Short-term cardiac memory and mother rotor fibrillation

Short-term cardiac memory refers to the effects of pacing history on action potential duration (APD). Although the ionic mechanisms for short-term memory occurring over many heartbeats (also called APD accommodation) are poorly understood, they may have important effects on reentry and fibrillation. To explore this issue, we incorporated a generic memory current into the Phase I Luo and Rudy action potential model, which lacks short-term memory. The properties of this current were matched to simulate quantitatively human ventricular monophasic action potential accommodation. We show that, theoretically, short-term memory can resolve the paradox of how mother rotor fibrillation is initiated in heterogeneous tissue by physiological pacing. In simulated heterogeneous two-dimensional tissue and three-dimensional ventricles containing an inward rectifier K(+) current gradient, short-term memory could spontaneously convert multiple wavelet fibrillation to mother rotor fibrillation or to a mixture of both fibrillation types. This was due to progressive acceleration and stabilization of rotors as accumulation of memory shortened APD and flattened APD restitution slope nonuniformly throughout the tissue.     

In Silico Analysis of Synaptonemal Complex Protein 1 (SYCP1) and Acrosin Binding Protein (ACRBP) Antigens to Design Novel Multiepitope Peptide Cancer Vaccine Against Breast Cancer

Multiepitope cancer vaccines are manifesting as the future of breast cancer immunotherapy. In the present study, high immunogenic fragments of synaptonemal complex protein 1 (SYCP1) and acrosin binding protein (ACRBP) antigens were selected according to MHCs binding affinity and CD8⁺ cytotoxic T lymphocytes’ (CTL) epitopes by various immunoinformatic servers. (RCQHKIAEMVALMEKHKHQYDKI) residue from p702–724 SYCP1 and the (YIQYPNYCSFKSQQCL) residue from p481–496 ACRBP were selected as the immunodominant fragments. Then, the selected fragments were fused together with a furin-sensitive linker to form the final peptide vaccine construct. The cleavage sites, TAP transport efficiency, CTL epitopes, post-translational modifications, and B cells epitopes were predicted for the final construct. The final construct contained appropriate CTLs epitopes and also, several linear and conformational B cell epitopes. Also, it exhibited 90.37% HLA population coverage in the world. Therefore, these preliminary results require validation by in vitro and in vivo experiments.

     

Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining

The nonhomologous end-joining (NHEJ) pathway is essential for the preservation of genome integrity, as it efficiently repairs DNA double-strand breaks (DSBs). Previous biochemical and genetic investigations have indicated that, despite the importance of this pathway, the entire complement of genes regulating NHEJ remains unknown. To address this, we employed a plasmid-based NHEJ DNA repair screen in budding yeast (Saccharomyces cerevisiae) using 369 putative nonessential DNA repair-related components as queries. Among the newly identified genes associated with NHEJ deficiency upon disruption are two spindle assembly checkpoint kinases, Bub1 and Bub2. Both observation of resulting phenotypes and chromatin immunoprecipitation demonstrated that Bub1 and -2, either alone or in combination with cell cycle regulators, are recruited near the DSB, where phosphorylated Rad53 or H2A accumulates. Large-scale proteomic analysis of Bub kinases phosphorylated in response to DNA damage identified previously unknown kinase substrates on Tel1 S/T-Q sites. Moreover, Bub1 NHEJ function appears to be conserved in mammalian cells. 53BP1, which influences DSB repair by NHEJ, colocalizes with human BUB1 and is recruited to the break sites. Thus, while Bub is not a core component of NHEJ machinery, our data support its dual role in mitotic exit and promotion of NHEJ repair in yeast and mammals.     

Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs

Here, we report the use of an in vivo protein-protein interaction detection approach together with focused follow-up experiments to study the function of the DeaD protein in Escherichia coli. In this method, functions are assigned to proteins based on the interactions they make with others in the living cell. The assigned functions are further confirmed using follow-up experiments. The DeaD protein has been characterized in vitro as a putative prokaryotic factor required for the formation of translation initiation complexes on structured mRNAs. Although the RNA helicase activity of DeaD has been demonstrated in vitro, its in vivo activity remains controversial. Here, using a method called sequential peptide affinity (SPA) tagging, we show that DeaD interacts with certain ribosomal proteins as well as a series of other nucleic acid binding proteins. Focused follow-up experiments provide evidence for the mRNA helicase activity of the DeaD protein complex during translation initiation. DeaD overexpression compensates for the reduction of the translation activity caused by a structure placed at the initiation region of a chloramphenicol acetyltransferase gene (cat) used as a reporter. Deletion of the deaD gene, encoding DeaD, abolishes the translation activity of the mRNA with an inhibitory structure at its initiation region. Increasing the growth temperature disrupts RNA secondary structures and bypasses the DeaD requirement. These observations suggest that DeaD is involved in destabilizing mRNA structures during translation initiation. This study also provides further confirmation that large-scale protein-protein interaction data can be suitable to study protein functions in E. coli.     

