Abstract: Salt stress adversely affects plant growth at various stages of development including seed germination, seedling establishment, vegetative growth and finally reproduction. Because of their immobile nature, plants have evolved mechanisms to sense and respond to salt stress. Seed dormancy is an adaptive trait that enables seed germination to coincide with favorable environmental conditions. We identified a novel locus of Arabidopsis, designated SHG1 (salt hypersensitive germination 1), whose disruption leads to reduced germination rate under moderate salt stress conditions. SHG1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. The shg1-disrupted Arabidopsis mutant died at the cotyledon stage when sown on salt-containing medium, although wild-type plants could form true leaves under the same conditions. On the other hand, this mutant showed similar phenotypes to wild-type plants when sown on medium without salt and transferred to salt-containing medium at the vegetative stage. These results suggested that SHG1 played indispensable role in the seed germination and seedling establishment under moderate salt stress conditions. SHG1 may be involved in the release of seed dormancy.
Abstract: Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.
Abstract: Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.
Abstract: Bioinformatics methods for predicting the T cell
coreceptor usage from the array of membrane protein of HIV-1 are
investigated. In this study, we aim to propose an effective prediction
method for dealing with the three-class classification problem of
CXCR4 (X4), CCR5 (R5) and CCR5/CXCR4 (R5X4). We made
efforts in investigating the coreceptor prediction problem as follows: 1)
proposing a feature set of informative physicochemical properties
which is cooperated with SVM to achieve high prediction test
accuracy of 81.48%, compared with the existing method with
accuracy of 70.00%; 2) establishing a large up-to-date data set by
increasing the size from 159 to 1225 sequences to verify the proposed
prediction method where the mean test accuracy is 88.59%, and 3)
analyzing the set of 14 informative physicochemical properties to
further understand the characteristics of HIV-1coreceptors.
Abstract: The prediction of transmembrane helical segments
(TMHs) in membrane proteins is an important field in the
bioinformatics research. In this paper, a method based on discrete
wavelet transform (DWT) has been developed to predict the number
and location of TMHs in membrane proteins. PDB coded as 1F88 was
chosen as an example to describe the prediction of the number and
location of TMHs in membrane proteins by using this method. One
group of test data sets that contain total 19 protein sequences was
utilized to access the effect of this method. Compared with the
prediction results of DAS, PRED-TMR2, SOSUI, HMMTOP2.0 and
TMHMM2.0, the obtained results indicate that the presented method
has higher prediction accuracy.
Abstract: The prediction of transmembrane helical segments
(TMHs) in membrane proteins is an important field in the
bioinformatics research. In this paper, a new method based on discrete
wavelet transform (DWT) has been developed to predict the number
and location of TMHs in membrane proteins. PDB coded as 1KQG
was chosen as an example to describe the prediction of the number and
location of TMHs in membrane proteins by using this method. To
access the effect of the method, 80 proteins with known 3D-structure
from Mptopo database are chosen at random as the test objects
(including 325 TMHs), 308 of which can be predicted accurately, the
average predicted accuracy is 96.3%. In addition, the above 80
membrane proteins are divided into 13 groups according to their
function and type. In particular, the results of the prediction of TMHs
of the 13 groups are satisfying.
Abstract: The aim of this study was to estimate the frequency of
EBV infection in Hodgkin's lymphoma (HL) and non-Hodgkin's
lymphoma (NHL) occurring in Jordanian patients. A total of 55
patients with lymphoma were examined in this study. Of 55 patients,
30 and 25 were diagnosed as HL and NHL, respectively. The four
HL subtypes were observed with the majority of the cases exhibited
the mixed cellularity (MC) subtype followed by the nodular sclerosis
(NS). The high grade was found to be the commonest subtype of
NHL in our sample, followed by the low grade. The presence of EBV
virus was detected by immunostating for expression of latent
membrane protein-1 (LMP-1). The frequency of LMP-1 expression
occurred more frequent in patients with HL (60.0%) than in patients
with NHL (32.0%). The frequency of LMP-1 expression was also
higher in patients with MC subtype (61.11%) than those patients with
NS (28.57%). No age or gender difference in occurrence of EBV
infection was observed among patient with HL. By contrast, the
prevalence of EBV infection in NHL patients aged below 50 was
lower (16.66%) than in NHL patients aged 50 or above (46.15%). In
addition, EBV infection was more frequent in females with NHL
(38.46%) than in male with NHL (25%). In NHL cases, the
frequency of EBV infection in intermediate grade (60.0%) was high
when compared with frequency of low (25%) or high grades (25%).
In conclusion, analysis of LMP-1 expression indicates an important
role for this viral oncogene in the pathogenesis of EBV-associated
malignant lymphomas. These data also support the previous findings
that people with EBV may develop lymphoma and that efforts to
maintain low lymphoma should be considered for people with EBV
infection.
Abstract: We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.
Abstract: Bones are dynamic and responsive organs, they
regulate their strength and mass according to the loads which they are subjected. Because, the Wnt/β-catenin pathway has profound
effects on the regulation of bone mass, we hypothesized that mechanical loading of bone cells stimulates Wnt/β-catenin signaling, which results in the generation of new bone mass.
Mechanical loading triggers the secretion of the Wnt molecule, which after binding to transmembrane proteins, causes GSK-3β (Glycogen synthase kinase 3 beta) to cease the phosphorylation of β-catenin. β-catenin accumulation in the cytoplasm, followed by its
transport into the nucleus, binding to transcription factors (TCF/LEF)
that initiate transcription of genes related to bone formation. To test this hypothesis, we used TOPGAL (Tcf Optimal Promoter
β-galactosidase) mice in an experiment in which cyclic loads were
applied to the forearm. TOPGAL mice are reporters for cells effected
by the Wnt/β-catenin signaling pathway. TOPGAL mice are genetically engineered mice in which transcriptional activation of β-
catenin, results in the production of an enzyme, β-galactosidase. The
presence of this enzyme allows us to localize transcriptional
activation of β-catenin to individual cells, thereby, allowing us to quantify the effects that mechanical loading has on the Wnt/β-catenin pathway and new bone formation. The ulnae of loaded TOPGAL
mice were excised and transverse slices along different parts of the
ulnar shaft were assayed for the presence of β-galactosidase.
Our results indicate that loading increases β-catenin transcriptional
activity in regions where this pathway is already primed (i.e. where basal activity is already higher) in a load magnitude dependent
manner. Further experiments are needed to determine the temporal and spatial activation of this signaling in relation to bone formation.
Abstract: Aptamers are useful tools in microorganism
researches, diagnoses, and treatment. Aptamers are specific target
molecules formed by oligonucleic acid molecules, and are not
decomposed by alcohol. Aptamers used to detect Mycobacterium
tuberculosis (MTB) have been proved to have specific affinity to the
outer membrane proteins of MTB. This article presents a biosensor
chip set with aptamers for early detection of MTB with high specificity
and sensitivity, even in very low concentration. Meanwhile, we have
already made a modified hydrophobic facial mask module with
internal rendering hydrophobic for effectively collecting M.
tuberculosis.