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MOHAMMED Yusuf

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Universitat de València

Kansas State University

Armando Marques-Guedes

UNL - New University of Lisbon

Field Museum

National Institute of Technology, Calicut

Visvesvaraya Technological University

Suresh Muthusamy

Kongu Engineering College

Viacheslav Kuleshov

Stockholm University

Yildiz Technical University

State University of Jakarta

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Papers by MOHAMMED Yusuf

Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions

BMC Biotechnology, 2011

Background Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH)... more Background Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified. Results Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection. Conclusions Although the exploitation of the unique optical properties of QD nanocrystals, such...

Correction to: X-ray ptychography imaging of human chromosomes after low-dose irradiation

Chromosome Research, 2021

Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes

Chromosoma, Jan 3, 2018

The high-order structure of metaphase chromosomes remains still under investigation, especially t... more The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be adequately combined. This mini review highlights 3D imaging used for chromosome analysis so far with future imaging directions also highlighted.

Nuclear incorporation of iron during the eukaryotic cell cycle

Journal of synchrotron radiation, Nov 1, 2016

Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe wit... more Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe within cell nuclei. Nuclei, which may have originated at different phases of the cell cycle, are found to show very different levels of Fe present with a strongly inhomogeneous distribution. P and S signals, presumably from DNA and associated nucleosomes, are high and relatively uniform across all the nuclei; these agree with X-ray phase contrast projection microscopy images of the same samples. Possible reasons for the Fe incorporation are discussed.

Addition of Zinc and Selenium to papaya extract enhances its efficiency of wound healing

Wound Repair and Regeneration

Wounds due to injuries for various reasons and for the diabetic patients have been a major public... more Wounds due to injuries for various reasons and for the diabetic patients have been a major public health concern. In search for a wound healing agent of herbal origin, earlier we have reported the eﬃciency of the green (unripe) Carica papaya extracts (GPE) for wound healing [1]. Here we report that addition of zinc and selenium with GPE results in further improvement of wound healing eﬃciency. Induced epidermal wounds on mouse (n= 5–7 for each group) were topically treated with GPE, prepared either in PBS or water as solvent. Zinc was added at concentration of 100 micro M and 200 micro M while selenium was added at a concentration of 2.5 micro M and 5 micro M. Zinc addition at 100 micro M was resulted in highest rate of wound healing compared to the addition of either 200 micro M of Zn or Se (either at 2.5 micro M or 5 micro M). During the ﬁrst phase (0–4 days) of wound healing addition of 100 micro M Zn to GPE resulted in about 50% reduction of the initial wound size (5 mm diameter...

Nanofluidics to Enhance Single Molecule DNA Imaging: Detecting Genomic Structural Variation in Humans

Biophysical Journal, 2014

The stability of tretinoin in tretinoin gel microsphere 0.1%

Cutis, 2002

Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. In studi... more Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. In studies to determine the degree of tretinoin photo degradation (isomerization), 2 tretinoin formulations, tretinoin gel microsphere 0.1% and tretinoin gel 0.025%, alone or in combination with erythromycin-benzoyl peroxide topical gel, were exposed to fluorescent light, incandescent light, or darkness for up to 24 hours. Results of the investigations revealed that after 24 hours of exposure to fluorescent light, 98% of the initial tretinoin in the tretinoin gel microsphere 0.1% formulation remained unchanged. When tretinoin gel microsphere 0.1% was combined with erythromycin-benzoyl peroxide topical gel and exposed to fluorescent light, 99% and 87% of the tretinoin was recovered after 4 and 24 hours, respectively, indicating only a limited amount of degradation. In contrast, exposure of tretinoin gel 0.025% to 24 hours of fluorescent light resulted in up to 69% tretinoin degradation and up to ...

