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"v1_Abstract": "Little is known about effects of large storm systems on mesophotic reefs. This study reports on how Typhoon 17 (Jelawat) affected Ryugu Reef on Okinawa-jima, Japan in September 2012. Benthic communities were surveyed before and after the typhoon using line intercept transect method. Comparison of the benthic assemblages showed highly significant differences in coral coverage at depths of 25-32 m before and after Typhoon 17. A large deep stand of Pachyseris foliosa was apparently less resistant to the storm than the shallower high diversity area of this reef. Contradictory to common perception, this research shows that large foliose corals at deeper depths are just as susceptible to typhoon damage as shallower branching corals. However, descriptive functional group analyses resulted in only minor changes after the disturbance, suggesting the high likelihood of recovery and the high resilience capacity of this mesophotic reef.",
"v1_col_introduction": "introduction : Typhoon damage from direct physical disturbances, turbidity, sedimentation, and salinity\nchanges can be destructive to shallow coral reefs and has been well studied (Van Woesik, Ayling & Mapstone, 1991; Harmelin-Vivien, 1994; Ninio et al., 2000; Cheal et al., 2002; Hongo, Kawamata & Goto, 2012). Declines in coral cover on shallow reefs (<25 m in depth) has been documented, specifically in genera such as Acropora, Montastraea, Porites, Agaracia, Diploria, Millepora, Siderastrea, Pocillopora, Pachyseris, Montipora, and Merulina (Harmelin-Vivien, 1994; Van Woesik, De Vantier & Glazebrook, 1995; Fabricius et al., 2008). Although massive corals such as Montipora, Montastraea, Siderastrea, and Diploria can be overturned during typhoons, they are often the most resistant to storms and therefore tend to dominate or increase in cover after a disturbance (Harmelin-Vivien, 1994; Fabricius et al., 2008; Hongo, Kawamata & Goto, 2012). Increase in cover of genera Porites, Montipora, and Lobophyllia, unattached fungiids and even Acropora species with high regeneration efficiencies have been documented after disturbances (Harmelin-Vivien, 1994; Van Woesik , De Vantier & Glazebrook, 1995; Fabricius et al., 2008; Kuo et al., 2010).\nRecent observational data of a mesophotic reef (35\u201340 m) near Kume-jima, Okinawa,\nJapan before and after a typhoon reported that newly broken Acropora pieces fused to new branches, producing clones, and the reef made a quick recovery after typhoon damage (Fujita, Kimura, & Atsuo, 2012).\nHowever, comparatively little has been published on the effects of tropical cyclones on\ndeeper reefs (Randall & Eldredge, 1977; Woodley et al., 1981; Walsh, 1983; Pfeffer & Tribble, 1985; Harmelin-Vivien & Laboute, 1986; Van Woesik, Ayling & Mapstone, 1991). In general, reefs at depths greater than 25 meters appear to be less affected by tropical cyclones than shallower reefs (Harmelin-Vivien, 1994; Bongaerts et al., 2011; Bridge & Guinotte, 2012). Harmelin-Vivien (1994) reported that most physical damage to deep reefs was due to rolling\n16\n17\n18\n19\n20\n21\n22\n23\n24\n25\n26\n27\n28\n29\n30\n31\n32\n33\n34\n35\n36\n37\n38\n39\n40\nPeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013)\nR ev ie w in g M an\nus cr ip t\ncolonies dislodged from shallower areas. However, as reported in Harmelin-Vivien (1994), tropical cyclone induced coral destruction was observed to depths of 25 m in Belize (Highsmith, Riggs, & D\u2019Antonio,1980), to 30 m on the Great Barrier Reef (Van Woesik, Ayling & Mapstone, 1991), to 30 m in Guam and Hawaii (Walsh, 1983), to 50 m in Jamaica (Woodley et al., 1981), to 50 m in Hawaii (Pfeffer & Tribble, 1985), to 50-65 m on the Great Barrier Reef (Bongaerts et al., 2013), and to 90-100 m in French Polynesia (Laboute, 1985; Harmelin-Vivien & Laboute, 1986). Bridge and Guinotte (2012) concluded that although depth does have an impact on coral community survival, rugosity and angle of slope play large roles in the protection of species on a reef. Large communities of of broadcast spawning species are important to the recovery of reefs and are more likely to survive in deeper waters than in shallower waters during a typhoon (Madin & Connolly, 2006; Bridge et al., 2012), and recruitment of coral larvae is likely the most effective method of recovery for disturbed reefs (Harmelin-Vivien, 1994).\nTyphoon 17 (Jelawat) struck the west coast of Okinawa-jima Island on 29 September\n2012 (Fig. 1)., heading from the southwest to the northeast with a general wind direction of northwest. The Japan Meteorological Agency (JMA) and the United States Navy Joint Typhoon Warning Center (JTW) documented this record-breaking typhoon as the third strongest typhoon to hit Okinawa-jima Island since weather radar observations were started in 1954 with maximum wave heights of 12 m. The Okinawa Meteorological Observatory (OMO) recorded the following maximum measurements for Typhoon 17 at the northern end of Okinawa-jima Island (Nago Meteorological Station): 32.2 m/s sustained winds, 57.4 m/s wind gusts, 947.4 hPa atmospheric pressure.\nRecently, Ohara et al. (2013) reported on a previously undiscovered shallow mesophotic\ncoral reef in Okinawa, Japan. The Japanese name for this reef is \u201cRyugu,\u201d based on its resemblance to the undersea palace of Ry\u016bjin, the dragon god of the sea. The deeper sections of Ryugu (32\u201342 m) were reported to be primarily composed of Pachyseris foliosa Veron, 1990,\n41\n42\n43\n44\n45\n46\n47\n48\n49\n50\n51\n52\n53\n54\n55\n56\n57\n58\n59\n60\n61\n62\n63\n64\n65\nPeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013)\nR ev ie w in g M an\nus cr ip t\nwith shallower sections (25\u201332 m) showing much higher diversity (Ohara et al., 2013). Little is known about Pachyseris foliosa, although the depth range of this species appears to be deeper than previously reported by Hoeksema, Rogers & Quibilan in 2008 (25-30 m).\nThis study reports on how Typhoon 17 affected Ryugu Reef with before and after transect\ndata. Objectives of this study include examination of coral communities at different depths and the identification of species and functional groups most affected by typhoons. One hypothesis tested was that shallow mesophotic reefs with large monospecific stands are more resistant to storm damage.",
