Biogeographic analysis of the Tortugas Ecological Reserve: Examining the refuge effect following reserve establishment

Almost 120 days at sea aboard three NOAA research vessels and one fishing vessel over the past three years have supported biogeographic characterization of Tortugas Ecological Reserve (TER). This work initiated measurement of post-implementation effects of TER as a refuge for exploited species. In Tortugas South, seafloor transect surveys were conducted using divers, towed operated vehicles (TOV), remotely operated vehicles (ROV), various sonar platforms, and the Deepworker manned submersible. ARGOS drifter releases, satellite imagery, ichthyoplankton surveys, sea surface temperature, and diver census were combined to elucidate potential dispersal of fish spawning in this environment. Surveys are being compiled into a GIS to allow resource managers to gauge benthic resource status and distribution. Drifter studies have determined that within the ~ 30 days of larval life stage for fishes spawning at Tortugas South, larvae could reach as far downstream as Tampa Bay on the west Florida coast and Cape Canaveral on the east coast. Together with actual fish surveys and water mass delineation, this work demonstrates that the refuge status of this area endows it with tremendous downstream spillover and larval export potential for Florida reef habitats and promotes the maintenance of their fish communities. In Tortugas North, 30 randomly selected, permanent stations were established. Five stations were assigned to each of the following six areas: within Dry Tortugas National Park, falling north of the prevailing currents (Park North); within Dry Tortugas National Park, falling south of the prevailing currents (Park South); within the Ecological Reserve falling north of the prevailing currents (Reserve North); within the Ecological Reserve falling south of the prevailing currents (Reserve South); within areas immediately adjacent to these two strata, falling north of the prevailing currents (Out North); and within areas immediately adjacent to these two strata, falling south of the prevailing currents (Out South). Intensive characterization of these sites was conducted using multiple sonar techniques, TOV, ROV, diver-based digital video collection, diver-based fish census, towed fish capture, sediment particle-size, benthic chlorophyll analyses, and stable isotope analyses of primary producers, fish, and, shellfish. In order to complement and extend information from studies focused on the coral reef, we have targeted the ecotone between the reef and adjacent, non-reef habitats as these areas are well-known in ecology for indicating changes in trophic relationships at the ecosystem scale. Such trophic changes are hypothesized to occur as top-down control of the system grows with protection of piscivorous fishes. Preliminary isotope data, in conjunction with our prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be the source of a significant amount of the primary production ultimately fueling fish production throughout TER and downstream throughout the range of larval fish dispersal. Therefore, the status and influence of the previously neglected, non-reef habitat within the refuge (comprising ~70% of TER) appears to be intimately tied to the health of the coral reef community proper. These data, collected in a biogeographic context, employing an integrated Before-After Control Impact design at multiple spatial scales, leave us poised to document and quantify the postimplementation effects of TER. Combined with the work at Tortugas South, this project represents a multi-disciplinary effort of sometimes disparate disciplines (fishery oceanography, benthic ecology, food web analysis, remote sensing/geography/landscape ecology, and resource management) and approaches (physical, biological, ecological). We expect the continuation of this effort to yield critical information for the management of TER and the evaluation of protected areas as a refuge for exploited species. (PDF contains 32 pages.)

Preliminary comparison of natural versus model-predicted recovery of vessel-generated seagrass injuries in Florida Keys National Marine Sanctuary

Each year, more than 500 motorized vessel groundings cause widespread damage to seagrasses in Florida Keys National Marine Sanctuary (FKNMS). Under Section 312 of the National Marine Sanctuaries Act (NMSA), any party responsible for the loss, injury, or destruction of any Sanctuary resource, including seagrass, is liable to the United States for response costs and resulting damages. As part of the damage assessment process, a cellular automata model is utilized to forecast seagrass recovery rates. Field validation of these forecasts was accomplished by comparing model-predicted percent recovery to that which was observed to be occurring naturally for 30 documented vessel grounding sites. Model recovery forecasts for both Thalassia testudinum and Syringodium filiforme exceeded natural recovery estimates for 93.1% and 89.5% of the sites, respectively. For Halodule wrightii, the number of over- and under-predictions by the model was similar. However, where under-estimation occurred, it was often severe, reflecting the well-known extraordinary growth potential of this opportunistic species. These preliminary findings indicate that the recovery model is consistently generous to Responsible Parties in that the model forecasts a much faster recovery than was observed to occur naturally, particularly for T. testudinum, the dominant seagrass species in the region and the species most often affected. Environmental setting (i.e., location, wave exposure) influences local seagrass landscape pattern and may also play a role in the recovery dynamics for a particular injury site. An examination of the relationship between selected environmental factors and injury recovery dynamics is currently underway. (PDF file contains 20 pages.)

