Rapid genome sequencing identifies a novel de novo SNAP25 variant for neonatal congenital myasthenic syndrome

Congenital myasthenic syndrome (CMS) is a group of 32 disorders involving genetic dysfunction at the neuromuscular junction resulting in skeletal muscle weakness that worsens with physical activity. Precise diagnosis and molecular subtype identification are critical for treatment as medication for one subtype may exacerbate disease in another (Engel et al., Lancet Neurol 14: 420 [2015]; Finsterer, Orphanet J Rare Dis 14: 57 [2019]; Prior and Ghosh, J Child Neurol 36: 610 [2021]). The SNAP25-related CMS subtype (congenital myasthenic syndrome 18, CMS18; MIM #616330) is a rare disorder characterized by muscle fatigability, delayed psychomotor development, and ataxia. Herein, we performed rapid whole-genome sequencing (rWGS) on a critically ill newborn leading to the discovery of an unreported pathogenic de novo SNAP25 c.529C > T; p.Gln177Ter variant. In this report, we present a novel case of CMS18 with complex neonatal consequence. This discovery offers unique insight into the extent of phenotypic severity in CMS18, expands the reported SNAP25 variant phenotype, and paves a foundation for personalized management for CMS18.

Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia

BACKGROUND

Genetic disorders contribute to significant morbidity and mortality in critically ill newborns. Despite advances in genome sequencing technologies, a majority of neonatal cases remain unsolved. Complex structural variants (SVs) often elude conventional genome sequencing variant calling pipelines and will explain a portion of these unsolved cases.

METHODS

As part of the Utah NeoSeq project, we used a research-based, rapid whole-genome sequencing (WGS) protocol to investigate the genomic etiology for a newborn with a left-sided congenital diaphragmatic hernia (CDH) and cardiac malformations, whose mother also had a history of CDH and atrial septal defect.

RESULTS

Using both a novel, alignment-free and traditional alignment-based variant callers, we identified a maternally inherited complex SV on chromosome 8, consisting of an inversion flanked by deletions. This complex inversion, further confirmed using orthogonal molecular techniques, disrupts the ZFPM2 gene, which is associated with both CDH and various congenital heart defects.

CONCLUSIONS

Our results demonstrate that complex structural events, which often are unidentifiable or not reported by clinically validated testing procedures, can be discovered and accurately characterized with conventional, short-read sequencing and underscore the utility of WGS as a first-line diagnostic tool.

Abstract P1-14-06: Selective internal radiation therapy (SIRT) with Yttrium-90 resin microspheres and FOLFOX/5FU chemotherapy in pre-treated breast cancer patients with liver metastases: A retrospective analysis of response rates, times to progression and survival of patients treated in Manchester UK between 2010 and 2016

Background:

SIRT is a globally licensed technique of Radio-Embolization (RE) of hepatic tumors via intra-arterial infusion of β-particle emitting Yttrium-90 (Y-90) radio-labelled microspheres. It increases response rates and hepatic time to progression in metastatic colorectal cancer when used in combination with 5FU/Oxaliplatin (FOLFOX) chemotherapy with acceptable toxicity profile. FOLFOX gives a radio-sensitizing effect and also controls disease outside the liver. Breast cancer liver metastases (BCLM) patients often have extra-hepatic disease and respond to multiple lines of systemic therapy and SIRT is infrequently used.

Methods and patients

Between 2010 and 2016 we treated 25 BCLM patients with Y-90 SIRT.

Receptor status: 20 ER+ve/HER-2 -ve, 3 ER-ve/HER-2 +ve, 2 triple -ve.

Eleven patients had liver only disease with 14 also having known extra-hepatic disease. Average number of previous lines of therapy in metastatic setting: chemotherapy = 2.4; endocrine = 1. Sixty-four % patients had prior Capecitabine (n=16); 12% platinum (n=3, all Carboplatin). Twenty patients received chemotherapy with SIRT: 17 had modified FOLFOX6 (Oxaliplatin/bolus 5FU day1, infusional 5FU day 1-3 (46 hrs); 3 patients had Modified de Gramont style 5FU alone. Five patients had no chemotherapy.

Sir-spheres were inserted on day 2 of FOLFOX with the 5FU infusion pump continuing to day 3. Further 2-weekly FOLFOX chemo cycles were at clinician's discretion: average number delivered 3.8. Four patients had the liver treated in two halves, approximately 6 weeks apart. One patient received SIRT only to half the liver. Patients were imaged with PET-CT/CT before and 2-3 months after SIRT. Retrospective case note review was performed and data correlated to evaluate tumor response (RR); hepatic and extra hepatic progression free survival (HPFS and EHPFS) and overall survival (OS). Accurate toxicity data was not recorded.

