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We obtained a dataset through beach and submarine topography surveys around Hujeoung coast in Uljin. We conducted the beach and submarine topography surveys using small vessels from July 8 to July 11, 2016. The surveying instruments used for the surveys were Shipborne Mobile LiDAR System and Multi-beam Echo Sounder (Kongsberg EM3001). The beach topography was observed up to about 6 m from the shoreline. The width of the beach is about 30 m to 40 m. In the southeast of the survey area, there is an exposed rock with a depth of about 20 m. The area around the rock has sandy sediments. Datasets of the Hujeong coast area can be used for continuous monitoring to development of coastal erosion control system.

Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1’s association with two large hook shaped proteins called SA (yeast: Scc3) and Nipbl (Scc2). The latter’s replacement by Pds5 recruits Wapl, which induces release from chromatin via a process requiring dissociation of Scc1’s N-terminal domain (NTD) from Smc3. If blocked by Esco (Eco)-mediated Smc3 acetylation, cohesin containing Pds5 merely maintains pre-existing loops, but a third fate occurs during DNA replication, when Pds5-containing cohesin associates with Sororin and forms structures that hold sister DNAs together. How Wapl induces and Sororin blocks release has hitherto remained mysterious. In the twenty years since their discovery, not a single testable hypothesis has been proposed as to their role. Here, AlphaFold 2 (AF) three-dimensional protein structure predictions lead us to propose formation of a quarternary complex between Wapl, SA, Pds5, and Scc1’s NTD, in which the latter is juxtaposed with (and subsequently sequestered by) a highly conserved cleft within Wapl’s C-terminal domain (CTD). AF also reveals how Scc1’s dissociation from Smc3 arises from a distortion of Smc3’s CC induced by engagement of SMC ATPase domains, how Esco acetyl transferases are recruited to Smc3 by Pds5, and how Sororin prevents release by binding to the Smc3/Scc1 interface. Our hypotheses explain the phenotypes of numerous existing mutations and are highly testable.

The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease.

Condensin is a Structural Maintenance of Chromosomes (SMC) complex needed for the compaction of DNA into chromatids during mitosis. Lengthwise DNA compaction by condensin is facilitated by ATPase-driven loop extrusion, a process that is believed to be the fundamental activity of most, if not all SMC complexes. In order to obtain molecular insights, we obtained cryo-EM structures of yeast condensin in the presence of a slowly-hydrolysable ATP analogue and linear, as well as circular DNAs. The DNAs were shown to be “clamped” between the engaged heterodimeric SMC ATPase heads and the Ycs4 subunit, in a manner similar to previously reported DNA-bound SMC complex structures. Ycgl, the other non-SMC subunit was only flexibly bound to the complex, while also binding DNA tightly, and often remaining at a distance from the head module. In the clamped state, the DNA is encircled, or topologically entrapped, by the kleisin Brnl and the two engaged head domains of Smc2 and Smc4, and this tripartite ring is closed at all interfaces, including at the neck of Smc2. We show that the neck gate opens upon head engagement in the absence of DNA, but it remains shut when DNA is present. Our work demonstrates that condensin and other SMC complexes go through similar conformations of the head modules during their ATPase cycle. In contrast, the behaviour of the Ycgl subunit in the condensin complex might indicate differences in the implementation of the extrusion reactions and our findings will constrain further mechanistic models of loop extrusion by SMC complexes.SIGNIFICANCE STATEMENTDNA needs to be compacted dramatically to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolysed. The DNA is clamped within a compartment that has been reported previously in other SMC complexes, including Rad50, cohesin and MukBEF. With the caveat of important differences that we also uncovered, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolysing ATP and translocating DNA.

The ClpP serine peptidase is a tetradecameric degradation machine involved in many physiological processes. It becomes a competent ATP-dependent protease with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause dysregulation and activation of ClpP without ATPases, and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed the structural details, conformational changes, and activation mechanism. Although product release by the side exit pores has been proposed, the detailed driving force for product release remains elusive. Here, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures revealed various conformational states at different pH conditions. To understand the conformational change for product release, we investigated the relationship between substrate hydrolysis and the pH lowering process. Our data, together with previous findings, provide insight into the molecular mechanism of product release by ClpP self-compartmentalizing protease.

Cohesin’s association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being ‘clamped’ by Scc2 and ATP-dependent engagement of cohesin’s Smc1 and Smc3 head domains. Scc2’s replacement by Pds5 abrogates cohesin’s ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1’s ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin’s coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1’s hinge that alters how Scc2 and Pds5 interact with Smc1’s hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin’s hinge, which in turn requires coiled coil folding.