Physical circulation measurements in Pamlico Sound, used to locate new oyster sanctuaries

The population of eastern oyster, C. virginica, has declined over the last century on most areas of the east and gulf coasts. North Carolina’s restoration efforts depend on the construction of subtidal oyster reefs to be used as broodstock sanctuaries in Pamlico Sound, NC. Successful restoration of the oyster population requires several thriving reefs connected as a meta-population. C. virginica has a 2-3 week larval stage, during which it gradually settles through the water column. Larvae that can travel from one reef to another during that stage form the basis of a meta-population. (PDF contains 3 pages)

The Coastal Barrier Island Network (CBIN): Future management strategies for barrier islands

Barrier islands are ecosystems that border coastal shorelines and form a protective barrier between continental shorelines and the wave action originating offshore. In addition to forming and maintaining an array of coastal and estuarine habitats of ecological and economic importance, barrier island coastlines also include some of the greatest concentrations of human populations and accompanying anthropogenic development in the world. These islands have an extremely dynamic nature whereby major changes in geomorphology and hydrology can occur over short time periods (i.e. days, hours) in response to extreme episodic storm events such as hurricanes and northeasters. The native vegetation and geological stability of these ecosystems are tightly coupled with one another and are vulnerable to storm-related erosion events, particularly when also disturbed by anthropogenic development. (PDF contains 4 pages)

Mitigating Scarring and Inflammation during Corneal Wound Healing using Nanofiber-Hydrogel Scaffolds

Due to the universal lack of donor tissue, there has been emerging interest in engineering materials to stimulate living cells to restore the features and functions of injured organs. We are particularly interested in developing materials for corneal use, where the necessity to maintain the tissue’s transparency presents an additional challenge. Every year, there are 1.5 – 2 million new cases of monocular blindness due to irregular healing of corneal injuries, dwarfing the approximately 150,000 corneal transplants performed. The large gap between the need and availability of cornea transplantation motivates us to develop a wound-healing scaffold that can prevent corneal blindness.

To develop such a scaffold, it is necessary to regulate the cells responsible for repairing the damaged cornea, namely myofibroblasts, which are responsible for the disordered and non-refractive index matched scar that leads to corneal blindness. Using in vitro assays, we identified that protein nanofibers of certain orientation can promote cell migration and modulate the myofibroblast phenotype. The nanofibers are also transparent, easy to handle and non-cytotoxic. To adhere the nanofibers to a wound bed, we examined the use of two different in situ forming hydrogels: an artificial extracellular matrix protein (aECM)-based gel and a photo-crosslinkable heparin-based gel. Both hydrogels can be formed within minutes, are transparent upon gelation and are easily tunable.

Using an in vivo mouse model for epithelial defects, we show that our corneal scaffolds (nanofibers together with hydrogel) are well-tolerated (no inflammatory response or turbidity) and support epithelium regrowth. We developed an ex vivo corneal tissue culture model where corneas that are wounded and treated with our scaffold can be cultured while retaining their ability to repair wounds for up to 21 days. Using this technique, we found that the aECM-based treatment induced a more favorable wound response than the heparin-based treatment, prompting us to further examine the efficacy of the aECM-based treatment in vivo using a rabbit model for stromal wounds. Results show that treated corneas have fewer myofibroblasts and immune cells than untreated ones, indicating that our corneal scaffold shows promise in promoting a calmer wound response and preventing corneal haze formation.

The Status of Eelgrass, Zostera marina, as Bay Scallop Habitat: Consequences for the Fishery in the Western Atlantic

Zostera marina is a member of a widely distributed genus of seagrasses, all commonly called eelgrass. The reported distribution of eelgrass along the east coast of the United States is from Maine to North Carolina. Eelgrass inhabits a variety of coastal habitats, due in part to its ability to tolerate a wide range of environmental parameters. Eelgrass meadows provide habitat, nurseries, and feeding grounds for a number of commercially and ecologically important species, including the bay scallop, Argopecten irradians. In the early 1930’s, a marine event, termed the “wasting disease,” was responsible for catastrophic declines in eelgrass beds of the coastal waters of North America and Europe, with the virtual elimination of Z. marina meadows in the Atlantic basin. Following eelgrass declines, disastrous losses were documented for bay scallop populations, evidence of the importance of eelgrass in supporting healthy scallop stocks. Today, increased turbidity arising from point and non-point source nutrient loading and sediment runoff are the primary threats to eelgrass along the Atlantic coast and, along with recruitment limitation, are likely reasons for the lack of recovery by eelgrass to pre-1930’s levels. Eelgrass is at a historical low for most of the western Atlantic with uncertain prospects for systematic improvement. However, of all the North American seagrasses, eelgrass has a growth rate and strategy that makes it especially conducive to restoration and several states maintain ongoing mapping, monitoring, and restoration programs to enhance and improve this critical resource. The lack of eelgrass recovery in some areas, coupled with increasing anthropogenic impacts to seagrasses over the last century and heavy fishing pressure on scallops which naturally have erratic annual quantities, all point to a fishery with profound challenges for survival.

