bluuebunny/crossref_metadata_2025_split huggingface dataset:
The conserved AAA-ATPase Msp1 confers organelle specificity to tail-anchored proteins
Authors: Okreglak Voytek , Walter Peter 
Published: May 2014

Significance
Membrane protein targeting to the endoplasmic reticulum, peroxisomes, and mitochondria requires specialized machinery to ensure the appropriate localization of proteins, which is important for defining organelle identity. Additional specificity is provided by sensing and degrading proteins that are mistargeted to an inappropriate compartment. One class of membrane proteins, which contain a hydrophobic segment at their extreme C terminus (called tail-anchored proteins), are prone to be mistargeted; however, how cells cope with this burden is unknown. In this work, we identify a conserved ATPase of the outer mitochondrial membrane, Msp1, which we propose functions as an extraction engine to remove and initiate degradation of an inappropriately targeted tail-anchored protein. In this way, Msp1 serves to enhance the fidelity of protein localization.
Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing
Authors: Li Guosheng , Wang Dongfang , Yang Ruolin , Logan Kyle , Chen Hao , Zhang Shanshan , Skaggs Megan I. , Lloyd Alan , Burnett William J. , Laurie John D. , Hunter Brenda G. , Dannenhoffer Joanne M. , Larkins Brian A. , Drews Gary N. , Wang Xiangfeng , Yadegari Ramin 
Published: May 2014

Significance
In flowering plants, double fertilization gives rise to an embryo and the endosperm, an absorptive storage structure that supports embryogenesis and seedling germination. In cereal grains, endosperm comprises a large proportion of the mature seed, contains large amounts of carbohydrates and proteins, and is an important source of food, feed, and industrial raw materials. This study provides a comprehensive profile of the genes expressed in the early developing endosperm in maize. We also show how a series of temporal programs of gene expression correlate with progressive functional and cellular specializations.
Redemption of autoantibodies on anergic B cells by variable-region glycosylation and mutation away from self-reactivity
Authors: Sabouri Zahra , Schofield Peter , Horikawa Keisuke , Spierings Emily , Kipling David , Randall Katrina L. , Langley David , Roome Brendan , Vazquez-Lombardi Rodrigo , Rouet Romain , Hermes Jana , Chan Tyani D. , Brink Robert , Dunn-Walters Deborah K. , Christ Daniel , Goodnow Christopher C. 
Published: May 2014

Significance
Antibodies are selected to bind microbial but not self-antigens, because binding to self would compete with binding microbes, shorten antibody half-life, and cause autoimmunity. Self-tolerance is actively acquired in part by discarding self-binding antibodies before the body is exposed to a microbe or vaccine. The experiments here provide evidence of an opposite mechanism, allowing antibodies that initially bind both foreign and self-antigens to acquire self/non-self discrimination during the course of an immune response through somatic hypermutation away from self-reactivity. In addition to selection for lower-affinity binding to self, antibody variants were selected with fewer binding sites available to bind self-antigen because most were occupied by N-linked carbohydrate, possibly explaining the frequent occurrence of N-linked glycosylation of antibody variable domains.
Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense
Authors: Lassen Kara G. , Kuballa Petric , Conway Kara L. , Patel Khushbu K. , Becker Christine E. , Peloquin Joanna M. , Villablanca Eduardo J. , Norman Jason M. , Liu Ta-Chiang , Heath Robert J. , Becker Morgan L. , Fagbami Lola , Horn Heiko , Mercer Johnathan , Yilmaz Omer H. , Jaffe Jacob D. , Shamji Alykhan F. , Bhan Atul K. , Carr Steven A. , Daly Mark J. , Virgin Herbert W. , Schreiber Stuart L. , Stappenbeck Thaddeus S. , Xavier Ramnik J. 
Published: May 2014

Significance
Although advances in human genetics have shaped our understanding of many complex diseases, little is known about the mechanism of action of alleles that influence disease. By using mice expressing a Crohn disease (CD)-associated risk polymorphism (Atg16L1 T300A), we show that Atg16L1 T300A-expressing mice demonstrate abnormalities in Paneth cells (similar to patients with the risk polymorphism) and goblet cells. We show that Atg16L1 T300A protein is more susceptible to caspase-mediated cleavage than WT autophagy related 16-like 1 (Atg16L1), resulting in decreased protein stability and effects on antibacterial autophagy and inflammatory cytokine production. We also identify interacting proteins that contribute to autophagy-dependent immune responses. Understanding how ATG16L1 T300A modulates autophagy-dependent immune responses sheds light on the mechanisms that underlie initiation and progression of CD.
Survey of Intersex Largemouth Bass from Impoundments in Georgia USA
Authors: Kellock Kristen A. , Trushel Brittany E. , Ely Patrick C. , Jennings Cecil A. , Bringolf Robert B. 
Published: May 2014

