Identification of key gene modules and pathways of human platelet transcriptome in acute myocardial infarction patients through co-expression network

stjosephs-hospital

Acute myocardial infarction (AMI) seriously threatens human life. In this study we aimed to systemically analyze the function of key gene modules in human platelets in AMI. We used weighted gene co-expression network analysis (WGCNA) to construct a co-expression module, and analyzed the relationship between potential modules and clinical characteristics based on platelet RNA-seq RPKM count reads of 16 ST-segment elevation myocardial infarction (STEMI) patients and 16 non-STEMI (NSTEMI) patients provided by the GEO database.

Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed with the DAVID tool. Hub genes were calculated by the Cytohubba package. A total of 3653 genes was selected to construct the co-expression modules.

A significant correlation between BMI and the module with color of sky-blue in STEMI. In NSTEMI, there was a significant correlation between the sky blue module and CAD, the Salmon module and HT, and the Cyan module and HT. In STEMI, the Hub genes were mainly enriched in functions related to cell membrane signal transduction including Aqp1, Armcx1, Gsta4, Hist3h2a and Il17re.

In NSTEMI, the Hub genes are related mainly to energy metabolism in the sky-blue module including Olr1, Nap1l3, Gfer, Dohh, Crispld1 and Ccdc8b; they are mainly related to extracellular space and calcium binding in the Cyan module, including Clec12b, Chd4, Asgr1, Armcx4, Chid1 and Alkbh7.

The hub genes in the Salmon module include Ell3, Aldh1b1, Cavin4, Cabp4, Eif1ay and Dus3l. Our results provide a framework for co-expression gene modules in STEMI and NSTEMI patients, and identify key targets as biomarkers for patients with different subtypes of AMI.

Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S

In response to COVID-19, the international water community rapidly developed methods to quantify the SARS-CoV-2 genetic signal in untreated wastewater. Wastewater surveillance using such methods has the potential to complement clinical testing in assessing community health. This interlaboratory assessment evaluated the reproducibility and sensitivity of 36 standard operating procedures (SOPs), divided into eight method groups based on sample concentration approach and whether solids were removed.

Two raw wastewater samples were collected in August 2020, amended with a matrix spike (betacoronavirus OC43), and distributed to 32 laboratories across the U.S. Replicate samples analyzed in accordance with the project’s quality assurance plan showed high reproducibility across the 36 SOPs: 80% of the recovery-corrected results fell within a band of ±1.15 log10 genome copies per L with higher reproducibility observed within a single SOP (standard deviation of 0.13 log10).

The inclusion of a solids removal step and the selection of a concentration method did not show a clear, systematic impact on the recovery-corrected results. Other methodological variations (e.g., pasteurization, primer set selection, and use of RT-qPCR or RT-dPCR platforms) generally resulted in small differences compared to other sources of variability.

These findings suggest that a variety of methods are capable of producing reproducible results, though the same SOP or laboratory should be selected to track SARS-CoV-2 trends at a given facility. The methods showed a 7 log10 range of recovery efficiency and limit of detection highlighting the importance of recovery correction and the need to consider method sensitivity when selecting methods for wastewater surveillance.

stjosephs-hospital

stjosephs-hospital

ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs

Motivation: Access to large-scale genomics and transcriptomics data from various tissues and cell lines allowed the discovery of wide-spread alternative splicing events and alternative promoter usage in mammalians. Between human and mouse, gene-level orthology is currently present for nearly 16k protein-coding genes spanning a diverse repertoire of over 200k total transcript isoforms.

Results: Here, we describe a novel method, ExTraMapper, which leverages sequence conservation between exons of a pair of organisms and identifies a fine-scale orthology mapping at the exon and then transcript level. ExTraMapper identifies more than 350k exon mappings, as well as 30k transcript mappings between human and mouse using only sequence and gene annotation information.

We demonstrate that ExTraMapper identifies a larger number of exon and transcript mappings compared to previous methods. Further, it identifies exon fusions, splits, and losses due to splice site mutations, and finds mappings between microexons that are previously missed.

