Interactive Visualization and Industrial Ecology: Applications,Challenges, and Opportunities

The emergence of increasingly complex data in industrial ecology (IE) has caused scholarly interest in interactive visualization (IV). IV allows users to interact with data, aiding in processing and interpreting complex datasets, processes, and simulations. Consequently, IV can help IE practitioners communicate the complexities of their methods and results, shed light on the underlying research assumptions, and enable more transparent monitoring of data quality and error. This can significantly increase the reach and impact of research, promote transparency, reproducibility, and open science, as well as improve the clarity and presentation of IE research. A review of current IV applications reveals that, while data exploration has received some attention among IE practitioners, IV applications in scientific communication are clearly lacking. With the help of a working example, we explore the value of IV, discuss its operationalization, and highlight challenges that the IE community must face during IV uptake. Such challenges include technical and knowledge limitations, limits on user interaction, and implementation strategies. With these challenges in mind, we outline key aspects needed to lift the IE field to the forefront of scientific communication in the coming years. Among these, we draft the basic principles of a “Hub for Interactive Visualization in Industrial Ecology” (HIVE), a point of encounter where IE practitioners could find an array of data visualization tools that are geared toward IE datasets. IV is here to stay, and its inceptive stage presents many opportunities to IE practitioners to shape its operationalization and benefit from early adoption.     

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network

Background  

Localized network patterns are assumed to represent an optimal design principle in different biological networks. A widely used method for identifying functional components in biological networks is looking for network motifs – over-represented network patterns. A number of recent studies have undermined the claim that these over-represented patterns are indicative of optimal design principles and question whether localized network patterns are indeed of functional significance. This paper examines the functional significance of regulatory network patterns via their biological annotation and evolutionary conservation.     

Analysis of unassisted translesion replication by the DNA polymerase III holoenzyme

DNA damage-induced mutations are formed when damaged nucleotides present in single-stranded DNA are replicated. We have developed a new method for the preparation of gapped plasmids containing site-specific damaged nucleotides, as model DNA substrates for translesion replication. Using these substrates, we show that the DNA polymerase III holoenzyme from Escherichia coli can bypass a synthetic abasic site analogue with high efficiency (30% bypass in 16 min), unassisted by other proteins. The theta and tau subunits of the polymerase were not essential for bypass. No bypass was observed when the enzyme was assayed on a synthetic 60-mer oligonucleotide carrying the same lesion, and bypass on a linear gapped plasmid was 3-4-fold slower than on a circular gapped plasmid. There was no difference in the bypass when standing-start and running-start replication were compared. A comparison of translesion replication by DNA polymerase I, DNA polymerase II, the DNA polymerase III core, and the DNA polymerase III holoenzyme clearly showed that the DNA polymerase III holoenzyme was by far the most effective in performing translesion replication. This was not only due to the high processivity of the pol III holoenzyme, because increasing the processivity of pol II by adding the gamma complex and beta subunit, did not increase bypass. These results support the model that SOS regulation was imposed on a fundamentally constitutive translesion replication reaction to achieve tight control of mutagenesis.     

DNA binding by yeast Mlh1 and Pms1: implications for DNA mismatch repair

The yeast Mlh1–Pms1 heterodimer required for mismatch repair (MMR) binds to DNA. Here we map DNA binding to N-terminal fragments of Mlh1 and Pms1. We demonstrate that Mlh1 and Pms1 N-terminal domains (NTDs) independently bind to double-stranded and single-stranded DNA, in the absence of dimerization and with different affinities. Full-length Mlh1p alone, which can homodimerize, also binds to DNA. Substituting conserved positively charged amino acids in Mlh1 produces mutator phenotypes in a haploid yeast strain characteristic of reduced MMR. These substitutions strongly reduce DNA binding by the Mlh1 NTD and, to a lesser extent, they also reduce DNA binding by full-length Mlh1 and the Mlh1–Pms1 heterodimer. Replacement of a homologous Pms1 residue has a much smaller effect on mutation rate and does not reduce DNA binding. The results demonstrate that NTDs of yeast Mlh1 and Pms1 contain independent DNA binding sites and they suggest that the C-terminal region of Mlh1p may also contribute to DNA binding. The differential mutator effects and binding properties observed here further suggest that Mlh1 and Pms1 differ in their interactions with DNA. Finally, the results are consistent with the hypothesis that DNA binding by Mlh1 is important for MMR.     

An improved GC/MS-based procedure for the quantitation of the isoprostane 15-F2t-IsoP in rat plasma

This article describes a procedure for the quantitation of the isoprostane 15-F_2t-IsoP (9a,11a,15S-trihydroxy-(8b)-prosta-5Z,13E-dien-1-oic acid [CAS#27415-26-5] formerly known as 8-epi-PGF_2a or 8-iso-PGF_2a, and also as iPF_2a-III). We have combined features from several earlier methods for 15-F_2t-IsoP and prostaglandins, and identified and modified those steps that may lead to poor recoveries. The resulting protocol is precise and reliable, and was validated by a blind time-course study of plasma levels in rats treated with 120 and 1200 mg CCl₄/kg body weight. Plasma levels of 15-F_2t-IsoP, as measured according to the procedure described above, are good indicators of acute oxidative stress as induced by CCl₄. The precision of the measurements allows detection of elevated plasma 15-F_2t-IsoP levels as long as 16 h after an acute exposure of 120 mg CCl₄/kg body weight, and 2 h after an exposure of 1 mg CCl₄/kg body weight. The results of this low-dose, pilot study suggest that this method has sufficient analytical precision to allow the detection of the small changes in plasma isoprostane levels, which result from chronic and/or lower-level exposures to agents causing oxidative stress.     

