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Here, we report on a patient with a 625 kb duplication in Xp22.12, detected by array comparative genomic hybridization (CGH). The duplicated region contains only one gene, RPS6KA3, that results in partial duplication. The same duplication was present in his mother and his maternal uncle. This partial duplication inhibits the RPS6KA3 expression, mimicking the effect of loss-of-function mutations associated with Coffin-Lowry syndrome (CLS). The phenotype of the patient here presented is not fully evocative of this syndrome because he does not present some of the facial, digital and skeletal abnormalities that are considered the main diagnostic features of CLS. This case is one of the few examples where RPS6KA3 mutations are associated with a non-specific X-linked mental retardation.

22q11.2 is a region prone to chromosomal rearrangements due to the presence of eight large blocks of low-copy repeats (LCR22s). The 3 Mb 22q11.2 “typical deletion”, between LCR22-A and D, causes a fairly well-known clinical picture, while the effects of smaller CNVs harbored in this interval are still to be fully elucidated. Nested deletions, flanked by LCR22B-D, LCR22B-C, or LCR22C-D, are very rare and are collectively described as “central deletions”. The LCR22C-D deletion (CDdel) has never been separately analyzed. In this paper, we focused only on CDdel, evaluating its gene content and reviewing the literature and public databases in order to obtain new insights for the classification of this CNV. At first glance, CDdels are associated with a broad phenotypic spectrum, ranging from clinically normal to quite severe phenotypes. However, the frequency of specific clinical traits highlights that renal/urinary tract abnormalities, cardiac defects, and neurological/behavioral disorders are much more common in CDdel than in the general population. This frequency is too high to be fortuitous, indicating that CDdel is a predisposing factor for these phenotypic traits. Among the genes present in this interval, CRKL is an excellent candidate for cardiac and renal defects. Even if further data are necessary to confirm the role of CDdels, according to our review, this CNV fits into the class of ‘likely pathogenic’ CNVs.

Neurodevelopmental disorders (NDDs) are considered synaptopathies, as they are due to anomalies in neuronal connectivity during development. DLG2 is a gene involved insynaptic function; the phenotypic effect of itsalterations in NDDs has been underestimated since few cases have been thoroughly described.We report on eight patients with 11q14.1 imbalances involving DLG2, underlining its potential effects on clinical presentation and its contribution to NDD comorbidity by accurate neuropsychiatric data collection. DLG2 is a very large gene in 11q14.1, extending over 2.172 Mb, with alternative splicing that gives rise to numerous isoforms differentially expressed in brain tissues. A thorough bioinformatic analysis of the altered transcripts was conducted for each patient. The different expression profiles of the isoforms of this gene and their influence on the excitatory–inhibitory balance in crucial brain structures could contribute to the phenotypic variability related to DLG2 alterations. Further studies on patients would be helpful to enrich clinical and neurodevelopmental findings and elucidate the molecular mechanisms subtended to NDDs.

The NFIA (nuclear factor I/A) gene encodes for a transcription factor belonging to the nuclear factor I family and has key roles in various embryonic differentiation pathways. In humans, NFIA is the major contributor to the phenotypic traits of “Chromosome 1p32p31 deletion syndrome”. We report on two new cases with deletions involving NFIA without any other pathogenic protein-coding gene alterations. A cohort of 24 patients with NFIA haploinsufficiency as the sole anomaly was selected by reviewing the literature and public databases in order to analyze all clinical features reported and their relative frequencies. This process was useful because it provided an overall picture of the phenotypic outcome of NFIA haploinsufficiency and helped to define a cluster of phenotypic traits that can facilitate clinicians in identifying affected patients. NFIA haploinsufficiency can be suspected by a careful observation of the dysmorphisms (macrocephaly, craniofacial, and first-finger anomalies), and this potential diagnosis is strengthened by the presence of intellectual and developmental disabilities or other neurodevelopmental disorders. Further clues of NFIA haploinsufficiency can be provided by instrumental tests such as MRI and kidney urinary tract ultrasound and confirmed by genetic testing.

The NFIA (nuclear factor I/A) gene encodes for a transcription factor belonging to the nuclear factor I family and has key roles in various embryonic differentiation pathways. In humans, NFIA is the major contributor to the phenotypic traits of “Chromosome 1p32p31 deletion syndrome”. We report on two new cases with deletions involving NFIA without any other pathogenic protein-coding gene alterations. A cohort of 24 patients with NFIA haploinsufficiency as the sole anomaly was selected by reviewing the literature and public databases in order to analyze all clinical features reported and their relative frequencies. This process was useful because it provided an overall picture of the phenotypic outcome of NFIA haploinsufficiency and helped to define a cluster of phenotypic traits that can facilitate clinicians in identifying affected patients. NFIA haploinsufficiency can be suspected by a careful observation of the dysmorphisms (macrocephaly, craniofacial, and first-finger anomalies), and this potential diagnosis is strengthened by the presence of intellectual and developmental disabilities or other neurodevelopmental disorders. Further clues of NFIA haploinsufficiency can be provided by instrumental tests such as MRI and kidney urinary tract ultrasound and confirmed by genetic testing.