"v2_Abstract": "Little is known about effects of large storm systems on mesophotic reefs. This study reports on how Typhoon 17 (Jelawat) affected Ryugu Reef on Okinawa-jima, Japan in September 2012. Benthic communities were surveyed before and after the typhoon using line intercept transect method. Comparison of the benthic assemblages showed highly significant differences in coral coverage at depths of 25-32 m before and after Typhoon 17. A large deep stand of Pachyseris foliosa was apparently less resistant to the storm than the shallower high diversity area of this reef. Contradictory to most current literature, this research shows that large foliose corals at deeper depths are just as susceptible to typhoon damage as shallower branching corals. However, descriptive functional group analyses resulted in only minor changes after the disturbance, suggesting the high likelihood of recovery and the high resilience capacity of this mesophotic reef.",
"v2_col_introduction": "introduction : Typhoon damage from direct physical disturbances, turbidity, sedimentation, and salinity\nchanges can be destructive to shallow coral reefs and has been well studied (Van Woesik, Ayling & Mapstone, 1991; Harmelin-Vivien, 1994; Ninio et al., 2000; Cheal et al., 2002; Hongo, Kawamata & Goto, 2012). Declines in coral cover on shallow reefs (<25 m in depth) has been documented, specifically in genera such as Acropora, Montastrea, Porites, Agaracia, Diploria, Millepora, Siderastrea, Pocillopora, Pachyseris, Montipora, and Merulina (Harmelin-Vivien, 1994; Van Woesik, De Vantier & Glazebrook, 1995; Fabricius et al., 2008). Although massive corals such as Montipora, Montastrea, Siderastrea, and Diploria can be overturned during\nPeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013)\nR ev ie w in g M an\nus cr ip t\ntyphoons, they are often the most resistant to storms and therefore tend to dominate or increase in cover after a disturbance (Harmelin-Vivien, 1994; Fabricius et al., 2008; Hongo, Kawamata & Goto, 2012). Increase in cover of genera Porites, Montipora, and Lobophyllia, unattached fungiids and even Acropora species with high regeneration efficiencies have been documented after disturbances (Harmelin-Vivien, 1994; Van Woesik , De Vantier & Glazebrook, 1995; Fabricius et al., 2008; Kuo et al., 2010).\nRecent observational data of a mesophotic reef (35\u201340 m) near Kume-jima, Okinawa,\nJapan before and after a typhoon reported that newly broken Acropora pieces fused to new branches, producing clones, and the reef made a quick recovery after typhoon damage (Fujita, Kimura, & Atsuo, 2012).\nHowever, comparatively little has been published on the effects of tropical cyclones on\ndeeper reefs (Randall & Eldredge, 1977; Woodley et al., 1981; Walsh, 1983; Pfeffer & Tribble, 1985; Harmelin-Vivien & Laboute, 1986; Van Woesik, Ayling & Mapstone, 1991). In general, reefs at depths greater than 25 meters appear to be less affected by tropical cyclones than shallower reefs (Harmelin-Vivien, 1994; Bongaerts et al., 2011; Bridge & Guinotte, 2012). Harmelin-Vivien (1994) reported that most physical damage to deep reefs was due to rolling colonies dislodged from shallower areas. Bridge and Guinotte (2012) concluded that although depth does have an impact on coral community survival, rugosity and angle of slope play large roles in the protection of species on a reef. Large communities of plating corals that are important to the recovery of broadcast spawning species are more likely to survive in deeper waters than in shallower waters during a typhoon (Madin & Connolly, 2006; Bridge et al., 2012), and recruitment of coral larvae is likely the most effective method of recovery for disturbed reefs (Harmelin-Vivien, 1994).\nPeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013)\nR ev ie w in g M an\nus cr ip t\nTyphoon 17 (Jelawat) struck the west coast of Okinawa-jima Island on 29 September\n2012 (Fig. 1)., heading from the southwest to the northeast with a general wind direction of northwest. The Japan Meteorological Agency (JMA) and the United States Navy Joint Typhoon Warning Center (JTW) documented this record-breaking typhoon as the third strongest typhoon to hit Okinawa-jima Island since weather radar observations were started in 1954 with maximum wave heights of 12 m. The Okinawa Meteorological Observatory (OMO) recorded the following maximum measurements for Typhoon 17 at the northern end of Okinawa-jima Island (Nago Meteorological Station): 32.2 m/s sustained winds, 57.4 m/s wind gusts, 947.4 hPa atmospheric pressure.\nRecently, Ohara et al. (2013) reported on a previously undiscovered shallow mesophotic\ncoral reef in Okinawa, Japan. The Japanese name for this reef is \u201cRyugu,\u201d based on its resemblance to the undersea palace of Ry\u016bjin, the dragon god of the sea. The deeper sections of Ryugu (32\u201342 m) were reported to be primarily composed of Pachyseris foliosa Veron, 1990, with shallower sections (25\u201332 m) showing much higher diversity (Ohara et al., 2013). Little is known about Pachyseris foliosa, although the depth range of this species appears to be deeper than previously reported by Hoeksema, Rogers & Quibilan in 2008 (25-30 m).\nThis study reports on how Typhoon 17 affected Ryugu Reef with before and after transect\ndata. Objectives of this study include examination of coral communities at different depths and the identification of species and functional groups most affected by typhoons. One hypothesis tested was that deeper reefs with large monospecific stands are more resistant to storm damage.",
"v1_text": "materials and methods : Five stations were designated at the Ryugu site (Fig 1). Station 1 was the deepest (42 m) and station 5 the shallowest (17 m). Stations are shown in Fig. 1 and summarized in Table 1. Temperature was recorded every 30 minutes using temperature loggers (HOBO U22 Temp Pro v2 logger, Onset Corp., Massachusetts, U.S.A.) placed approximately 30-50 cm from the substrate at each station from 12 September 2012 to 10 January 2013. Water motion was estimated at each station (except station 1) by the dissolution of plaster balls. Plaster balls (10.5 cm diameter) were made following Komatsu and Kawai (1992). The balls were set approximately 50 cm above the substrate at stations 2\u20135 on 11 January 2013 and removed on 16 January 2013. Water speeds for each station were calculated following the equations provided in Yokoyama, Inoue & Abo (2004). Ten meter line transects were surveyed both before (17 April 2012 and 11\u201312 September 2012) and after (14 December 2012) Typhoon 17 at locations near stations 2 (7 transects before, 9 transects after) and 3 (10 transects