Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

BACKGROUND

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.

RESULTS

We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.

CONCLUSION

We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.

Parameter estimation for discretely observed linear birth-and-death processes

Birth-and-death processes are widely used to model the development of biological populations. Although they are relatively simple models, their parameters can be challenging to estimate, as the likelihood can become numerically unstable when data arise from the most common sampling schemes, such as annual population censuses. A further difficulty arises when the discrete observations are not equi-spaced, for example, when census data are unavailable for some years. We present two approaches to estimating the birth, death, and growth rates of a discretely observed linear birth-and-death process: via an embedded Galton-Watson process and by maximizing a saddlepoint approximation to the likelihood. We study asymptotic properties of the estimators, compare them on numerical examples, and apply the methodology to data on monitored populations.

Short-term effects of simulated microgravity on morphology and gene expression in human breast cancer cells

Introduction

Microgravity has been shown to impose various effects on breast cancer cells. We exposed human breast cancer cells to simulated microgravity and studied morphology and alterations in gene expression.

Materials and methods

Human breast cancer cells were exposed to simulated microgravity in a random positioning machine (RPM) for 24 h. Morphology was observed under light microscopy, and gene alteration was studied by qPCR.

Results

After 24 h, formation of three-dimensional structures (spheroids) occurred. BRCA1 expression was significantly increased (1.9×, p < 0.05) in the adherent cells under simulated microgravity compared to the control. Expression of KRAS was significantly decreased (0.6×, p < 0.05) in the adherent cells compared to the control. VCAM1 was significantly upregulated (6.6×, 2.0×, p < 0.05 each) in the adherent cells under simulated microgravity and in the spheroids. VIM expression was significantly downregulated (0.45×, 0.44×, p < 0.05 each) in the adherent cells under simulated microgravity and in the spheroids. There was no significant alteration in the expression of MAPK1, MMP13, PTEN, and TP53.

Conclusions

Simulated microgravity induces spheroid formation in human breast cancer cells within 24 h and alters gene expression toward modified adhesion properties, enhanced cell repair, and phenotype preservation. Further insights into the underlying mechanisms could open up the way toward new therapies.

Short-term effects of simulated microgravity on morphology and gene expression in human breast cancer cells

INTRODUCTION

Microgravity has been shown to impose various effects on breast cancer cells. We exposed human breast cancer cells to simulated microgravity and studied morphology and alterations in gene expression.

MATERIALS AND METHODS

Human breast cancer cells were exposed to simulated microgravity in a random positioning machine (RPM) for 24 h. Morphology was observed under light microscopy, and gene alteration was studied by qPCR.

RESULTS

After 24 h, formation of three-dimensional structures (spheroids) occurred. BRCA1 expression was significantly increased (1.9×, p < 0.05) in the adherent cells under simulated microgravity compared to the control. Expression of KRAS was significantly decreased (0.6×, p < 0.05) in the adherent cells compared to the control. VCAM1 was significantly upregulated (6.6×, 2.0×, p < 0.05 each) in the adherent cells under simulated microgravity and in the spheroids. VIM expression was significantly downregulated (0.45×, 0.44×, p < 0.05 each) in the adherent cells under simulated microgravity and in the spheroids. There was no significant alteration in the expression of MAPK1, MMP13, PTEN, and TP53.

CONCLUSIONS

Simulated microgravity induces spheroid formation in human breast cancer cells within 24 h and alters gene expression toward modified adhesion properties, enhanced cell repair, and phenotype preservation. Further insights into the underlying mechanisms could open up the way toward new therapies.

Likely Transiting Exocomets Detected By Kepler

We present the first good evidence for exocomet transits of a host star in continuum light in data from the Kepler mission. The Kepler star in question, KIC 3542116, is of spectral type F2V and is quite bright at Kp = 10. The transits have a distinct asymmetric shape with a steeper ingress and slower egress that can be ascribed to objects with a trailing dust tail passing over the stellar disk. There are three deeper transits with depths of ≃ 0.1% that last for about a day, and three that are several times more shallow and of shorter duration. The transits were found via an exhaustive visual search of the entire Kepler photometric data set, which we describe in some detail. We review the methods we use to validate the Kepler data showing the comet transits, and rule out instrumental artefacts as sources of the signals. We fit the transits with a simple dust-tail model, and find that a transverse comet speed of ∼35-50 km s-1 and a minimum amount of dust present in the tail of ∼ 1016 g are required to explain the larger transits. For a dust replenishment time of ∼10 days, and a comet lifetime of only ∼300 days, this implies a total cometary mass of ≳ 3 × 1017 g, or about the mass of Halley's comet. We also discuss the number of comets and orbital geometry that would be necessary to explain the six transits detected over the four years of Kepler prime-field observations. Finally, we also report the discovery of a single comet-shaped transit in KIC 11084727 with very similar transit and host-star properties.