Observations of the 1992 U.S. Pelagic Pair Trawl Fishery in the Northwest Atlantic

Pelagic pair trawling for tuna, Thunnus spp., and swordfish, Xiphias gladius, was introduced in U.S. Northwest Atlantic waters in 1991. During autumn (October-November) of 1992 under the authority oft he Federal Atlantic Swordfish Regulations, the National Marine Fisheries Service placed observers aboard pelagic pair trawl vessels to document the catch, bycatch, discard, and gear used in this new fishery. The fishery is conducted primarily at night along shelf-edge waters from June to November. In late 1991, revised regulations restricted swordfish to bycatch in this fishery resulting in pelagic pair trawl vessels targeting tuna throughout 1992. Analyses of 1992 data indicate that albacore, T. alalunga, was the predominant species caught, although yellowfin tuna, T. albaeares, and bigeye tuna, T. obesus, were the preferred target species. Bycatch also included swordfish, large sharks, pelagic rays and other pelagic fishes, other tunas, and marine mammals.

Prioritizing seagrass restoration sites: study examines predictors of seagrass bed recovery

Ecologic researchers are modeling the impact of vessel grounding to seagrass beds using GIS in the Florida Keys National Marine Sanctuary. The surface creation tools in the ArcGIS 3D Analyst extension help assess both the damage and recovery of these seagrass beds.

Sensitivity of Lake Sturgeon population dynamics and genetics to demographic parameters [Powerpoint Slide]

Lake sturgeon Acipenser fulvescens restoration is a priority throughout the Great Lakes basin, where sturgeon have been reduced to less than 1% of historic levels due to habitat degradation, overharvest, and fragmentation of spawning populations. The population parameters most important to long-term lake sturgeon persistence are unknown.