before, 8 transects after). Based on the amount of data available, only stations 2 and 3 were included in analyses. For each line transect, a 10 meter tape measure was laid out along a constant dedpth contour and overlapping photographs or video was 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t taken along the line. Photographs or videos taken along the transects were used to report the total distance occupied by each operational taxonomic unit (OTU) identified. When feasible, OTUs were identified to species level following Hoeksema (1989) and Gittenberger, Reignen & Hoeksema (2011) for Fungiidae and Veron (2000) for other species. Community data were analyzed using PRIMER 6 statistical software in order to find differences in coral communities before and after the typhoon (Clarke and Warwick, 2001). All percent cover data were square-root transformed prior to analysis to moderately down-weight the importance of large space occupying operational taxonomic units (OTU). Bray-Curtis similarity matrices were calculated at stations 2 and 3. A one-way analysis of similarities test (ANOSIM) was performed to determine the difference and magnitude of difference in the assemblages before and after Typhoon 17. Non-Metric Multidimensional scaling (nMDS) was used to visualize multivariate patterns on the basis of the Bray-Curtis matrix. Bubble plot (square-root transformed cover data) was added to the plots to visualize variation in relevant OTUs. Each circle in figure 4 displays relative abundance of livecoral species (based on square root transformed data of the species' occurrence along each transect). Finally, the percentage contributions of each benthic grouping for observed differences between locations were assessed with the SIMPER routine. To assess potential changes in the functionality of the coral community after the typhoon coral taxa were classified into functional groups according to the shapes of the colonies following Denis et al. (2013). Each OTU was assigned to one or more of eight functional groups: massive, encrusting, foliose, columnar, plate-like, bushy, arborescent, and unattached (Supplementary Table 1). These were defined by each colony\u2019s growth form as described in Veron (2000), Wallace (1999) and by visual observation. Functional composition of the coral assemblages were calculated based on the relative abundance of coral OTU and plot for stations 2 and 3 before and after the typhoon. 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t results : Temperature sensors showed that the temperature was typically 0.1\u20130.2 degrees lower at station 5 (shallowest station) than at any of the other stations, although the temperature appeared to fluctuate the most at this station. Temperature drops were observed at all stations during and directly after typhoons, with the largest decrease in temperature at station 1 (20.9\u00b0C after Typhoon 17) (Fig. 2). Based on plaster ball weight loss, station 2 had the lowest amount of water movement compared to the other stations. The weight loss of each plaster ball and water speed for each station were as follows: Station 2: lost 254 g, 9.2 cm/s; Station 3: lost 284 g, 11.2 cm/s; Station 4: lost 292 g, 11.7 cm/s; Station 5: lost 294 g, 12.5 cm/s. Supplementary table 1 lists all OTUs documented on transects and their percent cover change before and after Typhoon 17. Live coral cover decreased and coral rubble increased by 33.3% at station 2 and by 11.4% at station 3 after Typhoon 17. Figure 3 shows before and after images at stations 2 and 3. Composition of the benthic communities before and after Typhoon 17 (Fig. 4) presented a significant difference at both station 2 (ANOSIM test, R = 0.572, p = 0.001) and station 3 (ANOSIM test, R = 0.24, p = 0.009). At station 2, the change in the occurrence of coral rubble on the transects contributed the most to this difference (Simper-test, 33.0% - Fig. 4), followed by the coverage of Lithophyllon repanda (12.7%), Pachyseris foliosa (11.6%), then Galaxea sp. 1 (11.2%). At station 3, every OTU contributed to <10% of the difference observed. Change in the occurrence of coral rubble contributed to only 6% of this difference (Fig. 4). Interestingly, the difference observed at station 3 was not significant (R = 0.07, p = 0.137) when the effects of the dominant OTU were not reduced using square root transformation. Functionality of the coral communities (Fig. 5) at both stations seems only slightly affected by the typhoon. Among the major differences observed at station 2, the encrusting group decreased by 8%, while the foliose group increased by 15%. At station 3, bushy (8%), columnar (6%) and plate-like (3%) groups 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t suffered the most from the path of the typhoon while encrusting (7%) and foliose (11%) corals were more resistant to this disturbance. acknowledgements : Thanks go to the boat captain, Tokunobu Toyama and diving staff, Sakiko Kawabata and Yoko Fudesaka, for their assistance during transect surveys. V. Denis is the recipient of a Post-Doctoral fellowship by the National Science Council of Taiwan. J.D. Reimer was funded by the Rising Star Program, and International Research Hub Project for Climate Change and Coral Reef/Island Dynamics, both at the University of the Ryukyus. 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t discussion : Typhoon 17 resulted in highly significant changes to the live coral abundance at Ryugu stations 2 and 3. The depth of this reef does not appear to have sheltered corals from drastic damage with notable increases in coral rubble in many of the study areas. Most interestingly, P. foliosa was among those species most affected by Typhoon 17. Apparently more diverse and complex communities, such as at station 3, are more resistant to typhoons in terms of survivability and functional group distribution, perhaps due to the lower impact on individual species. Based on SIMPER tests, there were many small differences in diverse OTUs at station 3 compared to station 2, where only 4 OTUs contributed to 70% of the typhoon effects. Station 2, primarily composed of P. foliosa, was heavily impacted by this storm, despite the fact that it was deeper than station 3, suggesting that the foliose structure of P. foliosa is vulnerable to physical disturbances. The large monospecific stand found here is also in a more stable environment, likely making it more sensitive to disturbance (Hughes, 1989; Rogers, 1992, 1993; HarmelinVivien, 1994). Therefore, our