Possibilities for increasing the efficiency of distribution centers: the case of company X

Darbo objektas. Paskirstymo centro veiklos efektyvumas. Darbo tikslas - įvertinti paskirstymo centrų veiklos efektyvumo didinimo galimybes „X“ įmonės atveju. Darbo uždaviniai: 1. Atskleisti paskirstymo centrų veiklos efektyvumo didinimo svarbą ir problemas. 2. Išanalizuoti paskirstymo centrų veiklos efektyvumo ir jo didinimo galimybes teoriniu aspektu. 3. Atlikti „X“ paskirstymo centro veiklos efektyvumo didinimo poreikio ir galimybių tyrimą. 4. Pagrįsti veiklos efektyvumo didinimo priemonių diegimo „X“ paskirstymo centre sprendimus. Darbo metodai: • mokslinės literatūros sisteminė loginė analizė; • kokybinis tyrimas - pusiau struktūruotas interviu; • daugiakriterinis vertinimas.Objectives: 1. Reveal the importance and problems of increasing the efficiency of distribution centers. 2. Analyze the efficiency of distribution centers and the possibilities of increasing it from a theoretical point of view. 3. Study of the need and possibilities for increasing the efficiency of the X distribution center. 4. Substantiate the decisions on the implementation of operational efficiency improvement measures in the X distribution center. Research methods: systematic logical analysis of scientific literature; qualitative research - semi-structured interview; multi-criteria evaluation. Research results: • in the first part of the work it was established that the problems of the distribution center of UAB X are losses caused by inefficient use of human resources, insufficient automation of warehouse operations processes. • an analysis of the scientific literature has shown that the traditional activity of a distribution center is to break down incoming goods into smaller parts and to collect consumer orders. • The benefits of the yard management system proposed to be installed in the X distribution center are based on the fact that it provides opportunities to see and effectively control the movement of arriving vehicles and their drivers in real time, as well as the progress of processing transport orders; allows local and external users, employees of other companies, to book arrival and loading time in the warehouse..Bioekonomikos plėtros fakultetasVerslo ir kaimo vystymosi tyrimų instituta

Building protein structure-specific rotamer libraries /

MOTIVATION: Identifying the probable positions of the protein side-chains is one of the protein modelling steps that can improve the prediction of protein-ligand and protein-protein interactions. Most of the strategies predicting the side-chain conformations use predetermined dihedral angle lists, also called rotamer libraries, that are usually generated from a subset of high-quality protein structures. Although these methods are fast to apply, they tend to average out geometries instead of taking into account the surrounding atoms and molecules and ignore structures not included in the selected subset. Such simplifications can result in inaccuracies when predicting possible side-chain atom positions. RESULTS: We propose an approach that takes into account both of these circumstances by scanning through sterically accessible side-chain conformations and generating dihedral angle libraries specific to the target proteins. The method avoids the drawbacks of lacking conformations due to unusual or rare protein structures and successfully suggests potential rotamers with average RMSD closer to the experimentally determined side-chain atom positions than other widely used rotamer libraries. AVAILABILITY AND IMPLEMENTATION: The technique is implemented in open-source software package rotag and available at GitHub: https://www.github.com/agrybauskas/rotag, under GNU Lesser General Public License

Domain organization of DNase from Thioalkalivibrio sp. provides insights into retention of activity in high salt environments

Our study indicates that DNA binding domains are common in many halophilic or halotolerant bacterial DNases and they are potential activators of enzymatic activity at high ionic strength. Usually, proteins adapt to high ionic strength by increasing the number of negatively charged residues on the surface. However, in DNases such adaptation would hinder the binding to negatively charged DNA, a step critical for catalysis. In our study we demonstrate how evolution has solved this dilemma by engaging the DNA binding domain. We propose a mechanism, which enables the enzyme activity at salt concentrations as high as 4 M of sodium chloride, based on collected experimental data and domain structure analysis of a secreted bacterial DNase from the extremely halotolerant bacterium Thioalkalivibrio sp. K90mix. The enzyme harbors two domains: an N-terminal domain, that exhibits DNase activity, and a C-terminal domain, comprising a duplicate DNA binding helix-hairpin-helix motif. Here we present experimental data demonstrating that the C-terminal domain is responsible for the enzyme’s resistance to high ionic strength

The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein /

Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15–30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprising only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here we show that Geobacter sulfurreducens short pAgo and the NAD$^+$-bound Sir2 protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD$^+$ depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD$^+$ depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD$^+$ to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids, underscoring the diversity of mechanisms of prokaryotic Agos