Caulobacter crescentus, which has been a model system for studying the bacterial cell cycle, has an RNA degradosome assembly that is formed by the endoribonuclease RNase E and includes the DEAD-box RNA helicase RhlB. Immunoprecipitations of extracts from cells expressing an epitope-tagged RNase E reveal that RhlE, another member of the DEAD-box helicase family, associates with the degradosome at temperatures below those optimum for growth. Phenotype analyses of rhlE, rhlB, and rhlE rhlB mutant strains show that RhlE is important for cell fitness at low temperature and its role may not be substituted by RhlB. Transcriptional and translational fusions of rhlE to the lacZ reporter gene and immunoblot analysis of an epitope-tagged RhlE indicate that its expression is induced upon temperature decrease, mainly through posttranscriptional regulation. RNase E pulldown assays show that other proteins, including the transcription termination factor Rho, a second DEAD-box RNA helicase, and ribosomal protein S1, also associate with the degradosome at low temperature. The results suggest that the RNA degradosome assembly can be remodeled with environmental change to alter its repertoire of helicases and other accessory proteins.In diverse bacterial lineages, multienzyme assemblies have evolved that are central elements of RNA metabolism and RNA-mediated regulation. The aquatic Gram-negative bacterium IMPORTANCE DEAD-box RNA helicases are often present in the RNA degradosome complex, helping unwind secondary structures to facilitate degradation. Caulobacter crescentus is an interesting organism to investigate degradosome remodeling with change in temperature, because it thrives in freshwater bodies and withstands low temperature. In this study, we show that at low temperature, the cold-induced DEAD-box RNA helicase RhlE is recruited to the RNA degradosome, along with other helicases and the Rho protein. RhlE is essential for bacterial fitness at low temperature, and its function may not be complemented by RhlB, although RhlE is able to complement for rhlB loss. These results suggest that RhlE has a specific role in the degradosome at low temperature, potentially improving adaptation to this condition. The complex structures that RNA can adopt underlie the capacity of the nucleic acid to regulate diverse cellular processes. RNA structure is likely to be in dynamic equilibrium in living cells, and when altered by environmental changes or in response to signals, the cell must quickly respond by ensuring that no misfolded RNA molecules accumulate. One such environmental condition is low temperature, which causes an increase in RNA secondary structure stability that could lead to altered function, particularly of mRNAs. A common response to cold temperature is the induction of RNA binding proteins and enzymes, such as the small cold shock proteins (CSPs), RNA helicases, and ribonucleases (RNases), which prevent or unwind secondary structures and turnover RNA and are important for cold adaptation , dbpA, rhlB, rhlE, and srmB. These enzymes have specific functional roles: SrmB and CsdA participate in ribosome biogenesis , CCNA_01546, CCNA_01923 (encoded by rhlB), and CCNA_02121  strain at 15°C.The nsertion , indicatnsertion . In ordeonitored . The rhlperature . At 15°Cmutation . These dmutation , with thrhlE mutant shows smaller colonies  or oxidative stress (potassium dichromate or paraquat) but increased when cells were grown at low temperature . The FLAG-RhlE protein accumulation upon incubation at low temperature reached maximal levels after 2 h at 10°C, with no further increase observed when cold incubation was continued until 5 h . To further explore the cold induction of rhlE, the cells were grown at 30°C and then transferred to 10°C for 60 min, returning to 30°C for another 90 min  of the rhlE mRNA is 186 nucleotide (nt) long . These results indicate that the 5′ UTR is necessary for maximal expression of the rhlE gene, probably due to mRNA stabilization, since the translation of the lacZ gene in these constructs was determined by the vector sequences  long  and is pnt) long . In ordeand 10°C . Althougwas used , indicatC. crescentus degradosome at 30°C   .in vivo. Some metabolic enzymes were found: the tricarboxylic acid (TCA) cycle enzyme 2-oxoglutarate dehydrogenase E1 component (CCNA_00342), the dicarboxylate metabolism enzyme acetoacetyl coenzyme A (acetoacetyl-CoA) reductase (CCNA_00545), a NUDIX family pyrophosphatase (CCNA_00267), which converts NAD+ into nicotinamide d-ribonucleotide, and a methionine adenosyltransferase (CCNA_00048). Proteins involved in RNA metabolism were also present, such as the small subunit ribosomal protein S1 (CCNA_03702), the transcription terminator Rho (CCNA_03876), and two DEAD-box RNA helicases, RhlE and CCNA_01546.Further comparison of the composition of the RNA degradosome at 15°C and 30°C was performed using the FLAG-RNase E strain at both temperatures and also by pretreating the cell extracts at 15°C with RNase A to eliminate interactions mediated by RNA. rhlB mutant  necessary for cold induction, but this sequence is not present in the 5′ UTR of rhlE (data not shown). The results indicated that RhlE could be regulating its own mRNA levels, either by mRNA stabilization mediated by the 5′ UTR and/or by enhancement of translation. Several bacterial DEAD-box RNA helicases have been shown to be induced by cold shock  and Hfq  and CC1847-E∕CC1847-F (downstream fragment)  strain (rhlB), MM74 (NA1000 rhlE::mini-Tn5), MM71 (NA1000 ΔrhlB FLAG-RNE), and MM82 (NA1000 ΔrhlB rhlE::mini-Tn5).s NA1000  was useds NA1000 . E. colipurposes . The rhlragment) . The frae 30-10H  was trane 30-10H  into the) strain . The resrhlE gene with primers that introduced a single FLAG peptide at the amino terminus (primer pairs RhlE12/RhlE11 and RhlE10/RhlE13). The two fragments were sequentially cloned into pNPTS138 using the restriction enzymes EcoRI and NcoI, and NcoI and ApaI, respectively. The vectors were introduced into E. coli S17-1 .The FLAG-RhlE strain was generated by amplification of the li S17-1  and tranE medium  containiEscherichia coli strains were grown at 37°C in Luria-Bertani (LB) medium. When necessary, antibiotics were added at the following concentrations: tetracycline, 12.5 μg/ml; ampicillin, 100 μg/ml; or kanamycin, 50 μg/ml. Generation times were calculated from four individual growth curves for each strain.The strains were grown in PYE medium and incubated at 30°C or 15°C with agitation. When necessary, antibiotics were added at the following concentrations: tetracycline, 1 μg/ml; kanamycin, 5 μg/ml; nalidixic acid, 20 μg/ml; or gentamicin, 5 μg/ml. 600) of 0.1 and incubated at 30°C or 15°C with agitation until an OD600 of 0.5 was reached. Samples were collected and mounted on slides with agarose pads . Microscopy was performed with a Nikon E800 microscope equipped with 100× differential interference contrast (DIC) . Images were captured with a Nikon DS-Ri1 camera and were analyzed with the UVP Doc-ItLS software (Life Science Software).Overnight cultures were diluted in PYE medium to an optical density at 600 nm  and ccRhlB-DUET.f/ccHel.REV2 (rhlB) and cloned into pET15 and pET DUET, respectively. Each fragment was isolated by digestion with NdeI and BamHI (rhlE) or NdeI and XhoI (rhlB) and was cloned into the pBV-MCS-4 vector  were grown asynchronously in 1 liter of PYE medium per pulldown experiment to an OD600 of 0.4 at 30°C. For cold treatments, cells were grown in 1 liter of PYE to an OD600 of 0.2 at 30°C before the temperature was lowered to 15°C and growth continued for a further 5 h, resulting in a final OD600 of ∼0.4. Cells were then harvested by centrifugation, resuspended in 30 ml of lysis buffer , flash-frozen, and stored at −80°C until required. Cell pellets were thawed on ice and then lysed by two passages through a high-pressure homogenizer at 50,000 kPa . The lysate was clarified by centrifugation , and the supernatant was incubated with 50 μl of anti-FLAG M2 affinity gel per pulldown experiment (Sigma-Aldrich) prewashed in lysis buffer . The anti-FLAG affinity gel was collected by gravity sedimentation, transferred to a minichromatography column (Thermo Scientific), and washed three times with 500 μl of lysis buffer. To elute bound proteins, the anti-FLAG resin was incubated with 30 μl of FLAG peptide diluted to 0.25 mg/ml in elution buffer  for 10 min at 4°C, and the eluate was collected by centrifugation and analyzed by SDS-PAGE using a 4 to 12% polyacrylamide NuPAGE gel (Thermo Scientific). Protein bands were identified by in-gel matrix-assisted laser desorption ionization (MALDI) mass spectrometry fingerprinting .Proteins were separated by SDS-PAGE in either 10% polyacrylamide gels or 4 to 12% polyacrylamide NuPAGE gels (Invitrogen), electrotransferred to cellulose or polyvinylidene difluoride (PVDF) membranes, and treated as described by Towbin et al. . For the2, 100 mM NaCl).For the detection of FLAG-RhlE, the membranes were incubated for 16 h with anti-FLAG monoclonal antibody (Sigma) at a 1:20,000 dilution in TBSTT , followed by incubation with alkaline phosphatase-conjugated anti-mouse IgG (Sigma) at a 1:5,000 dilution in TBS containing 5% milk. As a control, anti-Fur polyclonal antiserum 1:1,000 dilutions were used, followed by alkaline phosphatase-conjugated anti-rabbit IgG (Sigma) diluted 1:5,000 in TBS. Bands were developed with 0.5 mg/ml nitroblue tetrazolium (NBT) and 0.15 mg/ml 5-bromo-4-chloro-3-indolylphosphate (BCIP) in alkaline phosphatase buffer (100 mM Tris-Cl [pH 9.5], 5 mM MgCl