Neurodevelopmental disorders (NDDs) are considered synaptopathies, as they are due to anomalies in neuronal connectivity during development. DLG2 is a gene involved insynaptic function; the phenotypic effect of itsalterations in NDDs has been underestimated since few cases have been thoroughly described.We report on eight patients with 11q14.1 imbalances involving DLG2, underlining its potential effects on clinical presentation and its contribution to NDD comorbidity by accurate neuropsychiatric data collection. DLG2 is a very large gene in 11q14.1, extending over 2.172 Mb, with alternative splicing that gives rise to numerous isoforms differentially expressed in brain tissues. A thorough bioinformatic analysis of the altered transcripts was conducted for each patient. The different expression profiles of the isoforms of this gene and their influence on the excitatory–inhibitory balance in crucial brain structures could contribute to the phenotypic variability related to DLG2 alterations. Further studies on patients would be helpful to enrich clinical and neurodevelopmental findings and elucidate the molecular mechanisms subtended to NDDs.

Hydrogeological perturbations in response to earthquakes are widely described worldwide. In carbonate aquifers, a post-seismic discharge increase is often attributed to an increase of bulk permeability due to co-seismic fracturing and the attention on the role of faults to explain the diversion of groundwater is increasing. We focus on the reaction of carbonate hydrogeological basins to extensional seismicity, taking as an example the effects of the Central Italy 2016–2017 seismic sequence, on the Basal aquifer of the Sibillini Mountains area. Geo-structural, seismological and ground deformation data were collected and merged with artificial tracer tests results and with a 4-years discharge and geochemical monitoring campaign. The main NNW-directed groundwater flow was diverted to the west and a discharge deficit was observed at the foot-wall of the activated fault system with a relevant discharge increase, accompanied by geochemical variations, at the fault system hanging-wall. The observed variations are consistent with the combined action of a permeability increase along the activated fault systems, which modified the predominant pre-seismic along-strike regional flow, and with hydraulic conductivity increase due to fracturing, determining a fast aquifers emptying. We show that the prevailing mechanism depends on the aquifer systems position with respect to the activated faults.

Agricultural terraces are an important element of the Italian landscape. However, abandonment of agricultural areas and increase in the frequency of destructive rainfall events has made it mandatory to increase conservation efforts of terraces to reduce hydrological risks. This requires the development of new approaches capable of identifying and mapping failed or prone-to-fail terraces over large areas. The present work focuses on the development of a more cost-effective alternative, to help public administrators and private land owners to identify fragile areas that may be subject to failure due to the abandonment of terracing systems. We developed a simple field protocol to acquire quantitative measurements of the degree of damage—dry stone wall deformation—and establish a damage classification system. This new methodology is tested at two different sites in Tuscany, central Italy. The processing is based on existing DTMs derived from Airborne Laser Scanner (ALS) data and open source software. The main GIS modules adopted are flow accumulation and water discharge, processed with GRASS GIS. Results show that the damage degree and terrace wall deformation are correlated with flow accumulation even if other factors other than those analyzed can contribute to influence the instability of dry stone walls. These tools are useful for local land management and conservation efforts.

Several studies have been carried out to investigate soil compaction and rutting after logging vehicle traffic, based on time consuming and punctual field measurements. The objective of this study was to measure soil disturbances with two methods: (i) a new, image-based models derived by a structure-from-motion (SfM) photogrammetry approach; and (ii) a traditional soil sampling (bulk density and shear strength). Two trails were selected in a logging area (central Italy), one trafficked by a forwarder (FT) and one trafficked by a skidder (ST). Data collection was conducted before, during and after timber extraction. Image-based models derived by SfM photogrammetry was used to highlight the differences in the shape and distribution of the disturbances along ST and FT. Results showed that the physical parameters of soil significantly changed due to both FT and ST traffic. Machine passes increased bulk density (111% and 31% for FT and ST, respectively), penetration resistance (29% and 24% for FT and ST, respectively) and shear resistance (14% and 6% for FT and ST, respectively), whereas porosity decreased (46% and 9% for FT and ST, respectively). Significant differences between FT and ST were found when comparing ruts removal and bulges with SfM photogrammetry. After logging, FT clearly showed ruts and bulges, whereas in ST ruts and bulges were not visible, but soil displacement in the direction of extraction was evident and measurable. Nevertheless, although our result shows a larger soil disturbance caused by forwarders than skidders, it is not possible to draw any general conclusions about differences between the two machines. Data about the machine passes, or the wood volumes transported over each trial area were not available; therefore, any general conclusion is misleading. SfM photogrammetry give information not available via traditional methods, thus improving impact assessment.