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Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890–9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70–80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health. [ABSTRACT FROM AUTHOR]

The lethal malaria parasite Plasmodium falciparum needs to constantly respond and adapt to changes within the human host in order to survive and transmit. One such change is composed of nutritional limitation, which is augmented with increased parasite loads and intimately linked to severe disease development. Extracellular vesicles released from infected red blood cells have been proposed as important mediators of disease pathogenesis and intercellular communication but whether important for the parasite response to nutritional availability is unknown. Therefore, we investigated the abundance and small RNA cargo of extracellular vesicles released upon short-term nutritional starvation of P. falciparum in vitro cultures. We show that primarily ring-stage parasite cultures respond to glucose and amino acid deprivation with an increased release of extracellular vesicles. Small RNA sequencing of these extracellular vesicles further revealed human miRNAs and parasitic tRNA fragments as the main constituent biotypes. Short-term starvations led to alterations in the transcriptomic profile, most notably in terms of the over-represented biotypes. These data suggest a potential role for extracellular vesicles released from P. falciparum infected red blood cells in the response to nutritional perturbations, their potential as prognostic biomarkers and point towards an evolutionary conserved role among protozoan parasites. [ABSTRACT FROM AUTHOR]

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common upper respiratory tract complication where the pathogenesis is largely unknown. Herein, we investigated the transcriptome profile in nasal mucosa biopsies of CRSwNP patients and healthy individuals. We further integrated the transcriptomics data with genes located in chromosomal regions containing genome-wide significant gene variants for COVID-19. Among the most significantly upregulated genes in polyp mucosa were CCL18, CLEC4G, CCL13 and SLC9A3. Pathways involving "Ciliated epithelial cells" were the most differentially expressed molecular pathways when polyp mucosa and non-polyp mucosa from the same patient was compared. Natural killer T-cell (NKT) and viral pathways were the most statistically significant pathways in the mucosa of CRSwNP patients compared with those of healthy control individuals. Upregulated genes in polyp mucosa, located within the genome-wide associated regions of COVID-19, included LZTFL1, CCR9, SLC6A20, IFNAR1, IFNAR2 and IL10RB. Interestingly, the second most over-expressed gene in our study, CLEC4G, has been shown to bind directly to SARS-CoV-2 spike's N-terminal domain and mediate its entry and infection. Our results on altered expression of genes related to cilia and viruses point to the de-regulation of viral defenses in CRSwNP patients, and may give clues to future intervention strategies. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Erratum: A Constrained Metropolis–Hastings Robbins–Monro Algorithm for Q Matrix Estimation in DINA Models" published in the journal Psychometrika. The correction addresses an error in the acknowledgement section of the original article. The correct acknowledgement section is provided, acknowledging the Gustafsson and Skrondal Visiting Scholarship and the funding from the Research Council of Norway. The correction notice also includes a statement from the publisher, Springer Nature, emphasizing their neutrality and impartiality. The authors of the article are Chen-Wei Liu, Björn Andersson, and Anders Skrondal. [Extracted from the article]

Validation of models for plant disease management is a crucial part in the development of decision support systems in plant protection. Bespoke field trials are usually conducted to determine the performance of a model under practical conditions. However, field trials are very resource-demanding, and the use of already existing field trial data could significantly reduce costs for model validation. In this study, we took this novel approach to verify the performance of models for determining the need of fungicide applications against leaf blotch diseases in wheat by utilising historical weather data and yield data available from fungicide efficacy field trials. Two models based on humidity factors were used in the study. To estimate how specific humidity settings in the two models affect the number of recommended fungicide treatments per season, historical weather data from a 5-year period from weather stations in Denmark, Sweden, Norway, Finland, and Lithuania was used. The model output shows major differences between seasons and regions, typically recommending between one and three treatments per season. To determine the prediction potential of the models, data on yield gains from either one or two fungicide applications in fungicide efficacy trials conducted in wheat over a 5-year period in the five countries was utilised. The yield responses from fungicide treatments in the efficacy trials varied considerably between years and countries, as did the proportion of predictions of profitable treatments. In general, there was a tendency for the models to overestimate the need to apply fungicides (low specificity), but they rarely failed to recommend an application that was needed (high sensitivity). Despite the importance of having specific trials across regions in order to adjust models to local cropping and weather conditions, our study shows that historical weather data and existing field trial data have the potential to be used in model validation. [ABSTRACT FROM AUTHOR]