Results

Hepatic CT response rates: PR 56% (n=14), SD 28% (n=7) and PD 16% (n=4). Hepatic PET response rates: CR 32% (n=8), PR 40% (n=10), SD 12% (n=3), PD 16%(n=4). (Overall PET liver disease control rate = 84%).

Eight patients (32%) had extra-hepatic PD at first assessment. Of them, 4 had PR, 2 SD and 2 PD in the liver at that assessment. Two HER-2 +ve patients had brain metastases as first sign of PD within 75 days, an area not previously screened. Of 16 pre-treated with Capecitabine, liver CT response rates: 62.5% PR, 18.75% SD (n=10,3). Post SIRT/FOLFOX, average number of therapy lines: 2 for chemo and 0.75 for endocrine, with 8 patients still alive at time of censoring.

Median OS: 766 HPFS: 210 days (CI 140-286). Median EHPFS in patients with extra-hepatic disease: 152 days (CI 96-636).

Conclusions

SIRT with FOLFOX in previously treated BCLM patients produces high response rates, excellent tumor control and time to progression in the liver with good overall survival. It does not seem to decrease the ability to give further lines of chemotherapy and can be considered as an option for breast cancer patients with liver metastases.

Citation Format: Wilson G, Mullamitha S, Bentley D, Bell J, Mullan D, Carter L, Chittalia A, Howell S, Laasch H-U, Westwood T, Jeans S, Tipping J, Ryder D, Farquharson F, Arumugam P, Sheen A, Rajashanker B, Armstrong A, Misra V, Manoharan P, Lawrance J. Selective internal radiation therapy (SIRT) with Yttrium-90 resin microspheres and FOLFOX/5FU chemotherapy in pre-treated breast cancer patients with liver metastases: A retrospective analysis of response rates, times to progression and survival of patients treated in Manchester UK between 2010 and 2016 [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-14-06.

Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome

BACKGROUND

Glioblastoma (GBM) is the most common malignant brain cancer occurring in adults, and is associated with dismal outcome and few therapeutic options. GBM has been shown to predominantly disrupt three core pathways through somatic aberrations, rendering it ideal for precision medicine approaches.

METHODS

We describe a 35-year-old female patient with recurrent GBM following surgical removal of the primary tumour, adjuvant treatment with temozolomide and a 3-year disease-free period. Rapid whole-genome sequencing (WGS) of three separate tumour regions at recurrence was carried out and interpreted relative to WGS of two regions of the primary tumour.

RESULTS

We found extensive mutational and copy-number heterogeneity within the primary tumour. We identified a TP53 mutation and two focal amplifications involving PDGFRA, KIT and CDK4, on chromosomes 4 and 12. A clonal IDH1 R132H mutation in the primary, a known GBM driver event, was detectable at only very low frequency in the recurrent tumour. After sub-clonal diversification, evidence was found for a whole-genome doubling event and a translocation between the amplified regions of PDGFRA, KIT and CDK4, encoded within a double-minute chromosome also incorporating miR26a-2. The WGS analysis uncovered progressive evolution of the double-minute chromosome converging on the KIT/PDGFRA/PI3K/mTOR axis, superseding the IDH1 mutation in dominance in a mutually exclusive manner at recurrence, consequently the patient was treated with imatinib. Despite rapid sequencing and cancer genome-guided therapy against amplified oncogenes, the disease progressed, and the patient died shortly after.

CONCLUSION

This case sheds light on the dynamic evolution of a GBM tumour, defining the origins of the lethal sub-clone, the macro-evolutionary genomic events dominating the disease at recurrence and the loss of a clonal driver. Even in the era of rapid WGS analysis, cases such as this illustrate the significant hurdles for precision medicine success.

Opera and madness: Britten's Peter Grimes--a case study

In this paper, Britten's opera Peter Grimes (1945) is used as an illustrative case study through which to examine the depiction of psychiatric disorders in opera. It is argued that Peter Grimes is a powerful example of how opera, in the hands of a great composer, can become an invaluable tool for examining subjective human experience. After a brief discussion of opera as a vehicle to express emotions, various operas are drawn upon to provide a historical perspective and to demonstrate the long interconnection existing between opera and madness. An in-depth analysis of Peter Grimes, its background and central character, is then provided, in order to demonstrate how opera can elicit empathy for individuals affected by mental health problems.

