1.Comparative domain modeling of human EGF-like module EMR2 and study of interaction of the fourth domain of EGF with chondroitin 4-sulphate. J Biomed Res, 2011; 25(2):100-110

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1.

Comparative domain modeling of human EGF
-
like module EMR2 and study
of interaction of the fourth domain of EGF with chondroitin 4
-
sulphate
.

J
Biomed Res, 2011; 2
5(2):
100
-
110

Mukta Rani, Manas R. Dikhit, Ganesh C Sahoo, Pradeep Das

Biomedical Informatics Di
vision, Rajendra Memorial Research Institute of
Medical Sciences, Agam Kuan, Patna
-
800007, India.


Abstract:
EMR2 is an EGF
-
like module containing mucin
-
like hormone receptor
-
2
precursor, a G
-
protein coupled receptor (G
-
PCR). Mutation in EMR2 causes
compl
icated disorders like polycystic kidney disease (PKD). The structure of EMR2
shows that the fifth domain is comprised of EGF
-
TM7 helices. Functional assignment
of EMR2 by support vector machine (SVM) revealed that along with transporter
activity, several n
ovel functions are predicted. A twenty amino acid sequence
"MGGRVFLVFLAFCVWLTLPG" acts as the signal peptide responsible for
post
-
translational transport. Eight amino acids are involved in N
-
glycosylation sites
and two cleavage sites are Leu
517

and Ser
518

in EMR2. The residue Arg
241

is
responsible for interaction with glycosaminoglycan and chondroitin sulfate. On the
basis of structure, function and ligand binding sites, competitive EMR2 inhibitors
designed may decrease the rate of human diseases like Usher

s syndrome, bilateral
frontoparietal polymicrogyria and PKD.


http://www.jbr
-
pub.org/ch/reader/view_abstract.aspx?file_no=jbr110203&flag=1


2.

Identification of distant co
-
evolving residues in antigen 85C from
Mycobacterium tuberculosis using statistical cou
pling analysis of the esterase
family proteins
.

J Biomed Res, 2011; 2
5(3):
165
-
169

Veeky Baths, Utpal Roy

Department of Biological Sciences, BITS Pilani K. K Birla Goa Campus, GOA
403726, India
.


Abstract:
A fundamental goal in cellular signaling is to unde
rstand allosteric
communication, the process by which signals originating at one site in a protein
propagate reliably to affect distant functional sites. The general principles of protein
structure that underlie this process remain unknown. Statistical cou
pling analysis
(SCA) is a statistical technique that uses evolutionary data of a protein family to
measure correlation between distant functional sites and suggests allosteric
communication. In proteins, very distant and small interactions between collecti
ons of
amino acids provide the communication which can be important for signaling process.
In this paper, we present the SCA of protein alignment of the esterase family (pfam
ID: PF00756) containing the sequence of antigen 85C secreted by
Mycobacterium
tub
erculosis

to identify a subset of interacting residues. Clustering analysis of the
pairwise correlation highlighted seven important residue positions in the esterase
family alignments. These residues were then mapped on the crystal structure of
antigen 85C

(PDB ID: 1DQZ). The mapping revealed correlation between 3 distant
residues (Asp38, Leu123 and Met125) and suggests allosteric communication
between them. This information can be used for a new drug against this fatal disease.


http://www.jbr
-
pub.org/ch/r
eader/view_abstract.aspx?file_no=jbr110302&flag=1


3.

MiR
-
148a inhibits angiogenesis by targeting ERBB3
.

J Biomed Res, 2011;
2
5(3):
170
-
177

Jing Yu
a
, Qi Li
a
, Qing Xu
a
, Lingzhi Liu
a
, Binghua Jiang
a,b

a
Lab of Reproductive Medicine, Department of Pathology, Jiang
su Key Lab of
Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical
University, Nanjing ,Jiangsu 210029, China;

b
Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson
University, Philadelphia, PA, USA.