By reanalysis of RNA-seq data from 13 matched human and mouse tissues, we show that ExTraMapper improves the correlation of transcript-specific expression levels suggesting a more accurate mapping of human and mouse transcripts. We also applied the method to detect conserved exon and transcript pairs between human and rhesus macaque genomes to highlight the point that ExTraMapper is applicable to any pair of organisms that have orthologous gene pairs.

Availability: The source code and the results are available

Unconventional viral gene expression mechanisms as therapeutic targets

Unlike the human genome that comprises mostly noncoding and regulatory sequences, viruses have evolved under the constraints of maintaining a small genome size while expanding the efficiency of their coding and regulatory sequences.

As a result, viruses use strategies of transcription and translation in which one or more of the steps in the conventional gene-protein production line are altered. These alternative strategies of viral gene expression (also known as gene recoding) can be uniquely brought about by dedicated viral enzymes or by co-opting host factors (known as host dependencies).

Targeting these unique enzymatic activities and host factors exposes vulnerabilities of a virus and provides a paradigm for the design of novel antiviral therapies. In this Review, we describe the types and mechanisms of unconventional gene and protein expression in viruses, and provide a perspective on how future basic mechanistic work could inform translational efforts that are aimed at viral eradication.

 

GCNF Conjugated Antibody

C48479 100ul
EUR 476.4

Anti-GCNF antibody

PAab03390 100 ug
EUR 426

anti- GCNF antibody

FNab03390 100µg
EUR 606.3
Description: Antibody raised against GCNF

anti-GCNF

YF-PA23769 50 ul
EUR 400.8
Description: Mouse polyclonal to GCNF

anti-GCNF

YF-PA11986 50 ul
EUR 435.6
Description: Mouse polyclonal to GCNF

anti-GCNF

YF-PA11987 50 ug
EUR 435.6
Description: Mouse polyclonal to GCNF

anti-GCNF

YF-PA11988 100 ul
EUR 483.6
Description: Rabbit polyclonal to GCNF

anti-GCNF

YF-PA11989 100 ug
EUR 483.6
Description: Rabbit polyclonal to GCNF

GCNF ELISA KIT|Human

EF009808 96 Tests
EUR 826.8

Germ Cell Nuclear Factor (GCNF) Antibody

20-abx131389
  • EUR 510.00
  • EUR 159.60
  • EUR 1446.00
  • EUR 693.60
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  • 100 ug
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  • 50 ug

Polyclonal NR6A1 / GCNF Antibody (Ligand-binding Domain)

AMM06820G 0.05mg
EUR 580.8
Description: A polyclonal antibody raised in Rabbit that recognizes and binds to Human NR6A1 / GCNF (Ligand-binding Domain). This antibody is tested and proven to work in the following applications:

Recombinant Germ Cell Nuclear Factor (GCNF)

4-RPC509Hu01
  • EUR 560.83
  • EUR 273.60
  • EUR 1773.12
  • EUR 671.04
  • EUR 1222.08
  • EUR 451.20
  • EUR 4252.80
  • 100 ug
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  • 1 mg
  • 200 ug
  • 500 ug
  • 50ug
  • 5 mg
Description: Recombinant Human Germ Cell Nuclear Factor expressed in: E.coli

pGL4.19-TA-GCNF response element Plasmid

PVTB00989-2a 2 ug
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Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human)

4-PAC509Hu01
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  • EUR 3012.00
  • EUR 750.00
  • EUR 372.00
  • EUR 256.80
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF)

GCNF (anti human nuclear recepter antibody, clone# H7921)

PP-H7921-00 0.1mg/100uL
EUR 747.6
Description: The GCNF (anti human nuclear recepter antibody, clone# H7921) is available in Europe and for worldwide shipping via Gentaur.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), APC

4-PAC509Hu01-APC
  • EUR 414.00
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  • EUR 1094.40
  • EUR 528.00
  • EUR 262.80
  • 100ul
  • 10ml
  • 1ml
  • 200ul
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Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with APC.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), Biotinylated