hypothesis that shallow mesophotic reefs with large monospecific stands are more resistant to storm damage is rejected. Consistent with previous shallow water typhoon damage studies (Harmelin-Vivien, 1994; Van Woesik, De Vantier & Glazebrook, 1995; Fabricius et al., 2008; Kuo et al., 2010) corals in the genus Acropora were strongly affected and were mostly dead at Ryugu after Typhoon 17 whereas unattached Fungiidae corals were mostly healthy. The fungiid corals may have been hidden under other living corals and after Typhoon 17 became more visible with the other corals having been damaged. Away from the transect locations; however, several Fungiidae corals were completely buried by newly generated Acropora rubble and other branching coral 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t rubble. Accordingly, despite minor changes in the functionality of the coral community observed before and after Typhoon 17, the groups the most affected at station 3 were the bushy, columnar and plate-like corals. At station 2, the dominance of P. foliosa may have masked any differences. Most damaged colonies of P. foliosa were still alive after Typhoon 17, suggesting that species composition of this area may not change. This opposes the common idea that only massive corals would remain after disturbance (Harmelin-Vivien, 1994), suggesting a strong potential for the recovery and resilience of Ryugu Reef. Pachyseris species are typically gonochoric spawners that are most likely unable to fuse and create clones (Richmond and Hunter, 1990). If Pachyseris species reproduce only by spawning, Pachyseris-dominated reefs such as Ryugu should have a much slower recovery rate than Acropora-dominated reefs such as the one found near Kumejima. However, recruitment of coral larvae may allow this reef to recover relatively quickly. During this study, new P. foliosa polyps were observed growing two to three months after Typhoon 17, suggesting that the Pachyseris portion of the reef had already started to recover from the damage it incurred. Based on plaster ball data, Ryugu is a fairly calm reef and the lower currents at station 2 may be due to less tides or wave impacts, and is worth investigating further in future studies. The lower temperature observed during Typhoon 17 at station 1 (42 m) may be due to upwelling or thermal averaging due to wind driven vertical mixing with deeper cooler water that was enhanced by the onset of the typhoon, as seen during other large storms. Figure 2 shows large changes in temperature on 18 September (drop to 26.0\u00b0C) and 30 September (drop to 20.9\u00b0C), both of which correspond with large typhoon systems (Fig. 1; Typhoons 16 and 17, respectively). Many studies have found that increasing sea surface temperatures and global climate change have and will continue to cause increases in typhoon frequency, power dissipation, and storm intensity (Emanuel, 2005; Trenberth, 2005; Webster et al., 2005; Emanuel, Sundararajan & Williams, 2008; Tu et al., 2009). Tu et al. (2009) have documented a northward shift in typhoon 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t tracks in the western North Pacific-East Asia region with an increase in typhoon frequency in the Taiwan/East China Sea region (3.3 per year from 1970-1999; 5.7 per year from 2000-2006). Emanuel (2005) documented an increase in destructiveness of cyclones since the 1970s and has predicted a continued increase with global climate change. Global climate change is expected to bring larger and stronger typhoons to Okinawa, which will likely affect the survivability of some coral populations. A potential increase in storms makes it even more important to understand their effect on mesophotic reefs, which have been thought to act as refugia for many marine organisms during disturbances on shallow reefs. This study has shown that despite their depth, shallow mesophotic reefs may also be strongly affected by disturbances. It is, therefore, critical to document the succession of this reef after disturbances such as Typhoon 17 to understand its resilience and the role that mesophotic reefs may play in the future of coral reefs. 2013; station 3, c) 12 september 2012, d) 01 january 2013 : PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t Figure 4 Non-metric dimensional scaling of the benthic communities at Ryugu Reef Non-metric dimensional scaling of the benthic communities at Ryugu Reef based on the Bray-Curtis similarities matrices. Each circle in the bubble plot displays relative abundance of live coral or percent cover of coral rubble (based on square root transformed data of the species' occurrence along each transect) a) Station 2: live coral species, b) Station 2: coral rubble, c) Station 3: live coral species, d) Station 3: coral rubble. Red circle: before typhoon, blue circle: after typhoon. PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t Figure 5 Functional composition of the coral assemblage before and after Typhoon 17 at Ryugu Reef Functional composition of the coral assemblage before and after Typhoon 17 at Ryugu Reef, Stations 2 and 3 based on relative abundance of the coral OTUs. Axes represent the relative contribution of each of the 8 functional groups. PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t Table 1(on next page) stations at ryugu reef : PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t Station Location/Description Depth (m) 1 Outside outer edge of dense Pachyseris foliosa area, sandy 42 2 Upper edge of dense Pachyseris foliosa area 31.2 3 Upper edge of high diversity area 26.5 4 Upper edge of Fungiidae/rubble area 21.3 5 Sand, coral rubble 17 PeerJ reviewing PDF | (v2013:07:651:1:0:REVIEW 13 Aug 2013) R ev ie w in g M an us cr ip t",
