Genome-wide analysis of Solanum lycopersicum L. cyclophilins

Khadiza Khatun,Arif Hasan Khan Robin,Md Rafiqul Islam,Subroto Das Jyoti,Do-Jin Lee,김창길,정미영 한국식물생명공학회 2022 JOURNAL OF PLANT BIOTECHNOLOGY Vol.49 No.1

Cyclophilins (CYPs) are highly conserved ubiquitous proteins belong to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily. These proteins are present in a wide range of organisms; they contain a highly conserved peptidylprolyl cis/trans isomerase domain. A comprehensive database survey identified a total of 35 genes localized in all cellular compartments of Solanum lycopersicum L., but largely in the cytosol. Sequence alignment and conserved motif analyses of the SlCYP proteins revealed a highly conserved CLD motif. Evolutionary analysis predicted the clustering of a large number of gene pairs with high sequence similarity. Expression analysis using the RNA-Seq data showed that the majority of the SlCYP genes were highly expressed in mature leaves and blooming flowers, compared with their expression in other organs. This study provides a basis for the functional characterization of individual CYP genes in the future to elucidate their role(s) in protein refolding and long-distance signaling in tomatoes and in plant biology, in general

Riverbank erosion and its impact on rural women: Case study of Ulania village in Bangladesh

Khadiza Akter,Soma Dey,Shaakeel Hasan 이화여자대학교 아시아여성학센터 2019 Asian Journal of Women's Studies(AJWS) Vol.25 No.1

Riverbank erosion is one of the major natural hazards that have long-term consequences for human life. Bangladesh, a riverine country, regularly suffers from serious riverbank erosion. As a result, thousands of people, living near or along riverbanks, are displaced every year. Based on a field investigation undertaken in a village of Southern Bangladesh, this study examines how rural women cope with riverbank erosion. It reveals that women remain highly dependent on their surrounding environment to perform a wide range of activities. As a result, displacement due to riverbank erosion severely affects them. This article also shows that despite the socio-economic, cultural and gender barriers, women build diverse strategies to carry on with their lives in a new environment. Our findings identify women's capacity to face adversities due to natural hazards and how they use their own agency to influence social transformation.

Expression Profiling of the CSDP Transcription Factor Gene Family Points to Roles in Organ Development and Abiotic Stress Response in Tomato (Solanum lycopersicum L.)

Khatun, Khadiza,Nath, Ujjal Kumar,Park, Jong-In,Kim, Chang Kil,Nou, Ill Sup,Chung, Mi-Young Springer-Verlag 2018 Plant molecular biology reporter Vol.36 No.2

Molecular Characterization and Expression Profiling of Tomato GRF Transcription Factor Family Genes in Response to Abiotic Stresses and Phytohormones

Khatun, Khadiza,Robin, Arif Hasan Khan,Park, Jong-In,Nath, Ujjal Kumar,Kim, Chang Kil,Lim, Ki-Byung,Nou, Ill Sup,Chung, Mi-Young MDPI 2017 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.18 No.5

<P>Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (<I>Solanum lycopersicum</I>) have not been extensively explored. In this study, we characterized the 13 <I>SlGRF</I> genes. In silico analysis of protein motif organization, intron–exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the <I>SlGRF</I> genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that <I>SlGRFs</I> are important during growth and development of these tissues. Some of the <I>SlGRF</I> genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different <I>SlGRFs</I> under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of <I>SlGRF</I> genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.</P>

Comparison between Visual Inspection of Cervix and Cytology Based Screening Procedures in Bangladesh

Nessa, Ashrafun,Nahar, Khadiza Nurun,Begum, Shirin Akhter,Anwary, Shahin Ara,Hossain, Fawzia,Nahar, Khairun Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.12

