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Hardy-Weinberg equilibrium is the fundamental principle of population genetics. In this article, we present a new NetLogo model called “Hardy-Weinberg Basic model v 2.0”, characterized by a strict adherence to the original assumptions made by Hardy and Weinberg in 1908. A particularly significant feature of this model is that the algorithm does not make use of the binomial expansion formula. Instead, we show that using a procedure based on dynamic random networks, diploid equilibrium can be achieved spontaneously by a population of agents reproducing sexually in a Mendelian fashion. The model can be used to conduct simulations with a wide range of initial population sizes and genotype distributions for a single biallelic autosomal locus. Moreover, we also show that without any mathematical formalism the algorithm is also able to confirm the prediction of Kimura’s diffusion equations on the time required to fix a new neutral allele in a population, due to genetic drift alone.

Perovskites have emerged as promising light harvesters in photovoltaics. The resulting solar cells (i) are thin and lightweight, (ii) can be produced through solution processes, (iii) mainly use low-cost raw materials, and (iv) can be flexible. These features make perovskite solar cells intriguing as space technologies; however, the extra-terrestrial environment can easily cause the premature failure of devices. In particular, the presence of high-energy radiation is the most dangerous factor that can damage space technologies. This Review discusses the status and perspectives of perovskite photovoltaics in space applications. The main factors used to describe the space environment are introduced, and the results concerning the radiation hardness of perovskites toward protons, electrons, neutrons, and γ-rays are presented. Emphasis is given to the physicochemical processes underlying radiation damage in such materials. Finally, the potential use of perovskite solar cells in extra-terrestrial conditions is discussed by considering the effects of the space environment on the choice of the architecture and components of the devices.

Background The AHNAK2 gene encodes a large nucleoprotein expressed in several tissues, including brain, squamous epithelia, smooth muscle, and neuropil. Its role in calcium signaling has been suggested and to date, clear evidence about its involvement in the pathogenesis of clinical disorders is still lacking. Methods Here, we report a female 24-year-old patient diagnosed with a cardio-facio-cutaneous-like phenotype (CFC-like), characterized by epilepsy, psychomotor development delay, atopic dermatitis, congenital heart disease, hypotonia, and facial dysmorphism, who is compound heterozygote for two missense mutations in the AHNAK2 gene detected by exome sequencing. Results This patient had no detectable variant in any of the genes known to be associated with the cardio-facio-cutaneous syndrome. Moreover, the mode of inheritance does not appear to be autosomal dominant, as it is in typical CFC syndrome. We have performed in silico assessment of mutation severity separately for each missense mutation, but this analysis excludes a severe effect on protein function. Protein structure predictions indicate the mutations are located in flexible regions possibly involved in molecular interactions. Conclusion We discuss an alternative interpretation on the potential involvement of the two missense mutations in the AHNAK2 gene on the expression of CFC-like phenotype in this patient based on inter-allelic complementation. publishedVersion

Advancements in electrochemical double-layer capacitor (EDLC) technology require the concomitant use of novel efficient electrode materials and viable electrode manufacturing methods. Cost-effectiveness, scalability and sustainability are key-drivers for fulfilling product development chain accepted by worldwide legislations. Herein, we report a scalable and sprayable “green” electrode material-based ink based on activated carbon and single-/few-layer graphene (SLG/FLG) flakes. We show that, contrary to commercial reduced graphene oxide, defect-free and flat SLG/FLG flakes reduce the friction of ions over the electrode films, while spray coating deposition of our ink maximises the electrolyte accessibility to the electrode surface area. Sprayed SLG/FLG flakes-based EDLCs display superior rate capability performance (e.g., specific energies of 31.5, 23.7 and 12.5 Wh kg−1 at specific powers of 150, 7500 and 30000 W kg−1, respectively) compared to both SLG/FLG flakes-free devices and commercial-like EDLCs produced by slurry-coating method. The use of SLG/FLG flakes enables our sprayed EDLCs to operate in a wide range of temperature (−40/+100°C) compatible with ionic liquid/organic solvent-based electrolytes, overcoming the specific power limits of AC-based EDLCs. A prototype EDLCs stack consisting of multiple large-area EDLCs, each one displaying a capacitance of 25 F, demonstrates the industrial potential of our technology.

Solar-to-fuel direct conversion devices are a key component to realize a full transition to a renewable-energy based chemistry and energy, but their limits and possibilities are still under large debate. In this review article, we focus on the current density as a fundamental figure of merit to analyse these aspects and to compare different device configurations and types of solar fuels produced from small molecules such as H$_2$O, CO$_2$ and N$_2$. Devices with physical separation of the anodic and cathodic zones, photoelectrochemical-type (PEC) or with a photovoltaic element integrated in an electrochemical cell (PV/EC), are analysed. The physico-chemical mechanisms involved in device operation that affect the current density and relations with device architecture are first discussed. Aspects relevant to device design in relation to practical use are also commented on. Then discussion is moved towards the relevance of these aspects to compare the behaviour in the state-of-the-art of the conversion of these small molecules, with focus on solar fuels from H$_2$O, CO$_2$ and N$_2$ conversion, highligthing the gaps and perspectives of such technologies. The still significant lack of crucial data, notwithstanding the extensive literature on the topic, has to be remarked on, particularly in terms of the need to operate these cells in conjunction with sun concentration (in the 50-100 sun range) which emerges as the necessary direction from this analysis, with consequent aspects in terms of cell and materials design to operate in these conditions. The work provides a guide for the optimisation of the investigated technology and the fixing of their practical limits for large-scale applications.