"v2_text": "abstract : Little is known about effects of large storm systems on mesophotic reefs. This study reports on how Typhoon 17 (Jelawat) affected Ryugu Reef on Okinawa-jima, Japan in September 2012. Benthic communities were surveyed before and after the typhoon using line intercept transect method. Comparison of the benthic assemblages showed highly significant differences in coral coverage at depths of 25\u201332 m before and after Typhoon 17. A large deep stand of Pachyseris foliosa was apparently less resistant to the storm than the shallower high diversity area of this reef. Contradictory to most current literature, this research shows that large foliose corals at deeper depths are just as susceptible to typhoon damage as shallower branching corals. However, descriptive functional group analyses resulted in only minor changes after the disturbance, suggesting the high likelihood of recovery and the high resilience capacity of this mesophotic reef. materials and methods : PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Five stations were designated at the Ryugu site (Fig 1). Station 1 was the deepest (42 m) and station 5 the shallowest (17 m). Stations are shown in Fig. 1 and summarized in Table 1. Temperature was recorded every 30 minutes using temperature loggers (HOBO U22 Temp Pro v2 logger, Onset Corp., Massachusetts, U.S.A.) placed approximately 30-50 cm from the substrate at each station from 12 September 2012 to 10 January 2013. Water motion was estimated at each station (except station 1) by the dissolution of plaster balls. Plaster balls (10.5 cm diameter) were made following Komatsu and Kawai (1992). The balls were set approximately 50 cm above the substrate at stations 2\u20135 on 11 January 2013 and removed on 16 January 2013. Water speeds for each station were calculated following the equations provided in Yokoyama, Inoue & Abo (2004). Ten meter line transects were surveyed both before (17 April 2012 and 11\u201312 September 2012) and after (14 December 2012) Typhoon 17 at locations near stations 2 (7 transects before, 9 transects after) and 3 (10 transects before, 8 transects after). Based on the amount of data available, only stations 2 and 3 were included in analyses. For each line transect, a 10 meter tape measure was laid out and overlapping photographs or video was taken along the line. Photographs or videos taken along the transects were used to report the total distance occupied by each operational taxonomic unit (OTU) identified. When feasible, OTUs were identified to species level following Hoeksema (1989) and Gittenberger, Reignen & Hoeksema (2011) for Fungiidae and Veron (2000) for other species. Community data were analyzed using PRIMER 6 statistical software in order to find differences in coral communities before and after the typhoon (Clarke and Warwick, 2001). All percent cover data were square-root transformed prior to analysis to moderately down-weight the importance of large space occupying operational taxonomic units (OTU). Bray-Curtis similarity PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t matrices were calculated at stations 2 and 3. A one-way analysis of similarities test (ANOSIM) was performed to determine the difference and magnitude of difference in the assemblages before and after Typhoon 17. Non-Metric Multidimensional scaling (nMDS) was used to visualize multivariate patterns on the basis of the Bray-Curtis matrix. Bubble plot (square-root transformed cover data) was added to the plots to visualize variation in relevant OTUs. Each circle in figure 4 displays relative abundance of the species (based on square root transformed data of the species' occurrence along each transect). Finally, the percentage contributions of each benthic grouping for observed differences between locations were assessed with the SIMPER routine. To assess potential changes in the functionality of the coral community after the typhoon coral taxa were classified into functional groups according to the shapes of the colonies following Denis et al. (2013). Each OTU was assigned to one or more of eight functional groups: massive, encrusting, foliose, columnar, plate-like, bushy, arborescent, and unattached (Supplementary Table 1). These were defined by each colony\u2019s growth form as described in Veron (2000), Wallace (1999) and by visual observation. Functional composition of the coral assemblages were calculated based on the relative abundance of coral OTU and plot for stations 2 and 3 before and after the typhoon. results : Temperature sensors showed that the temperature was typically 0.1\u20130.2 degrees lower at station 5 (shallowest station) than at any of the other stations, although the temperature appeared to fluctuate the most at this station. Temperature drops were observed at all stations during and directly after typhoons, with the largest decrease in temperature at station 1 (20.9\u00b0C after PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Typhoon 17) (Fig. 2). Based on plaster ball weight loss, station 2 had the lowest amount of water movement compared to the other stations. The weight loss of each plaster ball and water speed for each station were as follows: Station 2: lost 254 g, 9.2 cm/s; Station 3: lost 284 g, 11.2 cm/s; Station 4: lost 292 g, 11.7 cm/s; Station 5: lost 294 g, 12.5 cm/s. Supplementary table 1 lists all OTUs documented on transects and their percent cover change before and after Typhoon 17. Coral rubble increased by 33.3% at station 2 and by 11.4% at station 3 after Typhoon 17. Figure 3 shows before and after images at stations 2 and 3. Composition of the benthic communities before and after Typhoon 17 (Fig. 4) presented a significant difference at both station 2 (ANOSIM test, R = 0.572, p = 0.001) and station 3 (ANOSIM test, R = 0.24, p = 0.009). At station 2, the change in the occurrence of coral rubble on the transects contributed the most to this difference (Simper-test, 33.0% - Fig. 4), followed by the coverage of Lithophyllon repanda (12.7%), Pachyseris foliosa (11.6%), then Galaxea sp. 1 (11.2%). At station 3, every OTU contributed to <10% of the difference observed. Change in the occurrence of coral rubble contributed to only 6% of this difference (Fig. 4). Interestingly, the difference observed at station 3 was not significant (R = 0.07, p = 0.137) when the effects of the dominant OTU were not reduced using square root transformation. Functionality of the coral communities (Fig. 5) at both stations seems only slightly affected by the typhoon. Among the major differences observed at station 2, the encrusting group decreased by 8%, while the foliose group increased by 15%. At station 3, bushy (8%), columnar (6%) and plate-like (3%) groups suffered the most from the path of the typhoon while encrusting (7%) and foliose (11%) corals were more resistant to this disturbance. figure legends : Figure 1. a)Map showing track of Typhoon 17 (Jelawat) around Okianwa-jima Island with position and b) studied stations of Ryugu Reef. Data on the track indicates date, time, central atmospheric pressure and maximum wind speed at each \"X\" mark. In b), dotted areas indicate positions of transects. Figure 2. Graph showing daily temperature change for Ryugu Reef, Stations 1\u20135, 12 September 2012 to 10 January 2013. Figure 3. Ryugu Reef photographs before