AbstractIntersex fish are increasingly being reported worldwide, primarily in rivers that receive treated wastewater, but few studies have investigated intersex in waters that do not receive wastewater. In a recent reconnaissance survey of intersex fish in North America, a high rate of intersex was reported for Largemouth Bass Micropterus salmoides in some southeastern U.S. rivers; however, the occurrence of intersex in impoundments has not been well described, especially on a statewide scale. Therefore, our objective for this project was to survey the occurrence of intersex Largemouth Bass in a variety of impoundment habitats across Georgia. Largemouth Bass were collected from 11 impoundments without direct municipal or agricultural wastewater inputs. Gonads from all male Largemouth Bass were evaluated for the incidence and severity of the intersex condition based on presence and arrangement of testicular oocytes. Overall 48% of male Largemouth Bass collected from impoundments were intersex, which was found in 9 of the 11 impoundments. Among impoundments, incidence of intersex ranged from 0 to 82% of the males sampled and surface area of the impoundment was a significant predictor of intersex incidence. Intersex fish were smaller than normal males, but population‐level effects of intersex and causative factors of endocrine disruption in the impoundments remain unknown. The high incidence of intersex males in small impoundments demonstrates that the condition is not confined to rivers and suggests that factors other than those previously associated with intersex (i.e., municipal wastewater) may be involved.
Determinate Versus Indeterminate Fecundity in American Shad, an Anadromous Clupeid
Authors: Hyle A. Reid , McBride Richard S. , Olney John E. 
Published: May 2014

AbstractHistorical fecundity estimates of American Shad Alosa sapidissima used a determinate method that estimated annual fecundity as the standing stock of oocytes at a single point of time prior to spawning. Such fecundity estimates have been (1) reported for populations from the Canadian Maritimes to Florida, (2) applied to hypothesis tests of life history evolution, and (3) used in demographic models to advise management policy. However, American Shad have asynchronous development of yolked oocyte clutches, which suggests that new oocytes could arise after spawning commences, biasing the results of a determinate fecundity method downward. If so, annual fecundity should be a product of batch size and the number of batches—an indeterminate fecundity method. We investigated oocyte recruitment, atresia, and spawning intervals using gonad histology of females from the Mattaponi River, Virginia. Batch size (i.e., the number of hydrated oocytes prior to a spawning event) was estimated using a gravimetric method. Spawning duration was obtained from an independent acoustic tagging study. A size hiatus between primary and secondary oocytes was only evident in some individuals during spawning, so we conclude that an indeterminate fecundity method is necessary for this population of American Shad. Atresia was evident during spawning but was low at the end of the 2002 spawning season. Females spawned every 2.2–2.9 d, releasing 11–17 batches per season. Batch fecundity (range: 12,700–81,400) was 23% higher for repeat versus virgin spawners. A bootstrapped estimate of potential annual fecundity for a virgin female—as calculated with an indeterminate fecundity method—was 478,000–544,000 eggs (95% confidence interval), about double the previous (determinate) estimates from this river system (260,000 and 288,000). Until more comparisons are done with other populations, we urge caution in using the many published determinate fecundity estimates of American Shad and other Alosa species.
Abundance, Distribution, and Diet of a Small‐Bodied Ecotype of Windowpane
Authors: Hanson John Mark , Wilson Tamara 
Published: May 2014

AbstractWindowpanes Scophthalmus aquosus were collected during demersal trawl surveys in Northumberland Strait in the southern Gulf of St. Lawrence, Canada, during July and August 2001–2012. Abundance indices showed relatively little variation between years. Windowpanes were widely distributed in the strait, with 95% of the population occurring in water <23m deep and with a temperature of >9.5°C. The Windowpanes collected were small, all <30cm total length. Fish of all sizes fed mainly on sevenspine bay shrimp Crangon septemspinosa, followed by mysids and (for fish >20cm) sand lances Ammodytes spp. and juvenile Atlantic Herring Harengus harengus. Small (<10‐cm) individuals also ate crab megalops larvae. The mysids consumed on sandy–gravel substrates were Mysis spp.; those consumed on mud bottom were mainly Neomysis americana. Cannibalism was low, consisting of two individuals <1.6cm.
Passive Acoustic Monitoring to Detect Spawning in Large‐Bodied Catostomids
Authors: Straight Carrie A. , Freeman Byron J. , Freeman Mary C. 
Published: May 2014