Solar cells (SCs) are the most ubiquitous and reliable energy generation systems for aerospace applications. Nowadays, III–V multijunction solar cells (MJSCs) represent the standard commercial technology for powering space-craft, thanks to their high-power conversion efficiency and certified reliability/stability while operating in orbit. Nevertheless, spacecraft companies are still using cheaper Si-based SCs to amortize the launching costs of satellites. Moreover, in recent years, new SCs technologies based on Cu(In,Ga)Se2(CIGS) and perovskite solar cells (PSCs) have emerged as promising candi-dates for aerospace power systems, because of their appealing properties such as lightweightness, flexibility, cost-effective manufacturing, and excep-tional radiation resistance. In this review the current advancements and future challenges of SCs for aerospace applications are critically discussed. In particular, for each type of SC, a description of the device’s architecture, a summary of its performance, and a quantitative assessment of the radia-tion resistance are presented. Finally, considering the high potential that 2D-materials (such as graphene, transition metal dichalcogenides, and transition metal carbides, nitrides, and carbonitrides) have in improving both performance and stability of SCs, a brief overview of some important results concerning the influence of radiation on both 2D materials-based devices and monolayer of 2D materials is also included.

Flexible energy storage devices and supercapacitors in particular have become very attractive due to the growing demand for wearable consumer devices. To obtain supercapacitors with improved performance, it is useful to resort to hybrid electrodes, usually nanocomposites, that combine the excellent charge transport properties and high surface area of nanostructured carbon with the electrochemical activity of suitable metal oxides or conjugated polymers. In this work, electrochemically active conducting inks are developed starting from commercially available polypyrrole and graphene nanoplatelets blended with dodecylbenzenesulfonic acid. Films prepared by applying the developed inks are characterized by means of Raman measurements, Fourier Transform Infrared (FTIR) analysis, and Atomic Force Microscopy (AFM) investigations. Planar supercapacitor prototypes with an active area below ten mm2 are then prepared by applying the inks onto transparency sheets, separated by an ion-permeable nafion layer impregnated with lithium hexafluorophospate, and characterized by means of electrical measurements. According to the experimental results, the devices show both pseudocapacitive and electric double layer behavior, resulting in areal capacitance that, when obtained from about 100 mF⋅cm−2 in the sample with polypyrrole-based electrodes, increases by a factor of about 3 when using electrodes deposited from inks containing polypyrrole and graphene nanoplateles.

The Mediterranean islands and their population history are of considerable importance to the interpretation of the population history of Europe as a whole. In this context, Sicily, because of its geographic position, represents a bridge between Africa, the Near East, and Europe that led to the stratification of settlements and admixture events. The genetic analysis of extant and ancient human samples has tried to reconstruct the population dynamics associated with the cultural and demographic changes that took place during the prehistory and history of Sicily. In turn, genetic, demographic and cultural changes need to be understood in the context of the environmental changes that took place over the Holocene. Based on this framework, this paper aims to discuss the cultural and demographic dimension of the island by reviewing archaeogenetic studies, and lastly, we discuss the ecological constraints related to human peopling in times of change in landscapes that occurred on the island in various periods. Finally, possible directions for future archaeogenetic studies of Sicily are discussed. Despite its long human history, Sicily is still one of the world’s biodiversity hotspots. The lessons we learn from the past use of landscape provide models for sustainable future management of the Mediterranean’s landscapes.

Intellectual disability (ID) is a pathological condition characterized by limited intellectual functioning and adaptive behaviors. It affects 1–3% of the worldwide population, and no pharmacological therapies are currently available. More than 1000 genes have been found mutated in ID patients pointing out that, despite the common phenotype, the genetic bases are highly heterogeneous and apparently unrelated. Bibliomic analysis reveals that ID genes converge onto a few biological modules, including cytoskeleton dynamics, whose regulation depends on Rho GTPases transduction. Genetic variants exert their effects at different levels in a hierarchical arrangement, starting from the molecular level and moving toward higher levels of organization, i.e., cell compartment and functions, circuits, cognition, and behavior. Thus, cytoskeleton alterations that have an impact on cell processes such as neuronal migration, neuritogenesis, and synaptic plasticity rebound on the overall establishment of an effective network and consequently on the cognitive phenotype. Systems biology (SB) approaches are more focused on the overall interconnected network rather than on individual genes, thus encouraging the design of therapies that aim to correct common dysregulated biological processes. This review summarizes current knowledge about cytoskeleton control in neurons and its relevance for the ID pathogenesis, exploiting in silico modeling and translating the implications of those findings into biomedical research.

Invited for this month's cover are collaborators from University of Pavia, Ecole Polytechnique Federale de Lausanne, University of Messina and Istituto Italiano di Tecnologia. The cover picture shows the crystal structure of a Ruddlesden-Popper quasi-2D perovskite with chemical formula (PEA)2 MA39 Pb40 I121 (with PEA: phenylethylammonium and MA: methylammonium). The subscript 40 indicates the number of PbI6 octahedra separated by a double layer of PEA cations. Such quasi-2D perovskites exhibit efficient photovoltaic performances and higher stability with respect to the pure 3D counterpart (MAPbI3 ). This article is part of the Special Collection on "Perovskite Materials and Devices". Read the full text of the article at 10.1002/cplu.202000777.