and after Typhoon 17. Station 2, a) 12 September 2012, b) 01 January 2013; Station 3, c) 12 September 2012, d) 01 January 2013. Figure 4. Non-metric dimensional scaling of the benthic communities at Ryugu Reef based on the Bray-Curtis similarities matrices. Each circle displays relative abundance of the species (based on square root transformed data of the species' occurrence along each transect) a) Station 2, b) Station 2: bubble plot of coral rubble, c) Station 3, d) Station 3: bubble plot of coral rubble. Empty circle: before typhoon, full circle: after typhoon. Figure 5. Functional composition of the coral assemblage before and after Typhoon 17 at Ryugu Reef, Stations 2 and 3 based on relative abundance of the coral OTUs. Axes represent the relative contribution of each of the 8 functional groups. PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Figure 1 Map of typhoon track and Ryugu Reef stations a) Map showing track of Typhoon 17(Jelawat) around Okinawa-jima Island with position and b) studied stations of Ryugu Reef. Data on the track indicate date, time, central atmospheric pressure and maximum wind speed at each \"X\" mark. In b), dotted areas indicate positions of transects. PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Table 1(on next page) acknowledgements : Thanks go to the boat captain, Tokunobu Toyama and diving staff, Sakiko Kawabata and Yoko Fudesaka, for their assistance during transect surveys. V. Denis is the recipient of a Post-Doctoral fellowship by the National Science Council of Taiwan. J.D. Reimer was funded by the Rising Star Program, and International Research Hub Project for Climate Change and Coral Reef/Island Dynamics, both at the University of the Ryukyus. PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t discussion : PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Typhoon 17 resulted in highly significant changes to the coral communities at Ryugu stations 2 and 3. The depth of this reef does not appear to have sheltered corals from drastic damage with notable increases in coral rubble in many of the study areas. Most interestingly, P. foliosa was among those species most affected by Typhoon 17. It appears that more diverse and complex communities, such as at station 3, are more resistant to typhoons, perhaps due to the lower impact on individual species. Based on SIMPER tests, there were many small differences in diverse OTUs at station 3 compared to station 2, where only 4 OTUs contributed to 70% of the typhoon effects. Station 2, primarily composed of P. foliosa, was heavily impacted by this storm, despite the fact that it was deeper than station 3, suggesting that the foliose structure of P. foliosa is vulnerable to physical disturbances. The large monospecific stand found here is also in a more stable environment, likely making it more sensitive to disturbance (Hughes, 1989; Rogers, 1992, 1993; Harmelin-Vivien, 1994). Therefore, our hypothesis that deeper reefs with large monospecific stands are more resistant to storm damage is rejected. Consistent with previous shallow water typhoon damage studies (Harmelin-Vivien, 1994; Van Woesik, De Vantier & Glazebrook, 1995; Fabricius et al., 2008; Kuo et al., 2010) corals in the genus Acropora were strongly affected and were mostly dead at Ryugu after Typhoon 17 whereas unattached Fungiidae corals were mostly healthy. The fungiid corals may have been hidden under other living corals and after Typhoon 17 became more visible with the other corals having been damaged. Away from the transect locations; however, several Fungiidae corals were completely buried by newly generated Acropora rubble and other branching coral rubble. Accordingly, despite minor changes in the functionality of the coral community observed before and after Typhoon 17, the groups the most affected at station 3 were the bushy, columnar and plate-like corals. At station 2, the dominance of P. foliosa may have masked any differences. PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Most damaged colonies of P. foliosa were still alive after Typhoon 17, suggesting that species composition of this area may not change. This opposes the common idea that only massive corals would remain after disturbance (Harmelin-Vivien, 1994), suggesting a strong potential for the recovery and resilience of Ryugu Reef. Pachyseris species are typically gonochoric spawners (Richmond and Hunter, 1990), suggesting that they are most likely unable to fuse and create clones. If this is the case, Pachyseris-dominated reefs such as Ryugu should have a much slower recovery rate than Acropora-dominated reefs such as the one found near Kume-jima. However, recruitment of coral larvae may allow this reef to recover relatively quickly. During this study, new P. foliosa polyps were observed growing two to three months after Typhoon 17, suggesting that the Pachyseris portion of the reef had already started to recover from the damage it incurred. Based on plaster ball data, Ryugu is a fairly calm reef and the lower currents at station 2 may be due to less tides or wave impacts, and is worth investigating further in future studies. It is likely that the lower temperature observed during Typhoon 17 at station 1 (42 m) is due to upwelling or a thermocline that was enhanced by the onset of the typhoon, as seen during other large storms. Figure 2 shows large changes in temperature on 18 September (drop to 26.0\u00b0C) and 30 September (drop to 20.9\u00b0C), both of which correspond with large typhoon systems (Fig. 1; Typhoons 16 and 17, respectively). Many studies have found that increasing sea surface temperatures and global climate change have and will continue to result in increases in typhoon frequency, power dissipation, and storm intensity (Emanuel, 2005; Trenberth, 2005; Webster et al., 2005; Emanuel, Sundararajan & Williams, 2008; Tu et al., 2009). Tu et al. (2009) have documented a northward shift in typhoon tracks in the western North Pacific-East Asia region with an increase in typhoon frequency in the Taiwan/East China Sea region (3.3 per year from 1970-1999; 5.7 per year from 2000-2006). PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Emanuel (2005) documented an increase in destructiveness of cyclones since the 1970s and has predicted a continued increase with global climate change. With global climate change expected to bring larger and stronger typhoons to Okinawa, and the likelihood of these storms affecting the survivability of some coral populations, it is even more important to