Managing livestock enterprises in Australia's extensive rangelands for greenhouse gas and environment outcomes: a pastoral company perspective

Extensive grazing of beef cattle is the principal use of the northern Australia land area. While north Australian beef production has traditionally utilised a low-input, low-output system of land management, recent innovations have increased the efficiency with which beef is produced. Investment to raise efficiency of cattle production by improving herd genetics, property infrastructure, the seasonal feed-base and its utilisation, as well as promoting feedlot finishing can all be expected to reduce the number of unproductive animals and reduce age-at-slaughter. Consequently, these innovations can all be expected to contribute to a reduction in the emissions intensity of greenhouse gases (GHG; t GHG/t liveweight gain). The North Australian Pastoral Company (NAPCO) has adopted these technologies to enhance reproductive and growth efficiency of the herd and has coupled them with changes in other aspects of property operation, such as use of solar energy systems, establishment of introduced perennial pastures and minimum tillage, to achieve production and operational gains, which also reduce the emissions intensity of their pastoral properties. Investments to improve production efficiency have been consistent with both financial and, in principle, environmental objectives of NAPCO. While NAPCO supports the development and implementation of new mitigation strategies, the company requires greater knowledge on pastoral emission levels and clarity on the future position of agriculture in a carbon economy. This information would enable confirmation of current emission levels, modelling of mitigation options and evaluation of the efficacy of potential on-farm carbon sinks. This paper presents NAPCO’s perspective on GHG emissions in the context of its pastoral enterprise, including current and future research and mitigation objectives.

Four weeks one-leg training and high fat diet does not alter PPARalpha protein or mRNA expression in human skeletal muscle

Fatty acid metabolism is influenced by training and diet with exercise training mediating this through activation of nuclear hormone receptor peroxisome proliferator-activated receptor alpha (PPARalpha) in skeletal muscle. This study investigated the effect of training and high fat or normal diet on PPARalpha expression in human skeletal muscle. Thirteen men trained one leg (T) four weeks (31.5 h in total), while the other leg (UT) served as control. During the 4 weeks six subjects consumed high fat (FAT) diet and seven subjects maintained a normal (CHO) diet. Biopsies were obtained from vastus lateralis muscle in both legs before and after training. After the biopsy, one-leg extension exercise was performed in random order with both legs 30 min at 95% of workload max. A training effect was evident as citrate synthase activity increased (P < 0.05) by 15% in the trained, but not the control leg in both groups. During exercise respiratory exchange ratio was lower in FAT (0.86 +/- 0.01, 0.83 +/- 0.01, mean +/- SEM) than CHO (0.96 +/- 0.02, 0.94 +/- 0.03) and in UT than T legs, respectively. The PPARalpha protein (144 +/- 44, 104 +/- 28, 79 +/- 15, 79 +/- 14, % of pre level) and PPARalpha mRNA (69 +/- [2, 2], 78 +/- [7, 6], 92 +/- [22, 18], 106 +/- [21, 18], % of pre level, geometric mean +/- SEM) expression remained unchanged by diet and training in FAT (UT, T) and CHO (UT, T), respectively. After the training and diet CS, HAD, PPARalpha, UCP2, UCP3 and mFABP mRNA content remained unchanged, whereas GLUT4 mRNA was lower in both groups and LDHA mRNA was lower (P < 0.05) only in FAT.

IN CONCLUSION

4 weeks one leg knee extensor training did not affect PPARalpha protein or mRNA expression. Furthermore, higher fat oxidation during exercise after fat rich diet was not accompanied by an increased PPARalpha protein or mRNA expression after 4 weeks.

Implantation of pure cultured olfactory ensheathing cells in an animal model of parkinsonism

BACKGROUND

Implantation of neural cells has been proposed as a therapeutic strategy for repairing the injured or diseased brain. In the present study we have examined the potential of olfactory ensheathing cells (OEC) to promote brain repair after surgical implantation in a rodent model of parkinsonism.

METHODS

Neonatal OECs were implanted in the striatum after a 6-hydroxydopamine lesion of the ipsilateral substantia nigra. Amphetamine-induced rotational asymmetry scores were determined 48 hours before and 4, 6 and 8 weeks after OEC implantation. The density of immunostaining for tyrosine hydroxylase and synaptophysin in the striatum and the number of tyrosine hydroxylase-positive cells remaining in the substantia nigra were also determined.

RESULTS

Rotational asymmetry scores were similar in OEC-implanted and vehicle-treated groups at all time points examined, and at each time were similar to those observed prior to implantation. Levels of striatal tyrosine-hydroxylase and synaptophysin immunoreactivity were similar in OEC- and vehicle-treated groups. The number of tyrosine-hydroxylase-positive cells in the substantia nigra was similar in both groups indicating that severity of the lesion was similar. Visualisation of GFP-labelled OECs one week after implantation in a separate group of animals revealed the cells to be located in the area immediately surrounding the needle tract.