Background: Cervical cancer continues to be a major problem in Bangladesh with approximately 18,000 new cases annually of which over 10,000 women die from it. Visual inspection of the cervix after 3-5% acetic acid (VIA) application is a simple and easy to learn method for cervical cancer screening, although cytology-based screening is more often applied in developed countries where it has successfully reduced the prevalence of cervical cancer. Objective: To compare the efficacy of VIA and cytology-based primary methods for cervical cancer screening in Bangladesh. Materials and Methods: This hospital based comparative study was conducted at the VIA centre and Colposcopy Clinic of Bangabandhu Sheikh Mujib Medical University (BSMMU) from October 2008 to October 2010. Results: Among 650 women, 74 (11.4%) were VIA+ve and 8 (1.2%) had abnormalities in their Pap smear reports. During colposcopy, 38 (7.7%) women had different grades of CIN and 4 (0.6%) had cervical cancer. The gold standard histology findings proved 20 women had CIN I, 14 had CIN II/II and 4 had cervical cancer. Among the 38 histology diagnosed abnormalities, VIA test could identify 30 abnormalities including two cervical cancers. However, Pap smear could detect only 8 cases of histological abnormalities (2 low grade and 6 had high grade lesion) and it missed all the cervical cancer cases. The sensitivity and specificity of VIA were 88.9% and 52.1%. The positive predictive value (PPV) and negative predictive value (NPV) were 41.0%, and 92.6% respectively. Moreover, the sensitivity, specificity, PPV and NPV of Pap smear were 33.3%, 95.8%, 75.0% and 79.3%, respectively. Conclusions: VIA test should be used as the primary screening tool even with its low sensitivity and specificity in low resource countries like Bangladesh. False positive results may be greater, but overtreatment can be minimized by colposcopy evaluation of the VIA positive women.

In vitro propagation of Phaleonopsis hybrid ‘Little gem’ by culturing apical part and axillary bud of flower stalk

정미영,AUNG HTAY NAING,Khadiza Khatun,안형근,임기병,김창길 한국식물생명공학회 2016 JOURNAL OF PLANT BIOTECHNOLOGY Vol.43 No.4

The in vitro propagation of the commercially important Phalaeonopsis hybrid ‘Little gem’ was achieved by culturing the apical part and axillary buds excised from flower stalks. The explants were cultured on 5 different basal media: 3.0 g・L-1 Hyponex and 4.0 g・L-1 peptone (H3P4) and Murashige & Skoog (MS) media were shown to be suitable for shoot regeneration. The MS medium supplemented with 5.0 mg・L-1 6-benzylaminopurine (BA) was found to be more efficient for shoot regeneration. However, the number of shoots induced by axillary buds was higher than that induced by the apical part. Incubation of the apical part under darkness for one week, as well as of the explants in the same medium with activated charcoal (AC) 0.5 g・L-1 promoted shoot regeneration and shoot growth; similar growth was not observed with axillary buds.

In vitro propagation of Phaleonopsis hybrid 'Little gem' by culturing apical part and axillary bud of flower stalk

Chung, Mi Young,Naing, Aung Htay,Khatun, Khadiza,Ahn, Hyung Geun,Lim, Ki Byung,Kim, Chang Kil The Korean Society of Plant Biotechnology 2016 식물생명공학회지 Vol.43 No.4

The in vitro propagation of the commercially important Phalaeonopsis hybrid 'Little gem' was achieved by culturing the apical part and axillary buds excised from flower stalks. The explants were cultured on 5 different basal media: $3.0{\cdot}L^{-1}$ Hyponex and $4.0{\cdot}L^{-1}$ peptone ($H_3P_4$) and Murashige & Skoog (MS) media were shown to be suitable for shoot regeneration. The MS medium supplemented with $5.0mg{\cdot}L^{-1}$ 6-benzylaminopurine (BA) was found to be more efficient for shoot regeneration. However, the number of shoots induced by axillary buds was higher than that induced by the apical part. Incubation of the apical part under darkness for one week, as well as of the explants in the same medium with activated charcoal (AC) $0.5g{\cdot}L^{-1}$ promoted shoot regeneration and shoot growth; similar growth was not observed with axillary buds.

Modification of Fatty Acid Profiles of Rapeseed (Brassica napus L.) Oil for Using as Food, Industrial Feed-Stock and Biodiesel

( Ujjal Kumar Nath ),( Hoy Taek Kim ),( Khadiza Khatun ),( Jong In Park ),( Kwon Kyoo Kang ),( Ill Sup Nou ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.2

