ACA‐specific RNA sequence recognition is acquired via the loop 2 region of MazF mRNA interferase

MazF is an mRNA interferase that cleaves mRNAs at a specific RNA sequence. MazF from E. coli (MazF‐ec) cleaves RNA at A and CA. To date, a large number of MazF homologs that cleave RNA at specific three‐ to seven‐base sequences have been identified from bacteria to archaea. MazF‐ec forms a dimer, in which the interface between the two subunits is known to be the RNA substrate‐binding site. Here, we investigated the role of the two loops in MazF‐ec, which are closely associated with the interface of the MazF‐ec dimer. We examined whether exchanging the loop regions of MazF‐ec with those from other MazF homologs, such as MazF from Myxococcus xanthus (MazF‐mx) and MazF from Mycobacterium tuberculosis (MazF‐mt3), affects RNA cleavage specificity. We found that exchanging loop 2 of MazF‐ec with loop 2 regions from either MazF‐mx or MazF‐mt3 created a new cleavage sequence at (A/U)(A/U)AA and C in addition to the original cleavage site, A and CA, whereas exchanging loop 1 did not alter cleavage specificity. Intriguingly, exchange of loop 2 with 8 or 12 consecutive Gly residues also resulted in a new RNA cleavage site at (A/U)(A/U)AA and C. The present study suggests a method for expanding the RNA cleavage repertoire of mRNA interferases, which is crucial for potential use in the regulation of specific gene expression and for biotechnological applications. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium

Methenyltetrahydromethanopterin cyclohydrolase (Mch) is involved in the methanogenesis pathway of archaea as a C₁ unit carrier where N⁵‐formyl‐tetrahydromethanopterin is converted to methenyl‐tetrahydromethanopterin. Mch from Methanobrevibacter ruminantium was cloned, purified, crystallized and its crystal structure solved at 1.37 Å resolution. A biologically active trimer, the enzyme is composed of two domains including an N‐terminal domain of six α‐helices encompassing a series of four β‐sheets and a predominantly anti‐parallel β–sheet at the C‐terminus flanked on one side by α‐helices. Sequence and structural alignments have helped identify residues involved in substrate binding and trimer formation. Proteins 2013; 81:2064–2070. © 2013 Wiley Periodicals, Inc.     

Combined effect of cyprid age and lipid content on larval attachment and metamorphosis of Balanus amphitrite darwin

Various algal diets of different lipid content and composition were used to rear batches of naupliar larvae of Balanus amphitrite. The cyprids in these larval batches differed in lipid content and were used to investigate the combined effect of cyprid lipid content and cyprid age on attachment and metamorphosis. For this purpose, cyprids were aged for 0,3 and 6 d at 8°C prior to utilization in laboratory attachment assays. The percentage attachment of cyprids with similar lipid content differed significantly among the three age categories. A strong and a weak positive relationship between cyprid lipid content and attachment were monitored in young and old cyprids, respectively. A significant interaction (two‐way ANOVA) between cyprid age and lipid content was observed, indicating that these factors jointly affect larval attachment and metamorphosis in B. amphitrite from the beginning of the cyprid stage.     

Dimethylsulphopropionate (DMSP) and proline from the surface of the brown alga Fucus vesiculosus inhibit bacterial attachment

It was demonstrated previously that polar and non-polar surface extracts of the brown alga Fucus vesiculosus collected during winter from the Kiel Bight (Germany) inhibited bacterial attachment at natural concentrations. The present study describes the bioassay-guided identification of the active metabolites from the polar fraction. Chromatographic separation on a size-exclusion liquid chromatography column and bioassays identified an active fraction that was further investigated using nuclear magnetic resonance spectroscopy and mass spectrometry. This fraction contained the metabolites dimethylsulphopropionate (DMSP), proline and alanine. DMSP and proline caused the anti-attachment activity. The metabolites were further quantified on the algal surface together with its associated boundary layer. DMSP and proline were detected in the range 0.12–1.08 ng cm^?2 and 0.09–0.59 ng cm^?2, respectively. These metabolites were tested in the concentration range from 0.1 to 1000 ng cm^?2 against the attachment of five bacterial strains isolated from algae and sediment co-occurring with F. vesiculosus. The surface concentrations for 50% inhibition of attachment of these strains were always <0.38 ng cm^?2 for DMSP and in four cases <0.1 ng cm^?2 for proline, while one strain required 1.66 ng cm^?2 of proline for 50% inhibition. Two further bacterial strains that had been directly isolated from F. vesiculosus were also tested, but proved to be the least sensitive. This study shows that DMSP and proline have an ecologically relevant role as surface inhibitors against bacterial attachment on F. vesiculosus.     

