Are There Rearrangement Hotspots in the Human Genome?

In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), postulating that the human genome is a mosaic of solid regions (with low propensity for rearrangements) and fragile regions (rearrangement hotspots). However, the rebuttal of RBM caused a controversy and led to a split among researchers studying genome evolution. In particular, it remains unclear whether some complex rearrangements (e.g., transpositions) can create an appearance of rearrangement hotspots. We contribute to the ongoing debate by analyzing multi-break rearrangements that break a genome into multiple fragments and further glue them together in a new order. In particular, we demonstrate that (1) even if transpositions were a dominant force in mammalian evolution, the arguments in favor of FBM still stand, and (2) the "gene deletion" argument against FBM is flawed.     

Computer Assessment of the Xenobiotic Metabolites Formation’s Probability in the Human Body

Biophysics - Abstract—Xenobiotics undergo biotransformation in the human body and the resulting metabolites may greatly differ in their physical, chemical, and biological properties from the...     

Comparison of Human and Animal Surveillance Data for H5N1 Influenza A in Egypt 2006–2011

Background

The majority of emerging infectious diseases are zoonotic (transmissible between animals and humans) in origin, and therefore integrated surveillance of disease events in humans and animals has been recommended to support effective global response to disease emergence. While in the past decade there has been extensive global surveillance for highly pathogenic avian influenza (HPAI) infection in both animals and humans, there have been few attempts to compare these data streams and evaluate the utility of such integration.

Methodology

We compared reports of bird outbreaks of HPAI H5N1 in Egypt for 2006–2011 compiled by the World Organisation for Animal Health (OIE) and the UN Food and Agriculture Organization (FAO) EMPRESi reporting system with confirmed human H5N1 cases reported to the World Health Organization (WHO) for Egypt during the same time period.

Principal Findings

Both human cases and bird outbreaks showed a cyclic pattern for the country as a whole, and there was a statistically significant temporal correlation between the data streams. At the governorate level, the first outbreak in birds in a season usually but not always preceded the first human case, and the time lag between events varied widely, suggesting regional differences in zoonotic risk and/or surveillance effectiveness. In a multivariate risk model, lower temperature, lower urbanization, higher poultry density, and the recent occurrence of a bird outbreak were associated with increased risk of a human case of HPAI in the same governorate, although the positive predictive value of a bird outbreak was low.

Conclusions

Integrating data streams of surveillance for human and animal cases of zoonotic disease holds promise for better prediction of disease risk and identification of environmental and regional factors that can affect risk. Such efforts can also point out gaps in human and animal surveillance systems and generate hypotheses regarding disease transmission.     

Whose Turn? Chromosome Research and the Study of the Human Genome

A common account sees the human genome sequencing project of the 1990s as a “natural outgrowth” of the deciphering of the double helical structure of DNA in the 1950s. The essay aims to complicate this neat narrative by putting the spotlight on the field of human chromosome research that flourished at the same time as molecular biology. It suggests that we need to consider both endeavors – the human cytogeneticists who collected samples and looked down the microscope and the molecular biologists who probed the molecular mechanisms of gene function – to understand the rise of the human genome sequencing project and the current genomic practices. In particular, it proposes that what has often been described as the “molecularization” of cytogenetics could equally well be viewed as the turn of molecular biologists to human and medical genetics – a field long occupied by cytogeneticists. These considerations also have implications for the archives that are constructed for future historians and policy makers.     

Cloning of Porcine Platelet Glycoprotein Ibα and Comparison with the Human Homolog