Abstract:
Micro
RNAs (miRNAs) play an important role in carcinogenesis in various
solid cancers including breast cancer. Down
-
regulation of
microRNA
-
148a

(
miR
-
148a
)
has been reported in certain cancer types. However, the biological role of
miR
-
148a

and its related targets

in breast cancer are unknown yet. In this study, we showed that
the level of
miR
-
148a

was lower in MCF7 cells than that in MCF10A cells. V
-
erb
-
b2
erythroblastic leukemia viral oncogene homolog 3 (
ERBB3
) is a direct target of
miR
-
148a

in human breast cance
r cells through direct binding of
miR
-
148a
to
ERBB3

3

-
UTR region. Overexpression of
miR
-
148a

in MCF7 cells inhibited
ERBB3

expression, blocked the downstream pathway activation including activation of AKT,
ERK1/2, and p70S6K1, and decreased HIF
-
1
α

express
ion. Furthermore, forced
expression of
miR
-
148a

attenuated tumor angiogenesis
in vivo
. Our results identify
ERBB3

as a direct target of
miR
-
148a
, and provide direct evidence that
miR
-
148a

inhibits tumor angiogenesis through
ERBB3
and its downstream signali
ng molecules.
This information would be helpful for targeting the
miR
-
148a
/
ERBB3
pathway for
breast cancer prevention and treatment in the future.


http://www.jbr
-
pub.org/ch/reader/view_abstract.aspx?file_no=jbr110303&flag=1


4.

Molecular screening of patient
s with nonsyndromic hearing loss from
Nanjing city of China
.

J Biomed Res, 2011; 2
5(5):
309
-
318

Yajie Lu
a
, Dachun Dai
b
, Zhibin Chen
b
, Xin Cao
a
, Xingkuan Bu
b
, Qinjun Wei
a
,
Guangqian Xing
b

a
Department of Biotechnology, Nanjing Medical University, Nanjing, Jia
ngsu
210029, China;

b
Department of Otolaryngology, the First Affiliated Hospital of Nanjing Medical
University, Nanjing, Jiangsu 210029,China.


Abstract:
Hearing loss is the most frequent sensory disorder involving a multitude of
factors, and at least 50%
of cases are due to genetic etiology. To further characterize
the molecular etiology of hearing loss in the Chinese population, we recruited a total
of 135 unrelated patients with nonsyndromic sensorineural hearing loss (NSHL) for
mutational screening of
G
JB2, GJB3, GJB6, SLC26A4, SLC26A5
IVS2
-
2A>G and
mitochondrial
12SrRNA, tRNA
Ser(UCN)

by PCR amplification and direct DNA
sequencing. The carrier frequencies of deafness
-
causing mutations in these patients
were 35.55% in
GJB2
, 3.70% in
GJB6
, 15.56% in
SLC26A
4
and 8.14% in
mitochondrial
12SrRNA
, respectively. The results indicate the necessity of genetic
screening for mutations of these causative genes in Chinese population with
nonsyndromic hearing loss.


http://www.jbr
-
pub.org/ch/reader/view_abstract.aspx?f
ile_no=jbr110502&flag=1


5.

Generation of conditional knockout alleles for PRL
-
3
.

J Biomed Res, 2011;
2
5(6
):
438
-
443

Hong Yan
a, b
, Dong Kong
b
, Xiaomei Ge
b
, Xiang Gao
b
, Xiao Han
a

a
Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing
Medical
University, Nanjing, Jiangsu 210029, China;

b
Model Animal Research Center, Nanjing University, Nanjing, Jiangsu 210093,
China.


Abstract:
Phosphatase of regenerating liver
-
3 (PRL
-
3) is a member of the protein
tyrosine phosphatase (PTP) superfamily and is
highly expressed in cancer metastases.
For better understanding of the role of PRL
-
3 in tumor metastasis, we applied a rapid
and efficient method for generating
PRL
-
3

floxed mice and investigated its
phenotypes. A BAC retrieval strategy was applied to cons
truct the
PRL
-
3

conditional
gene
-
targeting vector. Exon 4 was selected for deletion to generate a nonfunctional
prematurely terminated short peptide as it will cause a frame
-
shift mutation.
Conditional knockout
PRL
-
3

mice were generated by using the
Crelox
P

system and
were validated by Southern blot and RT
-
PCR analysis. Further analysis revealed the
phenotype characteristics of PRL
-
3 knockout mice and wildtype mice. In this study,
we successfully constructed the
PRL
-
3

conditional knockout mice, which will b
e
helpful to clarify the roles of PRL
-
3 and the mechanisms in tumor metastasis.


http://www.jbr
-
pub.org/ch/reader/view_abstract.aspx?file_no=JBR110609&flag=1


6.