AbstractDocumenting timing, locations, and intensity of spawning can provide valuable information for conservation and management of imperiled fishes. However, deep, turbid or turbulent water, or occurrence of spawning at night, can severely limit direct observations. We have developed and tested the use of passive acoustics to detect distinctive acoustic signatures associated with spawning events of two large‐bodied catostomid species (River RedhorseMoxostoma carinatumand Robust RedhorseMoxostoma robustum) in river systems in north Georgia. We deployed a hydrophone with a recording unit at four different locations on four different dates when we could both record and observe spawning activity. Recordings captured 494 spawning events that we acoustically characterized using dominant frequency, 95% frequency, relative power, and duration. We similarly characterized 46 randomly selected ambient river noises. Dominant frequency did not differ between redhorse species and ranged from 172.3 to 14,987.1Hz. Duration of spawning events ranged from 0.65 to 11.07s, River Redhorse having longer durations than Robust Redhorse. Observed spawning events had significantly higher dominant and 95% frequencies than ambient river noises. We additionally tested software designed to automate acoustic detection. The automated detection configurations correctly identified 80–82% of known spawning events, and falsely indentified spawns 6–7% of the time when none occurred. These rates were combined over all recordings; rates were more variable among individual recordings. Longer spawning events were more likely to be detected. Combined with sufficient visual observations to ascertain species identities and to estimate detection error rates, passive acoustic recording provides a useful tool to study spawning frequency of large‐bodied fishes that displace gravel during egg deposition, including several species of imperiled catostomids.
Relationships among Walleye Population Characteristics and Genetic Diversity in Northern Wisconsin Lakes
Authors: Waterhouse Matthew D. , Sloss Brian L. , Isermann Daniel A. 
Published: May 2014

AbstractThe maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age‐0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density‐dependent factors. An isolation‐by‐distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic diversity and stocking appeared to alter allelic frequencies and the genetic structure of Walleye populations in Wisconsin, possibly resulting in disruption of local adaptation.
How Much Cleaning is Needed When Processing Otoliths from Fish Larvae for Microchemical Analysis?
Authors: Gover Theodore R. , Nims Megan K. , Van Tassell Jason J. , Collingsworth Paris D. , Olesik John W. , Ludsin Stuart A. , Marschall Elizabeth A. 
Published: May 2014

AbstractOtolith microchemistry is a widely used tool in fish ecology and fisheries management. Cleaning‐protocol assessments are lacking, however, especially for larval fish otoliths, which are more fragile and difficult to manipulate than larger otoliths. Herein, we assess the value of cleaning larval fish otoliths with sonication, a commonly used technique that is time consuming and risks loss or breakage of small otoliths, as well as with a lesser‐known technique using a low‐power laser cleaning pulse (LPLCP). We measured trace elements in larval Walleye Sander vitreus reared in different water strontium concentrations. Strontium and Ba did not differ among any cleaning treatments, indicating that neither sonication nor a LPLCP is necessary. Likewise, Mn did not differ between sonicated and nonsonicated treatments; however, Mn was lower when a LPLCP was used. We suggest omitting the sonication step when preparing otoliths for trace element analysis of Sr, Ba, Mn, and other trace elements found in high abundances. The addition of a LPLCP is useful, although more research in this arena is warranted. Our findings should greatly reduce otolith processing time and the risk of losing and breaking larval otoliths during the cleaning process.
Fish and Benthic Macroinvertebrate Densities in Small Streams with and without American Eels
Authors: Stranko Scott A. , Ashton Matthew J. , Hilderbrand Robert H. , Weglein Sara L. , Kazyak David C. , Kilian Jay V. 
Published: May 2014

AbstractThe American Eel Anguilla rostrata has been excluded from many streams along the Atlantic slope of the USA because of movement barriers such as large dams. Loss of this formerly common top predator has the potential to influence many aspects of headwater streams. We used existing survey data for a landscape‐scale comparison of fish, benthic macroinvertebrate, and crayfish densities at 95 sites where American Eel access was excluded by dams and 74 sites containing eels. Benthic fish densities were significantly lower at eel‐containing sites, whereas benthic macroinvertebrate densities were significantly higher. Densities of nonbenthic fish, non‐eel top predators, and crayfish were not different between eel occurrence categories. While these initial results are correlative, we believe that American Eel may be capable of influencing lower trophic levels, and their presence may produce noticeable changes to headwater stream ecosystems.
Influence of Natural and Anthropogenic Disturbances on Spawning Sockeye Salmon Distributions in the Cedar River, Washington
Authors: Timm Raymond K. , Wissmar Robert C. 
Published: May 2014

