Insects and packaging — A review

This paper reviews the interactions of insects with food packaging, and measures which may be taken to limit damage.     

DNA packaging in bacteriophage: is twist important?

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces.     

Collagen formation — observations on its intracellular packaging and transport

Summary Odontoblasts, osteoblasts and fibroblasts of young rats were examined in the electron microscope after staining thin sections either with lead citrate alone or with uranyl acetate prior to lead citrate.With lead citrate alone, collagen fibrils in the extracellular matrix stand out as lucent structures against a moderately electron dense background. Within the cells, lucency is restricted to certain dilated portions of the Golgi saccules as well as to the secretory granules located nearby and in the secretory pole of the cells. The lucency present in these compartments may be attributed to fibrils that are similar to the lucent collagen fibrils in the extracellular matrix. Other cellular compartments, e.g. the rough ER, do not display lucency.When preparations are stained with uranyl acetate prior to lead citrate, lucency is observed neither in the matrix nor in the cells. In the matrix, collagen fibrils are easily identifiable by their cross banded pattern. In the odontoblasts, dilated portions of Golgi saccules between the outer and inner face contain filaments aligned in parallel that are approximately 3 000 Å in length. In saccules on the inner face filament aggregates are present, some of them exhibiting a cross banding pattern. In secretory granules, however, the contents appear rather homogeneous.It is suggested that filament aggregates of collagen can assemble in the Golgi apparatus from filamentous units. These are transported through the cell by way of secretion granules and are discharged to the extracellular matrix by exocytosis.This investigation was supported by grants of the Medical Research Council of Canada. The author wishes to express appreciation to Dr. C. P. Leblond for his guidance in the course of this work.     

Role of φ29 connector channel loops in late-stage DNA packaging

Double-stranded DNA bacteriophages and their eukaryotic virus counterparts have 12-fold head-tail connector assemblages embedded at a unique capsid vertex. This vertex is the site of assembly of the DNA packaging motor, and the connector has a central channel through which viral DNA passes during genome packaging and subsequent host infection. Crystal structures of connectors from different phages reveal either disordered residues or structured loops that project into the connector channel. Given the proximity to the translocating DNA substrate, these loops have been proposed to play a role in DNA packaging. Previous models have proposed structural motions in either the packaging ATPase or the connector channel loops as the driving force that translocates the DNA into the prohead. Here, we mutate the channel loops of the Bacillus subtilis bacteriophage φ29 connector and show that these loops have no active role in translocation of DNA. Instead, they appear to have an essential function near the end of packaging, acting to retain the packaged DNA in the head in preparation for motor detachment and subsequent tail assembly and virion completion.     

Compostable packaging materials – test methods and limit values for biodegradation

In order to classify packaging materials as capable of organic recovery according to the packaging regulation of the European Union, the intended materials must be tested for their compostability. An important prerequisite is the determination of biodegradability by standardized test methods. Details of the intended tests are not comprehensible without further knowledge of the problems of biodegradation testing. The test methods and the limit values used to evaluate the biodegradation results are presented and discussed against the background of established test methods and limit values for chemicals. Furthermore the problem of ecotoxicity tests in connection with compost quality is discussed and an overview of European test laboratories is given. Received: 27 August 1998 / Received revision: 4 November 1998 / Accepted: 7 November 1998     

In vivo studies of genomic packaging in the dsRNA bacteriophage Φ8

Background  

Φ8 is a bacteriophage containing a genome of three segments of double-stranded RNA inside a polyhedral capsid enveloped in a lipid-containing membrane. Plus strand RNA binds and is packaged by empty procapsids. Whereas Φ6, another member of the Cystoviridae, shows high stringency, serial dependence and precision in its genomic packaging in vitro and in vivo, Φ8 packaging is more flexible. Unique sequences (pac) near the 5' ends of plus strands are necessary and sufficient for Φ6 genomic packaging and the RNA binding sites are located on P1, the major structural protein of the procapsid.     

