achieved by using a pair of aligned IDTs, whereas by using the two offset IDTs, effective liquid mixing and jetting are observed which can be used in bioprinting applications

Dynamic Behavior of Droplet Impact on Inclined Surfaces with Acoustic Waves

Droplet impact on arbitrary inclined surfaces is of great interest for applications such as antifreezing, self-cleaning, and anti-infection. Research has been focused on texturing the surfaces to alter the contact time and rebouncing angle upon droplet impact. In this paper, using propagating surface acoustic waves (SAWs) along the inclined surfaces, we present a novel technique to modify and control key droplet impact parameters, such as impact regime, contact time, and rebouncing direction. A high-fidelity finite volume method was developed to explore the mechanisms of droplet impact on the inclined surfaces assisted by SAWs. Numerical results revealed that applying SAWs modifies the energy budget inside the liquid medium, leading to different impact behaviors. We then systematically investigated the effects of inclination angle, droplet impact velocity, SAW propagation direction, and applied SAW power on the impact dynamics and showed that by using SAWs, droplet impact on the nontextured hydrophobic and inclined surface is effectively changed from deposition to complete rebound. Moreover, the maximum contact time reduction up to ∼50% can be achieved, along with an alteration of droplet spreading and movement along the inclined surfaces. Finally, we showed that the rebouncing angle along the inclined surface could be adjusted within a wide range

Pengenalpastian protein membran putatif dalam sporozoit eimeria tenella melalui penyaringan imuno

Dalam parasit intrasel obligat seperti Eimeria tenella, protein membran dipercayai memainkan peranan yang penting dalam pengecaman dan pelekatan pada sel perumah supaya proses penyerangan parasit ke dalam sel perumah dapat disempurnakan. Untuk mengenalpasti protein pada membran E. tenella, penyaringan imuno telah dilakukan dengan menggunakan antiserum terhadap fraksi subsel yang telah diperkayakan dengan protein membran sporozoit. Usaha penyaringan imuno ini berjaya memencilkan 21 klon positif. Daripada jumlah ini, 13 klon menunjukkan pemadanan bermakna dengan jujukan dalam pangkalan data, iaitu 11 dengan protein mikronem EtMIC4, satu dengan EtMIC1 dan satu lagi dengan EtMIC2. Lapan klon selebihnya yang tidak menunjukkan sebarang pemadanan bermakna dengan jujukan dalam pangkalan data didapati membawa lima gen yang berlainan. Secara keseluruhannya, hasil kajian ini menunjukkan bahawa kaedah penyaringan imuno berupaya mengenalpasti gen baru yang kemungkinan besar mengekodkan protein membran dalam sporozoit E. tenella

Concentrated vertical jetting mechanism for isotropically focused Zno/Si surface acoustic waves

This paper investigates vertical droplet jetting using circular surface acoustic wave (CSAW) devices with annular interdigitated transducers (AIDTs) fabricated on ZnO film coated silicon substrate. The surface vibration on the CSAW devices was simulated using finite element analysis and characterised using laser vibrometry. Results showed that focused wave patterns and compact nodal distributions of vibration were formed at the centre of ZnO/Si CSAW device, which is contrast to an anisotropic wave distribution patterns generated by the same pattern of AIDTs fabricated on 128° Y-cut LiNbO3. Simulation of liquid jetting induced by the isotropically focused CSAW was performed using coupled Volume of Fluid and Level-Set method. Results showed that a sharp and cylindrical liquid column was generated from the ZnO/Si CSAW device induced by acoustic energy coming from all directions within the plane due to the in-plane isotropic nature of the ZnO thin films. The simulation enabled us to capture the different streaming/jetting processes induced by the anisotropic distributions of acoustic pressure generated by the AIDTs on the 128° Y-cut LiNbO3 CSAW device. The concentrated vertical droplet jetting behaviour from the ZnO/Si CSAW devices was investigated experimentally and supported the simulated results

Transcription factor trapping by RNA in gene regulatory elements

Transcription factors (TFs) bind specific sequences in promoter-proximal and -distal DNA elements to regulate gene transcription. RNA is transcribed from both of these DNA elements, and some DNA binding TFs bind RNA. Hence, RNA transcribed from regulatory elements may contribute to stable TF occupancy at these sites. We show that the ubiquitously expressed TF Yin-Yang 1 (YY1) binds to both gene regulatory elements and their associated RNA species across the entire genome. Reduced transcription of regulatory elements diminishes YY1 occupancy, whereas artificial tethering of RNA enhances YY1 occupancy at these elements. We propose that RNA makes a modest but important contribution to the maintenance of certain TFs at gene regulatory elements and suggest that transcription of regulatory elements produces a positive-feedback loop that contributes to the stability of gene expression programs.National Institutes of Health (U.S.) (HG002668)Biogen, Inc

