Expression of epidermal growth factor receptor tyrosine kinase family in fine needle aspiration and permanent specimens of invasive lobular and ductal breast cancers

Recently, the role of HER-2/Neu gene amplification has been enthusiastically investigated in breast cancer. Determining the HER-2/Neu status could be achieved by evaluating either histologic samples or cytologic specimens obtained by Fine Needle Aspiration (FNA). This study aimed at determining the concordance of HER-2/Neu expression in FNA and histologic sections. FNA samples, as well as their corresponding histologic sections of 90 cases with breast cancer were evaluated in Tabriz Sina Teaching Center in a 13-month period of time. The immunohistochemistry was employed for determining the HER-2/Neu amplification for both methods. The concordance rate and agreement were determined between the two methods. Ninety specimens of women with a mean age of 50.93 +/- 10.64 (29-84) years were assessed. There were 84 cases with invasive ductal carcinoma and 6 cases with invasive lobular carcinoma. Lymph nodes were involved in 50 cases and there were vascular and neural involvement in 40 and 35 cases, respectively. Her-2/Neu was not detected in 27 cases (30%) with weak and strong amplifications in 47 (52.2%) and 16 (17.8%) cases of FNA specimens, respectively. Her-2/Neu was not detected in 29 cases (32.2%) with weak and strong amplifications in 42 (46.7%) and 19 (21.1%) cases of histologic specimens, respectively. The concordance rate was 70% between the two methods. The agree ment was statistically significant between the two methods, as well (kappa = 0.51, p < 0.001). HER-2/neu gene amplification can be reliably estimated by immunohistochemistry on breast cancer FNAs and a good correlation has been found between this and results on histological sections.     

Structural and functional analysis of KIT gene encoding receptor tyrosine kinase and its interaction with sunitinib and HDAC inhibitors: an in silico approach

KIT is a growth factor receptor, important for normal germ cell migration and development. The malfunction of KIT gene results in constitutive activation of the tyrosine kinase activity of c-KIT which is believed to be the major oncogenic event in stomach, small intestine mastocytosis, acute leukemias, melanomas and colon tumors. The genetics of these diseases could be better understood by knowing the functional relevance of their SNP variation. In this study, a computational analysis to detect the most deleterious nonsynonymous SNPs of KIT gene was performed and investigated its binding affinity to native and predicted mutant protein structure (D816V) with sunitinib and HDAC (Trichostatin A and Panobinostat) inhibitors was investigated. Out of 1,288 SNPs retrieved from dbSNP database against KIT gene, 11 non-synonymous SNPs were detected to be damaging and deleterious by SIFT, PolyPhen and I-Mutant2.0 servers. Further, we modeled the mutant protein based on the deleterious nsSNP (rs121913507) and showed that the mutation from Aspartic acid to Valine at 816 position exhibit greatest impact on stability. The RMSD values of mutant and native structures are found to be 0.40 and 1.9 A, respectively. Furthermore, the binding affinity of sunitinib and HDAC inhibitors were compared with native and mutant protein. In this regard, it was found that trichostatin A has a high binding efficacy towards the mutant protein with a binding energy of -35.274 kcal mol(-1), as compared to the native structure which has a binding energy of -25.996 kcal mol(-1). Also, the FastSNP tool suggested that 3 SNPs found to affect protein splicing site and splicing regulation. From present results, it was clear that the non-synonymous SNP rs121913507 (D816V) could be the most deleterious SNP for KIT gene and HDAC inhibitors can serve as a best drug for the mutant protein.     

Introgressive Hybridization in Potato Revealed by Novel Cytogenetic and Genomic Technologies

Potato is the third most important food crop in the world and is crucial to ensure food security. However, increasing biotic and abiotic stresses jeopardize its stable production. Fortunately, breeders count on a rich pool of wild relatives that provide sources for disease resistance and tolerance to environmental stresses. To use such traits effectively, breeders require tools that facilitate exploration and exploitation of the genetic diversity of potato wild relatives. Introgression programs to incorporate such alien chromatin into the crop have so far relied on cytogenetic and genetic studies to tap desired traits from these wild resources. The available genetic and cytogenetic tools, supplemented with more recent genomic technologies, can assist in the use of potato relatives in pre-breeding. This information can also facilitate cisgenesis and genome editing to improve potato cultivars. Despite the abundant and rapidly growing genomic information of potato, that of its wild relatives is still limited.     