Colorful virus-like particles: fluorescent protein packaging by the Qβ capsid

Qβ virus-like particles encapsulating multiple copies of fluorescent proteins were generated in high yields using a modular system enhanced by specific engineered RNA--protein interactions. The resulting particles were structurally indistinguishable from recombinant Qβ alone. The encapsidated proteins were nearly identical in photochemical properties to monomeric analogues, were more stable toward thermal degradation, and were protected from proteolytic cleavage. Residues on the outer capsid surface were chemically derivatized by acylation and azide--alkyne cycloaddition without affecting the fluorescence properties of the packaged proteins. A high-affinity carbohydrate-based ligand of the CD22 receptor was thereby attached, and specific cell labeling by the particles was successfully detected by flow cytometry and confocal laser microscopy.     

Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates

The initial assembly product of bacteriophage ?6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state.     

Structure of the RNA claw of the DNA packaging motor of bacteriophage ?29

Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage ϕ29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33–35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.     

Role of the CCA bulge of prohead RNA of bacteriophage ø29 in DNA packaging

The oligomeric ring of prohead RNA (pRNA) is an essential component of the ATP-driven DNA packaging motor of bacteriophage ?29. The A-helix of pRNA binds the DNA translocating ATPase gp16 (gene product 16) and the CCA bulge in this helix is essential for DNA packaging in vitro. Mutation of the bulge by base substitution or deletion showed that the size of the bulge, rather than its sequence, is primary in DNA packaging activity. Proheads reconstituted with CCA bulge mutant pRNAs bound the packaging ATPase gp16 and the packaging substrate DNA-gp3, although DNA translocation was not detected with several mutants. Prohead/bulge-mutant pRNA complexes with low packaging activity had a higher rate of ATP hydrolysis per base pair of DNA packaged than proheads with wild-type pRNA. Cryoelectron microscopy three-dimensional reconstruction of proheads reconstituted with a CCA deletion pRNA showed that the protruding pRNA spokes of the motor occupy a different position relative to the head when compared to particles with wild-type pRNA. Therefore, the CCA bulge seems to dictate the orientation of the pRNA spokes. The conformational changes observed for this mutant pRNA may affect gp16 conformation and/or subsequent ATPase-DNA interaction and, consequently, explain the decreased packaging activity observed for CCA mutants.     

LCA studies comparing beverage cartons and alternative packaging: can overall conclusions be drawn?

Background and purpose

Numerous life cycle assessments (LCAs) have been conducted on the environmental impacts of beverage packaging systems. With such a potentially rich source of knowledge available, it seemed worthwhile to conduct a comprehensive evaluation of those existing studies. This paper describes a recent ‘meta analysis’, whose goal it was to provide a structured overview of LCAs on beverage cartons and other packaging systems from past years in order to answer two key questions: (1) Is it possible to draw general conclusions regarding the environmental performance (in terms of strengths and weaknesses) of beverage cartons in comparison to alternative packaging systems from these existing LCAs? (2) If certain trends arise across these LCA studies regarding the environmental performance of beverage cartons compared to other packaging systems for beverages, what can be said on their validity and limitations?

Methods

The meta analysis presented covers 22 LCA studies, all of which fulfil three criteria: (1) full life cycle approach, (2) beverage carton must be among the products evaluated in study, and (3) comparative approach. Each of these studies was categorised either as a core study (if focussed on Europe, conducted in 2000 or later, and peer reviewed) or as a basic study. Next to providing detailed comparisons of the analysed studies, the full report on the meta analysis was designed to allow a quick understanding of their main characteristics (or ‘profiles’). Similarities and differences were highlighted both in terms of results and the applied methodologies (e.g., key settings) and the validity and limitations of the findings were stated. Additionally, further environment-related topics of special interest to stakeholders in the beverage packaging industry were addressed.

Results, discussion, and conclusions

For certain environmental impact indicators/inventory categories, the LCA studies covered in this meta analysis indicate general trends regarding the performance of beverage cartons versus alternative packaging systems. For climate change, cumulated energy demand/fossil resource consumption, and acidification, all regarded by the majority of all studies, beverage cartons mostly have the most favourable results, while in terms of land use for forestry, they clearly require the largest area. For summer smog and terrestrial eutrophication, the result ‘pattern’ points towards a favourable picture for beverage cartons; however, fewer LCA studies provide results for these impact categories. For other environmental aspects, where the results of the analysed studies vary strongly, no clear pattern can be made out. Several aspects were covered in too few LCA studies in order for an overall trend or lack thereof to become visible, and still others—which in part have been receiving increased attention in the past years—are not addressed in any of the analysed core or basic studies.