小麦×玉米的小麦DH后代的分子生物学分析

植物远缘杂交是作物育种实践及其相关的基础遗传中应用最广泛的技术之一，几乎涉及到所有与栽培作物有关的科属内相对近缘的植物种类。除核型稳定的种间杂交可得到杂种外，还可以利用核型不稳定的种间杂交过程中父本染色体全部被消除的现象，通过胚培养和加倍处理获得大量的双单倍体（DH）杂交后代。然而，这种从小麦与玉米杂交获得的小麦DH后代与其理论上应完全同质的遗传表现却不相符，总有2-5%的DH植株发生了形态学变异，虽然没有明显的来自玉米的性状特征，而且一些研究者也认为它们是配子无性系变异，但是，不论是理论上还是一些间接的细胞学和生化证据都表明，有玉米的染色体DNA通过受精过程转移到小麦DH后代的基因组中，然而到目前为止，仍缺乏DNA水平上的直接证据。 本文在对来自小麦 * 玉米的谱通小麦DH系进行生化分析取得初步证据的基础上，构建玉米的随机基因组文库，从中筛选玉米的重复DNA序列作探针分别对普通小麦和波斯小麦的DH群体进行了系统的RFLP分析，并用有关的玉米重复列克隆对一些禾本科种和不同的玉米生物型基因组进行了比较研究，主要结果如下： 1、八种同工酶电泳分析表明，MDH、ADH、GDH、SKDH4种脱氢酶和GOT在后代中没有检测到任何变异，但21株普通小麦的DH后代群体中有7株在PER同工酶的慢区出现了增加一条酶带的变异，这条带在亲本小麦和玉米中均没有，它们与通常报道的无性系变异十分类似。其中有一株（第4号株）在迁移率为0.22的位置上出现了一条小麦所不具有的酶活性较强的EST带，在玉米同迁移率的位置上也有一条带，但活性十分微弱。此外，大部分小麦DH后代的AMY同工酶恬性有十分明显的增强。 2、可溶性蛋白质的SDS-PAGE分析，在小麦的DH后代中，有几株的变异很明显，其中第4、7、19号株（图2）在分子量为43000道尔顿的位置上出现了和玉米同迁移率而小麦不具有的蛋白质带，这强烈地暗示了玉米DNA的确通过受精作用导入小麦。 3、构建了玉米的随机基因组文库，依据菌落原位杂交结果，从中挑出了500个重组克隆。用其中的100个强信号的重复DNA克隆为探针对亲本小麦和玉米进行了RFLP筛选，其中80多个为玉米基因组特异的，9个与小麦有部分同源性，随后用它们探针分别对两个小麦DH群体进行RFLP分析。 4、用上文筛选的玉米特异的重复DNA克隆作探针进行RFLP分析，只有玉米的MR64克隆同时导入到两个小麦群体的各一株后代中，即普通小麦DH系的18号株和波斯小麦DH系的15号株检测到强杂交信号;另外一个克隆MR72只在4株波斯小麦DH后代中有杂交信号，这个结果首次从DNA水平上证明，的确有某些玉米特异的DNA序列通过受精作用以很低的频率转移到小麦DH后代的基因组中。 5、与小麦有部分同源性的玉米克隆MR13和MR50在一些普通小麦DH后代中检测到了缺失变异。特别是用MR13在普通小麦DH系的18号株（即导入了玉米特异的MR64的DNA的那一株小麦DH后代）的基因组中检测到了大幅度的限制性片段长度的变化，即原来的4.3kb的强信号带消失了，取而代之的是增加40kb、15kb、2.5kb和2.0kb四条杂交带，这要么与小麦基因组DNA较大的重俳事件有关，要么是由外源的玉米DNA插入造成的，但从增加的片段长度如此之大以及杂交信号变弱来看，它很可能就是玉米DNA插入到这个较强信号的小麦单拷贝序列中的结果。用小麦的DNA克隆pTa71也检测到了明显的变异。 6、测序分析发现，克隆MP64的插入片段长度为695bp，A+T含量为58%，经在GENEBANK中检索证实它是一个新克隆的DNA序列。序列中分别含有两对正向和反向重 序列及三个回文序列，对多种酶切的玉米基因组的RFLP分析表明它是一个带1-3个主串联重复单位的散布重复序列，在序列中的CCGG的第二个C高度甲基化，拷贝数约为5600左右。染色体原位杂交表明，MR64在玉米的每条染色体上均有分布，但拷贝数不同，这暗示它可能与玉米基因组的演化历程有密切的关系。 7、比较分析发现，MR64是玉米基因组特异的;而MR72在高粱、珍株粟、糜子和狼尾草等四个和玉米较近缘的种的基因组中有部分同源序列，这个比较结果更加肯定了小麦DH系所新增的DNA序列的确是异源的玉米DNA通过受精过程导入的。 8、初步分析发现，玉米的卫星DNA克隆MR4和其它卫星DNA一样也有严谨的重复等级结构，而且在主要禾本科种基因组中有较低的同源性。经在GENEBANK检索，串联重复DNA克隆MR68是一个新克隆的DNA序列，它在不同的玉米生物型基因组中表现出明显的分化特征，可用它作进一步的基因组的比较分析。 9、本文对染色体消除过程度中异源小片段DNA导入的可能机制和散布重复序列在远缘杂交的异源DNA鉴定中的应用进行了讨论，并分析了染色体消除型远缘杂交所获得的DH后代的变异来源。

Lobster trap debris in the Florida Keys National Marine Sanctuary: distribution, abundance, density, and patterns of accumulation

The fishery for spiny lobster Panulirus argus in the Florida Keys National Marine Sanctuary is well chronicled, but little information is available on the prevalence of lost or abandoned lobster traps. In 2007, towed-diver surveys were used to identify and count pieces of trap debris and any other marine debris encountered. Trap debris density (debris incidences/ha) in historic trap-use zones and in representative benthic habitats was estimated. Trap debris was not proportionally distributed with fishing effort. Coral habitats had the greatest density of trap debris despite trap fishers’ reported avoidance of coral reefs while fishing. The accumulation of trap debris on coral emphasizes the role of wind in redistributing traps and trap debris in the sanctuary. We estimated that 85,548 ± 23,387 (mean ± SD) ghost traps and 1,056,127 ± 124,919 nonfishing traps or remnants of traps were present in the study area. Given the large numbers of traps in the fishery and the lack of effective measures for managing and controlling the loss of gear, the generation of trap debris will likely continue in proportion to the number of traps deployed in the fishery. Focused removal of submerged trap debris from especially vulnerable habitats such as reefs and hardbottom, where trap debris density is high, would mitigate key habitat issues but would not address ghost fishing or the cost of lost gear.

El Niño reconstructions and confirmation of a pan-Californian model via Radiolarian evidence

Radiolarian number and/or flux rates extracted from Holocene and fossil sediments are used to help detect the presence of, type of (weak or strong), and exact location of the depocenter under an El Niño. These data, along with known provenances of certain radiolarians, support an earlier model that suggests a weak El Niño is a northern and coupled expression of a more southerly strong component dominated by eastern tropical Pacific water underlain by California current and gyre water.