Bias and Sampling Error of the Estimated Proportion of Genotypic Variance Explained by Quantitative Trait Loci Determined From Experimental Data in Maize Using Cross Validation and Validation With Independent Samples.

Cross validation (CV) was used to analyze the effects of different environments and different genotypic samples on estimates of the proportion of genotypic variance explained by QTL (p). Testcrosses of 344 F(3) maize lines grown in four environments were evaluated for a number of agronomic traits. In each of 200 replicated CV runs, this data set was subdivided into an estimation set (ES) and various test sets (TS). ES were used to map QTL and estimate p for each run (p(ES)) and its median (p(ES)) across all runs. The bias of these estimates was assessed by comparison with the median (p(TS.ES)) obtained from TS. We also used two independent validation samples derived from the same cross for further comparison. The median p(ES) showed a large upward bias compared to p(TS.ES). Environmental sampling generally had a smaller effect on the bias of p(ES) than genotypic sampling or both factors simultaneously. In independent validation, p(TS.ES) was on average only 50% of p(ES). A wide range among p(ES) reflected a large sampling error of these estimates. QTL frequency distributions and comparison of estimated QTL effects indicated a low precision of QTL localization and an upward bias in the absolute values of estimated QTL effects from ES. CV with data from three QTL studies reported in the literature yielded similar results as those obtained with maize testcrosses. We therefore recommend CV for obtaining asymptotically unbiased estimates of p and consequently a realistic assessment of the prospects of MAS.     

Avidin related protein 2 shows unique structural and functional features among the avidin protein family

Background  

The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin.     

Specific Genetic Interactions Between Spindle Assembly Checkpoint Proteins and B-Type Cyclins in Saccharomyces cerevisiae