Autism Spectrum Disorders (ASDs) stand out as a relevant example where omics-data approaches have been extensively and successfully employed. For instance, an outstanding outcome of the Autism Genome Project relies in the identification of biomarkers and the mapping of biological processes potentially implicated in ASDs’ pathogenesis. Several of these mapped processes are related to molecular and cellular events (e.g., synaptogenesis and synapse function, axon growth and guidance, etc.) that are required for the development of a correct neuronal connectivity. Interestingly, these data are consistent with results of brain imaging studies of some patients. Despite these remarkable progresses it is still quite a challenge to reconstruct the causal chain of events linking mutations, epimutations and other molecular defects to the spectrum of phenotypes and endophenotypes present in autistic patients. In this article we review the state-of-art of omics-data research in ASDs and present how the use of in silico dynamics modeling of biochemical networks becomes a powerful approach to investigate ASDs omics-data from a different perspective to extract more information. To this end, we generated—for the first time—a protein network regulating the dynamics of the growth cone and we then transformed it into the equivalent Boolean model. Using in silico mutagenesis we show that simulations of this model lead to a more comprehensive and systemic understanding of the cellular and molecular effects of gene mutations in ASDs compared to conventional analyses of static pathways. Such powerful tool might constitute a significant twist in the analysis of in silico genotype-phenotype relationship for ASDs and other multi-genic neurodevelopmental disorders, especially when combined with the latest sequencing technologies applied to single patients.

Structural changes of (Ag2O)x(B2O3)1-x glasses, over the range between X = 0.0 and X = 0.14, have been monitored by Raman spectroscopy. Low temperature heat capacity measurements have been also performed between 0.4 K and 25 K to investigate along with low frequency Raman scattering the behavior of the low-energy vibrational dynamics. A progressively decreasing intensity of the main band at 808 cm−1 and the appearance of a band at about 775 cm−1 with increasing Ag2O content have been observed and analyzed in detail. The strongly polarized band at 808 cm−1 is ascribed to the breathing vibration of boroxol rings and the decrease of its intensity indicates the reduction of the number of these units in the network. The band at 775 cm−1 is assigned to vibrations of pentaborate units, formed from two boroxol rings linked by a tetrahedral BO4 group. The rate of formation of BO4 groups appears to increase as X/(1-X). Raman investigation has been extended to very low frequencies, where a broad intense band, the Boson peak (BP), dominates the spectrum of all the samples below 100 cm−1. Addition of Ag2O shifts the BP position from 26 cm−1 up to 33 cm−1 and gives rise to a decrease of its intensity up to X = 0.09 and a sudden increase for X = 0.14, which has been explained as due to rattling motion of silver ions whose contribution is added to that of localized vibrations. The formation of tetrahedral BO4 groups stiffens the network and leads to a decrease of the excess heat capacity over the Debye prediction below 20 K, which is not taken into account by the simple hardening of the elastic continuum but seems to follow the reduction of boroxol rings. This result contrasts the observations on borate glasses with high Ag content and emphasizes the crucial role of the network continuity on the vibrational dynamics of a glass.

The DHRS9 gene is involved in several pathways including the synthesis of allopregnanolone from progesterone. Allopregnanolone is a positive modulator of gamma aminobutyric acid (GABA) action and plays a role in the control of neuronal excitability and seizures. Whole-exome sequencing performed on a girl with an early onset epilepsy revealed that she was a compound heterozygote for two novel missense mutations of the DHRS9 gene likely to disrupt protein function. No previous studies have reported the implication of this gene in epilepsy. We discuss a new potential pathogenic mechanism underlying epilepsy in a child, due to a defective progesterone pathway.

The last decade has witnessed the advance of metal halide perovskites as a promising low-cost and efficient class of light harvesters used in solar cells (SCs). Remarkably, the efficiency of lab-scale perovskite solar cells (PSCs) reached a power conversion efficiency of 25.5% in just ~10 years of research, rivalling the current record of 26.1% for Si-based PVs. To further boost the performances of PSCs, the use of 2D materials (such as graphene, transition metal dichalcogenides and transition metal carbides, nitrides and carbonitrides) has been proposed, thanks to their remarkable optoelectronic properties (that can be tuned with proper chemical composition engineering) and chemical stability. In particular, 2D materials have been demonstrated as promising candidates for (i) accelerating hot carrier transfer across the interfaces between the perovskite and the charge extraction layers; (ii) improving the crystallization of the perovskite layers (when used as additives in the precursor solution); (iii) favoring electronic bands alignment through tuning of the work function. In this mini-review, we discuss the physical mechanisms underlying the increased efficiency of 2D material-based PSCs, focusing on the three aforementioned effects.

Among the large family of transition metal dichalcogenides, recently ReS

This study highlights plastics occurrence in five demersal fish species from the Southern Tyrrhenian Sea: the Red mullet Mullus barbatus barbatus, the Piper gurnard Trigla lyra, the Blackmouth catshark Galeus melastomus, the Lesser spotted dogfish Scyliorhinus canicula and the Brown ray Raja miraletus. Overall, 125 fish were examined: 21 Red mullets, 16 Piper gurnards, 75 Blackmouth catsharks, 72 Dogfish and 1 Brown ray. The percentage of fish with ingested plastics was 14.4% with 0.24 items per specimen. The majority of the debris were fibers and the application of infrared and Raman spectroscopy allowed the identification and discrimination of plastic and non-plastic fibers. The plastic debris isolated were mainly microplastics (94.1%), while macroplastics occurrence was very low (5.9%). The plastics were identified as polypropylene, Teflon, nylon, kraton G (triblock copolymer) and polyethylene. Also cellulose was detected. S. canicula was the species with the highest number of plastic pollutants.