Structural maintenance of chromosomes (SMC)-kleisin complexes organize chromosomal DNAs in all domains of life, where they have key roles in chromosome segregation, DNA repair and regulation of gene expression. They function through topological entrapment and active translocation of DNA, but the underlying conformational changes are largely unclear. Using structural biology, mass spectrometry and cross-linking, we investigated the architecture of two evolutionarily distant SMC-kleisin complexes: proteobacterial MukBEF and eukaryotic cohesin. We show that both contain a dynamic coiled-coil discontinuity, the elbow, near the middle of their arms that permits a folded conformation. Bending at the elbow brings into proximity the hinge dimerization domain and the head/kleisin module, situated at opposite ends of the arms. Our findings favor SMC activity models that include a large conformational change in the arms, such as a relative movement between DNA contact sites during DNA loading and translocation.

SUMMARYIn addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are “clamped” in a sub-compartment created by Scc2’s association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.

Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.

Generally, risk assessment for a ship collision can be performed by analyzing the trajectories of two ships as they get close to each other. A near-miss collision between ships is an undesired event that did not result in collision, but had a high risk of doing so. Due to the high frequency of these occurrences, many actual accident data samples can be obtained. In this paper, we extract various variables related to near-miss collisions from this data, such as Distance to Closest Point of Approach (DCPA), Time to Closest Point of Approach (TCPA) and Collision Avoidance Variance (CAV). To assess near-miss collision risk, logistic regression analysis is performed by categorizing encounter types based on ship trajectories collected over 4 months in coastal water areas.

The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae , and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined K M and k cat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.

Summary Sister chromatid cohesion is mediated by cohesin, whose Smc1, Smc3, and kleisin (Scc1) subunits form a ring structure that entraps sister DNAs. The ring is opened either by separase, which cleaves Scc1 during anaphase, or by a releasing activity involving Wapl, Scc3, and Pds5, which bind to Scc1 and open its interface with Smc3. We present crystal structures of Pds5 from the yeast L. thermotolerans in the presence and absence of the conserved Scc1 region that interacts with Pds5. Scc1 binds along the spine of the Pds5 HEAT repeat fold and is wedged between the spine and C-terminal hook of Pds5. We have isolated mutants that confirm the observed binding mode of Scc1 and verified their effect on cohesin by immunoprecipitation and calibrated ChIP-seq. The Pds5 structure also reveals architectural similarities to Scc3, the other large HEAT repeat protein of cohesin and, most likely, Scc2., Graphical Abstract, Highlights • The crystal structure of the cohesin subunit Pds5 was determined • The crystal structure of Pds5 in complex with Scc1 binding region was determined • Structure-based mutants in Pds5 and Scc1 were analyzed by coIP and ChIP-seq • Pds5 shows some similarity to Scc3, the other large HEAT repeat cohesin subunit, Cohesin entraps DNA in a ring, facilitating sister chromatid cohesion during mitosis and meiosis. Lee et al. describe the structure of the cohesin subunit Pds5 in complex with Scc1, cohesin’s kleisin, mutants disrupting the Pds5:Scc1 interaction, and structural similarity to another cohesin subunit, Scc3.

Recently, the e-Navigation is main flow of worldwide maritime communications. The eNavigation suggested by the International Maritime Organization (IMO) and International Association of Lighthouse Authorities (IALA) is about collecting/integrating/expressing /analyzing/exchanging the marine data between ships and the land in harmony through the electronic method for protecting marine environment, keeping safe navigation, and maintaining marine safety/security [2]. However, the e-Navigation is concentrated only the maritime service and a common data structure to share maritime information, so security considerations especially when ship starts to communicate other ships is insufficient. In this paper, we analyze the e-Navigation Maritime Service Portfolios (MSPs) and ship-to-ship information sharing protocol. We propose security requirements of MSPs and secure ship-to-ship information sharing scheme to provide reliable communication between ships based on the analysis results. Our proposed scheme has 3 steps to authenticate each other using the each ship’s Maritime Mobile Sevice Identify (MMSI) is a unique key of each ship and increases the security of reliable ship-to-ship communication.