The B-type cyclin Clb5 is involved primarily in control of DNA replication in Saccharomyces cerevisiae. We conducted a synthetic genetic array (SGA) analysis, testing for synthetic lethality between the clb5 deletion and a selected 87 deletions related to diverse aspects of cell cycle control based on GO annotations. Deletion of the spindle checkpoint genes BUB1 and BUB3 caused synthetic lethality with clb5. The spindle checkpoint monitors the attachment of spindles to the kinetochore or spindle tension during early mitosis. However, another spindle checkpoint gene, MAD2, could be deleted without ill effects in the absence of CLB5, suggesting that the bub1/3 clb5 synthetic lethality reflected some function other than the spindle checkpoint of Bub1 and Bub3. To characterize the lethality of bub3 clb5 cells, we constructed a temperature-sensitive clb5 allele. At nonpermissive temperature, bub3 clb5-ts cells showed defects in spindle elongation and cytokinesis. High-copy plasmid suppression of bub3 clb5 lethality identified the C-terminal fragment of BIR1, the yeast homolog of survivin; cytologically, the BIR1 fragment rescued the growth and cytokinesis defects. Bir1 interacts with IplI (Aurora B homolog), and the addition of bub3 clb5-ts significantly enhanced the lethality of the temperature-sensitive ipl1-321. Overall, we conclude that the synthetic lethality between clb5 and bub1 or bub3 is likely related to functions of Bub1/3 unrelated to their spindle checkpoint function. We tested requirements for other B-type cyclins in the absence of spindle checkpoint components. In the absence of the related CLB3 and CLB4 cyclins, the spindle integrity checkpoint becomes essential, since bub3 or mad2 deletion is lethal in a clb3 clb4 background. clb3 clb4 mad2 cells accumulated with unseparated spindle pole bodies. Thus, different B-type cyclins are required for distinct aspects of spindle morphogenesis and function, as revealed by differential genetic interactions with spindle checkpoint components.CELL cycle progression is achieved by series of activations of cyclins/cyclin-dependent kinase (CDK) complexes (Morgan 2003). CDK becomes active only when it is associated with cyclins. The process has to proceed sequentially and in a timely fashion. In Saccharomyces cerevisiae, there are six B-type cyclins, Clb1–6 (Nasmyth 1993). Clb1–4 are mitotic cyclins (Surana et al. 1991), and Clb5,6 are S-phase cyclins (Epstein and Cross 1992; Schwob and Nasmyth 1993). While different cyclins/CDK complexes promote distinct cell cycle events, these B-type cyclins also share overlapping functions. The primary role of Clb5,6 is to trigger DNA replication (Epstein and Cross 1992; Schwob and Nasmyth 1993). Mitotic cyclins Clb1–4 trigger entering into mitosis (Fitch et al. 1992; Richardson et al. 1992), and they also have functions in spindle pole body (SPB) separation (Fitch et al. 1992) and spindle elongation (Rahal and Amon 2008). Clb2 inhibits mitotic exit; therefore, degradation of Clb2 is required for mitotic exit (Wasch and Cross 2002).CLB5 is a nonessential gene, although Clb5,6 are the primary drivers of DNA replication in wild-type cells (Schwob and Nasmyth 1993). Clb-Cdk1 activity also inhibits rereplication within a single cell cycle by phosphorylation of the prereplicative complex (Labib et al. 1999; Drury et al. 2000; Nguyen et al. 2000, 2001; Liku et al. 2005). Binding of Clb5 to Orc6 also contributes to preventing DNA rereplication (Wilmes et al. 2004). The Clb5 hydrophobic patch mutant, Clb5-hpm, cannot bind to Orc6 (Wilmes et al. 2004).There are several known mitotic functions for Clb5. When clb5 was combined with cdc28-4 (CDC28 is the only CDK in S. cerevisiae), cells exhibited defects in nuclear positioning (Segal et al. 1998) and spindle polarity (Segal et al. 2000). Phosphorylation of Fin1 by Clb5-Cdk1 inhibits Fin1 association with the spindle, which affects spindle integrity (Woodbury and Morgan 2007). Consistently, Clb5 is present long after completion of replication and is degraded at the metaphase–anaphase transition by Cdc20/APC (anaphase promoting complex) (Shirayama et al. 1999).Synthetic genetic array analysis (SGA; Tong et al. 2001) can identify novel functions or pathways controlled by a nonessential protein. This analysis carried out with clb5 led to a study of the interaction of different B-type cyclins with components of the spindle assembly checkpoint. The spindle assembly checkpoint ensures the proper attachment between mitotic spindles and kinetochores. The checkpoint thus inhibits anaphase entry when spindles do not attach to the kinetochores properly. Components of the spindle checkpoint are mitotic-arrest-defective genes (MAD1, MAD2, MAD3) and the budding uninhibited by benzimidazole genes (BUB1 and BUB3) (Amon 1999). There is a functional difference between BUB and MAD genes. Deletion of BUB1 or BUB3 causes chromosome mis-segregation compared to the deletion of MAD genes (Warren et al. 2002). Bub1p and Bub3p are recruited to the kinetochore in early mitosis independently from spindle–kinetochore attachment status, whereas Mad1p and Mad2p are bound to kinetochores in response to the unattached kinetochores (Gillett et al. 2004). Thus, unlike Mad1p and Mad2p, Bub1p and Bub3p have functions that are independent and distinct from their checkpoint function in chromosome segregation. In this study, we discuss the genetic interactions between CLB5 and spindle checkpoint genes, emphasizing the difference between Mad and Bub proteins.     

Serum netrin and VCAM-1 as biomarker for Egyptian patients with type IΙ diabetes mellitus