In this work it is reported for the first time the characterization of microplastics from sea water samples and in two congener species of seabreams: Pagellus erythrinus and P. bogaraveo, Mediterranean fish species of great commercial importance. An experimental survey was conducted on May-June 2017 in the southernmost part of the Tyrrhenian Sea. Microplastics found in the sea water and in the grastrointestinal tract of two teleosts were characterized by Raman and IR spectroscopies. Microplastics found in sea water samples appeared in the form of fragments made of plastics of low and high density (PVC and LPDE). All the microplastics found in fish belonged to Nylon 66, typical fibers used in industry and in fisheries. Our findings highlighted the importance of further studies along the food web chain for a better understanding of the diffusion and possible consequences of this terrible threat.

Several nuclear genes have been found to be linked to ichthyosis, and Next Generation Sequencing approach on panels of targeted genes has turned out to be particularly useful in analyzing diseases characterized by significant genetic and phenotypic heterogeneity. We developed a panel of 26 genes to be screened with the Ion Personal Genome Machine (PGM) for causative mutations relating to ichthyosis. Sequencing runs were obtained from a patient with ichthyosis using the Ion Torrent PGM and then processed with Ion Torrent Suite, Variant Caller, Coverage Analysis and wANNOVER tools. No causative mutations were found using Variant Caller and wANNOVER softwares, whereas the “Coverage Analysis” tool revealed a common large deletion in STS gene in a patient with X-linked ichthyosis. Identification of indels in Next Generation Sequencing (NGS) data is a veritable challenge. This study demonstrates the efficacy and effectiveness of using NGS approach to detect large deletions without resorting to specific algorithms for “indel” detection. Our results indicate that the NGS panel is a useful, rapid and cost-effective screening test for patients whose features are suggestive of a genetic etiology involving one of the genes embedded in the panel. It is an excellent alternative to Sanger sequencing as for costs, ease of analysis, and turnaround time.

The efficient production of molecular hydrogen (H2) is a fundamental step toward an environmentally friendly economy. Photocathodes using organic bulk heterojunction (BHJ) films as light harvesters represent an attracting technology for low-cost photoelectrochemical water splitting. These photocathodes need charge transporting layers (CTLs) to efficiently separate and transport either holes or electrons toward the back-current collector and electrolyte, respectively. Therefore, it is pivotal to control the energy band edge levels and the work function (WF) of the CTLs to match the ones of the BHJ film, current collector, and electrolyte. Herein, the use of 2D p-doped WS2flakes as hole transporting material for H2-evolving photocathodes based on the regioregular poly(3-hexylthiophene):phenyl-C61-butyric acid methyl ester (rr-P3HT:PCBM) BHJ film is proposed. The WS2flakes are produced through scalable liquid-phase exfoliation of the bulk crystal, whereas p-type chemical doping allows the tuning of the WS2WF. This approach boosts the performances of the photocathodes, reaching photocurrent densities up to 4.14 mA cm−2at 0 V versus reversible hydrogen electrode (RHE), an onset potential of 0.66 V versus RHE, and a ratiometric power-saved metric of 1.28% (under 1 sun illumination). To the best of the authors' knowledge, these performances represent the current record for 2D materials-based CTLs.

Among the large family of transition metal dichalcogenides (TMDCs), recently ReS2 has stood out due to its nearly layer-independent optoelectronic and physicochemical properties. These are related to its 1T distorted octahedral structure, which leads to strong in-plane anisotropy and the presence of active sites at its surface, which makes ReS2 interesting for applications such as gas sensors and catalysts for H2 production. However, the current fabrication methods for ReS2 use chemical or physical vapor deposition (CVD or PVD) processes that are costly and involve complex and lengthy fabrication procedures, therefore limiting their large-scale production and exploitation. To address this issue, we developed a colloidal synthesis approach, which allows the production of ReS2 to be attained at temperatures below 360 Celsius degrees and with reaction times < 2 h, resulting in a more cost-efficient strategy than the CVD and PVD methods. By combining the solution-based synthesis with surface functionalization strategies, we demonstrate the feasibility of colloidal ReS2 nanosheet films for gas sensing of different toxic gases, moisture and other volatile compounds with highly competitive performance in comparison with devices built with CVD-grown ReS2 and MoS2. In addition, the integration of the ReS2 nanosheet films in assemblies, in which they are deposited on top of networks of carbon nanotubes, allowed us to fabricate electrodes for electrocatalysis for H2 production in both acid and alkaline conditions. Results from proof-of-principle devices show an electrocatalytic overpotential that is competitive with devices based on ReS2 produced by CVD, and even with MoS2, WS2 and MoSe2 electrocatalysts.

Since the beginning of intensive studies on graphene and graphitic materials, Raman spectroscopy has always been used as a characterisation technique. This is due to two main reasons: the non-destructive nature of this experimental technique and its ability to distinguish between the plethora of existing carbon materials. One of the most challenging research activities concerns the production of graphene microcircuits. To address this issue, a possible strategy is to directly reduce and pattern graphite oxide (GO) film by laser irradiation. The objective of this study is to evaluate the laser irradiation-induced structural changes on thin GO films by using Micro-Raman spectroscopy. We used as a source a Nd:YAG laser (1064 nm) and different laser fluences: 15 J/cm2, 7.5 J/cm2 and 5 J/cm2. We have analyzed the modifications of the main Raman contributions of these graphitic materials: the D band (defect induced band), the G band (band due to sp2 hybridized carbon atoms) and the 2D band (D band overtone). In particular, we found out that our figure of merit (FOM) parameters, i.e. the intensity ratio ID/IG (for the D band and G band) and I2D/IG (for the 2D band and G band), change with the laser fluences, revealing a different effect induced by the laser irradiation. The best results are found in the sample irradiated with 5 J/cm2, suggesting that higher fluences do not lead to better results.