Glycoprotein Ib–IX–V (GPIb–IX–V) is a platelet adhesion receptor complex that initiates platelet aggregation. Glycoprotein Ibα (GPIbα) is the central component of the GPIb–IX–V complex, anchoring the complex to the cytoskeleton and harboring the binding site for von Willebrand factor (vWF). Previous studies suggest that the coagulation function in pigs differs from that in humans, especially with respect to the interaction between vWF and platelets. However, we have little knowledge about the function of porcine platelets, which is important with regard to studies of cardiovascular disease, clotting, and surgery that use pigs as animal models. To extend this information, we cloned and analyzed the porcine GPIbα sequence. Porcine GPIbα contains 1891 nucleotides and includes an open reading frame that encodes 627 amino acids. The nucleotide sequence showed 67% identity with human GPIbα, whereas the deduced amino acid sequences were 59% identical. The vWF binding domain shares the highest identity among different species, whereas the PEST domain shows variations. Evaluation of platelet function by using ristocetin-induced platelet aggregation revealed remarkably lower levels of aggregation in porcine than human platelets. According to the sequence analysis and platelet aggregation tests, we propose that the function of GPIbα, especially regarding the ristocetin–vWF–GPIbα interaction, differs between pigs and humans. This characterization of porcine GPIbα will enhance our knowledge of the porcine coagulation system.Abbreviations: GPIbα, glycoprotein Ibα, vWF, von Willebrand factorGlycoprotein (GP) Ib–IX–V is one of the major adhesive receptors expressed on the surface of circulating platelets and is essential for platelet adhesion and clot formation at sites of vascular injury.² Platelet adhesion in high-shear areas is initiated by GPIbα, a subunit of the GPIb–IX–V complex, via binding to von Willebrand factor (vWF), a multimeric adhesive protein associated with collagen in the vessel wall.^3,13,27 After GPIbα-dependent adhesion to vWF, platelets become activated and undergo cytoskeletal rearrangements associated with shape changes, spreading, and the secretion of platelet agonists that amplify the platelet aggregation and activation mediated by platelet integrin α_IIbβ₃.¹The GPIb–IX–V complex consists of 4 transmembrane subunits—GPIbα, GPIbβ, GP IX, and GP V—which are present at a ratio of 2:2:2:1.²⁶ The entire ligand-binding capacity of the GPIb–IX–V complex is situated in the N-terminal globular region (amino acids 1 through 282) of GPIbα.²⁸ Mutations in GPIbα lead to Bernard–Soulier syndrome and pseudo-von Willebrand disease.^15,24 Thrombi that cause complications in arterial thrombosis are associated with GPIb–IX–V, especially GPIbα.²¹ Because the interactions between GPIbα and its ligand are critical to the vascular processes of thrombosis and inflammation, the complex is under intense scrutiny as a potential therapeutic target.²⁹Pigs share many physiologic and anatomic similarities with humans and offer several breeding and handling advantages relative to nonhuman primates, making the pig an optimal species for preclinical experimentation. During the last several years, porcine animal models have gained a great deal of importance^23,30 in cardiovascular diseases,^6,33 ischemia–reperfusion injury,¹⁰ transplant surgery, and many other areas of biomedical research.¹⁷ In particular, the pig has been identified as an ideal cell, tissue, and organ donor for xenotransplantation. Because differences exist between species, it is necessary to take the physiologic differences between pigs and humans into account when developing animal models and when analyzing the results obtained by using these models.Our early studies revealed differences in the process of coagulation between pigs and humans.⁵ Currently we know little about which functions of platelets are conserved between species or about porcine GPIb–IX–V and its differences from the human complex. In the current study, we cloned the coding sequences of porcine GPIbα and compared its nucleotide sequence, deduced protein sequence, and 3D structure model with those of human GPIbα, focusing on important functional domains and vWF interaction sites. We also investigated the ability of porcine platelets to be agglutinated or activated when treated with ristocetin. This work represents a step toward understanding the value and limitations of the pig as a preclinical model for coagulation-related studies.     

Decreased External Skeletal Robustness in Schoolchildren – A Global Trend? Ten Year Comparison of Russian and German Data

Objectives

Obesity and a reduced physical activity are global developments. Physical activity affects the external skeletal robustness which decreased in German children. It was assumed that the negative trend of decreased external skeletal robustness can be found in other countries. Therefore anthropometric data of Russian and German children from the years 2000 and 2010 were compared.