AbstractHuman management of river ecosystems dampens natural disturbance regimes that drive critical habitat‐forming processes. However, the quantification of processes can be difficult and is typically accomplished through surrogate analyses. In 2001, a channel‐damming landslide in the Cedar River, Washington, changed habitat conditions and spawning distributions of Sockeye Salmon Oncorhynchus nerka. We evaluated annual changes in a number of key indicators of river processes during the pre‐ and post‐disturbance periods. We used an exhaustive chi‐square automatic interaction detection (CHAID) model to evaluate the effect of changes in habitat complexity, discharge characteristics, and parental generation spawning distributions on 54years (1952–2006) of weekly spawning fish surveys. Before the landslide, the spatial and temporal patterns of Sockeye Salmon distributions were heavily influenced by the spawning locations of their parents. Densities of spawning fish were highest in the uppermost river reaches. After the landslide, habitat complexity and fish densities increased in the lower, landslide‐affected river reaches. The CHAID model analyses indicated that fluvial habitat complexity, river discharge characteristics, and the density of fish in respective parental generations were significant factors explaining the spawning distributions by reach. Our analyses of the salmon population response to annual changes in habitat complexity affirm that our metrics were useful surrogates for measuring the habitat‐forming processes restored when the landslide reconnected the river channel with its floodplain. Furthermore, this study provides an “order of magnitude” insight into the amount of restoration that will elicit a population‐scale response in salmon.
Contingents of Southern Flounder from Subtropical Estuaries Revealed by Otolith Chemistry
Authors: Nims Megan K. , Walther Benjamin D. 
Published: May 2014

AbstractThe identification of contingents within populations that exhibit distinct migratory behaviors and patterns of habitat use can lead to the understanding of the fitness consequences of individual variability in a population and an increased understanding of population dynamics. This study examines the variation in migratory behavior and habitat use patterns in Southern Flounder Paralichthys lethostigma in the northwestern Gulf of Mexico, whose populations have declined rapidly over the last 25–30years. The putative life history for this species includes short postsettlement movements into low‐salinity habitats, followed by estuarine and marine residency for the remainder of life. However, using otolith Ba:Ca in wild‐captured fish, two primary contingents were observed: (1) 54% of fish showed marine–estuarine residency for their entire lifetimes, and (2) 46% showed residence in oligohaline habitats for some portion of their lifetimes. For the second group, oligohaline residence varied widely with life history profiles, having between < 5% up to > 95% of values above the oligohaline threshold. Relationships between the proportion of life spent in oligohaline waters and proxies of growth performance were not significant, indicating no apparent difference in the relative advantage of specific residency patterns. Residence in oligohaline habitats thus appears to be facultative for this population, which may be a local adaptation to interannual drought cycles and variable freshwater inputs in the region.
Age and Growth of the Bull Shark in the Western North Atlantic Ocean
Authors: Natanson Lisa J. , Adams Douglas H. , Winton Megan V. , Maurer Jasmine R. 
Published: May 2014

AbstractAge and growth estimates for the Bull Shark Carcharhinus leucas were derived from 121 vertebral centra collected from Bull Sharks (59.1–223.5cm FL) between 1966 and 2010 in the western North Atlantic Ocean. Size at birth was confirmed with an additional 20 embryos (44.2–54.4cm FL). The maximum age based on vertebral band pair counts was 25 (184cm FL) and 27 (196cm FL) years for males and females, respectively. The logistic and Gompertz growth models fitted the size‐at‐age data best for males and females, respectively. Based on previously published estimates of length at maturity, males mature at 15–17years (176–185cm FL) and females at 15years (189cm FL). Bull Sharks in the western North Atlantic Ocean and the Gulf of Mexico have similar growth rates and reach similar sizes at age.
Regulation of intestinal health and disease by innate lymphoid cells
Authors: Sonnenberg Gregory F. 
Published: May 2014

Abstract
Innate lymphoid cells (ILCs) are a recently appreciated immune cell population that is constitutively found in the healthy mammalian gastrointestinal (GI) tract and associated lymphoid tissues. Translational studies have revealed that alterations in ILC populations are associated with GI disease in patients, such as inflammatory bowel disease, HIV infection and colon cancer, suggesting a potential role for ILCs in either maintaining intestinal health or promoting intestinal disease. Mouse models identified that ILCs have context-dependent protective and pathologic functions either during the steady state, or following infection, inflammation or tissue damage. This review will discuss the associations of altered intestinal ILCs with human GI diseases, and the functional consequences of targeting ILCs in mouse models. Collectively, our current understanding of ILCs suggests that the development of novel therapeutic strategies to modulate ILC responses will be of significant clinical value to prevent or treat human GI diseases.