The main objective of this study was to provide a methodological insight in the archaeometric field of ceramic provenance and technology, through the identification of the scale of representative differences in terms of clay composition. For this purpose, a total of 78 clay specimens-representative of the three types of Daunian clayey raw materials (Sub-Apennine clays, alluvial deposits and terraced alluvial deposits)- was collected and geochemically investigated, with the aim of determining up to which geographical scale, the exclusive application of geochemical analyses can provide reliable results for the reconstruction of clayey raw materials supply. For the Daunian territory, the scale has been identified with that of a ‘riverine province’, i.e. between the local and the regional extension of the north Apulian fluvial courses. In practice, the Sub-Apennine clays can be chemically distinguished into a northern group, including the Salsola, Vulgano, Celone and Lorenzo streams and a southern group, including the Carapelle stream and the Ofanto river. Moreover, the comparison between the geochemical composition of the clay samples and that of local ceramic productions (previously investigated) has shown that the Sub-Apennine clays were either used as received (Clay 1 group) or refined through decantation (Clay 2 group), before being shaped into fine wares or building materials; conversely, both the alluvial and the terraced alluvial deposits were used “as received” for the production of coarse wares. Furthermore, for the first time, the geospatial network analysis was further applied to the investigation of ancient raw materials exploitation. This analysis was performed in order to reach a reasonable reconstruction of both routes and travel times linking supply areas with production and distribution sites. Surprisingly, the results have shown that, at small distances, the transportation of clayey raw materials is not only reliable but rather highly likely, especially in those sites where Sub-Apennine clays are not readily available.

Greek colonisation of South Italy and Sicily (Magna Graecia) was a defining event in European cultural history, although the demographic processes and genetic impacts involved have not been systematically investigated. Here, we combine high-resolution surveys of the variability at the uni-parentally inherited Y chromosome and mitochondrial DNA in selected samples of putative source and recipient populations with forward-in-time simulations of alternative demographic models to detect signatures of that impact. Using a subset of haplotypes chosen to represent historical sources, we recover a clear signature of Greek ancestry in East Sicily compatible with the settlement from Euboea during the Archaic Period (eighth to fifth century BCE). We inferred moderate sex-bias in the numbers of individuals involved in the colonisation: a few thousand breeding men and a few hundred breeding women were the estimated number of migrants. Last, we demonstrate that studies aimed at quantifying Hellenic genetic flow by the proportion of specific lineages surviving in present-day populations may be misleading.European Journal of Human Genetics advance online publication, 15 July 2015; doi:10.1038/ejhg.2015.124.

Spinal muscular atrophy (SMA) is an autosomal-recessive neuromuscular disorder characterized by motor neuron degeneration in the anterior horn of the spinal cord and brain stem, resulting in progressive muscle weakness and atrophy. The responsible survival motor neuron gene (SMN1; HGNC: 11117) is localized in 5q11.2-13.3. Screening for carriers of SMA is necessary for effective clinical/prenatal diagnosis and genetic counselling. In this study, the copy number of SMN1 gene was determined from a southern Italian population to estimate carrier frequency. This is the first report addressing the estimation of SMA carrier frequency in an Italian population. Our results show that the SMA carrier frequency in Sicily is higher than in the European populations and lower than in Mediterranean/Middle Eastern countries. The carrier testing could be a helpful tool for genetic counselling, to individuals with a positive family history. SMA is the second most common severe autosomalrecessive disorder after cystic fibrosis and the most frequent genetic cause of infant mortality, with an incidence of one per 6000–10,000 live births (Pearn 1980). Mutations in the survival motor neuron gene (SMN1; HGNC: 11117), localized in 5q11.2-13.3 within a large inverted duplicated element, cause SMA types I, II, III and IV (Lefebvre et al. 1995). Further, between 95% and 98% of individuals with recessive SMA have two deletion mutations (deletion of exons 7–8) and the remaining 2–5% have one deletion mutation (exons 7–8) and a second, different type of mutation (Ogino and Wilson 2002). People generally have between one and three copies of the SMN1 gene. Usually, people with two copies

The gastrin-releasing peptide receptor (GRPR) was implicated for the first time in the pathogenesis of Autism spectrum disorders (ASD) by Ishikawa-Brush et al. [Ishikawa-Brush et al. (1997): Hum Mol Genet 6: 1241-1250]. Since this original observation, only one association study [Marui et al. (2004): Brain Dev 26: 5-7] has further investigated, though unsuccessfully, the involvement of the GRPR gene in ASD. With the aim of contributing further information to this topic we have sequenced the entire coding region and the intron/exon junctions of the GRPR gene in 149 Italian autistic patients. The results of this study led to the identification of four novel point mutations, two of which, that is, C6S and L181F, involve amino acid changes identified in two patients with ASD and Rett syndrome, respectively. Both the leucine at position 181 and the cysteine at position 6 are strongly conserved in vertebrates. C6S and L181F mutant proteins were expressed in COS-7 and BALB/3T3 cells, but they did not affect either GRP's binding affinity or its potency for stimulating phospholipase C-mediated production of inositol 1,4,5-trisphosphate. In summary, our results do not provide support for a major role of the GRPR gene in ASD in the population of patients we have studied. However, there is a potential role of C6S and L181F mutations on GRPR function, and possibly in the pathogenesis of the autistic disorders in the two patients.