Fungal plant diseases driven by weather factors are common in European wheat and barley crops. Among these, septoria tritici blotch (Zymoseptoria tritici), tan spot (Pyrenophora tritici-repentis), and stagonospora nodorum blotch (Parastagonospora nodorum) are common in the Nordic-Baltic region at variable incidence and severity both in spring and winter wheat fields. In spring barley, net blotch (Pyrenophora teres), scald (Rhynchosporium graminicola, syn. Rhynchosporium commune) and ramularia leaf spot (Ramularia collo-cygni) are common yield limiting foliar diseases. We analysed data from 449 field trials from 2007 to 2017 in wheat and barley crops in the Nordic-Baltic region and explored the differences in severity of leaf blotch diseases between countries and years, and the impact of the diseases on yield. In the experiments, septoria tritici blotch dominated in winter wheat in Denmark and southern Sweden; while in Lithuania, both septoria tritici blotch and tan spot were common. In spring wheat, stagonospora nodorum blotch dominated in Norway and tan spot in Finland. Net blotch and ramularia leaf blotch were the most severe barley diseases over large areas, while scald occurred more locally and had less yield impact in all countries. Leaf blotch diseases, with severity >50% at DC 73–77, caused an average yield loss of 1072 kg/ha in winter wheat and 1114 kg/ha in spring barley across all countries over 5 years. These data verify a large regional and yearly variation in disease severity, distribution and impact on yield, emphasizing the need to adapt fungicide applications to the actual need based on locally adapted risk assessment systems. [ABSTRACT FROM AUTHOR]

We applied latent class analysis and the rule space model to verify the cumulative characteristic of conceptual change by developing a learning progression for buoyancy. For this study, we first abstracted seven attributes of buoyancy and then developed a hypothesized learning progression for buoyancy. A 14-item buoyancy instrument was administered to 1089 8th grade students to verify and refine the learning progression. The results suggest four levels of progression during conceptual change when 8th grade students understand buoyancy. Students at level 0 can only master Density. When students progress to level 1, they can grasp Direction, Identification, Submerged volume, and Relative density on the basis of the prior level. Then, students gradually master Archimedes' theory as they reach level 2. The most advanced students can further grasp Relation with motion and arrive at level 3. In addition, this four-level learning progression can be accounted for by the Qualitative–Quantitative–Integrative explanatory model. [ABSTRACT FROM AUTHOR]

Risk models for decisions on fungicide use based on weather data, disease monitoring, and control thresholds are used as important elements in a sustainable cropping system. The need for control of leaf blotch diseases in wheat (caused by Zymoseptoria tritici, Parastagonospora nodorum and Pyrenophora tritici-repentis) vary significantly across years and locations. Disease development is mainly driven by humidity events during stem elongation and heading. Two risk models were tested in field trials in order to identify situations favourable for the development of leaf blotch diseases in Lithuania, Norway, Sweden, Finland and Denmark. The Crop Protection Online (CPO) model uses days with precipitation (>1 mm), while the humidity model (HM) uses 20 continuous hours with relative humidity (RH) ≥ 85% as criteria for the need of a fungicide application. Forty-seven field trials were carried out during two seasons to validate these two risk-models against reference fungicide treatments. The season 2018 was dry and 2019 had an average precipitation profile. The two risk models with few exceptions provided acceptable disease control. In 2018, very few treatments were recommended by the models, saving 85–98% of treatments compared to the reference treatments, while in the wetter season 2019, 31% fewer applications were recommended. Based on specific criteria including fungicide input and net yield responses the models gave correct recommendations in 95% of the trials in 2018 and in 54–58% of the trials in 2019 compared with reference treatments dominated by 2–3 sprays. In comparison with single spray references, the models gave correct recommendations in 54–69% of the situations. [ABSTRACT FROM AUTHOR]

