International Journal Publication: Large-scale production and evaluation of marker-free indica rice IR64 expressing phytoferritin genes

For those interested to read our latest publication about iron transporter genes in Rice variety IR64 Oryza sativa  entitled: Large-scale production and evaluation of marker-free indica rice IR64 expressing phytoferritin genes.Please click the link and download the pdf file Iron transporter genes. My contribution to this research publication was mainly on gene expression.Thank you for reading.

Endometrial Cancer in a Hypothetical Patient

Hypothetical Patient is XY
54 yo G4P3 (3013)
Pre-op Diagnosis: Endometrial adenocarcinoma secretory type with cervical extension IIA
Operative Findings:
Uterus measures 11x6.5x 3cm
cervix 3.5x3.5x2.5
Right ovary 2x1.5x0.5
Left ovary 2x1x0.5
Right Fallopian tube 8x0.5
Left Fallopian tube 8x0.5
Endocervical canal 2.5cm
UC 8.5
myometrium 2cm
endometrium 0.5cm
obturator nerve (L) 3.5x4x1.0
omentum 10x 8x3cm

Post Operative Diagnosis: Endometrial adenocarcinoma secretory type intraoperative stage  IIIC1
Management; Chemotherapy+ Pelvic EBRT+ Brachytherapy

Surgery done: Exploratory laparotomy,Peritoneal fluid cytology, Extrafascial hesterectomy with bilateral salpingooophorectomy, Random peritoneal biopsy,bilateral lymph node dissection, infracolic omentectomy,paraaortic lymph node sampling/CLEA

Infracolic omentectomy was done:
1.) poor histologic type *
2.) ovarian metastasis
3.) serosal extension*( yellowish at the back)
Plan:
Chemotherapy: Carboplatin-Paclitaxel

Notes:
Women who are at high risk for endometrial cancer are those known to carry HNPCC associated
mutations(pedigree showed 3 generations).

"Kadar and associates and Lurain and colleagues noted that positive peritoneal cytology was associated primarily with adverse features such as extrauterine disease and that therapy  for positive peritoneal cytology as an isolated finding did not appear to improve survival"-Compre Gyne

International Publication on Springer

I cant believe that in the next few months my international  publication about Rice iron transporter genes will be out. Im so  happy  and proud about it. 

Routine Labs and Basis

Liver Function test-  AST and ALT are ordered

Renal Function Test-BUN and Crea

Thyroid Function Test- FT4, FT3 and TSH

Chest Xray
Why it is usually done?
1.to check for the presence of pulmonary infiltrates in the lung especially in patients living in the Asia Pacific Region
when apica infiltrates-pertain to Tuberculosis
2. to check for pulmonary mass or nodules in the case of metastasis/spread is via hematogeneous/ blood route -such as  the case of lung cancer and patient with probable Gestational Trophoblastic Neoplasia
; this might warrant Chest CT scan to determine the extent of the mass and its distribution

3. to check for cardiomegaly, atherosclerotic aorta


The rationale for each will be discussed in detail  in  the next update.

Detailed Steps on Primer Design

I list here the steps on how to design a good working primer.

1.       Get the sequence of your gene  from published literature for example OsNAS3.

2.       Using the TIGR Blast/ NCBI Blast, check the whole sequence if it specifies the gene of interest. It is important that the gene sequence is 100% homologous to the plant where the sequence is derived and the most important is that the whole sequence specifies only one distinct gene.

3.       Put your sequence inside the box of   Primer 3 online software. Specify in the software what are the parameters of the primer you want to have. Click generate. You would get something like this.

Important Notes:

When designing primers take note of the following:

GC content, melting temp (Tm) of primer, 3’ ends of the primer

PCR product size- It depends on what your purpose is. If your going to used the conventional PCR you can create a primer with a product size of 400bp and up. If you’re going to use the primer for real time PCR design a primers with 100-350 size only.  

4.       To be extra sure if your primer is really  specific,  Blast them again with NCBI blast. This would look like this. With the use of Vector NTI/Bioedit you can check the size of your PCR product.

5.       You are now ready to order your primers at SBS and proligo.

Erythrocyte Sedimentation Rate

Erythrocyte sedimentation rate (ESR) AKA  sedimentation rate or Westergren ESR, is the rate at which red blood cells sediment/precipitate in a duartion of one hour. It is a very common blood test, and is a NON-specific measure of inflammation. In order to conduct this test, anticoagulated blood is placed in an upright tube, known as a Westergren tube, and the rate at which the red blood cells fall is measured and reported in mm/h. 

Diagnostic Use: 
 ESR increased can be triggered  by any cause or focus of inflammation.It may be increased in pregnancy, inflammation, anemia or rheumatoid arthritis. However it may  be  decreased in polycythemia, sickle cell anemia, hereditary spherocytosis, and congestive heart failure. Studies reiterated that it may be increased in kidney cancer.It should be taken note that basal ESR is slightly higher in females(Medline).

Commonly Use:
 useful in diagnosing some diseases such as:
 multiple myeloma, 
temporal arteritis,
 polymyalgia rheumatica,
 systemic lupus erythematosus, 
rheumatoid arthritis,
chronic kidney diseases.

 In many of such cases, the ESR may exceed 100 mm/hour.

.

Blood Works: Absolute Neutrophil Count

How to compute for absolute neutrophil count?

ANC= (% bands + % neutrophils) X WBC

             --------------------------------

                          100

          = (0+ .0078)X 9.36 X 10E6/mm3

          = 7,300

How to interpret?

NCI Risk Category ANC

0 Within normal limits

1 ≥1500 - <2000 mm3="">

2 ≥1000 - <1500 mm3="">

3 ≥500 - <1000 mm3="">

4 <500/mm³