The incorporation of reference DNA is crucial to the validation of any DNA typing protocol. This paper aims to provide a panel of reference DNAs for actual forensic profiling strategies, i.e. autosomal and gonosomal STR typing as well as mtDNA sequencing. We have characterised three human lymphoid cell lines, GM9947, GM9948 and GM3657, and considered 58 autosomal and gonosomal microsatellites as well as the mitochondrial control region sequence. Well-established markers and STRs recently developed for forensic use were involved. K562 DNA samples which we purchased from two different suppliers were also analysed. They revealed conflicting results with regard to the ChrX STR marker genotype. Hence, we suggest that K562 is no longer used for the calibration of profiling techniques. Our investigation establishes a panel of one female and two male DNA samples as an STR allelic ladder calibration tool and offers information on six alleles of each autosome (AS) marker, three alleles of each X chromosome (ChrX) marker and two alleles of each ChrY marker. In addition, sequences of the mitochondrial control region of the three DNAs are communicated in order to provide sequencing quality control.

Pah(enu2) mice, created by chemically induced genetic mutation, are characterized by biochemical phenotypes closely resembling untreated human phenylketonuria (PKU). However, studies conducted in adult Pah(enu2) mice have shown no indices of the severe mental retardation that characterizes untreated PKU. The present experiments explored recognition of novel spatial and non-spatial information in Pah(enu2) mice by two nonassociative tests that do not use explicit reinforcement and avoid lengthy training. Moreover, we evaluated emotional reactivity by the Elevated Plus Maze. Finally, the performance of affected mutants was compared with that of their unaffected and heterozygous littermates and also with that of mice of the C57BL/6 (C57) inbred strain, an increasingly used background for genetic targeted organisms, and with DBA/2 (DBA) mice, known for their nonpathological deficits in spatial learning. The results demonstrated that mutant Pah(enu2) mice are characterized by deficits involving both spatial and nonspatial recognition, that are not related to motor impairment or to high emotional reactivity to novelty. These results indicate that Pah(enu2) mice show pathological cognitive deficits and support their use to test hypotheses about neurodevelopmental disturbances involved in mental retardation.

a Department of Biological Sciences, Wichita State University, Wichita, Kansas, USA b OASI Istituto per la ricerca sul ritardo mentale e l’involuzione cerebrale, Troina, Sicily, Italy c Department of Biopathology and Biomedical Methodology, University of Palermo, Palermo, Sicily, Italy d Department of Psychology, University of Rome, and Fondazione Santa Lucia IRCCS, Rome, Italy e McGill University—Montreal Children’s Hospital Research Institute, Montreal, Que., Canada f Laboratory of Cerebral Metabolism, National Institute of Mental Health, Bethesda, MD, USA

In forensic science and in legal medicine Y chromosomal typing is indispensable for sex determination, for paternity testing in the absence of the father and for distinguishing males in multiple rape cases. Another potential application is the estimation of paternal geographic origin or family name from a crime stain to narrow down the range of suspects and thus reduce costs of mass screenings. However, Y typing alone cannot provide a sufficiently resolved DNA fingerprint as required for court convictions. Thus, there is a dilemma whether or not to sacrifice valuable material for the sake of extensive Y chromosomal investigations when stain DNA is limited (typically allowing only few PCR amplifications). We here describe a Y-chromosome-specific nucleotide insertion in the duplicate short tandem repeat (STR) locus DXYS156 which allows us to distinguish males from females as does the commonly used amelogenin system, but with the advantage that this locus is multi-allelic, thus substantially contributing towards DNA fingerprinting of a sample and furthermore enabling the detection of sample contamination. Yet another bonus is that both the X and the Y copies of DXYS156 have alleles specific to different parts of the world, offering separate estimates of maternal and paternal descent of that sample. We therefore recommend the inclusion of DXYS156 in standard multiplexing kits for forensic, archaeological and genealogical applications.

When the mtDNA profile of a crime scene matches that of a suspect, it is necessary to determine the probability of a chance match by consulting the frequencies of the identified allele in a "reference population". The ceiling principle suggests that that population should be chosen in which the allele of the suspect is found at the highest frequency, in order to give the suspect the maximum benefit of doubt. Recently, we advocated the use of a worldwide mitochondrial database combined with a geographical information system to identify the regions of the world with the highest frequencies of matching mtDNA types. Here, we demonstrate that the alternative approach of defining a ceiling reference population on the basis of continent or phenotype (race) is too coarse for a non-negligible percentage of mtDNA control region types.

We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1,2,3,4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ∼44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages., Instituto Multidisciplinario de Biología Celular

Autism Spectrum Disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies have investigated the role of de novo Copy Number Variants (CNVs) and microRNAs as important but distinct etiological factors in ASD. We developed a novel computational procedure to assess the potential pathogenic role of microRNA genes overlapping de novo CNVs in ASD patients. Here we show that for chromosomes # 1, 2 and 22 the actual number of miRNA loci affected by de novo CNVs in patients was found significantly higher than that estimated by Monte Carlo simulation of random CNV events. Out of 24 miRNA genes over-represented in CNVs from these three chromosomes only hsa-mir-4436b-1 and hsa-mir-4436b-2 have not been detected in CNVs from non-autistic subjects as reported in the Database of Genomic Variants. Altogether the results reported in this study represent a first step towards a full understanding of how a dysregulated expression of the 24 miRNAs genes affect neurodevelopment in autism. We also propose that the procedure used in this study can be effectively applied to CNVs/miRNA genes association data in other genomic disorders beyond autism.