In diagnostic classification models (DCMs), the Q matrix encodes in which attributes are required for each item. The Q matrix is usually predetermined by the researcher but may in practice be misspecified which yields incorrect statistical inference. Instead of using a predetermined Q matrix, it is possible to estimate it simultaneously with the item and structural parameters of the DCM. Unfortunately, current methods are computationally intensive when there are many attributes and items. In addition, the identification constraints necessary for DCMs are not always enforced in the estimation algorithms which can lead to non-identified models being considered. We address these problems by simultaneously estimating the item, structural and Q matrix parameters of the Deterministic Input Noisy "And" gate model using a constrained Metropolis–Hastings Robbins–Monro algorithm. Simulations show that the new method is computationally efficient and can outperform previously proposed Bayesian Markov chain Monte-Carlo algorithms in terms of Q matrix recovery, and item and structural parameter estimation. We also illustrate our approach using Tatsuoka's fraction–subtraction data and Certificate of Proficiency in English data. [ABSTRACT FROM AUTHOR]

Acute appendicitis is the most common surgical emergency in children. Nonoperative treatment of nonperforated acute appendicitis in children is an alternative to appendectomy. The purpose of this systematic review and meta-analysis was to determine the outcomes of nonoperative treatment of nonperforated acute appendicitis in children in the literature. Databases were searched to identify abstracts, using predefined search terms. The abstracts were reviewed by two independent reviewers and articles were selected according to inclusion and exclusion criteria. Data were extracted by the two reviewers and analyzed. The literature search yielded 2743 abstracts. Twenty-one articles were selected for analysis. The study design was heterogenous, with only one randomized controlled study. The symptoms resolved in 92% [95% CI (88; 96)] of the nonoperatively treated patients. Meta-analysis showed that an additional 16% (95% CI 10; 22) of patients underwent appendectomy after discharge from initial hospital stay. Complications and length of hospital stay was not different among patients treated with antibiotics compared with those who underwent appendectomy. Nonoperative treatment of nonperforated acute appendicitis children is safe and efficient. There is a lack of large randomized controlled trials to compare outcomes of nonoperative treatment with appendectomy. [ABSTRACT FROM AUTHOR]

Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt Pleurodeles waltl, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the Myb-like proto-oncogene have expanded dramatically in the Pleurodeles waltl genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates. [ABSTRACT FROM AUTHOR]

Item response theory (IRT) observed-score kernel equating is introduced for the non-equivalent groups with anchor test equating design using either chain equating or post-stratification equating. The equating function is treated in a multivariate setting and the asymptotic covariance matrices of IRT observed-score kernel equating functions are derived. Equating is conducted using the two-parameter and three-parameter logistic models with simulated data and data from a standardized achievement test. The results show that IRT observed-score kernel equating offers small standard errors and low equating bias under most settings considered. [ABSTRACT FROM AUTHOR]

In multi-core systems, main memory is a major shared resource among processor cores. A task running on one core can be delayed by other tasks running simultaneously on other cores due to interference in the shared main memory system. Such memory interference delay can be large and highly variable, thereby posing a significant challenge for the design of predictable real-time systems. In this paper, we present techniques to reduce this interference and provide an upper bound on the worst-case interference on a multi-core platform that uses a commercial-off-the-shelf (COTS) DRAM system. We explicitly model the major resources in the DRAM system, including banks, buses, and the memory controller. By considering their timing characteristics, we analyze the worst-case memory interference delay imposed on a task by other tasks running in parallel. We find that memory interference can be significantly reduced by (i) partitioning DRAM banks, and (ii) co-locating memory-intensive tasks on the same processing core. Based on these observations, we develop a memory interference-aware task allocation algorithm for reducing memory interference. We evaluate our approach on a COTS-based multi-core platform running Linux/RK. Experimental results show that the predictions made by our approach are close to the measured worst-case interference under workloads with both high and low memory contention. In addition, our memory interference-aware task allocation algorithm provides a significant improvement in task schedulability over previous work, with as much as 96 % more tasksets being schedulable. [ABSTRACT FROM AUTHOR]