Endocrine Control of Exaggerated Trait Growth in Rhinoceros Beetles

Juvenile hormone (JH) is a key insect growth regulator frequently involved in modulating phenotypically plastic traits such as caste determination in eusocial species, wing polymorphisms in aphids, and mandible size in stag beetles. The jaw morphology of stag beetles is sexually-dimorphic and condition-dependent; males have larger jaws than females and those developing under optimum conditions are larger in overall body size and have disproportionately larger jaws than males raised under poor conditions. We have previously shown that large males have higher JH titers than small males during development, and ectopic application of fenoxycarb (JH analog) to small males can induce mandibular growth similar to that of larger males. What remains unknown is whether JH regulates condition-dependent trait growth in other insects with extreme sexually selected structures. In this study, we tested the hypothesis that JH mediates the condition-dependent expression of the elaborate horns of the Asian rhinoceros beetle, Trypoxylus dichotomus. The sexually dimorphic head horn of this beetle is sensitive to nutritional state during larval development. Like stag beetles, male rhinoceros beetles receiving copious food produce disproportionately large horns for their body size compared with males under restricted diets. We show that JH titers are correlated with body size during the late feeding and early prepupal periods, but this correlation disappears by the late prepupal period, the period of maximum horn growth. While ectopic application of fenoxycarb during the third larval instar significantly delayed pupation, it had no effect on adult horn size relative to body size. Fenoxycarb application to late prepupae also had at most a marginal effect on relative horn size. We discuss our results in context of other endocrine signals of condition-dependent trait exaggeration and suggest that different beetle lineages may have co-opted different physiological signaling mechanisms to achieve heightened nutrient-sensitive weapon growth.

Anoctamin 6 is localized in the primary cilium of renal tubular cells and is involved in apoptosis-dependent cyst lumen formation

Primary cilia are antenna-like structures projected from the apical surface of various mammalian cells including renal tubular cells. Functional or structural defects of the cilium lead to systemic disorders comprising polycystic kidneys as a key feature. Here we show that anoctamin 6 (ANO6), a member of the anoctamin chloride channel family, is localized in the primary cilium of renal epithelial cells in vitro and in vivo. ANO6 was not essential for cilia formation and had no effect on in vitro cyst expansion. However, knockdown of ANO6 impaired cyst lumen formation of MDCK cells in three-dimensional culture. In the absence of ANO6, apoptosis was reduced and epithelial cells were incompletely removed from the center of cell aggregates, which form in the early phase of cystogenesis. In line with these data, we show that ANO6 is highly expressed in apoptotic cyst epithelial cells of human polycystic kidneys. These data identify ANO6 as a cilium-associated protein and suggest its functional relevance in cyst formation.

Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Treatment of intraarticular middle phalanx fractures using the Ligamentotaxor®

BACKGROUND

We evaluated the outcome of intraarticular middle phalanx fractures after dynamic treatment with the Ligamentotaxor® system.

MATERIALS AND METHODS

Ten consecutive patients (seven male, three female; mean age 52 years) with intraarticular middle phalanx fractures were treated with the Ligamentotaxor® between 2009 and 2011. Proximal interphalangeal joint mobility, grip strength and 'Disabilities of the Arm, Shoulder and Hand' (DASH) score were evaluated in a 15-month follow-up. The reconstitution of the intraarticular space was measured immediately after trauma, at 6 weeks and at 15 months by radiograph control. The severity of the trauma was classified according to AO.

