Discontinuous phenomena in bioreactor and membrane reactor systems

In this work, we analyze the existence of discontinuous bifurcation and stability issues in discontinuous flow of bioreactor and membrane reactor models with or without recycle. The reaction is assumed to be governed by certain types of discontinuities in Monod growth kinetics curve leading to discontinuous dynamical system. The criteria for the existence and stability of steady-states of these models are established. More generally, our analysis highlights the presence of several types of bifurcation depending upon the effect of the dilution factor (residence time), biomass concentration and solid-liquid-gas separator efficiency. As well, we present bifurcation conditions defining the dynamics near steady-state branches on the border, providing a possible framework for existing of saddle-node, nonsmooth fold, persistence and grazing-sliding scenarios. It is shown that the critical values of residence time dependence upon recycle ratio, decay rate and existence of discontinuity surface. Further, the performance of the reactor at largest residence times will be discussed. In addition, numerical simulations to illustrate and confirm the results will be carried out.     

Effect of salt stress on photosystem Ⅱ heterogeneity in wheat leaves

In order to study the effects of salt stress on photosystem Ⅱ (PSⅡ) heterogeneity, signal from the fluorometer was digitized via a microcomputer interface to record PSⅡ fluorescence induction kinetics. Changes of parameters (Fm, Fp1 and F0) from the fast phase of fluorescence induction curve showed that the percentage of QB-nonreducing PSⅡ reaction centers dropped at first, and then rose with the increase of stress intensity and time. This indicated that the electron transfer from QA to QB is one of the sites where the photochemical and photophysical processes of PSⅡ are damaged by the salt stress.     

Sorting by restricted-length-weighted reversals

Classical sorting by reversals uses the unit-cost model, that is, each reversal consumes an equal cost. This model limits the biological meaning of sorting by reversal. Bender and his colleagues extended it by assigning a cost function f（1） = l^a for all a≥ 0, where l is the length of the reversed subsequence. In this paper, we extend their results by considering a model in which long reversals are prohibited. Using the same cost function above for permitted reversals, we present tight or nearly tight bounds for the worst-case cost of sorting by reversals. Then we develop algorithms to approximate the optimal cost to sort a given 0/1 sequence as well as a given permutation. Our proposed problems are more biologically meaningful and more algorithmically general and challenging than the problem considered by Bender et al. Furthermore, our bounds are tight and nearly tight, whereas our algorithms provide good approximation ratios compared to the optimal cost to sort 0/1 sequences or permutations by reversals.     

A novel algorithm for finding interspersed repeat regions

The analysis of repeats in the DNA sequences is an important subject in bioinformatics. In this paper, we propose a novel projection-assemble algorithm to find unknown interspersed repeats in DNA sequences. The algorithm employs random projection algorithm to obtain a candidate fragment set, and exhaustive search algorithm to search each pair of fragments from the candidate fragment set to find potential linkage, and then assemble them together. The complexity of our projection-assemble algorithm is nearly linear to the length of the genome sequence, and its memory usage is limited by the hardware. We tested our algorithm with both simulated data and real biology data, and the results show that our projection-assemble algorithm is efficient. By means of this algorithm, we found an un-labeled repeat region that occurs five times in Escherichia coil genome, with its length more than 5,000 bp, and a mismatch probability less than 4%.     

Viral RNA-based transfection and expression of enhanced green fluorescent protein in the parasitic protozoan Eimeria stiedae

Eimeria stiedae(E.stiedae),the most common protozoan pathogen of rabbits,causes coccidiosis.This disease is problematic for rabbit breeders [1].There is little information about the cellular and molecular biology of this pathogen and a lack of genetic tools.Genetic manipulation is necessary to advance our understanding of parasite biology and ultimately develop vaccines and treat diseases.DNA-mediated and viral RNA-mediated transfection systems have successfully been established in many protozoan parasites [2,3].It was discovered that E.stiedae possesses a dsRNA virus(EsRV1),and more recently,the genome of this virus has been sequenced.To date,however,there is no report on the use of viral RNA-mediated transfection for E.stiedae.In this study,we report a transient viral RNA-mediated transfection of E.stiedae using enhanced green fluorescent protein(EGFP)as a reporter gene.Our study provides a valuable genetic tool for studying the biology of E.stiedae.     

Molecular Phylogeny Supports the Validity of Polypedates impresus Yang 2008

The taxonomy of the Asian tree frogs of the Polypedates leucomystax complex, a group of widespread and morphologically similar species, is very controversial. To ascertain the taxonomic status of these species, we investi- gated the historical relationships among representative samples based on ～ 2 kb of nucleotide sequences from the mitochondrial 12S rRNA, tRNAvaline, and 16S rRNA genes. Our phylogeny resolved five well supported lineages(A, B, C, D and E) in the P. leucomystax complex. Polypedates impresus from Yunnan, China, Polypedates cf. mutus and Polypedates cf. megacephalus from Guangxi and Yunnan, China, and Laos constructed Clade C, which is monophyletic. In order to recognize the unique position of this clade, we considered P. impresus in Clade C as a valid species. Following our phylogeny, Chinese Polypedates, corresponding to the other four clades, should include four species: P. mutus(Clade A); P. braueri(Clade B); P. impresus(Clade C) and P. megacephalus(Clade D). P. leucomystax(Clade E) is mainly distributed in the Malaysia, Indonesia and Philippines.     