Methods

Russian (2000/2010 n = 1023/268) and German (2000/2010 n = 2103/1750) children aged 6–10 years were investigated. Height, BMI and external skeletal robustness (Frame-Index) were examined and compared for the years and the countries. Statistical analysis was performed by Mann-Whitney-Test.

Results

Comparison 2010 and 2000: In Russian children BMI was significantly higher; boys were significantly taller and exhibited a decreased Frame-Index (p = .002) in 2010. German boys showed significantly higher BMI in 2010. In both sexes Frame-Index (p = .001) was reduced in 2010. Comparison Russian and German children in 2000: BMI, height and Frame-Index were different between Russian and German children. German children were significantly taller but exhibited a lower Frame-Index (p<.001). Even German girls showed a significantly higher BMI. Comparison Russian and German children in 2010: BMI and Frame-Index were different. Russian children displayed a higher Frame-Index (p<.001) compared with Germans.

Conclusions

In Russian children BMI has increased in recent years. Frame-Index is still higher in Russian children compared with Germans however in Russian boys Frame-Index is reduced. This trend and the physical activity should be observed in the future.     

Maximising Acute Kidney Injury Alerts – A Cross-Sectional Comparison with the Clinical Diagnosis

Background

Acute kidney injury (AKI) is serious and widespread across healthcare (1 in 7 hospital admissions) but recognition is often delayed causing avoidable harm. Nationwide automated biochemistry alerts for AKI stages 1-3 have been introduced in England to improve recognition. We explored how these alerts compared with clinical diagnosis in different hospital settings.

Methods

We used a large population cohort of 4464 patients with renal impairment. Each patient had case-note review by a nephrologist, using RIFLE criteria to diagnose AKI and chronic kidney disease (CKD). We identified and staged AKI alerts using the new national NHS England AKI algorithm and compared this with nephrologist diagnosis across hospital settings.

Results

Of 4464 patients, 525 had RIFLE AKI, 449 had mild AKI, 2185 had CKD (without AKI) and 1305 were of uncertain chronicity. NHS AKI algorithm criteria alerted for 90.5% of RIFLE AKI, 72.4% of mild AKI, 34.1% of uncertain cases and 14.0% of patients who actually had CKD.The algorithm identified AKI particularly well in intensive care (95.5%) and nephrology (94.6%), but less well on surgical wards (86.4%). Restricting the algorithm to stage 2 and 3 alerts reduced the over-diagnosis of AKI in CKD patients from 14.0% to 2.1%, but missed or delayed alerts in two-thirds of RIFLE AKI patients.

Conclusion

Automated AKI detection performed well across hospital settings, but was less sensitive on surgical wards. Clinicians should be mindful that restricting alerts to stages 2-3 may identify fewer CKD patients, but including stage 1 provides more sensitive and timely alerting.     

EGFR Intron Recombination in Human Gliomas: Inappropriate Diversion of V(D)J Recombination?

The epidermal growth factor receptor (EGFR) is a membrane-bound, 170 kDa, protein tyrosine kinase that plays an important role in tumorigenesis. The EGFR gene, which is composed of over 168 kb of sequence, including a 123-kb first intron, is frequently amplified and rearranged in malignant gliomas leading to the expression of oncogenic deletion (DM) and tandem duplication (TDM) mutants. The most common DM in gliomas is EGFRvIII, which arises from recombination between introns 1 and 7 with deletion of exons 2 through 7 and intervening introns. In addition, some human gliomas express 180- to 190-kDa TDM, which are constitutively active and highly oncogenic. Both DM and TDM arise by recombination of introns that contain sequences with homology to the recombination signal sequence (RSS) heptamers and nonamers present in the V(D)J region of the immunoglobin and T lymphocyte antigen receptor genes. V(D)J RSS have also been identified in certain proto-oncogenes like bcl-2 that are involved in translocations associated with the development of human lymphomas and in other genes such as hypoxanthine-guainine phosphoribosyl transferase (HPRT) in which deletion mutations and intron rearrangements are a common phenomenon. Together with the expression of recombination associated gene (RAG) and nonhomologous end-joining (NHEJ) proteins in gliomas, these observation suggest that aberrant activity of the V(D)J recombinase may be involved in the activation of proto-oncogenes in both liquid and solid tumors.     