Rapeseed is a member of family Brassicaceae, cultivated as oil crop. Rapeseed oil is being utilized from early civilization, but its popularity being declined from the mid-nineteenth century due to presence of erucic acid (C22:1) and glucosinolates. Thereby, several attempts have been made to develop cultivars free from those toxins. In the past 20 years, breeders got success in developing ``00``- quality rapeseed, known as ``Canola``. The target mutagenesis of fae-1 and fae-2 of Brassica napus ensured such success. Thereafter, ``canola`` regains its market as a healthy vegetable oil. Moreover, high oleic acid rapeseed lines, with 86% oleic acid, have been developed by using chemical mutagenesis of FAD2 alleles responsible for desaturation of oleic acid (C18:1) to linoleic acid (C18:2). Recently, high erucic acid rapeseed oil regained interest for biodegradable plastic, cosmetic, emollient industries and for biodiesel. Therefore, breeding approaches have been pursued; unfortunately, that were failed to reach erucic acid level beyond 50% in seed-oil. Rapeseed genotypes over-expressed with Ld-LPAAT separately and Ld-LPAAT-FAE chimaric construct together were tried but failed to reach the erucic acid content more than 60%. Thereof, combined effort of conventional breeding and transgenic approaches are brought together to overcome three hypothesized bottlenecks; reviewed in this article, which restricted erucic acid level near to 60%. Finally, rapeseed genotypes with 78% erucic acid were developed successfully. This material is now available in Germany for using in emollient industries and for biodiesel. Therefore, this article is reviewed on the current status and future outlook for modification of fatty acid profiles of rapeseed oil for its end-use as food, industrial feed-stock and biodiesel.

Assessment of the Therapeutic Potential of Persimmon Leaf Extract on Prediabetic Subjects

Mohd M. Khan,Bao Quoc Tran,장윤진,박수현,William E. Fondrie,Khadiza Chowdhury,윤성환,David R. Goodlett,채수완,채한정,서승영,구영아 한국분자세포생물학회 2017 Molecules and cells Vol.40 No.7

Dietary supplements have exhibited myriads of positive health effects on human health conditions and with the advent of new technological advances, including in the fields of proteomics, genomics, and metabolomics, biological and pharmacological activities of dietary supplements are being evaluated for their ameliorative effects in human ailments. Recent interests in understanding and discovering the molecular targets of phytochemical-gene-protein-metabolite dynamics resulted in discovery of a few protein signature candidates that could potentially be used to assess the effects of dietary supplements on human health. Persimmon (Diospyros kaki) is a folk medicine, commonly used as dietary supplement in China, Japan, and South Korea, owing to its different beneficial health effects including anti-diabetic implications. However, neither mechanism of action nor molecular biomarkers have been discovered that could either validate or be used to evaluate effects of persimmon on human health. In present study, Mass Spectrometry (MS)-based proteomic studies were ac-complished to discover proteomic molecular signatures that could be used to understand therapeutic potentials of persimmon leaf extract (PLE) in diabetes amelioration. Saliva, serum, and urine samples were analyzed and we propose that salivary proteins can be used for evaluating treatment effectiveness and in improving patient compliance. The present discovery proteomics study demonstrates that salivary proteomic profile changes were found as a result of PLE treatment in prediabetic subjects that could specifically be used as potential protein signature candidates.

Assessment of the Therapeutic Potential of Persimmon Leaf Extract on Prediabetic Subjects

Khan, Mohd M.,Tran, Bao Quoc,Jang, Yoon-Jin,Park, Soo-Hyun,Fondrie, William E.,Chowdhury, Khadiza,Yoon, Sung Hwan,Goodlett, David R.,Chae, Soo-Wan,Chae, Han-Jung,Seo, Seung-Young,Goo, Young Ah Korean Society for Molecular and Cellular Biology 2017 Molecules and cells Vol.40 No.7

Dietary supplements have exhibited myriads of positive health effects on human health conditions and with the advent of new technological advances, including in the fields of proteomics, genomics, and metabolomics, biological and pharmacological activities of dietary supplements are being evaluated for their ameliorative effects in human ailments. Recent interests in understanding and discovering the molecular targets of phytochemical-gene-protein-metabolite dynamics resulted in discovery of a few protein signature candidates that could potentially be used to assess the effects of dietary supplements on human health. Persimmon (Diospyros kaki) is a folk medicine, commonly used as dietary supplement in China, Japan, and South Korea, owing to its different beneficial health effects including anti-diabetic implications. However, neither mechanism of action nor molecular biomarkers have been discovered that could either validate or be used to evaluate effects of persimmon on human health. In present study, Mass Spectrometry (MS)-based proteomic studies were accomplished to discover proteomic molecular signatures that could be used to understand therapeutic potentials of persimmon leaf extract (PLE) in diabetes amelioration. Saliva, serum, and urine samples were analyzed and we propose that salivary proteins can be used for evaluating treatment effectiveness and in improving patient compliance. The present discovery proteomics study demonstrates that salivary proteomic profile changes were found as a result of PLE treatment in prediabetic subjects that could specifically be used as potential protein signature candidates.