The effect of simulated solar UV irradiation on tretinoin in tretinoin gel microsphere 0.1% and tretinoin gel 0.025%

Cutis, 2006

Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. Tretinoi... more Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. Tretinoin gel microsphere 0.1% (TGM)--alone or in combination with erythromycin-benzoyl peroxide (EBP) or clindamycin-benzoyl peroxide (CBP) topical gels-and tretinoin gel 0.025% (TG)--alone or, combined with EBP-were exposed to simulated solar UV irradiation to determine the degree of tretinoin photodegradation/isomerization. The investigation revealed that 94% and 84% of the initial tretinoin in the TGM formulation remained stable after 2 and 6 hours, respectively, of simulated solar UV irradiation. When combined with EBP topical gel, 89% and 81% of the initial tretinoin remained stable after 2 and 6 hours, respectively, of exposure to simulated solar UV irradiation; 86% and 80% of the tretinoin remained stable after 2 and 6 hours, respectively, when combined with CBP topical gel. In contrast, only 19% and 10% of the tretinoin remained unchanged after 2 and 6 hours, respectively, of simulated ...

Platinum blue staining of cells grown in electrospun scaffolds

BioTechniques, 2014

Fibroblast cells grown in electrospun polymer scaffolds were stained with platinum blue, a heavy ... more Fibroblast cells grown in electrospun polymer scaffolds were stained with platinum blue, a heavy metal stain, and imaged using scanning electron microscopy. Good contrast on the cells was achieved compared with samples that were gold sputter coated. The cell morphology could be clearly observed, and the cells could be distinguished from the scaffold fibers. Here we optimized the required concentration of platinum blue for imaging cells grown in scaffolds and show that a higher concentration causes platinum aggregation. Overall, platinum blue is a useful stain for imaging cells because of its enhanced contrast using scanning electron microscopy (SEM). In the future it would be useful to investigate cell growth and morphology using three-dimensional imaging methods.

Altered Intra-Nuclear Organisation of Heterochromatin and Genes in ICF Syndrome

PLoS ONE, 2010

The ICF syndrome is a rare autosomal recessive disorder, the most common symptoms of which are im... more The ICF syndrome is a rare autosomal recessive disorder, the most common symptoms of which are immunodeficiency, facial anomalies and cytogenetic defects involving decondensation and instability of chromosome 1, 9 and 16 centromeric regions. ICF is also characterised by significant hypomethylation of the classical satellite DNA, the major constituent of the juxtacentromeric heterochromatin. Here we report the first attempt at analysing some of the defining genetic and epigenetic changes of this syndrome from a nuclear architecture perspective. In particular, we have compared in ICF (Type 1 and Type 2) and controls the large-scale organisation of chromosome 1 and 16 juxtacentromeric heterochromatic regions, their intra-nuclear positioning, and co-localisation with five specific genes (BTG2, CNN3, ID3, RGS1, F13A1), on which we have concurrently conducted expression and methylation analysis. Our investigations, carried out by a combination of molecular and cytological techniques, demonstrate the existence of specific and quantifiable differences in the genomic and nuclear organisation of the juxtacentromeric heterochromatin in ICF. DNA hypomethylation, previously reported to correlate with the decondensation of centromeric regions in metaphase described in these patients, appears also to correlate with the heterochromatin spatial configuration in interphase. Finally, our findings on the relative positioning of hypomethylated satellite sequences and abnormally expressed genes suggest a connection between disruption of long-range geneheterochromatin associations and some of the changes in gene expression in ICF. Beyond its relevance to the ICF syndrome, by addressing fundamental principles of chromosome functional organisation within the cell nucleus, this work aims to contribute to the current debate on the epigenetic impact of nuclear architecture in development and disease.

Characterization of a Dominant Cone Degeneration in a Green Fluorescent Protein–Reporter Mouse with Disruption of Loci Associated with Human Dominant Retinal Dystrophy