     

Distinct stages in the recognition,sorting, and packaging of proTGFα into COPII-coated transport vesicles

In addition to its role in forming vesicles from the endoplasmic reticulum (ER), the coat protein complex II (COPII) is also responsible for selecting specific cargo proteins to be packaged into COPII transport vesicles. Comparison of COPII vesicle formation in mammalian systems and in yeast suggested that the former uses more elaborate mechanisms for cargo recognition, presumably to cope with a significantly expanded repertoire of cargo that transits the secretory pathway. Using proTGFα, the transmembrane precursor of transforming growth factor α (TGFα), as a model cargo protein, we demonstrate in cell-free assays that at least one auxiliary cytosolic factor is specifically required for the efficient packaging of proTGFα into COPII vesicles. Using a knockout HeLa cell line generated by CRISPR/Cas9, we provide functional evidence showing that a transmembrane protein, Cornichon-1 (CNIH), acts as a cargo receptor of proTGFα. We show that both CNIH and the auxiliary cytosolic factor(s) are required for efficient recruitment of proTGFα to the COPII coat in vitro. Moreover, we provide evidence that the recruitment of cargo protein by the COPII coat precedes and may be distinct from subsequent cargo packaging into COPII vesicles.     

Uptake of bacteriophage λ DNA in Escherichia coli by electroporation: An alternative to in vitro packaging

Summary By using a high field strength DC pulse of 15 kV/cm and a pulse duration of 5 ms for the transfection of E. coli by bacteriophage DNA, we obtained efficiencies of 1.1 × 10⁶ (pfu/g bacteriophage , DNA). This represents a 100-fold improvement over the traditional CaCl₂/heat shock method and is a viable alternative to the more costly in vitro packaging of recombinant bacteriophage DNA for the production of cDNA and genomic libraries.     

3’-UTR sequence of Macrobrachium rosenbergii extra small virus(XSV) is important for viral RNA packaging

正Dear Editor,The packaging of viral genomic RNA into virus par-ticles is a critical step for virus maturation.This stepincludes the recognition and interaction between the nu-cleocapsid protein and viral RNA.The necessity of viralRNA packaging signals has been described for manyRNA viruses(Cologna R,et al.,2000;Narayanan K,et al.,2001;Tchatalbachev S,et al.,2001).Occasionalpackaging of nongenomic viral RNAs and cellular RNAs     

The environmental impact of packaging in food supply chains—does life cycle assessment of food provide the full picture?

Purpose

Due to the urgency and the magnitude of the environmental problems caused by food supply chains, it is important that the recommendations for packaging improvements given in life cycle assessment (LCA) studies of food rest on a balanced consideration of all relevant environmental impacts of packaging. The purpose of this article is to analyse the extent to which food LCAs include the indirect environmental impact of packaging in parallel to its direct impact. While the direct environmental impact of food packaging is the impact caused by packaging materials’ production and end-of-life, its indirect environmental impact is caused by its influence on the food product’s life cycle, e.g. by its influence on food waste and on logistical efficiency.

Methods

The article presents a review of 32 food LCAs published in peer-reviewed scientific journals over the last decade. The steps of the food product’s life cycle that contribute to the direct and indirect environmental impacts of packaging provide the overall structure of the analytical framework used for the review. Three aspects in the selected food LCAs were analysed: (1) the defined scope of the LCAs, (2) the sensitivity and/or scenario analyses and (3) the conclusions and recommendations.

Results and discussion

While in packaging LCA literature, there is a trend towards a more systematic consideration of the indirect environmental impact of packaging, it is unclear how food LCAs handle this aspect. The results of the review show that the choices regarding scope and sensitivities/scenarios made in food LCAs and their conclusions about packaging focus on the direct environmental impact of packaging. While it is clear that not all food LCAs need to analyse packaging in detail, this article identifies opportunities to increase the validity of packaging-related conclusions in food LCAs and provides specific recommendations for packaging-related food LCA methodology.