A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip? for Methylome Profiling

DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome.     

Comparison of the Levels of Pro-Inflammatory Cytokines Released in the Vastus Lateralis Muscle of Patients with Fibromyalgia and Healthy Controls during Contractions of the Quadriceps Muscle – A Microdialysis Study

Objective

Fibromyalgia is associated with central hyperexcitability, but it is suggested that peripheral input is important to maintain central hyperexcitability. The primary aim was to investigate the levels of pro-inflammatory cytokines released in the vastus lateralis muscle during repetitive dynamic contractions of the quadriceps muscle in patients with fibromyalgia and healthy controls. Secondarily, to investigate if the levels of pro-inflammatory cytokines were correlated with pain or fatigue during these repetitive dynamic contractions.

Material and Methods

32 women with fibromyalgia and 32 healthy women (controls) participated in a 4 hour microdialysis session, to sample IL-1β, IL-6, IL-8, and TNF from the most painful point of the vastus lateralis muscle before, during and after 20 minutes of repeated dynamic contractions. Pain (visual analogue scale; 0–100) and fatigue Borg’s Rating of Perceived Exertion Scale; 6–20) were assessed before and during the entire microdialysis session.

Results

The repetitive dynamic contractions increased pain in the patients with fibromyalgia (P < .001) and induced fatigue in both groups (P < .001). Perceived fatigue was significantly higher among patients with fibromyalgia than controls (P < .001). The levels of IL-1β did not change during contractions in either group. The levels of TNF did not change during contractions in patients with fibromyalgia, but increased in controls (P < .001) and were significantly higher compared to patients with fibromyalgia (P = .033). The levels of IL-6 and IL-8 increased in both groups alike during and after contractions (P’s < .001). There were no correlations between pain or fatigue and cytokine levels after contractions.

Conclusion

There were no differences between patients with fibromyalgia and controls in release of pro-inflammatory cytokines, and no correlations between levels of pro-inflammatory cytokines and pain or fatigue. Thus, this study indicates that IL-1β, IL-6, IL-8, and TNF do not seem to play an important role in maintenance of muscle pain in fibromyalgia.     

3D Participatory Sensing with Low-Cost Mobile Devices for Crop Height Assessment – A Comparison with Terrestrial Laser Scanning Data

The integration of local agricultural knowledge deepens the understanding of complex phenomena such as the association between climate variability, crop yields and undernutrition. Participatory Sensing (PS) is a concept which enables laymen to easily gather geodata with standard low-cost mobile devices, offering new and efficient opportunities for agricultural monitoring. This study presents a methodological approach for crop height assessment based on PS. In-field crop height variations of a maize field in Heidelberg, Germany, are gathered with smartphones and handheld GPS devices by 19 participants. The comparison of crop height values measured by the participants to reference data based on terrestrial laser scanning (TLS) results in R² = 0.63 for the handheld GPS devices and R² = 0.24 for the smartphone-based approach. RMSE for the comparison between crop height models (CHM) derived from PS and TLS data is 10.45 cm (GPS devices) and 14.69 cm (smartphones). Furthermore, the results indicate that incorporating participants’ cognitive abilities in the data collection process potentially improves the quality data captured with the PS approach. The proposed PS methods serve as a fundament to collect agricultural parameters on field-level by incorporating local people. Combined with other methods such as remote sensing, PS opens new perspectives to support agricultural development.     

Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-than Genome Length ‘Imprecise’ Intermediates

Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of ‘evolution by duplication’ in the positive-strand RNA viruses.     

Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes?