In Australia, those who migrate as children or adolescents (1.5 generation migrants) may have entered a new cultural environment at a crucial time in their psychosexual development. These migrants may have to contend with constructions of sexual and reproductive health from at least two cultures which may be at conflict on the matter. This study was designed to investigate the role of culture in constructions of sexual and reproductive health and health care seeking behaviour from the perspective of 1.5 generation migrants.Forty-two adults from various ethno-cultural backgrounds took part in this Q methodological study. Online, participants rank-ordered forty-two statements about constructions of sexual and reproductive health and health seeking behaviours based on the level to which they agreed or disagreed with them. Participants then answered a series of questions about the extent to which their ethnic/cultural affiliations influenced their identity. A by-person factor analysis was then conducted, with factors extracted using the centroid technique and a varimax rotation.A seven-factor solution provided the best conceptual fit for constructions of sexual and reproductive health and help-seeking. Factor A compared progressive and traditional sexual and reproductive health values. Factor B highlighted migrants’ experiences through two cultural lenses. Factor C explored migrant understandings of sexual and reproductive health in the context of culture. Factor D explained the role of culture in migrants’ intimate relationships, beliefs about migrant sexual and reproductive health and engagement of health care services. Factor E described the impact of culture on sexual and reproductive health related behaviour. Factor F presented the messages migrant youth are given about sexual and reproductive health. Lastly, Factor G compared constructions of sexual and reproductive health across cultures.This study has demonstrated that when the cultural norms of migrants’ country of origin are maintained it has a significant influence on how 1.5 generation migrants construct, experience and understand various aspects of sexual and reproductive health. Policy makers, health care professionals and resettlement service providers are advised to engage with migrant parents and youth in exploring, discussing, reframing and reconstructing SRH in an Australian context. In Australia, those who migrate as children or adolescents (1.5 generation migrants) may have entered a new cultural environment at a crucial time in their psychosexual development. These migrants may have to contend with constructions of sexual and reproductive health from at least two cultures which may be in conflict. This study, using Q methodology, investigated the role of culture in constructions of sexual and reproductive health from the perspective of 1.5 generation migrants. Analysis resulted in seven distinct yet interrelated factors. The findings of this study demonstrate that young migrants vary in their acculturation journeys. Notably, when the cultural norms of migrants’ country of origin persist post-migration it has a significant influence on how 1.5 generation migrants construct, experience and understand sexual and reproductive health. The findings indicate that as norms take on more cross-cultural constructions they can reshape to produce multicultural ways of understanding and experiencing sexual and reproductive health without young migrants having to lose their relationship with their culture of origin. Policy makers, health care professionals and resettlement service providers are advised to engage with migrant communities, parents and youth in exploring, discussing, reframing and reconstructing SRH in an Australian context.Migration within an international context has increased exponentially especially in the past two decades . Of partCultural differences between a migrant’s country of origin and that of immigration are linked to reduced help-seeking behaviour across a range of health outcomes  and espeSuch differences and outcomes often relate to a wide range of SRH issues including, but not limited to, abortion, contraceptives, gender and gender equality, sexual intercourse and behaviour, sexual pleasure and satisfaction . While tHere SRH refers to “a state of complete physical, mental and social well-being in all matters relating to the reproductive system. It implies that people are able to have a satisfying and safe sex life, the capability to reproduce, and the freedom to decide if, when, and how often to do so” . Good SRThis is of particular relevance to 1.5 generation migrants who are culturally from two worlds. 1.5 generation migrants are not conventional first generation migrants, who are often adults eligible to emigrate on their own, nor are they the conventional second generation migrant, the offspring of the first-generation migrant born in the adoptive country. 1.5 generation migrants are often expected to uphold  particular norms about SRH  while atDiscourse around the experiences of 1.5 generation migrants, given their unique cross-cultural position, is increasing. Extant research has explored 1.5 generation migrants experiences of sociocultural identity , 16, effRecent research reinforces this connection between 1.5 generation migrants’ cross-cultural standpoint, sexuality and SRH. For instance, one paper compared sexual partner risk among Latino adolescents  in San Francisco . The stuThis paper is part of a larger project which aimed to investigate the role of culture in constructions of SRH and SRH help-seeking from the perspective of 1.5 generation migrants. Using a mixed methods approach  the larger study sought to define the key aspects of one’s culture and its messages about sexuality that shape how people within this cohort understand and experience SRH. This paper will focus on the results of the Q methodology portion of the project.Q methodology allows for the sampling of subjective viewpoints, and can assist in identifying patterns, including areas of difference or overlap, across various perspectives on a given phenomenon . Q methoThe concourse represents thoughts and opinions or verbalisations about the subject being studied. To develop the concourse a literature review was conducted regarding migrants’ constructions of SRH and help-seeking in Australia. In addition, related materials from online newspapers, websites and clinical guidelines were reviewed to include constructions of SRH not captured in the literature review.Semi-structured interviews were also conducted with two 1.5 generation migrants . A total of 120 items were pooled from these steps. Included items were then grouped under four themes: the role of culture on experiences of SRH; constructions and understanding of SRH; the healthcare system and SRH help-seeking behaviour; and external perceptions of migrant sexuality. Within each theme statements were again refined until a final set of items was prepared. This was performed with the purpose of ensuring that all aspects of the topic were covered and not inclined towards a particular viewpoint . The finWith the help of community stakeholders 1.5 generation migrants were recruited via advertisements posted at seven Western Sydney University campuses and surrounding off-campus venues . This was done in an effort to strategically engage participants from several suburbs within the Greater Western Sydney region to ensure that the Q sorts collected were from as many ethnocultural groups as possible. Following an online survey examining 1.5 generation migrants’ experiences of SRH and help-seeking, 42 out of 112 participants agreed to take part in the Q sort activity. The other 70 declined to participant due to personal time constraints. According to Rogers , a samplParticipants performed the Q sorting task in three phases using web-based software Q-Assessor . First, In order to identify perspectives shared by participants, a bi-person factor analysis was performed – a commonly applied statistical method in Q methodology. Factor analysis begins with the calculation of correlation matrix which reveals the degree of agreement or disagreement between the sorts or the similarity or dissimilarity in the views of the Q sorters. From this matrix, initial sets of factors were extracted using the centroid method. The extracted factors were then subjected to varimax rotation; varimax positions factors so that it maximizes the amount of study variance explained . It alsoage = 22.8, SD = 4.4). Migrants had arrived in Australia as follows, Pre-1999 (4), 2000–2005 (19), 2006–2010 (11) and 2011–2015 (7). The majority migrated from sub-Saharan Africa (18: 42.8%) with the others migrating from South East Asia (8), East Asia (4), Eastern Europe (4), Western Europe (3), the Middle East (2) and the Americas (1). Age upon arrival to Australia ranged from 5 to 19 years with the majority (22: 52.3%) having arrived between the ages of 11 and 15. Other participants arrived between the ages of 0–5 (1), 6–10 (12) and 16–19 (6). Thirty-five (83.3%) participants came to Australia with their immediate family members, 5 came with extended family and 2 came alone. With regards to religion, 23 (54.7%) identified as Catholic/Christian, 7 as Islamic, 2 as Hindu, 2 as Greek Orthodox, 1 as Druze, and 5 indicated that they did not follow any religion. The majority of participants (26: 61.9%) spoke a language other than English at home and 16 only spoke English at home. Table The P set consisted of 1.5 generation migrants who ranged in age from 18 to 39 . With the majority being from non-Western countries and identifying as religious these migrants may experience challenges in their efforts to compare, assess, review and re/construct their SRH values.Factor B accounted for 9.51% of the total variance with the Q sorts of 6 participants defining this factor. Factor B demonstrated the influence of culture on SRH constructs within cross-cultural contexts. Socially participants felt that Australians should take on SRH values from migrant cultures (40: +4). Participants also believed that migrants who identify most as being Australian have more SRH problems than other Australians (36: +3). This may be a criticism of Australian culture and its influence on SRH. Criticism is also seen in migrants’ evaluation of their own cultures. Cultural support can be seen in participants’ belief that if confronted with an unplanned pregnancy their family and community would be supportive (4:−2). Even so, there was a moderate sense that going to a clinic for an SRH issue without family or community knowing was preferred (3: +2). It seems that the migrants had a more liberal set of SRH values. This is reflected in the respondents’ belief that how SRH is dealt with in Australia was not very different to their culture of origin (9:−3). They also believed that people born in Australia did not necessarily have an easier time with SRH compared to migrants like themselves (13:−2) or that non-migrants understood SRH differently than they did (26:−1).The post-Q questionnaire indicates that all exemplars strongly identified with their culture of origin (sub-Saharan Africa (50%), South East Asia (33.3%) and Eastern Europe (16.6%)). This may explain their critique of how SRH is constructed in Australian culture. This is further corroborated as 83.3% strongly agreed or agreed that they had a robust relationship with their community based on their culture of origin.Factor C accounted for 8.28% of the total variance with the Q sorts of 4 participants defining this factor. Factor C exemplars strongly believed that culture played a large role in how people understand SRH (28: +4). These participants were keen to pass on values about SRH from their culture of origin to future generations (8: +3) and indicated that Australian values did not lead their understanding of SRH (21:−4). They also felt that the way in which SRH is understood in their culture of origin and in Australia were quite different (26: +3) with Australia being more liberal in this regard (17:−3). A key difference was having no words in their mother tongue for SRH (27: +2) which would have a significant impact on how SRH was constructed. Further, the potential differences between one’s culture of origin and those within Australia can cause confusion about SRH (7: +4). For example, exemplars moderately agreed that “migrants from certain cultures are carriers of sexually transmitted infections” (38: +2) and that migrants who identify most with their culture of origin have more SRH issues than other Australians (37: +1).Although exemplars perceived differences regarding SRH between their culture of origin and in Australia there are some aspects of cultural community support which resemble those in Australia. For instance, in the participants’ culture of origin discussing SRH is encouraged (10: +2) and they would not feel uncomfortable if their family or community knew that they had sex outside of marriage (2:−2). If they were confronted with an unplanned pregnancy their community and family would also be supportive (4:−2). Although support is present, the exemplars indicated that their ability to seek professional help for an SRH issue would be impacted by others’ perceptions (5: +2). This hindrance does not seem linked specifically to one cultural context as participants indicated that Australians do not get help for SRH issues more easily than their migrant counterparts (30:−2). Further, help-seeking was not influenced by health care workers’ understanding of SRH within various cultures (32:−3). As such, participants felt that health care workers were moderately well-equipped to handle the SRH needs of people from their own background (29: +1).The questions posed after the Q sort indicate that half of the exemplars identified most with their culture of origin while the other half were neutral. Although these exemplars see culture as an important factor in constructions of SRH the salience of their culture of origin seems less prominent in their SRH behaviour and help-seeking. With the majority coming from sub-Saharan Africa and being Christian/Catholic their culture of origin was important but may not have been the most important element in their constructions of SRH.Factor D accounted for 6.22% of the total variance with the Q sorts of 6 participants defining this factor. Factor D describes the role of culture in migrants’ intimate relationships, beliefs about SRH and engagement of health care services. For these participants, culture played a large role both in how SRH is understood (15: +4) and experienced (28: +4). Australian values also led their understanding of SRH (21: +2). Participants felt that Australians can have intimate relationships with whomever they liked and that no one would mind (14: +3). Based on this belief the exemplars did not avoid casual sexual encounters in fear that their family or community would not approve (19:−4) nor did they feel that their family or community would frown upon sex outside of marriage (2:−2). Participants also reported that their SRH help-seeking would not be impacted by the perception of others (5:−3). This way of understanding SRH, and thus, engaging in intimate relationships in Australia was not that different to understandings of SRH in the migrants’ culture of origin (26:−1). This liberal way of interacting with SRH is perhaps a result of being encouraged to discuss SRH within their culture of origin (10: +2) e.Cultural differences were, however, implied as participants agreed that migrants need more assistance from SRH health services than people born in Australia (31: +3). Exemplars may have felt this way as they indicated that health care workers had limited knowledge about the SRH beliefs within their culture of origin (32: +1) and may not be equipped (29: +1) to handle their needs. Even so these exemplars did not perceive major differences between migrant groups and other Australians. For instance, they disagreed that migrants who identified most with Australian culture had more SRH issues (36:−2), that migrants who do not take on Australian ways of understanding SRH had failed to assimilate (39:−2) and they disagreed that migrants from certain cultural groups were carriers of STIs (38:−4).The post-Q sort questions indicate that the majority of exemplars identified with the culture and values of their country of origin (83.3% strongly agreed or agreed) and had strong relationships with their family and community as a result of these values (66.6% strongly agreed or agreed).Factor E accounted for 7.88% of the total variance with the Q sorts of 4 participants defining this factor. Factor E describes the impact of culture on SRH related behaviour. For these exemplars, there was quite a difference in the way SRH is understood in Australia and in their culture of origin (26: +3). For instance, they perceived that in Australia people are encouraged to discuss SRH (12: +4) and that people born in Australia have an easier time with SRH than migrants like themselves (13: +4). Part of having an easier time with SRH included the perception that Australians are better able to access support for SRH issues over their migrant counterparts (30: +3). These participants also avoided casual sexual encounters because their family or community would perceive such behaviour as disrespectful (19: +3). Participants’ behaviour moderation was not necessarily in an effort to avoid STIs or unplanned pregnancy (25:−4) but was instead in an effort to avoid disapproval. For example, participants also agreed that their family or community would not be supportive if they had to manage an unplanned pregnancy (4: +4).While migrants’ SRH behaviours may have been dictated by cultural pressures this did not seem to result in a culture clash between their culture of origin and Australian culture. For instance, participants disagreed that going through puberty and adolescence was difficult as a result of being exposed to differing messages