Genetic analyses of grain-filling rate and duration in maize

Grain-filling rate and duration influence grain yield in maize (Zea mays L.), but very little information on their inheritance exists. To devise effective breeding strategies, the genetic nature of these traits must be understood. The objectives of this study were to (1) examine general combining ability (GCA) and specific combining ability (SCA) for grain-filling rate, grain-filling duration, and related agronomic traits via North Carolina Design II, (2) determine the inter-relationships among these traits and their influence on yield via correlation and path coefficient analyses, and (3) identify an indirect selection criterion for yield. Design II crosses among four inbred lines used as males and a set of four inbred lines as female parents were grown in 1996. Combining ability analyses indicated that both GCA (V_g) and SCA mean squares (V_s) were significant for grain-filling rate (on a kernel or an ear basis) and effective filling duration. General combining ability was more important than SCA for both kernel-filling rate and effective filling duration, whereas SCA effect was more important for ear-filling rate. The ratio 2V_g/(2V_g + V_s) was 0.85, 0.88, and 0.45 for kernel-filling rate, effective filling duration, and ear-filling rate, respectively. Kernel-filling rate had a positive phenotypic correlation with kernel weight and was negatively correlated with midsilk date and effective filling duration. Kernel number per ear was more important than kernel-filling rate in influencing grain yield. These relationships were confirmed by results from a 1997 experiment using nine commercial hybrids. Chlorophyll readings taken with SPAD chlorophyll meter at a late developmental stage gave a positive genetic correlation with single-plant yield (r = 0.73). A path coefficient analysis revealed that chlorophyll concentration had a small direct effect on grain yield, whereas it had a large indirect effect on grain yield via kernel number per ear and grain-filling duration. Kernel weight and midsilk date could serve as indirect selection criteria for effective grain-filling duration and kernel-filling rate. Chlorophyll concentration at a late developmental stage could also be an indirect selection criterion for final grain yield.     

Magnetic resonance imaging and analyses of tempering processes in rice kernels

This research involved a magnetic resonance imaging (MRI) technique that was applied to examine water distribution and migration in single rice kernels during the tempering process. The imaging experiments were performed in a Bruker 9.4T MRI system. Three-dimensional spin-echo (SE) imaging sequences were optimized by adjusting the scanning parameters of echo time (TE) and repetition time (TR) to obtain images with maximum contrast. The MR images showed that the moisture distribution in the rice kernel is non-uniform and compartmental. The embryo region exhibited much higher MR signal intensity than the starchy endosperm portion. The tempering process was analyzed with spatial-temporal signal intensities of the endosperm following the drying process of the rice kernel. The transient change of the signal intensities in the endosperm was well fitted with a double exponential function suggesting that both convection and diffusion contributed to the reduction of the moisture gradient within the rice kernel during tempering. This hypothesis was further supported by the experimental data of the insulated rice kernel whose convective mass transfer was excluded. The experimental results revealed that MR imaging of rice kernels could be used as an efficient tool to examine the mechanisms of moisture migration within cereal grains.     

Cardiac involvement of major thalassemia and evaluation of total serum creatine kinase and creatine kinase-mB isoenzyme and cardiac troponinI in these patients

The goal of this study was the evaluation of specific markers of myocardial injury that includes CK-MB and troponin I in major thalassemic patients. Regular blood transfusion is the main treatment in major thalassemia. One of the most important complications of regular blood transfusion is iron overload that eventually involves many organs like heart and cause myocardial injury. Sixty patients with transfusion-dependent major thalassemia, at the age range of 8 to 15 years in Tabriz Pediatric Medical Center were chosen. Measurement of Hb, Hct and serum ferritin were performed in hospital laboratory, but total serum Creatine Kinase (CK) by photometric and isoenzyme of CK-MB by immunologic DGKC and cardiac troponin I (cTnI) were tested by ELISA methods in Shaheed Madani heart center laboratory before blood transfusion. For all patients echocardiography and ECG assessment of cardiac function were done by a pediatric cardiologist and results were statistically analyzed. Forty nine patients (group A) had normal left ventricular ejection fraction (LVEF = 50-70%) and 11 patients (group B) had reduced LVEF (20-45%). There was no statistical difference between two groups in average volume of blood transfusion (p = 0.074). Although total CK and CK-MB isoenzyme were higher in group B but there was no statistically meaningful difference between two groups (p = 0.123, p = 0.111). Troponin I also was higher in group B but statistically analysis showed no correlation between cardiac function and troponin I level in these groups (p = 0.827). This study showed that cardiac markers are not helpful for recognition of cardiac involvement in major thalassemia.     