CONCLUSION

This study demonstrates that implantation of OECs alone is not sufficient to promote tissue repair and functional recovery in a rodent model of parkinsonism. The results add to a growing number of studies that propose a caveat for the use of pure OECs as a neurosurgical strategy for the treatment of brain disease or injury.

The effects of a nucleotide supplement on the immune and metabolic response to short term, high intensity exercise performance in trained male subjects

AIM

The aim of this work was to determine the ergogenic effects of a nucleotide supplement on the metabolic and immune responses to short term high intensity exercise in volunteer, trained, male subjects.

METHODS

Thirty moderately trained male subjects were randomly divided into 3 equal sized groups, control (C), placebo (P) or experimental (E). Each subject undertook a 2 min maximal exercise test prior to, and after 60 days, on either a nucleotide (E) or placebo supplement. Prior to exercise testing unstimulated saliva samples and blood samples were taken. Saliva was analysed for cortisol and IgA, while blood was analysed for lactate, lactate dehydrogenase and creatine kinase.

RESULTS

The postexercise C value was significantly higher than the pre-exercise concentration (P<0.0001; for C, P, and E). In the postsupplement C analysis, the E postexercise group was significantly lower than either the C (P<0.005) or the P group (P<0.05). In the pre- and postsupplementation periods, the pre-exercise SIgA values were significantly higher than the postexercise values (P<0.0001). However, in the postsupplementation period, the SIgA value in the E group was significantly higher than either the P (P<0.05) or C (P<0.05) groups. There were no significant changes in blood lactate, lactate dehydrogenase, or creatine kinase concentrations post supplementation.

CONCLUSIONS

We concluded that a chronically ingested nucleotide supplement blunts the response of the hormones associated with physiological stress.

Specificity of VO2MAX and the ventilatory threshold in free swimming and cycle ergometry: comparison between triathletes and swimmers

OBJECTIVES

To compare maximal heart rate (HRmax), maximal oxygen consumption (VO2MAX), and the ventilatory threshold (VT; %VO2MAX) during cycle ergometry and free swimming between swimmers and triathletes.

METHODS

Nine swimmers and ten triathletes completed an incremental swimming and cycling test to exhaustion. Whole body metabolic responses were determined in each test.

RESULTS

The swimmers exhibited a significantly higher VO2MAX in swimming than in cycling (58.4 (5.6) v 51.3 (5.1) ml/kg/min), whereas the opposite was found in the triathletes (53.0 (6.7) v 68.2 (6.8) ml/kg/min). HRmax was significantly different in the maximal cycling and swimming tests for the triathletes (188.6 (7.5) v 174.8 (9.0) beats/min). In the maximal swimming test, HRmax was significantly higher in the swimmers than in the triathletes (174.8 (9.0) v 184.6 (9.7) beats/min). No significant differences were found for VT measured in swimming and cycling in the triathletes and swimmers.

CONCLUSION

This study confirms that the exercise testing mode affects the VO2MAX value, and that swimmers have very specific training adaptations even compared with triathletes. This may be a function of acute physiological responses combined with the specialist training status of the different athletes influencing maximal cardiac output or oxygen extraction. In contrast, the different training regimens do not seem to influence the VT, as this variable did not differ between the two testing modes in either group.

Common VKORC1 and GGCX polymorphisms associated with warfarin dose

We report a novel combination of factors that explains almost 60% of variable response to warfarin. Warfarin is a widely used anticoagulant, which acts through interference with vitamin K epoxide reductase that is encoded by VKORC1. In the next step of the vitamin K cycle, gamma-glutamyl carboxylase encoded by GGCX uses reduced vitamin K to activate clotting factors. We genotyped 201 warfarin-treated patients for common polymorphisms in VKORC1 and GGCX. All the five VKORC1 single-nucleotide polymorphisms covary significantly with warfarin dose, and explain 29-30% of variance in dose. Thus, VKORC1 has a larger impact than cytochrome P450 2C9, which explains 12% of variance in dose. In addition, one GGCX SNP showed a small but significant effect on warfarin dose. Incorrect dosage, especially during the initial phase of treatment, carries a high risk of either severe bleeding or failure to prevent thromboembolism. Genotype-based dose predictions may in future enable personalised drug treatment from the start of warfarin therapy.