Investigative Opthalmology & Visual Science, 2011

To characterize anatomically and functionally the retinal degeneration observed in a transgenic m... more To characterize anatomically and functionally the retinal degeneration observed in a transgenic mouse line (OPN1LW-EGFP) expressing enhanced green fluorescent protein (EGFP) in a subpopulation of cone photoreceptors, and to map the location of the transgenic insertion. METHODS. An anatomic comparison of cone survival was carried out between wild type (WT) and transgenic mice at three postnatal time points (P80, P140, and P245). Retinal function was assessed at P245 by ERG and included an ultraviolet flicker stimulus to isolate S-cone function. Chromosomal mapping by FISH and high-resolution mapping on DNA fibers (Fiber-FISH) were performed to identify the location of the transgenic insertion. RESULTS. GFP expression was largely absent in S-cones. Cone numbers were significantly reduced in OPN1LW-EGFP mice at all time points compared to WT, with cone loss independent of GFP expression. Anatomic loss correlated with a functional deficit in dark-and light-adapted ERG responses, including a reduction in UV-flicker response, confirming the degeneration of S-cones. The phenotype of heterozygote mice was slightly less severe than in homozygotes, consistent with a dominantly inherited cone dystrophy. The transgenic insertion mapped to a specific region on chromosome 10 orthologous with loci for progressive bifocal chorioretinal atrophy and North Carolina macular dystrophy on human chromosome 6. Cone loss is global in OPN1LW-EGFP mice and is independent of GFP expression. The mechanism underlying the degeneration remains elusive; however, disruption of loci associated with dominantly inherited retinal degenerations in humans makes this mouse of great interest. (Invest Ophthal-

Some tribal medicinal plants of Chittagong Hill Tracts, Bangladesh

Bangladesh Journal of Plant Taxonomy, 2007

A survey was carried out in different localities of Rangamati and Bandarban Districts of Banglade... more A survey was carried out in different localities of Rangamati and Bandarban Districts of Bangladesh between 2001 and 2002 to document medicinal plants. A total of 69 medicinal plants under 40 families were documented during this work, which the tribal use to treat about 50 diseases. Scientific names, tribal names of the plants, parts used, names of the diseases and names of the user communities are mentioned. Key words: Hill Tracts, Medicinal plants, Traditional knowledge, Bangladesh DOI: 10.3329/bjpt.v14i2.531 Bangladesh J. Plant Taxon. 14(2): 117-128, 2007 (December)

Applications of graphene and related nanomaterials in analytical chemistry

New Journal of Chemistry, 2015

Graphene and its related materials remain a very bright and exciting prospect in analytical chemi... more

Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions

BMC Biotechnology, 2011

Background Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH)... more Background Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified. Results Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection. Conclusions Although the exploitation of the unique optical properties of QD nanocrystals, such...

Correction to: X-ray ptychography imaging of human chromosomes after low-dose irradiation

Chromosome Research, 2021

Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes

Chromosoma, Jan 3, 2018

The high-order structure of metaphase chromosomes remains still under investigation, especially t... more The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be adequately combined. This mini review highlights 3D imaging used for chromosome analysis so far with future imaging directions also highlighted.

Nuclear incorporation of iron during the eukaryotic cell cycle

Journal of synchrotron radiation, Nov 1, 2016

Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe wit... more Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe within cell nuclei. Nuclei, which may have originated at different phases of the cell cycle, are found to show very different levels of Fe present with a strongly inhomogeneous distribution. P and S signals, presumably from DNA and associated nucleosomes, are high and relatively uniform across all the nuclei; these agree with X-ray phase contrast projection microscopy images of the same samples. Possible reasons for the Fe incorporation are discussed.

Addition of Zinc and Selenium to papaya extract enhances its efficiency of wound healing

Wound Repair and Regeneration

Wounds due to injuries for various reasons and for the diabetic patients have been a major public... more Wounds due to injuries for various reasons and for the diabetic patients have been a major public health concern. In search for a wound healing agent of herbal origin, earlier we have reported the eﬃciency of the green (unripe) Carica papaya extracts (GPE) for wound healing [1]. Here we report that addition of zinc and selenium with GPE results in further improvement of wound healing eﬃciency. Induced epidermal wounds on mouse (n= 5–7 for each group) were topically treated with GPE, prepared either in PBS or water as solvent. Zinc was added at concentration of 100 micro M and 200 micro M while selenium was added at a concentration of 2.5 micro M and 5 micro M. Zinc addition at 100 micro M was resulted in highest rate of wound healing compared to the addition of either 200 micro M of Zn or Se (either at 2.5 micro M or 5 micro M). During the ﬁrst phase (0–4 days) of wound healing addition of 100 micro M Zn to GPE resulted in about 50% reduction of the initial wound size (5 mm diameter...