RESULTS

We found B1 30 %, C1 (Seno I + II) 50 % and C3 (Seno III-V) 20 %. In 60 % of the cases, fractures were localized on the middle base of the fifth digit, in 20 % on the third digit and in 20 % on the index finger. The dynamic treatment lasted 7 weeks; patients were exposed to full workload after 9 weeks. The mean flexion mobility after 15 months reached 73° (range 60-100°), and the extension deficit was 13° (range 0-20°) on average. Grip strength attained 71.3 % (range 60-87 %) of the contralateral side. Initial x-ray after trauma compared to the x-ray after 15 months showed an intraarticular space reconstitution average of 0.5 mm (range 0.1-0.9 mm) anterior-posterior and 0.6 mm (range 0.1-1 mm) lateral. Patients evaluated their outcome with an average of 14.6 points (range 3.3-26.7) using the DASH score.

CONCLUSION

Good results can be obtained with the Ligamentotaxor®. We recommend it for the dynamic treatment of intraarticular middle phalanx finger fractures. Larger series and long-term results are needed.

A strong magnetic field around the supermassive black hole at the centre of the Galaxy

Earth's nearest candidate supermassive black hole lies at the centre of the Milky Way. Its electromagnetic emission is thought to be powered by radiatively inefficient accretion of gas from its environment, which is a standard mode of energy supply for most galactic nuclei. X-ray measurements have already resolved a tenuous hot gas component from which the black hole can be fed. The magnetization of the gas, however, which is a crucial parameter determining the structure of the accretion flow, remains unknown. Strong magnetic fields can influence the dynamics of accretion, remove angular momentum from the infalling gas, expel matter through relativistic jets and lead to synchrotron emission such as that previously observed. Here we report multi-frequency radio measurements of a newly discovered pulsar close to the Galactic Centre and show that the pulsar's unusually large Faraday rotation (the rotation of the plane of polarization of the emission in the presence of an external magnetic field) indicates that there is a dynamically important magnetic field near the black hole. If this field is accreted down to the event horizon it provides enough magnetic flux to explain the observed emission--from radio to X-ray wavelengths--from the black hole.

Oral magnesium supplementation reduces insulin resistance in non-diabetic subjects - a double-blind, placebo-controlled, randomized trial

The incidence of insulin resistance and metabolic syndrome correlates with the availability of magnesium (Mg). We studied the effect of oral Mg supplementation on insulin sensitivity and other characteristics of the metabolic syndrome in normomagnesemic, overweight, insulin resistant, non-diabetic subjects. Subjects were tested for eligibility using oral glucose tolerance test (OGTT) and subsequently randomized to receive either Mg-aspartate-hydrochloride (n = 27) or placebo (n = 25) for 6 months. As trial endpoints, several indices of insulin sensitivity, plasma glucose, serum insulin, blood pressure and lipid profile were determined. Mg supplementation resulted in a significant improvement of fasting plasma glucose and some insulin sensitivity indices (ISIs) compared to placebo. Blood pressure and lipid profile did not show significant changes. The results provide significant evidence that oral Mg supplementation improves insulin sensitivity even in normomagnesemic, overweight, non-diabetic subjects emphasizing the need for an early optimization of Mg status to prevent insulin resistance and subsequently type 2 diabetes.

Four-digit replantation in a mentally retarded person: a case report

This report describes a case where 4 digits were replanted in a mentally retarded patient with a history of smoking and the inability to follow postoperative arrangements.

Script-driven imagery of self-injurious behavior in patients with borderline personality disorder: a pilot FMRI study

OBJECTIVE

Self-injurious behavior (SIB) is one of the most distinctive features of borderline personality disorder (BPD) and related to impulsivity and emotional dysregulation.

METHOD

Female patients with BPD (n = 11) and healthy controls (n = 10) underwent functional magnetic resonance imaging while listening to a standardized script describing an act of self-injury. Experimental sections of the script were contrasted to the neutral baseline section and group-specific brain activities were compared.

RESULTS

While imagining the reactions to a situation triggering SIB, patients with BPD showed significantly less activation in the orbitofrontal cortex compared with controls. Furthermore, only patients with BPD showed increased activity in the dorsolateral prefrontal cortex during this section and a decrease in the mid-cingulate while imagining the self-injurious act itself.

CONCLUSION

This pattern of activation preliminary suggests an association with diminished emotion regulation, impulse control as well as with response selection and reappraisal during the imagination of SIB.