about SRH (6:−3). Exemplars also disagreed that moving from one country to another during childhood/adolescence caused confusion about SRH (7:−1).Interestingly, the post-Q sort questions show that the majority of the exemplars were neutral or disagreed (75%) with identifying most with the values of their culture of origin and were neutral or disagreed (75%) with identifying most with Australian culture. This contextual information suggests that these migrants did not explicitly retain or denounce the SRH values of their culture of origin nor do they take on the values of their adoptive culture.Factor F accounted for 9.39% of the total variance with the Q sorts of 8 participants defining this factor. Factor F delves into the messages which the participants may have been given as they grew up. There was strong agreement that culture plays a large role in how people experience SRH (15: +4) and the ways in which SRH is dealt with in Australia and their culture of origin is very different (9: +3). As such, participants may have decided to take on Australian values which now lead their understanding of SRH (21: +2). The process of making such a decision was however complicated. For instance, participants agreed that going through puberty and adolescence was sometimes difficult because of conflicting SRH messages from school or media and their family or community (6: +3).However, the content of the messages received from their culture of origin may not have been specific to SRH. For instance, SRH did not simply refer to contraception (24:−4) or linking SRH risks to promiscuity (25:−4). The content may have been more morally bound or religious in nature as exemplars would never let their family or community know that they had had sex outside of marriage (2: +4). Given the variety of messages and ways of understanding SRH, the participants indicated that health care workers may have a hard time managing the needs of migrant populations. Notably, participants perceived that health care workers were not well equipped (29:−2) and health care services did not do enough to cater to the needs of migrants (35:−2). Given the varying messages regarding SRH it is not surprising that health care workers would find it hard to keep up.The post-Q questionnaire showed that most identified (75%) with the values of their culture of origin with 62.5% being neutral or disagreeing about identifying most with Australian culture. While 75% of the exemplars came from Western Europe the majority identified as religious (62.5% Muslim and 25% Christian/Catholic). As such the impact of multiple messages may have had a confusing effect on their constructions of acceptable SRH behaviour.Factor G accounted for 2.67% of the total variance with the Q sorts of 2 participants defining this factor. Factor G revealed many similarities between Australian and migrant cultures. For instance, exemplars agreed that in Australia people are encouraged to discuss SRH (12: +4) and that SRH was not a taboo subject in their culture of origin (16:−4). Further, the migrants note that there are many words in their culture of origin to facilitate such discussions (27:−4) and that that women have control over their SRH (11: +3). Participants agreed that Australians may believe that some migrant groups have out-dated ideas about SRH (42: +4) but that Australia was in fact quite conservative with regards to SRH (17: +3). As such, these exemplars felt that young migrants are not confused about SRH (7:−1) which may be linked to their belief that failure to adopt Australian values regarding SRH is an indication of a migrant’s failure to assimilate (39: 1). This is further corroborated by participants’ agreement that migrants who identify most with their culture of origin experience more SRH issues than other Australians (37: +1).Participants believed that others’ perceptions would have an impact on how and when they got professional help for an SRH issue (5: +2) – perhaps because they believed that SRH is something promiscuous people generally have to contend with (25: +1). Although their family or community would be very supportive if they found out the participant had contracted an STI (1:−2) this was not so if the participants were involved in an unplanned pregnancy (4: +2). Considering their perception that both their culture of origin and Australian culture are equally conservative on these matters, limitations in community or family support were no different in either context.The post-Q sort questions indicate that all exemplars identified strongly with their culture of origin as well as Australian culture. As they deemed their culture of origin and Australian culture to be similar, there would be little SRH related culture clash.This study investigated the role of culture in constructions of SRH and help-seeking from the perspective of 1.5 generation migrants. The results show a range of processes involved in comparing, assessing, reviewing and re/constructing SRH and help-seeking between and across cultures. For some migrants the meaning of SRH constructs changed when in a different cultural context . On the With the majority of participants being religious 83.3%) it may not be their ethnic culture which drove their understandings of SRH but instead their religious values. Through this lens extracting or cherry-picking which SRH constructs could stay and which could go may not have made sense as they were intertwined with deeply held religious beliefs. Within the context of Islam for example Smerecnik, Schaalma, Gerjo, Meijer and Poelman  explain .3% it maThe age of arrival in Australia may have a significant influence on the ways in which participants re/constructed SRH and help-seeking. For instance, participants who arrived before the age of 10 may have little to no understanding of SRH constructs of their country of origin . Those wThis study unearthed several interesting and previously undocumented findings with regards to constructions and understandings of SRH across cultures. The study has also highlighted key areas which require further consideration and investigation. For instance, SRH values include a very broad range of concepts which could mean and comprise of different things for different migrant groups. Further research on the content of these values would be beneficial and would provide a better sense of which values from migrants’ country of origin are difficult to integrate with Australian values and the impact this may have on SRH help-seeking and outcomes.The purposeful nature of the sampling strategy helped to achieve a varied sample with the aim of capturing perspectives from various ethnic, religious and migration histories. However, the country of origin of the sample was not proportional as most participants were from sub-Saharan Africa. In addition, the majority of participants were Catholic or Christian which may not reflect many 1.5 generation migrants who do not prescribe to Christianity. This cultural similarity may mean the full breadth of cross-cultural constructions of SRH have yet to be explored. Thus, generalisations cannot be made about the different perspectives among such groups, and further study is recommended to assess the effect of country of origin and religious background on constructions of SRH amongst young migrants in Australia.Although participants of this study were recruited from a number of Western Sydney suburbs this was done in relation to seven Western Sydney University campuses and surrounding off-campus venues. As a result, the participants are likely to have been university students or staff and therefore engaged with higher education. As such, the sample may not be representative of the many 1.5 generation migrants who may not have high levels of education. With lower levels of education come lower levels of health literacy . ConsequA range of seven distinct perspectives that indicate variation in 1.5 generation migrants’ constructions of SRH and help-seeking were revealed using Q methodology. The data highlights that young migrants vary in their acculturation journeys. Such variation may have less to do with culture or even age upon arrival and more to do with religiosity. This is important to consider as migrants are expected to culturally adapt, in this case, to “Australia’s way of life”  while onThe data highlights potential complications to the development and delivery of cross-cultural SRH education and services. As such, further research with migrant youth can provide insight about effective strategies for cross-cultural, intercultural and/or multicultural SRH education. This would be used to inform the development of a responsive, flexible and adaptable model to address this gap in migrant resettlement service delivery. It would also assist migrant parents and youth in exploring, discussing, reframing and reconstructing SRH in an Australian context. Australia’s unique experience of multiculturalism, relatively short history of migration as well as its legal and political frameworks requires that Australian migrant communities and organisations be central in the identification and exploration of keys issues and strategies relevant to the Australian context .