ObjectiveThis study aimed to evaluate the serum level of netrin and soluble vascular cell adhesion molecule 1 (VCAM-I) in patients with type IΙ diabetes mellitus (T2DM) and evaluate the association of their levels with the development of a diabetic complication.Patients and methodsThis study was carried out on type II diabetic patients with and without complications and healthy individuals served as controls. All subjects were submitted to the estimation of serum lipid profile, serum creatinine, urinary albumin/creatinine ratio (ACR), fasting blood glucose (FBG), glycated hemoglobin (HbA1c), visceral adiposity index (VAI), atherogenic index of plasma (AIP), lipid accumulation product (LAP) and detection of serum level of netrin1 and VCAM1.ResultsDiabetic patients with complications had significantly higher serum levels of creatinine, ACR, cholesterol, Triglyceride, low-density lipoprotein, netrin1, and VCAM1 than diabetic patients without complications. Likewise, the level of VAI and LAP as markers of excessive body fat were significantly higher in diabetic patients with complications than diabetic patients without complications. The netrin1 and VCAM1 were a significant discriminator of T2DM renal complications with a sensitivity of 96%, 90%, and specificity of 82.7%, 91.3% respectively.ConclusionIt can be concluded that serum netrin1 and VCAM1 correlated significantly with markers of excessive body fat, a renal complication in the patient with type 2 diabetes mellitus.     

A Yeast GSK-3 Kinase Mck1 Promotes Cdc6 Degradation to Inhibit DNA Re-Replication

Cdc6p is an essential component of the pre-replicative complex (pre-RC), which binds to DNA replication origins to promote initiation of DNA replication. Only once per cell cycle does DNA replication take place. After initiation, the pre-RC components are disassembled in order to prevent re-replication. It has been shown that the N-terminal region of Cdc6p is targeted for degradation after phosphorylation by Cyclin Dependent Kinase (CDK). Here we show that Mck1p, a yeast homologue of GSK-3 kinase, is also required for Cdc6 degradation through a distinct mechanism. Cdc6 is an unstable protein and is accumulated in the nucleus only during G1 and early S-phase in wild-type cells. In mck1 deletion cells, CDC6p is stabilized and accumulates in the nucleus even in late S phase and mitosis. Overexpression of Mck1p induces rapid Cdc6p degradation in a manner dependent on Threonine-368, a GSK-3 phosphorylation consensus site, and SCF^CDC4. We show evidence that Mck1p-dependent degradation of Cdc6 is required for prevention of DNA re-replication. Loss of Mck1 activity results in synthetic lethality with other pre-RC mutants previously implicated in re-replication control, and these double mutant strains over-replicate DNA within a single cell cycle. These results suggest that a GSK3 family protein plays an unexpected role in preventing DNA over-replication through Cdc6 degradation in Saccharomyces cerevisiae. We propose that both CDK and Mck1 kinases are required for Cdc6 degradation to ensure a tight control of DNA replication.     

Measurements of several metallic elements and matrix metalloproteinases (MMPs) in saliva from patients with taste disorder

We have measured and compared several metallic elements and matrix metalloproteinases (MMPs) in saliva from patients with taste disorder and healthy subjects. Stimulated whole saliva was collected from 20 patients and 35 healthy subjects. Inductively coupled plasma mass spectrometry (ICP-MS) was used for the determination of metallic elements in saliva. Amounts of MMP-1, MMP-3, MMP-9 and IL-1alpha, IL-6 in saliva were measured using an enzyme-linked immunosorbent assay systems. Zinc in the serum was determined by flame atomic absorption spectrometry. Our results provide evidence that levels of zinc, manganese and the amount of MMP-3 in saliva are significantly decreased in the patients with taste disorder compared to the healthy subjects; Zn (p.p.b.): healthy subjects 79.8 +/- 42.6, patients 47.22 +/- 17.1, (P < 0.001), Mn (p.p.b.): healthy subjects 4.48 +/- 2.46, patients 2.78 +/- 1.23, (P < 0.004), MMP-3 (ng/ml), healthy subjects 0.820 +/- 0.417, patients 0.594 +/- 0.179 (P < 0.01). In contrast, copper is significantly increased in the patients; Cu (p.p.b.): healthy subjects 34.5 +/- 13.5, patients 45.9 +/- 20.8 (P < 0.049). These differences may be closely related with this disease. ICP-MS is an easy and accurate instrument for measurements of salivary metallic elements and may be useful in establishing a diagnosis of taste disorder.