Sequence composition and genome organization of maize

Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome approximately 80% the size of the human genome. To gain global insight into the organization of its genome, we have sequenced the ends of large insert clones, yielding a cumulative length of one-eighth of the genome with a DNA sequence read every 6.2 kb, thereby describing a large percentage of the genes and transposable elements of maize in an unbiased approach. Based on the accumulative 307 Mb of sequence, repeat sequences occupy 58% and genic regions occupy 7.5%. A conservative estimate predicts approximately 59,000 genes, which is higher than in any other organism sequenced so far. Because the sequences are derived from bacterial artificial chromosome clones, which are ordered in overlapping bins, tagged genes are also ordered along continuous chromosomal segments. Based on this positional information, roughly one-third of the genes appear to consist of tandemly arrayed gene families. Although the ancestor of maize arose by tetraploidization, fewer than half of the genes appear to be present in two orthologous copies, indicating that the maize genome has undergone significant gene loss since the duplication event.     

An Attempt to Evaluate Selected Aspects of “Bone–Fat Axis” Function in Healthy Individuals and Patients With Pancreatic Cancer

Recently, much attention has been paid to a potential biochemical cross-talk between the metabolism of the adipose tissue (AT) and bone (marrow), termed “bone–fat axis.” We hypothesized that selected substances, participating in this “dialog,” are associated with body mass and peripheral trafficking of bone marrow-derived stem cells (BMSCs) in both healthy individuals and patients with obesity-associated malignancies such as pancreatic adenocarcinoma.We performed an analysis of the systemic levels of selected substances involved in the regulation of bone (marrow) homeostasis (parathormone, calcitonin, osteopontin, osteonectin, stem cell factor [SCF], and fibroblast growth factor-23) in 35 generally healthy volunteers and 35 patients with pancreatic cancer. Results were correlated with the absolute number of circulating BMSCs and body mass values. Additionally, subcutaneous and visceral/omental AT levels of the aforementioned molecules were analyzed in lean and overweight/obese individuals.Intensified steady-state trafficking of only Lin-CD45 + CD133 + hematopoietic stem/progenitor cells was observed in overweight/obese individuals and this was associated with BMI values and elevated levels of both osteonectin and SCF, which also correlated with BMI. In comparison to healthy individuals, patients with cancer had significantly higher osteopontin levels and lower values of both osteonectin and osteonectin/osteopontin ratio. While no significant correlation was observed between BMI and the number of circulating BMSCs in patients with cancer, peripheral trafficking of CD34 + KDR + CD31 + CD45-endothelial progenitor cells and CD105 + STRO-1 + CD45-mesenchymal stem cells was associated with the osteonectin/osteopontin ratio, which also correlated with BMI (r = 0.52; P < 0.05). AT levels of the examined substances were similar to those measured in the plasma, except for osteonectin, which was about 10 times lower.Our study highlights the potential role of osteonectin, osteopontin, and SCF as communication signals between the bone (marrow) and AT in both healthy individuals and patients with pancreatic cancer. We postulate that these molecules may be overlooked biochemical players linking body mass and BMSCs with obesity-associated cancer development and/or progression in humans.     