Effect of cyprid age on the settlement of balanus amphitrite darwin in response to natural biofilms

Larval settlement of the barnacle Balanus amphitrite Darwin (Cirripedia, Balanidae) is influenced by natural biofilms. In previous work by others, discriminatory settlement of aged cyprids has been observed in response to biofilms of different age. This study extends prior work by considering the effect of the age of cyprids on the outcome of settlement assays. Settlement was investigated with 0‐day‐old (newly metamorphosed) and 5‐day‐old cyprids. Biofilms under investigation were developed in the field for periods of 5 d and 1 month, and were subsequently included in laboratory settlement assays with a choice between a filmed and an unfilmed substratum. The bioassay was modified from the conventional horizontal dish design in order to generate a low water surface‐to‐volume ratio, which served to suppress larval entrapment in an organic layer on the water surface. Irrespective of cyprid age, a clear discrimination between a filmed and an unfilmed substrata was observed, and the preference for filmed or unfilmed substratum was dependent on the age of the cyprids. Settlement of 0‐day‐old cyprids was inhibited by a biofilmed substratum whereas induction occurred with aged cyprids. This pattern of settlement was independent of biofilm age. Bacterial abundance on unfilmed substrata in treatments and controls was significantly lower than that on biofilmed surfaces, confirming that bacterial contamination did not change the qualitative option during the assay.     

Civilization,wilderness and secrecy: Making two Nigerian films

This paper draws on fieldwork and filmmaking experiences and explores the interpretive process shared between the object, filmmaker, and audience. Mammy Water: In Search of the Water Spirits in Nigeria [1989] is the result of extensive field research and close collaboration between the local community, the researcher/filmmaker and team. Mammy Water priviledges local views on the subject over the academic discourse taking place elsewhere. This has evoked diverse reactions. Some miss the (Western) analytical level, others engage in the discourse itself, or assume the film's own position. The issue of cultural perspective is carried even further in cinematography. Both films discussed here were made not only in close collaboration with African communities but also photographed by an African cinematographer, Alhaji Yusufu Mohammed. His camera evokes diametrically opposed reactions from African and Western viewers. Where Westerners perceive “distance”, African audiences perceive “closeness”, where Westerners perceive a scene as “staged”, African audiences perceive it as “natural”. This contrast of perception is further highlighted in Owu: Chidi Joins the Okoroshi Secret Society [1991], mostly filmed by Alhaji, but complemented by two video inserts by my daughter, Saskia Jell, who produced additional behind‐the‐scenes footage in Coming to Nigeria.

Reviewers have raised another important topic. Owu points to three different levels of secrecy surrounding the masquerade and initiation into Oguta's Okoroshi society. This in turn raises questions on if and how to represent secrecy and the dichotomy between civilization and wilderness on film.

A discussion of post‐production at the IWF introduces a negative dimension and questions the undue impact of politics, German rigidity, and other impediments.

In conclusion, my films are strongly grounded in long‐term field research, and indebted to the people whose cultures I have researched, as well as to Alhaji Yusufu Mohammed's cinematic representation. Situated between Africa and the Western world, my films contain elements of both African and Western cultures, as they attempt to mediate between them. 1 am looking to the genre of ethnographic film primarily for its effort to create meaning in interpreting and representing cultures, for its position between the cultural worlds, and for its possibilities for transcultural communication. This goal could be served by a plurality of methods, different film styles, and varied authors within the same genre.     

Masking the mask: An Israeli response to the threat of chemical warfare

This paper analyzes a form of visual euphemism which we call “masking the mask.” During the Gulf War, Iraq fired 40 missiles on Israel. Citizens were issued with gas mask kits and were ordered into sealed rooms in their homes during attacks. Thousands of Israelis of all ages decorated or covered their gas mask kits. Although no chemical warheads were fired on the country, Israelis were unusually fearful of gassing because of associations with the Holocaust. Masking the mask served important psychological and communicative functions. It provided a means to express one's fears, to attempt a modest form of mastery over a threatening environment, as well as to rebel against dehumanization and personalization, and to express solidarity with the group under threat, while reasserting one's individual identity.