SummaryIn addition to sharing with condensin an ability to organize DNA into chromatids, cohesin regulates enhancer-promoter interactions and confers sister chromatid cohesion. Association with chromosomes is regulated by hook-shaped HEAT repeat proteins that Associate With its Kleisin (Scc1) subunit (HAWKs), namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently displaces Pds5 during loading. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesin’s ATPase activity, loading, and translocation while Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesin’s initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2’s association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states, one with Pds5 bound to Scc1 that is not able to hydrolyse ATP efficiently but is capable of release from chromosomes and another in which Scc2, transiently replacing Pds5, stimulates the ATP hydrolysis necessary for loading and translocation away from loading sites.

In this paper, we provide a mechanism to be able to save time and human resources to predict the time of occurrence of accidents at sea this time of the incident are not clear and to extract the suspected vessel-related accidents at sea. The proposed mechanism, it save such amount of data and time to trajectory extraction by managing separate the control area in a grid pattern, and is characterized as possible through trajectory analysis for a particular area. It also can be reduced 30 times faster than existing marine accident analysis time using the playback function in VTS operating system, so it is effective in saving human resource and time.

In most sea surveillance radars based on non-coherent integration, the scan integration which improves signal to noise ratio and mitigates unwanted echo with a small correlation time such as sea clutter is widely used. The problems of the conventional scan integration are: (a) the target trail is generated through integrating prior scan and current scan; (b) it is difficult to detect a small and fast moving target because of the attenuated small target echo caused by scan integration. In this paper, the conventional scan integration algorithm is analyzed in order to overcome the above problems, and then a simple and efficient scan correlation algorithm is proposed to remove the target trail. The proposed scan correlation algorithm uses the difference the current and the prior CFAR processed scan video. Compared to the conventional scan correlation algorithm, the proposed method is very simple and efficiently removes the target trail. The computer simulation results show that the proposed algorithm can extract a fast moving target without a target trail.

Despite of modern navigation devices, there are problems in navigation of vessels in waterways due to the geographical structures, disturbances in water, dynamic nature, and heavily environmental influenced sea traffic. Even though all vessels are equipped with modern navigation devices, the accidents are reported caused by various reasons and mainly by human factor according to investigation. We propose an effective and efficient composition collision risk calculation method for finding the collision probability and avoiding the collision between ships in possible collision situations. The proposed composition collision risk calculation method at ship’s position using combination of fuzzy and fuzzy comprehensive evaluation methods. The algorithm is straightforward to implement and is shown to be effective in automatic ship handling for ships involved in complex navigation situations. Experiments are carried out with indigenous data and the results show the effectiveness of the proposed approach.

International Association of Lighthouse Authorities (IALA) is developing the standard intersystem VTS exchange format (IVEF) protocol for exchange of navigation and vessel information between VTS systems and between VTS and vessels. VTS (vessel traffic system) is an important marine traffic monitoring system which is designed to improve the safety and efficiency of navigation and the protection of the marine environment. And the demand of Inter-VTS networking has been increased for realization of e-Navigation as shore side collaboration for maritime safety. And IVEF (inter-VTS data exchange format) for inter-VTS network has become a hot research topic of VTS system. Currently, the IVEF developed by the International Association of Lighthouse Authorities (IALA) does not include any highly trusted certification technology for the connectors. The output of standardization is distributed as the IALA recommendation V-145, and the protocol is implemented with an open source. The IVEF open source, however, is the code used to check the functions of standard protocols. It is too slow to be used in the field and requires a large memory. And the vessel traffic information requires high security since it is highly protected by the countries. Therefore, this paper suggests the authentication protocol to increase the security of the VTS systems using the main certification server and IVEF.

The forthcoming Internet of Things - an intelligent collaboration of resource-limited static/mobile devices that are embedded in the daily lives of users - poses new challenges to security and end-user privacy. One of the most challenging problems is how to thwart replica attacks. Once a device is captured physically by an attacker or contaminated by malicious code, it can be reprogrammed and the secret information inside can be duplicated into a large number of replicas that maliciously occupy the network and collect users private information without authorisation. In this study, the authors focus on studying the detection of replicas in mobile applications; which can consist of resource-limited static devices attached to mobile entities. Most existing solutions for detecting replicas have been designed for static devices, and cannot be immediately applied to mobile devices because of their unique properties, in particular, their node mobility. The authors present two efficient methods for detecting replicas in mobile devices. Through performance evaluations, they find that the proposed methods provide highly accurate replica detection with nearly zero detection errors. Furthermore, the distributed and cooperative strategy of the methods significantly reduces the energy required to detect replicas while providing faster replica detection than the existing solutions.