Expression, purification and characterization of Mycobacterium tuberculosis
RpfE protein
.

J Biom
ed Res, 2012; 2
6(1
):
17
-
23

Ying Xue
a
, Yinlan Bai
b
, Xue Gao
b
, Hong Jiang
b
, Limei Wang
b
, Hui Gao
b
, Zhikai Xu
b

a
Department of Radiation Therapy, Xijing Hospital, the Fourth Military Medical
University, Xian, Shaanxi 710032, China;

b
Department of Microbiology,

School of Basic Medicine, the Fourth Military
Medical University, Xian, Shaanxi 710032, China.


Abstract:
Resuscitation promoting factor E (RpfE) is one of the five Rpf
-
like proteins
in
Mycobacterium tuberculosis (M. tuberculosis)
. These Rpf
-
like proteins

are
secretory, which make them candidates for recognition by the host immune system. In
this study, the
RpfE

gene was amplified from
M. tuberculosis
, cloned into the
expression vectors pDE22 and pPRO EXHT, and were expressed in
Mycobacterium
vaccae (M. va
ccae)
and
Escherichia coli
DH5
α
, respectively. Both recombinant RpfE
proteins were purified by Ni
-
Sepharose affinity chromatography, and were given to
C57BL/6 mice. The RpfE proteins elicited T cell proliferation, and stimulated the
production of gamma int
erferon (IFN
-
γ
), interleukin
-
10 (IL
-
10) and IL
-
12. Our results
indicated that the RpfE protein expressed in
M. vaccae
could more efficiently
stimulate cellular immune response, making it a promising candidate as a subunit
vaccine.


http://www.jbr
-
pub.org/c
h/reader/view_abstract.aspx?file_no=JBR120103&flag=1


7.

Overexpression of the mTERT gene by adenoviral vectors promotes the
proliferation of neuronal stem cells in vitro and stimulates neurogenesis in
the hippocampus of mice
.
J Biomed Res
,

2012;

26
(5):381
-
38
8


Mengying Liu,

Yao Hu,

Lijuan Zhu,

Chen Chen,

Yu Zhang,

Weixiang Sun,

Qigang
Zhou

Department of Pharmacology, Pharmacy College, Nanjing Medical University,
Nanjing, Jiangsu 210029, China
.


Abstrac
t:

We sought to construct the adenoviral vector carrying t
he gene encoding
mouse telomerase reverse transcriptase (mTERT), as well as detect its expression and
effect on the proliferation of neuronal stem cells. mTERT was amplified by RT
-
PCR
and then the eukaryotic expression vector of pDC
-
EGFP
-
TERT w
as constructed. After
DNA sequence analysis, we detected that there were 293 cells transfected with
pDC
-
EGFP
-
TERT and helper adenovirus plasmid pBHG lox ΔE1, and three Cre using
Lipofectamine 2000 mediation, named Ad
-
mTERT
-
GFP, to package adenoviral
partic
les. The Ad
-
mTERT
-
GFP was used to infect neuronal stem cells and then the
expression and activity of mTERT were detected. In addition, Bromodeoxyuridine
labeling test identified the impact of mTERT overexpression on proliferation of
neuronal stem cells. Th
e recombinant adenoviral vector confirmed that mTERT was
successfully constructed. Overexpression of mTERT stimulated the proliferation of
neuronal stem cells both in vitro and in vivo. mTERT overexpression via adenoviral
vector carrying mTERT cDNA upregul
ated the ability of proliferation in neuronal
stem cells.


http://www.jbr
-
pub.org/ch/reader/view_abstract.aspx?file_no=JBR120510&flag=1