Long-term changes in hydrographic conditions in northern Adriatic and its relationship to hydrological and atmospheric processes

A very long data series (1921–2000) of hydrographic parameters (temperature, salinity and density) collected in surface and bottom layers at a station in the coastal zone in the northeastern Adriatic was analyzed. Seasonal and interannual variability of the three parameters is described on the basis of monthly and yearly averages. The seasonal cycles obtained were found to be typical for the northern Adriatic. Interannual analysis showed that there was no trend in temperature, salinity and density in the region during the interval analyzed. The long-term series of yearly means of hydrographic parameters were related to the long-term series of yearly means of several hydrological/atmospheric parameters using different time lags of between 0 and 4 years. These parameters are surface heat flux gained by insolation Qs computed for Trieste, precipitation P in Trieste, Po River discharge rate R and two atmospheric oscillation indexes, a Mediterranean Oscillation (MO) index and North Atlantic Oscillation (NAO) index. At zero time lag the interannual changes at the surface were found to be significantly related to changes in the Qs and NAO index (temperature) and R (salinity and density). At the same time lag the changes in the bottom were found to be related to the MO index (temperature, salinity and density). Additionally, bottom salinity and density were significantly related to R at a time lag of 1 year.<br><br> <b>Key words.</b> Oceanography: Physical (air-sea interactions; hydrography

Destructive M6.2 Petrinja Earthquake (Croatia) in 2020—Preliminary Multidisciplinary Research

On 28 December 2020, seismic activity in the wider Petrinja area strongly intensified after a period of relative seismological quiescence that had lasted more than 100 years (since the well-known M5.8 Kupa Valley earthquake of 1909, which is known based on the discovery of the Mohorovičić discontinuity). The day after the M5 foreshock, a destructive M6.2 mainshock occurred. Outcomes of preliminary seismological, geological and SAR image analyses indicate that the foreshocks, mainshock and aftershocks were generated due to the (re)activation of a complex fault system—the intersection of longitudinal NW–SE right-lateral and transverse NE–SW left-lateral faults along the transitional contact zone of the Dinarides and the Pannonian Basin. According to a survey of damage to buildings, approximately 15% of buildings were very heavily damaged or collapsed. Buildings of special or outstanding historical or cultural heritage significance mostly collapsed or became unserviceable. A preliminary analysis of the earthquake ground motion showed that in the epicentral area, the estimated peak ground acceleration PGA values for the bedrock ranged from 0.29 to 0.44 g. In the close Petrinja epicentral area that is characterized by the superficial deposits, significant ground failures were reported within local site effects. Based on that finding and building damage, we assume that the resulting peak ground acceleration (PGAsite) values were likely between 0.4 and 0.6 g depending on the local site characteristics and the distance from the epicentre

Cas3 is a limiting factor for CRISPR-Cas immunity in Escherichia coli cells lacking H-NS

Background: CRISPR-Cas systems provide adaptive immunity to mobile genetic elements in prokaryotes. In many bacteria, including E. coli, a specialized ribonucleoprotein complex called Cascade enacts immunity by “an interference reaction" between CRISPR encoded RNA (crRNA) and invader DNA sequences called “protospacers”. Cascade recognizes invader DNA via short “protospacer adjacent motif” (PAM) sequences and crRNA-DNA complementarity. This triggers degradation of invader DNA by Cas3 protein and in some circumstances stimulates capture of new invader DNA protospacers for incorporation into CRISPR as “spacers” by Cas1 and Cas2 proteins, thus enhancing immunity. Co-expression of Cascade, Cas3 and crRNA is effective at giving E. coli cells resistance to phage lysis, if a transcriptional repressor of Cascade and CRISPR, H-NS, is inactivated (Δhns). We present further genetic analyses of the regulation of CRISPR-Cas mediated phage resistance in Δhns E. coli cells. Results: We observed that E. coli Type I-E CRISPR-Cas mediated resistance to phage λ was strongly temperature dependent, when repeating previously published experimental procedures. Further genetic analyses highlighted the importance of culture conditions for controlling the extent of CRISPR immunity in E. coli. These data identified that expression levels of cas3 is an important limiting factor for successful resistance to phage. Significantly, we describe the new identification that cas3 is also under transcriptional control by H-NS but that this is exerted only in stationary phase cells. Conclusions: Regulation of cas3 is responsive to phase of growth, and to growth temperature in E. coli, impacting on the efficacy of CRISPR-Cas immunity in these experimental systems