Simulating the Folding Pathway of RNA Secondary Structure Using the Modified Ant Colony Algorithm

<正> A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial stage.Furthermore,a more realistic formula is used to compute the energy ofmulti-branch loop in the following iteration.Then a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different stems.Finally by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values forparameters.The measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.     

Analysis of a predator-prey model with herd behavior and disease in prey incorporating prey refuge

In this work,we have introduced an eco-epidemiological model of an infected predator prey system.Incorporation of prey refuge gives that a fraction of the infected prey is available to the predator for consumption.Moreover,to make the model more realistic to the environment,we have introduced strong Allee effect in the susceptible population.Boundedness and positivity of the solution have been established.Local stability conditions of the equilibrium points have been found with the help of Routh-Hurwitz criterion and it has been observed that if a prey population is infected with a lethal disease,then both the prey(susceptible and infected)and predator cannot survive simultaneously in the system for any parametric values.The disease transmission rate and the attack rate on the susceptible have an important role to control the system dynamics.For different values of these two key parameters,we have got only healthy or disease-free or predation-free or a fluctuating disease-free or even a fluctuating predator-free system with some certain parametric conditions.     

Photo-induced electron transfer between hypocrellins and nano-sized semiconductor CdS——EPR study on the kinetics of photosensitized reduction in HA-CdS and HB-CdS systems

Both HA-CdS and HB-CdS (Hys-CdS, Hys represents HA, HB) complex systems were established according to the dynamics of heterogeneous electron-transfer process μ = Es/s+-ECB <0. In these systems, the electron transferring from 1Hys* to conduction band ofCdS is feasible. Determined from the fluorescence quenching, the apparent association constants (Kapp) between Hypocrellin A(HA), Hypocrellin B (HB) and CdS sol. were about 940 (mol/L)-1, 934 (mol/L)-1, respectively. Fluorescence lifetime measurements gave the rate constant for the electron transfer process from 1HA*, 1HB* into conduction band of CdS semiconductor as 5.16×109 s-1, 5.10×109 s-1, respectively. TEMPO (2,2,6,6-tetramethy-1-piperdinyloxy), a stable nitroxide radical, was used in the kinetic study of the reduction reaction taking place on the surface of a CdS colloidal semiconductor, kinetics equation of the reaction was determined with the electron paramagnetic resonance (EPR) method, and the reaction order of TEMPO is zero. When Hys were add     

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase. In addition to factor for inversion stimulation(Fis), histone-like nucleoid structuring protein(H-NS), heat-unstable nucleoid protein(HU) and integration host factor(IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells(Dps), host factor for phage Qβ(Hfq) and suppressor of td- phenotype A(Stp A). Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, Stp A and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli.     

Entry of severe fever with thrombocytopenia syndrome virus

Severe fever with thrombocytopenia syndrome virus(SFTSV) is a globe-shaped virus covered by a dense icosahedral array of glycoproteins Gn/Gc that mediate the attachment of the virus to host cells and the fusion of viral and cellular membranes. Several membrane factors are involved in virus entry, including C-type lectins and nonmuscle myosin heavy chain ⅡA. The post-fusion crystal structure of the Gc protein suggests that it is a class Ⅱ membrane fusion protein, similar to the E/E1 protein of flaviviruses and alphaviruses. The virus particles are internalized into host cell endosomes through the clathrin-dependent pathway, where the low pH activates the fusion of the virus with the cell membrane. With information from studies on other bunyaviruses, herein we will review our knowledge of the entry process of SFTSV.     

Appetite control： why we fail to stop eating even when we are full？

We often eat more than our body needs. We live in an environment where high calorie food is abundant and physical activities are limited. Living in this environment, maintaining healthy bodyweight becomes challenging and obesity becomes a social burden. Why do we continue to eat even after the metabolic needs are satisfied？ Feeding is an ancient behavior essential to survive. Thus the mechanisms to regulate appetite, energy expenditure, and energy storage are well conserved throughout animals. Based on this conservation, we study why we fail to control appetite using a simple genetic model system C. elegans. We have discovered certain genetic components that when misregulated have animals eat more and store more fat. In this review we discuss how these genes work in the appetite control circuit to ultimately understand overall appetite control behavior. We will also briefly discuss how social influence affects feeding regardless of the metabolic status of an animal.     