The DNA sequence and comparative analysis of human chromosome 10

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

The components of the "critical quartet" log Kow values assessed by four commercial software packages

Partition coefficient (log Kow) values of 103 compounds in four different solvent-water systems (alkane-water, octanol-water, chloroform-water and propylene glycol dipelargonate (PGDP)-water--the "critical quartet") were published by Leahy et al. (1992). J. Chem. Soc. Perkin Trans. 2, pp. 723-731. They used the Abraham LSER (linear solvation energy relationship) descriptors to model the log Kow values in the four systems. The calculation of Abraham LSER descriptors has now been computerized in the ABSOLV program, and we have used ABSOLV, and three other commercial software packages (HYBOT-PLUS, Molecular Modeling Pro and QsarIS) that calculate descriptors of similar classes, to model partitioning in the four solvent-water systems. Stepwise regression selected broadly similar types of descriptor from each software package to model logKow values in each solvent-water system. Overall, HYBOT-PLUS gave the best results. The rĵle of the various classes of descriptor (size, polarity, polarizability, hydrogen bonding) in modeling partitioning in the four different solvent-water systems is discussed.

Regulation of the stem cell leukemia (SCL) gene: a tale of two fishes

The stem cell leukemia (SCL) gene encodes a tissue-specific basic helix-loop-helix (bHLH) protein with a pivotal role in hemopoiesis and vasculogenesis. Several enhancers have been identified within the murine SCL locus that direct reporter gene expression to subdomains of the normal SCL expression pattern, and long-range sequence comparisons of the human and murine SCL loci have identified additional candidate enhancers. To facilitate the characterization of regulatory elements, we have sequenced and analyzed 33 kb of the SCL genomic locus from the pufferfish Fugu rubripes, a species with a highly compact genome. Although the pattern of SCL expression is highly conserved from mammals to teleost fish, the genes flanking pufferfish SCL were unrelated to those known to flank both avian and mammalian SCL genes. These data suggest that SCL regulatory elements are confined to the region between the upstream and downstream flanking genes, a region of 65 kb in human and 8.5 kb in pufferfish. Consistent with this hypothesis, the entire 33-kb pufferfish SCL locus directed appropriate expression to hemopoietic and neural tissue in transgenic zebrafish embryos, as did a 10.4-kb fragment containing the SCL gene and extending to the 5' and 3' flanking genes. These results demonstrate the power of combining the compact genome of the pufferfish with the advantages that zebrafish provide for studies of gene regulation during development. Furthermore, the pufferfish SCL locus provides a powerful tool for the manipulation of hemopoiesis and vasculogenesis in vivo.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence

The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]

Dynamic association of capping enzymes with transcribing RNA polymerase II

The C-terminal heptad repeat domain (CTD) of RNA polymerase II (pol II) is proposed to target pre-mRNA processing enzymes to nascent pol II transcripts, but this idea has not been directly tested in vivo. In vitro, the yeast mRNA capping enzymes Ceg1 and Abd1 bind specifically to the phosphorylated CTD. Here we show that yeast capping enzymes cross-link in vivo to the 5' ends of transcribed genes and that this localization requires the CTD. Both the extent of CTD phosphorylation at Ser 5 of the heptad repeat and the binding of capping enzymes decreased as polymerase moved from the 5' to the 3' ends of the ACT1, ENO2, TEF1, GAL1, and GAL10 genes. Ceg1 is released early in elongation, but Abd1 can travel with transcribing pol II as far as the 3' end of a gene. The CTD kinase, Kin28, is required for binding, and the CTD phosphatase, Fcp1, is required for dissociation of capping enzymes from the elongation complex. CTD phosphorylation and dephosphorylation therefore control the association of capping enzymes with pol II as it transcribes a gene.

Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q

The organization of centromeric heterochromatin has been established in a number of eucaryotes but remains poorly defined in human. Here we present 1025 kb of contiguous human genomic sequence which links pericentromeric satellites to the RET proto-oncogene in 10q11.2 and is presumed to span the transition from centric heterochromatin to euchromatin on this chromosome arm. Two distinct domains can be defined within the sequence. The proximal approximately 240 kb consists of arrays of satellites and other tandem repeats separated by tracts of complex sequence which have evolved by pericentromeric-directed duplication. Analysis of 32 human paralogues of these sequences indicates that most terminate at or within repeat arrays, implicating these repeats in the interchromosomal duplication process. Corroborative PCR-based analyses establish a genome-wide correlation between the distribution of these paralogues and the distribution of satellite families present in 10q11. In contrast, the distal approximately 780 kb contains few tandem repeats and is largely chromosome specific. However, a minimum of three independent intrachromosomal duplication events have resulted in >370 kb of this sequence sharing >90% identity with sequences on 10p. Using computer-based analyses and RT-PCR we confirm the presence of three genes within the sequence, ZNF11/33B, KIAA0187 and RET, in addition to five transcripts of unknown structure. All of these transcribed sequences map distal to the satellite arrays. The boundary between satellite-rich interchromosomally duplicated DNA and chromosome-specific DNA therefore appears to define a transition from pericentromeric heterochromatin to euchromatin on the long arm of this chromosome.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Hybrid (BDBB) interferon-alpha: preformulation studies