Vessel traffic system uses multiple sea surveillance radars as a primary sensor to obtain maritime traffic information like as ship's position, speed, course. The systematic errors such as the range bias and the azimuth bias of the two-dimensional radar system can significantly degrade the accuracy of the radar image and target tracking information. Therefore, the systematic errors of the radar system should be corrected precisely in order to provide the accurate target information in the vessel traffic system. In this paper, it is proposed that the method compensates the range bias and the azimuth bias using AtoN information installed at VTS coverage. The radar measurement residual error model is derived from the standard error model of two-dimensional radar measurements and the position information of AtoN, and then the linear Kalman filter is designed for estimation of the systematic errors of the radar system. The proposed method is validated via Monte-Carlo runs. Also, the convergence characteristics of the designed filter and the accuracy of the systematic error estimates according to the number of AtoN information are analyzed.

Recently, researches of technology and standardization for maritime safety are proceeding internationally. In particular, some technologies and strategies for e-Navigation have been developed and the necessity of development of next generation VTS (Vessel Traffic Service) has been raised in Korea. In order to construct user oriented VTS system for domestic environment, VTS operators are asked for their requirements related to developing VTS and the opinions should be reflected in the VTS. So in this paper, we collect the requirements from fifteen VTS centers in the country and we also analyze them. Furthermore, we propose an ASM (Application Specific Messages) service, which was not supported by current VTS, and we verify the proposed ASM through AIS (Automatic Identification System) system and simulation terminal for maritime safety.

Due to brisk industrial growth, the marine traffic has become an imperative subject in the open sea nowadays. The crew inside the vehicle traffic service (VTS) centre is facing challenging issues on account of continuous growth in vessel number. Currently, most of VTS centers' are using the ARPA RADAR based conventional vehicle traffic management system and VTS staff has to carry out most of the things manually to guide the ship's captain properly. Therefore, there is a strong impetus in the field of ocean engineering to develop a smart system which can take the data from RADAR and autonomously manipulate it, to calculate the degree of collision risk among all vessels from the VTS centre. Later on, the traffic management officer utilizes this information for intelligent decision making. In the past, several researchers have addressed this issue to facilities the VTS crew and captain of the ship but mostly, their research work was for academic purposes and could not get popularity because of extra manual workload. Our proposed vessel collision risk assessment system is an intelligent solution which is based on fuzzy inference system and has the ability to solve the said issues. We calculated the DCPA, TCPA, bearing and VCD among all vessels ships from the VTS centre by using conventional marine equipments and exploited the extracted information to calculate and display the degree of collision risk among all vessels. Furthermore, we developed the RADAR filtration algorithm which helps the VTS officer to gauge out the degree of collision risk around a particular ship. To authenticate the validity and to monitor the performance efficiency, we developed RADAR operated intelligent software which directly gets the required data from RADAR and displays the vessels list based on their degree of collision severity. The laboratory experiments confirm the validity of the proposed system.

In order to provide for the safe and expeditious passage of maritime traffic in congested waters, every country establishes, operates, and maintains Vessel Traffic Services where needed. In larger areas, a VTS will generally require a communication system to enable the vessel traffic center and the participating vessels to exchange information. There are some kinds of commercial VTS. Generally, these consists of several systems which have its own role such as operating system, video extracting and tracking system, warning and integration system, VTS logging and replaying system and so on. These are connected each other directly. In this paper, we introduce the centralized VTS which is separated by VTS Gateway System between VTS Operating System and the other subsystems. In case of VGWS, three kinds of messages are considered in the message arrival process. First is check in/check out messages which are basic as gateway. Second is VTS operating system supporting message which is always applied to all VTS operating system including VTOS user login, VTOS user environment configuration info setting and common info for VTS system and so on. Last is compulsory message transmission for VTOS logging and playback. The centralized VTS running tests show that the message processing delay of VGWS is acceptable compared to the predefined delay metric for VGWS performance.

Recent malicious attempts in Cyber space are intended to emerge national threats such as Suxnet as well as to get financial benefits through a large pool of comprised botnets. The evolved botnets use the Domain Name System(DNS) to communicate with the C&C server and zombies. DNS is one of the core and most important components of the Internet and DNS traffic are continually increased by the popular wireless Internet service. On the other hand, domain names are popular for malicious use. This paper studies on DNS-based cyber threats domain detection by data classification based on supervised learning. Furthermore, the developed cyber threats domain detection system using DNS traffic analysis provides collection, analysis, and normal/abnormal domain classification of huge amounts of DNS data.