The E protein is a multifunctional membrane protein of SARS-CoV

The E (envelope) protein is the smallest structural protein in all coronaviruses and is the only viral structural protein in which no variation has been detected. We conducted genome sequencing and phylogenetic analyses of SARS-CoV. Based on genome sequencing, we predicted the E protein is a transmembrane (TM) protein characterized by a TM region with strong hydrophobicity and α-helix conformation. We identified a segment (NH2-_L-Cys-A-Y-Cys-Cys-N_-COOH) in the carboxyl-terminal region of the E protein that appears to form three disulfide bonds with another segment of corresponding cysteines in the carboxyl-terminus of the S (spike) protein. These bonds point to a possible structural association between the E and S proteins. Our phylogenetic analyses of the E protein sequences in all published coronaviruses place SARS-CoV in an independent group in Coronaviridae and suggest a non-human animal origin.     

Protein product encoded by a human novel gene E9730 enhances AP-1 activity through interacting with Jab1

A novel human gene, named E9730 (a clone number of fetal liver cDNA library), has been identified from more than 14,000 expressed sequence tags (ESTs) based on our large scale sequencing of human fetal liver cDNA libraries. Although sequencing of this novel human gene indicates that it is a leucine zipper protein, the function of E9730 and its homologous genes among species is unknown yet. To find out physiological functional clue of E9730, the yeast two-hybrid system was used to screen the E9730-interac-ting protein(s), and one clone containing a cDNA insert with almost the entire coding sequence (amino acids 39-335) of human Jabl (Jun-activating domain binding protein 1) that interacted specifically with E9730 was identified. A specific association between Jabl and E9730 was shown by co-immunoprecipitation and co-localization experiments. Furthermore, E9730 appeared to enhance Jab 1 -induced AP-1 activity in a concentration-dependent manner and Jabl may be involved in the intracellular signaling trans     

Modeling and dynamics of an ecological-economic model

In this paper, an eco-economic model with harvesting on biological population is established, which takes the form of a differential-algebra system. The impact of the economic profit from harvesting upon the dynamics of the model is studied. By using a suitable parameterization for the differential-algebra system, we derive an equivalent parameterized system which gives the stability results for the positive equilibrium point of our model. Moreover, based on the parameterized system as well as the approaches of normal form and formal series, the conditions on the Hopf bifurcation and the stability of center are obtained. Several numerical simulations for demonstrating the theoretical results are also presented. Lastly, according to the dynamical analysis, we provide a threshold value for the economic profit, which can maintain the sustainable development of our eco-economic system.     

YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.     

Effects of Three Commonly-used Diuretics on the Urinary Proteome

bstract Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic,rine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker ource than blood. However, since the urinary proteome is affected by many factors, including iuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker iscovery. Here, we evaluated the effects of three commonly-used diuretics(furosemide, F; hydrochlorothiazide,H; and spirolactone, S) on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the roteomes were analyzed using label-free liquid chromatography–tandem mass spectrometry LC–MS/MS). Based on the criteria of P 6 0.05, a fold change P2, a spectral count P5, and false ositive rate(FDR) 61%, 14 proteins(seven for F, five for H, and two for S) were identified by rogenesis LC–MS. The human orthologs of most of these 14 proteins are stable in the healthy uman urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results uggest that the effects of diuretics deserve more attention in future urinary protein biomarker tudies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to     

Roles of sphingosine 1-phosphate on tumorigenesis

Sphingosine 1-phosphate (S1P) is a bioactive sphingolipid with a variety of biological activities.It is generated from the conversion of ceramide to sphingosine by ceramidase and the subsequent conversion of sphingosine to S1P,which is catalyzed by sphingosine kinases.Through increasing its intracellular levels by sphingolipid metabolism and binding to its cell surface receptors,S1P regulates several physiological and pathological processes,including cell proliferation,migration,angiogenesis and autophagy.These processes are responsible for tumor growth,metastasis and invasion and promote tumor survival.Since ceramide and S1P have distinct functions in regulating in cell fate decision,the balance between the ceramide/sphingosine/S1P rheostat becomes a potent therapeutic target for cancer cells.Herein,we summarize our current understanding of S1P signaling on tumorigenesis and its potential as a target for cancer therapy.     

Cold adaptation of a mesophilic cellulase,EG Ⅲ from Trichoderma reesei,by directed evolution

Cold-active enzymes have received little research attention although they are very useful in industries. Since the structure bases of cold adaptation of enzymes are still unclear, it is also very difficult to obtain cold-adapted enzymes for industrial applications using routine protein engineering methods. In this work, we employed directed evolution method to randomly mutate a mesophilic cellulase, endoglucanase Ⅲ (EG Ⅲ) from Trichoderma reesei, and obtained a cold-adapted mutant, designated as w-3. DNA sequence analysis indicates that w-3 is a truncated form of native EG Ⅲ with a deletion of 25 consecutive amino acids at C-terminus. Further examination of enzymatic kinetics and thermal stability shows that mutant w-3 has a higher Kcat value and becomes more thermolabile than its parent. In addition, activation energies of w-3 and wild type EG Ⅲ calculated from Arrhenius equation are 13.3 kJ· mol-1 and 26.2 kJ ·mol-1, respectively. Therefore, the increased specific activity of w-3 at lower tempera