Nutritive value of rapeseed proteins and fractions supplemented with methionine and tyrosine in rats

Rapeseed protein concentrate (RPC), rapeseed 2S and 12S fractions, a blend of 2S and 12S fractions, retentate (RET) and precipitate (PRE) proteins obtained during rapeseed fractionation were compared to casein for nutritive value as determined by net protein ratio (NPR) and apparent digestibility coefficient (ADC). Tyrosine concentration in rapeseed 2S fraction was the lowest compared to all other protein sources and methionine was the first limiting amino acid. The NPR and ADC of RPC, RET, and fraction 12S did not change significantly (P<0.05) following supplementation with methionine, but for PRE the NPR was decreased significantly (P<0.05). However, the rapeseed 2S fraction supplemented with tyrosine had a NPR significantly (P<0.05) higher than that of RPC and not significant (P<0.05) different from that of casein. The NPR of the 2S and 12S blend was significantly (P<0.05) higher than that of RET and PRE; however, no significant (P<0.05) difference was observed in NPR and ADC of the blend when supplemented with tyrosine. The nutritive value and digestibility of rapeseed 2S fraction were improved by supplementation with tyrosine and by blending with the 12S fraction.     

Correlating karyomorphology and molecular marker analyses in turmeric: a case study

India is the largest producer and exporter of turmeric (Curcuma longa), and different cultivars of this crop are traditionally characterized using agronomic traits, such as rhizome weight, yield potential, color and aroma of rhizome, curcumin content, and stability of curcumin content, which are influenced by environmental factors. The purpose of the present study was to probe whether karyomorphological and molecular marker attributes of turmeric cultivars could be correlated to validate their distinctiveness. Detailed karyomorphological analyses revealed uniform somatic chromosome number (2n = 63), with symmetric karyotype in all the studied cultivars. Chromosomes varied from 0.67 to 2.03 µm in length, with up to 72% bearing primary constrictions in the nearly median region (i-value ranging from 27.17 to 50). Asymmetry indices also indicated overall karyotypic symmetry among cultivars. On the contrary, random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker analyses revealed significant variability in the genetic constitution among them; Jaccard’s similarity coefficient value ranged from 0.569 to 0.969. Unweighted pair group method with arithmetic average (UPGMA) dendrogram and principal coordinate analysis based on the Jaccard’s coefficient produced four distinct clusters, which showed no geographical bias. Thus, it was concluded that although significant genetic variability that exists among the turmeric cultivars can be utilized for examining their authenticity, practicality of the use of karyomorphological characters for identification is significantly limited by the gross karyotypic similarity. Cryptic genetic changes accumulate in the genome of these plants because of their interaction with the environment. However, these remain confined within each cultivar in the absence of large-scale hybridizations and predominant vegetative propagation. This probably leads to variability in agronomic characters and may even help in developing novel characters in different cultivars. However, detection of any such change in the chromosomal structure would require fluorescent hybridization techniques.     

Glycogen synthase kinase 3, circadian rhythms, and bipolar disorder: a molecular link in the therapeutic action of lithium

Background  

Bipolar disorder (BPD) is a widespread condition characterized by recurring states of mania and depression. Lithium, a direct inhibitor of glycogen synthase kinase 3 (GSK3) activity, and a mainstay in BPD therapeutics, has been proposed to target GSK3 as a mechanism of mood stabilization. In addition to mood imbalances, patients with BPD often suffer from circadian disturbances. GSK3, an essential kinase with widespread roles in development, cell survival, and metabolism has been demonstrated to be an essential component of the Drosophila circadian clock. We sought to investigate the role of GSK3 in the mammalian clock mechanism, as a possible mediator of lithium's therapeutic effects.     

Water and nitrogen limitations in soybean grain production II. Field and model analyses

A short-season and a long-season soybean (Glycine max (L.) Merr) cultivar were grown on two different soil types under both irrigated and water-limited conditions in a semi-arid tropical environment. In addition to differences in water holding capacity, the clay soil had less available soil nitrogen than the sandy loam soil. The experimental water regimes coupled with the differing soil types gave a wide range in yield response. A model analysis was done to simulate the crop growth to identify those factors that limited yield. Under irrigated conditions, the yields of crops grown on the clay soil were found in the model to be especially limited by low amounts of available soil nitrogen. With weekly irrigation of the sandy loam soil, the long-season cultivar in the simulation experienced brief episodes of water shortage which reduced the nitrogen fixation rate. An optimal irrigation schedule was simulated based on soil water depletion, which improved yield and saved water compared to the simulated weekly schedule. Terminal water deficits reduced yields more for the long-season cultivar both experimentally and in the simulations, as the short-season cultivar initiated seed growth earlier and produced greater seed mass before water shortage terminated crop growth.A model analysis of the water limitations showed that water deficits at the beginning of seed fill had the greatest effect on yields. Greater soil water storage as simulated by greater depth of water extraction resulted in increased yields. Increased nitrogen supply to the crop simulated by either greater soil nitrogen availability or increased nitrogen fixation rates resulted in substantial yield increases.     