High sediment loads were expected on inner-shelf reefs due to their proximity to the mainland, however, terrigenous siliceous sediments only accounted for 13–24% of total mass. On inner-shelf reef crests parrotfishes would take three months to produce the equivalent mass of sediment found in the EAM. On the outer-shelf it would take just three days, suggesting that inner-shelf EAMs are characterised by low rates of sediment turnover. By contrast, on-reef sediment production by parrotfishes is high on outer-shelf crests. However, exposure to oceanic swells means that much of this production is likely to be lost. Hydrodynamic activity also appears to structure sediment patterns at within-reef scales, with coarser sediments (> 250 μm) typifying exposed reef crest EAMs, and finer sediments (< 250 μm) typifying sheltered back-reef EAMs. As both the load and grain size of EAM sediments mediate a number of important ecological processes on coral reefs, the observed sediment gradients are likely to play a key role in the structure and function of the associated coral reef communities.Sediments are found in the epilithic algal matrix (EAM) of all coral reefs and play important roles in ecological processes. Although we have some understanding of patterns of EAM sediments across individual reefs, our knowledge of patterns across broader spatial scales is limited. We used an underwater vacuum sampler to quantify patterns in two of the most ecologically relevant factors of EAM sediments across the Great Barrier Reef: total load and grain size distribution. We compare these patterns with rates of sediment production and reworking by parrotfishes to gain insights into the potential contribution of parrotfishes to EAM sediments. Inner-shelf reef EAMs had the highest sediment loads with a mean of 864.1 g m Sediments can be found on all coral reefs and are derived from a number of sources ranging from on-reef production via bioerosion to inputs from terrestrial systems –3. WhileMost sediment in reef systems is in the off-reef apron, i.e. as sand or mud around the reef. However, almost every hard surface on the reef is also covered with some sediment, and it is these sediments, especially those within the epilithic algal matrix (EAM), that may have the most long-lasting effect on coral reef organisms ,25. It iAcross the continental shelf of the Great Barrier Reef (GBR) there are numerous ecological gradients in terms of the community composition of benthic components, corals, cryptofauna and fishes –41. WateIn addition to our understanding of how EAM sediments vary across broad spatial scales, we also have a limited knowledge of the factors which are responsible for maintaining EAM sediment loads on coral reefs. The factors contributing to variation in suspended sediments across broad spatial scales have received some attention ,43,49, aParrotfishes can be divided into three distinct functional groups, browsers, scrapers and excavators, each fulfilling a different role on coral reefs . The twoA variety of non-fish coral reef organisms are also associated with the on-reef production of sediment through bioerosion, including sea urchins and endolithic boring organisms such as polychaetes and sponges ,52,54. HWhile there is some information available pertaining to the dynamics of suspended sediments, and sediment production and reworking across broader spatial scales ,54,61,62This study was conducted in accordance with all permitting requirements of the Great Barrier Reef Marine Park Authority including authorisation to collect sediments using a vacuum sampler (permit numbers: G12/35057.1 and G13/36627.1). Ethics approval was not required for this study because the sediment collection and processing did not involve vertebrates or cephalopods and data on parrotfishes was sourced from a previously published study. Data are available in the supplementary material  Tables.2 PVC ring on a suitable EAM-covered surface and collecting the enclosed particulates using a submersible electronic vacuum sampler  < 0.05), and between individual reefs within the same shelf position . Pairwise analyses revealed that the significant difference in grain size distribution between reefs was a result of differences between individual outer-  and mid-shelf reefs  only. The PERMDISP analysis found that grain size distributions from back reef habitats were more dispersed than distributions from reef crest habitats . However, habitat separation as revealed by the PERMANOVA was clear based on a greater abundance of coarse sediments (> 250 μm) on reef crests, while back-reefs had more fine sediments (< 250 μm)  .-2 day-1 of sediment. Given that EAMs in this location contain 220 g m-2, parrotfishes could produce the equivalent of all EAM sediments in just three days (-2 day-1 sediment production vs. 915 g m-2 in EAMs [Table A in -2 day-1) approximate total EAM sediment loads (120 g m-2) . The contribution of other bioeroding organisms, including endolithic boring organisms and sea urchins, may be higher on inner-shelf reefs than offshore, but they remain a fraction of parrotfish sediment production rates [Carbonate sediments on reefs are generally coarser than siliceous sediments  and are on rates ,59,62. Hon rates  as well on rates ,79 also on rates ,54. ThusInner-shelf reefs are not exposed to the same degree of wave energy compared to outer-shelf, and to a lesser extent, mid-shelf reefs ,81. On i-2 day-1 of sediment compared to 220 g m-2 in the EAM. The high bioerosion rates and subsequent sediment inputs are chiefly driven by the bumphead parrotfish, B. muricatum, which often defecate in feeding areas . Much of the sediment produced by B. muricatum is therefore available for incorporation into the EAM. However, although sediment inputs are high, the retention of sediments within the EAM is likely to be quite low. The outer-shelf of the GBR is very exposed to oceanic swells and associated hydrodynamic activity [Compared to inner-shelf EAMs, those found on outer-shelf reef crests appear to be fundamentally different due to the high-turnover nature of this environment. On outer-shelf reef crests the on-reef production of sediment is particularly high: in this location bioerosion by parrotfishes approximates total calcification . The paractivity ,81 and cactivity  when exaB. muricatum [C. microrhinos, export of sediment off the reef may also be significant. It is estimated that approximately one third of defecation events by this species take place away from EAM-dominated feeding areas [Ctenochaetus striatus, is likely to contribute significantly to the export of sediment from EAMs to deeper water on mid-shelf reefs [C. striatus ingests substantial quantities of sediment when feeding on EAMs [C. striatus-mediated sediment export is largely absent from inner-shelf reefs as this species is only found in high abundances on mid- and outer-shelf reefs where it is one of the most abundant herbivorous/detritivorous coral reef fishes [The lowest EAM sediment loads were found on mid-shelf coral reefs. Similarly low EAM sediment loads have previously been reported for mid-shelf coral reefs on the GBR ,47. The uricatum . As mid-ng areas . Additiolf reefs . C. stri on EAMs ,86 and af fishes ,87,88.Along with hydrodynamic and biological processes the geomorphology of the reefs in question can also shape sedimentary patterns. The wave energy that leaks past the reef crest is critical in sediment transport, but the dissipation and transformation of wave energy is dependent on the tidal elevation and reef morphology . Inner-,Furthermore, it must be noted that the current study only represents a single snapshot in time of the documented cross-shelf EAM sediment patterns. Sampling over temporal time spans would be necessary to see if changes were occurring; the results of the current study, however, provide a baseline for future work. In addition, comparing static values (EAM sediment loads) to rates of sediment production (parrotfish bioerosion) can only highlight the potential importance of this particular sediment input at different locations. It is currently unclear how suspended sediment loads and parrotfish sediment production actually relate to the amount of sediment which is retained within the EAM. EAM sediment loads have the potential to represent a chronic long-term stressor on coral reefs ,25 and cIn addition to total EAM sediment loads, the particle size of the EAM sediments can directly affect ecological processes including herbivory/detritivory ,34, coraHydrodynamic forces and differences in reef morphology may also explain the differences between reefs in the same shelf position. Hydrodynamic energy decreases towards the coast , and altThe reworking of sediment by parrotfishes also has the potential to contribute to the general patterns documented for EAM grain size distributions. When parrotfishes rework sediments they grind them in their pharyngeal jaws, potentially reducing the size of particles , a proceOn some reefs parrotfishes are likely to play a substantial role in EAM sediment dynamics, particularly in terms of sediment production on the outer-shelf. However, hydrodynamic activity, reef geomorphology and other physical processes are likely to be pivotal in structuring EAM sediment patterns. Unfortunately we do not know if the broad scale patterns of EAM sediments documented herein are temporally stable or how increased sediment inputs ,95,96 maS1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S3 TableModels are compared using the corrected Akaike Information Criterion (AICc). Shown are degrees of freedom (df), model maximum log-likelihood (logLik), AICc, change in AICc (Δ) and AICc weight (wAICc).(PDF)Click here for additional data file.S4 TableThe generalised linear mixed effects model was based on a GAMMA distribution with a log link and contained shelf position as a fixed effect and individual reef as a random effect. SE = standard error, df = degrees of freedom.(PDF)Click here for additional data file.S5 TableThe PERMANOVA was based on a Bray-Curtis similarity matrix of standardised, log (χ + 1)-transformed sediment grain size data.(PDF)Click here for additional data file.S6 Table(PDF)Click here for additional data file.S1 Text(PDF)Click here for additional data file.