4-PAC509Hu01-Biotin
  • EUR 373.20
  • EUR 2952.00
  • EUR 872.40
  • EUR 457.20
  • EUR 262.80
  • 100ul
  • 10ml
  • 1ml
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Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with Biotin.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), Cy3

4-PAC509Hu01-Cy3
  • EUR 502.80
  • EUR 5190.00
  • EUR 1410.00
  • EUR 654.00
  • EUR 301.20
  • 100ul
  • 10ml
  • 1ml
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Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with Cy3.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), FITC

4-PAC509Hu01-FITC
  • EUR 355.20
  • EUR 3168.00
  • EUR 900.00
  • EUR 446.40
  • EUR 234.00
  • 100ul
  • 10ml
  • 1ml
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Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with FITC.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), HRP

4-PAC509Hu01-HRP
  • EUR 379.20
  • EUR 3426.00
  • EUR 968.40
  • EUR 477.60
  • EUR 247.20
  • 100ul
  • 10ml
  • 1ml
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Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with HRP.

Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), PE

4-PAC509Hu01-PE
  • EUR 355.20
  • EUR 3168.00
  • EUR 900.00
  • EUR 446.40
  • EUR 234.00
  • 100ul
  • 10ml
  • 1ml
  • 200ul
  • 20ul
Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with PE.

Human Germ Cell Nuclear Factor (GCNF) Protein

20-abx650014
  • EUR 777.60
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Germ Cell Nuclear Factor (GCNF) Polyclonal Antibody (Human), APC-Cy7

4-PAC509Hu01-APC-Cy7
  • EUR 685.20
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  • EUR 2046.00
  • EUR 912.00
  • EUR 382.80
  • 100ul
  • 10ml
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Description: A Rabbit polyclonal antibody against Human Germ Cell Nuclear Factor (GCNF). This antibody is labeled with APC-Cy7.

CD11b Antibody Antibody

ABD2911 100 ug
EUR 525.6

ASAP1 antibody Antibody

DF8746 200ul
EUR 420

anti- Antibody^Polyclonal antibody control antibody

LSMab09882 100 ug
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ARHGDIA Antibody / RHOGDI Antibody

F54788-0.08ML 0.08 ml
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ARHGDIA Antibody / RHOGDI Antibody

F54788-0.4ML 0.4 ml
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Antibody

A1360-500 Ask for price

Anti-Glycolipid Antibody (AGA) Antibody

20-abx004855
  • EUR 493.20
  • EUR 710.40
  • EUR 218.40
  • EUR 376.80
  • 100 ul
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Ly1 Antibody Reactive (LYAR) Antibody

20-abx008109
  • EUR 360.00
  • EUR 526.80
  • EUR 226.80
  • 100 ul
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Ly1 Antibody Reactive (LYAR) Antibody

20-abx123734
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Ly1 Antibody Reactive (LYAR) Antibody

20-abx014333
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Ly1 Antibody Reactive (LYAR) Antibody

abx033330-400ul 400 ul
EUR 627.6

Ly1 Antibody Reactive (LYAR) Antibody

abx033330-80l 80 µl
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Anti-Glycolipid Antibody (AGA) Antibody

abx036399-100ug 100 ug
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Anti-Glycoprotein Antibody (GP) Antibody

20-abx319900
  • EUR 493.20
  • EUR 2214.00
  • EUR 718.80
  • EUR 218.40
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Anti-Glycoprotein Antibody (GP) Antibody

20-abx319901
  • EUR 493.20
  • EUR 2214.00
  • EUR 718.80
  • EUR 218.40
  • EUR 360.00
  • 100 ug
  • 1 mg
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Anti-Glycoprotein Antibody (GP) Antibody

20-abx319905
  • EUR 493.20
  • EUR 2214.00
  • EUR 718.80
  • EUR 218.40
  • EUR 360.00
  • 100 ug
  • 1 mg
  • 200 ug
  • 20 ug
  • 50 ug