Nipple-areola reconstruction: satisfaction and clinical determinants

After performing a chart review, the authors identified 120 patients who underwent breast cancer-related reconstruction. All charts were evaluated with regard to breast mound reconstruction type, nipple-areola reconstruction type, the interval between breast mound and nipple-areola reconstruction, the number of procedures needed to achieve nipple-areola reconstruction, patient history of radiation therapy, and complications. A questionnaire was then developed and mailed to all of the patients who underwent both breast mound and nipple/areola reconstruction (n = 105) to evaluate their level of satisfaction. Of the 43 patients who returned the questionnaire, 41 completed all portions correctly. The questionnaire evaluated patient satisfaction with breast mound reconstruction; patient satisfaction with nipple-areola reconstruction; what the patient disliked most about the nipple-areola reconstruction; and whether or not the patient would choose to have breast reconstruction again. Several parameters were then tested statistically against the reported patient satisfaction.A review of all patients who underwent breast reconstruction revealed that their breast mound reconstructions were done using either a TRAM flap (59 percent), a latissimus dorsi flap and an implant (19 percent), an expander followed by an implant (9 percent), an implant only (4 percent), or other means (9 percent). The nipple-areola was reconstructed in these patients with either a star flap (36 percent), nipple sharing (10 percent), a keyhole flap (9 percent), a skate flap (9 percent), an S-flap (8 percent), a full-thickness skin graft (6 percent), or by another means (22 percent). The number of procedures needed to achieve nipple-areola reconstruction was either one (in 66 percent of the patients), two (in 32 percent of the patients), or three or more (2 percent of the patients). Eleven percent of the patients experienced the complication of nipple necrosis.Satisfaction with breast mound reconstruction was reported by 81 percent of patients to be excellent/good, by 14 percent of patients to be fair, and by 5 percent of patients to be poor. Reported satisfaction with nipple-areola reconstruction was excellent/good for 64 percent of patients, fair for 22 percent of patients, and poor for 14 percent of patients. The factors patients disliked most about their nipple-areola reconstruction were, in descending order, lack of projection, color match, shape, size, texture, and position. Statistical analysis of the data revealed inferior patient satisfaction when there was a longer interval between breast mound and nipple areola reconstruction (p = 0.003). No significant difference was observed in nipple/areola reconstruction satisfaction ratings when compared with breast mound reconstruction type (p = 0.46), nipple-areola reconstruction type (p = 0.98), and history of radiation therapy (p = 0.23). There was also no significant difference when breast mound reconstruction was compared with technique (p = 0.51) and history of radiation therapy (p = 0.079). Overall, there was a greater satisfaction with breast mound reconstruction than with nipple-areola reconstruction (p = 0.0001).     

Evaluation of the binding between potential anti-HIV DNA-based drugs and viral envelope glycoprotein gp120 by capillary electrophoresis with laser-induced fluorescence detection

The fusion of the human immunodeficiency virus (HIV) with the target cell was assisted by the interaction between the viral envelope glycoprotein HIV-1 gp120 and a chemokine receptor. Studies have shown that the efficiency of the binding depends on the presence of the V3 loop of the gp120 which is known to interact with polyanions, such as phosphorothioate oligodeoxynucleotides (Sd, potential anti-HIV drugs). In this study, capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) was used to systematically evaluate binding between Sd and HIV-1 gp120. A 25-mer fluorescently tagged phosphorothioate oligodeoxynucleotide (GEM) was employed as a probe to study this interaction. The dissociation constant (K(d)) between GEM and gp120 was determined to be 0.98 nM by Scatchard analysis. The competition constants (K(c)) of a set of Sd that compete with GEM for binding to gp120 were also determined. The results showed that the interaction had a strong dependence on the sulfur phosphorothioate backbone. Chain length and the sequence of Sd also affect the ability of binding to gp120. The ability to study the protein-drug binding in the solution with minimal sample consumption makes CE-LIF very attractive for biological studies.     

Nest Etiquette—Where Ants Go When Nature Calls

Sanitary behaviour is an important, but seldom studied, aspect of social living. Social insects have developed several strategies for dealing with waste and faecal matter, including dumping waste outside the nest and forming specialised waste-storage chambers. In some cases waste material and faeces are put to use, either as a construction material or as a long-lasting signal, suggesting that faeces and waste may not always be dangerous. Here we examine a previously undescribed behaviour in ants – the formation of well-defined faecal patches. Lasius niger ants were housed in plaster nests and provided with coloured sucrose solution. After two months, 1–4 well defined dark patches, the colour of the sucrose solution, formed within each of the plaster nests. These patches never contained other waste material such as uneaten food items, or nestmate corpses. Such waste was collected in waste piles outside the nest. The coloured patches were thus distinct from previously described ‘kitchen middens’ in ants, and are best described as ‘toilets’. Why faeces is not removed with other waste materials is unclear. The presence of the toilets inside the nest suggests that they may not be an important source of pathogens, and may have a beneficial role.