understand their effect on mesophotic reefs, which have been thought to act as refugia for many marine organisms during disturbances on shallow reefs. This study has shown that despite their depth, these deeper reefs may also be strongly affected by disturbances. It is, therefore, critical to document the succession of this mesophotic reef after disturbances such as Typhoon 17 to understand its resilience and the role that mesophotic reefs may play in the future of coral reefs. stations at ryugu reef : PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Station Location/Description Depth (m) 1 Outside outer edge of dense Pachyseris foliosa area, sandy 42 2 Upper edge of dense Pachyseris foliosa area 31.2 3 Upper edge of high diversity area 26.5 4 Upper edge of Fungiidae/rubble area 21.3 5 Sand, coral rubble 17 PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Figure 2 temperature change graph : Graph showing daily temperature change for Ryugu Reef, Stations 1-5, 12 September 2012 to 10 January 2013. PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Figure 3 Ryugu Reef photographs before and after Typhoon 17. Station 2, a) 12 September 2012, b) 01 January 2013; Station 3, c) 12 September 2012, d) 01 January 2013 PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Figure 4 Non-metric dimensional scaling of benthic communities at Ryugu Reef Non-metric dimensional scaling of the benthic communities at Ryugu Reef based on the Bray-Curtis similarities matrices. Each circle displays relative abundance of the species a) Station 2, bubble plot of live coral; b) Station 2, bubble plot of coral rubble; c) Station 3, bubble plot of live coral; d)Station 3, bubble plot of coral rubble. Empty circle: before typhoon, full circle: after typhoon PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t Figure 5 Functional composition of coral assemblage before and after typhoon Functional composition of the coral assemblage before and after Typhoon 17 at Ryugu Reef, Stations 2 and 3 based on relative abundance of the coral OYUs. Axes represent the relative contribution of each of the 8 functional groups PeerJ reviewing PDF | (v2013:07:651:0:0:NEW 16 Jul 2013) R ev ie w in g M an us cr ip t",
"url": "https://peerj.com/articles/152/reviews/",
"review_1": "Howard Young \u00b7 Aug 14, 2013 \u00b7 Academic Editor\nACCEPT\nYou changes were accepted and the manuscript is now ready for publication. Congratulations.",
"review_2": "Howard Young \u00b7 Jun 27, 2013 \u00b7 Academic Editor\nMAJOR REVISIONS\nDear Authors,\n\nI believe that your paper is worthy of publication but please try to especially address the concerns of the first reviewer. I am not concerned about comment 3 but I do believe that a response to the first 2 concerns is needed.",
"review_3": "Balamurugan Kuppusamy \u00b7 Jun 26, 2013\nBasic reporting\nSee below\nExperimental design\nSee below\nValidity of the findings\nSee below\nAdditional comments\nThe manuscript by Baysal et al studies the effect of hypoxia on C to U RNA editing of SDHB gene in monocytes. Previous studies show that SDH is a heterotetrameric tumor suppressor complex mutated in paraganglioma tumors due to hypoxia-inducible activation pathways. The authors studied regulation, extent and cell type origin of SDHB RNA editing. The authors found that RNA editing is low in monocyte-enriched PBMCs under normal condition, however, markedly increased under hypoxic conditions. This leads to down regulation of SDHB gene and consequently an increase in monocyte cell survival. Overall these findings add the mechanistic details to our understanding of the RNA editing under physiologically relevant conditions such as hypoxia, however additional data would support and strengthen their conclusions.\n\nMajor concerns:\n\n1. The authors show that hypoxia, one of the physiological conditions, increased the C136U RNA editing of SDHB transcripts in CD14+ monocytes.\n- Are HIF-factors (HIF-1alpha/HIF-2alpha) involved in this process?\n- Does the knockdown of these would rescue the change in the C136U RNA editing of SDHB transcripts in CD14+ monocytes?\n- Is the RNA editing pattern changed when these CD14+ monocytes are treated with inflammatory conditions (for example LPS) which is also one of the microenvironmental conditions.\n-\n2. On page 22, the authors state that \u201cthe suppression of SDH might be an evolutionarily conserved metabolic adaptation to hypoxia\u2026.. due to enhanced glycolysis\u201d. Though the data suggest that the C136U RNA editing is increased which should supposedly decrease the express, however, SDHB protein levels were unchanged under hypoxic conditions compared to normoxia (Figure 4D). I do not think that changes in the RNA editing of this gene is sufficient to conclude that SDHB expression is downregulated leading to enhanced glycolysis.\n\n3. The authors showed RNA editing pattern in peripheral blood mononuclear cells (lymphocytes and monocyte-enriched population). Did the authors by chance look at the status of RNA editing in polymorphonuclear cells, especially neutrophils, which are also part of the immune system and have key role(s) in the immunological processes.\n\nMinor issues:\n1. Provide p values for the figures: 1C-E, 2C and 4A, B and E\n2. Figure 4 legends, line 8, change C13U into C136U RNA editing\nCite this review as\nKuppusamy B (2013) Peer Review #1 of \"Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes (v0.1)\". PeerJ https://doi.org/10.7287/peerj.152v0.1/reviews/1",
"review_4": "Jianyun Liu \u00b7 Jun 24, 2013\nBasic reporting\n1. In line 322, \u201c>= fold change\u201d, a \u201c3\u201d is missing.\n2. In Fig.1A, 9 lymphoblastoid cell lines and one fibroblastic cell line were included, but the authors did not provide names and sources of these cell lines.\nExperimental design\nNo Comments\nValidity of the findings\nNo Comments\nAdditional comments\nIn this manuscript, Baysal investigated RNA editing of SDHB (C136U) in different cell types and human tissues using both bioinformatics tools and wet lab tools. They provided massive amount of data to support their hypothesis that hypoxia induces RNA editing of SDHB and downregulates its expression in monocytes. The authors have performed many hypothesis-driven and well-designed experiments. Overall, this manuscript is well-written and the results are properly interpreted with some speculations. Two minor points are listed below:\n1. In line 322, \u201c>= fold change\u201d, a \u201c3\u201d is missing.\n2. In Fig.1A, 9 lymphoblastoid cell lines and one fibroblastic cell line were included, but the authors did not provide names and sources of these cell lines.\nCite this review as\nLiu J (2013) Peer Review #2 of \"Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes (v0.1)\". PeerJ https://doi.org/10.7287/peerj.152v0.1/reviews/2",