Nanofluidics to Enhance Single Molecule DNA Imaging: Detecting Genomic Structural Variation in Humans

Biophysical Journal, 2014

The stability of tretinoin in tretinoin gel microsphere 0.1%

Cutis, 2002

Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. In studi... more Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. In studies to determine the degree of tretinoin photo degradation (isomerization), 2 tretinoin formulations, tretinoin gel microsphere 0.1% and tretinoin gel 0.025%, alone or in combination with erythromycin-benzoyl peroxide topical gel, were exposed to fluorescent light, incandescent light, or darkness for up to 24 hours. Results of the investigations revealed that after 24 hours of exposure to fluorescent light, 98% of the initial tretinoin in the tretinoin gel microsphere 0.1% formulation remained unchanged. When tretinoin gel microsphere 0.1% was combined with erythromycin-benzoyl peroxide topical gel and exposed to fluorescent light, 99% and 87% of the tretinoin was recovered after 4 and 24 hours, respectively, indicating only a limited amount of degradation. In contrast, exposure of tretinoin gel 0.025% to 24 hours of fluorescent light resulted in up to 69% tretinoin degradation and up to ...

The effect of simulated solar UV irradiation on tretinoin in tretinoin gel microsphere 0.1% and tretinoin gel 0.025%

Cutis, 2006

Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. Tretinoi... more Topical tretinoin is highly effective and widely used in the treatment of acne vulgaris. Tretinoin gel microsphere 0.1% (TGM)--alone or in combination with erythromycin-benzoyl peroxide (EBP) or clindamycin-benzoyl peroxide (CBP) topical gels-and tretinoin gel 0.025% (TG)--alone or, combined with EBP-were exposed to simulated solar UV irradiation to determine the degree of tretinoin photodegradation/isomerization. The investigation revealed that 94% and 84% of the initial tretinoin in the TGM formulation remained stable after 2 and 6 hours, respectively, of simulated solar UV irradiation. When combined with EBP topical gel, 89% and 81% of the initial tretinoin remained stable after 2 and 6 hours, respectively, of exposure to simulated solar UV irradiation; 86% and 80% of the tretinoin remained stable after 2 and 6 hours, respectively, when combined with CBP topical gel. In contrast, only 19% and 10% of the tretinoin remained unchanged after 2 and 6 hours, respectively, of simulated ...

Platinum blue staining of cells grown in electrospun scaffolds

BioTechniques, 2014

Fibroblast cells grown in electrospun polymer scaffolds were stained with platinum blue, a heavy ... more Fibroblast cells grown in electrospun polymer scaffolds were stained with platinum blue, a heavy metal stain, and imaged using scanning electron microscopy. Good contrast on the cells was achieved compared with samples that were gold sputter coated. The cell morphology could be clearly observed, and the cells could be distinguished from the scaffold fibers. Here we optimized the required concentration of platinum blue for imaging cells grown in scaffolds and show that a higher concentration causes platinum aggregation. Overall, platinum blue is a useful stain for imaging cells because of its enhanced contrast using scanning electron microscopy (SEM). In the future it would be useful to investigate cell growth and morphology using three-dimensional imaging methods.