There have been conflicting findings regarding the relationship between body mass index (BMI) and self-rated health (SRH) worldwide. The purpose of this study was to examine the association between BMI and SRH by comparing its relationship in four East Asian countries: South Korea, China, Japan, and Taiwan. Using data from the East Asian Social Survey, the relationship between weight status and SRH status was investigated and compared between four countries, China, Japan, South Korea, and Taiwan. An ordinal logit regression model was estimated for each country, and the results were compared. We found that the relationship between weight status and SRH status differed across the four countries. In China, people who were overweight reported better SRH scores than those of normal weight, whereas in Japan, obese and severely obese people reported poor scores. In contrast, South Koreans who were underweight, obese, or severely obese reported poor ratings of health status than those of normal weight. In Taiwan, however, no differences in respondents’ weight status were found across SRH scores. There were notable differences in the relationship between BMI and SRH status in four East Asian countries. Individual countries should consider these relationships when designing and implementing obesity intervention programs. Obesity is a major global health concern, with a prevalence of more than 1.9 million adults worldwide in 2014. The prevalence has grown steadily and has nearly doubled since 1980  and SRH status  were significant. There was no difference among the four countries for gender distribution of the study participants . However, there were significant differences in terms of marital status , living in an urban area , smoking status , alcohol consumption habits , age , and years of education   = 4.63 , p = 0.001], and South Korea . However, this difference was not found in Taiwan . Specifically, respondents from China who were underweight reported poorer SRH scores [M (SD) = 3.32 (1.24)] than those who were of normal weight [M (SD) = 3.63 (1.10)], overweight [M (SD) = 3.69 (1.09)], or obese [M (SD) = 3.65 (1.14)]. In Japan, respondents who were obese reported poorer SRH scores [M (SD) = 2.79 (0.72)] than their normal weight counterparts [M (SD) = 2.95 (0.83)], but no differences were found among other weight groups in their SRH scores. Korean respondents with normal weight reported the best SRH scores [M (SD) = 3.56 (1.15)] followed by overweight [M (SD) = 3.47 (1.22)], underweight [M (SD) = 3.24 (1.30)], obese [M (SD) = 3.14 (1.29)], and severely obese [M (SD) = 2.56 (1.21)]. Differences in SRH scores between normal and obese or severely obese groups were significant in South Korea. In Taiwan, however, no group differences in their SRH scores were found among the weight status groups. Furthermore, the best SRH scores were reported by the overweight group in Taiwan or China, whereas the same were found in normal weight groups in Japan or South Korea (th Korea .p = 0.001] reported poorer SRH scores while those who were overweight  reported better scores than those of normal weight after adjusting for other covariates. In Japan, respondents who were obese  and severely obese  reported poorer SRH than their counterparts in the normal weight group. Korean respondents who were underweight , obese , or severely obese  reported poorer SRH than the normal weight group. In Taiwan, however, no significant differences were found between weight groups compared to the normal weight group (ht group .The present study was conducted to explore the relationships between BMI and SRH status in four East Asian countries: China, Japan, South Korea, and Taiwan. The findings suggest that the relationships between BMI with SRH status vary across countries.Traditionally, East Asian cultures, including China, Japan, South Korea, and Taiwan, are strongly influenced by Confucianism. In the view of Confucianism, human beings are “organic and network-based entities that are interconnected with each other, family, community, and society” . HoweverDifferences in cultural background and in stages of socioeconomic development may lead to differences in social meanings of weight and interpretations of SRH status ,16. The In South Korea, a high-income developing country, both underweight and obese/severely obese were significantly associated with poor SRH status in the current study. South Korea is one of the most rapidly aging counties because of decreasing birth rate and increasing life expectancy and has recently experienced rapid growth in its economy . TherefoJapan is a very highly developed country, but is aging faster than any other developed country . In the In contrast to South Korea and Japan, being underweight was a significant factor associated with a poorer SRH after adjusting for covariates in China. This result is consistent with the findings of a previous study that only underweight was associated with poor SRH status . Lee andTaiwan is a high-income developing country, but there was no significant relationship between obesity and SRH status, unlike South Korea. One study in Taiwan found that being underweight was associated with poor SRH status by both the adolescents and their parents, while overweight and obesity were not associated with poor SRH status ; these fIn a systematic review by Dinsa and colleagues , socioecThis study has several limitations. First, this study was a cross-sectional study that could not establish cause-and-effect relationships between BMI and SRH status. Second, this study could not control for other factors that may be related to SRH status, such as medical conditions and physical activity. Lastly, this study measured obesity using self-reported BMI, but did not consider other measures, such as percent body fat or central fat distribution. Thus, BMI might not accurately portray fat mass and, therefore, risk of obesity-related conditions in some individuals, such as those with high amounts of muscle. Despite the limitations, this study was the first to compare the relationship between BMI and SRH status in four East Asian countries using a single data source; previous studies only examined the relationship between BMI and SRH status in one or two countries ,37,45. TIn conclusion, this study revealed that the relationships between BMI and SRH status varied in four neighboring Asian countries that are all influenced by Confucian culture and that interact with each other. Differences in the stage of economic development, the economic growth rate, and health-related culture may influence the differences in the relationship between BMI and SRH status in the four countries. Obesity and SRH status should be interpreted in the economic and cultural context of each country.