Molecular analysis of 289 chromosomes has been performed in a cohort of phenylketonuria (PKU) patients whose ancestors lived in five Italian regions, Calabria, Campania, Piemonte, Puglia/Basilicata and Sicilia. Phenylalaninehydroxylase (PAH) gene mutations and minihaplotypes (combinations of PAH gene STR and VNTR systems) have been determined for 78.5 and 64%, respectively, of the chromosomes studied. 21 different minihaplotypes and 24 PKU mutations were found. Heterogeneity tests carried out for the frequencies of mutations and minihaplotypes show that the distribution of eight mutations and four minihaplotypes is statistically heterogeneous in the five Italian regions. Although the evolutionary rate of microsatellites or the age of these mutations is difficult to estimate with accuracy, our findings taken together show a genetic stratification of the Italian population. These results rule out allelic homogeneity of PKU at the molecular level between regions of Italy, yet minihaplotype data may be of practical use for a multistep approach to PAH gene genotyping.

Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

SummaryPhenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) are allelic disorders caused by mutations in the gene encoding phenylalanine hydroxylase (PAH). Previous studies have suggested that the highly variable metabolic phenotypes of PAH deficiency correlate with PAH genotypes. We identified both causative mutations in 686 patients from seven European centers. On the basis of the phenotypic characteristics of 297 functionally hemizygous patients, 105 of the mutations were assigned to one of four arbitrary phenotype categories. We proposed and tested a simple model for correlation between genotype and phenotypic outcome. The observed phenotype matched the predicted phenotype in 79% of the cases, and in only 5 of 184 patients was the observed phenotype more than one category away from that expected. Among the seven contributing centers, the proportion of patients for whom the observed phenotype did not match the predicted phenotype was 4%–23% (P10,000 genotypes, which may be useful for the management of hyperphenylalaninemia in newborns.

This report identifies eight new mutations of the phenylalanine hydroxylase gene detected in Italian patients with hyperphenylalaninemia. The trivial name of the mutations, predicted phenotypic effect, and population of origin (Italian region) are as follows: F55L (nonconservative change: classic, moderate, mild PKU ?; Sicily), IVS2nt-13 (splicing defect, classic PKU; Tuscany), I65N (nonconservative change classic, moderate, mild PKU ?; Sicily), H201Y (non-PKU HPA; Sicily), I269L (non-PKU HPA, or polymorphism; Sicily), IVS7nt3 (splicing defect or polymorphism; Sicily), I283N (classic PKU; Sicily), IVS12nt2 (splicing defect, classic PKU; Sicily and Apulia). In Sicily, the relative frequency of mutations F55L, I65N, H201Y, I269L, IVS7nt3, I283N, IVS12nt2 is < 1%. The seven new mutations identified in the Sicilian population increase the remarkable genetic heterogeneity typical of this population with an estimated homozygosity value at the PAH locus of 0.041. Hum Mutat 11:240‐243, 1998. © 1998 Wiley-Liss, Inc.

We developed a new application of comparative multiplex dosage analysis (CMDA) for evaluation of the ataxin 2 gene. Expansions of the triplet CAG can cause spinocerebellar ataxia type 2 (SCA2), a neurodegenerative disease with an autosomal-dominant mode of inheritance. Molecular diagnosis of SCA2 is routinely based on the use of conventional PCR to detect the CAG expansion. However, PCR does not amplify an allele with an expansion of many triplets (>80), which is typically found in infantile and juvenile forms of SCA2, thus leading to false negatives. We propose the analysis of the ATXN2 gene by CMDA to complement existing methods currently used for the detection of large expansions of the CAG repeat. Using CMDA, the presence of any longer mutated allele in a heterozygous patient or fetus would be inferred due to dosage variation of the very frequent normal allele #22. CMDA can be completed in 1 day, at very low cost, and would be a useful tool for prenatal diagnosis and for diagnosis of presymptomatic forms of early-onset SCA2.

Rubinstein-Taybi syndrome is a rare autosomal dominant congenital disorder characterized by postnatal growth retardation, psychomotor developmental delay, skeletal anomalies, peculiar facial morphology, and tumorigenesis. Mutations in the gene encoding the cAMP response element-binding protein (CREB, also known as CREBBP or CBP) on chromosome 16p13.3 have been identified. In addition, some patients with low intelligence quotients and autistic features bear large deletions. Based on these observations, we used multiplex ligation-dependent probe amplification to search for large deletions affecting the CREBBP gene in a Rubinstein-Taybi syndrome patient. We identified a novel heterozygote deletion removing five exons (exons 17-21), encoding the histone acetyltransferase domain. We propose the use of multiplex ligation-dependent probe amplification as a fast, accurate and cheap test for detecting large deletions in the CREBBP gene in the sub-group of Rubinstein-Taybi syndrome patients with low intelligence quotients and autistic features.