A number of techniques, including RP-HPLC, HP-SEC and SDS-PAGE have been used in the delineation of degradative mechanisms of recombinant hybrid (BDBB) interferon-alpha (IFN-alpha) in the solution phase. Different degradation profiles are found according to medium pH. At pH 4.0 the major routes of degradation are via chemical transformation of the monomeric protein to a species which retains antiviral activity, and by self-proteolytic hydrolysis. At pH 7.6, methionine-oxidation is the major chemical degradative process. Protein aggregation is also a significant route of degradation at the higher pH. The results have assisted in a targeted preformulation screen of potentially stabilising excipients and possible parenteral solution dosage forms have been identified. Preliminary 'real-time' storage data confirm excellent chemical and physical stability of IFN-alpha in vehicles formulated at pH 7.6 or, especially, pH 4.0 under the proposed shelf conditions.

Induction of filopodia by direct local elevation of intracellular calcium ion concentration

In neuronal growth cones, cycles of filopodial protrusion and retraction are important in growth cone translocation and steering. Alteration in intracellular calcium ion concentration has been shown by several indirect methods to be critically involved in the regulation of filopodial activity. Here, we investigate whether direct elevation of [Ca2+]i, which is restricted in time and space and is isolated from earlier steps in intracellular signaling pathways, can initiate filopodial protrusion. We raised [Ca2+]i level transiently in small areas of nascent axons near growth cones in situ by localized photolysis of caged Ca2+ compounds. After photolysis, [Ca2+]i increased from approximately 60 nM to approximately 1 microM within the illuminated zone, and then returned to resting level in approximately 10-15 s. New filopodia arose in this area within 1-5 min, and persisted for approximately 15 min. Elevation of calcium concentration within a single filopodium induced new branch filopodia. In neurons coinjected with rhodamine-phalloidin, F-actin was observed in dynamic cortical patches along nascent axons; after photolysis, new filopodia often emerged from these patches. These results indicate that local transient [Ca2+]i elevation is sufficient to induce new filopodia from nascent axons or from existing filopodia.

Coupling RNA polymerase II transcription with pre-mRNA processing

How are transcription and processing of mRNA precursors co-ordinated? The past two years has witnessed exciting insights into the mechanism which targets the mRNA processing machinery to RNA polymerase II (pol II) transcription complexes and closely integrates processing with transcription. Protein-protein contacts have been discovered between the pol II transcription machinery and RNA processing factors; furthermore, a unique domain of pol II has been identified that not only recruits processing factors but also controls their activity.

The discovery of orally available thrombin inhibitors: optimisation of the P1 pharmacophore

Thrombin inhibitors have been designed with the replacement of the strongly basic guanidine P1 pharmocophore with a group that exploits the lipophilicity of the S1 pocket. The approach has lead to the discovery of potent thrombin inhibitors demonstrating good intra-duodenal absorption.

Studies towards the identification of potent, selective and bioavailable thrombin inhibitors

The application of selection criteria, based on potency and physicochemical parameters, to a candidate library of thrombin inhibitors is described. The utility of the approach is exemplified by the discovery of a potent, selective and bioavailable thrombin inhibitor 62.

CE marking--what does it really mean?

Compliance with the Medical Devices Directive (93/42/EEC) became compulsory for all medical devices placed on the European market in June 1998. Under the directive, manufacturers are required to fulfil a number of requirements leading to the placing of the CE mark on their devices. However, many questions still remain. Not all manufacturers are aware of their responsibilities and not all purchasers are aware of the true meaning of the CE mark. It is vital to understand the purpose of the regulations, the definition of 'medical device', the importance of complying with the manufacturer's intended purpose and instructions, the role of quality systems and clinical investigations in the compliance process, and the decisions which may be made by the manufacturers. It is also important to realise that whilst the directive, if correctly applied and enforced, brings benefits to the medical industry and patients, it is not a substitute for professional judgement in the purchasing process.

A new candidate region for the positional cloning of the XLP gene

X-linked lymphoproliferative disease (XLP) is an inherited immunodeficiency characterised by selective susceptibility to Epstein-Barr virus and frequent association with malignant lymphomas chiefly located in the ileocecal region, liver, kidney and CNS. Taking advantage of a large bacterial clone contig, we obtained a genomic sequence of 197620 bp encompassing a deletion (XLP-D) of 116 kb in an XLP family, whose breakpoints were identified. The study of potential exons from this region in 40 unrelated XLP patients did not reveal any mutation. To define the critical region for XLP and investigate the role of the XLP-D deletion, detailed haplotypes in a region of approximately 20 cM were reconstructed in a total of 87 individuals from 7 families with recurrence of XLP. Two recombination events in a North American family and a new microdeletion (XLP-G) in an Italian family indicate that the XLP gene maps in the interval between DXS1001 and DXS8057, approximately 800 kb centromeric to the previously reported familial microdeletion XLP-D.