Consider the problem of scheduling a task set τ of implicit-deadline sporadic tasks to meet all deadlines on a t-type heterogeneous multiprocessor platform where tasks may access multiple shared resources. The multiprocessor platform has m processors of type-k, where k∈{1,2,..., t}. The execution time of a task depends on the type of processor on which it executes. The set of shared resources is denoted by R. For each task τ, there is a resource set R⊆ R such that for each job of τ, during one phase of its execution, the job requests to hold the resource set R exclusively with the interpretation that (i) the job makes a single request to hold all the resources in the resource set R and (ii) at all times, when a job of τ holds R, no other job holds any resource in R. Each job of task τ may request the resource set R at most once during its execution. A job is allowed to migrate when it requests a resource set and when it releases the resource set but a job is not allowed to migrate at other times. Our goal is to design a scheduling algorithm for this problem and prove its performance. We propose an algorithm, LP-EE-vpr, which offers the guarantee that if an implicit-deadline sporadic task set is schedulable on a t-type heterogeneous multiprocessor platform by an optimal scheduling algorithm that allows a job to migrate only when it requests or releases a resource set, then our algorithm also meets the deadlines with the same restriction on job migration, if given processors $4 \times (1 + \operatorname{MAXP}\times \lceil \frac{\vert P\vert \times\operatorname{MAXP}}{\min \{m_{1}, m_{2}, \ldots, m_{t} \}} \rceil )$ times as fast. (Here $\operatorname{MAXP}$ and | P| are computed based on the resource sets that tasks request.) For the special case that each task requests at most one resource, the bound of LP-EE-vpr collapses to $4 \times (1 + \lceil \frac{\vert R\vert }{\min \{m_{1}, m_{2}, \ldots, m_{t} \}} \rceil )$. To the best of our knowledge, LP-EE-vpr is the first algorithm with proven performance guarantee for real-time scheduling of sporadic tasks with resource sharing on t-type heterogeneous multiprocessors. [ABSTRACT FROM AUTHOR]

Consider the problem of assigning implicit-deadline sporadic tasks on a heterogeneous multiprocessor platform comprising two different types of processors—such a platform is referred to as two-type platform. We present two low degree polynomial time-complexity algorithms, SA and SA-P, each providing the following guarantee. For a given two-type platform and a task set, if there exists a task assignment such that tasks can be scheduled to meet deadlines by allowing them to migrate only between processors of the same type (intra-migrative), then (i) using SA, it is guaranteed to find such an assignment where the same restriction on task migration applies but given a platform in which processors are $1+\frac{\alpha}{2}$ times faster and (ii) SA-P succeeds in finding a task assignment where tasks are not allowed to migrate between processors (non-migrative) but given a platform in which processors are 1+ α times faster. The parameter 0< α≤1 is a property of the task set; it is the maximum of all the task utilizations that are no greater than 1. We evaluate average-case performance of both the algorithms by generating task sets randomly and measuring how much faster processors the algorithms need (which is upper bounded by $1+\frac{\alpha}{2}$ for SA and 1+ α for SA-P) in order to output a feasible task assignment (intra-migrative for SA and non-migrative for SA-P). In our evaluations, for the vast majority of task sets, these algorithms require significantly smaller processor speedup than indicated by their theoretical bounds. Finally, we consider a special case where no task utilization in the given task set can exceed one and for this case, we (re-)prove the performance guarantees of SA and SA-P. We show, for both of the algorithms, that changing the adversary from intra-migrative to a more powerful one, namely fully-migrative, in which tasks can migrate between processors of any type, does not deteriorate the performance guarantees. For this special case, we compare the average-case performance of SA-P and a state-of-the-art algorithm by generating task sets randomly. In our evaluations, SA-P outperforms the state-of-the-art by requiring much smaller processor speedup and by running orders of magnitude faster. [ABSTRACT FROM AUTHOR]