"pdf_1": "https://peerj.com/articles/152v0.2/submission",
"pdf_2": "https://peerj.com/articles/152v0.1/submission",
"all_reviews": "Review 1: Howard Young \u00b7 Aug 14, 2013 \u00b7 Academic Editor\nACCEPT\nYou changes were accepted and the manuscript is now ready for publication. Congratulations.\nReview 2: Howard Young \u00b7 Jun 27, 2013 \u00b7 Academic Editor\nMAJOR REVISIONS\nDear Authors,\n\nI believe that your paper is worthy of publication but please try to especially address the concerns of the first reviewer. I am not concerned about comment 3 but I do believe that a response to the first 2 concerns is needed.\nReview 3: Balamurugan Kuppusamy \u00b7 Jun 26, 2013\nBasic reporting\nSee below\nExperimental design\nSee below\nValidity of the findings\nSee below\nAdditional comments\nThe manuscript by Baysal et al studies the effect of hypoxia on C to U RNA editing of SDHB gene in monocytes. Previous studies show that SDH is a heterotetrameric tumor suppressor complex mutated in paraganglioma tumors due to hypoxia-inducible activation pathways. The authors studied regulation, extent and cell type origin of SDHB RNA editing. The authors found that RNA editing is low in monocyte-enriched PBMCs under normal condition, however, markedly increased under hypoxic conditions. This leads to down regulation of SDHB gene and consequently an increase in monocyte cell survival. Overall these findings add the mechanistic details to our understanding of the RNA editing under physiologically relevant conditions such as hypoxia, however additional data would support and strengthen their conclusions.\n\nMajor concerns:\n\n1. The authors show that hypoxia, one of the physiological conditions, increased the C136U RNA editing of SDHB transcripts in CD14+ monocytes.\n- Are HIF-factors (HIF-1alpha/HIF-2alpha) involved in this process?\n- Does the knockdown of these would rescue the change in the C136U RNA editing of SDHB transcripts in CD14+ monocytes?\n- Is the RNA editing pattern changed when these CD14+ monocytes are treated with inflammatory conditions (for example LPS) which is also one of the microenvironmental conditions.\n-\n2. On page 22, the authors state that \u201cthe suppression of SDH might be an evolutionarily conserved metabolic adaptation to hypoxia\u2026.. due to enhanced glycolysis\u201d. Though the data suggest that the C136U RNA editing is increased which should supposedly decrease the express, however, SDHB protein levels were unchanged under hypoxic conditions compared to normoxia (Figure 4D). I do not think that changes in the RNA editing of this gene is sufficient to conclude that SDHB expression is downregulated leading to enhanced glycolysis.\n\n3. The authors showed RNA editing pattern in peripheral blood mononuclear cells (lymphocytes and monocyte-enriched population). Did the authors by chance look at the status of RNA editing in polymorphonuclear cells, especially neutrophils, which are also part of the immune system and have key role(s) in the immunological processes.\n\nMinor issues:\n1. Provide p values for the figures: 1C-E, 2C and 4A, B and E\n2. Figure 4 legends, line 8, change C13U into C136U RNA editing\nCite this review as\nKuppusamy B (2013) Peer Review #1 of \"Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes (v0.1)\". PeerJ https://doi.org/10.7287/peerj.152v0.1/reviews/1\nReview 4: Jianyun Liu \u00b7 Jun 24, 2013\nBasic reporting\n1. In line 322, \u201c>= fold change\u201d, a \u201c3\u201d is missing.\n2. In Fig.1A, 9 lymphoblastoid cell lines and one fibroblastic cell line were included, but the authors did not provide names and sources of these cell lines.\nExperimental design\nNo Comments\nValidity of the findings\nNo Comments\nAdditional comments\nIn this manuscript, Baysal investigated RNA editing of SDHB (C136U) in different cell types and human tissues using both bioinformatics tools and wet lab tools. They provided massive amount of data to support their hypothesis that hypoxia induces RNA editing of SDHB and downregulates its expression in monocytes. The authors have performed many hypothesis-driven and well-designed experiments. Overall, this manuscript is well-written and the results are properly interpreted with some speculations. Two minor points are listed below:\n1. In line 322, \u201c>= fold change\u201d, a \u201c3\u201d is missing.\n2. In Fig.1A, 9 lymphoblastoid cell lines and one fibroblastic cell line were included, but the authors did not provide names and sources of these cell lines.\nCite this review as\nLiu J (2013) Peer Review #2 of \"Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes (v0.1)\". PeerJ https://doi.org/10.7287/peerj.152v0.1/reviews/2\nReview 5: nan\nReview 6: \n",
"LLM_extracted_review": "['Review 1: You changes were accepted and the manuscript is now ready for publication. Congratulations.\\n\\nReview 2: I believe that your paper is worthy of publication but please try to especially address the concerns of the first reviewer. I am not concerned about comment 3 but I do believe that a response to the first 2 concerns is needed.\\n\\nReview 3: The authors found that RNA editing is low in monocyte-enriched PBMCs under normal condition, however, markedly increased under hypoxic conditions. This leads to down regulation of SDHB gene and consequently an increase in monocyte cell survival. Overall these findings add the mechanistic details to our understanding of the RNA editing under physiologically relevant conditions such as hypoxia, however additional data would support and strengthen their conclusions. Major concerns include the involvement of HIF-factors in the RNA editing process, the sufficiency of RNA editing changes to conclude downregulation of SDHB expression, and whether RNA editing status was examined in polymorphonuclear cells. Minor issues include the need for p values in certain figures and a correction in the figure legend.\\n\\nReview 4: The authors have performed many hypothesis-driven and well-designed experiments. Overall, this manuscript is well-written and the results are properly interpreted with some speculations. Minor points include a missing \"3\" in line 322 regarding fold change and the lack of names and sources for the included cell lines in Fig.1A.']"
} |