Recombination patterns in maize reveal limits to crossover homeostasis

During meiotic recombination, double-strand breaks (DSBs) are formed in chromosomal DNA and then repaired as either crossovers (COs) or non–crossovers (NCOs). In most taxa, the number of DSBs vastly exceeds the number of COs. COs are required for generating genetic diversity in the progeny, as well as proper chromosome segregation. Their formation is tightly controlled so that there is at least one CO per pair of homologous chromosomes whereas the maximum number of COs per chromosome pair is fairly limited. One of the main mechanisms controlling the number of recombination events per meiosis is CO homeostasis, which maintains a stable CO number even when the DSB number is dramatically altered. The existence of CO homeostasis has been reported in several species, including mouse, yeast, and Caenorhabditis elegans. However, it is not known whether homeostasis exists in the same form in all species. In addition, the studies of homeostasis have been conducted using mutants and/or transgenic lines exhibiting fairly severe meiotic phenotypes, and it is unclear how important homeostasis is under normal physiological conditions. We found that, in maize, CO control is robust only to ensure one CO per chromosome pair. However, once this limit is reached, the CO number is linearly related to the DSB number. We propose that CO control is a multifaceted process whose different aspects have a varying degree of importance in different species.Meiotic recombination creates genetic diversity by generating new allelic combinations in the progeny. In the first step of the recombination pathway, double-strand breaks (DSBs) are formed in chromosomal DNA by a topoisomerase-like protein, SPO11 (1). The DSBs are subsequently repaired in a process that involves several recombination proteins. First, the MRN complex, which includes MRE11, RAD50, and NBS1, resects the DSB ends, leading to formation of 3′ overhangs (2). The single-stranded DNAs created in this way are then coated by two recA-like proteins, RAD51 and DMC1. These proteins catalyze the invasion of homologous double-stranded DNA regions, resulting in single-end invasion (SEI) events (3). Eventually, DSBs are repaired as either crossovers (COs) or non–crossovers (NCOs). Besides generating genetic diversity, crossing-over creates physical connections between homologous chromosomes, which are essential for accurate segregation of the homologs during the first meiotic division. Defects in this process can lead to aneuploidy. Consequently, CO formation, including the number and distribution of COs, is under stringent control (4, 5).To ensure proper segregation of chromosomes during anaphase I, at least one CO must be formed for each homolog pair (6). Failure to meet this requirement leads to chromosome missegregation. Consequently, nonexchange chromosomes are extremely rare in WT meiosis in most species, including maize (7). Even in Caenorhabditis elegans, which forms only one CO per bivalent, the rate of nonexchange chromosomes is less than 1% (8, 9). These observations led to the proposal of an obligate CO model, which posits that there must be a regulatory mechanism, called CO assurance, that ensures the formation of at least one obligate CO per bivalent (6).In contrast to the lower limit, regulation of the upper limit of CO number per homolog pair is less understood. Both the number of COs and the spacing between them are affected by CO interference. Interference reduces the probability of two COs forming next to each other. Thus, it limits the number of COs and increases their spacing. The strength of interference diminishes with the distance along the chromosome. Not all COs are subject to interference, but data from numerous species, including budding yeast, mouse, and maize, show that only a small fraction of COs are independent of interference (10–13). In maize, ∼15% of COs belong to the noninterfering class (12).Due to these constraints on CO number and placement, it is quite likely that the number of COs per bivalent is largely similar among eukaryotes although variation exists both between and within species (14–16). Major differences, however, have been observed among species with respect to the number of meiotic DSBs. In most cases, the number of DSBs far exceeds the number of COs (17, 18). For instance, in maize, nearly 500 DSBs lead to the formation of ∼20 COs (15, 19).Mechanisms determining which DSBs result in COs or NCOs are poorly understood. CO rates are unlikely to be limited by the structural properties of chromosomes (20). Instead, they are controlled by an intricate regulatory mechanism influencing DSB fate. Mutating components of this mechanism can dramatically increase CO number (20, 21). In contrast, studies in budding yeast, C. elegans, and mouse have shown that CO numbers are not affected by DSB number, even if the variation in the number of DSBs is substantial (18, 22–24). This phenomenon is known as CO homeostasis (22). However, it is not known whether homeostasis operates in all species. In addition, the studies of homeostasis have been conducted using mutants and/or transgenic lines exhibiting fairly severe meiotic phenotypes, and it is unclear how important homeostasis is under normal physiological conditions.To understand CO control, we examined the substantial intraspecies variation in CO and DSB numbers that exists in maize. Surprisingly, we found a strong correlation between the number of meiotic DSBs and the number of COs. Our data suggest that, whereas CO control in maize maintains CO assurance (i.e., ensures the presence of one obligate CO per bivalent), it does not operate beyond this limit. Instead, once the requirement for the obligate CO is met, the number of COs becomes proportional to the DSB number. We propose that the control of the CO number is a multifaceted process whose different aspects have a varying degree of importance in different species.     

Mathematical modelling of the growth of human fetus anatomical structures

The goal of this study was to present a procedure that would enable mathematical analysis of the increase of linear sizes of human anatomical structures, estimate mathematical model parameters and evaluate their adequacy. Section material consisted of 67 foetuses—rectus abdominis muscle and 75 foetuses- biceps femoris muscle. The following methods were incorporated to the study: preparation and anthropologic methods, image digital acquisition, Image J computer system measurements and statistical analysis method. We used an anthropologic method based on age determination with the use of crown-rump length—CRL (V–TUB) by Scammon and Calkins. The choice of mathematical function should be based on a real course of the curve presenting growth of anatomical structure linear size ? in subsequent weeks t of pregnancy. Size changes can be described with a segmental-linear model or one-function model with accuracy adequate enough for clinical purposes. The interdependence of size–age is described with many functions. However, the following functions are most often considered: linear, polynomial, spline, logarithmic, power, exponential, power-exponential, log-logistic I and II, Gompertz’s I and II and von Bertalanffy’s function. With the use of the procedures described above, mathematical models parameters were assessed for V-PL (the total length of body) and CRL body length increases, rectus abdominis total length h, its segments hI, hII, hIII, hIV, as well as biceps femoris length and width of long head (LHL and LHW) and of short head (SHL and SHW). The best adjustments to measurement results were observed in the exponential and Gompertz’s models.     

Study of the behavior of <Emphasis Type="Italic">Euglena viridis</Emphasis>, <Emphasis Type="Italic">Euglena gracilis</Emphasis> and <Emphasis Type="Italic">Lepadella patella</Emphasis> cultured in all-glass microaquarium

In the paper, the microaquarium fabricated in a form of entirely glass lab-on-a-chip for culturing and microscale study of microorganisms has been presented. A new approach towards cellular studies that brings a significant improvement over commonly utilized – polymer-based solutions has been shown. For the first time, all-borosilicate glass chip was applied for the culturing of the selected microorganisms and enabled notable population growth and behaviorism investigation. The chip fabrication method in comparison to typical glass chip technology was notably simplified, including quick patterning and low temperature bonding in 80 °C. In the studies, both a single-cell (Euglena gracilis and Euglena viridis) and multi-cell microorganisms (Lepadella patella) were cultured in the microaquarium. Behaviorism of the selected microorganisms was investigated by supplying various proportions of carbon dioxide, nitrogen and air into the chip. Tests included studies of microorganisms chemotaxis, viability (mostly based on photosynthesis process) and coexistence in the lab-on-a-chip environment. The experiments confirmed that the developed chip is a tool that fits the requirements for the culturing and behavioral studies of microorganisms and constitute ground-works to propel its further application in broadly defined cellular study field.     