Conclusions

Overall, we conclude that the indirect environmental impact of packaging is insufficiently considered in current food LCA practice. Based on these results, this article calls for a more systematic consideration of the indirect environmental impact of packaging in future food LCAs. In addition, it identifies a need for more packaging research that can provide the empirical data that many food LCA practitioners currently lack. In particular, LCA practitioners would benefit if there were more knowledge and data available about the influence of certain packaging characteristics (e.g. shape, weight and type of material) on consumer behaviour.

     

Biological and biochemical properties of the small viral RNA(pRNA) essential for the packaging of the dsDNA of phage ø29

The genome of the lineal double-stranded DNA viruses of both prokaryotes and eukaryotes is packaged into a preformed procapsid during maturation. Common features exist in this step of the viral life cycle. Bacteriophage ø29 is an ideal model in this study because its DNA can be efficiently packaged in vitro with all components overproduced and purified. An exciting aspect is the discovery that a small viral RNA (pRNA) encoded by ø29 has a novel and essential role in viral DNA packaging. This pRNA is not a structural component of the mature virion, nor is it required for the assembly of the procapsid. The discovery of pRNA as a non-protein participant in viral DNA packaging extends previously demonstrated RNA functions.     

Construction and packaging of pseudotype retrovirus containing human N—ras cDNA antisense sequence and its biological effects on human hepatoma cells

N-ras is one of the transforming genes in human hepatic cancer cells.It has been found that N-ras was overexpressed at the mRNA and protein level in hepatoma cells.In order to explore the biological roles of N-ras in human hepatic carcinogenesis and the potential application in control of cancer cell growth,a preudotype retrovirus containing antisense sequence of human N-ras was constructed and packaged.A recombinant retrovirus vector containing antisense or sense sequences of N-ras cDNA was constructed by pZIP-NeoSV(X)1.The pseudotype virus was packaged ang rescued by transfection and infection in PA317 and ψ 2 helper cells.It has been demonstrated that the pseudotype retrovirus containing antisense N-ras sequence did inhibit the growth of human PLC/PRF/5 hepatoma cells accompanied with inhibition of p21 expression,while the retrovirus containing sense sequence had none.The pseudotype virus had no effect on human diploid fibroblasts.     

An analytical framework for social life cycle impact assessment—part 2: case study of labor impacts in an IC packaging company

Purpose

The pressure on brand firms in the electronics industry to improve the labor conditions of their workers in their global production networks is increasing. Given the significance of mitigating the impacts of production on labor, this study used the new development method of social life cycle impact assessment (SLCIA) for conducting labor impact assessment. An illustrative example in an integrated circuit (IC) packaging company is presented to demonstrate the assessment of the impacts and the identification of the potential for improvement of labor practices among three factories.

Methods

SLCIA method was proposed based on the UNEP/SETAC Guidelines that were reviewed in our previous work, Part 1 (in a previous article): Methodology. The proposed method was used to assess the impacts of operations on labor in the three factories of an IC packaging company. Nineteen indicators of labor–stakeholders were used to collect data from factories and organizations in 2012. The obtained values from these three factories were translated into social impact scores that ranged from 1 to 5. The score of each indicator was multiplied by the weights of each indicator, and a final score of labor situations was generated to identify the hotspots of labor impacts and to identify the factory with better labor performance.

Results and discussion

The main goal of this study is to demonstrate the effectiveness of our proposed SLCIA method in assessing the labor impacts in the electronics industry. Among three factories of IC packaging, factory C was ranked as having the lowest social impact on labor with a higher performance, followed by factories B and A. In addition, the results show that four indicators, “lacking labor union,” “did not hire a sufficient number of disabled employees,” “overtime work that exceeded the legal limit,” and “excessive number of dispatched workers,” were recognized as the main social impacts on labor in IC packaging production.

Conclusions

The SLCA technique was used to assess the impacts of the production processes of three IC packaging factories on the labor conditions of their factory workers. The proposed method shed light on the significant impacts of such processes. The proposed model demonstrated its potential advantage by systematically and effectively identifying the labor impact hotspots, which could assist managers in devising strategies that could improve the labor situations within their organizations.