The evolution of genome size as well as structure and organization of genomes belongs among the key questions of genome biology. Here we show, based on a comparative analysis of 30 genomes, that there is generally a tight correlation between the number of genes per chromosome and the length of the respective chromosome in eukaryotic genomes. The surprising exceptions to this pattern are placental mammalian genomes. We identify the number and, more importantly, the uneven distribution of gene deserts among chromosomes, i.e., long (>500 kb) stretches of DNA that do not encode for genes, as the main contributing factor for the observed anomaly of eutherian genomes. Gene-rich placental mammalian chromosomes have smaller proportions of gene deserts and vice versa. We show that the uneven distribution of gene deserts is a derived character state of eutherians. The functional and evolutionary significance of this particular feature of eutherian genomes remains to be explained.     

High-Pass Filter Characteristics of the Baroreflex – A Comparison of Frequency Domain and Pharmacological Methods

Pharmacological methods to assess baroreflex sensitivity evoke supra-physiological blood pressure changes whereas computational methods use spontaneous fluctuations of blood pressure. The relationships among the different baroreflex assessment methods are still not fully understood. Although strong advocates for each technique exist, the differences between these methods need further clarification. Understanding the differences between pharmacological and spontaneous baroreflex methods could provide important insight into the baroreflex physiology. We compared the modified Oxford baroreflex gain and the transfer function modulus between spontaneous RR interval and blood pressure fluctuations in 18 healthy subjects (age: 39±10 yrs., BMI: 26±4.9). The transfer function was calculated over the low-frequency range of the RR interval and systolic blood pressure oscillations during random-frequency paced breathing. The average modified Oxford baroreflex gain was lower than the average transfer function modulus (15.7±9.2 ms/mmHg vs. 19.4±10.5 ms/mmHg, P<0.05). The difference between the two baroreflex measures within the individual subjects comprised a systematic difference (relative mean difference: 20.7%) and a random variance (typical error: 3.9 ms/mmHg). The transfer function modulus gradually increased with the frequency within the low-frequency range (LF), on average from 10.4±7.3 ms/mmHg to 21.2±9.8 ms/mmHg across subjects. Narrowing the zone of interest within the LF band produced a decrease in both the systematic difference (relative mean difference: 0.5%) and the random variance (typical error: 2.1 ms/mmHg) between the modified Oxford gain and the transfer function modulus. Our data suggest that the frequency dependent increase in low-frequency transfer function modulus between RR interval and blood pressure fluctuations contributes to both the systematic difference (bias) and the random variance (error) between the pharmacological and transfer function baroreflex measures. This finding suggests that both methodological and physiological factors underlie the observed disagreement between the pharmacological and the transfer function method. Thus both baroreflex measures contribute complementary information and can be considered valid methods for baroreflex sensitivity assessment.     

Differential Distribution of Both IL-12Rβ Chains in the Plasma Membrane of Human T Cells

IL-12 is a cytokine that stimulates the expression of CD26, a T cell– and raft-associated ectopeptidase. IL-12 also enhances the interaction between CD26 and CD45RO, which removes the phosphatase CD45RO from raft microdomains. Since Janus kinases are known CD45 substrates, our hypothesis was that this relocation of CD45RO in nonraft areas of the membrane could be important to switch off the signaling via cytokine receptors, e.g., the IL-12 receptor (IL-12R). Accordingly, both IL-12R and CD45RO should be equally positioned in the cell membrane upon IL-12R ligation. However, there were no data available on the membrane distribution of IL-12R on human T cells. Working with phytohemagglutinin (PHA) lymphoblasts, we tried to fill that gap. The high-affinity IL-12R is made of two chains: IL-12Rβ1 and IL-12Rβ2. Using flow cytometry, Western blot and confocal microscopy, we obtained data suggesting that IL-12Rβ1 is mainly associated to phospholipid-rich membrane areas, a location even enhanced upon IL-12 incubation of PHA blasts. Instead, IL-12Rβ2 is found more segregated into membrane rafts, which could explain why two IL-12-triggered events, T-cell proliferation and ERK1/2 activation, are both methyl-β-cyclodextrin-sensitive events. Ligation of IL-12R with IL-12 seems to induce a partial enrichment of IL-12Rβ2 in phospholipid-rich areas, where according to our data IL-12Rβ1 is already present. Therefore, although new data will be required, the present results support the initial hypothesis.