Reconstruction of cranial cruciate ligament in rabbits using polyester implants saturated with PRP,antlerogenic stem cells MIC-1 and their homogenate

Aim of the study: The attempt to limit the negative effects of polyester implants on the articular cavity by using preparations containing growth factors. Materials and Methods: Polyester implants used for the reconstruction of a rabbit’s cranial cruciate ligament (CCL) were saturated with autogenic platelet-rich plasma (PRP), antlerogenic stem cells MIC-1 and their homogenate prior to the surgery. Six months after CCL reconstruction, morphological, and biochemical blood tests were carried out, including proteinogram and acute phase proteins. The knee joints were also examined macro- and microscopically. Results: The results, compared to the control group, showed a favorable effect of the PRP and homogenate of antlerogenic cells on limiting the inflammation caused by the presence of polyester implant in the knee joint. The addition of growth factors caused covering the implant faster with the recipient’s connective tissue, thus contributing to reducing the inflammatory reaction of the articular capsule to the presence of polyester. At the same time, no enhanced local or general reaction of the rabbit organism was observed to the presence of xenogenic antlerogenic stem cells MIC-1 homogenate which, like the PRP, may provide an easily available source of growth factors, increasingly often used in regenerative medicine. Conclusions: Applying antlerogenic stem cells, their homogenate or PRP increases the volume of connective tissue that surrounds and intertwines polyester CCL implant, separating it from synovial cavity environment.     

Quality and performance of validated prognostic models for survival after resection of intrahepatic cholangiocarcinoma: a systematic review and meta-analysis

BackgroundThe objective of this systematic review was to evaluate the performance of prognostic survival models for intrahepatic cholangiocarcinoma (iCCA) when validated in an external dataset. Furthermore, it sought to identify common prognostic factors across models, and assess methodological quality of the studies in which the models were developed.MethodsThe PRISMA guidelines were followed. External validation studies of prognostic models for patients with iCCA were searched in 5 databases. Model performance was assessed by discrimination and calibration.ResultsThirteen external validation studies were identified, validating 18 different prognostic models. The Wang model was the sole model with good performance (C-index above 0.70) for overall survival. This model incorporated tumor size and number, lymph node metastasis, direct invasion into surrounding tissue, vascular invasion, Carbohydrate antigen (CA) 19-9, and carcinoembryonic antigen (CEA). Methodological quality was poor in 11/12 statistical models. The Wang model had the highest score with 13 out of 17 points.ConclusionThe Wang model for prognosis after resection of iCCA has good quality and good performance at external validation, while most prognostic models for iCCA have been developed with poor methodological quality and show poor performance at external validation.     

Erysipelothrix rhusiopathiae Endocarditis in a Patient With Severe Unicuspid Aortic Valve Damage Complicated With Acquired Ventricular Septal Defect

Erysipelothrix rhusiopathiae, is an important animal pathogen, but rarely reported in humans. To date, only fa ew cases of infective E rhusiopathiae endocarditis of the aortic valve have been described. We introduce the first reported case of severe damage of the native unicuspid aortic valve complicated with acquired ventricular septal defect caused by E rhusiopathiae endocarditis. This case may provide a better understanding of the disease process and transmission and underscores the need to include this pathogen in the differential diagnosis of infective endocarditis.     

Structural Characterization of Al65Cu20Fe15 Melt-Spun Alloy by X-ray,Neutron Diffraction,High-Resolution Electron Microscopy and Mössbauer Spectroscopy

The aim of the work was to characterize the structure of Al₆₅Cu₂₀Fe₁₅ alloy obtained with the use of conventional casting and rapid solidification-melt-spinning technology. Based on the literature data, the possibility of an icosahedral quasicrystalline phase forming in the Al-Cu-Fe was verified. Structure analysis was performed based on the results of X-ray diffraction, neutron diffraction, ⁵⁷Fe Mössbauer and transmission electron microscopy. Studies using differential scanning calorimetry were carried out to describe the crystallization mechanism. Additionally, electrochemical tests were performed in order to characterize the influence of the structure and cooling rate on the corrosion resistance. On the basis of the structural studies, the formation of a metastable icosahedral phase and partial amorphous state of ribbon structure were demonstrated. The possibility of the formation of icosahedral quasicrystalline phase I-AlCuFe together with the crystalline phases was indicated by X-ray diffraction (XRD), neutron diffraction (ND) patterns, Mössbauer spectroscopy, high-resolution transmission electron microscopy (HRTEM) observations and differential scanning calorimetry (DSC) curves. The beneficial effect of the application of rapid solidification on the corrosive properties was also confirmed.