Activated transcription independent of the RNA polymerase II holoenzyme in budding yeast

We investigated whether the multisubunit holoenzyme complex of RNA polymerase II (Pol II) and mediator is universally required for transcription in budding yeast. DeltaCTD Pol II lacking the carboxy-terminal domain of the large subunit cannot assemble with mediator but can still transcribe the CUP1 gene. CUP1 transcripts made by DeltaCTD Pol II initiated correctly and some extended past the normal poly(A) site yielding a novel dicistronic mRNA. Most CUP1 transcripts made by DeltaCTD Pol II were degraded but could be stabilized by deletion of the XRN1 gene. Unlike other genes, transcription of CUP1 and HSP82 also persisted after inactivation of the CTD kinase Kin28 or the mediator subunit Srb4. The upstream-activating sequence (UAS) of the CUP1 promoter was sufficient to drive Cu2+ inducible transcription without Srb4 and heat shock inducible transcription without the CTD. We conclude that the Pol II holoenzyme is not essential for all UAS-dependent activated transcription in yeast.

Transcriptional control: Tat cofactors and transcriptional elongation

HIV-1 gene expression requires the transactivator Tat, which stimulates viral transcript elongation. Recent results show that two cellular cyclin-dependent kinases, which phosphorylate the carboxy-terminal domain of the RNA polymerase II large subunit, contact Tat and contribute to the control of transcriptional elongation.

The guanylyltransferase domain of mammalian mRNA capping enzyme binds to the phosphorylated carboxyl-terminal domain of RNA polymerase II

We have conducted a biochemical and genetic analysis of mouse mRNA capping enzyme (Mce1), a bifunctional 597-amino acid protein with RNA triphosphatase and RNA guanylyltransferase activities. The principal conclusions are as follows: (i) the mammalian capping enzyme consists of autonomous and nonoverlapping functional domains; (ii) the guanylyltransferase domain Mce1(211-597) is catalytically active in vitro and functional in vivo in yeast in lieu of the endogenous guanylyltransferase Ceg1; (iii) the guanylyltransferase domain per se binds to the phosphorylated RNA polymerase II carboxyl-terminal domain (CTD), whereas the triphosphatase domain, Mce1(1-210), does not bind to the CTD; and (iv) a mutation of the active site cysteine of the mouse triphosphatase elicits a strong growth-suppressive phenotype in yeast, conceivably by sequestering pre-mRNA ends in a nonproductive complex or by blocking access of the endogenous yeast triphosphatase to RNA polymerase II. These findings contribute to an emerging model of mRNA biogenesis wherein RNA processing enzymes are targeted to nascent polymerase II transcripts through contacts with the CTD. The phosphorylation-dependent interaction between guanylyltransferase and the CTD is conserved from yeast to mammals.

The pufferfish SLP-1 gene, a new member of the SCL/TAL-1 family of transcription factors

The SCL/TAL-1 gene encodes a basic helix-loop-helix (bHLH) transcription factor essential for the development of all hemopoietic lineages and also acts as a T-cell oncogene. Four related genes have been described in mammals (LYL-1, TAL-2, NSCL1, and NSCL2), all of which exhibit a high degree of sequence similarity to SCL/TAL-1 in the bHLH domain and two of which (LYL-1 and TAL-2) have also been implicated in the pathogenesis of T-cell acute lymphoblastic leukemia. In this study we describe the identification and characterization of a pufferfish gene termed SLP-1, which represents a new member of this gene family. The genomic structure and sequence of SLP-1 suggests that it forms a subfamily with SCL/TAL-1 and LYL-1 and is most closely related to SCL/TAL-1. However, unlike SCL/TAL-1, SLP-1 is widely expressed. Sequence analysis of a whole cosmid containing SLP-1 shows that SLP-1 is flanked upstream by a zinc finger gene and a fork-head-domain gene and downstream by a heme-oxygenase and a RING finger gene.