The effect of photobiomodulation therapy in common maxillofacial injuries: Current status

The use of photobiomodulation therapy (PBMT) may be used for treating trauma to the maxillofacial region. The effects of PBMT on maxillofacial injuries were discussed in this review article. The electronic databases Pubmed, Scopus, and Web of Science were thoroughly searched. This review included in vitro, in vivo, and clinical studies describing how PBMT can be used in maxillofacial tissue engineering and regenerative medicine. Some studies suggest that PBMT may offer a promising therapy for traumatic maxillofacial injuries because it can stimulate the differentiation and proliferation of various cells, including dental pulp cells and mesenchymal stem cells, enhancing bone regeneration and osseointegration. PBMT reduces pain and swelling after oral surgery and tooth extraction in human and animal models of maxillofacial injuries. Patients with temporomandibular disorders also benefit from PBMT in terms of reduced inflammation and symptoms. PBMT still has some limitations, such as the need for standardizing parameters. PBMT must also be evaluated further in randomized controlled trials in various maxillofacial injuries. As a result, PBMT offers a safe and noninvasive treatment option for patients suffering from traumatic maxillofacial injuries. PBMT still requires further research to establish its efficacy in clinical practice and determine the optimal parameters.     

Effects of nerve graft on nitric oxide synthase, NAD(P)H oxidase, and antioxidant enzymes in chronic spinal cord injury

Oxidative stress and nitrosative stress play important roles in the pathogenesis of secondary spinal cord injury. Recently, we demonstrated that peripheral nerve grafts (PNG) with acidic fibroblast growth factor (aFGF) partially restore hind limb locomotion in adult rats with completely transected spinal cords. This study investigated the protein abundances of the superoxide (O2*)-generating enzyme nicotinamide adenine dinucleotide (phosphate) oxidase (NAD(P)H oxidase; gp91phox subunit), nitric oxide synthases (NOS), antioxidant enzymes, superoxide dismutases (Cu Zn SOD, Mn SOD), catalase, and glutathione peroxidase (GPX) as well as nitrotyrosine in the spinal cord tissue 4 months after spinal cord transection in rats with and without PNG and aFGF. The protein abundances of the gp91phox subunit of NAD(P)H oxidase, Mn SOD, catalase, GPX, eNOS, and nitrotyrosine were significantly upregulated, whereas Cu Zn SOD and nNOS were unchanged in the injury group compared to the sham controls. The nerve graft with aFGF treated group showed significantly better hind limb locomotion recovery than the injury group. Although the protein abundances of gp91phox, nitrotyrosine, and Cu Zn SOD were similar in the treated group (nerve graft with aFGF) compared to the injury group, Mn SOD, GPX, catalase, and eNOS protein abundances were significantly higher, whereas nNOS was markedly lower in the treated group. We conclude that the combination of nerve graft and aFGF enhances the local antioxidant defense system after spinal cord transection in rats.     

On the Relation between the Small World Structure and Scientific Activities

The modern science has become more complex and interdisciplinary in its nature which might encourage researchers to be more collaborative and get engaged in larger collaboration networks. Various aspects of collaboration networks have been examined so far to detect the most determinant factors in knowledge creation and scientific production. One of the network structures that recently attracted much theoretical attention is called small world. It has been suggested that small world can improve the information transmission among the network actors. In this paper, using the data on 12 periods of journal publications of Canadian researchers in natural sciences and engineering, the co-authorship networks of the researchers are created. Through measuring small world indicators, the small worldiness of the mentioned network and its relation with researchers’ productivity, quality of their publications, and scientific team size are assessed. Our results show that the examined co-authorship network strictly exhibits the small world properties. In addition, it is suggested that in a small world network researchers expand their team size through getting connected to other experts of the field. This team size expansion may result in higher productivity of the whole team as a result of getting access to new resources, benefitting from the internal referring, and exchanging ideas among the team members. Moreover, although small world network is positively correlated with the quality of the articles in terms of both citation count and journal impact factor, it is negatively related with the average productivity of researchers in terms of the number of their publications.     

Type-IV Pilus Deformation Can Explain Retraction Behavior

Polymeric filament like type IV Pilus (TFP) can transfer forces in excess of 100 pN during their retraction before stalling, powering surface translocation(twitching). Single TFP level experiments have shown remarkable nonlinearity in the retraction behavior influenced by the external load as well as levels of PilT molecular motor protein. This includes reversal of motion near stall forces when the concentration of the PilT protein is loweblack significantly. In order to explain this behavior, we analyze the coupling of TFP elasticity and interfacial behavior with PilT kinetics. We model retraction as reaction controlled and elongation as transport controlled process. The reaction rates vary with TFP deformation which is modeled as a compound elastic body consisting of multiple helical strands under axial load. Elongation is controlled by monomer transport which suffer entrapment due to excess PilT in the cell periplasm. Our analysis shows excellent agreement with a host of experimental observations and we present a possible biophysical relevance of model parameters through a mechano-chemical stall force map.