Bony remodelling in unilateral dermatomal cavernous haemangiomatosis of the arm

We report a case of a massive unilateral dermatomal cavernous haemangioma (UDCH) affecting the left arm and adjacent neck in the region of the C4-C8 dermatomes, with associated bony remodelling. To our knowledge, this is the first report of the rare condition UDCH with bony abnormalities.

A cross-sectional investigation of discontinuation of self-injury and normalizing pain perception in patients with borderline personality disorder

OBJECTIVE

Several studies have shown reduced pain perception in patients with borderline personality disorder (BPD) and current self-injurious behavior (SIB). The aim of the present study was to test whether pain perception in patients with current SIB is different from that of patients who had stopped SIB, and whether pain perception of the latter group differs from healthy controls (HC).

METHOD

We investigated 24 borderline patients and 24 HC. Thirteen patients showed current SIB (BPD-SIB) and 11 patients did not exhibit SIB anymore (BPD-non-SIB). Pain thresholds were assessed using thermal stimuli and laser radiant heat pulses.

RESULTS

We found significant linear trends for all pain measures. The BPD-SIB group was less sensitive than the BPD-non-SIB group and the latter were less sensitive than HC. The pain sensitivity negatively correlated with borderline symptom severity.

CONCLUSION

The results suggest an association between the termination of SIB, decline of psychopathology and normalization of pain perception in borderline patients.

Concepts and developments in peripheral nerve surgery

Nerve injuries may result in sensory and motor deficits when not treated appropriately. Especially the surgical management of nerve defects still represents a challenge for the surgeon. In these cases the grafting of autologous nerves represents the only reasonable approach. Due to the side effects associated with this method (sacrifice of donor nerves, neuroma formation in the harvesting area, limited availability of donor nerves, etc.), numerous alternatives were proposed in order to avoid the transplantation of autologous tissue. This review provides a general view on the state of the art of how to supply gaping injuries in the peripheral nerve. Furthermore new approaches emphasizing tubulization techniques for the reconstruction of lost nerve tissue are described with a special focus on various materials with their advantages and disadvantages.

[Is intraoperative luxation of the ulnar nerve a criterion for transposition?]

BACKGROUND

The relevance of subcutaneous transposition of the ulnar nerve in the therapy of cubital tunnel syndrome is still under debate. The aim of this study was to compare the results after decompression to additional transposition in cases of intraoperative luxation.

METHODS

A total of 54 cases after surgery of cubital tunnel syndrome between 2000 and 2006 were analyzed. Nerve transposition was performed in cases of intraoperatively apparent nerve luxation.

RESULTS

Of the patients 12 were treated by decompression alone and 42 by additional subcutaneous transposition. There was no significant difference concerning symptom amelioration, usage properties of the hand, sensation impairment and duration of disability. Force measurements of grip strength and pinch strength revealed no significant differences between either hand in both groups. The 2-point discrimination ability of the 8th to 10th finger nerves was not significantly different between the groups either.

CONCLUSION

Nerve transposition revealed no benefits in the treatment of cubital tunnel syndrome when performed in cases of intraoperative nerve luxation.

[Characteristics of Pseudomonas aurantiaca DNA supramolecular complexes at various developmental stages]

Differences in viscoelasticity (eta) and molecular mass (M) values, as well as in the fatty acid profile of lipids in DNA supramolecular complexes (SC) isolated from Pseudomonas aurantiaca cultures at the exponential and stationary growth phases were established for the first time. Typical characteristics of DNA SC from actively growing cells were the following: eta = 315 +/- 15 dl/g, M(DNA) = 39 x 10(6) Da, C16:0 > C18:0 > C18:1 present as basic fatty acids (FA) in a pool of loosely DNA-bound lipids; the tightly DNA-bound lipid fraction consisted of only two acids C18:0 > C16:0. Significantly higher values of viscoelasticity eta = 779 +/- 8 dl/g and M(DNA) = 198 x 10(6) Da were observed for DNA SC of the stationary phase cells; one more FA, C14:0, was detected in the loosely bound lipid fraction, while lipids tightly bound to DNA contained mainly C16:0 > C18:1 > > C18:0 > C14:0 FA. The content of saturated FA in the DNA-bound lipids in the stationary phase cells was twice as high as in the exponential phase cells. The fraction of tightly bound lipids from the stationary phase cells contained nine times more unsaturated fatty acids than the fraction from proliferating cells. These differences in FA composition of DNA-bound lipids demonstrate the importance of lipids for the structural organization and functioning of genomic DNA during bacterial culture development.