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease, is the leading monogenic cause of infant mortality. Homozygous loss of the gene survival of motor neuron 1 (SMN1) causes the selective degeneration of lower motor neurons and subsequent atrophy of proximal skeletal muscles. The SMN1 protein product, survival of motor neuron (SMN), is ubiquitously expressed and is a key factor in the assembly of the core splicing machinery. The molecular mechanisms by which disruption of the broad functions of SMN leads to neurodegeneration remain unclear. We used an antisense oligonucleotide (ASO)-based inducible mouse model of SMA to investigate the SMN-specific transcriptome changes associated with neurodegeneration. We found evidence of widespread intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induction, which was then rescued by a therapeutic ASO. Intron retention was concomitant with a strong induction of the p53 pathway and DNA damage response, manifesting as gamma-H2A.X positivity in neurons of the spinal cord and brain. Widespread intron retention and markers of the DNA damage response were also observed with SMN depletion in human SH-SY5Y neuroblastoma cells and human induced pluripotent stem cell-derived motor neurons. We also found that retained introns, high in GC content, served as substrates for the formation of transcriptional R-loops. We propose that defects in intron removal in SMA promote DNA damage in part through the formation of RNA:DNA hybrid structures, leading to motor neuron death

Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions.

On December 17, 2018, the North American branch of the International Life Sciences Institute (ILSI North America) convened a workshop "Can We Begin to Define a Healthy Gut Microbiome Through Quantifiable Characteristics?" with >40 invited academic, government, and industry experts in Washington, DC. The workshop objectives were to 1) develop a collective expert assessment of the state of the evidence on the human gut microbiome and associated human health benefits, 2) see if there was sufficient evidence to establish measurable gut microbiome characteristics that could serve as indicators of "health," 3) identify short- and long-term research needs to fully characterize healthy gut microbiome-host relationships, and 4) publish the findings. Conclusions were as follows: 1) mechanistic links of specific changes in gut microbiome structure with function or markers of human health are not yet established; 2) it is not established if dysbiosis is a cause, consequence, or both of changes in human gut epithelial function and disease; 3) microbiome communities are highly individualized, show a high degree of interindividual variation to perturbation, and tend to be stable over years; 4) the complexity of microbiome-host interactions requires a comprehensive, multidisciplinary research agenda to elucidate relationships between gut microbiome and host health; 5) biomarkers and/or surrogate indicators of host function and pathogenic processes based on the microbiome need to be determined and validated, along with normal ranges, using approaches similar to those used to establish biomarkers and/or surrogate indicators based on host metabolic phenotypes; 6) future studies measuring responses to an exposure or intervention need to combine validated microbiome-related biomarkers and/or surrogate indicators with multiomics characterization of the microbiome; and 7) because static genetic sampling misses important short- and long-term microbiome-related dynamic changes to host health, future studies must be powered to account for inter- and intraindividual variation and should use repeated measures within individuals

AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors

YesAlternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95 (AKAP8), has a remarkable activity in enhancing chromatin transcription. In this study, we have shown that AKAP95 physically interacts with many factors involved in transcription and RNA processing, and functionally regulates pre-mRNA splicing. AKAP95 directly promotes splicing in vitro and the inclusion of a specific exon of an endogenous gene FAM126A. The N-terminal YG-rich domain of AKAP95 is important for its binding to RNA processing factors including selective groups of hnRNP proteins, and its zinc finger domains are critical for pre-mRNA binding. Genome-wide binding assays revealed that AKAP95 bound preferentially to proximal intronic regions on a large number of pre-mRNAs in human transcriptome, and AKAP95 depletion predominantly resulted in reduced inclusion of many exons. AKAP95 also selectively coordinates with hnRNP H/F and U proteins in regulating alternative splicing events. We have further shown that AKAP95 directly interacts with itself. Taken together, our results establish AKAP95 as a novel and mostly positive regulator of premRNA splicing and a possible integrator of transcription and splicing regulation, and support a model that AKAP95 facilitates the splice site communication by looping out introns through both RNA-binding and protein-protein interaction.This work was supported by a UAB start-up fund to H.J