A detailed study of the mutant phenylalanine hydroxylase (PAH) gene from the eastern part of the Czech Republic (Moravia) is reported. A total of 190 mutant alleles from 95 phenylketonuria (PKU) families were analyzed for 21 prevalent Caucasian mutations and restriction fragment length polymorphism/variable number of tandem repeats (RFLP/VNTR) haplotypes. Eighty per cent of all mutant alleles were found to carry 11 mutations. The most common molecular defect was the mutation R408W (55.3%), with a very high degree of homozygosity (34.6%). Each of four other mutations (R158Q, R243X, G272X, IVS12nt1) accounted for more than 3% of PKU alleles. Rarely present were mutations IVS10nt546 (2.6%), R252W (2.6%), L48S (2.1%), R261Q (1.6%), Y414C (1.0%) and 165T (0.5%). Mutations that have been predominantly described in southern Europe (IVS7nt1, A259V, Y277D, R241H, T278N) were not detected. A total of 14 different mutant haplotypes were observed. Three unusual genotype-haplotype associations were identified (R158Q on haplotypes 2.3 and 7.8 and R252W on haplotype 69.3). There was a strong association between the mutation R408W and haplotype 2.3 (54.7%). Heterogeneity was found at mutations R408W (haplotypes 2.3 and 5.9), R158Q (haplotypes 4.3, 2.3 and 7.8) and IVS10nt546 (haplotypes 6.7 and 34.7). The molecular basis of PKU in the Moravian area appears to be relatively homogeneous in comparison with other southern and western European populations, thus providing a good starting point for prenatal diagnosis and early clinical classification.

The results of the neonatal screening for phenylalanine hydroxylase (PAH) deficiency in Sicily show that its incidence is higher than previously reported for mainland Italians and that non-PKU HPA is in excess of classical and mild PKU. The latter finding suggests that a high number of non-PKU HPA mutations would occur in the Sicilian population compared to populations with an inverted PKU/non-PKU HPA ratio. Previous studies have identified 40 mutations accounting for the majority (98%) of mutant alleles underlying PAH deficiency in Sicily. In order to study the molecular basis of the distribution of PAH deficiency phenotypes in the Sicilian population, we have correlated 31 of those mutations with clinical and metabolic phenotypes in 12 mentally retarded patients, 14 treated patients with classic or mild PKU, and 13 subjects presenting the non-PKU HPA phenotype. The present study proposes a tentative classification for a large number (26) of PAH gene mutations which may represent an additional tool for establishing a differential diagnosis for PAH deficiency in the Sicilian population.

A polymorphic short tandem repeat (STR) in intron 3 (Goltsov et al., 1993) and a variable number of tandem repeats (Hind III-VNTR) flanked by two constant Hind III sites (Golstov et al., 1992) have been recently identified in the human phenylalanine hydroxylase (PAH) gene. These polymorphisms are easily detected by the polymerase chain reaction (PCR) and gel electrophoresis. We report on the use of these two novel polymorphisms in three Italian families with pregnancies at risk for classical phenylketonuria (PKU). A carrier status for PKU was ascertained in two fetuses; the third family refused prenatal diagnosis, although informativeness was shown to be complete.

Hyperphenylalaninemia due to a deficiency of hepatic phenylalanine hydroxylase (PAH) is the most common inborn error of amino acid metabolism. Clinically, the disorder is highly heterogeneous, spanning from nonphenylketonuria hyperphenylalaninemia to classical phenylketonuria. Only little is known about the molecular defects underlying hyperphenylalaninemia in Southern Europe. In this study, we conducted a systematic analysis of 53 patients from the Sicilian population. Each patient included in the study had persistently elevated blood levels of phenylalanine and met the differential criteria for PAH deficiency. Genomic DNA was analysed by scanning all PAH-coding exons for mutations by PCR in combination with denaturing gradient gel electrophoresis (DGGE). 52 patients were completely genotyped. A spectrum of 40 different mutations was established including 17 novel PAH mutations. Our results explain the clinical heterogeneity of hyperphenylalaninemia in Southern Europe, and form the basis for the establishment of phenotype-genotype correlations in Sicily and surrounding countries.

The forensic application of mtDNA typing requires large databases which are regionally well defined. To further this aim, we have typed mtDNA in a sample of 111 French and 106 Sicilians. The French were typed for both hypervariable segments (HVR1 and HVR2) of the mtDNA control region, whereas the Sicilians were only typed for HVR1, but in addition for the coding region RFLP markers for mtDNA groups H, I, J, K, L, M, T, U, V and X. In both samples, the predominant sequence type by far was the Cambridge reference sequence. Comparing HVR1 sequences, we found that the French sample was twice as diverse as the Sicilian sample as measured by sequence matches. A further set of sequence match comparisons including the French, Sicilian, and the published British mtDNA samples, demonstrate that sequence matching probabilities within samples differ by less than a factor of 2 from the matching probabilities between samples.

Angelman syndrome (AS) is a severe neurobehavioural disorder caused by failure of expression of the maternal copy of the imprinted domain located on 15q11-q13. There are different mechanisms leading to AS: maternal microdeletion, uniparental disomy, defects in a putative imprinting centre, mutations of the E3 ubiquitin protein ligase (UBE3A) gene. However, some of suspected cases of AS are still scored negative to all the latter mutations. Recently, it has been shown that a proportion of negative cases bear large deletions overlapping one or more exons of the UBE3A gene. These deletions are difficult to detect by conventional gene-scanning methods due to the masking effect by the non-deleted allele. In this study, we have used for the first time multiplex ligation-dependent probe amplification (MLPA) and comparative multiplex dosage analysis (CMDA) to search for large deletions affecting the UBE3A gene. Using this approach, we identified a novel causative deletion involving exon 8 in an affected sibling. Based on our results, we propose the use of MLPA as a fast, accurate and inexpensive test to detect large deletions in the UBE3A gene in a small but significant percentage of AS patients.