Altered Intra-Nuclear Organisation of Heterochromatin and Genes in ICF Syndrome

PLoS ONE, 2010

The ICF syndrome is a rare autosomal recessive disorder, the most common symptoms of which are im... more The ICF syndrome is a rare autosomal recessive disorder, the most common symptoms of which are immunodeficiency, facial anomalies and cytogenetic defects involving decondensation and instability of chromosome 1, 9 and 16 centromeric regions. ICF is also characterised by significant hypomethylation of the classical satellite DNA, the major constituent of the juxtacentromeric heterochromatin. Here we report the first attempt at analysing some of the defining genetic and epigenetic changes of this syndrome from a nuclear architecture perspective. In particular, we have compared in ICF (Type 1 and Type 2) and controls the large-scale organisation of chromosome 1 and 16 juxtacentromeric heterochromatic regions, their intra-nuclear positioning, and co-localisation with five specific genes (BTG2, CNN3, ID3, RGS1, F13A1), on which we have concurrently conducted expression and methylation analysis. Our investigations, carried out by a combination of molecular and cytological techniques, demonstrate the existence of specific and quantifiable differences in the genomic and nuclear organisation of the juxtacentromeric heterochromatin in ICF. DNA hypomethylation, previously reported to correlate with the decondensation of centromeric regions in metaphase described in these patients, appears also to correlate with the heterochromatin spatial configuration in interphase. Finally, our findings on the relative positioning of hypomethylated satellite sequences and abnormally expressed genes suggest a connection between disruption of long-range geneheterochromatin associations and some of the changes in gene expression in ICF. Beyond its relevance to the ICF syndrome, by addressing fundamental principles of chromosome functional organisation within the cell nucleus, this work aims to contribute to the current debate on the epigenetic impact of nuclear architecture in development and disease.

Characterization of a Dominant Cone Degeneration in a Green Fluorescent Protein–Reporter Mouse with Disruption of Loci Associated with Human Dominant Retinal Dystrophy

Investigative Opthalmology & Visual Science, 2011

To characterize anatomically and functionally the retinal degeneration observed in a transgenic m... more To characterize anatomically and functionally the retinal degeneration observed in a transgenic mouse line (OPN1LW-EGFP) expressing enhanced green fluorescent protein (EGFP) in a subpopulation of cone photoreceptors, and to map the location of the transgenic insertion. METHODS. An anatomic comparison of cone survival was carried out between wild type (WT) and transgenic mice at three postnatal time points (P80, P140, and P245). Retinal function was assessed at P245 by ERG and included an ultraviolet flicker stimulus to isolate S-cone function. Chromosomal mapping by FISH and high-resolution mapping on DNA fibers (Fiber-FISH) were performed to identify the location of the transgenic insertion. RESULTS. GFP expression was largely absent in S-cones. Cone numbers were significantly reduced in OPN1LW-EGFP mice at all time points compared to WT, with cone loss independent of GFP expression. Anatomic loss correlated with a functional deficit in dark-and light-adapted ERG responses, including a reduction in UV-flicker response, confirming the degeneration of S-cones. The phenotype of heterozygote mice was slightly less severe than in homozygotes, consistent with a dominantly inherited cone dystrophy. The transgenic insertion mapped to a specific region on chromosome 10 orthologous with loci for progressive bifocal chorioretinal atrophy and North Carolina macular dystrophy on human chromosome 6. Cone loss is global in OPN1LW-EGFP mice and is independent of GFP expression. The mechanism underlying the degeneration remains elusive; however, disruption of loci associated with dominantly inherited retinal degenerations in humans makes this mouse of great interest. (Invest Ophthal-

Some tribal medicinal plants of Chittagong Hill Tracts, Bangladesh

Bangladesh Journal of Plant Taxonomy, 2007

A survey was carried out in different localities of Rangamati and Bandarban Districts of Banglade... more A survey was carried out in different localities of Rangamati and Bandarban Districts of Bangladesh between 2001 and 2002 to document medicinal plants. A total of 69 medicinal plants under 40 families were documented during this work, which the tribal use to treat about 50 diseases. Scientific names, tribal names of the plants, parts used, names of the diseases and names of the user communities are mentioned. Key words: Hill Tracts, Medicinal plants, Traditional knowledge, Bangladesh DOI: 10.3329/bjpt.v14i2.531 Bangladesh J. Plant Taxon. 14(2): 117-128, 2007 (December)

Applications of graphene and related nanomaterials in analytical chemistry

New Journal of Chemistry, 2015

Graphene and its related materials remain a very bright and exciting prospect in analytical chemi... more