While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots , and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at  Therefore, in the study of RNA functions, it may be more relevant to look at global topological patterns than individual base-pairs [Once seen as a simple scaffold, RNA is now known to play important regulatory and catalytic roles. RNA is involved in processes including transcriptional regulation , RNA matse-pairs , 8. RNAsse-pairs , 9–11. Ose-pairs ; in Grouse-pairs ; in ribose-pairs  and stimse-pairs .As only a small number of functional RNA classes have been identified, we believe that the majority of regulatory and functional RNA motifs are yet to be identified. Eukaryotic genomes are pervasively transcribed ; almost et al., which is an abstract tree where the nodes represent structural elements [et al. implemented the homeomorphically irreducible tree (HIT) that represents an RNA secondary structure as a contracted topology in which each node represents a structural element weighted by size [et al. have developed the element-contact graphs (ECGs) with size-weighted nodes as well [et al., which represents RNA structures as abstract shapes and aims for efficient RNA structure comparisons, has been shown useful in topologically clustering RNA families; however, RNAshapes does not perform well on families with pseudoknots [et al. developed a graph-based pipeline called GraphClust [Just as conserved structural topologies are important for RNA function, the identification of novel conserved topologies provides an approach to discovering the functions of currently unknown classes of biologically important RNAs. An analogy can be made to the importance of sequence alignment and database searching programs in identifying novel proteins and DNA regulatory elements. While typical functional RNA structures are pseudoknotted, the current computational approaches to RNA structure comparison only consider structures without pseudoknots. Because of their importance to RNA function, we believe that incorporating pseudoknots in structural comparisons is critical to identifying biologically important classes of molecules. In this paper we propose a straightforward approach to comparing RNA structural topologies, including pseudoknots, and identifying known and unknown conserved topologies. Waterman  introducelements –20, and elements . Fontana by size . Shu et  as well , which u as well , 24, the as well , 24. Alt as well  were dev as well , 8 of Giudoknots . BuildinaphClust  for fastaphClust . However2, the second eigenvalue of the Laplacian matrix [2 and linear combinations of α and β , for categorizing the structural similarity of RNA graphs, and for predicting whether randomly generated RNA topologies are similar to biological examples (RNA-like). These numerical descriptors, however, have never been shown to be able to group RNAs into structural/functional classes. Moreover, these approaches, which rely on a small number of numeric descriptors, cannot identify similarity between specific substructures nested within fairly large graphs .The Schlick group has developed the RNA-As-Graphs procedure, which combines elements from several sources to develop a database of mathematically possible RNA graphs in which RNA structures are represented as Shapiro tree graphs, without pseudoknots, or as dual graphs, with inclusion of pseudoknots –32. Numen matrix –35, measThere are several aspects of RNA structure that make it particularly hard to identify topologically similar structures. Structures from the same functional family may have little or no sequence similarity; they typically have a similar arrangement of stems (topology), but different local base-pairing; our knowledge of the structures may be incomplete due to lack of a high-quality three-dimensional structure or structural prediction; structures may lack biologically important pseudoknots since tractable computational approaches based on dynamic programming often do not include these important features; or in the case of graph comparison, the computation itself may require infeasible amounts of time. The RNA XIOS graph  explicitA set of curated RNA structures have been collected from the literature and a variety of biological databases , and is In a XIOS graph, RNA stems are shown as vertices and the relationships between stems are shown as edges . Edges me.g., the 23S rRNA can have more than 50 stems [This work focuses on the topological similarity between RNA structures, that is, similarity in the relative location and nesting of stems, and the location of pseudoknots. In principle, this should provide the broadest range of matching since individual structures often differ in the length of stems and the length of single-stranded regions between stems. As mentioned before, the sequences themselves can be even more variable with little or no sequence conservation detectable, even between RNAs with similar structures. Topologically similar substructures in a pair of RNAs correspond to isomorphous subgraphs in their respective XIOS graphs. The maximal common subgraph (MCS) represents the greatest possible topological match between RNAs, similar to the maximal alignment between two sequences. But the MCS is difficult to identify because of the large size of biologically important structures; 50 stems . Finding50 stems , making We have exhaustively enumerated a non-redundant set of all physically possible RNA topological motifs containing from one to seven stems . The graObviously, this procedure generates multiple copies (isomorphs) of some topologies, for instance  and , as well as some graphs that are not connected . Some of the isomorphs can be eliminated by imposing two restrictions. First, the graph must be connected, and second, the first instances  of each object (stem) must occur in numerical order. Even these restrictions do not entirely eliminate permutations that correspond to isomorphic XIOS graphs. For instance, the sets  and  are mirror images of each other, and correspond to the same XIOS graph. These symmetry-related topologies are detected and removed using the gSpan , 49 apprUsing this approach, we have enumerated a library of all unique physically possible RNA topologies with 2 to 7 stem structures . BecauseThe topologies in the library are not independent; two unique 5-stem XIOS graphs, for instance, may share a common 4-stem subgraph as shown in A XIOS graph corresponding to a single structure can be characterized by the set of fixed-size subgraphs it contains. This set of constituent subgraphs is the RNA fingerprint , which csimple fingerprint. We define the extended fingerprint as the simple fingerprint plus all of the ancestral subgraphs . It is essential, therefore to consider whether the results in Figs i.e., graphs with no information from real biological structures except the frequency of occurrence of subgraphs in the known structures. Both the expanded and the decoy graph sets should be completely free of size effects since they all have exactly the same number of stems. The two sets were mixed and graphs compared using the Extended Fingerprint Jaccard Similarity. There is only a minor decrease in performance , where n is the number of graphs in the library , and m is the number of edges in the query graph. The subgraph random sampling algorithm can be parallelized by simultaneously running independent instances on multiple processors. The algorithm identifies the fingerprint of all 206 curated RNA graphs in a reasonable time, especially when it is run on multiple cores  . FunctioThe XIOS graph is a topological graph approach  that speExhaustively enumerating the set of subgraphs present in a XIOS graph is time consuming because each subgraph in the entire motif database must be separately tested against the query to determine whether there is a match. Because the dictionary of subgraphs is large , a brute force approach is slow. In this work we suggest a sampling approach to enumerating the subgraph spectrum. The computational complexity of motif sampling depends on both the size and structure of the query graph, and on the number of vertices sampled in each iteration. As most of RNA XIOS graphs are highly connected, an increase in graph size can result in a large increase in the time required to completely sample the fingerprint. Fortunately, the motif sampling is completely parallelizable; any number of processors can independently sample subgraphs from the query, and the time required per query graph is modest. Furthermore, our results suggest that a complete fingerprint may not be necessary; that even incomplete fingerprints (such as fingerprints derived from structures where part of the structure has been removed) are sufficient to identify topologically similar structures. The question of whether absolutely every subgraph has been detected, which a sampling strategy cannot guarantee, is therefore somewhat moot.Experimental determination of RNA structures by X-ray crystallography or NMR is difficult, and a relatively small number of complete structures are available. Instead, structures are often predicted using a combination of biochemical information , secondary structure prediction, and phylogenetic conservation (covariance). This results in “known” structures that are incomplete (missing important stems) or inaccurate . It is therefore important that the structural/topological comparison be robust with respect to incompleteness or error in the structures, a salient characteristic of the RNA fingerprint comparison we describe here. The extended-fingerprint Jaccard Similarity correctly identifies topologically similar RNAs across a broad range of sizes, and biological functions, but its potential application is far more general. RNA structure prediction is commonly judged to be 60 to 80 percent accurate , 68, 82.S1 Fig(PDF)Click here for additional data file.S2 Fig(PDF)Click here for additional data file.S3 Fig(PDF)Click here for additional data file.S4 Fig(PDF)Click here for additional data file.S5 Fig(PDF)Click here for additional data file.S1 Table(PDF)Click here for additional data file.S2 Table(PDF)Click here for additional data file.S3 Table(PDF)Click here for additional data file.S4 Table(PDF)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.