Anti-Glycoprotein Antibody (GP) Antibody

20-abx319913
  • EUR 493.20
  • EUR 2214.00
  • EUR 718.80
  • EUR 218.40
  • EUR 360.00
  • 100 ug
  • 1 mg
  • 200 ug
  • 20 ug
  • 50 ug

Anti-Glycolipid Antibody (AGA) Antibody

abx230204-100ug 100 ug
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Ly1 Antibody Reactive (LYAR) Antibody

20-abx324434
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Ly1 Antibody Reactive (LYAR) Antibody

20-abx311665
  • EUR 493.20
  • EUR 2214.00
  • EUR 718.80
  • EUR 218.40
  • EUR 360.00
  • 100 ug
  • 1 mg
  • 200 ug
  • 20 ug
  • 50 ug

Ly1 Antibody Reactive (LYAR) Antibody

abx234901-100ug 100 ug
EUR 661.2

Anti-Anti-SEPT6 antibody antibody

STJ11100949 100 µl
EUR 332.4
Description: This gene is a member of the septin family of GTPases. Members of this family are required for cytokinesis. One version of pediatric acute myeloid leukemia is the result of a reciprocal translocation between chromosomes 11 and X, with the breakpoint associated with the genes encoding the mixed-lineage leukemia and septin 2 proteins. This gene encodes four transcript variants encoding three distinct isoforms. An additional transcript variant has been identified, but its biological validity has not been determined.

Anti-Anti-SEPT9 Antibody antibody

STJ111369 100 µl
EUR 332.4
Description: This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.

Anti-Anti-SEPT11 Antibody antibody

STJ111530 100 µl
EUR 332.4

Anti-Anti-SEPT4 Antibody antibody

STJ112276 100 µl
EUR 332.4
Description: This gene is a member of the septin family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse, and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. This gene is highly expressed in brain and heart. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. One of the isoforms (known as ARTS) is distinct; it is localized to the mitochondria, and has a role in apoptosis and cancer.

Anti-Anti-MARCH9 Antibody antibody

STJ112609 100 µl
EUR 332.4

Anti-Anti-SEPT11 Antibody antibody

STJ113941 100 µl
EUR 332.4

Anti-Anti-SEPT11 Antibody antibody

STJ114081 100 µl
EUR 332.4

Anti-Anti-SEPT5 Antibody antibody

STJ114819 100 µl
EUR 332.4
Description: This gene is a member of the septin gene family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. This gene is mapped to 22q11, the region frequently deleted in DiGeorge and velocardiofacial syndromes. A translocation involving the MLL gene and this gene has also been reported in patients with acute myeloid leukemia. Alternative splicing results in multiple transcript variants. The presence of a non-consensus polyA signal (AACAAT) in this gene also results in read-through transcription into the downstream neighboring gene (GP1BB; platelet glycoprotein Ib), whereby larger, non-coding transcripts are produced.

Anti-Anti-MARCH8 Antibody antibody

STJ114828 100 µl
EUR 332.4

Anti-Anti-SEPT7 Antibody antibody

STJ116214 100 µl
EUR 332.4
Description: This gene encodes a protein that is highly similar to the CDC10 protein of Saccharomyces cerevisiae. The protein also shares similarity with Diff 6 of Drosophila and with H5 of mouse. Each of these similar proteins, including the yeast CDC10, contains a GTP-binding motif. The yeast CDC10 protein is a structural component of the 10 nm filament which lies inside the cytoplasmic membrane and is essential for cytokinesis. This human protein functions in gliomagenesis and in the suppression of glioma cell growth, and it is required for the association of centromere-associated protein E with the kinetochore. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified on chromosomes 5, 7, 9, 10, 11, 14, 17 and 19.

Anti-Anti-SEPT8 Antibody antibody

STJ117206 100 µl
EUR 332.4
Description: This gene is a member of the septin family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse, and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Anti-Anti-SEPT12 Antibody antibody

STJ117759 100 µl
EUR 332.4
Description: This gene encodes a guanine-nucleotide binding protein and member of the septin family of cytoskeletal GTPases. Septins play important roles in cytokinesis, exocytosis, embryonic development, and membrane dynamics. Multiple transcript variants encoding different isoforms have been found for this gene.