Consider the problem of partitioned scheduling of an implicit-deadline sporadic task set on heterogeneous multiprocessors to meet all deadlines. Each processor is either of type-1 or type-2. We present a new algorithm, FF-3C, for this problem. FF-3C offers low time-complexity and provably good performance. Specifically, FF-3C offers (i) a time-complexity of O( n⋅max( m,log n)+ m⋅log m), where n is the number of tasks and m is the number of processors and (ii) the guarantee that if a task set can be scheduled by an optimal partitioned-scheduling algorithm to meet all deadlines then FF-3C meets all deadlines as well if given processors at most $\frac{1}{1-\alpha}$ times as fast (referred to as speed competitive ratio) and tasks are scheduled using EDF; where α is a property of the task set. The parameter α is in the range (0,0.5] and for each task, it holds that its utilization is no greater than α or greater than 1− α on each processor type. Thus, the speed competitive ratio of FF-3C can never exceed 2. We also present several extensions to FF-3C; these offer the same performance guarantee and time-complexity but with improved average-case performance. Via simulations, we compare the performance of our new algorithms and two state-of-the-art algorithms (and variations of the latter). We evaluate algorithms based on (i) running time and (ii) the necessary multiplication factor, i.e., the amount of extra speed of processors that the algorithm needs, for a given task set, so as to succeed, compared to an optimal task assignment algorithm. Overall, we observed that our new algorithms perform significantly better than the state-of-the-art. We also observed that our algorithms perform much better in practice, i.e., the necessary multiplication factor of the algorithms is much smaller than their speed competitive ratio. Finally, we also present a clustered version of the new algorithm. [ABSTRACT FROM AUTHOR]

Known algorithms capable of scheduling implicit-deadline sporadic tasks over identical processors at up to 100% utilisation invariably involve numerous preemptions and migrations. To the challenge of devising a scheduling scheme with as few preemptions and migrations as possible, for a given guaranteed utilisation bound, we respond with the algorithm NPS-F. It is configurable with a parameter, trading off guaranteed schedulable utilisation (up to 100%) vs preemptions. For any possible configuration, NPS-F introduces fewer preemptions than any other known algorithm matching its utilisation bound. A clustered variant of the algorithm, for systems made of multicore chips, eliminates (costly) off-chip task migrations, by dividing processors into disjoint clusters, formed by cores on the same chip (with the cluster size being a parameter). Clusters are independently scheduled (each, using non-clustered NPS-F). The utilisation bound is only moderately affected. We also formulate an important extension (applicable to both clustered and non-clustered NPS-F) which optimises the supply of processing time to executing tasks and makes it more granular. This reduces processing capacity requirements for schedulability without increasing preemptions. [ABSTRACT FROM AUTHOR]

We present a 12(1+3 R/(4 m)) competitive algorithm for scheduling implicit-deadline sporadic tasks on a platform comprising m processors, where a task may request one of R shared resources. [ABSTRACT FROM AUTHOR]