DNA End Resection Controls the Balance between Homologous and Illegitimate Recombination in Escherichia coli

Even a partial loss of function of human RecQ helicase analogs causes adverse effects such as a cancer-prone Werner, Bloom or Rothmund-Thompson syndrome, whereas a complete RecQ deficiency in Escherichia coli is not deleterious for a cell. We show that this puzzling difference is due to different mechanisms of DNA double strand break (DSB) resection in E. coli and humans. Coupled helicase and RecA loading activities of RecBCD enzyme, which is found exclusively in bacteria, are shown to be responsible for channeling recombinogenic 3′ ending tails toward productive, homologous and away from nonproductive, aberrant recombination events. On the other hand, in recB1080/recB1067 mutants, lacking RecBCD’s RecA loading activity while preserving its helicase activity, DSB resection is mechanistically more alike that in eukaryotes (by its uncoupling from a recombinase polymerization step), and remarkably, the role of RecQ also becomes akin of its eukaryotic counterparts in a way of promoting homologous and suppressing illegitimate recombination. The sickly phenotype of recB1080 recQ mutant was further exacerbated by inactivation of an exonuclease I, which degrades the unwound 3′ tail. The respective recB1080 recQ xonA mutant showed poor viability, DNA repair and homologous recombination deficiency, and very increased illegitimate recombination. These findings demonstrate that the metabolism of the 3′ ending overhang is a decisive factor in tuning the balance of homologous and illegitimate recombination in E. coli, thus highlighting the importance of regulating DSB resection for preserving genome integrity. recB mutants used in this study, showing pronounced RecQ helicase and exonuclease I dependence, make up a suitable model system for studying mechanisms of DSB resection in bacteria. Also, these mutants might be useful for investigating functions of the conserved RecQ helicase family members, and congruently serve as a simpler, more defined model system for human oncogenesis

Long-term changes in hydrographic conditions in northern Adriatic and its relationship to hydrological and atmospheric processes

A very long data series (1921–2000) of hydrographic parameters (temperature, salinity and density) collected in surface and bottom layers at a station in the coastal zone in the northeastern Adriatic was analyzed. Seasonal and interannual variability of the three parameters is described on the basis of monthly and yearly averages. The seasonal cycles obtained were found to be typical for the northern Adriatic. Interannual analysis showed that there was no trend in temperature, salinity and density in the region during the interval analyzed. The long-term series of yearly means of hydrographic parameters were related to the long-term series of yearly means of several hydrological/atmospheric parameters using different time lags of between 0 and 4 years. These parameters are surface heat flux gained by insolation Qs computed for Trieste, precipitation P in Trieste, Po River discharge rate R and two atmospheric oscillation indexes, a Mediterranean Oscillation (MO) index and North Atlantic Oscillation (NAO) index. At zero time lag the interannual changes at the surface were found to be significantly related to changes in the Qs and NAO index (temperature) and R (salinity and density). At the same time lag the changes in the bottom were found to be related to the MO index (temperature, salinity and density). Additionally, bottom salinity and density were significantly related to R at a time lag of 1 year. Key words. Oceanography: Physical (air-sea interactions; hydrography

Cas1-Cas2 physically and functionally interacts with DnaK to modulate CRISPR Adaptation

Data Availability: The data underlying this article are available in the article and in its online supplementary material....BBSRC grant number BB/T006625-1 (ELB) and BB/T007168/1 (CJR); Croatian Science Foundation grant IP-2016-06-8861 (IIB)

INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing

Comprehensive characterisation of genome engineering technologies is relevant for their development and safe use in human gene therapy. Short-read based methods can overlook insertion events in repetitive regions. We develop INSERT-seq, a method that combines targeted amplification of integrated DNA, UMI-based correction of PCR bias and Oxford Nanopore long-read sequencing for robust analysis of DNA integration. The experimental pipeline improves the number of mappable insertions at repetitive regions by 4.8-7.3% and larger repeats are processed with a computational peak calling pipeline. INSERT-seq is a simple, cheap and robust method to quantitatively characterise DNA integration in diverse ex vivo and in vivo samples.We thank funding received from UPGRADE (European Union Horizon 2020, grant agreement No 825825), Fundación Ramón Areces (“Advanced gene editing technologies to restore LAMA2 on merosin-deficient congenital muscular dystrophy type 1A”), MdM projecte de recerca “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M)