Increasing levels of carbon dioxide in the atmosphere put shallow, warm-water coral reef ecosystems, and the people who depend upon them at risk from two key global environmental stresses: 1) elevated sea surface temperature , and 2) ocean acidification. These global stressors: cannot be avoided by local management, compound local stressors, and hasten the loss of ecosystem services. Impacts to people will be most grave where a) human dependence on coral reef ecosystems is high, b) sea surface temperature reaches critical levels soonest, and c) ocean acidification levels are most severe. Where these elements align, swift action will be needed to protect people’s lives and livelihoods, but such action must be informed by data and science.2-related global environmental stresses could cause the most severe impacts. Mapping indicators has been proposed as a way of combining natural and social science data to identify policy actions even when the needed science is relatively nascent. To identify where people are at risk and where more science is needed, we map indicators of biological, physical and social science factors to understand how human dependence on coral reef ecosystems will be affected by globally-driven threats to corals expected in a high-CO2 world. Western Mexico, Micronesia, Indonesia and parts of Australia have high human dependence and will likely face severe combined threats. As a region, Southeast Asia is particularly at risk. Many of the countries most dependent upon coral reef ecosystems are places for which we have the least robust data on ocean acidification. These areas require new data and interdisciplinary scientific research to help coral reef-dependent human communities better prepare for a high CO2 world.Designing policies to offset potential harm to coral reef ecosystems and people requires a better understanding of where CO Hundreds of millions of people worldwide depend on coral reef ecosystems. Coral r2 [2-emitting nations  to reduce carbon emissions that cause both climate change and OA, 2) reduce damages to corals caused by local environmental stressors that can make these problems worse, and 3) improve and/or restore associated ecosystems (e.g. mangroves) to a state that could replace lost ecosystem services and thus minimize impacts on people. Engineering responses, other than green infrastructure and restoration, to counter these global threats have also been proposed [Increasing levels of carbon dioxide in the atmosphere put shallow, warm-water coral reef ecosystems, and the people who depend upon them at risk from two key global environmental stresses: 1) elevated sea surface temperature , and 2) ocean acidification (OA). Bleaching and OA can compound local reef stresses that will hasten the loss of the ecosystem services provided by reefs . Structu2 : 1) urgeproposed ,13, but 2-related threats to reefs will not be the same across the globe[2 will cause the most immediate and serious problems where a) human dependence on coral reef ecosystems is high, b) sea surface temperature reaches critical levels soonest, and c) OA levels are most severe. Where these elements align, swift action will be needed to protect people’s lives and livelihoods, but such policy action must be informed by data and science. Correspondingly, places where the threats of OA and climate change are low may serve as potential refugia for coral reef organisms and larvae.The ecological and social impacts of COthe globe,5,14. In2 world and the people and countries that will be affected. Two previous studies examined the combined threats faced by coral reefs from local and global stressors as well as an array of human dimensions that include human dependence and adaptive capacity [2 future. Our analysis also differs from previous studies in that we focus on the dependence of people on coral reef ecosystem services without attempting to assess their adaptive capacity. Adaptive capacity, while an important factor in evaluating vulnerability and risk within a region, is often represented with metrics that do not accurately convey conditions of coastal communities [2 threats to human outcomes.Sufficient indicator data exist to create preliminary maps of the potential threats to coral reef ecosystems posed by a high-COcapacity ,1. We upmunities . By focu2 in the atmosphere can help us identify where new science and data are needed to help people deal with these environmental changes and coral reef decline.There still is much to be learned about the impacts of global change on coral reef ecosystems and the people who depend on them. We need to better understand the ecological science regarding how coral reefs are affected by both global and local environmental stressors and how people, in turn, respond to these changes. Social and economic factors should be directly considered in setting research priorities about locations for new science. An examination of current human dependence on coral reef ecosystems and our current state of knowledge about the large scale and unavoidable threats that will result from increasing concentrations of COCoral bleaching, mortality, and disease caused by elevated sea surface temperature, have direct impacts on coral reef ecosystems . Sustain2 world. Van Hooidonk et al. [2, known as OA and often measured by aragonite saturation state (Ωar), also poses a severe threat to corals and reef ecosystems[ar levels of 3.1 or less, a level some coral reefs will experience in the next decade, are known to impair larval recruitment of some corals[The ability of coral reef ecosystems to recover from damaging events is likely to be suppressed by the elevated sea surface temperature and OA expected to occur in a high-COk et al. ,25 used cosystems. While mcosystems–28, OA cme corals,30. Simime corals. Experimme corals, which cme corals,33.2 world may put coral reef-dependent people most at risk [We use an indicator approach to identify places where key environmental factors driven by a high-CO at risk . Mapping at risk . As such2-driven threats to coral reefs, we map indicators of two key aspects of current human dependence on coral reefs (people who benefit from the shoreline protection provided by reefs and reef-related fisheries) and two key indicators of oceanic change in a high CO2 world  projections that show when sea surface temperature may reach levels that will cause bleaching  for the year 2050 under the business-as-usual (RCP8.5) emissions scenario [ar is a measure of carbonate chemistry, related to OA, that reflects the level of carbon saturation of ocean water. It is a measure originally intended to reflect the challenge that OA poses for organisms with calcium carbonate skeletons. Lower levels of aragonite indicate more severe OA. To calculate Ωar in year 2050, we use the same technique provided by [ar in 2050 using the projected atmospheric pCO2 and sea surface temperature in 2050 under the RCP8.5 emissions scenario, in-situ total alkalinity , as well as the salinity, silicate, and phosphate data, as well as calculated surface water pCO2 from the base year 2000. Data regarding the predicted Ωar levels for 2050 are available in the supplementary materials  are highly concentrated, mostly in the Western and Eastern Tropical Pacific. Because OA and increasing sea surface temperature follow different latitudinal gradients [To understand where coastal communities will face high combined stress from both increased bleaching and more intense OA, we rescale  each gloap these . Areas tradients , no areaHuman dependence on coral reefs and a high combined score for stress from both OA and coral bleaching (e.g. scores approaching 15) are projected to occur along the coasts of much of Western Mexico and Micronesia as well as the coastlines of Indonesia and Australia on the Timor Sea and parts of Southeast Asia. These places may require swift action to protect people from the combined impacts of warming seas and increasingly acidified oceans (e.g. many parts of Southeast Asia).2 world, we merge coral reef areas into the biological ocean provinces proposed by both Donner [ar, ar = 3.07, which is below the level known to cause reduced growth and recruitment in some corals [The ecological response of coral reefs is likely to vary regionally due to different species composition, varying rates of change in temperature and acidification conditions, and differences in the conditions that promote coral reef resilience  bottom . To visuh Donner  and Mainh Donner . Within e corals ,29). Sou2, we need to do more. Our analysis shows, however, that in many places . CollecThe Global Ocean Acidification Observing Network (GOA-ON) was established to better achieve “socially relevant” OA monitoring  , and cou2, but we recognize that the ecological health of coral reefs depends on many factors [We focus only on two key stressors associated with increased atmospheric CO factors ,35. Cora factors ,53). Kno2 world has already started, for example through the UNFCCC process [Finally, we need more and better social and economic science to understand how humans will respond to projected environmental changes in coral reef ecosystems . New research on human responses to coral reef change is emerging –58. Whil process , science2 world, new, interdisciplinary science should be conducted in regions where the likely social and economic impacts of bleaching and OA on humans could be high, and thus the potential societal relevance of such science could also be high. Unfortunately, carrying out science and data collection in many of the coral reef regions most at risk of global environmental change is a challenge. Many of these regions lack the financial or human capacity to carry out large-scale experiments and routine data collection. It is often difficult for scientists to obtain permission to sample in coastal ocean areas or where national maritime jurisdictions are disputed. Both international and regional efforts are needed to overcome the impediments to obtaining data in these areas. GOA-ON and other international bodies (e.g. the United Nations Environment Program) should begin to facilitate such cooperation without delay because elevated sea surface temperatures and critical levels of OA are upon us. While reducing atmospheric CO2 should remain a primary goal, a portion of international climate change funding that will become available for developing countries in the coming years should go towards supporting this research.To expedite action to combat the changes corals may experience in a high COS1 Data(NC)Click here for additional data file.S2 Data(NC)Click here for additional data file.S3 Data(NC)Click here for additional data file.S1 TableDerived from an ensemble of models that are included in the IPCC Fifth Assessment Report (CMIP5) for the emission scenario RCP8.5, OISST V2 1982–2005 climatology.(DOCX)Click here for additional data file.S2 TableBased on GLODAP, CARINA and PACIFICA data .(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.