Arginine kinase expression and localization in growth cone migration

Migrating neuronal growth cones exert traction forces that are generated by ATP-driven F-actin/myosin interactions. Sustained generation of these forces may require an energy supply mediated by the guanidino kinases, creatine kinase and arginine kinase. We cloned and sequenced grasshopper arginine kinase and examined its expression during embryogenesis and its subcellular localization in vivo and in vitro. During the first half of embryogenesis, arginine kinase is expressed selectively in a small percentage of ectodermal cells (dorsal closure cells), in a small percentage of mesodermal cells (muscle pioneers), and throughout the developing CNS. Most of these cell types are motile, including nascent neurons, muscle pioneers, dorsal closure cells, and many CNS glia. Neuroblasts also strongly express arginine kinase; they are nonmotile but are undergoing repeated rounds of (ATP-dependent) mitosis. Arginine kinase is colocalized with F-actin in a narrow band along the leading edges of lamellipodia of migrating glia. In neurons undergoing axonogenesis, arginine kinase is concentrated in growth cones and extends to the tips of filopodia. The amount of arginine kinase varies widely between growth cones, even between different growth cones of the same neuron. Energy for growth cone migration appears to be mobilized by (1) selective expression of arginine kinase by neurons, (2) localization of arginine kinase within growth cones, and (3) concentration of arginine kinase within specific growth cones, depending on the traction forces being generated. Mobilization of guanidino kinases may participate in the selective growth of specific growth cones.

A gene map of the human genome

The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.

DNA ligase I is required for fetal liver erythropoiesis but is not essential for mammalian cell viability

Four distinct DNA ligase activities (I-IV) have been identified within mammalian cells. Evidence has indicated that DNA ligase I is central to DNA replication, as well as being involved in DNA repair processes. A patient with altered DNA ligase I displayed a phenotype similar to Bloom's syndrome, being immunodeficient, growth retarded and predisposed to cancer. Fibroblasts isolated from this patient (46BR) exhibited abnormal lagging strand synthesis and repair deficiency. It has been reported that DNA ligase I is essential for cell viability, but here we show that cells lacking DNA ligase I are in fact viable. Using gene targeting in embryonic stem (ES) cells, we have produced DNA ligase I-deficient mice. Embryos develop normally to mid-term when haematopoiesis usually switches to the fetal liver. Thereupon acute anaemia develops, despite the presence of erythroid-committed progenitor cells in the liver. Thus DNA ligase I is required for normal development, but is not essential for replication. Hence a previously unsuspected redundancy must exist between mammalian DNA ligases.

Blackjack, a novel protein associated with microtubules in embryonic neurons

Microtubule-associated proteins can influence the organization, stability and dynamics of microtubules. We characterize a novel protein that associates with microtubules as assessed by immunofluorescence, immunoelectron microscopy, and co-sedimentation. The protein is expressed heavily in embryonic neurons and, to a lesser extent, in epithelial and mesodermal cells. The cDNA sequence predicts a protein of 1,547 amino acids and approximately 170 kDa. Immunoblot of embryo lysate demonstrates bands of approximately 240 and 260 kDa. The predicted amino acid sequence contains 77 potential serine/threonine phosphorylation sites. A distinctive feature is a predicted alpha-helical central domain comprising 21 identical repeats of an 11 amino acid sequence (PLEELRKDAAE). The protein is thermostable and has two major charge-domains: the amino-terminal 80% has an estimated pI of 4.0 and the carboxy-terminal 20%, a pI of 12.2. The protein shares several general biochemical and molecular features of MAPs, but its sequence is not similar to that of any described MAP.

Three functional classes of transcriptional activation domain

We have studied the abilities of different transactivation domains to stimulate the initiation and elongation (postinitiation) steps of RNA polymerase II transcription in vivo. Nuclear run-on and RNase protection analyses revealed three classes of activation domains: Sp1 and CTF stimulated initiation (type I); human immunodeficiency virus type 1 Tat fused to a DNA binding domain stimulated predominantly elongation (type IIA); and VP16, p53, and E2F1 stimulated both initiation and elongation (type IIB). A quadruple point mutation of VP16 converted it from a type IIB to a type I activator. Type I and type IIA activators synergized with one another but not with type IIB activators. This observation implies that synergy can result from the concerted action of factors stimulating two different steps in transcription: initiation and elongation. The functional differences between activators may be explained by the different contacts they make with general transcription factors. In support of this idea, we found a correlation between the abilities of activators, including Tat, to stimulate elongation and their abilities to bind TFIIH.

Antimicrobial use in long-term-care facilities

There is intense antimicrobial use in long-term-care facilities (LTCF), and studies repeatedly document that much of this use is inappropriate. The current crisis in antimicrobial resistance, which encompasses the LTCF, heightens concerns of antimicrobial use. Attempts to improve antimicrobial use in the LTCF are complicated by characteristics of the patient population, limited availability of diagnostic tests, and virtual absence of relevant clinical trials. This article recommends approaches to management of common LTCF infections and proposes minimal standards for an antimicrobial review program. In developing these recommendations, the article acknowledges the unique aspects of provision of care in the LTCF.