Myeloma responses and tolerance following combined kidney and nonmyeloablative marrow transplantation: in vivo and in vitro analyses

Six patients with renal failure due to multiple myeloma (MM) received simultaneous kidney and bone marrow transplantation (BMT) from HLA-identical sibling donors following nonmyeloablative conditioning, including cyclophosphamide (CP), peritransplant antithymocyte globulin and thymic irradiation. Cyclosporine (CyA) was given for approximately 2 months posttransplant, followed by donor leukocyte infusions. All six patients accepted their kidney grafts long-term. Three patients lost detectable chimerism but accepted their kidney grafts off immunosuppression for 1.3 to >7 years. One such patient had strong antidonor cytotoxic T lymphocyte (CTL) responses in association with marrow rejection. Two patients achieved full donor chimerism, but resumed immunosuppression to treat graft-versus-host disease. Only one patient experienced rejection following CyA withdrawal. He responded to immunosuppression, which was later successfully withdrawn. The rejection episode was associated with antidonor Th reactivity. Patients showed CTL unresponsiveness to cultured donor renal tubular epithelial cells. Initially recovering T cells were memory cells and were enriched for CD4+CD25+ cells. Three patients are in sustained complete remissions of MM, despite loss of chimerism in two. Combined kidney/BMT with nonmyeloablative conditioning can achieve renal allograft tolerance and excellent myeloma responses, even in the presence of donor marrow rejection and antidonor alloresponses in vitro.

Gas chromatographic determination of benzene, toluene, ethylbenzene and xylenes using flame ionization detector in water samples with direct aqueous injection up to 250 μl

A simple method of solventless extraction of volatile organic compounds (benzene, toluene, ethylbenzene and xylenes) from aqueous samples was developed. This method allows direct injection of large volume of water sample into a gas chromatograph using the sorption capacity of the sorbent Chromosorb P NAW applied directly in the injection port of gas chromatograph. The system prevent water penetration into a column, keep it adsorbed on its surface until the analytes are stripped into a column, and the residual water is purging using split flow. The limit of detection ranging from 0.6 for benzene to 1.1 microg l(-1) for o-xylene and limit of quantification ranging 2.0-3.6 microg l(-1) are lower that those reached by gas chromatography with flame ionization detection and direct aqueous injection before.

Biochemical deficiency of pyridoxine does not affect interleukin-2 production of lymphocytes from patients with Sjögren's syndrome

BACKGROUND

There is evidence that pyridoxine deficiency may alter the immune response. It is not known whether a deficiency of this vitamin is evident in subjects with primary Sjögren's syndrome (SS).

OBJECTIVE

We studied whether subjects with primary SS showed a biochemical deficiency of pyridoxine, and if it is associated with abnormal production of interleukin-2 from lymphocytes stimulated in vitro with phytohemagglutinin (PHA).

DESIGN

Two studies were conducted, (i) biochemical and nutritional assessments were performed in a cross-over study in subjects with primary SS, who were supplemented with 25 mg/day of pyridoxine or placebo for 3 months. After 1 month washout, they were supplemented for 3 months with placebo, (ii) patients with SS and matched controls received pyridoxine or placebo for 45 days, and a blood sample was obtained to study IL-2 production and expression in T-lymphocytes stimulated with PHA.

RESULTS

Subjects with primary SS showed limited dietary intake of pyridoxine and biochemical deficiency of this vitamin assessed through the activation coefficient of the erythrocyte aspartate aminotransferase. The biochemical deficiency did not affect production nor mRNA expression of IL-2 from T-lymphocytes stimulated in vitro with PHA compared with the control group. Supplementation of subjects with primary SS with 25 mg/day with pyridoxine for 45 days did not produce any significant change as compared to those patients supplemented with placebo.

CONCLUSIONS

Subjects with primary SS showed biochemical deficiency of pyridoxine, possibly due to limited intake of this vitamin which was corrected by supplementation with pyridoxine. However, IL-2 production and mRNA expression from stimulated lymphocytes were unaffected by supplementation, probably because the deficiency was not severe enough to affect the immune system.

SPONSORSHIP

This work was supported by the National Council of Science and Technology (CONACYT), Mexico, grant no. 212226-5-0902PM.