The occurrence of obesity, eating disorders, and related diseases has increased in many parts of the world. Given that few strong genetic factors have been found, it is clear that these are complex multi-factorial diseases. The serotonin receptor 2C, a member of the 5-HTergic system, has been implicated in the control of phagia and obesity. We report a detailed investigation of linkage disequilibrium (LD) within and between the HTR2C promoter and the flanking sequences around a commonly utilized marker in the second coding exon of HTR2C. We suggest that inconsistent associations between HTR2C and several phenotypes, including obesity, may be due to the LD pattern across the gene in which recombination and gene conversion have been influential. The nucleotide and haplotype distribution is consistent with that of the neutral mutation model. The number of haplotypes suggests demographic influences or over dominant selection that may have a function in HTR2C expression. Using the fine LD pattern, we describe a possible association with promoter haplotypes and diplotypes, including a GT microsatellite, and body mass index (BMI) ≥30 kgm−2 ( P<0.0001). SNP −995G>A heterozygotes, as well as promoter diplotypes, were found to marginally influence higher serum leptin corrected for percentage body fat ( P=0.01), which might suggest that these subjects are leptin resistant. Our results complement previous studies of HTR2C in both mice and humans, and suggest the importance of genetic variation and elucidating the fine LD structure in uncovering the genetic factors of obesity. [ABSTRACT FROM AUTHOR]

We analyzed 137 kb covering human neurofibromatosis 2 (NF2) tumor suppressor locus and orthologous loci from baboon, mouse, rat, and pufferfish Takifugurubripes. A predominant feature of human-rodent conservation is a very similar distribution of conserved islands, regarding length, position, and degree of identity. By use of a threshold of 75% identity over ≥100 bp of gap-free alignment, comparisons of human-mouse sequences resulted in 3.58% for extra-exonic conservation, which can be compared to 4.5% of exonic sequence content within the human locus. We identified a duplication of neurofibromin 2 in pufferfish, which resulted in two putative proteins with 74% and 76% identity to the human protein. One distinct island (called inter 1), conserved between all analyzed species, was located between promoters of the NIPSNAP1 and NF2 genes. Inter1 might represent a novel regulatory element, important for the function of this locus. The high level of intronic conservation in the NF2 locus suggests that a number of unknown regulatory elements might exist within this gene. These elements could be affected by disease-causing mutations in NF2 patients and NF2-associated tumors. Alternatively, this conservation might be explained by presence of not yet characterized transcriptional unit(s) within this locus. [ABSTRACT FROM AUTHOR]

Translocation t(11;22)(q23;q11) is the most common constitutional reciprocal translocation in man. Balanced carriers are phenotypically normal, except for decreased fertility, an increased spontaneous abortion rate and a possible predisposition to breast cancer in some families. Here, we report the high resolution mapping of the t(11;22)(q23;q11) breakpoint. We have localised the breakpoint, by using fluorescence in situ hybidisation (FISH) walking, to a region between D11S1340 and WI-8564 on chromosome 11, and D22S134 and D22S264 on chromosome 22. We report the isolation of a bacterial artificial chromosome (BAC) clone spanning the breakpoint in 11q23. We have narrowed down the breakpoint to an 80-kb sequenced region on chromosome 11 and FISH analysis has revealed a variation of the breakpoint position between patients. In 22q11, we have sequenced two BACs (BAC2280L11 and BAC41C4) apparently mapping to the region; these contain low copy repeats (LCRs). Southern blot analysis with probes from BAC2280L11 has revealed different patterns between normal controls and translocation carriers, indicating that sequences similar/identical to these probes flank the translocation breakpoint. The occurrence of LCRs has previously been associated with genomic instability and "unclonable" regions. Hence, the presence of such repeats renders standard translocation breakpoint cloning techniques ineffective. Thus, we have used high resolution fiber-FISH to study this region in normal and translocation cases by using probes from 22q11, LCRs and 11q23. We demonstrate that the LCR containing the gap in 22q11 is probably substantially larger than the previous estimates of 100 kb. Using fiber-FISH, we have localised the breakpoint in 22q11 to approximately 20–40 kb from the centromeric border of the LCR (i.e. the telomeric end of AC006547) and have confirmed the breakpoint position on 11q23. [ABSTRACT FROM AUTHOR]