Anti-Anti-MARCH6 Antibody antibody

STJ118549 100 µl
EUR 332.4

Anti-Anti-MARCH6 Antibody antibody

STJ118550 100 µl
EUR 332.4

Anti-Anti-MARCH7 Antibody antibody

STJ118752 100 µl
EUR 332.4

Anti-Anti-SEPT3 Antibody antibody

STJ118990 100 µl
EUR 332.4

Anti-Anti-SEPT2 Antibody antibody

STJ28365 100 µl
EUR 332.4

Anti-Anti-SEPT7 Antibody antibody

STJ28963 100 µl
EUR 332.4
Description: This gene encodes a protein that is highly similar to the CDC10 protein of Saccharomyces cerevisiae. The protein also shares similarity with Diff 6 of Drosophila and with H5 of mouse. Each of these similar proteins, including the yeast CDC10, contains a GTP-binding motif. The yeast CDC10 protein is a structural component of the 10 nm filament which lies inside the cytoplasmic membrane and is essential for cytokinesis. This human protein functions in gliomagenesis and in the suppression of glioma cell growth, and it is required for the association of centromere-associated protein E with the kinetochore. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified on chromosomes 5, 7, 9, 10, 11, 14, 17 and 19.

Anti-Anti-SEPT2 Antibody antibody

STJ25475 100 µl
EUR 332.4

Anti-Anti-SEPT5 Antibody antibody

STJ25477 100 µl
EUR 332.4
Description: This gene is a member of the septin gene family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. This gene is mapped to 22q11, the region frequently deleted in DiGeorge and velocardiofacial syndromes. A translocation involving the MLL gene and this gene has also been reported in patients with acute myeloid leukemia. Alternative splicing results in multiple transcript variants. The presence of a non-consensus polyA signal (AACAAT) in this gene also results in read-through transcription into the downstream neighboring gene (GP1BB; platelet glycoprotein Ib), whereby larger, non-coding transcripts are produced.

Anti-Anti-SEPT8 Antibody antibody

STJ25479 100 µl
EUR 332.4
Description: This gene is a member of the septin family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse, and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Anti-Anti-SEPT1 antibody antibody

STJ119580 100 µl
EUR 332.4
Description: This gene is a member of the septin family of GTPases. Members of this family are required for cytokinesis and the maintenance of cellular morphology. This gene encodes a protein that can form homo- and heterooligomeric filaments, and may contribute to the formation of neurofibrillary tangles in Alzheimer's disease. Alternatively spliced transcript variants have been found but the full-length nature of these variants has not been determined. [provided by RefSeq, Dec 2012]

CLCN5 Antibody / CIC-5 antibody

RQ6462 100ug
EUR 419
Description: The CLCN5 gene encodes the chloride channel Cl-/H+ exchanger ClC-5. This gene encodes a member of the ClC family of chloride ion channels and ion transporters. The encoded protein is primarily localized to endosomal membranes and may function to facilitate albumin uptake by the renal proximal tubule. Mutations in this gene have been found in Dent disease and renal tubular disorders complicated by nephrolithiasis. Alternatively spliced transcript variants have been found for this gene.

Cytokeratin 7 antibody-Cytoskeleton Marker Antibody

48169-100ul 100ul
EUR 399.6

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Genetic diversity of circumsporozoite protein in Plasmodium knowlesi isolates from Malaysian Borneo and Peninsular MalaysiaGenetic diversity of circumsporozoite protein in Plasmodium knowlesi isolates from Malaysian Borneo and Peninsular Malaysia

 Background: Understanding the genetic variety of candidate genes for malaria vaccines comparable to circumsporozoite protein (csp) might improve the event of vaccines for treating Plasmodium knowlesi. Therefore, the goal of this