我国油菜生产应对气候变化的对策和措施分析

摘要：本文分析了近年来气候变化特点及对我国油菜生态环境及油菜生产的影响。结果表明,随着气温升高,冬油菜潜在种植面积显著增加,传统的油菜生产格局发生改变,体现出明显的“东减、北移、西扩”特征;由于降水分布不均、极端气候事件频繁,油菜单产增加趋势减缓,油菜生产的不稳定性显著增加。根据当前油菜生产所面临的问题,提出了整合育种和栽培措施的应对策略。     

Differences in free and protein-bound tyrosine among potato genotypes and the relationship to internal blackspot resistance

Twelve potato clones were selected to represent the full range of internal blackspot response in order to determine the relationships between tuber protein, free tyrosine, and blackspot susceptibility. The blackspot reaction for each clone was consistent over five growing seasons, including tubers grown over a normal season (mature), and short season (immature) during one year. The blackspot index, determined by either an abrasive peel test or an impact bruise test, was highly correlated with the tyrosine content of the tubers (r = 0.90 p = 0.001 for the means of each clone over five location-years). Tubers with free tyrosine levels below 4 μmole/g dry weight consistently showed a resistant blackspot response. The relationship between tyrosine and blackspot susceptibility was also found in stolon and bud ends from five of the clones which represented the extremes of blackspot reaction and genetic diversity. Bud end samples of each of the clones had lower tyrosine content and a corresponding reduction in blackspot compared with stolon ends. Phenols, other than tyrosine, showed no consistent relationship to the blackspot reaction. There was a very high negative correlation between free tyrosine and estimated protein-bound tyrosine. R values ranged from ?0.85 to ?0.97 (p = 0.001) for mature tubers of the 12 clones over 4 growing seasons. Total tyrosine (free, plus protein-bound) remained relatively constant. There were no significant differences in mean total tyrosine content among the 12 clones over five location-years of testing; and there were no significant differences among the five growing seasons except for the short season (immature) tubers which were 14% lower in total tyrosine content. These results indicate a remarkably constant level of total tyrosine production in the twelve clones studied, that represented diverse genetic backgrounds. Mature tubers of all genotypes contained 26 ± 1 μmole/g dry weight total tyrosine. Partitioning of tyrosine between tuber protein and the free amino acid pool varied with genotype and appeared to be a major determinate of blackspot resistance.     

Assessment and analyses for the interpretation of potato late blight response in field studies

Potato seedlings and cultivars were successfully subjected to moderate to heavy late blight pressure in field plots to which a race complex of the pathogen was applied. Multiple assessments through the course of the epidemics revealed differences in overall disease susceptibility or resistance. Differences were also demonstrated in disease response patterns among potato lines with similar overall disease ratings. Use of principal component and cluster analyses established discrete groupings of potato lines. This provides a basis for a more objective interpretation of the results in identifying both overall disease response and pattern (slow or fast) of response of potato cultivars and breeding lines.     

Comparative analyses of LMW glutenin alleles in bread wheat using allele-specific PCR and SDS-PAGE

One hundred and eighty-two bread wheat cultivars developed in India were characterized for low molecular weight (LMW) glutenins using SDS-PAGE and allele-specific polymerase chain reaction (PCR) to assess allelic diversity encoded by Glu-3 loci, as well as their utility for correctly identifying different alleles. SDS-PAGE indicated Glu-A3c is present in 64.6% of the cultivars, Glu-A3b in 13.8%, Glu-A3d in 12.7% and Glu-A3e/f in 8.8%. Seven types of alleles were present at the Glu-B3 locus: Glu-B3b (29.3%), Glu-B3g (27.0%), Glu-B3h (13.8%), Glu-B3i (16.1%), Glu-B3j (12.1%), Glu-B3c (0.6%) and Glu-B3d (1.1%). SDS-PAGE found three types of Glu-D3 alleles: Glu-D3a (30.2%), Glu-D3b (67.1%) and Glu-D3c (2.7%). However, PCR found two different alleles in cultivars classified as carrying Glu-D3a and three alleles in those identified as carrying Glu-D3b cultivars, indicating a more complex nature of the Glu-D3 locus. In conclusion, the data found greater consistency between the SDS-PAGE and PCR amplification patterns of alleles such as Glu-A3c, Glu-A3d, Glu-B3g, Glu-B3h and Glu-B3i, and less consistency between those same patterns in the Glu-A3b, Glu-A3e/f and Glu-B3b alleles. More studies are needed in order to achieve unambiguous identification of the Glu-3 alleles and thereby allow their greater utility in germplasm evaluation and breeding.     

Starch accumulation in the microspores of a solanum species and possible implications in mutation breeding

Waxy-like microspores have been observed during the specific period of starch accumulation in developing buds ofSolanum verrucosum. It is considered that appropriate mutagenic treatment of meiotic buds might perhaps increase the frequency of these waxy-like microspores to such a high proportion that the mutation could be transmitted to the next generation. Should such be the case it would become possible to test the double hypothesis that the waxy-like mutants are really amylose-free and that the waxy character can also express itself in the tubers.