Diamond-Blackfan anaemia (DBA) is a constitutional erythroblastopenia characterized by absent or decreased erythroid precursors. The disease, previously mapped to human chromosome 19q13, is frequently associated with a variety of malformations. To identify the gene involved in DBA, we cloned the chromosome 19q13 breakpoint in a patient with a reciprocal X;19 chromosome translocation. The breakpoint occurred in the gene encoding ribosomal protein S19. Furthermore, we identified mutations in RPS19 in 10 of 40 unrelated DBA patients, including nonsense, frameshift, splice site and missense mutations, as well as two intragenic deletions. These mutations are associated with clinical features that suggest a function for RPS19 in erythropoiesis and embryogenesis. [ABSTRACT FROM AUTHOR]

Full exon-intron structures are presented for the NIK serine/threonine protein kinase gene and a novel gene termed C17orf1. By in situ hybridisation and radiation hybrid mapping, a cosmid (cDD-Z) that contains regions of both of these genes has been localised between markers D17S800 and D17S791 at chromosome 17q21. The two genes are thus positional candidates for the mutant locus underlying frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17), a disease for which NIK is also a good biological candidate. Using exon-intron maps, a genomic DNA sequencing based mutation screen has been performed for the NIK and C17orf1 genes in a chromosome 17-linked FTDP-17 pedigree. Two silent single-base variations were detected in C17orf1. No alterations were restricted to DNA samples from patients, thus excluding the C17orf1 and NIK genes as likely sites of mutation FTDP-17. [ABSTRACT FROM AUTHOR]

A nonsense mutation at the CpG-site in the codon for Arg(169) in the gene for hypoxanthine phosphoribosyltransferase (hprt) was identified by genomic polymerase chain reaction (PCR) and DNA sequencing in cultured fibroblasts from two brothers with Lesch Nyhan's syndrome. The recurrence of mutation at this CpG-site in several unrelated Lesch-Nyhan families suggests that deamination of 5-methylcytosine is a possible mechanism for mutagenesis. The level of hprt-mRNA in the fibroblasts of the patients was similar to that in healthy controls, whereas hprt-enzyme activity was not detectable. The mutation in this family was also identified in five female relatives and prenatally in a male fetus. Unexpectedly, results from hair follicle analyses and fibroblast selection studies in 8-azaguanine and 6-thioguanine medium showed a non-carrier phenotype in three of the female heterozygotes, whereas X-inactivation mosaicism was demonstrated in one heterozygote. A possible explanation for the apparent non-random X-inactivation in this family is the co-existence of the hprt mutation with an undefined X-linked lethal mutation. This observation is of practical relevance for carrier detection in other Lesch-Nyhan families. [ABSTRACT FROM AUTHOR]

Two previously unidentified mutations at the phenylalanine hydroxylase locus were found during a study of the relationship between genotype and phenotype in phenylketonuria and hyperphenylalaninemia. One mutation eliminates the BamHI site in exon 7 and the other eliminates the HindIII site in exon 11 of the phenylalanine hydroxylase gene. They were suspected because of deviating restriction fragment patterns and confirmed by amplification, via the polymerase chain reaction, of exon 7 and exon 11, respectively, followed by digestion with the appropriate restriction enzyme. Direct sequencing of amplified mutant exon 7 revealed a G/C to T/A transversion at the first base of codon 272, substituting a GGA glycine codon for a UGA stop codon. Direct sequencing of amplified mutant exon 11 revealed a deletion of codon 364, a CTT leucine codon. The exon 7 mutation can be expected to result in a truncated protein and the exon 11 mutation in the elimination of an amino acid in the catalytic region of the enzyme. A patient who is a compound heterozygote for these two mutations has classical phenylketonuria. It is concluded that each of the two mutations leads to a profound loss of enzymatic activity. The segregation of these mutations with disease alleles in 4 and 2 families, respectively, supports the hypothesis that multiple mutations at the phenylalanine hydroxylase locus explain the variable phenylalanine tolerance in patients with phenylalanine hydroxylase deficiency. [ABSTRACT FROM AUTHOR]

Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM. [ABSTRACT FROM AUTHOR]